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Sample records for actin-related protein arp

  1. Sequences, structural models, and cellular localization of the actin- related proteins Arp2 and Arp3 from Acanthamoeba

    PubMed Central

    1995-01-01

    We cloned and sequenced the two actin-related proteins (Arps) present in the profilin-binding complex of Acanthamoeba (Machesky, L. M., S. J. Atkinson, C. Ampe, J. Vandekerckhove, and T. D. Pollard. 1994, J. Cell Biol. 127:107-115). The sequence of Arp2 is more similar to other Arp2s than to actin, while the sequence of Arp3 is more similar to other Arp3s than to actin. Phylogenetic analysis of all known Arps demonstrates that most group into three major families, which are likely to be shared across all eukaryotic phyla. Together with conventional actins, the Arps form a larger family distinct from structurally related ATPases such as Hsp70's and sugar kinases. Atomic models of the Arps based on their sequences and the structure of actin provide some clues about function. Both Arps have atoms appropriately placed to bind ATP and divalent cation. Arp2, but not Arp3, has a conserved profilin-binding site. Neither Arp has the residues required to copolymerize with actin, but an Arp heterodimer present in the profilin-binding complex might serve as a pointed end nucleus for actin polymerization. Both Acanthamoeba Arps are soluble in cell homogenates, and both are concentrated in the cortex of Acanthamoeba. The cellular concentrations are 1.9 microM Arp2 and 5.1 microM Arp3, substoichiometric to actin (200 microM) but comparable to many actin- binding proteins. PMID:7593166

  2. Yeast Actin-Related Protein ARP6 Negatively Regulates Agrobacterium-Mediated Transformation of Yeast Cell

    PubMed Central

    Luo, Yumei; Chen, Zikai; Zhu, Detu; Tu, Haitao; Pan, Shen Quan

    2015-01-01

    The yeasts, including Saccharomyces cerevisiae and Pichia pastoris, are single-cell eukaryotic organisms that can serve as models for human genetic diseases and hosts for large scale production of recombinant proteins in current biopharmaceutical industry. Thus, efficient genetic engineering tools for yeasts are of great research and economic values. Agrobacterium tumefaciens-mediated transformation (AMT) can transfer T-DNA into yeast cells as a method for genetic engineering. However, how the T-DNA is transferred into the yeast cells is not well established yet. Here our genetic screening of yeast knockout mutants identified a yeast actin-related protein ARP6 as a negative regulator of AMT. ARP6 is a critical member of the SWR1 chromatin remodeling complex (SWR-C); knocking out some other components of the complex also increased the transformation efficiency, suggesting that ARP6 might regulate AMT via SWR-C. Moreover, knockout of ARP6 led to disruption of microtubule integrity, higher uptake and degradation of virulence proteins, and increased DNA stability inside the cells, all of which resulted in enhanced transformation efficiency. Our findings have identified molecular and cellular mechanisms regulating AMT and a potential target for enhancing the transformation efficiency in yeast cells. PMID:26425545

  3. Yeast Actin-Related Protein ARP6 Negatively Regulates Agrobacterium-Mediated Transformation of Yeast Cell.

    PubMed

    Luo, Yumei; Chen, Zikai; Zhu, Detu; Tu, Haitao; Pan, Shen Quan

    2015-01-01

    The yeasts, including Saccharomyces cerevisiae and Pichia pastoris, are single-cell eukaryotic organisms that can serve as models for human genetic diseases and hosts for large scale production of recombinant proteins in current biopharmaceutical industry. Thus, efficient genetic engineering tools for yeasts are of great research and economic values. Agrobacterium tumefaciens-mediated transformation (AMT) can transfer T-DNA into yeast cells as a method for genetic engineering. However, how the T-DNA is transferred into the yeast cells is not well established yet. Here our genetic screening of yeast knockout mutants identified a yeast actin-related protein ARP6 as a negative regulator of AMT. ARP6 is a critical member of the SWR1 chromatin remodeling complex (SWR-C); knocking out some other components of the complex also increased the transformation efficiency, suggesting that ARP6 might regulate AMT via SWR-C. Moreover, knockout of ARP6 led to disruption of microtubule integrity, higher uptake and degradation of virulence proteins, and increased DNA stability inside the cells, all of which resulted in enhanced transformation efficiency. Our findings have identified molecular and cellular mechanisms regulating AMT and a potential target for enhancing the transformation efficiency in yeast cells. PMID:26425545

  4. Yeast Actin-Related Protein ARP6 Negatively Regulates Agrobacterium-Mediated Transformation of Yeast Cell.

    PubMed

    Luo, Yumei; Chen, Zikai; Zhu, Detu; Tu, Haitao; Pan, Shen Quan

    2015-01-01

    The yeasts, including Saccharomyces cerevisiae and Pichia pastoris, are single-cell eukaryotic organisms that can serve as models for human genetic diseases and hosts for large scale production of recombinant proteins in current biopharmaceutical industry. Thus, efficient genetic engineering tools for yeasts are of great research and economic values. Agrobacterium tumefaciens-mediated transformation (AMT) can transfer T-DNA into yeast cells as a method for genetic engineering. However, how the T-DNA is transferred into the yeast cells is not well established yet. Here our genetic screening of yeast knockout mutants identified a yeast actin-related protein ARP6 as a negative regulator of AMT. ARP6 is a critical member of the SWR1 chromatin remodeling complex (SWR-C); knocking out some other components of the complex also increased the transformation efficiency, suggesting that ARP6 might regulate AMT via SWR-C. Moreover, knockout of ARP6 led to disruption of microtubule integrity, higher uptake and degradation of virulence proteins, and increased DNA stability inside the cells, all of which resulted in enhanced transformation efficiency. Our findings have identified molecular and cellular mechanisms regulating AMT and a potential target for enhancing the transformation efficiency in yeast cells.

  5. The actin-related protein hArp8 accumulates on the mitotic chromosomes and functions in chromosome alignment

    SciTech Connect

    Aoyama, Naoki; Oka, Asako; Kitayama, Kumiko; Kurumizaka, Hitoshi; Harata, Masahiko

    2008-02-15

    The actin family consists of conventional actin and various actin-related proteins (Arps). Some of these Arps are localized in the nucleus, and a fraction of each of these nuclear Arps is functionally involved in chromatin remodeling and histone acetyltransferase complexes. On the other hand, in mitotic cells, the localization and function of the nuclear Arps are largely unknown. Human Arp8 (hArp8), an ortholog of yeast nuclear Arp8, was recently found to be associated with the hINO80-chromatin remodeling complex along with hArp5. Here we report that hArp8, but not hArp5, accumulates on mitotic chromosomes. This is the first example where a member of the actin family is found to be associated with mitotic chromosomes. Expression of truncated hArp8 proteins and depletion of endogenous hArp8 by RNA interference caused misalignment of mitotic chromosomes, suggesting that chromosome-associated hArp8 has a role in chromosome behavior. In contrast, depletion of hIno80 and hArp5 did not cause misalignment of chromosomes, suggesting that the role of hArp8 at mitotic chromosomes is independent of the activity of hINO80 complexes. These findings provide the first insight into a novel function of actin family members in mitosis.

  6. The human actin-related protein hArp5: Nucleo-cytoplasmic shuttling and involvement in DNA repair

    SciTech Connect

    Kitayama, Kumiko; Kamo, Mariko; Oma, Yukako; Matsuda, Ryo; Uchida, Takafumi; Ikura, Tsuyoshi; Tashiro, Satoshi; Ohyama, Takashi; Winsor, Barbara; Harata, Masahiko

    2009-01-15

    Certain actin-related proteins (Arps) of budding yeast are localized in the nucleus, and have essential roles as stoichiometric components of histone acetyltransferase (HAT) and chromatin remodeling complexes. On the other hand, identification of vertebrate nuclear Arps and their functional analyses are just beginning. We show that human Arp5 (hArp5) proteins are localized in the nucleus, and that arp5{delta} yeast cells are partially complemented by hArp5. Thus, hArp5 is a novel member of the nuclear Arps of vertebrates, which possess evolutionarily conserved functions from yeast to humans. We show here that hArp5 shuttles between the nucleus and the cytoplasm. Furthermore, after the induction of DNA double strand breaks (DSB), cell growth and the accumulation of phosphorylated histone H2AX ({gamma}-H2AX) are impaired by hArp5 depletion. Association of hArp5 with the hIno80 chromatin remodeling enzyme and decrease of chromatin-bound hIno80 by hArp5-depletion indicate that hArp5 may have a role in the recruitment of the hINO80 complex to chromatin. Overexpression of hArp5 and hIno80 enhanced {gamma}-H2AX accumulation. These observations suggest that hArp5 is involved in the process of DSB repair through the regulation of the chromatin remodelling machinery.

  7. DNA Binding Properties of the Actin-Related Protein Arp8 and Its Role in DNA Repair

    PubMed Central

    Murakami, Hirokazu; Otawa, Kenji; Tachiwana, Hiroaki; Oma, Yukako; Nishijima, Hitoshi; Shibahara, Kei-ich; Kurumizaka, Hitoshi; Harata, Masahiko

    2014-01-01

    Actin and actin-related proteins (Arps), which are members of the actin family, are essential components of many of these remodeling complexes. Actin, Arp4, Arp5, and Arp8 are found to be evolutionarily conserved components of the INO80 chromatin remodeling complex, which is involved in transcriptional regulation, DNA replication, and DNA repair. A recent report showed that Arp8 forms a module in the INO80 complex and this module can directly capture a nucleosome. In the present study, we showed that recombinant human Arp8 binds to DNAs, and preferentially binds to single-stranded DNA. Analysis of the binding of adenine nucleotides to Arp8 mutants suggested that the ATP-binding pocket, located in the evolutionarily conserved actin fold, plays a regulatory role in the binding of Arp8 to DNA. To determine the cellular function of Arp8, we derived tetracycline-inducible Arp8 knockout cells from a cultured human cell line. Analysis of results obtained after treating these cells with aphidicolin and camptothecin revealed that Arp8 is involved in DNA repair. Together with the previous observation that Arp8, but not γ-H2AX, is indispensable for recruiting INO80 complex to DSB in human, results of our study suggest an individual role for Arp8 in DNA repair. PMID:25299602

  8. Assembly of the Arp5 (Actin-related Protein) Subunit Involved in Distinct INO80 Chromatin Remodeling Activities.

    PubMed

    Yao, Wei; Beckwith, Sean L; Zheng, Tina; Young, Thomas; Dinh, Van T; Ranjan, Anand; Morrison, Ashby J

    2015-10-16

    ATP-dependent chromatin remodeling, which repositions and restructures nucleosomes, is essential to all DNA-templated processes. The INO80 chromatin remodeling complex is an evolutionarily conserved complex involved in diverse cellular processes, including transcription, DNA repair, and replication. The functional diversity of the INO80 complex can, in part, be attributed to specialized activities of distinct subunits that compose the complex. Furthermore, structural analyses have identified biochemically discrete subunit modules that assemble along the Ino80 ATPase scaffold. Of particular interest is the Saccharomyces cerevisiae Arp5-Ies6 module located proximal to the Ino80 ATPase and the Rvb1-Rvb2 helicase module needed for INO80-mediated in vitro activity. In this study we demonstrate that the previously uncharacterized Ies2 subunit is required for Arp5-Ies6 association with the catalytic components of the INO80 complex. In addition, Arp5-Ies6 module assembly with the INO80 complex is dependent on distinct conserved domains within Arp5, Ies6, and Ino80, including the spacer region within the Ino80 ATPase domain. Arp5-Ies6 interacts with chromatin via assembly with the INO80 complex, as IES2 and INO80 deletion results in loss of Arp5-Ies6 chromatin association. Interestingly, ectopic addition of the wild-type Arp5-Ies6 module stimulates INO80-mediated ATP hydrolysis and nucleosome sliding in vitro. However, the addition of mutant Arp5 lacking unique insertion domains facilitates ATP hydrolysis in the absence of nucleosome sliding. Collectively, these results define the requirements of Arp5-Ies6 assembly, which are needed to couple ATP hydrolysis to productive nucleosome movement.

  9. Sequence and comparative genomic analysis of actin-related proteins.

    PubMed

    Muller, Jean; Oma, Yukako; Vallar, Laurent; Friederich, Evelyne; Poch, Olivier; Winsor, Barbara

    2005-12-01

    Actin-related proteins (ARPs) are key players in cytoskeleton activities and nuclear functions. Two complexes, ARP2/3 and ARP1/11, also known as dynactin, are implicated in actin dynamics and in microtubule-based trafficking, respectively. ARP4 to ARP9 are components of many chromatin-modulating complexes. Conventional actins and ARPs codefine a large family of homologous proteins, the actin superfamily, with a tertiary structure known as the actin fold. Because ARPs and actin share high sequence conservation, clear family definition requires distinct features to easily and systematically identify each subfamily. In this study we performed an in depth sequence and comparative genomic analysis of ARP subfamilies. A high-quality multiple alignment of approximately 700 complete protein sequences homologous to actin, including 148 ARP sequences, allowed us to extend the ARP classification to new organisms. Sequence alignments revealed conserved residues, motifs, and inserted sequence signatures to define each ARP subfamily. These discriminative characteristics allowed us to develop ARPAnno (http://bips.u-strasbg.fr/ARPAnno), a new web server dedicated to the annotation of ARP sequences. Analyses of sequence conservation among actins and ARPs highlight part of the actin fold and suggest interactions between ARPs and actin-binding proteins. Finally, analysis of ARP distribution across eukaryotic phyla emphasizes the central importance of nuclear ARPs, particularly the multifunctional ARP4.

  10. A mutation in the Cc.arp9 gene encoding a putative actin-related protein causes defects in fruiting initiation and asexual development in the agaricomycete Coprinopsis cinerea.

    PubMed

    Nakazawa, Takehito; Ando, Yuki; Hata, Takeshi; Nakahori, Kiyoshi

    2016-08-01

    Agaricomycetes exhibit a remarkable morphological differentiation from vegetative mycelia to huge fruiting bodies. To investigate the molecular mechanism underlying the fruiting body development, we have isolated and characterized many Coprinopsis cinerea mutant strains defective in fruiting initiation to date. Dikaryon formation in agaricomycetes, which is followed by fruiting development, is governed by the mating type loci, A and B. Recently, mutations in the Cc.snf5 gene, which encodes a putative component of the chromatin remodeling complex switch/sucrose non-fermentable (SWI/SNF), were shown to cause defects in A-regulated clamp cell morphogenesis, as well as in fruiting initiation. Here, we demonstrate that Cc.arp9, which encodes a putative actin-related protein associated with two chromatin remodeling complexes, SWI/SNF and remodels the structure of chromatin (RSC), is also essential for fruiting initiation. In contrast to Cc.snf5 mutants, Cc.arp9 mutants were not defective in clamp cell formation. The effects of mutations in Cc.arp9 and Cc.snf5 on oidia production and the transcriptional expression levels of clp1 and pcc1, which are under the control of the A gene, were also examined. These indicated that Cc.Snf5 is involved in A-regulated pathways, whereas Cc.Arp9 is not apparently. Cc.arp9/Cc.snf5 double-gene disruptants were generated and their phenotypes were analyzed, which suggested a complicated developmental regulation mechanism mediated by chromatin remodeling.

  11. A mutation in the Cc.arp9 gene encoding a putative actin-related protein causes defects in fruiting initiation and asexual development in the agaricomycete Coprinopsis cinerea.

    PubMed

    Nakazawa, Takehito; Ando, Yuki; Hata, Takeshi; Nakahori, Kiyoshi

    2016-08-01

    Agaricomycetes exhibit a remarkable morphological differentiation from vegetative mycelia to huge fruiting bodies. To investigate the molecular mechanism underlying the fruiting body development, we have isolated and characterized many Coprinopsis cinerea mutant strains defective in fruiting initiation to date. Dikaryon formation in agaricomycetes, which is followed by fruiting development, is governed by the mating type loci, A and B. Recently, mutations in the Cc.snf5 gene, which encodes a putative component of the chromatin remodeling complex switch/sucrose non-fermentable (SWI/SNF), were shown to cause defects in A-regulated clamp cell morphogenesis, as well as in fruiting initiation. Here, we demonstrate that Cc.arp9, which encodes a putative actin-related protein associated with two chromatin remodeling complexes, SWI/SNF and remodels the structure of chromatin (RSC), is also essential for fruiting initiation. In contrast to Cc.snf5 mutants, Cc.arp9 mutants were not defective in clamp cell formation. The effects of mutations in Cc.arp9 and Cc.snf5 on oidia production and the transcriptional expression levels of clp1 and pcc1, which are under the control of the A gene, were also examined. These indicated that Cc.Snf5 is involved in A-regulated pathways, whereas Cc.Arp9 is not apparently. Cc.arp9/Cc.snf5 double-gene disruptants were generated and their phenotypes were analyzed, which suggested a complicated developmental regulation mechanism mediated by chromatin remodeling. PMID:26746642

  12. Crystals of the Arp2/3 complex in two new space groups with structural information about actin-related protein 2 and potential WASP binding sites.

    PubMed

    Jurgenson, Christopher T; Pollard, Thomas D

    2015-09-01

    Co-crystals of the bovine Arp2/3 complex with the CA motif from N-WASP in two new space groups were analyzed by X-ray diffraction. The crystals in the orthorhombic space group P212121 contained one complex per asymmetric unit, with unit-cell parameters a = 105.48, b = 156.71, c = 177.84 Å, and diffracted to 3.9 Å resolution. The crystals in the tetragonal space group P41 contained two complexes per asymmetric unit, with unit-cell parameters a = b = 149.93, c = 265.91 Å, and diffracted to 5.0 Å resolution. The electron-density maps of both new crystal forms had densities for small segments of subdomains 1 and 2 of Arp2. Both maps had density at the binding site on Arp3 for the C-terminal EWE tripeptide from N-WASP and a binding site proposed for the C motif of N-WASP in the barbed-end groove of Arp2. The map from the tetragonal crystal form had density near the barbed end of Arp3 that may correspond to the C helix of N-WASP. The noise levels and the low resolution of the maps made the assignment of specific molecular structures for any of these CA peptides impossible.

  13. Rho GTPases and the Downstream Effectors Actin-related Protein 2/3 (Arp2/3) Complex and Myosin II Induce Membrane Fusion at Self-contacts*

    PubMed Central

    Sumida, Grant M.; Yamada, Soichiro

    2015-01-01

    Actin regulation is required for membrane activities that drive cell adhesion and migration. The Rho GTPase family plays critical roles in actin and membrane dynamics; however, the roles of the Rho GTPase family are not limited to cell adhesion and migration. Using micron-sized obstacles to induce the formation of self-contacts in epithelial cells, we previously showed that self-adhesion is distinct from cell-to-cell adhesion in that self-contacts are eliminated by membrane fusion. In the current study, we identified Rho GTPases, RhoA, Rac1, and Cdc42, as potential upstream regulators of membrane fusion. The RhoA downstream effector myosin II is required for fusion as the expression of mutant myosin light chain reduced membrane fusion. Furthermore, an inhibitor of the Arp2/3 complex, a downstream effector of Rac1 and Cdc42, also reduced self-contact-induced membrane fusion. At self-contacts, while the concentration of E-cadherin diminished, the intensity of GFP-tagged Arp3 rapidly fluctuated then decreased and stabilized after membrane fusion. Taken together, these data suggest that the Arp2/3 complex-mediated actin polymerization brings two opposing membranes into close apposition by possibly excluding E-cadherin from contact sites, thus promoting membrane fusion at self-contacts. PMID:25527498

  14. ACTIN-RELATED PROTEIN6 Regulates Female Meiosis by Modulating Meiotic Gene Expression in Arabidopsis.

    PubMed

    Qin, Yuan; Zhao, Lihua; Skaggs, Megan I; Andreuzza, Sebastien; Tsukamoto, Tatsuya; Panoli, Aneesh; Wallace, Kirsten N; Smith, Steven; Siddiqi, Imran; Yang, Zhenbiao; Yadegari, Ramin; Palanivelu, Ravishankar

    2014-04-15

    In flowering plants, meiocytes develop from subepidermal cells in anthers and ovules. The mechanisms that integrate gene-regulatory processes with meiotic programs during reproductive development remain poorly characterized. Here, we show that Arabidopsis thaliana plants deficient in ACTIN-RELATED PROTEIN6 (ARP6), a subunit of the SWR1 ATP-dependent chromatin-remodeling complex, exhibit defects in prophase I of female meiosis. We found that this meiotic defect is likely due to dysregulated expression of meiotic genes, particularly those involved in meiotic recombination, including DMC1 (DISRUPTED MEIOTIC cDNA1). Analysis of DMC1 expression in arp6 mutant plants indicated that ARP6 inhibits expression of DMC1 in the megasporocyte and surrounding nonsporogeneous ovule cells before meiosis. After cells enter meiosis, however, ARP6 activates DMC1 expression specifically in the megasporocyte even as it continues to inhibit DMC1 expression in the nonsporogenous ovule cells. We further show that deposition of the histone variant H2A.Z, mediated by the SWR1 chromatin-remodeling complex at the DMC1 gene body, requires ARP6. Therefore, ARP6 regulates female meiosis by determining the spatial and temporal patterns of gene expression required for proper meiosis during ovule development. PMID:24737671

  15. Plasma IgG autoantibody against actin-related protein 3 in liver fluke Opisthorchis viverrini infection.

    PubMed

    Rucksaken, R; Haonon, O; Pinlaor, P; Pairojkul, C; Roytrakul, S; Yongvanit, P; Selmi, C; Pinlaor, S

    2015-07-01

    Opisthorchiasis secondary to Opisthorchis viverrini infection leads to cholangiocellular carcinoma through chronic inflammation of the bile ducts and possibly inducing autoimmunity. It was hypothesized that plasma autoantibodies directed against self-proteins are biomarkers for opisthorchiasis. Plasma from patients with opisthorchiasis was tested using proteins derived from immortalized cholangiocyte cell lines, and spots reacting with plasma were excised and subjected to LC-MS/MS. Seven protein spots were recognized by IgG autoantibodies, and the highest matching scored protein was actin-related protein 3 (ARP3). The antibody against ARP3 was tested in plasma from 55 O. viverrini-infected patients, 24 patients with others endemic parasitic infections and 17 healthy controls using Western blot and ELISA. Immunoreactivity against recombinant ARP3 was significantly more prevalent in opisthorchiasis compared to healthy controls at Western blotting and ELISA (P < 0.05). Plasma ARP3 autoantibody titres were also higher in opisthorchiasis compared to healthy individuals (P < 0.01) and other parasitic infections including Strongyloides stercoralis (P < 0.001), echinostome (P < 0.05), hookworms (P < 0.001) and Taenia spp. (P < 0.05). It was further characterized in that the ARP3 autoantibody titre had a sensitivity of 78.18% and specificity of 100% for opisthorchiasis. In conclusion, it may be suggested that plasma anti-ARP3 might represent a new diagnostic antibody for opisthorchiasis. PMID:25809205

  16. Actin-related protein 2/3 complex-based actin polymerization is critical for male fertility.

    PubMed

    Lee, J S; Kwon, W S; Rahman, M S; Yoon, S J; Park, Y J; Pang, M G

    2015-09-01

    The actin-related protein 2/3 (Arp2/3) complex is critical for regulation of actin polymerization, which is associated with sperm motility and capacitation status. However, the function of the Arp2/3 complex in male fertility has not yet been fully elucidated. Therefore, this study was designed to investigate the role of the Arp2/3 complex in different processes in spermatozoa and its consequences on fertilization and early embryonic development. In this in vitro study, mouse spermatozoa were incubated with different concentrations (10, 100, and 500 μm) of CK-636, an Arp2/3 complex antagonist. Our results demonstrated that inhibition of the Arp2/3 complex by high concentrations (100 and 500 μm) of CK-636 induced hyper-activated motility and acrosomal reaction, whereas intracellular calcium and tyrosine phosphorylation levels in spermatozoa were inhibited. Moreover, exposure of spermatozoa to the highest concentration of CK-636 reduced fertilization and embryo development. Interestingly, fertilization was significantly increased after treatment with 100 μm CK-636, whereas embryonic development was significantly decreased. Therefore, we conclude that the Arp2/3 complex plays a decisive role in regulation of sperm function and male fertility via actin polymerization. We anticipate that the Arp2/3 complex may have clinical application as marker for male fertility and male contraceptive targeting.

  17. Mammalian actin-related protein 2/3 complex localizes to regions of lamellipodial protrusion and is composed of evolutionarily conserved proteins.

    PubMed Central

    Machesky, L M; Reeves, E; Wientjes, F; Mattheyse, F J; Grogan, A; Totty, N F; Burlingame, A L; Hsuan, J J; Segal, A W

    1997-01-01

    Human neutrophils contain a complex of proteins similar to the actin-related protein 2/3 (Arp2/3) complex of Acanthamoeba. We have obtained peptide sequence information for each member of the putative seven-protein complex previously described for Acanthamoeba and human platelets. From the peptide sequences we have identified cDNA species encoding three novel proteins in this complex. We find that in addition to Arp2 and Arp3, this complex contains a relative of the human (Suppressor of Profilin) SOP2Hs protein and four previously unknown proteins. These proteins localize in the cytoplasm of fibroblasts that lack lamellipodia, but are enriched in lamellipodia on stimulation with serum or platelet-derived growth factor. We propose a conserved and dynamic role for this complex in the organization of the actin cytoskeleton. PMID:9359840

  18. The actin family protein ARP6 contributes to the structure and the function of the nucleolus

    SciTech Connect

    Kitamura, Hiroshi; Matsumori, Haruka; Kalendova, Alzbeta; Hozak, Pavel; Goldberg, Ilya G.; Nakao, Mitsuyoshi; Saitoh, Noriko; Harata, Masahiko

    2015-08-21

    The actin family members, consisting of actin and actin-related proteins (ARPs), are essential components of chromatin remodeling complexes. ARP6, one of the nuclear ARPs, is part of the Snf-2-related CREB-binding protein activator protein (SRCAP) chromatin remodeling complex, which promotes the deposition of the histone variant H2A.Z into the chromatin. In this study, we showed that ARP6 influences the structure and the function of the nucleolus. ARP6 is localized in the central region of the nucleolus, and its knockdown induced a morphological change in the nucleolus. We also found that in the presence of high concentrations of glucose ARP6 contributed to the maintenance of active ribosomal DNA (rDNA) transcription by placing H2A.Z into the chromatin. In contrast, under starvation, ARP6 was required for cell survival through the repression of rDNA transcription independently of H2A.Z. These findings reveal novel pleiotropic roles for the actin family in nuclear organization and metabolic homeostasis. - Highlights: • ARP6, an actin related protein, is important for nucleolar function and structure. • A population of ARP6 is localized in the center of nucleolus. • Depletion of ARP6 resulted in aberrant shape of the nucleolus. • ARP6 maintains the active rDNA transcription under high glucose. • ARP6 is required for the repression of rDNA transcription under starvation.

  19. The actinome of Dictyostelium discoideum in comparison to actins and actin-related proteins from other organisms.

    PubMed

    Joseph, Jayabalan M; Fey, Petra; Ramalingam, Nagendran; Liu, Xiao I; Rohlfs, Meino; Noegel, Angelika A; Müller-Taubenberger, Annette; Glöckner, Gernot; Schleicher, Michael

    2008-07-09

    Actin belongs to the most abundant proteins in eukaryotic cells which harbor usually many conventional actin isoforms as well as actin-related proteins (Arps). To get an overview over the sometimes confusing multitude of actins and Arps, we analyzed the Dictyostelium discoideum actinome in detail and compared it with the genomes from other model organisms. The D. discoideum actinome comprises 41 actins and actin-related proteins. The genome contains 17 actin genes which most likely arose from consecutive gene duplications, are all active, in some cases developmentally regulated and coding for identical proteins (Act8-group). According to published data, the actin fraction in a D. discoideum cell consists of more than 95% of these Act8-type proteins. The other 16 actin isoforms contain a conventional actin motif profile as well but differ in their protein sequences. Seven actin genes are potential pseudogenes. A homology search of the human genome using the most typical D. discoideum actin (Act8) as query sequence finds the major actin isoforms such as cytoplasmic beta-actin as best hit. This suggests that the Act8-group represents a nearly perfect actin throughout evolution. Interestingly, limited data from D. fasciculatum, a more ancient member among the social amoebae, show different relationships between conventional actins. The Act8-type isoform is most conserved throughout evolution. Modeling of the putative structures suggests that the majority of the actin-related proteins is functionally unrelated to canonical actin. The data suggest that the other actin variants are not necessary for the cytoskeleton itself but rather regulators of its dynamical features or subunits in larger protein complexes.

  20. The role of Arabidopsis Actin-Related Protein 3 in amyloplast sedimentation and polar auxin transport in root gravitropism

    PubMed Central

    Zou, Jun-Jie; Zheng, Zhong-Yu; Xue, Shan; Li, Han-Hai; Wang, Yu-Ren; Le, Jie

    2016-01-01

    Gravitropism is vital for shaping directional plant growth in response to the forces of gravity. Signals perceived in the gravity-sensing cells can be converted into biochemical signals and transmitted. Sedimentation of amyloplasts in the columella cells triggers asymmetric auxin redistribution in root tips, leading to downward root growth. The actin cytoskeleton is thought to play an important role in root gravitropism, although the molecular mechanism has not been resolved. DISTORTED1 (DIS1) encodes the ARP3 subunit of the Arabidopsis Actin-Related Protein 2/3 (ARP2/3) complex, and the ARP3/DIS1 mutant dis1-1 showed delayed root curvature after gravity stimulation. Microrheological analysis revealed that the high apparent viscosity within dis1-1 central columella cells is closely associated with abnormal movement trajectories of amyloplasts. Analysis using a sensitive auxin input reporter DII-VENUS showed that asymmetric auxin redistribution was reduced in the root tips of dis1-1, and the actin-disrupting drug Latrunculin B increased the asymmetric auxin redistribution. An uptake assay using the membrane-selective dye FM4-64 indicated that endocytosis was decelerated in dis1-1 root epidermal cells. Treatment and wash-out with Brefeldin A, which inhibits protein transport from the endoplasmic reticulum to the Golgi apparatus, showed that cycling of the auxin-transporter PIN-FORMED (PIN) proteins to the plasma membrane was also suppressed in dis1-1 roots. The results reveal that ARP3/DIS1 acts in root gravitropism by affecting amyloplast sedimentation and PIN-mediated polar auxin transport through regulation of PIN protein trafficking. PMID:27473572

  1. The actin-related protein Act3p of Saccharomyces cerevisiae is located in the nucleus.

    PubMed Central

    Weber, V; Harata, M; Hauser, H; Wintersberger, U

    1995-01-01

    Actin-related proteins, a group of protein families that exhibit about 50% sequence identity among each other and to conventional actin, have been found in a variety of eukaryotic organisms. In the budding yeast Saccharomyces cerevisiae, genes for one conventional actin (ACT1) and for three actin-related proteins (ACT2, ACT3, and ACT5) are known. ACT3, which we recently discovered, is an essential gene coding for a polypeptide of 489 amino acids (Act3p), with a calculated molecular mass of 54.8 kDa. Besides its homology to conventional actin, Act3p possesses a domain exhibiting weak similarity to the chromosomal protein HMG-14 as well as a potential nuclear localization signal. An antiserum prepared against a specific segment of the ACT3 gene product recognizes a polypeptide band of approximately 55 kDa in yeast extract. Indirect immunofluorescence experiments with this antiserum revealed that Act3p is located in the nucleus. Nuclear staining was observed in all cells regardless of the stage of the cell cycle. Independently, immunoblotting experiments with subcellular fractions showed that Act3p is indeed highly enriched in the nuclear fraction. We suggest that Act3p is an essential constituent of yeast chromatin. Images PMID:8573785

  2. The actin family protein ARP6 contributes to the structure and the function of the nucleolus.

    PubMed

    Kitamura, Hiroshi; Matsumori, Haruka; Kalendova, Alzbeta; Hozak, Pavel; Goldberg, Ilya G; Nakao, Mitsuyoshi; Saitoh, Noriko; Harata, Masahiko

    2015-08-21

    The actin family members, consisting of actin and actin-related proteins (ARPs), are essential components of chromatin remodeling complexes. ARP6, one of the nuclear ARPs, is part of the Snf-2-related CREB-binding protein activator protein (SRCAP) chromatin remodeling complex, which promotes the deposition of the histone variant H2A.Z into the chromatin. In this study, we showed that ARP6 influences the structure and the function of the nucleolus. ARP6 is localized in the central region of the nucleolus, and its knockdown induced a morphological change in the nucleolus. We also found that in the presence of high concentrations of glucose ARP6 contributed to the maintenance of active ribosomal DNA (rDNA) transcription by placing H2A.Z into the chromatin. In contrast, under starvation, ARP6 was required for cell survival through the repression of rDNA transcription independently of H2A.Z. These findings reveal novel pleiotropic roles for the actin family in nuclear organization and metabolic homeostasis.

  3. Structure and Biochemical Properties of Fission Yeast Arp2/3 Complex Lacking the Arp2 Subunit

    SciTech Connect

    Nolen, B.; Pollard, T

    2008-01-01

    Arp2/3 (actin-related protein 2/3) complex is a seven-subunit complex that nucleates branched actin filaments in response to cellular signals. Nucleation-promoting factors such as WASp/Scar family proteins activate the complex by facilitating the activating conformational change and recruiting the first actin monomer for the daughter branch. Here we address the role of the Arp2 subunit in the function of Arp2/3 complex by isolating a version of the complex lacking Arp2 (Arp2? Arp2/3 complex) from fission yeast. An x-ray crystal structure of the ?Arp2 Arp2/3 complex showed that the rest of the complex is unperturbed by the loss of Arp2. However, the Arp2? Arp2/3 complex was inactive in actin nucleation assays, indicating that Arp2 is essential to form a branch. A fluorescence anisotropy assay showed that Arp2 does not contribute to the affinity of the complex for Wsp1-VCA, a Schizosaccharomyces pombe nucleation-promoting factor protein. Fluorescence resonance energy transfer experiments showed that the loss of Arp2 does not prevent VCA from recruiting an actin monomer to the complex. Truncation of the N terminus of ARPC5, the smallest subunit in the complex, increased the yield of Arp2? Arp2/3 complex during purification but did not compromise nucleation activity of the full Arp2/3 complex.

  4. A Novel Actin-Related Protein Is Associated with Daughter Cell Formation in Toxoplasma gondii▿ †

    PubMed Central

    Gordon, Jennifer L.; Beatty, Wandy L.; Sibley, L. David

    2008-01-01

    Cell division in Toxoplasma gondii occurs by an unusual budding mechanism termed endodyogeny, during which twin daughters are formed within the body of the mother cell. Cytokinesis begins with the coordinated assembly of the inner membrane complex (IMC), which surrounds the growing daughter cells. The IMC is compiled of both flattened membrane cisternae and subpellicular filaments composed of articulin-like proteins attached to underlying singlet microtubules. While proteins that comprise the elongating IMC have been described, little is known about its initial formation. Using Toxoplasma as a model system, we demonstrate that actin-like protein 1 (ALP1) is partially redistributed to the IMC at early stages in its formation. Immunoelectron microscopy localized ALP1 to a discrete region of the nuclear envelope, on transport vesicles, and on the nascent IMC of the daughter cells prior to the arrival of proteins such as IMC-1. The overexpression of ALP1 under the control of a strong constitutive promoter disrupted the formation of the daughter cell IMC, leading to delayed growth and defects in nuclear and apicoplast segregation. Collectively, these data suggest that ALP1 participates in the formation of daughter cell membranes during cell division in apicomplexan parasites. PMID:18408052

  5. Reduced myelin basic protein and actin-related gene expression in visual cortex in schizophrenia.

    PubMed

    Matthews, Paul R; Eastwood, Sharon L; Harrison, Paul J

    2012-01-01

    Most brain gene expression studies of schizophrenia have been conducted in the frontal cortex or hippocampus. The extent to which alterations occur in other cortical regions is not well established. We investigated primary visual cortex (Brodmann area 17) from the Stanley Neuropathology Consortium collection of tissue from 60 subjects with schizophrenia, bipolar disorder, major depression, or controls. We first carried out a preliminary array screen of pooled RNA, and then used RT-PCR to quantify five mRNAs which the array identified as differentially expressed in schizophrenia (myelin basic protein [MBP], myelin-oligodendrocyte glycoprotein [MOG], β-actin [ACTB], thymosin β-10 [TB10], and superior cervical ganglion-10 [SCG10]). Reduced mRNA levels were confirmed by RT-PCR for MBP, ACTB and TB10. The MBP reduction was limited to transcripts containing exon 2. ACTB and TB10 mRNAs were also decreased in bipolar disorder. None of the transcripts were altered in subjects with major depression. Reduced MBP mRNA in schizophrenia replicates findings in other brain regions and is consistent with oligodendrocyte involvement in the disorder. The decreases in expression of ACTB, and the actin-binding protein gene TB10, suggest changes in cytoskeletal organisation. The findings confirm that the primary visual cortex shows molecular alterations in schizophrenia and extend the evidence for a widespread, rather than focal, cortical pathophysiology.

  6. Phosphorylation of the Arp2 subunit relieves auto-inhibitory interactions for Arp2/3 complex activation.

    PubMed

    Narayanan, Arjun; LeClaire, Lawrence L; Barber, Diane L; Jacobson, Matthew P

    2011-11-01

    Actin filament assembly by the actin-related protein (Arp) 2/3 complex is necessary to build many cellular structures, including lamellipodia at the leading edge of motile cells and phagocytic cups, and to move endosomes and intracellular pathogens. The crucial role of the Arp2/3 complex in cellular processes requires precise spatiotemporal regulation of its activity. While binding of nucleation-promoting factors (NPFs) has long been considered essential to Arp2/3 complex activity, we recently showed that phosphorylation of the Arp2 subunit is also necessary for Arp2/3 complex activation. Using molecular dynamics simulations and biochemical assays with recombinant Arp2/3 complex, we now show how phosphorylation of Arp2 induces conformational changes permitting activation. The simulations suggest that phosphorylation causes reorientation of Arp2 relative to Arp3 by destabilizing a network of salt-bridge interactions at the interface of the Arp2, Arp3, and ARPC4 subunits. Simulations also suggest a gain-of-function ARPC4 mutant that we show experimentally to have substantial activity in the absence of NPFs. We propose a model in which a network of auto-inhibitory salt-bridge interactions holds the Arp2 subunit in an inactive orientation. These auto-inhibitory interactions are destabilized upon phosphorylation of Arp2, allowing Arp2 to reorient to an activation-competent state. PMID:22125478

  7. Visualizing Arp2/3 Complex Activation Mediated by Binding of ATP and WASp using Structural Mass Spectrometry

    SciTech Connect

    Kiselar,J.; Mahaffy, R.; Pollard, T.; Almo, S.; Chance, M.

    2007-01-01

    Actin-related protein (Arp) 2/3 complex nucleates new branches in actin filaments playing a key role in controlling eukaryotic cell motility. This process is tightly regulated by activating factors: ATP and WASp-family proteins. However, the mechanism of activation remains largely hypothetical. We used radiolytic protein footprinting with mass spectrometry in solution to probe the effects of nucleotide- and WASp-binding on Arp2/3. These results represent two significant advances in such footprinting approaches. First, Arp2/3 is the most complex macromolecular assembly yet examined; second, only a few picomoles of Arp2/3 was required for individual experiments. In terms of structural biology of Arp 2/3, we find that ATP binding induces conformational changes within Arp2/3 complex in Arp3 (localized in peptide segments 5-18, 212-225, and 318-327) and Arp2 (within peptide segment 300-316). These data are consistent with nucleotide docking within the nucleotide clefts of the actin-related proteins promoting closure of the cleft of the Arp3 subunit. However, ATP binding does not induce conformational changes in the other Arp subunits. Arp2/3 complex binds to WASp within the C subdomain at residue Met 474 and within the A subdomain to Trp 500. Our data suggest a bivalent attachment of WASp to Arp3 (within peptides 162-191 and 318-329) and Arp2 (within peptides 66-80 and 87-97). WASp-dependent protections from oxidation within peptides 54-65 and 80-91 of Arp3 and in peptides 300-316 of Arp2 suggest domain rearrangements of Arp2 and Arp3 resulting in a closed conformational state consistent with an 'actin-dimer' model for the active state.

  8. The actin-related protein Sac1 is required for morphogenesis and cell wall integrity in Candida albicans.

    PubMed

    Zhang, Bing; Yu, Qilin; Jia, Chang; Wang, Yuzhou; Xiao, Chenpeng; Dong, Yijie; Xu, Ning; Wang, Lei; Li, Mingchun

    2015-08-01

    Candida albicans is a common pathogenic fungus and has aroused widespread attention recently. Actin cytoskeleton, an important player in polarized growth, protein secretion and organization of cell shape, displays irreplaceable role in hyphal development and cell integrity. In this study, we demonstrated a homologue of Saccharomyces cerevisiae Sac1, in C. albicans. It is a potential PIP phosphatase with Sac domain which is related to actin organization, hyphal development, biofilm formation and cell wall integrity. Deletion of SAC1 did not lead to insitiol-auxotroph phenotype in C. albicans, but this gene rescued the growth defect of S. cerevisiae sac1Δ in the insitiol-free medium. Hyphal induction further revealed the deficiency of sac1Δ/Δ in hyphal development and biofilm formation. Fluorescence observation and real time PCR (RT-PCR) analysis suggested both actin and the hyphal cell wall protein Hwp1 were overexpressed and mislocated in this mutant. Furthermore, cell wall integrity (CWI) was largely affected by deletion of SAC1, due to the hypersensitivity to cell wall stress, changed content and distribution of chitin in the mutant. As a result, the virulence of sac1Δ/Δ was seriously attenuated. Taken together, this study provides evidence that Sac1, as a potential PIP phosphatase, is essential for actin organization, hyphal development, CWI and pathogenicity in C. albicans.

  9. ox-LDL induces endothelial dysfunction by promoting Arp2/3 complex expression.

    PubMed

    Tang, Yao; Zhao, Jianting; Shen, Liming; Jin, Yiqi; Zhang, Zhixuan; Xu, Guoxiong; Huang, Xianchen

    2016-06-24

    Oxidized low-density lipoproteins (ox-LDL) play a critical role in endothelial injury including cytoskeleton reorganization, which is closely related to actin-related protein 2/3 (Arp2/3) complex. The aim of this study was to investigate the role of Arp2/3 complex in ox-LDL-induced endothelial dysfunction. In this study, we found that Arp2 and Arp3 expression was increased under atherosclerotic conditions both in ApoE-/- mice and in ox-LDL-stimulated human coronary artery endothelial cells (HCAECs). Arp2/3 complex inhibitor CK666 significantly reduced ox-LDL-induced ROS generation and cytoskeleton reorganization, and increased NO release in HCAECs. Pretreatment with LOX-1- but not CD36-blocking antibody markedly decreased ox-LDL-induced Arp2 and Arp3 expression. Moreover, Rac-1 siRNA remarkably suppressed ox-LDL-stimulated Arp2 and Arp3 expression. Additionally, CK666 reduced endothelial nitric oxide synthase (eNOS) expression and atherosclerotic lesions in ApoE-/- mice. Collectively, ox-LDL induces endothelial dysfunction by activating LOX-1/Rac-1 signaling and upregulating Arp2/3 complex expression. PMID:27181356

  10. Characterization of Two Classes of Small Molecule Inhibitors of Arp2/3 Complex

    SciTech Connect

    Nolen, B.; Tomasevic, N; Russell, A; Pierce, D; Jia, Z; McCormick, C; Hartman, J; Sakowicz, R; Pollard, T

    2009-01-01

    Polymerization of actin filaments directed by the actin-related protein (Arp)2/3 complex supports many types of cellular movements. However, questions remain regarding the relative contributions of Arp2/3 complex versus other mechanisms of actin filament nucleation to processes such as path finding by neuronal growth cones; this is because of the lack of simple methods to inhibit Arp2/3 complex reversibly in living cells. Here we describe two classes of small molecules that bind to different sites on the Arp2/3 complex and inhibit its ability to nucleate actin filaments. CK-0944636 binds between Arp2 and Arp3, where it appears to block movement of Arp2 and Arp3 into their active conformation. CK-0993548 inserts into the hydrophobic core of Arp3 and alters its conformation. Both classes of compounds inhibit formation of actin filament comet tails by Listeria and podosomes by monocytes. Two inhibitors with different mechanisms of action provide a powerful approach for studying the Arp2/3 complex in living cells.

  11. The structural basis of actin filament branching by the Arp2/3 complex

    PubMed Central

    Rouiller, Isabelle; Xu, Xiao-Ping; Amann, Kurt J.; Egile, Coumaran; Nickell, Stephan; Nicastro, Daniela; Li, Rong; Pollard, Thomas D.; Volkmann, Niels; Hanein, Dorit

    2008-01-01

    The actin-related protein 2/3 (Arp2/3) complex mediates the formation of branched actin filaments at the leading edge of motile cells and in the comet tails moving certain intracellular pathogens. Crystal structures of the Arp2/3 complex are available, but the architecture of the junction formed by the Arp2/3 complex at the base of the branch was not known. In this study, we use electron tomography to reconstruct the branch junction with sufficient resolution to show how the Arp2/3 complex interacts with the mother filament. Our analysis reveals conformational changes in both the mother filament and Arp2/3 complex upon branch formation. The Arp2 and Arp3 subunits reorganize into a dimer, providing a short-pitch template for elongation of the daughter filament. Two subunits of the mother filament undergo conformational changes that increase stability of the branch. These data provide a rationale for why branch formation requires cooperative interactions among the Arp2/3 complex, nucleation-promoting factors, an actin monomer, and the mother filament. PMID:18316411

  12. The structural basis of actin filament branching by the Arp2/3 complex.

    PubMed

    Rouiller, Isabelle; Xu, Xiao-Ping; Amann, Kurt J; Egile, Coumaran; Nickell, Stephan; Nicastro, Daniela; Li, Rong; Pollard, Thomas D; Volkmann, Niels; Hanein, Dorit

    2008-03-10

    The actin-related protein 2/3 (Arp2/3) complex mediates the formation of branched actin filaments at the leading edge of motile cells and in the comet tails moving certain intracellular pathogens. Crystal structures of the Arp2/3 complex are available, but the architecture of the junction formed by the Arp2/3 complex at the base of the branch was not known. In this study, we use electron tomography to reconstruct the branch junction with sufficient resolution to show how the Arp2/3 complex interacts with the mother filament. Our analysis reveals conformational changes in both the mother filament and Arp2/3 complex upon branch formation. The Arp2 and Arp3 subunits reorganize into a dimer, providing a short-pitch template for elongation of the daughter filament. Two subunits of the mother filament undergo conformational changes that increase stability of the branch. These data provide a rationale for why branch formation requires cooperative interactions among the Arp2/3 complex, nucleation-promoting factors, an actin monomer, and the mother filament.

  13. Structural and Biochemical Characterization of Two Binding Sites for Nucleation-promoting Factor WASp-VCA on Arp2/3 Complex

    SciTech Connect

    S Ti; C Jurgenson; B Nolen; T Pollard

    2011-12-31

    Actin-related protein (Arp) 2/3 complex mediates the formation of actin filament branches during endocytosis and at the leading edge of motile cells. The pathway of branch formation is ambiguous owing to uncertainty regarding the stoichiometry and location of VCA binding sites on Arp2/3 complex. Isothermal titration calorimetry showed that the CA motif from the C terminus of fission yeast WASP (Wsp1p) bound to fission yeast and bovine Arp2/3 complex with a stoichiometry of 2 to 1 and very different affinities for the two sites (K{sub d}s of 0.13 and 1.6 {micro}M for fission yeast Arp2/3 complex). Equilibrium binding, kinetic, and cross-linking experiments showed that (i) CA at high-affinity site 1 inhibited Arp2/3 complex binding to actin filaments, (ii) low-affinity site 2 had a higher affinity for CA when Arp2/3 complex was bound to actin filaments, and (iii) Arp2/3 complex had a much higher affinity for free CA than VCA cross-linked to an actin monomer. Crystal structures showed the C terminus of CA bound to the low-affinity site 2 on Arp3 of bovine Arp2/3 complex. The C helix is likely to bind to the barbed end groove of Arp3 in a position for VCA to deliver the first actin subunit to the daughter filament.

  14. A pathogenesis related-10 protein CaARP functions as aldo/keto reductase to scavenge cytotoxic aldehydes.

    PubMed

    Jain, Deepti; Khandal, Hitaishi; Khurana, Jitendra Paul; Chattopadhyay, Debasis

    2016-01-01

    Pathogenesis related-10 (PR-10) proteins are present as multigene family in most of the higher plants. The role of PR-10 proteins in plant is poorly understood. A sequence analysis revealed that a large number of PR-10 proteins possess conserved motifs found in aldo/keto reductases (AKRs) of yeast and fungi. We took three PR-10 proteins, CaARP from chickpea, ABR17 from pea and the major pollen allergen Bet v1 from silver birch as examples and showed that these purified recombinant proteins possessed AKR activity using various cytotoxic aldehydes including methylglyoxal and malondialdehyde as substrates and the reduced form of nicotinamide adenine dinucleotide phosphate (NADPH) as co-factor. Essential amino acids for this catalytic activity were identified by substitution with other amino acids. CaARP was able to discriminate between the reduced and oxidized forms of NADP independently of its catalytic activity and underwent structural change upon binding with NADPH. CaARP protein was preferentially localized in cytosol. When expressed in bacteria, yeast or plant, catalytically active variants of CaARP conferred tolerance to salinity, oxidative stress or cytotoxic aldehydes. CaARP-expressing plants showed lower lipid peroxidation product content in presence or absence of stress suggesting that the protein functions as a scavenger of cytotoxic aldehydes produced by metabolism and lipid peroxidation. Our result proposes a new biochemical property of a PR-10 protein.

  15. A pathogenesis related-10 protein CaARP functions as aldo/keto reductase to scavenge cytotoxic aldehydes.

    PubMed

    Jain, Deepti; Khandal, Hitaishi; Khurana, Jitendra Paul; Chattopadhyay, Debasis

    2016-01-01

    Pathogenesis related-10 (PR-10) proteins are present as multigene family in most of the higher plants. The role of PR-10 proteins in plant is poorly understood. A sequence analysis revealed that a large number of PR-10 proteins possess conserved motifs found in aldo/keto reductases (AKRs) of yeast and fungi. We took three PR-10 proteins, CaARP from chickpea, ABR17 from pea and the major pollen allergen Bet v1 from silver birch as examples and showed that these purified recombinant proteins possessed AKR activity using various cytotoxic aldehydes including methylglyoxal and malondialdehyde as substrates and the reduced form of nicotinamide adenine dinucleotide phosphate (NADPH) as co-factor. Essential amino acids for this catalytic activity were identified by substitution with other amino acids. CaARP was able to discriminate between the reduced and oxidized forms of NADP independently of its catalytic activity and underwent structural change upon binding with NADPH. CaARP protein was preferentially localized in cytosol. When expressed in bacteria, yeast or plant, catalytically active variants of CaARP conferred tolerance to salinity, oxidative stress or cytotoxic aldehydes. CaARP-expressing plants showed lower lipid peroxidation product content in presence or absence of stress suggesting that the protein functions as a scavenger of cytotoxic aldehydes produced by metabolism and lipid peroxidation. Our result proposes a new biochemical property of a PR-10 protein. PMID:26577640

  16. ARP2/3 localization in Arabidopsis leaf pavement cells: a diversity of intracellular pools and cytoskeletal interactions

    PubMed Central

    Zhang, Chunhua; Mallery, Eileen L.; Szymanski, Daniel B.

    2013-01-01

    In plant cells the actin cytoskeleton adopts many configurations, but is best understood as an unstable, interconnected track that rearranges to define the patterns of long distance transport of organelles during growth. Actin filaments do not form spontaneously; instead filament nucleators, such as the evolutionarily conserved actin-related protein (ARP) 2/3 complex, can efficiently generate new actin filament networks when in a fully activated state. A growing number of genetic experiments have shown that ARP2/3 is necessary for morphogenesis in processes that range from tip growth during root nodule formation to the diffuse polarized growth of leaf trichomes and pavement cells. Although progress has been rapid in the identification of proteins that function in series to positively regulate ARP2/3, less has been learned about the actual function of ARP2/3 in cells. In this paper, we analyze the localization of ARP2/3 in Arabidopsis leaf pavement cells. We detect a pool of ARP2/3 in the nucleus, and also find that ARP2/3 is efficiently and specifically clustered on multiple organelle surfaces and associates with both the actin filament and microtubule cytoskeletons. Our mutant analyses and ARP2/3 and actin double labeling experiments indicate that the clustering of ARP2/3 on organelle surfaces and an association with actin bundles does not necessarily reflect an active pool of ARP2/3, and instead most of the complex appears to exist as a latent organelle-associated pool. PMID:23874346

  17. ARP2/3 localization in Arabidopsis leaf pavement cells: a diversity of intracellular pools and cytoskeletal interactions.

    PubMed

    Zhang, Chunhua; Mallery, Eileen L; Szymanski, Daniel B

    2013-01-01

    In plant cells the actin cytoskeleton adopts many configurations, but is best understood as an unstable, interconnected track that rearranges to define the patterns of long distance transport of organelles during growth. Actin filaments do not form spontaneously; instead filament nucleators, such as the evolutionarily conserved actin-related protein (ARP) 2/3 complex, can efficiently generate new actin filament networks when in a fully activated state. A growing number of genetic experiments have shown that ARP2/3 is necessary for morphogenesis in processes that range from tip growth during root nodule formation to the diffuse polarized growth of leaf trichomes and pavement cells. Although progress has been rapid in the identification of proteins that function in series to positively regulate ARP2/3, less has been learned about the actual function of ARP2/3 in cells. In this paper, we analyze the localization of ARP2/3 in Arabidopsis leaf pavement cells. We detect a pool of ARP2/3 in the nucleus, and also find that ARP2/3 is efficiently and specifically clustered on multiple organelle surfaces and associates with both the actin filament and microtubule cytoskeletons. Our mutant analyses and ARP2/3 and actin double labeling experiments indicate that the clustering of ARP2/3 on organelle surfaces and an association with actin bundles does not necessarily reflect an active pool of ARP2/3, and instead most of the complex appears to exist as a latent organelle-associated pool.

  18. Signalling to actin assembly via the WASP (Wiskott-Aldrich syndrome protein)-family proteins and the Arp2/3 complex.

    PubMed Central

    Millard, Thomas H; Sharp, Stewart J; Machesky, Laura M

    2004-01-01

    The assembly of a branched network of actin filaments provides the mechanical propulsion that drives a range of dynamic cellular processes, including cell motility. The Arp2/3 complex is a crucial component of such filament networks. Arp2/3 nucleates new actin filaments while bound to existing filaments, thus creating a branched network. In recent years, a number of proteins that activate the filament nucleation activity of Arp2/3 have been identified, most notably the WASP (Wiskott-Aldrich syndrome protein) family. WASP-family proteins activate the Arp2/3 complex, and consequently stimulate actin assembly, in response to extracellular signals. Structural studies have provided a significant refinement in our understanding of the molecular detail of how the Arp2/3 complex nucleates actin filaments. There has also been much progress towards an understanding of the complicated signalling processes that regulate WASP-family proteins. In addition, the use of gene disruption in a number of organisms has led to new insights into the specific functions of individual WASP-family members. The present review will discuss the Arp2/3 complex and its regulators, in particular the WASP-family proteins. Emphasis will be placed on recent developments in the field that have furthered our understanding of actin dynamics and cell motility. PMID:15040784

  19. Role and structural mechanism of WASP-triggered conformational changes in branched actin filament nucleation by Arp2/3 complex.

    PubMed

    Rodnick-Smith, Max; Luan, Qing; Liu, Su-Ling; Nolen, Brad J

    2016-07-01

    The Arp2/3 (Actin-related proteins 2/3) complex is activated by WASP (Wiskott-Aldrich syndrome protein) family proteins to nucleate branched actin filaments that are important for cellular motility. WASP recruits actin monomers to the complex and stimulates movement of Arp2 and Arp3 into a "short-pitch" conformation that mimics the arrangement of actin subunits within filaments. The relative contribution of these functions in Arp2/3 complex activation and the mechanism by which WASP stimulates the conformational change have been unknown. We purified budding yeast Arp2/3 complex held in or near the short-pitch conformation by an engineered covalent cross-link to determine if the WASP-induced conformational change is sufficient for activity. Remarkably, cross-linked Arp2/3 complex bypasses the need for WASP in activation and is more active than WASP-activated Arp2/3 complex. These data indicate that stimulation of the short-pitch conformation is the critical activating function of WASP and that monomer delivery is not a fundamental requirement for nucleation but is a specific requirement for WASP-mediated activation. During activation, WASP limits nucleation rates by releasing slowly from nascent branches. The cross-linked complex is inhibited by WASP's CA region, even though CA potently stimulates cross-linking, suggesting that slow WASP detachment masks the activating potential of the short-pitch conformational switch. We use structure-based mutations and WASP-Arp fusion chimeras to determine how WASP stimulates movement toward the short-pitch conformation. Our data indicate that WASP displaces the autoinhibitory Arp3 C-terminal tail from a hydrophobic groove at Arp3's barbed end to destabilize the inactive state, providing a mechanism by which WASP stimulates the short-pitch conformation and activates Arp2/3 complex. PMID:27325766

  20. The Interaction of Arp2/3 Complex with Actin: Nucleation, High Affinity Pointed End Capping, and Formation of Branching Networks of Filaments

    NASA Astrophysics Data System (ADS)

    Dyche Mullins, R.; Heuser, John A.; Pollard, Thomas D.

    1998-05-01

    The Arp2/3 complex is a stable assembly of seven protein subunits including two actin-related proteins (Arp2 and Arp3) and five novel proteins. Previous work showed that this complex binds to the sides of actin filaments and is concentrated at the leading edges of motile cells. Here, we show that Arp2/3 complex purified from Acanthamoeba caps the pointed ends of actin filaments with high affinity. Arp2/3 complex inhibits both monomer addition and dissociation at the pointed ends of actin filaments with apparent nanomolar affinity and increases the critical concentration for polymerization at the pointed end from 0.6 to 1.0 μ M. The high affinity of Arp2/3 complex for pointed ends and its abundance in amoebae suggest that in vivo all actin filament pointed ends are capped by Arp2/3 complex. Arp2/3 complex also nucleates formation of actin filaments that elongate only from their barbed ends. From kinetic analysis, the nucleation mechanism appears to involve stabilization of polymerization intermediates (probably actin dimers). In electron micrographs of quick-frozen, deep-etched samples, we see Arp2/3 bound to sides and pointed ends of actin filaments and examples of Arp2/3 complex attaching pointed ends of filaments to sides of other filaments. In these cases, the angle of attachment is a remarkably constant 70 ± 7 degrees. From these in vitro biochemical properties, we propose a model for how Arp2/3 complex controls the assembly of a branching network of actin filaments at the leading edge of motile cells.

  1. Proteomic analysis identifies an NADPH oxidase 1 (Nox1)-mediated role for actin-related protein 2/3 complex subunit 2 (ARPC2) in promoting smooth muscle cell migration.

    PubMed

    Al Ghouleh, Imad; Rodríguez, Andrés; Pagano, Patrick J; Csányi, Gábor

    2013-01-01

    A variety of vascular pathologies, including hypertension, restenosis and atherosclerosis, are characterized by vascular smooth muscle cell (VSMC) hypertrophy and migration. NADPH oxidase 1 (Nox1) plays a pivotal role in these phenotypes via distinct downstream signaling. However, the mediators differentiating these distinct phenotypes and their precise role in vascular disease are still not clear. The present study was designed to identify novel targets of VSMC Nox1 signaling using 2D Differential In-Gel Electrophoresis and Mass Spectrometry (2D-DIGE/MS). VSMC treatment with scrambled (Scrmb) or Nox1 siRNA and incubation with the oxidant hydrogen peroxide (H2O2; 50 µM, 3 h) followed by 2D-DIGE/MS on cell lysates identified 10 target proteins. Among these proteins, actin-related protein 2/3 complex subunit 2 (ARPC2) with no previous link to Nox isozymes, H2O2, or other reactive oxygen species (ROS), was identified and postulated to play an intermediary role in VSMC migration. Western blot confirmed that Nox1 mediates H2O2-induced ARPC2 expression in VSMC. Treatment with a p38 MAPK inhibitor (SB203580) resulted in reduced ARPC2 expression in H2O2-treated VSMC. Additionally, wound-healing "scratch" assay confirmed that H2O2 stimulates VSMC migration via Nox1. Importantly, gene silencing of ARPC2 suppressed H2O2-stimulated VSMC migration. These results demonstrate for the first time that Nox1-mediated VSMC migration involves ARPC2 as a downstream signaling target. PMID:24152438

  2. RasGRP3 regulates the migration of glioma cells via interaction with Arp3

    PubMed Central

    Lee, Hae Kyung; Finniss, Susan; Cazacu, Simona; Xiang, Cunli; Poisson, Laila M.; Blumberg, Peter M.; Brodie, Chaya

    2015-01-01

    Glioblastoma (GBM), the most aggressive primary brain tumors, are highly infiltrative. Although GBM express high Ras activity and Ras proteins have been implicated in gliomagenesis, Ras-activating mutations are not frequent in these tumors. RasGRP3, an important signaling protein responsive to diacylglycerol (DAG), increases Ras activation. Here, we examined the expression and functions of RasGRP3 in GBM and glioma cells. RasGRP3 expression was upregulated in GBM specimens and glioma stem cells compared with normal brains and neural stem cells, respectively. RasGRP3 activated Ras and Rap1 in glioma cells and increased cell migration and invasion partially via Ras activation. Using pull-down assay and mass spectroscopy we identified the actin-related protein, Arp3, as a novel interacting protein of RasGRP3. The interaction of RasGRP3 and Arp3 was validated by immunofluorescence staining and co-immunoprecipitation, and PMA, which activates RasGRP3 and induces its translocation to the peri-nuclear region, increased the association of Arp3 and RasGRP3. Arp3 was upregulated in GBM, regulated cell spreading and migration and its silencing partially decreased these effects of RasGRP3 in glioma cells. In summary, RasGRP3 acts as an important integrating signaling protein of the DAG and Ras signaling pathways and actin polymerization and represents an important therapeutic target in GBM. PMID:25682201

  3. Structural Characterization and Computer-aided Optimization of a Small Molecule Inhibitor of Arp2/3 Complex, a Key Regulator of the Actin Cytoskeleton

    PubMed Central

    Baggett, Andrew W.; Cournia, Zoe; Han, Min Suk; Patargias, George; Glass, Adam C.; Liu, Shih-Yuan; Nolen, Brad J.

    2012-01-01

    CK-666 (1) is a recently discovered small molecule inhibitor of the Arp2/3 complex, a key actin cytoskeleton regulator with roles in bacterial pathogenesis and motility of cancer cells. While 1 is commercially available, the crystal structure of Arp2/3 (Actin-related protein 2/3) complex with 1 bound has not been reported, making its mechanism of action uncertain. Furthermore, its relatively low potency increases its potential for off target effects in vivo, complicating interpretation of its influence in cell biological studies and precluding its use in clinical applications. Here we report the crystal structure of 1 bound to Arp2/3 complex, which reveals that 1 binds between the Arp2 and Arp3 subunits to stabilize the inactive conformation of the complex. Based on the crystal structure, we used computational docking and free energy perturbation calculations of monosubstituted derivatives of 1 to guide optimization efforts. Biochemical assays of ten newly synthesized compounds led to the identification of compound 2, which exhibits a 3 fold increase in inhibitory activity in vitro. In addition, our computational analyses unveiled a surface groove at the interface of the Arp2 and Arp3 subunits that can be exploited for additional structure-based optimization. PMID:22623398

  4. A Novel Neural Wiskott-Aldrich Syndrome Protein (N-Wasp) Binding Protein, Wish, Induces Arp2/3 Complex Activation Independent of Cdc42

    PubMed Central

    Fukuoka, Maiko; Suetsugu, Shiro; Miki, Hiroaki; Fukami, Kiyoko; Endo, Takeshi; Takenawa, Tadaomi

    2001-01-01

    We identified a novel adaptor protein that contains a Src homology (SH)3 domain, SH3 binding proline-rich sequences, and a leucine zipper-like motif and termed this protein WASP interacting SH3 protein (WISH). WISH is expressed predominantly in neural tissues and testis. It bound Ash/Grb2 through its proline-rich regions and neural Wiskott-Aldrich syndrome protein (N-WASP) through its SH3 domain. WISH strongly enhanced N-WASP–induced Arp2/3 complex activation independent of Cdc42 in vitro, resulting in rapid actin polymerization. Furthermore, coexpression of WISH and N-WASP induced marked formation of microspikes in Cos7 cells, even in the absence of stimuli. An N-WASP mutant (H208D) that cannot bind Cdc42 still induced microspike formation when coexpressed with WISH. We also examined the contribution of WISH to a rapid actin polymerization induced by brain extract in vitro. Arp2/3 complex was essential for brain extract–induced rapid actin polymerization. Addition of WISH to extracts increased actin polymerization as Cdc42 did. However, WISH unexpectedly could activate actin polymerization even in N-WASP–depleted extracts. These findings suggest that WISH activates Arp2/3 complex through N-WASP–dependent and –independent pathways without Cdc42, resulting in the rapid actin polymerization required for microspike formation. PMID:11157975

  5. Capping Protein Increases the Rate of Actin-based Motility by Promoting Filament Nucleation by the Arp2/3 Complex

    PubMed Central

    Akin, Orkun; Mullins, R. Dyche

    2008-01-01

    Summary Capping protein is an integral component of Arp2/3-nucleated actin networks that drive amoeboid motility. Increasing the concentration of capping protein, which caps barbed ends of actin filaments and prevents elongation, increases the rate of actin-based motility in vivo and in vitro. We studied the synergy between capping protein and Arp2/3 using an in vitro actin-based motility system reconstituted from purified proteins. We find that capping protein increases the rate of motility by promoting more frequent filament nucleation by the Arp2/3 complex, and not by increasing the rate of filament elongation as previously suggested. One consequence of this coupling between capping and nucleation is that, while the rate of motility depends strongly on the concentration of capping protein and Arp2/3, the net rate of actin assembly is insensitive to changes in either factor. By reorganizing their architecture, dendritic actin networks harness the same assembly kinetics to drive different rates of motility. PMID:18510928

  6. Insights into the Influence of Nucleotides on Actin Family Proteins from Seven Structures of Arp2/3 Complex

    SciTech Connect

    Nolen,B.; Pollard, T.

    2007-01-01

    ATP is required for nucleation of actin filament branches by Arp2/3 complex, but the influence of ATP binding and hydrolysis are poorly understood. We determined crystal structures of bovine Arp2/3 complex cocrystalized with various bound adenine nucleotides and cations. Nucleotide binding favors closure of the nucleotide binding cleft of Arp3, but no large scale conformational changes in the complex. Thus, ATP binding does not directly activate Arp2/3 complex, but is part of a network of interactions that contribute to nucleation. We compared nucleotide-induced conformational changes of residues lining the cleft in Arp3 and actin structures to construct a movie depicting the proposed ATPase cycle for the actin family. Chemical crosslinking stabilized subdomain 1 of Arp2, revealing new electron density for 69 residues in this subdomain. Steric clashes with Arp3 appear to be responsible for intrinsic disorder of subdomains 1 and 2 of Arp2 in inactive Arp2/3 complex.

  7. ARP2, a novel pro-apoptotic protein expressed in epithelial prostate cancer LNCaP cells and epithelial ovary CHO transformed cells.

    PubMed

    Mas-Oliva, Jaime; Navarro-Vidal, Enrique; Tapia-Vieyra, Juana Virginia

    2014-01-01

    Neoplastic epithelial cells generate the most aggressive types of cancers such as those located in the lung, breast, colon, prostate and ovary. During advanced stages of prostate cancer, epithelial cells are associated to the appearance of androgen-independent tumors, an apoptotic-resistant phenotype that ultimately overgrows and promotes metastatic events. We have previously identified and electrophysiologically characterized a novel Ca(2+)-permeable channel activated during apoptosis in the androgen-independent prostate epithelial cancer cell line, LNCaP. In addition, we reported for the first time the cloning and characterization of this channel-like molecule named apoptosis regulated protein 2 (ARP2) associated to a lethal influx of Ca(2+) in Xenopus oocytes. In the present study, LNCaP cells and Chinese hamster ovary cells (CHO cell line) transfected with arp2-cDNA are induced to undergo apoptosis showing an important impact on cell viability and activation of caspases 3 and 7 when compared to serum deprived grown cells and ionomycin treated cells. The subcellular localization of ARP2 in CHO cells undergoing apoptosis was studied using confocal microscopy. While apoptosis progresses, ARP2 initially localized in the peri-nuclear region of cells migrates with time towards the plasma membrane region. Based on the present results and those of our previous studies, the fact that ARP2 constitutes a novel cation channel is supported. Therefore, ARP2 becomes a valuable target to modulate the influx and concentration of calcium in the cytoplasm of epithelial cancer cells showing an apoptotic-resistant phenotype during the onset of an apoptotic event. PMID:24465888

  8. ARP2, a novel pro-apoptotic protein expressed in epithelial prostate cancer LNCaP cells and epithelial ovary CHO transformed cells.

    PubMed

    Mas-Oliva, Jaime; Navarro-Vidal, Enrique; Tapia-Vieyra, Juana Virginia

    2014-01-01

    Neoplastic epithelial cells generate the most aggressive types of cancers such as those located in the lung, breast, colon, prostate and ovary. During advanced stages of prostate cancer, epithelial cells are associated to the appearance of androgen-independent tumors, an apoptotic-resistant phenotype that ultimately overgrows and promotes metastatic events. We have previously identified and electrophysiologically characterized a novel Ca(2+)-permeable channel activated during apoptosis in the androgen-independent prostate epithelial cancer cell line, LNCaP. In addition, we reported for the first time the cloning and characterization of this channel-like molecule named apoptosis regulated protein 2 (ARP2) associated to a lethal influx of Ca(2+) in Xenopus oocytes. In the present study, LNCaP cells and Chinese hamster ovary cells (CHO cell line) transfected with arp2-cDNA are induced to undergo apoptosis showing an important impact on cell viability and activation of caspases 3 and 7 when compared to serum deprived grown cells and ionomycin treated cells. The subcellular localization of ARP2 in CHO cells undergoing apoptosis was studied using confocal microscopy. While apoptosis progresses, ARP2 initially localized in the peri-nuclear region of cells migrates with time towards the plasma membrane region. Based on the present results and those of our previous studies, the fact that ARP2 constitutes a novel cation channel is supported. Therefore, ARP2 becomes a valuable target to modulate the influx and concentration of calcium in the cytoplasm of epithelial cancer cells showing an apoptotic-resistant phenotype during the onset of an apoptotic event.

  9. ARP2/3-dependent growth in the plant kingdom: SCARs for life

    PubMed Central

    Yanagisawa, Makoto; Zhang, Chunhua; Szymanski, Daniel B.

    2013-01-01

    In the human experience SCARs (suppressor of cAMP receptors) are permanent reminders of past events, not always based on bad decisions, but always those in which an interplay of opposing forces leaves behind a clear record in the form of some permanent watery mark. During plant morphogenesis, SCARs are important proteins that reflect an unusual evolutionary outcome, in which the plant kingdom relies heavily on this single class of actin-related protein (ARP) 2/3 complex activator to dictate the time and place of actin filament nucleation. This unusually simple arrangement may serve as a permanent reminder that cell shape control in plants is fundamentally different from that of crawling cells in mammals that use the power of actin polymerization to define and maintain cell shape. In plant cells, actin filaments indirectly affect cell shape by determining the transport properties of organelles and cargo molecules that modulate the mechanical properties of the wall. It is becoming increasingly clear that polarized bundles of actin filaments operate at whole cell spatial scales to organize the cytoplasm and dictate the patterns of long-distance intracellular transport and secretion. The number of actin-binding proteins and actin filament nucleators that are known to participate in the process of actin network formation are rapidly increasing. In plants, formins and ARP2/3 are two important actin filament nucleators. This review will focus on ARP2/3, and the apparent reliance of most plant species on the SCAR/WAVE (WASP family verprolin homologous) regulatory complex as the sole pathway for ARP2/3 activation. PMID:23802001

  10. Radicicol but not geldanamycin evokes oxidative stress response and efflux protein inhibition in ARPE-19 human retinal pigment epithelial cells.

    PubMed

    Ryhänen, Tuomas; Mannermaa, Eliisa; Oksala, Niku; Viiri, Johanna; Paimela, Tuomas; Salminen, Antero; Atalay, Mustafa; Kaarniranta, Kai

    2008-04-28

    Drug delivery to retinal cells has represented a major challenge for ophthalmologists for many decades. However, drug targeting to the retina is essential in therapies against retinal diseases such as age-related macular degeneration, the most common reason of blindness in the developed countries. Retinal cells are chronically exposed to oxidative stress that contributes to cellular senescence and may cause neovascularization in the most severe age-related macular degeneration cases. Various pre- and clinical studies have revealed that heat shock protein 90 (HSP90) inhibitors, such as geldanamycin and radicicol, are promising drugs in the treatment of different malignant processes. In this study, our goal was to compare the effects of 0.1 microM, 1 microM or 5 microM geldanamycin or radicicol on the oxidative stress response, cytotoxicity, and efflux protein activity (a protein pump which removes drugs from cells) in ARPE-19 (human retinal pigment epithelial, RPE) cells. Our findings indicate that geldanamycin and radicicol increased HSP70 and HSP27 expression analyzed by western blotting. Cellular levels of protein carbonyls were increased in response to 0.1 microM (P=0.048 for 24 h, P=0.018 for 48 h) or 5 microM (P=0.030 for 24 h, P=0.046 for 48 h) radicicol but not to geldanamycin analyzed by ELISA assay. In addition, HNE-protein adducts were accumulated in the RPE cells exposed to 0.1 microM or 5 microM radicicol but not to geldanamycin analyzed by western blotting. However, MTT assay revealed that 5 microM geldanamycin reduced cellular viability 20-30% (P<0.05 for 24 h, P<0.01 for 48 h), but this was not observed at any radicicol concentration in RPE cells. Interestingly, the increased oxidative stress response was associated with efflux protein inhibition (20-30%) when the cells were exposed to 1 microM or 5 microM (P<0.05) radicicol, but not in geldanamycin-treated RPE cells. These novel findings help in understanding the influence of HSP90 inhibition and

  11. Protein Kinase Cδ and Calmodulin Regulate Epidermal Growth Factor Receptor Recycling from Early Endosomes through Arp2/3 Complex and Cortactin

    PubMed Central

    Lladó, Anna; Timpson, Paul; Vilà de Muga, Sandra; Moretó, Jemina; Pol, Albert; Grewal, Thomas; Daly, Roger J.

    2008-01-01

    The intracellular trafficking of the epidermal growth factor receptor (EGFR) is regulated by a cross-talk between calmodulin (CaM) and protein kinase Cδ (PKCδ). On inhibition of CaM, PKCδ promotes the formation of enlarged early endosomes and blocks EGFR recycling and degradation. Here, we show that PKCδ impairs EGFR trafficking due to the formation of an F-actin coat surrounding early endosomes. The PKCδ-induced polymerization of actin is orchestrated by the Arp2/3 complex and requires the interaction of cortactin with PKCδ. Accordingly, inhibition of actin polymerization by using cytochalasin D or by overexpression of active cofilin, restored the normal morphology of the organelle and the recycling of EGFR. Similar results were obtained after down-regulation of cortactin and the sequestration of the Arp2/3 complex. Furthermore we demonstrate an interaction of cortactin with CaM and PKCδ, the latter being dependent on CaM inhibition. In summary, this study provides the first evidence that CaM and PKCδ organize actin dynamics in the early endosomal compartment, thereby regulating the intracellular trafficking of EGFR. PMID:17959830

  12. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7

    PubMed Central

    Langer, Gerrit G; Cohen, Serge X; Lamzin, Victor S; Perrakis, Anastassis

    2008-01-01

    ARP/wARP is a software suite to build macromolecular models in X-ray crystallography electron density maps. Structural genomics initiatives and the study of complex macromolecular assemblies and membrane proteins all rely on advanced methods for 3D structure determination. ARP/wARP meets these needs by providing the tools to obtain a macromolecular model automatically, with a reproducible computational procedure. ARP/wARP 7.0 tackles several tasks: iterative protein model building including a high-level decision-making control module; fast construction of the secondary structure of a protein; building flexible loops in alternate conformations; fully automated placement of ligands, including a choice of the best fitting ligand from a “cocktail”; and finding ordered water molecules. All protocols are easy to handle by a non-expert user through a graphical user interface or a command line. The time required is typically a few minutes although iterative model building may take a few hours. PMID:18600222

  13. Expression of the ARPC4 Subunit of Human Arp2/3 Severely Affects Mycobacterium tuberculosis Growth and Suppresses Immunogenic Response in Murine Macrophages

    PubMed Central

    Ghosh, Anamika; Samuchiwal, Sachin K.; Bhalla, Kuhulika; Tharad, Megha; Kumar, Sushil; Prakash, Prem; Kumar, Purnima; Das, Gobardhan; Ranganathan, Anand

    2013-01-01

    Background The search for molecules against Mycobacterium tuberculosis is urgent. The mechanisms facilitating the intra-macrophage survival of Mycobacterium tuberculosis are as yet not entirely understood. However, there is evidence showing the involvement of host cell cytoskeleton in every step of establishment and persistence of mycobacterial infection. Methodology/Principal Findings Here we show that expression of ARPC4, a subunit of the Actin related protein 2/3 (Arp2/3) protein complex, severely affects the pathogen’s growth. TEM studies display shedding of the mycobacterial outer-coat. Furthermore, in infected macrophages, mycobacteria expressing ARPC4 were cleared off at a much faster rate, and were unable to mount a pro-inflammatory cytokine response. The translocation of ARPC4-expressing mycobacteria to the lysosome of the infected macrophage was also impaired. Additionally, the ARPC4 subunit was shown to interact with Rv1626, an essential secretory mycobacterial protein. Real-time PCR analysis showed that upon expression of ARPC4 in mycobacteria, Rv1626 expression is downregulated as much as six-fold. Rv1626 was found to also interact with mammalian cytoskeleton protein, Arp2/3, and enhance the rate of actin polymerization. Conclusions/Significance With crystal structures for Rv1626 and ARPC4 subunit already known, our finding lays out the effect of a novel molecule on mycobacteria, and represents a viable starting point for developing potent peptidomimetics. PMID:23894563

  14. Platelet actin nodules are podosome-like structures dependent on Wiskott–Aldrich syndrome protein and ARP2/3 complex

    PubMed Central

    Poulter, Natalie S.; Pollitt, Alice Y.; Davies, Amy; Malinova, Dessislava; Nash, Gerard B.; Hannon, Mike J.; Pikramenou, Zoe; Rappoport, Joshua Z.; Hartwig, John H.; Owen, Dylan M.; Thrasher, Adrian J.; Watson, Stephen P.; Thomas, Steven G.

    2015-01-01

    The actin nodule is a novel F-actin structure present in platelets during early spreading. However, only limited detail is known regarding nodule organization and function. Here we use electron microscopy, SIM and dSTORM super-resolution, and live-cell TIRF microscopy to characterize the structural organization and signalling pathways associated with nodule formation. Nodules are composed of up to four actin-rich structures linked together by actin bundles. They are enriched in the adhesion-related proteins talin and vinculin, have a central core of tyrosine phosphorylated proteins and are depleted of integrins at the plasma membrane. Nodule formation is dependent on Wiskott–Aldrich syndrome protein (WASp) and the ARP2/3 complex. WASp−/− mouse blood displays impaired platelet aggregate formation at arteriolar shear rates. We propose actin nodules are platelet podosome-related structures required for platelet–platelet interaction and their absence contributes to the bleeding diathesis of Wiskott–Aldrich syndrome. PMID:26028144

  15. ARP/wARP and molecular replacement: the next generation

    SciTech Connect

    Cohen, Serge X. Ben Jelloul, Marouane; Long, Fei; Vagin, Alexei; Knipscheer, Puck; Lebbink, Joyce; Sixma, Titia K.; Lamzin, Victor S.; Murshudov, Garib N.; Perrakis, Anastassis

    2008-01-01

    A systematic test shows how ARP/wARP deals with automated model building for structures that have been solved by molecular replacement. A description of protocols in the flex-wARP control system and studies of two specific cases are also presented. Automatic iterative model (re-)building, as implemented in ARP/wARP and its new control system flex-wARP, is particularly well suited to follow structure solution by molecular replacement. More than 100 molecular-replacement solutions automatically solved by the BALBES software were submitted to three standard protocols in flex-wARP and the results were compared with final models from the PDB. Standard metrics were gathered in a systematic way and enabled the drawing of statistical conclusions on the advantages of each protocol. Based on this analysis, an empirical estimator was proposed that predicts how good the final model produced by flex-wARP is likely to be based on the experimental data and the quality of the molecular-replacement solution. To introduce the differences between the three flex-wARP protocols (keeping the complete search model, converting it to atomic coordinates but ignoring atom identities or using the electron-density map calculated from the molecular-replacement solution), two examples are also discussed in detail, focusing on the evolution of the models during iterative rebuilding. This highlights the diversity of paths that the flex-wARP control system can employ to reach a nearly complete and accurate model while actually starting from the same initial information.

  16. Severe congenital actin related myopathy with myofibrillar myopathy features.

    PubMed

    Selcen, Duygu

    2015-06-01

    Mutations in ACTA1 have been associated with different pathologic findings including nemaline myopathy, intranuclear rod myopathy, actin myopathy, cap myopathy, congenital fiber type disproportion, and core myopathy. Myofibrillar myopathies are morphologically distinct but genetically heterogeneous muscular dystrophies arising from mutations in Z-disk related proteins. We report a 26-month-old boy with significantly delayed motor development requiring mechanical ventilation and tube-feeding since birth. The muscle biopsy displayed typical features of myofibrillar myopathy with abnormal expression of multiple proteins. Whole exome sequencing revealed two-amino-acid duplication in ACTA1. In cell culture system, mutant actin was expressed at ~11% of wild-type, and mutant actin formed pleomorphic cytoplasmic aggregates whereas wild-type actin appeared in filamentous structures. We conclude that mutations in ACTA1 can cause pathologic features consistent with myofibrillar myopathy, and mutations in ACTA1 should be considered in patients with severe congenital hypotonia associated with muscle weakness and features of myofibrillar myopathy. PMID:25913210

  17. Neutral Hydrogen in Arp 158

    NASA Astrophysics Data System (ADS)

    Iyer, Mansie G.; Simpson, Caroline E.; Gottesman, Stephen T.; Malphrus, Benjamin K.

    2004-09-01

    We present 21 cm observations of Arp 158. We have performed a study of the neutral hydrogen (H I) to help us understand the overall formation and evolution of this system. This is a disturbed system with distinct optical knots connected by a linear structure embedded in luminous material. There is also a diffuse spray to the southeast. The H I seems to be made up of three distinct, kinematically separate systems. Arp 158 bears a certain optical resemblance to NGC 520 (Arp 157), which has been identified as a mid-stage merger. From our 21 cm observations of Arp 158, we also see a comparable H I content with NGC 520. These similarities suggest that Arp 158 is also an intermediate-stage merger.

  18. Assessment of automatic ligand building in ARP/wARP

    PubMed Central

    Evrard, Guillaume X.; Langer, Gerrit G.; Perrakis, Anastassis; Lamzin, Victor S.

    2007-01-01

    The efficiency of the ligand-building module of ARP/wARP version 6.1 has been assessed through extensive tests on a large variety of protein–ligand complexes from the PDB, as available from the Uppsala Electron Density Server. Ligand building in ARP/wARP involves two main steps: automatic identification of the location of the ligand and the actual construction of its atomic model. The first step is most successful for large ligands. The second step, ligand construction, is more powerful with X-ray data at high resolution and ligands of small to medium size. Both steps are successful for ligands with low to moderate atomic displacement parameters. The results highlight the strengths and weaknesses of both the method of ligand building and the large-scale validation procedure and help to identify means of further improvement. PMID:17164533

  19. Dynactin integrity depends upon direct binding of dynamitin to Arp1

    PubMed Central

    Cheong, Frances Ka Yan; Feng, Lijuan; Sarkeshik, Ali; Yates, John R.; Schroer, Trina A.

    2014-01-01

    Dynactin is a multiprotein complex that works with cytoplasmic dynein and other motors to support a wide range of cell functions. It serves as an adaptor that binds both dynein and cargoes and enhances single-motor processivity. The dynactin subunit dynamitin (also known as p50) is believed to be integral to dynactin structure because free dynamitin displaces the dynein-binding p150Glued subunit from the cargo-binding Arp1 filament. We show here that the intrinsically disordered dynamitin N-terminus binds to Arp1 directly. When expressed in cells, dynamitin amino acids (AA) 1–87 causes complete release of endogenous dynamitin, p150, and p24 from dynactin, leaving behind Arp1 filaments carrying the remaining dynactin subunits (CapZ, p62, Arp11, p27, and p25). Tandem-affinity purification–tagged dynamitin AA 1–87 binds the Arp filament specifically, and binding studies with purified native Arp1 reveal that this fragment binds Arp1 directly. Neither CapZ nor the p27/p25 dimer contributes to interactions between dynamitin and the Arp filament. This work demonstrates for the first time that Arp1 can directly bind any protein besides another Arp and provides important new insight into the underpinnings of dynactin structure. PMID:24829381

  20. Infrared outburst in Arp 299

    NASA Astrophysics Data System (ADS)

    Mattila, Seppo; Meikle, Peter; Kotak, Rubina; Perez-Torres, Miguel; Romero-Canizales, Cristina; Alberdi, Antxon

    2011-05-01

    Arp 299 is one of the nearest examples of a luminous infrared galaxy. We discovered a strong outburst in Arp 299 which is apparent at infrared (IR) wavelengths but not in the optical indicating emission from warm dust and a high extinction. This source could originate from an IR 'dust echo' resulting either from a highly obscured outburst in an active galactic nucleus or an energetic supernova. To continue our study of the origin of this outburst we propose short IRAC observations.

  1. Characterizing PvARP, a novel Plasmodium vivax antigen

    PubMed Central

    2013-01-01

    Background Plasmodium vivax continues to be the most widely distributed malarial parasite species in tropical and sub-tropical areas, causing high morbidity indices around the world. Better understanding of the proteins used by the parasite during the invasion of red blood cells is required to obtain an effective vaccine against this disease. This study describes characterizing the P. vivax asparagine-rich protein (PvARP) and examines its antigenicity in natural infection. Methods The target gene in the study was selected according to a previous in silico analysis using profile hidden Markov models which identified P. vivax proteins that play a possible role in invasion. Transcription of the arp gene in the P. vivax VCG-1 strain was here evaluated by RT-PCR. Specific human antibodies against PvARP were used to confirm protein expression by Western blot as well as its subcellular localization by immunofluorescence. Recognition of recombinant PvARP by sera from P. vivax-infected individuals was evaluated by ELISA. Results VCG-1 strain PvARP is a 281-residue-long molecule, which is encoded by a single exon and has an N-terminal secretion signal, as well as a tandem repeat region. This protein is expressed in mature schizonts and is located on the surface of merozoites, having an apparent accumulation towards their apical pole. Sera from P. vivax-infected patients recognized the recombinant, thereby suggesting that this protein is targeted by the immune response during infection. Conclusions This study showed the characterization of PvARP and its antigenicity. Further assays orientated towards evaluating this antigen’s functional importance during parasite invasion are being carried out. PMID:23688042

  2. Clathrin- and Arp2/3-Independent Endocytosis in the Fungal Pathogen Candida albicans

    PubMed Central

    Epp, Elias; Nazarova, Elena; Regan, Hannah; Douglas, Lois M.; Konopka, James B.; Vogel, Jackie; Whiteway, Malcolm

    2013-01-01

    ABSTRACT Clathrin-mediated endocytosis (CME) is conserved among eukaryotes and has been extensively analyzed at a molecular level. Here, we present an analysis of CME in the human fungal pathogen Candida albicans that shows the same modular structure as those in other fungi and mammalian cells. Intriguingly, C. albicans is perfectly viable in the absence of Arp2/3, an essential component of CME in other systems. In C. albicans, Arp2/3 function remains essential for CME as all 15 proteins tested that participate in CME, including clathrin, lose their characteristic dynamics observed in wild-type (WT) cells. However, since arp2/3 cells are still able to endocytose lipids and fluid-phase markers, but not the Ste2 and Mup1 plasma membrane proteins, there must be an alternate clathrin-independent pathway we term Arp2/3-independent endocytosis (AIE). Characterization of AIE shows that endocytosis in arp2 mutants relies on actin cables and other Arp2/3-independent actin structures, as inhibition of actin functions prevented cargo uptake in arp2/3 mutants. Transmission electron microscopy (TEM) showed that arp2/3 mutants still formed invaginating tubules, cell structures whose proper functions are believed to heavily rely on Arp2/3. Finally, Prk1 and Sjl2, two proteins involved in patch disassembly during CME, were not correctly localized to sites of endocytosis in arp2 mutants, implying a role of Arp2/3 in CME patch disassembly. Overall, C. albicans contains an alternative endocytic pathway (AIE) that relies on actin cable function to permit clathrin-independent endocytosis (CIE) and provides a system to further explore alternate endocytic routes that likely exist in fungal species. PMID:23982070

  3. Sigma Factor RpoS Controls Alkylresorcinol Synthesis through ArpR, a LysR-Type Regulatory Protein, during Encystment of Azotobacter vinelandii

    PubMed Central

    Romero, Yanet; Moreno, Soledad; Guzmán, Josefina; Espín, Guadalupe

    2013-01-01

    Azotobacter vinelandii is a bacterium which undergoes a differentiation process leading to the formation of metabolically dormant cysts. During the encystment process, A. vinelandii produces alkylresorcinol lipids (ARs) that replace the membrane phospholipids and are also components of the layers covering the cyst. The synthesis of ARs in A. vinelandii has been shown to occur by the activity of enzymes encoded by the arsABCD operon, which is expressed only during the differentiation process. Also, the production of ARs has been shown to be dependent on the stationary-phase sigma factor RpoS, which is also implicated in the control of the synthesis of other cyst components (i.e., alginate and poly-β-hydroxybutyrate). In this study, we identified ArpR, a LysR-type transcriptional regulator expressed only during encystment that positively regulates arsABCD transcription. We show that this activation is dependent on acetoacetyl-coenzyme A (acetoacetyl-CoA), which might provide a metabolic signal for encystment. We also show that RpoS regulates arsABCD expression through the control of arpR transcription. PMID:23378510

  4. Arp2/3 complex-deficient mouse fibroblasts are viable and have normal leading-edge actin structure and function

    PubMed Central

    Di Nardo, Alessia; Cicchetti, Gregor; Falet, Hervé; Hartwig, John H.; Stossel, Thomas P.; Kwiatkowski, David J.

    2005-01-01

    RNA interference silencing of up to 90% of Arp3 protein expression, a major subunit of the Arp2/3 complex, proportionately decreases the intracellular motility of Listeria monocytogenes and actin nucleation activity ascribable to the Arp2/3 complex in mouse embryonic fibroblasts. However, the Arp2/3-deficient cells exhibit unimpaired lamellipodial actin network structure, translational locomotion, spreading, actin assembly, and ruffling responses. In addition, Arp3-silenced cells expressing neural Wiskott-Aldrich syndrome protein-derived peptides that inhibit Arp2/3 complex function in wild-type cells retained normal PDGF-induced ruffling. The Arp2/3 complex can be dispensable for leading-edge actin remodeling. PMID:16254049

  5. Identification of an ATP-controlled allosteric switch that controls actin filament nucleation by Arp2/3 complex

    PubMed Central

    Rodnick-Smith, Max; Liu, Su-Ling; Balzer, Connor J.; Luan, Qing; Nolen, Brad J.

    2016-01-01

    Nucleation of branched actin filaments by Arp2/3 complex is tightly regulated to control actin assembly in cells. Arp2/3 complex activation involves conformational changes brought about by ATP, Nucleation Promoting Factor (NPF) proteins, actin filaments and NPF-recruited actin monomers. To understand how these factors promote activation, we must first understand how the complex is held inactive in their absence. Here we demonstrate that the Arp3 C-terminal tail is a structural switch that prevents Arp2/3 complex from adopting an active conformation. The interaction between the tail and a hydrophobic groove in Arp3 blocks movement of Arp2 and Arp3 into an activated filament-like (short pitch) conformation. Our data indicate ATP binding destabilizes this interaction via an allosteric link between the Arp3 nucleotide cleft and the hydrophobic groove, thereby promoting the short-pitch conformation. Our results help explain how Arp2/3 complex is locked in an inactive state without activators and how autoinhibition is relieved. PMID:27417392

  6. Identification of an ATP-controlled allosteric switch that controls actin filament nucleation by Arp2/3 complex.

    PubMed

    Rodnick-Smith, Max; Liu, Su-Ling; Balzer, Connor J; Luan, Qing; Nolen, Brad J

    2016-01-01

    Nucleation of branched actin filaments by Arp2/3 complex is tightly regulated to control actin assembly in cells. Arp2/3 complex activation involves conformational changes brought about by ATP, Nucleation Promoting Factor (NPF) proteins, actin filaments and NPF-recruited actin monomers. To understand how these factors promote activation, we must first understand how the complex is held inactive in their absence. Here we demonstrate that the Arp3 C-terminal tail is a structural switch that prevents Arp2/3 complex from adopting an active conformation. The interaction between the tail and a hydrophobic groove in Arp3 blocks movement of Arp2 and Arp3 into an activated filament-like (short pitch) conformation. Our data indicate ATP binding destabilizes this interaction via an allosteric link between the Arp3 nucleotide cleft and the hydrophobic groove, thereby promoting the short-pitch conformation. Our results help explain how Arp2/3 complex is locked in an inactive state without activators and how autoinhibition is relieved. PMID:27417392

  7. Coronin3 regulates gastric cancer invasion and metastasis by interacting with Arp2

    PubMed Central

    Sun, Yi; Shang, Yulong; Ren, Gui; Zhou, Lin; Feng, Bin; Li, Kai; Deng, Lin; Liang, Jie; Lu, Yuanyuan; Wang, Xin

    2014-01-01

    Coronin3 expression is increased in gastric cancer (GC) tissues and can promote GC invasion and metastasis. However, the mechanisms underlying Coronin3 function in GC remain unclear. In this study, we aimed to explore the interacting molecules essential for the tumor-promoting effects of Coronin3 in GC. Using mass spectrometric analysis, functional studies, and immunohistochemistry, we found that Arp2 interacted with Coronin3, and ectopic expression of Arp2 promoted GC cell migration and invasion, while Arp2 knockdown suppressed whole-cell motility and attenuated the Coronin3-mediated upregulation of cell migration and invasion. In addition, both proteins correlated with the metastatic status of GC patients. Furthermore, survival analyses demonstrated that both Coronin3 and Arp2 correlated with overall GC patient survival, and the combination of Coronin3 and Arp2 most accurately predicted GC patient prognosis. Combined, these data demonstrate that Coronin3 can regulate GC invasion and metastasis through Arp2, and the combination of Coronin3 and Arp2 provides a potential marker for predicting GC prognosis. PMID:24918434

  8. Adjudin disrupts spermatogenesis via the action of some unlikely partners: Eps8, Arp2/3 complex, drebrin E, PAR6 and 14-3-3.

    PubMed

    Cheng, C Yan; Lie, Pearl Py; Wong, Elissa Wp; Mruk, Dolores D; Silvestrini, Bruno

    2011-10-01

    Adjudin, 1-(2,4-dichlorobenzyl)-1H-indazole-3-carbohydrazide (formerly called AF-2364), is a potent analog of lonidamine [1-(2,4-dichlorobenzyl)-1H-indazole-3-carboxylic acid] known to disrupt germ cell adhesion, most notably elongating and elongated spermatids, in the seminiferous epithelium of adult rat testes and thus, leads to infertility in rats. Since the population of spermatogonia and spermatogonial stem cells (SSCs) in the seminiferous tubules is not significantly reduced by the treatment of rats with adjudin, adjudin-induced infertility is highly reversible, which enables reinitiation of spermatogenesis and germ cell re-population of the voided seminiferous epithelium. Furthermore, adjudin appears to exert its effects at the testis-specific atypical adherens junction (AJ) type known as ectoplasmic specialization (ES), most notably the apical ES at the Sertoli cell-spermatid interface. Thus, the hypothalamic-pituitary-gonadal axis is not unaffected and systemic side-effects are minimal. This also makes adjudin a potential candidate for male contraceptive development. Herein, we critically evaluate recent findings in the field and provide an updated model regarding the mechanism underlying adjudin-induced apical ES disruption. In short, adjudin targets actin filament bundles at the apical ES, the hallmark ultrastructure of this testis-specific junction type not found in any other epithelia/endothelia in mammals, by suppressing the expression of Eps8 (epidermal growth factor receptor pathway substrate 8), an actin capping protein that also plays a role in actin bundling, so that actin filament bundles can no longer be maintained at the apical ES. This is concomitant with a mis-localization of Arp3 (actin-related protein 3, a component of the Arp2/3 complex that induces actin nucleation/branching) recruited by drebrin E, causing "unwanted" actin branching, further destabilizing actin filament bundles at the apical ES. Additionally, adjudin blocks the

  9. Tropomyosin Promotes Lamellipodial Persistence by Collaborating with Arp2/3 at the Leading Edge.

    PubMed

    Brayford, Simon; Bryce, Nicole S; Schevzov, Galina; Haynes, Elizabeth M; Bear, James E; Hardeman, Edna C; Gunning, Peter W

    2016-05-23

    At the leading edge of migrating cells, protrusion of the lamellipodium is driven by Arp2/3-mediated polymerization of actin filaments [1]. This dense, branched actin network is promoted and stabilized by cortactin [2, 3]. In order to drive filament turnover, Arp2/3 networks are remodeled by proteins such as GMF, which blocks the actin-Arp2/3 interaction [4, 5], and coronin 1B, which acts by directing SSH1L to the lamellipodium where it activates the actin-severing protein cofilin [6, 7]. It has been shown in vitro that cofilin-mediated severing of Arp2/3 actin networks results in the generation of new pointed ends to which the actin-stabilizing protein tropomyosin (Tpm) can bind [8]. The presence of Tpm in lamellipodia, however, is disputed in the literature [9-19]. Here, we report that the Tpm isoforms 1.8/9 are enriched in the lamellipodium of fibroblasts as detected with a novel isoform-specific monoclonal antibody. RNAi-mediated silencing of Tpm1.8/9 led to an increase of Arp2/3 accumulation at the cell periphery and a decrease in the persistence of lamellipodia and cell motility, a phenotype consistent with cortactin- and coronin 1B-deficient cells [2, 7]. In the absence of coronin 1B or cofilin, Tpm1.8/9 protein levels are reduced while, conversely, inhibition of Arp2/3 with CK666 leads to an increase in Tpm1.8/9 protein. These findings establish a novel regulatory mechanism within the lamellipodium whereby Tpm collaborates with Arp2/3 to promote lamellipodial-based cell migration. PMID:27112294

  10. Apigenin Attenuates Oxidative Injury in ARPE-19 Cells thorough Activation of Nrf2 Pathway

    PubMed Central

    Li, Min; Chen, Weiwei; Yu, Haitao; Yang, Yan; Hang, Li

    2016-01-01

    The current study was aimed at evaluating the therapeutic implication of apigenin and to elucidate the underlying mechanism. The tert-butyl hydroperoxide (t-BHP) at 200 μM was used to induce oxidative stress-associated injury in ARPE-19 cells. Apigenin at concentrations less than 800 μM did not cause cytotoxic effects on ARPE-19 cells. Cell viability assay showed that apigenin at 200 μM significantly promoted cell survival in t-BHP-treated ARPE-19 cells. Additionally, apigenin at 100 μM significantly protected ARPE-19 cells from t-BHP-induced apoptosis. Molecular examinations demonstrated that apigenin at 400 μM significantly upregulated the mRNA and protein expression of Nrf2 and stimulated its nuclear translocation in ARPE-19 cells treated with or without t-BHP. Apigenin 400 μM also significantly elevated the expression of HO-1, NQO1, and GCLM at both mRNA and protein levels in the presence or absence of t-BHP. Furthermore, apigenin at 400 μM significantly increased the activities of SOD, CAT, GSH-PX, and T-AOC and reduced the levels of ROS and MDA in t-BHP-treated ARPE-19 cells. However, these effects of apigenin were all abolished by being transfected with Nrf2 siRNA. Collectively, our current data indicated that apigenin exerted potent antioxidant properties in ARPE-19 cells challenged with t-BHP, which were dependent on activation of Nrf2 signaling.

  11. Apigenin Attenuates Oxidative Injury in ARPE-19 Cells thorough Activation of Nrf2 Pathway

    PubMed Central

    Li, Min; Chen, Weiwei; Yu, Haitao; Yang, Yan; Hang, Li

    2016-01-01

    The current study was aimed at evaluating the therapeutic implication of apigenin and to elucidate the underlying mechanism. The tert-butyl hydroperoxide (t-BHP) at 200 μM was used to induce oxidative stress-associated injury in ARPE-19 cells. Apigenin at concentrations less than 800 μM did not cause cytotoxic effects on ARPE-19 cells. Cell viability assay showed that apigenin at 200 μM significantly promoted cell survival in t-BHP-treated ARPE-19 cells. Additionally, apigenin at 100 μM significantly protected ARPE-19 cells from t-BHP-induced apoptosis. Molecular examinations demonstrated that apigenin at 400 μM significantly upregulated the mRNA and protein expression of Nrf2 and stimulated its nuclear translocation in ARPE-19 cells treated with or without t-BHP. Apigenin 400 μM also significantly elevated the expression of HO-1, NQO1, and GCLM at both mRNA and protein levels in the presence or absence of t-BHP. Furthermore, apigenin at 400 μM significantly increased the activities of SOD, CAT, GSH-PX, and T-AOC and reduced the levels of ROS and MDA in t-BHP-treated ARPE-19 cells. However, these effects of apigenin were all abolished by being transfected with Nrf2 siRNA. Collectively, our current data indicated that apigenin exerted potent antioxidant properties in ARPE-19 cells challenged with t-BHP, which were dependent on activation of Nrf2 signaling. PMID:27656262

  12. ARP101, a selective MMP-2 inhibitor, induces autophagy-associated cell death in cancer cells.

    PubMed

    Jo, Yoon Kyung; Park, So Jung; Shin, Ji Hyun; Kim, Yunha; Hwang, Jung Jin; Cho, Dong-Hyung; Kim, Jin Cheon

    2011-01-28

    Autophagy is a catabolic cellular process involving self-digestion and turnover of macromolecules and entire organelles. Autophagy is primarily a protective process in response to cellular stress, but it can be associated with cell death. Genetic evidence also supports autophagy function as a tumor suppressor mechanism. To identify specific regulators to autophagy, we screened the Lopac 1280 and the Prestwick chemical libraries using a cell-based screening system with autophagy marker (green fluorescence protein conjugated LC3 protein (GFP-LC3)). We identified ARP101, a selective matrix metalloproteinase-2 (MMP-2) inhibitor as one of the most potent inducer of autophagy. ARP101 treatment was highly effective in inducing the formation of autophagosome and conversion of LC3I into LC3II. Moreover, ARP101-induced autophagy was completely blocked in mouse embryo fibroblasts that lacked autophagy related gene 5 (ATG5(-/-) MEF). Interestingly, cell death induced by ARP101 was not inhibited by zVAD, a pan caspase inhibitor, whereas, it was efficiently suppressed by addition of 3-methyladenine, an autophagy inhibitor. These results suggest that the selective MMP-2 inhibitor, ARP101, induces autophagy and autophagy-associated cell death. PMID:21187062

  13. Applications of Laser and Synchrotron Based ARPES to Photocathode Research

    SciTech Connect

    Rameau J.; Smedley J.; Muller, E.; Kidd, T.; Johnson, P.; Allen, P.; Carr, L.; Valla, T.

    2010-10-12

    Laser angle resolved photoelectron spectroscopy (ARPES) provides unique information about angle and energy distribution of photoelectrons. Laser ARPES gives unique insight into how NEA materials work. ARPES combined with some ancillary measurements gives a very complete picture of system electronic physics. For H:C[100] there is now a clear program for engineering as well as development analogous systems. ARPES well suited for identifying 'ideal' photocathodes with intrinsically low emittance and high QE.

  14. The role of Arp2/3 in growth cone actin dynamics and guidance is substrate dependent.

    PubMed

    San Miguel-Ruiz, José E; Letourneau, Paul C

    2014-04-23

    During development extrinsic guidance cues modulate the peripheral actin network in growth cones to direct axons to their targets. We wanted to understand the role of the actin nucleator Arp2/3 in growth cone actin dynamics and guidance. Since growth cones migrate in association with diverse adhesive substrates during development, we probed the hypothesis that the functional significance of Arp2/3 is substrate dependent. We report that Arp2/3 inhibition led to a reduction in the number of filopodia and growth cone F-actin content on laminin and L1. However, we found substrate-dependent differences in growth cone motility, actin retrograde flow, and guidance after Arp2/3 inhibition, suggesting that its role, and perhaps that of other actin binding proteins, in growth cone motility is substrate dependent. PMID:24760849

  15. Actin and Arp2/3 localize at the centrosome of interphase cells

    SciTech Connect

    Hubert, Thomas; Vandekerckhove, Joel; Gettemans, Jan

    2011-01-07

    Research highlights: {yields} Actin was detected at the centrosome with the anti-actin antibody 1C7 that recognizes antiparallel ('lower dimer') actin dimers. {yields} Centrosomal actin was found in interphase but not mitotic MDA-MB-231 cells. {yields} Neither the anti-actin antibody C4 that binds to globular, monomer actin, nor the anti-actin antibody 2G2 that recognizes the nuclear conformation of actin detect actin at the centrosome. {yields} The Arp2/3 complex transiently localizes at the pericentriolar matrix but not at the centrioles of interphase HEK 293T cells. -- Abstract: Although many actin binding proteins such as cortactin and the Arp2/3 activator WASH localize at the centrosome, the presence and conformation of actin at the centrosome has remained elusive. Here, we report the localization of actin at the centrosome in interphase but not in mitotic MDA-MB-231 cells. Centrosomal actin was detected with the anti-actin antibody 1C7 that recognizes antiparallel ('lower dimer') actin dimers. In addition, we report the transient presence of the Arp2/3 complex at the pericentriolar matrix but not at the centrioles of interphase HEK 293T cells. Overexpression of an Arp2/3 component resulted in expansion of the pericentriolar matrix and selective accumulation of the Arp2/3 component in the pericentriolar matrix. Altogether, we hypothesize that the centrosome transiently recruits Arp2/3 to perform processes such as centrosome separation prior to mitotic entry, whereas the observed constitutive centrosomal actin staining in interphase cells reinforces the current model of actin-based centrosome reorientation toward the leading edge in migrating cells.

  16. Actin-Like Protein 1 (ALP1) is a component of dynamic, high molecular weight complexes in Toxoplasma gondii

    PubMed Central

    Gordon, Jennifer L.; Buguliskis, Jeffrey S.; Buske, Paul J.; David Sibley, L

    2009-01-01

    Apicomplexan parasites, such as Toxoplasma gondii, rely on actin-based motility for cell invasion, yet conventional actin does not appear to be required for cell division in these parasites. Apicomplexans also contain a variety of actin-related proteins (Arps); however, most of these not directly orthologous to Arps in well-studied systems. We recently identified an apicomplexan-specific member of this family called Actin-Like Protein 1, (ALP1), which plays a role in the assembly of vesicular components recruited to the inner membrane complex (IMC) of daughter cells during cell division. In addition to its enrichment at daughter cell membranes, ALP1 is localized throughout the cytoplasm both diffusely distributed and concentrated in clusters that are detected by fluorescence microscopy, suggesting it forms complexes. Using quantitative optical imaging methods, including fluorescence recovery after photobleaching (FRAP) and fluorescence loss in photobleaching (FLIP), we demonstrated that ALP1 is a component of a large complex, and that it readily exchanges between diffusible and complex-bound forms. Sedimentation and density gradient analyses revealed that ALP1 is found in a freely soluble state as well as high molecular weight complexes. During cell division, ALP1 was dynamically associated with the IMC, suggesting it rapidly cycles between freely diffusible and complex forms during daughter cell assembly. PMID:19701930

  17. Molecular characterization of the Brassica rapa auxin-repressed, superfamily genes, BrARP1 and BrDRM1.

    PubMed

    Lee, Jeongyeo; Han, Ching-Tack; Hur, Yoonkang

    2013-01-01

    Two auxin-repressed superfamily genes, auxin-repressed protein 1 (ARP1) and dormancy-associated protein 1 (DRM1), are highly expressed in both the dormant buds and non-growing tissues of several plant species. To further identify the function of these proteins in Chinese cabbage (Brassica rapa L. ssp. pekinensis), we examined comprehensive expression patterns of BrARP1 and BrDRM1 under various developmental and stress conditions. We also examined these same genes in transgenic Arabidopsis plants. Both genes were expressed in all tissues tested, but their levels were highest in mature tissues accompanied by low levels of the growth-associated marker, B. rapa ribosomal protein 27. Expression of both genes was induced by abiotic stresses, such as chilling, heat shock, and salt treatment. Overexpression of either BrARP1 or BrDRM1 in Arabidopsis causes a reduction in vegetative growth and seed productivity, without affecting morphology. The lengths of petioles and siliques were greatly reduced. Simultaneous expression of both genes showed an additive effect on the growth suppression, resulting in significant reduction in plant size. Knock-out of Arabidopsis ARP1, DRM1, or both, neither affected growth rate nor final size. Results suggest BrARP1 and BrDRM1 are either involved in growth arrest, or stop growth, possibly from inhibition of either cell elongation or cell expansion, thereby creating a "growth brake".

  18. Molecular characterization of the Brassica rapa auxin-repressed, superfamily genes, BrARP1 and BrDRM1.

    PubMed

    Lee, Jeongyeo; Han, Ching-Tack; Hur, Yoonkang

    2013-01-01

    Two auxin-repressed superfamily genes, auxin-repressed protein 1 (ARP1) and dormancy-associated protein 1 (DRM1), are highly expressed in both the dormant buds and non-growing tissues of several plant species. To further identify the function of these proteins in Chinese cabbage (Brassica rapa L. ssp. pekinensis), we examined comprehensive expression patterns of BrARP1 and BrDRM1 under various developmental and stress conditions. We also examined these same genes in transgenic Arabidopsis plants. Both genes were expressed in all tissues tested, but their levels were highest in mature tissues accompanied by low levels of the growth-associated marker, B. rapa ribosomal protein 27. Expression of both genes was induced by abiotic stresses, such as chilling, heat shock, and salt treatment. Overexpression of either BrARP1 or BrDRM1 in Arabidopsis causes a reduction in vegetative growth and seed productivity, without affecting morphology. The lengths of petioles and siliques were greatly reduced. Simultaneous expression of both genes showed an additive effect on the growth suppression, resulting in significant reduction in plant size. Knock-out of Arabidopsis ARP1, DRM1, or both, neither affected growth rate nor final size. Results suggest BrARP1 and BrDRM1 are either involved in growth arrest, or stop growth, possibly from inhibition of either cell elongation or cell expansion, thereby creating a "growth brake". PMID:23065269

  19. Protein pattern of Xenopus laevis embryos grown in simulated microgravity.

    PubMed

    Tedeschi, Gabriella; Pagliato, Lara; Negroni, Manuela; Montorfano, Gigliola; Corsetto, Paola; Nonnis, Simona; Negri, Armando; Rizzo, Angela Maria

    2011-03-01

    Numerous studies indicate that microgravity affects cell growth and differentiation in many living organisms, and various processes are modified when cells are placed under conditions of weightlessness. However, until now, there is no coherent explanation for these observations, and little information is available concerning the biomolecules involved. Our aim has been to investigate the protein pattern of Xenopus laevis embryos exposed to simulated microgravity during the first 6 days of development. A proteomic approach was applied to compare the protein profiles of Xenopus embryos developed in simulated microgravity and in normal conditions. Attention was focused on embryos that do not present visible malformations in order to investigate if weightlessness has effects at protein level in the absence of macroscopic alterations. The data presented strongly suggest that some of the major components of the cytoskeleton vary in such conditions. Three major findings are described for the first time: (i) the expression of important factors involved in the organization and stabilization of the cytoskeleton, such as Arp (actin-related protein) 3 and stathmin, is heavily affected by microgravity; (ii) the amount of the two major cytoskeletal proteins, actin and tubulin, do not change in such conditions; however, (iii) an increase in the tyrosine nitration of these two proteins can be detected. The data suggest that, in the absence of morphological alterations, simulated microgravity affects the intracellular movement system of cells by altering cytoskeletal proteins heavily involved in the regulation of cytoskeleton remodelling.

  20. WAVE binds Ena/VASP for enhanced Arp2/3 complex-based actin assembly.

    PubMed

    Havrylenko, Svitlana; Noguera, Philippe; Abou-Ghali, Majdouline; Manzi, John; Faqir, Fahima; Lamora, Audrey; Guérin, Christophe; Blanchoin, Laurent; Plastino, Julie

    2015-01-01

    The WAVE complex is the main activator of the Arp2/3 complex for actin filament nucleation and assembly in the lamellipodia of moving cells. Other important players in lamellipodial protrusion are Ena/VASP proteins, which enhance actin filament elongation. Here we examine the molecular coordination between the nucleating activity of the Arp2/3 complex and the elongating activity of Ena/VASP proteins for the formation of actin networks. Using an in vitro bead motility assay, we show that WAVE directly binds VASP, resulting in an increase in Arp2/3 complex-based actin assembly. We show that this interaction is important in vivo as well, for the formation of lamellipodia during the ventral enclosure event of Caenorhabditis elegans embryogenesis. Ena/VASP's ability to bind F-actin and profilin-complexed G-actin are important for its effect, whereas Ena/VASP tetramerization is not necessary. Our data are consistent with the idea that binding of Ena/VASP to WAVE potentiates Arp2/3 complex activity and lamellipodial actin assembly.

  1. WAVE binds Ena/VASP for enhanced Arp2/3 complex–based actin assembly

    PubMed Central

    Havrylenko, Svitlana; Noguera, Philippe; Abou-Ghali, Majdouline; Manzi, John; Faqir, Fahima; Lamora, Audrey; Guérin, Christophe; Blanchoin, Laurent; Plastino, Julie

    2015-01-01

    The WAVE complex is the main activator of the Arp2/3 complex for actin filament nucleation and assembly in the lamellipodia of moving cells. Other important players in lamellipodial protrusion are Ena/VASP proteins, which enhance actin filament elongation. Here we examine the molecular coordination between the nucleating activity of the Arp2/3 complex and the elongating activity of Ena/VASP proteins for the formation of actin networks. Using an in vitro bead motility assay, we show that WAVE directly binds VASP, resulting in an increase in Arp2/3 complex–based actin assembly. We show that this interaction is important in vivo as well, for the formation of lamellipodia during the ventral enclosure event of Caenorhabditis elegans embryogenesis. Ena/VASP's ability to bind F-actin and profilin-complexed G-actin are important for its effect, whereas Ena/VASP tetramerization is not necessary. Our data are consistent with the idea that binding of Ena/VASP to WAVE potentiates Arp2/3 complex activity and lamellipodial actin assembly. PMID:25355952

  2. Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression

    PubMed Central

    De Bodt, Stefanie; Proost, Sebastian; Vandepoele, Klaas; Rouzé, Pierre; Van de Peer, Yves

    2009-01-01

    Background Large-scale identification of the interrelationships between different components of the cell, such as the interactions between proteins, has recently gained great interest. However, unraveling large-scale protein-protein interaction maps is laborious and expensive. Moreover, assessing the reliability of the interactions can be cumbersome. Results In this study, we have developed a computational method that exploits the existing knowledge on protein-protein interactions in diverse species through orthologous relations on the one hand, and functional association data on the other hand to predict and filter protein-protein interactions in Arabidopsis thaliana. A highly reliable set of protein-protein interactions is predicted through this integrative approach making use of existing protein-protein interaction data from yeast, human, C. elegans and D. melanogaster. Localization, biological process, and co-expression data are used as powerful indicators for protein-protein interactions. The functional repertoire of the identified interactome reveals interactions between proteins functioning in well-conserved as well as plant-specific biological processes. We observe that although common mechanisms (e.g. actin polymerization) and components (e.g. ARPs, actin-related proteins) exist between different lineages, they are active in specific processes such as growth, cancer metastasis and trichome development in yeast, human and Arabidopsis, respectively. Conclusion We conclude that the integration of orthology with functional association data is adequate to predict protein-protein interactions. Through this approach, a high number of novel protein-protein interactions with diverse biological roles is discovered. Overall, we have predicted a reliable set of protein-protein interactions suitable for further computational as well as experimental analyses. PMID:19563678

  3. Genomic analysis of the biocontrol strain Pseudomonas fluorescens Pf29Arp with evidence of T3SS and T6SS gene expression on plant roots.

    PubMed

    Marchi, Muriel; Boutin, Morgane; Gazengel, Kévin; Rispe, Claude; Gauthier, Jean-Pierre; Guillerm-Erckelboudt, Anne-Yvonne; Lebreton, Lionel; Barret, Matthieu; Daval, Stéphanie; Sarniguet, Alain

    2013-06-01

    Several bacterial strains of the Pseudomonas genus provide plant growth stimulation, plant protection against pests or bioremediation. Among these bacteria, P. fluorescens Pf29Arp reduces the severity of take-all, a disease caused by the pathogenic fungus Gaeumannomyces graminis var. tritici (Ggt) on wheat roots. In this study, we obtained a draft genome of Pf29Arp and subsequent comparative genomic analyses have revealed that this bacterial strain is closely related to strains of the 'P. brassicacearum-like' subgroup including P. brassicacearum ssp. brassicacearum NFM421 and P. fluorescens F113. Despite an overall chromosomal organization similar to these strains, a number of features including antibiotic synthesis gene clusters from secondary metabolism are not found in the Pf29Arp genome. But Pf29Arp possesses different protein secretion systems including type III (T3SS) and type VI (T6SS) secretion systems. Pf29Arp is the first Pseudomonas sp. strain described with four T6SS clusters (cluster I, II, III and IV). In addition, some protein-coding genes involved in the assembly of these secretion systems are basally expressed during Pf29Arp colonization of healthy wheat roots and display different expression patterns on necrotized roots caused by Ggt. These data suggest a role of T3SS and T6SS in the Pf29Arp adaptation to different root environments.

  4. microARPES and nanoARPES at diffraction-limited light sources: opportunities and performance gains.

    PubMed

    Rotenberg, Eli; Bostwick, Aaron

    2014-09-01

    The scientific opportunities for microARPES and nanoARPES techniques are discussed, and the benefits to these techniques at diffraction-limited light sources are presented, in particular the impact on spectromicroscopic ARPES (angle-resolved photoemission spectroscopy) of upgrading the Advanced Light Source to diffraction-limited performance. The most important consideration is whether the space-charge broadening, impacting the energy and momentum resolution, will limit the possible benefits for ARPES. Calculations of energy broadening due to space-charge effects will be presented over a wide range of parameters, and optimum conditions for ARPES will be discussed. The conclusion is that spectromicroscopic ARPES will greatly benefit from the advent of diffraction-limited light sources; space-charge broadening effects will not be a limiting factor. PMID:25177993

  5. Robotic Reverberation Mapping of Arp 151

    NASA Astrophysics Data System (ADS)

    Valenti, S.; Sand, D. J.; Barth, A. J.; Horne, K.; Treu, T.; Raganit, L.; Boroson, T.; Crawford, S.; Pancoast, A.; Pei, L.; Romero-Colmenero, E.; Villforth, C.; Winkler, H.

    2015-11-01

    We present the first results from the Las Cumbres Observatory Global Telescope (LCOGT) Network's Active Galactic Nuclei (AGNs) Key Project, a large program devoted to using the robotic resources of LCOGT to perform time domain studies of active galaxies. We monitored the Seyfert 1 galaxy Arp 151 (Mrk 40) for ∼200 days with robotic imagers and with the FLOYDS robotic spectrograph at Faulkes Telescope North. Arp 151 was highly variable during this campaign, with V-band light curve variations of ∼0.3 mag and Hβ flux changing by a factor of ∼3. We measure robust time lags between the V-band continuum and the Hα, Hβ, and Hγ emission lines, with {τ }{cen}={13.89}-1.41+1.39, {7.52}-1.06+1.43, and {7.40}-1.32+1.50 days, respectively. The lag for the He iiλ4686 emission line is unresolved. We measure a velocity-resolved lag for the Hβ line, which is clearly asymmetric with higher lags on the blue wing of the line that decline to the red, possibly indicative of radial inflow, and is similar in morphology to past observations of the Hβ transfer function shape. Assuming a virialization factor of f = 5.5, we estimate a black hole mass of {M}{BH}={6.2}-1.2+1.4 × 106 M⊙, also consistent with past measurements for this object. These results represent the first step to demonstrate the powerful robotic capabilities of LCOGT for long-term AGN time domain campaigns that human intensive programs cannot easily accomplish. Arp 151 is now one of just a few AGNs where the virial product is known to remain constant against substantial changes in Hβ lag and luminosity.

  6. Beam emittance from ARPES for photoinjectors

    NASA Astrophysics Data System (ADS)

    Harkay, Katherine; Spentzouris, Linda; Nemeth, Karoly; Droubay, Timothy; Chambers, Scott; Joly, Alan; Hess, Wayne

    2014-03-01

    A commonly-used beam emittance measurement for photoinjector sources involves accelerating a low-charge beam to a few megavolts in an electron gun, then using a pepper-pot emittance diagnostic to image the transverse charge distribution. The emission distribution at the cathode surface could in principle be deduced through simulations, but cannot be measured directly with this method. In the quest to develop ultra-bright photoinjectors, it would be advantageous to be able to measure the emission distribution directly, and use this as a screening process to characterize different photocathode candidates. Angle-resolved photoemission sepctroscopy (ARPES), used widely in surface science, has been proposed [H. Padmore (private communication)] as a method to measure the photocathode intrinsic emittance. A promising novel photocathode, a thin layer of MgO on Ag was recently fabricated and ARPES measurements were carried out [T.C. Droubay et al., PRL (in press)]. The analysis of these data and resulting emittance will be presented. Implications for its use in simulations and design of future photoinjectors will also be presented. This work was supported by the U.S. DOE Office of Science (DE-AC02-06CH11357) and the National Science Foundation (No. PHY-0969989). The measurements were carried out at the EMSL user facility at PNNL.

  7. DS-ARP: a new detection scheme for ARP spoofing attacks based on routing trace for ubiquitous environments.

    PubMed

    Song, Min Su; Lee, Jae Dong; Jeong, Young-Sik; Jeong, Hwa-Young; Park, Jong Hyuk

    2014-01-01

    Despite the convenience, ubiquitous computing suffers from many threats and security risks. Security considerations in the ubiquitous network are required to create enriched and more secure ubiquitous environments. The address resolution protocol (ARP) is a protocol used to identify the IP address and the physical address of the associated network card. ARP is designed to work without problems in general environments. However, since it does not include security measures against malicious attacks, in its design, an attacker can impersonate another host using ARP spoofing or access important information. In this paper, we propose a new detection scheme for ARP spoofing attacks using a routing trace, which can be used to protect the internal network. Tracing routing can find the change of network movement path. The proposed scheme provides high constancy and compatibility because it does not alter the ARP protocol. In addition, it is simple and stable, as it does not use a complex algorithm or impose extra load on the computer system.

  8. Elucidating Key Motifs Required for Arp2/3-Dependent and Independent Actin Nucleation by Las17/WASP

    PubMed Central

    Urbanek, Agnieszka N.; Smaczynska-de Rooij, Iwona I.

    2016-01-01

    Actin nucleation is the key rate limiting step in the process of actin polymerization, and tight regulation of this process is critical to ensure actin filaments form only at specific times and at defined regions of the cell. Arp2/3 is a well-characterised protein complex that can promote nucleation of new filaments, though its activity requires additional nucleation promotion factors (NPFs). The best recognized of these factors are the WASP family of proteins that contain binding motifs for both monomeric actin and for Arp2/3. Previously we demonstrated that the yeast WASP homologue, Las17, in addition to activating Arp2/3 can also nucleate actin filaments de novo, independently of Arp2/3. This activity is dependent on its polyproline rich region. Through biochemical and in vivo analysis we have now identified key motifs within the polyproline region that are required for nucleation and elongation of actin filaments, and have addressed the role of the WH2 domain in the context of actin nucleation without Arp2/3. We have also demonstrated that full length Las17 is able to bind liposomes giving rise to the possibility of direct linkage of nascent actin filaments to specific membrane sites to which Las17 has been recruited. Overall, we propose that Las17 functions as the key initiator of de novo actin filament formation at endocytic sites by nucleating, elongating and tethering nascent filaments which then serve as a platform for Arp2/3 recruitment and function. PMID:27637067

  9. Elucidating Key Motifs Required for Arp2/3-Dependent and Independent Actin Nucleation by Las17/WASP.

    PubMed

    Allwood, Ellen G; Tyler, Joe J; Urbanek, Agnieszka N; Smaczynska-de Rooij, Iwona I; Ayscough, Kathryn R

    2016-01-01

    Actin nucleation is the key rate limiting step in the process of actin polymerization, and tight regulation of this process is critical to ensure actin filaments form only at specific times and at defined regions of the cell. Arp2/3 is a well-characterised protein complex that can promote nucleation of new filaments, though its activity requires additional nucleation promotion factors (NPFs). The best recognized of these factors are the WASP family of proteins that contain binding motifs for both monomeric actin and for Arp2/3. Previously we demonstrated that the yeast WASP homologue, Las17, in addition to activating Arp2/3 can also nucleate actin filaments de novo, independently of Arp2/3. This activity is dependent on its polyproline rich region. Through biochemical and in vivo analysis we have now identified key motifs within the polyproline region that are required for nucleation and elongation of actin filaments, and have addressed the role of the WH2 domain in the context of actin nucleation without Arp2/3. We have also demonstrated that full length Las17 is able to bind liposomes giving rise to the possibility of direct linkage of nascent actin filaments to specific membrane sites to which Las17 has been recruited. Overall, we propose that Las17 functions as the key initiator of de novo actin filament formation at endocytic sites by nucleating, elongating and tethering nascent filaments which then serve as a platform for Arp2/3 recruitment and function. PMID:27637067

  10. The unbearable opaqueness of Arp220

    NASA Astrophysics Data System (ADS)

    Martín, S.; Aalto, S.; Sakamoto, K.; González-Alfonso, E.; Muller, S.; Henkel, C.; García-Burillo, S.; Aladro, R.; Costagliola, F.; Harada, N.; Krips, M.; Martín-Pintado, J.; Mühle, S.; van der Werf, P.; Viti, S.

    2016-05-01

    Context. The origin of the enormous luminosities of the two opaque nuclei of Arp 220, the prototypical ultra-luminous infrared galaxy, remains a mystery because we lack observational tools to explore the innermost regions around the nuclei. Aims: We explore the potential of imaging vibrationally excited molecular emission at high angular resolution to better understand the morphology and physical structure of the dense gas in Arp 220 and to gain insight into the nature of the nuclear powering sources. Methods: The Atacama Large Millimeter/submillimeter Array (ALMA) provided simultaneous observations of HCN, HCO+, and vibrationally excited HCN v2 = 1f emission. Their J = 4-3 and 3-2 transitions were observed at a matching resolution of ~0.5'', which allows us to isolate the emission from the two nuclei. Results: The HCN and HCO+ lines within the ground-vibrational state poorly describe the central ~100 pc region around the nuclei because there are strong effects of cool absorbing gas in the foreground and severe line blending that is due to the prolific molecular emission of Arp 220. Vibrationally excited emission of HCN is detected in both nuclei with a very high ratio relative to the total LFIR, higher than in any other observed galaxy and well above what is observed in Galactic hot cores. HCN v2 = 1f is observed to be marginally resolved in ~60 × 50 pc regions inside the dusty ~100 pc sized nuclear cores. Its emission is centered on our derived individual nuclear velocities based on HCO+ emission (VWN = 5342 ± 4 and VEN = 5454 ± 8 km s-1, for the western and eastern nucleus, respectively). With virial masses within r ~ 25-30 pc based on the HCN v2 = 1f line widths, we estimate gas surface densities (gas fraction fg = 0.1) of 3 ± 0.3 × 104 M⊙ pc-2 (WN) and 1.1 ± 0.1 × 104 M⊙ pc-2 (EN). The 4-3/3-2 flux density ratio could be consistent with optically thick emission, which would further constrain the size of the emitting region to >15 pc (EN) and >22 pc

  11. Rapid high-resolution spin- and time-resolved ARPES

    NASA Astrophysics Data System (ADS)

    Lin, Chiu-Yun; Gotlieb, Kenneth; Jozwiak, Chris; Hussain, Zahid; Bostwick, Aaron; Lanzara, Alessandra; Advanced Light Source, Lawrence Berkeley National Laboratory Collaboration; Graduate Group in Applied Science; Technology, University of California, Berkeley Collaboration

    2015-03-01

    A high-efficiency spin- and angle-resolved photoemission spectroscopy (spin-ARPES) spectrometer, coupled with a lab-based 6 eV laser, will be presented in this talk. Combining time-of-flight(TOF) energy measurements with low-energy exchange scattering spin polarimetry, spin-TOF ARPES achieves unprecedented measurements of near-EF physics rapidly. In addition, the successful integration of the spectrometer with the pulsed laser system demonstrates its potential for simultaneous spin- and time-resolved ARPES with pump-probe based measurements.

  12. Diffusion, capture and recycling of SCAR/WAVE and Arp2/3 complexes observed in cells by single-molecule imaging.

    PubMed

    Millius, Arthur; Watanabe, Naoki; Weiner, Orion D

    2012-03-01

    The SCAR/WAVE complex drives lamellipodium formation by enhancing actin nucleation by the Arp2/3 complex. Phosphoinositides and Rac activate the SCAR/WAVE complex, but how SCAR/WAVE and Arp2/3 complexes converge at sites of nucleation is unknown. We analyzed the single-molecule dynamics of WAVE2 and p40 (subunits of the SCAR/WAVE and Arp2/3 complexes, respectively) in XTC cells. We observed lateral diffusion of both proteins and captured the transition of p40 from diffusion to network incorporation. These results suggest that a diffusive 2D search facilitates binding of the Arp2/3 complex to actin filaments necessary for nucleation. After nucleation, the Arp2/3 complex integrates into the actin network and undergoes retrograde flow, which results in its broad distribution throughout the lamellipodium. By contrast, the SCAR/WAVE complex is more restricted to the cell periphery. However, with single-molecule imaging, we also observed WAVE2 molecules undergoing retrograde motion. WAVE2 and p40 have nearly identical speeds, lifetimes and sites of network incorporation. Inhibition of actin retrograde flow does not prevent WAVE2 association and disassociation with the membrane but does inhibit WAVE2 removal from the actin cortex. Our results suggest that membrane binding and diffusion expedites the recruitment of nucleation factors to a nucleation site independent of actin assembly, but after network incorporation, ongoing actin polymerization facilitates recycling of SCAR/WAVE and Arp2/3 complexes.

  13. Application of SAE ARP4754A to Flight Critical Systems

    NASA Technical Reports Server (NTRS)

    Peterson, Eric M.

    2015-01-01

    This report documents applications of ARP4754A to the development of modern computer-based (i.e., digital electronics, software and network-based) aircraft systems. This study is to offer insight and provide educational value relative to the guidelines in ARP4754A and provide an assessment of the current state-of-the- practice within industry and regulatory bodies relative to development assurance for complex and safety-critical computer-based aircraft systems.

  14. Exo70 Stimulates the Arp2/3 Complex-mediated Actin Branching for Lamellipodia Formation and Cell Migration

    PubMed Central

    Liu, Jianglan; Zhao, Yuting; Sun, Yujie; He, Bing; Yang, Changsong; Svitkina, Tatyana; Goldman, Yale E.; Guo, Wei

    2012-01-01

    Summary Directional cell migration requires the coordination of actin assembly and membrane remodeling. The exocyst is an octameric protein complex essential for exocytosis and plasma membrane remodeling [1,2]. A component of the exocyst, Exo70, directly interacts with the Arp2/3 complex, a core nucleating factor for the generation of branched actin networks for cell morphogenesis and migration [3-9]. Using in vitro actin polymerization assay and time-lapse TIRF microscopy, we found Exo70 functions as a kinetic activator of the Arp2/3 complex that promotes actin filament nucleation and branching. We further found that the effect of Exo70 on actin is mediated by promoting the interaction of Arp2/3 complex with WAVE2, a member of the N-WASP/WAVE family of nucleation promoting factors (NPFs). At the cellular level, the stimulatory effect of Exo70 on Arp2/3 is required for lamellipodia formation and maintaining directional persistence of cell migration. Our findings provide a novel mechanism for regulating actin polymerization and branching for effective membrane protrusion during cell morphogenesis and migration. PMID:22748316

  15. DS-ARP: A New Detection Scheme for ARP Spoofing Attacks Based on Routing Trace for Ubiquitous Environments

    PubMed Central

    Song, Min Su; Lee, Jae Dong; Jeong, Hwa-Young; Park, Jong Hyuk

    2014-01-01

    Despite the convenience, ubiquitous computing suffers from many threats and security risks. Security considerations in the ubiquitous network are required to create enriched and more secure ubiquitous environments. The address resolution protocol (ARP) is a protocol used to identify the IP address and the physical address of the associated network card. ARP is designed to work without problems in general environments. However, since it does not include security measures against malicious attacks, in its design, an attacker can impersonate another host using ARP spoofing or access important information. In this paper, we propose a new detection scheme for ARP spoofing attacks using a routing trace, which can be used to protect the internal network. Tracing routing can find the change of network movement path. The proposed scheme provides high constancy and compatibility because it does not alter the ARP protocol. In addition, it is simple and stable, as it does not use a complex algorithm or impose extra load on the computer system. PMID:25243205

  16. Research on implementation of proxy Arp in IP DSLAM

    NASA Astrophysics Data System (ADS)

    Cheng, Chuanqing; Wang, Li; Huang, Qiugen

    2005-02-01

    While the ethernet is applied more and more in public network environment and xdsl service become the most common access mode ,IP kenel DSLAM undertakes some functions such as service distribution and convergence ,security management and customer management.Facing the contradiction of the need of port isolation and the shortage of ip address,VLAN aggregation technology is applied in DSLAM.How to implement the communicatio between the two vlan but share the same ip subnet,proxy arp does this. This paper introduces how to implement proxy arp in the DSLAM. TCP/IP communication detail procedure betweent two host ,the relation of VLAN and network segment are discussed. The proxy arp model and its implementation in IP DSLAM is also expatiated in this paper and a conformance tesing is given.

  17. The remarkable infrared galaxy Arp 220 = IC 4553

    NASA Technical Reports Server (NTRS)

    Soifer, B. T.; Neugebauer, G.; Helou, G.; Lonsdale, C. J.; Hacking, P.; Rice, W.; Houck, J. R.; Low, F. J.; Rowan-Robinson, M.

    1984-01-01

    IRAS observations of the peculiar galaxy Arp 220 = IC 4553 show that it is extremely luminous in the far-infrared, with a total luminosity of 2 x 10 to the 12th solar luminosities. The infrared-to-blue luminosity ratio of this galaxy is about 80, which is the largest value of the ratio for galaxies in the UGC catalog, and places it in the range of the 'unidentified' infrared sources recently reported by Houck et al. in the IRAS all-sky survey. Other observations of Arp 220, combined with the luminosity in the infrared, allow either a Seyfert-like or starburst origin for this luminosity.

  18. Protein interacting with C kinase 1 suppresses invasion and anchorage-independent growth of astrocytic tumor cells

    PubMed Central

    Cockbill, Louisa M. R.; Murk, Kai; Love, Seth; Hanley, Jonathan G.

    2015-01-01

    Astrocytic tumors are the most common form of primary brain tumor. Astrocytic tumor cells infiltrate the surrounding CNS tissue, allowing them to evade removal upon surgical resection of the primary tumor. Dynamic changes to the actin cytoskeleton are crucial to cancer cell invasion, but the specific mechanisms that underlie the particularly invasive phenotype of astrocytic tumor cells are unclear. Protein interacting with C kinase 1 (PICK1) is a PDZ and BAR domain–containing protein that inhibits actin-related protein 2/3 (Arp2/3)-dependent actin polymerization and is involved in regulating the trafficking of a number of cell-surface receptors. Here we report that, in contrast to other cancers, PICK1 expression is down-regulated in grade IV astrocytic tumor cell lines and also in clinical cases of the disease in which grade IV tumors have progressed from lower-grade tumors. Exogenous expression of PICK1 in the grade IV astrocytic cell line U251 reduces their capacity for anchorage-independent growth, two-dimensional migration, and invasion through a three-dimensional matrix, strongly suggesting that low PICK1 expression plays an important role in astrocytic tumorigenesis. We propose that PICK1 negatively regulates neoplastic infiltration of astrocytic tumors and that manipulation of PICK1 is an attractive possibility for therapeutic intervention. PMID:26466675

  19. Proton Calorimetry and Gamma-Rays in Arp 220

    NASA Astrophysics Data System (ADS)

    Yoast-Hull, Tova; Gallagher, John S.; Zweibel, Ellen Gould

    2014-08-01

    Until recently, it was thought that starburst galaxies were both electron and proton calorimeters, making them especially bright in gamma-rays. However, with detections of starburst galaxies M82 and NGC 253 by Fermi, HESS, and VERITAS, we find that such galaxies are only partial proton calorimeters due to significant advection by galactic winds. Thus, to find cosmic-ray proton calorimeters, we must look for much denser systems. Previous models of the cosmic ray interactions in Arp 220 (e.g. Torres 2004) suggest it is a proton calorimeter and that it should already be detectable by Fermi. The Torres model suggests that if Arp 220 is a calorimeter, then it should have been detected in gamma-rays by Fermi at levels above current upper limits. We therefore must question. whether Arp 220 is a true proton calorimeter, and if so what other properties could be responsible for its low gamma ray flux. Here, we further explore the observed ranges on environmental properties and model the central nuclei to predict both the radio and gamma-ray spectra. We test the proton calorimetry hypothesis and estimate the observation time needed for a detection by Fermi for a range of assumptions about conditions in Arp 220.

  20. Extreme-ultraviolet ultrafast ARPES at high repetition rates

    NASA Astrophysics Data System (ADS)

    Buss, Jan; Wang, He; Xu, Yiming; Stoll, Sebastian; Zeng, Lingkun; Ulonska, Stefan; Denlinger, Jonathan; Hussain, Zahid; Jozwiak, Chris; Lanzara, Alessandra; Kaindl, Robert

    Time- and angle-resolved photoemission spectroscopy (trARPES) represents a powerful approach to resolve the electronic structure and quasiparticle dynamics in complex materials, yet is often limited in either momentum space (incident photon energy), probe sensitivity (pulse repetition rate), or energy resolution. We demonstrate a novel table-top trARPES setup that combines a bright 50-kHz source of narrowband, extreme ultraviolet (XUV) pulses at 22.3 eV with UHV photoemission instrumentation to sensitively access dynamics for a large momentum space. The output of a high-power Ti:sapphire amplifier is split to provide the XUV probe and intense photoexcitation (up to mJ/cm2) . A vacuum beamline delivers spectral and flux characterization, differential pumping, as well as XUV beam steering and toroidal refocusing onto the sample with high incident flux of 3x1011 ph/s. Photoemission studies are carried out in a customized UHV chamber equipped with a hemispherical analyzer (R4000), six-axis sample cryostat, and side chambers for sample loading, storage and preparation. An ARPES energy resolution down to 70 meV with the direct XUV output is demonstrated. We will discuss initial applications of this setup including Fermi surface mapping and trARPES of complex materials.

  1. VLBI Images of 49 Radio Supernovae in Arp 220

    NASA Astrophysics Data System (ADS)

    Lonsdale, Colin J.; Diamond, Philip J.; Thrall, Hannah; Smith, Harding E.; Lonsdale, Carol J.

    2006-08-01

    We have used a very long baseline interferometry (VLBI) array at 18 cm wavelength to image the nucleus of the luminous IR galaxy Arp 220 at ~1 pc linear resolution, with very high sensitivity. The resulting map has an rms of 5.5 μJy beam-1, and careful image analysis results in 49 confirmed point sources ranging in flux density from 1.2 mJy down to ~60 μJy. Comparison with high-sensitivity data from 12 months earlier reveals at least four new sources. The favored interpretation of these sources is that they are radio supernovae, and if all new supernovae are detectable at this sensitivity, a resulting estimate of the supernova rate in the Arp 220 system is 4+/-2 per year. The implied star formation rate is sufficient to power the entire observed far-infrared luminosity of the galaxy. The two nuclei of Arp 220 exhibit striking similarities in their radio properties, although the western nucleus is more compact, and appears to be ~3 times more luminous than the eastern nucleus. There are also some puzzling differences, and differential free-free absorption, synchrotron aging, and expansion losses may all be playing a role. Comparison with the nearby starburst galaxy M82 supports the hypothesis that the activity in Arp 220 is essentially a scaled-up version of that in M82.

  2. Nutraceutical with Resveratrol and Omega-3 Fatty Acids Induces Autophagy in ARPE-19 Cells.

    PubMed

    Koskela, Ali; Reinisalo, Mika; Petrovski, Goran; Sinha, Debasish; Olmiere, Céline; Karjalainen, Reijo; Kaarniranta, Kai

    2016-05-11

    Impaired autophagic and proteasomal cleansing have been documented in aged retinal pigment epithelial (RPE) cells and age-related macular degeneration (AMD). Omega-3 fatty acids and resveratrol have many positive homeostatic effects in RPE cells. In this work, ARPE-19 cells were treated with 288 ng of Resvega, containing 30 mg of trans resveratrol and 665 mg of omega-3 fatty acids, among other nutrients, with proteasome inhibitor MG-132 or autophagy inhibitor bafilomycin A1 up to 48 h. Autophagy markers p62/SQSTM1 (p62) and LC3 (microtubule-associated protein 1A/1B-light chain 3) were analyzed by Western blotting. Fluorescence microscopy with mCherry-GFP-LC3 plasmid was applied to study the autophagy flux, and cytoprotective effects were investigated with colorimetric MTT and LDH assays. Resvega induced autophagy by showing increased autolysosome formation and autophagy flux, and the change in the p62 and LC3 protein levels further confirmed the fluorescent microscopy results. Moreover, Resvega provided a clear cytoprotection under proteasome inhibition. These findings highlight the potential of the nutraceuticals containing resveratrol, omega-3 fatty acids and other nutrients in the prevention of ARPE-19 cell damage.

  3. Nutraceutical with Resveratrol and Omega-3 Fatty Acids Induces Autophagy in ARPE-19 Cells.

    PubMed

    Koskela, Ali; Reinisalo, Mika; Petrovski, Goran; Sinha, Debasish; Olmiere, Céline; Karjalainen, Reijo; Kaarniranta, Kai

    2016-01-01

    Impaired autophagic and proteasomal cleansing have been documented in aged retinal pigment epithelial (RPE) cells and age-related macular degeneration (AMD). Omega-3 fatty acids and resveratrol have many positive homeostatic effects in RPE cells. In this work, ARPE-19 cells were treated with 288 ng of Resvega, containing 30 mg of trans resveratrol and 665 mg of omega-3 fatty acids, among other nutrients, with proteasome inhibitor MG-132 or autophagy inhibitor bafilomycin A1 up to 48 h. Autophagy markers p62/SQSTM1 (p62) and LC3 (microtubule-associated protein 1A/1B-light chain 3) were analyzed by Western blotting. Fluorescence microscopy with mCherry-GFP-LC3 plasmid was applied to study the autophagy flux, and cytoprotective effects were investigated with colorimetric MTT and LDH assays. Resvega induced autophagy by showing increased autolysosome formation and autophagy flux, and the change in the p62 and LC3 protein levels further confirmed the fluorescent microscopy results. Moreover, Resvega provided a clear cytoprotection under proteasome inhibition. These findings highlight the potential of the nutraceuticals containing resveratrol, omega-3 fatty acids and other nutrients in the prevention of ARPE-19 cell damage. PMID:27187449

  4. Nutraceutical with Resveratrol and Omega-3 Fatty Acids Induces Autophagy in ARPE-19 Cells

    PubMed Central

    Koskela, Ali; Reinisalo, Mika; Petrovski, Goran; Sinha, Debasish; Olmiere, Céline; Karjalainen, Reijo; Kaarniranta, Kai

    2016-01-01

    Impaired autophagic and proteasomal cleansing have been documented in aged retinal pigment epithelial (RPE) cells and age-related macular degeneration (AMD). Omega-3 fatty acids and resveratrol have many positive homeostatic effects in RPE cells. In this work, ARPE-19 cells were treated with 288 ng of Resvega, containing 30 mg of trans resveratrol and 665 mg of omega-3 fatty acids, among other nutrients, with proteasome inhibitor MG-132 or autophagy inhibitor bafilomycin A1 up to 48 h. Autophagy markers p62/SQSTM1 (p62) and LC3 (microtubule-associated protein 1A/1B-light chain 3) were analyzed by Western blotting. Fluorescence microscopy with mCherry-GFP-LC3 plasmid was applied to study the autophagy flux, and cytoprotective effects were investigated with colorimetric MTT and LDH assays. Resvega induced autophagy by showing increased autolysosome formation and autophagy flux, and the change in the p62 and LC3 protein levels further confirmed the fluorescent microscopy results. Moreover, Resvega provided a clear cytoprotection under proteasome inhibition. These findings highlight the potential of the nutraceuticals containing resveratrol, omega-3 fatty acids and other nutrients in the prevention of ARPE-19 cell damage. PMID:27187449

  5. Mid-infrared imaging of Markarian 231 and Arp 220

    SciTech Connect

    Keto, E.; Ball, R.; Arens, J.; Jernigan, G.; Meixner, M. Smithsonian Astrophysical Observatory, Cambridge, MA Lawrence Livermore National Laboratory, Livermore, CA Lawrence Livermore National Laboratory, Livermore, CA California University, Berkeley )

    1992-03-01

    High angular resolution observations of Arp 220 and Mrk 231 provide images of the nuclei and show that the source of the strong mid-IR emission is confined to regions less than about 0.5 arcsec or 400 pc in diameter in Mrk 231 and less than 1.5 arcsec x 0.9 arcsec or 320 x 530 pc in Arp 220. If much of the far-IR emission also derives from such a small region, the implied radiation densities are quite high, equivalent to one O star per cu pc. Although in normal galaxies the near-IR traces an older population of evolved, cool stars, such high radiation densities in the IR bright galaxies suggest the possibility that the spatial correlation observed between the near-IR, mid-IR, and radio may hold because emission in all three bands is associated with hot interstellar gas and dust. 23 refs.

  6. Mid-infrared imaging of Markarian 231 and Arp 220

    NASA Technical Reports Server (NTRS)

    Keto, Eric; Ball, Roger; Arens, John; Jernigan, Garrett; Meixner, Margaret

    1992-01-01

    High angular resolution observations of Arp 220 and Mrk 231 provide images of the nuclei and show that the source of the strong mid-IR emission is confined to regions less than about 0.5 arcsec or 400 pc in diameter in Mrk 231 and less than 1.5 arcsec x 0.9 arcsec or 320 x 530 pc in Arp 220. If much of the far-IR emission also derives from such a small region, the implied radiation densities are quite high, equivalent to one O star per cu pc. Although in normal galaxies the near-IR traces an older population of evolved, cool stars, such high radiation densities in the IR bright galaxies suggest the possibility that the spatial correlation observed between the near-IR, mid-IR, and radio may hold because emission in all three bands is associated with hot interstellar gas and dust.

  7. Phase Stability and the Velocity Dependence of the ARP Force

    NASA Astrophysics Data System (ADS)

    Elgin, John; Arnold, Brian; Inaki, Taichi; Fang, Yifan; Metcalf, Harold

    2016-05-01

    Adiabatic Rapid Passage (ARP) has been shown to produce optical forces much stronger than the usual radiative force. Recent work has found that the ARP force is very sensitive to the phase of the optical field. Thus, the use of two free running, oppositely detuned lasers is not the ideal way to achieve an accurate measurement of the velocity dependence by mimicking the Doppler shift. We believe that phase locking the two lasers to a third, master laser will address these phase concerns, thereby allowing a proper measure of the velocity dependence. We have implemented this in our experiment and will present the results obtained from this change. We will also compare these results to those obtained using independent lasers and comment on the implications. Supported by ONR and GAANN - Dept. of Education.

  8. Kv3.3 Channels Bind Hax-1 and Arp2/3 to Assemble a Stable Local Actin Network that Regulates Channel Gating.

    PubMed

    Zhang, Yalan; Zhang, Xiao-Feng; Fleming, Matthew R; Amiri, Anahita; El-Hassar, Lynda; Surguchev, Alexei A; Hyland, Callen; Jenkins, David P; Desai, Rooma; Brown, Maile R; Gazula, Valeswara-Rao; Waters, Michael F; Large, Charles H; Horvath, Tamas L; Navaratnam, Dhasakumar; Vaccarino, Flora M; Forscher, Paul; Kaczmarek, Leonard K

    2016-04-01

    Mutations in the Kv3.3 potassium channel (KCNC3) cause cerebellar neurodegeneration and impair auditory processing. The cytoplasmic C terminus of Kv3.3 contains a proline-rich domain conserved in proteins that activate actin nucleation through Arp2/3. We found that Kv3.3 recruits Arp2/3 to the plasma membrane, resulting in formation of a relatively stable cortical actin filament network resistant to cytochalasin D that inhibits fast barbed end actin assembly. These Kv3.3-associated actin structures are required to prevent very rapid N-type channel inactivation during short depolarizations of the plasma membrane. The effects of Kv3.3 on the actin cytoskeleton are mediated by the binding of the cytoplasmic C terminus of Kv3.3 to Hax-1, an anti-apoptotic protein that regulates actin nucleation through Arp2/3. A human Kv3.3 mutation within a conserved proline-rich domain produces channels that bind Hax-1 but are impaired in recruiting Arp2/3 to the plasma membrane, resulting in growth cones with deficient actin veils in stem cell-derived neurons.

  9. Kv3.3 Channels Bind Hax-1 and Arp2/3 to Assemble a Stable Local Actin Network that Regulates Channel Gating.

    PubMed

    Zhang, Yalan; Zhang, Xiao-Feng; Fleming, Matthew R; Amiri, Anahita; El-Hassar, Lynda; Surguchev, Alexei A; Hyland, Callen; Jenkins, David P; Desai, Rooma; Brown, Maile R; Gazula, Valeswara-Rao; Waters, Michael F; Large, Charles H; Horvath, Tamas L; Navaratnam, Dhasakumar; Vaccarino, Flora M; Forscher, Paul; Kaczmarek, Leonard K

    2016-04-01

    Mutations in the Kv3.3 potassium channel (KCNC3) cause cerebellar neurodegeneration and impair auditory processing. The cytoplasmic C terminus of Kv3.3 contains a proline-rich domain conserved in proteins that activate actin nucleation through Arp2/3. We found that Kv3.3 recruits Arp2/3 to the plasma membrane, resulting in formation of a relatively stable cortical actin filament network resistant to cytochalasin D that inhibits fast barbed end actin assembly. These Kv3.3-associated actin structures are required to prevent very rapid N-type channel inactivation during short depolarizations of the plasma membrane. The effects of Kv3.3 on the actin cytoskeleton are mediated by the binding of the cytoplasmic C terminus of Kv3.3 to Hax-1, an anti-apoptotic protein that regulates actin nucleation through Arp2/3. A human Kv3.3 mutation within a conserved proline-rich domain produces channels that bind Hax-1 but are impaired in recruiting Arp2/3 to the plasma membrane, resulting in growth cones with deficient actin veils in stem cell-derived neurons. PMID:26997484

  10. Fusion of the mouse IgG1 Fc domain to the VHH fragment (ARP1) enhances protection in a mouse model of rotavirus

    PubMed Central

    Günaydın, Gökçe; Yu, Shengze; Gräslund, Torbjörn; Hammarström, Lennart; Marcotte, Harold

    2016-01-01

    A variable fragment of a heavy chain antibody (VHH) directed against rotavirus, also referred to as anti-rotavirus protein 1 (ARP1), was shown to confer protection against rotavirus induced diarrhea in infant mouse model of rotavirus induced diarrhea. In this study, we have fused the mouse IgG1 Fc to ARP1 to improve the protective capacity of ARP1 by inducing an Fc-mediated effector function. We have shown that the Fc-ARP1 fusion protein confers significantly increased protection against rotavirus in a neonatal mouse model of rotavirus-induced diarrhea by reducing the prevalence, duration and severity of diarrhea and the viral load in the small intestines, suggesting that the Fc part of immunoglobulins may be engaged in Fc-mediated neutralization of rotavirus. Engineered conventional-like antibodies, by fusion of the Fc part of immunoglobulins to antigen-specific heavy-chain only VHH fragments, might be applied to novel antibody-based therapeutic approaches to enhance elimination of pathogens by activation of distinct effector signaling pathways. PMID:27439689

  11. Fusion of the mouse IgG1 Fc domain to the VHH fragment (ARP1) enhances protection in a mouse model of rotavirus.

    PubMed

    Günaydın, Gökçe; Yu, Shengze; Gräslund, Torbjörn; Hammarström, Lennart; Marcotte, Harold

    2016-01-01

    A variable fragment of a heavy chain antibody (VHH) directed against rotavirus, also referred to as anti-rotavirus protein 1 (ARP1), was shown to confer protection against rotavirus induced diarrhea in infant mouse model of rotavirus induced diarrhea. In this study, we have fused the mouse IgG1 Fc to ARP1 to improve the protective capacity of ARP1 by inducing an Fc-mediated effector function. We have shown that the Fc-ARP1 fusion protein confers significantly increased protection against rotavirus in a neonatal mouse model of rotavirus-induced diarrhea by reducing the prevalence, duration and severity of diarrhea and the viral load in the small intestines, suggesting that the Fc part of immunoglobulins may be engaged in Fc-mediated neutralization of rotavirus. Engineered conventional-like antibodies, by fusion of the Fc part of immunoglobulins to antigen-specific heavy-chain only VHH fragments, might be applied to novel antibody-based therapeutic approaches to enhance elimination of pathogens by activation of distinct effector signaling pathways. PMID:27439689

  12. WIP Provides an Essential Link between Nck and N-WASP during Arp2/3-Dependent Actin Polymerization

    PubMed Central

    Donnelly, Sara K.; Weisswange, Ina; Zettl, Markus; Way, Michael

    2013-01-01

    Summary Nck links phosphotyrosine-based signaling to Arp2/3-dependent actin polymerization during many different cellular processes as well as actin-based motility of enteropathogenic Escherichia coli (EPEC) [1, 2], vaccinia [3, 4], and other vertebrate poxviruses [5] by interacting with N-WASP/WASP [6, 7]. Nck also binds WASP-interacting protein (WIP) [8], which inhibits the ability of N-WASP to activate the Arp2/3 complex until it receives an appropriate signaling input [9, 10]. Using mouse embryonic fibroblasts (MEFs) lacking Nck, WIP, or N-WASP [3, 11, 12], we have investigated whether an interaction of Nck with both WIP and N-WASP is required for their recruitment to vaccinia during Arp2/3-dependent actin assembly. We find that WIP or its homolog WIRE is required for N-WASP recruitment and actin-based motility of the virus. WIP contains two Nck-binding sites and is recruited to the virus, bound to N-WASP, by interacting with the second SH3 domain of Nck. N-WASP also contains two Nck-binding sites, but its recruitment is dependent on its interaction with WIP rather than Nck. The first and third SH3 domains of Nck are not required to recruit the WIP:N-WASP complex but are essential to stimulate actin assembly. We have established that WIP acts as an essential link between Nck and N-WASP. Our observations provide important insights into the hierarchy and connections in one of the major cellular signaling networks stimulating Arp2/3 complex-dependent actin polymerization. PMID:23707428

  13. ARPES study of the Kitaev Candidate RuCl3

    NASA Astrophysics Data System (ADS)

    Zhou, Xiaoqing; Li, Haoxiang; Waugh, Justin; Parham, Stephen; Kim, Heung-Sik; Kee, Hae-Young; Sears, Jennifer; Kim, Young-June; Dessau, Daniel

    RuCl3 has been identified as a spin-orbital-assisted Mott insulator with possible Kitaev magnetic orders at low temperature by X-ray absorption, susceptibility, specific heat and Raman scattering. Here we report high resolution ARPES spectroscopy measurements on single crystal RuCl3, and compare it with DFT calculations with and without magnetic order. Furthermore, the possible spin-orbital-assisted Mott transition is investigated through electron doping

  14. EVLA Imaging of Methanimine and Hydrogen Cyanide in Arp 220

    NASA Astrophysics Data System (ADS)

    Rickert, Matthew; Momjian, E.; Sarma, A.; AO Arp 220 Team

    2011-01-01

    We used the EVLA in A configuration to image the C-band transitions of the pre-biotic molecule methanimine (H2CNH) and the J=5 direct l-type transition of hydrogen cyanide (HCN) in the nearest and the prototypical ultra-luminous IR galaxy, Arp 220. The observations were carried out as a result of the first definitive extragalactic detection of these transitions with Arecibo (Salter et al. 2008). These EVLA A-configuration observations spatially resolve the two nuclei of Arp 220, which are separated by about 1 arcsec. The results show that the emission line of the H2CNH and the absorption line of the HCN (J=5) are solely detected toward the western nucleus of Arp 220. The H2CNH emission is very likely due to a maser, because its brightness temperature is several times the decomposition temperature of the molecule. This is similar to the formaldehyde (H2CO) transition, which also shows a weak maser emission in Arp 220 and mostly toward the western nucleus. The confinement of the HCN (J=5) absorption line to the western nucleus is in contrast to previous detections of rotationally excited HCN transitions, which have been observed in emission from both nuclei. These EVLA observations, along with Arecibo's original detections, demonstrate that a new range of molecular transitions can now be detected and imaged at cm wavelengths, thus opening up new opportunities for the study of the physical and chemical characteristics of luminous IR galaxies. The National Radio Astronomy Observatory is a facility of the National Science Foundation operated under cooperative agreement by Associated Universities, Inc.

  15. Parsec-scale magnetic fields in Arp 220

    NASA Astrophysics Data System (ADS)

    McBride, James; Robishaw, Timothy; Heiles, Carl; Bower, Geoffrey C.; Sarma, Anuj P.

    2015-02-01

    We present the first very long baseline interferometry (VLBI) detections of Zeeman splitting in another galaxy. We used Arecibo Observatory, the Green Bank Telescope, and the Very Long Baseline Array to perform dual-polarization observations of OH maser lines in the merging galaxy Arp 220. We measured magnetic fields of ˜1-5 mG associated with three roughly parsec-sized clouds in the nuclear regions of Arp 220. Our measured magnetic fields have comparable strengths and the same direction as features at the same velocity identified in previous Zeeman observations with Arecibo alone. The agreement between single dish and VLBI results provides critical validation of previous Zeeman splitting observations of OH megamasers that used a single large dish. The measured magnetic field strengths indicate that magnetic energy densities are comparable to gravitational energy in OH maser clouds. We also compare our total intensity results to previously published VLBI observations of OH megamasers in Arp 220. We find evidence for changes in both structure and amplitude of the OH maser lines that are most easily explained by variability intrinsic to the masing region, rather than variability produced by interstellar scintillation. Our results demonstrate the potential for using high-sensitivity VLBI to study magnetic fields on small spatial scales in extragalactic systems.

  16. Following the Viterbi Path to Deduce Flagellar Actin-Interacting Proteins of Leishmania spp.: Report on Cofilins and Twinfilins

    NASA Astrophysics Data System (ADS)

    Pacheco, Ana Carolina L.; Araújo, Fabiana F.; Kamimura, Michel T.; Medeiros, Sarah R.; Viana, Daniel A.; Oliveira, Fátima de Cássia E.; Filho, Raimundo Araújo; Costa, Marcília P.; Oliveira, Diana M.

    2007-11-01

    For performing vital cellular processes, such as motility, eukaryotic cells rely on the actin cytoskeleton, whose structure and dynamics are tightly controlled by a large number of actin-interacting (AIP) or actin-related/regulating (ARP) proteins. Trypanosomatid protozoa, such as Leishmania, rely on their flagellum for motility and sensory reception, which are believed to allow parasite migration, adhesion, invasion and even persistence on mammalian host tissues to cause disease. Actin can determine cell stiffness and transmit force during mechanotransduction, cytokinesis, cell motility and other cellular shape changes, while the identification and analyses of AIPs can help to improve understanding of their mechanical properties on physiological architectures, such as the present case regarding Leishmania flagellar apparatus. This work conveniently apply bioinformatics tools in some refined pattern recognition techniques (such as hidden Markov models (HMMs) through the Viterbi algorithm/path) in order to improve the recognition of actin-binding/interacting activity through identification of AIPs in genomes, transcriptomes and proteomes of Leishmania species. We here report cofilin and twinfilin as putative components of the flagellar apparatus, a direct bioinformatics contribution in the secondary annotation of Leishmania and trypanosomatid genomes.

  17. SCARN a Novel Class of SCAR Protein That Is Required for Root-Hair Infection during Legume Nodulation.

    PubMed

    Qiu, Liping; Lin, Jie-Shun; Xu, Ji; Sato, Shusei; Parniske, Martin; Wang, Trevor L; Downie, J Allan; Xie, Fang

    2015-10-01

    Rhizobial infection of legume root hairs requires a rearrangement of the actin cytoskeleton to enable the establishment of plant-made infection structures called infection threads. In the SCAR/WAVE (Suppressor of cAMP receptor defect/WASP family verpolin homologous protein) actin regulatory complex, the conserved N-terminal domains of SCAR proteins interact with other components of the SCAR/WAVE complex. The conserved C-terminal domains of SCAR proteins bind to and activate the actin-related protein 2/3 (ARP2/3) complex, which can bind to actin filaments catalyzing new actin filament formation by nucleating actin branching. We have identified, SCARN (SCAR-Nodulation), a gene required for root hair infection of Lotus japonicus by Mesorhizobium loti. Although the SCARN protein is related to Arabidopsis thaliana SCAR2 and SCAR4, it belongs to a distinct legume-sub clade. We identified other SCARN-like proteins in legumes and phylogeny analyses suggested that SCARN may have arisen from a gene duplication and acquired specialized functions in root nodule symbiosis. Mutation of SCARN reduced formation of infection-threads and their extension into the root cortex and slightly reduced root-hair length. Surprisingly two of the scarn mutants showed constitutive branching of root hairs in uninoculated plants. However we observed no effect of scarn mutations on trichome development or on the early actin cytoskeletal accumulation that is normally seen in root hair tips shortly after M. loti inoculation, distinguishing them from other symbiosis mutations affecting actin nucleation. The C-terminal domain of SCARN binds to ARPC3 and ectopic expression of the N-terminal SCAR-homology domain (but not the full length protein) inhibited nodulation. In addition, we found that SCARN expression is enhanced by M. loti in epidermal cells and that this is directly regulated by the NODULE INCEPTION (NIN) transcription factor.

  18. SCARN a Novel Class of SCAR Protein That Is Required for Root-Hair Infection during Legume Nodulation

    PubMed Central

    Qiu, Liping; Lin, Jie-shun; Xu, Ji; Sato, Shusei; Parniske, Martin; Wang, Trevor L.; Downie, J. Allan; Xie, Fang

    2015-01-01

    Rhizobial infection of legume root hairs requires a rearrangement of the actin cytoskeleton to enable the establishment of plant-made infection structures called infection threads. In the SCAR/WAVE (Suppressor of cAMP receptor defect/WASP family verpolin homologous protein) actin regulatory complex, the conserved N-terminal domains of SCAR proteins interact with other components of the SCAR/WAVE complex. The conserved C-terminal domains of SCAR proteins bind to and activate the actin-related protein 2/3 (ARP2/3) complex, which can bind to actin filaments catalyzing new actin filament formation by nucleating actin branching. We have identified, SCARN (SCAR-Nodulation), a gene required for root hair infection of Lotus japonicus by Mesorhizobium loti. Although the SCARN protein is related to Arabidopsis thaliana SCAR2 and SCAR4, it belongs to a distinct legume-sub clade. We identified other SCARN-like proteins in legumes and phylogeny analyses suggested that SCARN may have arisen from a gene duplication and acquired specialized functions in root nodule symbiosis. Mutation of SCARN reduced formation of infection-threads and their extension into the root cortex and slightly reduced root-hair length. Surprisingly two of the scarn mutants showed constitutive branching of root hairs in uninoculated plants. However we observed no effect of scarn mutations on trichome development or on the early actin cytoskeletal accumulation that is normally seen in root hair tips shortly after M. loti inoculation, distinguishing them from other symbiosis mutations affecting actin nucleation. The C-terminal domain of SCARN binds to ARPC3 and ectopic expression of the N-terminal SCAR-homology domain (but not the full length protein) inhibited nodulation. In addition, we found that SCARN expression is enhanced by M. loti in epidermal cells and that this is directly regulated by the NODULE INCEPTION (NIN) transcription factor. PMID:26517270

  19. SCARN a Novel Class of SCAR Protein That Is Required for Root-Hair Infection during Legume Nodulation.

    PubMed

    Qiu, Liping; Lin, Jie-Shun; Xu, Ji; Sato, Shusei; Parniske, Martin; Wang, Trevor L; Downie, J Allan; Xie, Fang

    2015-10-01

    Rhizobial infection of legume root hairs requires a rearrangement of the actin cytoskeleton to enable the establishment of plant-made infection structures called infection threads. In the SCAR/WAVE (Suppressor of cAMP receptor defect/WASP family verpolin homologous protein) actin regulatory complex, the conserved N-terminal domains of SCAR proteins interact with other components of the SCAR/WAVE complex. The conserved C-terminal domains of SCAR proteins bind to and activate the actin-related protein 2/3 (ARP2/3) complex, which can bind to actin filaments catalyzing new actin filament formation by nucleating actin branching. We have identified, SCARN (SCAR-Nodulation), a gene required for root hair infection of Lotus japonicus by Mesorhizobium loti. Although the SCARN protein is related to Arabidopsis thaliana SCAR2 and SCAR4, it belongs to a distinct legume-sub clade. We identified other SCARN-like proteins in legumes and phylogeny analyses suggested that SCARN may have arisen from a gene duplication and acquired specialized functions in root nodule symbiosis. Mutation of SCARN reduced formation of infection-threads and their extension into the root cortex and slightly reduced root-hair length. Surprisingly two of the scarn mutants showed constitutive branching of root hairs in uninoculated plants. However we observed no effect of scarn mutations on trichome development or on the early actin cytoskeletal accumulation that is normally seen in root hair tips shortly after M. loti inoculation, distinguishing them from other symbiosis mutations affecting actin nucleation. The C-terminal domain of SCARN binds to ARPC3 and ectopic expression of the N-terminal SCAR-homology domain (but not the full length protein) inhibited nodulation. In addition, we found that SCARN expression is enhanced by M. loti in epidermal cells and that this is directly regulated by the NODULE INCEPTION (NIN) transcription factor. PMID:26517270

  20. Astaxanthin protects ARPE-19 cells from oxidative stress via upregulation of Nrf2-regulated phase II enzymes through activation of PI3K/Akt

    PubMed Central

    Li, Zhongrui; Dong, Xin; Liu, Hongling; Chen, Xi; Shi, Huanqi; Fan, Yan; Hou, Dingshan

    2013-01-01

    Purpose Oxidative stress on retinal pigment epithelial (RPE) cells is thought to play a crucial role in the development and progression of age-related macular degeneration. Astaxanthin (AST) is a carotenoid that shows significant antioxidant properties. This study was designed to investigate the protective effect of AST on ARPE-19 cells against oxidative stress and the possible underlying mechanism. Methods ARPE-19 cells exposed to different doses of H2O2 were incubated with various concentrations of AST and cell viability subsequently detected with the (4-[3-[4-iodophenyl]-2–4(4-nitrophenyl)-2H-5- tetrazolio-1,3-benzene disulfonate]; WST-1) assay. The apoptosis rate and intracellular levels of reactive oxygen species (ROS) were measured with flow cytometry. NAD(P)H quinine oxidoreductase 1 (NQO1), hemeoxygenase-1 (HO-1), glutamate-cysteine ligase modifier subunit (GCLM), and glutamate-cysteine ligase catalytic subunit (GCLC) expression were examined with real-time PCR and western blotting. The nuclear localization of nuclear factor (erythroid-derived 2)-like 2 (Nrf2) protein and the expression levels of cleaved caspase-3 and protein kinase B proteins were evaluated with western blotting. Results AST clearly reduced H2O2-induced cell viability loss, cell apoptosis, and intracellular generation of ROS. Furthermore, treatment with AST activated the Nrf2-ARE pathway by inducing Nrf2 nuclear localization. Consequently, Phase II enzymes NQO1, HO-1, GCLM, and GCLC mRNA and proteins were increased. AST inhibited expression of H2O2-induced cleaved caspase-3 protein. Activation of the phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt) pathway was involved in the protective effect of AST on the ARPE-19 cells. Conclusions AST protected ARPE-19 cells against H2O2-induced oxidative stress via Nrf2-mediated upregulation of the expression of Phase II enzymes involving the PI3K/Akt pathway. PMID:23901249

  1. The biocontrol bacterium Pseudomonas fluorescens Pf29Arp strain affects the pathogenesis-related gene expression of the take-all fungus Gaeumannomyces graminis var. tritici on wheat roots

    PubMed Central

    Daval, Stéphanie; Lebreton, Lionel; Gazengel, Kévin; Boutin, Morgane; Guillerm-Erckelboudt, Anne-Yvonne; Sarniguet, Alain

    2011-01-01

    The main effects of antagonistic rhizobacteria on plant pathogenic fungi are antibiosis, fungistasis or an indirect constraint through the induction of a plant defence response. To explore different biocontrol mechanisms, an in vitro confrontation assay was conducted with the rhizobacterium Pseudomonas fluorescens Pf29Arp as a biocontrol agent of the fungus Gaeumannomyces graminis var. tritici (Ggt) on wheat roots. In parallel with the assessment of disease extension, together with the bacterial and fungal root colonization rates, the transcript levels of candidate fungal pathogenicity and plant-induced genes were monitored during the 10-day infection process. The bacterial inoculation of wheat roots with the Pf29Arp strain reduced the development of Ggt-induced disease expressed as attack frequency and necrosis length. The growth rates of Ggt and Pf29Arp, monitored through quantitative polymerase chain reaction of DNA amounts with a part of the Ggt 18S rDNA gene and a specific Pf29Arp strain detection probe, respectively, increased throughout the interactions. Bacterial antagonism and colonization had no significant effect on root colonization by Ggt. The expression of fungal and plant genes was quantified in planta by quantitative reverse transcription-polymerase chain reaction during the interactions thanks to the design of specific primers and an innovative universal reference system. During the early stages of the tripartite interaction, several of the fungal genes assayed were down-regulated by Pf29Arp, including two laccases, a β-1,3-exoglucanase and a mitogen-activated protein kinase. The plant host glutathione-S-transferase gene was induced by Ggt alone and up-regulated by Pf29Arp bacteria in interaction with the pathogen. We conclude that Pf29Arp antagonism acts through the alteration of fungal pathogenesis and probably through the activation of host defences. PMID:21726382

  2. Protective effect of canolol from oxidative stress-induced cell damage in ARPE-19 cells via an ERK mediated antioxidative pathway

    PubMed Central

    Dong, Xin; Li, Zhongrui; Wang, Wei; Zhang, Wenjie; Liu, Shuizhong; Fang, Jun; Maeda, Hiroshi; Matsukura, Makoto

    2011-01-01

    Purpose Oxidative stress damage to retinal pigment epithelial (RPE) cells is thought to play a critical role in the pathogenesis of age-related macular degeneration (AMD). This study was conducted to investigate the protective effect of canolol against oxidative stress-induced cell death in ARPE-19 cells and its underlying mechanism. Methods ARPE-19 cells, a human retinal pigment epithelial cell line, were subjected to oxidative stress with 150 μM t-butyl hydroxide (t-BH) in the presence/absence of canolol in different concentrations. Cell viabilities were monitored by a 3-(4, 5-dimethylthiazol-2-yl)-2, 5 diphenyl tetrazolium bromide (MTT) assay. The apoptosis was measured by flow cytometry using Annexin V-FITC and PI staining and intracellular reactive oxygen species (ROS) levels were measured by a fluorescence spectrophotometer. Gene expression of NF-E2-related factor (Nrf-2), heme oxygenase-1 (HO-1), catalase and glutathione S-transferase-pi (GST-pi) were measured by a reverse transcription polymerase chain reaction (RT–PCR) assay. Activation of the extracellular signal regulated kinase (ERK) protein was evaluated by western blot analysis. Results Canolol showed relatively high safety for ARPE-19 cells and recovered the cell death caused by t-BH dose-dependently at a concentration of 50–200 μM. Canolol also reduced t-BH-induced intracellular ROS generation and thus protected ARPE-19 cells from cell apoptosis. HO-1, catalase, GST-pi, and Nrf-2 were elevated in ARPE-19 cells after treatment with different concentrations of canolol for 24 h. Finally, canolol was found to activate extracellular signal regulated kinase (ERK) phosphorylation in ARPE-19 cells under the condition, with or without t-BH. Conclusions Canolol protected ARPE-19 cells from t-BH-induced oxidative damage and the protective mechanism was associated, at least partly, with the upregulation (activation) of antioxidative enzymes, probably through an ERK mediated pathway. This suggests that

  3. A second Las17 monomeric actin-binding motif functions in Arp2/3-dependent actin polymerization during endocytosis.

    PubMed

    Feliciano, Daniel; Tolsma, Thomas O; Farrell, Kristen B; Aradi, Al; Di Pietro, Santiago M

    2015-04-01

    During clathrin-mediated endocytosis (CME), actin assembly provides force to drive vesicle internalization. Members of the Wiskott-Aldrich syndrome protein (WASP) family play a fundamental role stimulating actin assembly. WASP family proteins contain a WH2 motif that binds globular actin (G-actin) and a central-acidic motif that binds the Arp2/3 complex, thus promoting the formation of branched actin filaments. Yeast WASP (Las17) is the strongest of five factors promoting Arp2/3-dependent actin polymerization during CME. It was suggested that this strong activity may be caused by a putative second G-actin-binding motif in Las17. Here, we describe the in vitro and in vivo characterization of such Las17 G-actin-binding motif (LGM) and its dependence on a group of conserved arginine residues. Using the yeast two-hybrid system, GST-pulldown, fluorescence polarization and pyrene-actin polymerization assays, we show that LGM binds G-actin and is necessary for normal Arp2/3-mediated actin polymerization in vitro. Live-cell fluorescence microscopy experiments demonstrate that LGM is required for normal dynamics of actin polymerization during CME. Further, LGM is necessary for normal dynamics of endocytic machinery components that are recruited at early, intermediate and late stages of endocytosis, as well as for optimal endocytosis of native CME cargo. Both in vitro and in vivo experiments show that LGM has relatively lower potency compared to the previously known Las17 G-actin-binding motif, WH2. These results establish a second G-actin-binding motif in Las17 and advance our knowledge on the mechanism of actin assembly during CME.

  4. PWR Cross Section Libraries for ORIGEN-ARP

    SciTech Connect

    McGraw, Carolyn; Ilas, Germina

    2012-01-01

    New pressurized water reactor (PWR) cross-section libraries were generated for use with the ORIGEN-ARP depletion sequence in the SCALE nuclear analysis code system. These libraries are based on ENDF/B-VII nuclear data and were generated using the two-dimensional depletion sequence, TRITON/NEWT, in SCALE 6.1. The libraries contain multiple burnup-dependent cross-sections for seven PWR fuel designs, with enrichments ranging from 1.5 to 6 wt% 235U. The burnup range has been extended from the 72 GWd/MTU used in previous versions of the libraries to 90 GWd/MTU. Validation of the libraries using radiochemical assay measurements and decay heat measurements for PWR spent fuel showed good agreement between calculated and experimental data. Verification against detailed TRITON simulations for the considered assembly designs showed that depletion calculations performed in ORIGEN-ARP with the pre-generated libraries provide similar results as obtained with direct TRITON depletion, while greatly reducing the computation time.

  5. A Deep Arecibo Spectral Scan of Arp 220

    NASA Astrophysics Data System (ADS)

    Vick, Michelle; Ghosh, T.; Salter, C. J.; Minchin, R. F.

    2014-01-01

    A deep spectral scan of the prototype Ultra Luminous Infra-Red Galaxy (ULIRG), Arp 220, has been made over the frequency range 1.1 to 10.0 GHz using the 305-m Arecibo telescope. These new observations supersede a previous shallow scan of Arp 220 (Salter et al., 2008, Astron. J., 136, 389). The spectral lines seen in the previous scan were all re-detected with greatly improved signal-to-noise ratio. These lines include hydrogen cyanide (HCN v2=1) in absorption, formaldehyde (H2CO) in emission at 4.83 GHz, and hydroxyl (OH) in emission at 1.6 GHz and absorption at 4.7, 6.0 and 7.8 GHz. In addition, a large number of hydrogen recombination lines were detected, as was the H2CO line at 4.955 GHz, and two lines that are identified with excited transitions of methylidyne (CH) at 4.848 and 4.870 GHz. The identification of other possible detections is on-going.

  6. ARPES view of orbitally resolved quasiparticle lifetimes in iron pnictides

    NASA Astrophysics Data System (ADS)

    Brouet, Véronique; LeBoeuf, David; Lin, Ping-Hui; Mansart, Joseph; Taleb-Ibrahimi, Amina; Le Fèvre, Patrick; Bertran, François; Forget, Anne; Colson, Dorothée

    2016-02-01

    We study with angle-resolved photoemission spectroscopy (ARPES) the renormalization and quasiparticle lifetimes of the dx y and dx z/dy z orbitals in two iron pnictides, LiFeAs and Ba (Fe0.92Co0.08 )2As2 (Co8). We find that both quantities depend on orbital character rather than on the position on the Fermi surface (for example, hole or electron pocket). In LiFeAs, the renormalizations are larger for dx y, while they are similar for both types of orbitals in Co8. The most salient feature, which proved robust against all the ARPES caveats we could think of, is that the lifetimes for dx y exhibit a markedly different behavior than those for dx z/dy z. They have smaller values near EF and exhibit larger ω and temperature dependences. While the behavior of dx y is compatible with a Fermi-liquid description, that is not the case for dx z/dy z. This situation should have important consequences for the physics of iron pnictides, which have not been considered up to now. More generally, it raises interesting questions about how a Fermi-liquid regime can be established in a multiband system with small effective bandwidths.

  7. P CYGNI PROFILES OF MOLECULAR LINES TOWARD ARP 220 NUCLEI

    SciTech Connect

    Sakamoto, Kazushi; Aalto, Susanne; Black, John H.; Conway, John E.; Costagliola, Francesco; Wilner, David J.; Peck, Alison B.; Spaans, Marco; Wang, Junzhi; Wiedner, Martina C.

    2009-08-01

    We report {approx}100 pc (0.''3) resolution observations of (sub)millimeter HCO{sup +} and CO lines in the ultraluminous infrared galaxy Arp 220. The lines peak at two merger nuclei, with HCO{sup +} being more spatially concentrated than CO. Asymmetric line profiles with blueshifted absorption and redshifted emission are discovered in HCO{sup +}(3-2) and (4-3) toward the two nuclei and in CO(3-2) toward one nucleus. We suggest that these P Cygni profiles are due to {approx}100 km s{sup -1} outward motion of molecular gas from the nuclei. This gas is most likely outflowing from the inner regions of the two nuclear disks rotating around individual nuclei, clearing the shroud around the luminosity sources there.

  8. Predictions for the ARPES spectral function of kagome antiferromagnetic insulators

    NASA Astrophysics Data System (ADS)

    Pujari, Sumiran; Lawler, Michael J.

    2011-03-01

    There are now a number of spin liquid candidate materials possibly with exotic spin-1/2 ``spinon'' excitations. Motivation by these discoveries, we consider the scaling properties of the hole spectral function for the frustrated Kagome Heisenberg antiferromagnet assuming Dirac Spin Liquid(DSL) ground state proposed for Herbertsmithite [ 2 ] . We predict a sublinear in energy power law dependence of the ARPES spectral function at certain wave vectors. Using Renormalization group techniques, we show how (gauge) fluctuations of the DSL mean field give an anomalous exponent to spinons [ 2 ] and no anomalous exponent to holons thereby leading to the sublinear power law. If this behavior is observed in experiments, they would provide strong evidence for the existence of spinons in highly frustrated magnets. S.P. gratefully acknowledges support from NSF grant DMR-1005466.

  9. ARPES of single layer iron pnictide on STO

    NASA Astrophysics Data System (ADS)

    Shen, Zhi-Xun

    Quantum systems in confined geometries have been a very rich ground for discoveries. In this talk, I will discuss recent progresses in uncovering novel physics at ultra-thin limit, with focus on mono-unit-cell (UC) superconductor FeSe grown on SrTiO3, where the Cooper pairing temperature is reported to have dramatically enhanced from its bulk value of 8K to ~60K. Of interest are the cause of the enhanced pairing strength, and the nature of the superconducting state. We show angle-resolved photoemission spectroscopy (ARPES) data that provide clear evidence for strong cross-interface electron-phonon coupling in single UC limit, suggesting that pairing is significantly enhanced by the strong interface mode coupling. We will also show other results on the nature of the superconducting state in this system..

  10. ULTRALUMINOUS X-RAY SOURCES IN ARP 147

    SciTech Connect

    Rappaport, S.; Steinhorn, B.; Levine, A.; Pooley, D. E-mail: aml@space.mit.ed

    2010-10-01

    The Chandra X-Ray Observatory was used to image the collisional ring galaxy Arp 147 for 42 ks. We detect nine X-ray sources with luminosities in the range of (1.4-7) x 10{sup 39} erg s{sup -1} (assuming that the sources emit isotropically) in or near the blue knots of star formation associated with the ring. A source with an X-ray luminosity of 1.4 x 10{sup 40} erg s{sup -1} is detected in the nuclear region of the intruder galaxy. X-ray sources associated with a foreground star and a background quasar are used to improve the registration of the X-ray image with respect to Hubble Space Telescope (HST) high-resolution optical images. The intruder galaxy, which apparently contained little gas before the collision, shows no X-ray sources other than the one in the nuclear bulge which may be a poorly fed supermassive black hole. These observations confirm the conventional wisdom that collisions of gas-rich galaxies trigger large rates of star formation which, in turn, generate substantial numbers of X-ray sources, some of which have luminosities above the Eddington limit for accreting stellar-mass black holes (i.e., ultraluminous X-ray sources, 'ULXs'). We also utilize archival Spitzer and Galex data to help constrain the current star formation rate in Arp 147 to {approx}7 M{sub sun} yr{sup -1}. All of these results, coupled with binary evolution models for ULXs, allow us to tentatively conclude that the most intense star formation may have ended some 15 Myr in the past.

  11. The plant pathogenic fungus Gaeumannomyces graminis var. tritici improves bacterial growth and triggers early gene regulations in the biocontrol strain Pseudomonas fluorescens Pf29Arp.

    PubMed

    Barret, M; Frey-Klett, P; Boutin, M; Guillerm-Erckelboudt, A-Y; Martin, F; Guillot, L; Sarniguet, A

    2009-01-01

    In soil, some antagonistic rhizobacteria contribute to reduce root diseases caused by phytopathogenic fungi. Direct modes of action of these bacteria have been largely explored; however, commensal interaction also takes place between these microorganisms and little is known about the influence of filamentous fungi on bacteria. An in vitro confrontation bioassay between the pathogenic fungus Gaeumannomyces graminis var. tritici (Ggt) and the biocontrol bacterial strain Pseudomonas fluorescens Pf29Arp was set up to analyse bacterial transcriptional changes induced by the fungal mycelium at three time-points of the interaction before cell contact and up until contact. For this, a Pf29Arp shotgun DNA microarray was constructed. Specifity of Ggt effect was assessed in comparison with one of two other filamentous fungi, Laccaria bicolor and Magnaporthe grisea. During a commensal interaction, Ggt increased the growth rate of Pf29Arp. Before contact, Ggt induced bacterial genes involved in mycelium colonization. At contact, genes encoding protein of stress response and a patatin-like protein were up-regulated. Among all the bacterial genes identified, xseB was specifically up-regulated at contact by Ggt but down-regulated by the other fungi. Data showed that the bacterium sensed the presence of the fungus early, but the main gene alteration occurred during bacterial-fungal cell contact. PMID:19121038

  12. MERLIN radio observations of two recent supernovae in Arp299: SN2010O & SN2010P

    NASA Astrophysics Data System (ADS)

    Beswick, R. J.; Perez-Torres, M. A.; Mattila, S.; Garrington, S. T.; Kankare, E.; Ryder, S.; Alberdi, A.; Romero-Canizales, C.

    2010-02-01

    We report MERLIN radio observations of the two recent supernovae in Arp299; SN2010P and SN2010O (CBET #2145 and CBET #2144, respectively). Observations of Arp299 were made between 1900UT 29th Jan 2010 and 0150UT 1st Feb 2010 at 4994MHz. The previously known compact radio structure of Arp299, including the nuclear starburst components associated with A=IC694 and B1=the southernmost nucleus of NGC3690 are detected (Neff, Ulvestad & Teng 2004, ApJ, 611, 186; Ulvestad 2009 AJ, 138, 152; Perez-Torres et al 2009, A&A 507, 17).

  13. Implications of the ISO LWS spectrum of the prototypical ultraluminous galaxy: ARP 220

    NASA Technical Reports Server (NTRS)

    Fischer, J.; Satyapal, S.; Luhman, M. L.; Melnick, G.; Cox, P.; Cernicharo, J.; Stacey, G. J.; Smith, H. A.; Lord, S. D.; Greenhouse, M. A.

    1997-01-01

    The low resolution far infrared spectrum of the galaxy Arp 220, obtained with the low wavelength spectrometer (LWS) onboard the Infrared Space Observatory (ISO), is presented. The spectrum is dominated by the OH, H2O, CH, NH3 and O I absorption lines. The upper limits on the far infrared fine structure lines indicate a softer radiation in Arp 220 than in starburst galaxies.

  14. The core-collapse supernova rate in Arp 299 revisited

    NASA Astrophysics Data System (ADS)

    Romero-Cañizales, C.; Mattila, S.; Alberdi, A.; Pérez-Torres, M. A.; Kankare, E.; Ryder, S. D.

    2011-08-01

    We present a study of the core-collapse supernova (CCSN) rate in nuclei A and B1, of the luminous infrared galaxy (LIRG) Arp 299, based on ˜11 yr of Very Large Array (VLA) monitoring of their radio emission at 8.4 GHz. Significant variations in the nuclear radio flux density can be used to identify the CCSN activity in the absence of high-resolution very long baseline interferometry (VLBI) observations. In the case of the B1-nucleus, the small variations in its measured diffuse (synchrotron plus free-free) radio emission are below the fluxes expected from radio supernovae (RSNe), thus making it well-suited to detect RSNe through flux density variability. In fact, we find strong evidence for at least three RSNe this way, which results in a lower limit for the CCSN rate (νSN) of >0.28+0.27-0.15 yr-1. This value agrees within the uncertainties with the infrared (IR) luminosity based SN rate estimate, and with previously reported radio estimates. In the A-nucleus, we did not detect any significant variability and found a SN detection threshold luminosity of ≈3.1 × 1028 erg s-1 Hz-1, allowing only the detection of the most luminous RSNe known. Our method is basically blind to normal CCSN explosions occurring within the A-nucleus, which result in too small variations in the nuclear flux density, remaining diluted by the strong diffuse emission of the nucleus itself. Additionally, we have attempted to find near-IR (NIR) counterparts for the earlier reported RSNe in the Arp 299 nucleus A, by comparing NIR adaptive optics images from the Gemini-N Telescope with contemporaneous observations from the European VLBI Network (EVN). However, we were not able to detect NIR counterparts for the reported radio SNe within the innermost regions of nucleus A. While our NIR observations were sensitive to typical CCSNe at ˜300 mas (or 70 pc projected distance) from the centre of the nucleus A, suffering from extinction up to AV˜ 15 mag, they were not sensitive to such highly

  15. ARPES Studies of Cuprate Fermiology: Superconductivity, Pseudogap and Quasiparticle Dynamics

    SciTech Connect

    Vishik, Inna

    2011-06-23

    We present angle-resolved photoemission spectroscopy (ARPES) studies of the cuprate high-temperature superconductors which elucidate the relation between superconductivity and the pseudogap and highlight low-energy quasiparticle dynamics in the superconducting state. Our experiments suggest that the pseudogap and superconducting gap represent distinct states, which coexist below T{sub c}. Studies on Bi-2212 demonstrate that the near-nodal and near-antinodal regions behave differently as a function of temperature and doping, implying that different orders dominate in different momentum-space regions. However, the ubiquity of sharp quasiparticles all around the Fermi surface in Bi-2212 indicates that superconductivity extends into the momentum-space region dominated by the pseudogap, revealing subtlety in this dichotomy. In Bi-2201, the temperature dependence of antinodal spectra reveals particle-hole asymmetry and anomalous spectral broadening, which may constrain the explanation for the pseudogap. Recognizing that electron-boson coupling is an important aspect of cuprate physics, we close with a discussion of the multiple 'kinks' in the nodal dispersion. Understanding these may be important to establishing which excitations are important to superconductivity.

  16. Star clusters in the interacting galaxy system Arp 284

    NASA Astrophysics Data System (ADS)

    Peterson, Bradley W.; Struck, Curtis; Smith, Beverly J.; Hancock, Mark

    2009-12-01

    We present results from a study of protoglobular cluster candidates in the interacting galaxy system Arp 284 (NGC 7714/5) using data from the Hubble Space Telescope (HST). Previous studies of the Antennae and M51 have suggested that the majority of young massive star clusters dissolve within 20 Myr due to mass loss. We use the evolutionary synthesis code STARBURST99 to estimate ages and extinctions for approximately 175 clusters visible with HST. We also use lower resolution Galaxy Evolution Explorer and ground-based Hα data to estimate the ages of the giant HII regions in which these clusters are found, and compare the Spitzer colours of these HII regions to those of star-forming regions in other interacting systems. The ages are also used to aid in the interpretation of Chandra X-ray data. Clusters in the tidal tails of NGC 7714 are generally found to have ages less than 20 Myr, though observational limits make the significance of this result uncertain. Older clusters, though not numerous, have nearly the same spatial distribution within the imaged portion of NGC 7714 as young clusters. The cluster population in the bridge connecting the two galaxies appears to be older, but the data in this part of the system are too limited to draw firm conclusions. The ages of the giant HII regions in NGC 7714 are generally older than those of their constituent clusters, possibly indicating that the young clusters we detect are surrounded by their dispersed predecessors.

  17. Identification of early salt stress responsive proteins in seedling roots of upland cotton (Gossypium hirsutum L.) employing iTRAQ-based proteomic technique

    PubMed Central

    Li, Wu; Zhao, Fu'an; Fang, Weiping; Xie, Deyi; Hou, Jianan; Yang, Xiaojie; Zhao, Yuanming; Tang, Zhongjie; Nie, Lihong; Lv, Shuping

    2015-01-01

    Soil salinity is a major abiotic stress that limits plant growth and agricultural productivity. Upland cotton (Gossypium hirsutum L.) is highly tolerant to salinity; however, large-scale proteomic data of cotton in response to salt stress are still scant. Here, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic technique was employed to identify the early differentially expressed proteins (DEPs) from salt-treated cotton roots. One hundred and twenty-eight DEPs were identified, 76 of which displayed increased abundance and 52 decreased under salt stress conditions. The majority of the proteins have functions related to carbohydrate and energy metabolism, transcription, protein metabolism, cell wall and cytoskeleton metabolism, membrane and transport, signal transduction, in addition to stress and defense. It is worth emphasizing that some novel salt-responsive proteins were identified, which are involved in cell cytoskeleton metabolism (actin-related protein2, ARP2, and fasciclin-like arabinogalactan proteins, FLAs), membrane transport (tonoplast intrinsic proteins, TIPs, and plasma membrane intrinsic proteins, PIPs), signal transduction (leucine-rich repeat receptor-like kinase encoding genes, LRR-RLKs) and stress responses (thaumatin-like protein, TLP, universal stress protein, USP, dirigent-like protein, DIR, desiccation-related protein PCC13-62). High positive correlation between the abundance of some altered proteins (superoxide dismutase, SOD, peroxidase, POD, glutathione S-transferase, GST, monodehydroascorbate reductase, MDAR, and malate dehydrogenase, MDH) and their enzyme activity was evaluated. The results demonstrate that the iTRAQ-based proteomic technique is reliable for identifying and quantifying a large number of cotton root proteins. qRT-PCR was used to study the gene expression levels of the five above-mentioned proteins; four patterns are consistent with those of induced protein. These results showed that the proteome

  18. Arp2/3 complex and actin dynamics are required for actin-based mitochondrial motility in yeast.

    PubMed

    Boldogh, I R; Yang, H C; Nowakowski, W D; Karmon, S L; Hays, L G; Yates, J R; Pon, L A

    2001-03-13

    The Arp2/3 complex is implicated in actin polymerization-driven movement of Listeria monocytogenes. Here, we find that Arp2p and Arc15p, two subunits of this complex, show tight, actin-independent association with isolated yeast mitochondria. Arp2p colocalizes with mitochondria. Consistent with this result, we detect Arp2p-dependent formation of actin clouds around mitochondria in intact yeast. Cells bearing mutations in ARP2 or ARC15 genes show decreased velocities of mitochondrial movement, loss of all directed movement and defects in mitochondrial morphology. Finally, we observe a decrease in the velocity and extent of mitochondrial movement in yeast in which actin dynamics are reduced but actin cytoskeletal structure is intact. These results support the idea that the movement of mitochondria in yeast is actin polymerization driven and that this movement requires Arp2/3 complex.

  19. Zeaxanthin and α-tocopherol reduce the inhibitory effects of photodynamic stress on phagocytosis by ARPE-19 cells.

    PubMed

    Olchawa, Magdalena M; Herrnreiter, Anja M; Pilat, Anna K; Skumatz, Christine M B; Niziolek-Kierecka, Magdalena; Burke, Janice M; Sarna, Tadeusz J

    2015-12-01

    Zeaxanthin and α-tocopherol have been previously shown to efficiently protect liposomal membrane lipids against photosensitized peroxidation, and to protect cultured RPE cells against photodynamic killing. Here the protective action of combined zeaxanthin and α-tocopherol was analyzed in ARPE-19 cells subjected to photodynamic (PD) stress mediated by rose Bengal (RB) or merocyanine-540 (MC-540) at sub-lethal levels. Stress-induced cytotoxicity was analyzed by the MTT assay. The peroxidation of membrane lipids was determined by HPLC-EC (Hg) measurements of cholesterol hydroperoxides using cholesterol as a mechanistic reporter molecule. The specific phagocytosis of FITC-labeled photoreceptor outer segments (POS) isolated from bovine retinas was measured by flow cytometry, and the levels of phagocytosis receptor proteins αv integrin subunit, β5 integrin subunit and MerTK were quantified by Western blot analysis. Cytotoxicity measures confirmed that PD stress levels used for phagocytosis analysis were sub-lethal and that antioxidant supplementation protected against higher, lethal PD doses. Sub-lethal PD stress mediated by both photosensitizers induced the accumulation of 5α-OOH and 7α/β-OOH cholesterol hydroperoxides and the addition of the antioxidants substantially inhibited their accumulation. Antioxidant delivery prior to PD stress also reduced the inhibitory effect of stress on POS phagocytosis and partially reduced the stress-induced diminution of phagocytosis receptor proteins. The use of a novel model system where oxidative stress was induced at sub-lethal levels enable observations that would not be detectable using lethal stress models. Moreover, novel observations about the protective effects of zeaxanthin and α-tocopherol on photodynamic damage to ARPE-19 cell membranes and against reductions in the abundance of receptor proteins involved in POS phagocytosis, a process essential for photoreceptor survival, supports the importance of the

  20. Zeaxanthin and α-tocopherol reduce the inhibitory effects of photodynamic stress on phagocytosis by ARPE-19 cells

    PubMed Central

    Olchawa, Magdalena M.; Herrnreiter, Anja M.; Pilat, Anna K.; Skumatz, Christine M. B.; Niziolek-Kierecka, Magdalena; Burke, Janice M.; Sarna, Tadeusz J.

    2016-01-01

    Zeaxanthin and α-tocopherol have been previously shown to efficiently protect liposomal membrane lipids against photosensitized peroxidation, and to protect cultured RPE cells against photodynamic killing. Here the protective action of combined zeaxanthin and α-tocopherol was analyzed in ARPE-19 cells subjected to photodynamic (PD) stress mediated by rose Bengal (RB) or merocyanine-540 (MC-540) at sub-lethal levels. Stress-induced cytotoxicity was analyzed by the MTT assay. The peroxidation of membrane lipids was determined by HPLC-EC(Hg) measurements of cholesterol hydroperoxides using cholesterol as a mechanistic reporter molecule. The specific phagocytosis of FITC-labeled photoreceptor outer segments (POS) isolated from bovine retinas was measured by flow cytometry, and the levels of phagocytosis receptor proteins αv integrin subunit, β5 integrin subunit and MerTK were quantified by Western blot analysis. Cytotoxicity measures confirmed that PD stress levels used for phagocytosis analysis were sub-lethal and that antioxidant supplementation protected against higher, lethal PD doses. Sub-lethal PD stress mediated by both photosensitizers induced the accumulation of 5α-OOH and 7α/β-OOH cholesterol hydroperoxides and the addition of the antioxidants substantially inhibited their accumulation. Antioxidant delivery prior to PD stress also reduced the inhibitory effect of stress on POS phagocytosis and partially reduced the stress-induced diminution of phagocytosis receptor proteins. The use of a novel model system where oxidative stress was induced at sub-lethal levels enable observations that would not be detectable using lethal stress models. Moreover, novel observations about the protective effects of zeaxanthin and α-tocopherol on photodynamic damage to ARPE-19 cell membranes and against reductions in the abundance of receptor proteins involved in POS phagocytosis, a process essential for photoreceptor survival, supports the importance of the antioxidants

  1. An infrared study of starbursts in the interacting galaxy pair Arp 299 (NGC 3690+IC 694)

    SciTech Connect

    Nakagawa, Takao; Nagata, Tetsuya; Geballe, T.R.; Okuda, Haruyuki; Shibai, Hiroshi; Tokyo Univ.; Kyoto Univ.; Joint Astronomy Center, Hilo, HI; Institute of Space and Astronautical Science, Sagamihara )

    1989-05-01

    Extensive infrared observations have been obtained of the three active regions in Arp 299. Multiaperture JHK photometry reveals that the colors of the three regions are totally different from each other, and that there are very red nuclei smaller than 4 arcsec in two of them. Multiaperture spectroscopy of the Br-gamma and the shock-excited H2 lines shows that both the atomic and molecular lines are spatially extended, indicating that Arp 299 is undergoing an active episode of star formation not only in its nuclei but also well outside of them. Although there is some evidence that suggests the presence of a compact, active galactic nucleus, a simple starburst model can explain the bolometric luminosities, production rates of ionizing photons, and H24 line luminosities of each active region in Arp 299. However, each starburst cannot last longer than 10 to the 8th yr. 56 refs.

  2. OrigenArp Primer: How to Perform Isotopic Depletion and Decay Calculations with SCALE/ORIGEN

    SciTech Connect

    Bowman, Stephen M; Gauld, Ian C

    2010-08-01

    The SCALE (Standardized Computer Analyses for Licensing Evaluation) computer software system developed at Oak Ridge National Laboratory is widely used and accepted around the world for nuclear analyses. ORIGEN-ARP is a SCALE isotopic depletion and decay analysis sequence used to perform point-depletion calculations with the well-known ORIGEN-S code using problem-dependent cross sections. Problem-dependent cross-section libraries are generated using the ARP (Automatic Rapid Processing) module using an interpolation algorithm that operates on pre-generated libraries created for a range of fuel properties and operating conditions. Methods are provided in SCALE to generate these libraries using one-, two-, and three-dimensional transport codes. The interpolation of cross sections for uranium-based fuels may be performed for the variables burnup, enrichment, and water density. An option is also available to interpolate cross sections for mixed-oxide (MOX) fuels using the variables burnup, plutonium content, plutonium isotopic vector, and water moderator density. This primer is designed to help a new user understand and use ORIGEN-ARP with the OrigenArp Windows graphical user interface in SCALE. It assumes that the user has a college education in a technical field. There is no assumption of familiarity with nuclear depletion codes in general or with SCALE/ORIGEN-ARP in particular. The primer is based on SCALE 6 but should be applicable to earlier or later versions of SCALE. Information is included to help new users, along with several sample problems that walk the user through the different input forms and menus and illustrate the basic features. References to related documentation are provided. The primer provides a starting point for the nuclear analyst who uses SCALE/ORIGEN-ARP. Complete descriptions are provided in the SCALE documentation. Although the primer is self-contained, it is intended as a companion volume to the SCALE documentation. The SCALE Manual is

  3. Angle-resolved photoemission spectroscopy (ARPES) studies of cuprate superconductors

    SciTech Connect

    Palczewski, Ari Deibert

    2010-01-01

    This dissertation is comprised of three different angle-resolved photoemission spectroscopy (ARPES) studies on cuprate superconductors. The first study compares the band structure from two different single layer cuprates Tl2Ba2CuO6+δ (Tl2201) Tc, max ≈ 95 K and (Bi 1.35Pb0.85)(Sr1.47La0.38)CuO6+δ (Bi2201) Tc, max ≈ 35 K. The aim of the study was to provide some insight into the reasons why single layer cuprate's maximum transition temperatures are so different. The study found two major differences in the band structure. First, the Fermi surface segments close to (π,0) are more parallel in Tl2201 than in Bi2201. Second, the shadow band usually related to crystal structure is only present in Bi2201, but absent in higher Tc Tl2201. The second study looks at the different ways of doping Bi2Sr2CaCu2O8+δ (Bi2212) in-situ by only changing the post bake-out vacuum conditions and temperature. The aim of the study is to systematically look into the generally overlooked experimental conditions that change the doping of a cleaved sample in ultra high vacuum (UHV) experiments. The study found two major experimental facts. First, in inadequate UHV conditions the carrier concentration of Bi2212 increases with time, due to the absorption of oxygen from CO2/CO molecules, prime contaminants present in UHV systems. Second, in a very clean UHV system at elevated temperatures (above about 200 K), the carrier concentration decreases due to the loss of oxygen atoms from the Bi-O layer. The final study probed the particle-hole symmetry of the pseudogap phase in high temperature superconducting cuprates by looking at the thermally excited bands above the Fermi level. The data showed a particle-hole symmetric pseudogap which symmetrically closes away from the nested FS before the node. The data is consistent

  4. The Far-Infrared Spectrum of Arp 220

    NASA Technical Reports Server (NTRS)

    Gonzalez-Alfonso, Eduardo; Smith, Howard A.; Fischer, Jacqueline; Cernicharo, Jose

    2005-01-01

    ISO/LWS grating observations of the ultraluminous infrared galaxy Arp 220 shows absorption in molecular lines of OH, H(sub 2)O, CH, NH, and NH(sub 3), as well as in the [O I] 63 micron line and emission in the [C II] 158 micron line. We have modeled the continuum and the emission/absorption of all observed features by means of a non-local radiative transfer code. The continuum from 25 to 1300 microns is modeled as a warm (106 K) nuclear region that is optically thick in the far-infrared, attenuated by an extended region (size 2") that is heated mainly through absorption of nuclear infrared radiation. The molecular absorption in the nuclear region is characterized by high excitation due to the high infrared radiation density. The OH column densities are high toward the nucleus (2 - 6 x 10(exp 17) cm(exp -2)) and the extended region (approximately 2 x 10(exp 17) cm(exp -2)). The H(sub 2)O column density is also high toward the nucleus (2 - 10 x 10(exp 17) cm(exp -2)) and lower in the extended region. The column densities in a halo that accounts for the absorption by the lowest lying levels are similar to what are found in the diffuse clouds toward the star forming regions in the Sgr B2 molecular cloud complex near the Galactic Center. Most notable are the high column densities found for NH and NH(sub 3) toward the nucleus, with values of approximately 1.5 x 10(exp 16) cm(exp -2) and approximately 3 x 10(exp 16) cm(exp -2), respectively, whereas the NH(sub 2) column density is lower than approximately 2 x 10(exp 15) cm(exp -2). A combination of PDRs in the extended region and hot cores with enhanced H(sub 2)O photodissociation and a possible shock contribution in the nuclei may explain the relative column densities of OH and H(sub 2)O, whereas the nitrogen chemistry may be strongly affected by cosmic ray ionization. The [C II] 158 micron line is well reproduced by our models and its deficit relative to the CII/FIR ratio in normal and starburst galaxies is suggested to

  5. The Far-Infrared Spectrum of Arp 220

    NASA Technical Reports Server (NTRS)

    Gonzalez-Alfonso, Eduardo; Smith, Howard A.; Fischer, Jacqueline; Cernicharo, Jose

    2004-01-01

    ISO/LWS grating observations of the ultraluminous infrared galaxy Arp 220 shows absorption in molecular lines of OH, H 2 0 , CH, NH, and "3, well as in the [0 I] 63 pm line and emission in the [C 111 158 pm line. We have modeled the continuum and the emission/absorption of all observed features by means of a non-local radiative transfer code. The continuum from 25 to 1300 pm is modeled AS A WARM (106 K) NUCLEAR REGION THAT IS OPTICALLY THICK IN THE FAR-INFRARED, attenuated by an extended region (size 2") that is heated mainly through absorption of nuclear infrared radiation. The molecular absorption in the nuclear region is characterized by high excitation due to the high infrared radiation density. The OH column densities are high toward the nucleus and the extended region (about 2 x 10 sup 17 cm sup-2). The H2O column density is also high toward the nucleus (2 - 10 x 1017 cm-2) and lower in the extended region. The column densities in a halo that accounts for the absorption by the lowest lying levels are similar to what are found in the diffuse clouds toward the star forming regions in the Sgr B2 molecular cloud complex near the Galactic Center. Most notable are the high column densities found for NH and NH3 toward the nucleus, with values of about 1.5 x 10supl6 cmsup-2 and about 3 x 10supl6 cmsup-2, respectively, whereas the NH2 column density is lower than about 2 x 10sup15 cmsup-2. A combination of PDRs in the extended region and hot cores with enhanced H20 photodissociation and a possible shock contribution in the nuclei may explain the relative column densities of OH and H20, whereas the nitrogen chemistry may be strongly affected by cosmic ray ionization. The [C II] 158 pm line is well reproduced by our models and its "deficit" relative to the CII/FIR ratio in normal and starburst galaxies is suggested to be mainly a consequence of the dominant non-PDR component of far- infrared radiation, ALTHOUGH OUR MODELS ALONE CANNOT RULE OUT EXTINCTION EFFECTS IN THE

  6. Influence of k⊥ broadening on ARPES spectra of the (110) and (001) surfaces of SrVO3 films

    NASA Astrophysics Data System (ADS)

    Mitsuhashi, T.; Minohara, M.; Yukawa, R.; Kitamura, M.; Horiba, K.; Kobayashi, M.; Kumigashira, H.

    2016-09-01

    To examine the effect of k⊥ broadening on angle-resolved photoemission spectroscopy (ARPES) spectra, in situ ARPES using the variable polarization of synchrotron light has been performed for the (110) and (001) surfaces of SrVO3 films. Using the polarization dependence for the band structures of the V 3 d t2 g states, we have separately observed the dx y-derived states and the dy z/dz x ones for the (110) surface. It is found that ARPES images for the dy z/dz x states are considerably broader than those for the dx y states. Meanwhile, such a broadening is not observed in the identical dy z/dz x -derived band dispersion along the crystallographically equivalent direction on the (001) surface, indicating that the broadening of the ARPES image originates from the absence or presence of mirror symmetry in the respective states with respect to the ARPES-measurement planes. The observed spectroscopic behavior is well reproduced by the simulation where the k⊥ broadening in the photoelectron emission process is taken into account. These results indicate that the consideration of the mirror symmetry of the band structures with respect to the ARPES-measurement plane is important for analyzing the ARPES-spectral line shape in the case that the k⊥-broadening effect is dominant in ARPES spectra.

  7. ALMA Imaging of HCN, CS, and Dust in Arp 220 and NGC 6240

    NASA Astrophysics Data System (ADS)

    Scoville, Nick; Sheth, Kartik; Walter, Fabian; Manohar, Swarnima; Zschaechner, Laura; Yun, Min; Koda, Jin; Sanders, David; Murchikova, Lena; Thompson, Todd; Robertson, Brant; Genzel, Reinhard; Hernquist, Lars; Tacconi, Linda; Brown, Robert; Narayanan, Desika; Hayward, Christopher C.; Barnes, Joshua; Kartaltepe, Jeyhan; Davies, Richard; van der Werf, Paul; Fomalont, Edward

    2015-02-01

    We report ALMA Band 7 (350 GHz) imaging at 0.''4-0.''6 resolution and Band 9 (696 GHz) at ~0.''25 resolution of the luminous IR galaxies Arp 220 and NGC 6240. The long wavelength dust continuum is used to estimate interstellar medium masses for Arp 220 east and west and NGC 6240 of 1.9, 4.2, and 1.6 × 109 M ⊙within radii of 69, 65, and 190 pc. The HCN emission was modeled to derive the emissivity distribution as a function of radius and the kinematics of each nuclear disk, yielding dynamical masses consistent with the masses and sizes derived from the dust emission. In Arp 220, the major dust and gas concentrations are at radii less than 50 pc in both counter-rotating nuclear disks. The thickness of the disks in Arp 220 estimated from the velocity dispersion and rotation velocities are 10-20 pc and the mean gas densities are nH_2 ˜ 10^5 cm-3 at R <50 pc. We develop an analytic treatment for the molecular excitation (including photon trapping), yielding volume densities for both the HCN and CS emission with n H2 ~ 2 × 105 cm-3. The agreement of the mean density from the total mass and size with that required for excitation suggests that the volume is essentially filled with dense gas, i.e., it is not cloudy or like swiss cheese.

  8. Crucial roles of the Arp2/3 complex during mammalian corticogenesis

    PubMed Central

    Wang, Pei-Shan; Chou, Fu-Sheng; Ramachandran, Sreekumar; Xia, Sheng; Chen, Huei-Ying; Guo, Fengli; Suraneni, Praveen; Maher, Brady J.

    2016-01-01

    The polarity and organization of radial glial cells (RGCs), which serve as both stem cells and scaffolds for neuronal migration, are crucial for cortical development. However, the cytoskeletal mechanisms that drive radial glial outgrowth and maintain RGC polarity remain poorly understood. Here, we show that the Arp2/3 complex – the unique actin nucleator that produces branched actin networks – plays essential roles in RGC polarity and morphogenesis. Disruption of the Arp2/3 complex in murine RGCs retards process outgrowth toward the basal surface and impairs apical polarity and adherens junctions. Whereas the former is correlated with an abnormal actin-based leading edge, the latter is consistent with blockage in membrane trafficking. These defects result in altered cell fate, disrupted cortical lamination and abnormal angiogenesis. In addition, we present evidence that the Arp2/3 complex is a cell-autonomous regulator of neuronal migration. Our data suggest that Arp2/3-mediated actin assembly might be particularly important for neuronal cell motility in a soft or poorly adhesive matrix environment. PMID:27385014

  9. IR and dc magneto-transport and ARPES compared: p-type cuprates

    NASA Astrophysics Data System (ADS)

    Jenkins, Gregory S.; Schmadel, D. C.; Drew, H. D.; Tsukada, I.; Gu, G. D.; Kontani, H.

    2010-03-01

    We report IR Hall Effect measurements in the terahertz (THz) spectral region on optimally doped Bi2Sr2Ca Cu2O8+x (BSCCO) single crystals and in La2-xSrxCuO4 (LSCO) films as a function of doping ranging from 7% to 16.5%. Critical comparisons between the dc Hall coefficient RH and Hall angle θH, the IR RH and θH, and the values predicted by ARPES analyzed within the relaxation time approximation will be discussed. In optimally doped BSCCO, the temperature power law associated with the off-diagonal conductivity at frequencies up to 10 meV deviates strongly from that of the longitudinal conductivity, and the IR Hall response is significantly larger than that expected based upon ARPES results. Analysis of dc RH measurements and ARPES results show a significant anomalous Hall effect ˜100K even in severely overdoped Tl-2201. In LSCO, a rapid decrease of the Hall mass with underdoping, a hallmark signature of Fermi surface reconstruction, is shown to strongly deviate from that predicted by the ARPES measured Fermi arcs. These results will be discussed in terms of Fermi surface models. [G. S. Jenkins et al., arXiv:0901.1701.

  10. Impact Of Sodium Oxalate, Sodium Aluminosilicate, and Gibbsite/Boehmite on ARP Filter Performance

    SciTech Connect

    Poirier, M.; Burket, P.

    2015-11-01

    The Savannah River Site (SRS) is currently treating radioactive liquid waste with the Actinide Removal Process (ARP) and the Modular Caustic Side Solvent Extraction Unit (MCU). Recently, the low filter flux through the ARP of approximately 5 gallons per minute has limited the rate at which radioactive liquid waste can be treated. Salt Batch 6 had a lower processing rate and required frequent filter cleaning. Savannah River Remediation (SRR) has a desire to understand the causes of the low filter flux and to increase ARP/MCU throughput. SRR requested SRNL to conduct bench-scale filter tests to evaluate whether sodium oxalate, sodium aluminosilicate, or aluminum solids (i.e., gibbsite and boehmite) could be the cause of excessive fouling of the crossflow or secondary filter at ARP. The authors conducted the tests by preparing slurries containing 6.6 M sodium Salt Batch 6 supernate, 2.5 g MST/L slurry, and varying concentrations of sodium oxalate, sodium aluminosilicate, and aluminum solids, processing the slurry through a bench-scale filter unit that contains a crossflow primary filter and a dead-end secondary filter, and measuring filter flux and transmembrane pressure as a function of time. Among the conclusions drwn from this work are the following: (1) All of the tests showed some evidence of fouling the secondary filter. This fouling could be from fine particles passing through the crossflow filter. (2) The sodium oxalate-containing feeds behaved differently from the sodium aluminosilicate- and gibbsite/boehmite-containing feeds.

  11. Genetically encoded photoswitching of actin assembly through the Cdc42-WASP-Arp2/3 complex pathway

    PubMed Central

    Leung, Daisy W.; Otomo, Chinatsu; Chory, Joanne; Rosen, Michael K.

    2008-01-01

    General methods to engineer genetically encoded, reversible, light-mediated control over protein function would be useful in many areas of biomedical research and technology. We describe a system that yields such photo-control over actin assembly. We fused the Rho family GTPase Cdc42 in its GDP-bound form to the photosensory domain of phytochrome B (PhyB) and fused the Cdc42 effector, the Wiskott-Aldrich Syndrome Protein (WASP), to the light-dependent PhyB-binding domain of phytochrome interacting factor 3 (Pif3). Upon red light illumination, the fusion proteins bind each other, activating WASP, and consequently stimulating actin assembly by the WASP target, the Arp2/3 complex. Binding and WASP activation are reversed by far-red illumination. Our approach, in which the biochemical specificity of the nucleotide switch in Cdc42 is overridden by the light-dependent PhyB-Pif3 interaction, should be generally applicable to other GTPase-effector pairs. PMID:18728185

  12. The Arp2/3 complex has essential roles in vesicle trafficking and transcytosis in the mammalian small intestine.

    PubMed

    Zhou, Kang; Sumigray, Kaelyn D; Lechler, Terry

    2015-06-01

    The Arp2/3 complex is the only known nucleator of branched F-actin filaments. Work in cultured cells has established a wide array of functions for this complex in controlling cell migration, shape, and adhesion. However, loss of Arp2/3 complex function in tissues has yielded cell type-specific phenotypes. Here we report essential functions of the Arp2/3 complex in the intestinal epithelium. The Arp2/3 complex was dispensable for intestinal development, generation of cortical F-actin, and cell polarity. However, it played essential roles in vesicle trafficking. We found that in the absence of ArpC3, enterocytes had defects in the organization of the endolysosomal system. These defects were physiologically relevant, as transcytosis of IgG was disrupted, lipid absorption was perturbed, and neonatal mice died within days of birth. These data highlight the important roles of the Arp2/3 complex in vesicle trafficking in enterocytes and suggest that defects in cytoplasmic F-actin assembly by the Arp2/3 complex, rather than cortical pools, underlie many of the phenotypes seen in the mutant small intestine.

  13. The Arp2/3 complex has essential roles in vesicle trafficking and transcytosis in the mammalian small intestine

    PubMed Central

    Zhou, Kang; Sumigray, Kaelyn D.; Lechler, Terry

    2015-01-01

    The Arp2/3 complex is the only known nucleator of branched F-actin filaments. Work in cultured cells has established a wide array of functions for this complex in controlling cell migration, shape, and adhesion. However, loss of Arp2/3 complex function in tissues has yielded cell type–specific phenotypes. Here we report essential functions of the Arp2/3 complex in the intestinal epithelium. The Arp2/3 complex was dispensable for intestinal development, generation of cortical F-actin, and cell polarity. However, it played essential roles in vesicle trafficking. We found that in the absence of ArpC3, enterocytes had defects in the organization of the endolysosomal system. These defects were physiologically relevant, as transcytosis of IgG was disrupted, lipid absorption was perturbed, and neonatal mice died within days of birth. These data highlight the important roles of the Arp2/3 complex in vesicle trafficking in enterocytes and suggest that defects in cytoplasmic F-actin assembly by the Arp2/3 complex, rather than cortical pools, underlie many of the phenotypes seen in the mutant small intestine. PMID:25833710

  14. Involvement of the Rac1-IRSp53-Wave2-Arp2/3 Signaling Pathway in HIV-1 Gag Particle Release in CD4 T Cells

    PubMed Central

    Thomas, Audrey; Mariani-Floderer, Charlotte; López-Huertas, Maria Rosa; Gros, Nathalie; Hamard-Péron, Elise; Favard, Cyril; Ohlmann, Theophile; Alcamí, José

    2015-01-01

    ABSTRACT During HIV-1 assembly, the Gag viral proteins are targeted and assemble at the inner leaflet of the cell plasma membrane. This process could modulate the cortical actin cytoskeleton, located underneath the plasma membrane, since actin dynamics are able to promote localized membrane reorganization. In addition, activated small Rho GTPases are known for regulating actin dynamics and membrane remodeling. Therefore, the modulation of such Rho GTPase activity and of F-actin by the Gag protein during virus particle formation was considered. Here, we studied the implication of the main Rac1, Cdc42, and RhoA small GTPases, and some of their effectors, in this process. The effect of small interfering RNA (siRNA)-mediated Rho GTPases and silencing of their effectors on Gag localization, Gag membrane attachment, and virus-like particle production was analyzed by immunofluorescence coupled to confocal microscopy, membrane flotation assays, and immunoblot assays, respectively. In parallel, the effect of Gag expression on the Rac1 activation level was monitored by G-LISA, and the intracellular F-actin content in T cells was monitored by flow cytometry and fluorescence microscopy. Our results revealed the involvement of activated Rac1 and of the IRSp53-Wave2-Arp2/3 signaling pathway in HIV-1 Gag membrane localization and particle release in T cells as well as a role for actin branching and polymerization, and this was solely dependent on the Gag viral protein. In conclusion, our results highlight a new role for the Rac1-IRSp53-Wave2-Arp2/3 signaling pathway in the late steps of HIV-1 replication in CD4 T lymphocytes. IMPORTANCE During HIV-1 assembly, the Gag proteins are targeted and assembled at the inner leaflet of the host cell plasma membrane. Gag interacts with specific membrane phospholipids that can also modulate the regulation of cortical actin cytoskeleton dynamics. Actin dynamics can promote localized membrane reorganization and thus can be involved in

  15. Star Formation Rate and Gas Relations in the Arp 299 Merger from the VIXENS Survey

    NASA Astrophysics Data System (ADS)

    Heiderman, Amanda; Evans, Neal J.; Gebhardt, Karl; Blanc, Guillermo; Davis, Timothy; Papovich, Casey; van den Bosch, Remco; Iono, Daisuke; Yun, Min S.

    2015-08-01

    We highlight first results from the VIRUS-P Investigation of the eXtreme ENvironments of Starbursts (VIXENS) integral field unit survey. We investigate the relationship between star formation and gas content in late interaction phase merger Arp 299 from VIXENS. By comparing Hα, Paα, and 24μm images to CO(2→1), CO(3→2), HCN(1→0), HCO+(1→0), and HI maps, we explore the relation between the star formation rate and gas surface densities on spatially resolved ~kpc scales. We find that the SFR-gas relations for Arp 299 are discrepant from known extragalactic spatially resolved relations in nearby spiral galaxies and disk-averaged relations in high-z mergers.

  16. OSSE observations of the ultraluminous infrared galaxies ARP 220 and MRK 273

    NASA Technical Reports Server (NTRS)

    Dermer, C. D.; Shier, L. M.; Sturner, S. J.; McNaron-Brown, K.; Bland-Hawthorn, J.

    1997-01-01

    The results of oriented scintillation spectrometer experiment (OSSE) observations of the ultraluminous infrared galaxies Arp 220 and Mrk 273 are reported. The pointings of Arp 220 and Mrk 273 concentrated on their upper limits. The gamma ray luminosities from these sources were found to be between one and two orders of magnitude smaller than the infrared luminosities. Multiwavelength luminosity spectra are produced from the radio to the gamma ray regime, and are compared with the typical multiwavelength spectra of active galactic nuclei. The lack of measured gamma ray emission provides no evidence for the existence of buried active galactic nuclei in these ultraluminous infrared galaxies, but is consistent with an origin of the infrared luminosity from starburst activity.

  17. A test of the massive binary black hole hypothesis - Arp 102B

    NASA Technical Reports Server (NTRS)

    Helpern, J. P.; Filippenko, Alexei V.

    1988-01-01

    The emission-line spectra of several AGN have broad peaks which are significantly displaced in velocity with respect to the host galaxy. An interpretation of this effect in terms of orbital motion of a binary black hole predicts periods of a few centuries. It is pointed out here that recent measurements of the masses and sizes of many low-luminosity AGN imply orbital periods much shorter than this. In particular, it is found that the elliptical galaxy Arp 102B is the most likely candidate for observation of radial velocity variations; its period is expected to be about 3 yr. The H-alpha line profile of Arp 102B has been measured for 5 yr without detecting any change in velocity, and it is thus found that a rather restrictive observational test of the massive binary black hole hypothesis already exists, albeit for this one object.

  18. Structural analysis of the transitional state of Arp2/3 complex activation by two actin-WCAs

    PubMed Central

    Boczkowska, Malgorzata; Rebowski, Grzegorz; Kast, David J.; Dominguez, Roberto

    2015-01-01

    Actin filament nucleation and branching by Arp2/3 complex is activated by nucleation-promoting factors (NPFs), whose C-terminal WCA region contains binding sites for actin (W) and Arp2/3 complex (CA). It is debated whether one or two NPFs are required for activation. Here, we present conclusive evidence in support of the two-NPF model and show that actin plays a crucial role in the interactions of two mammalian NPFs, N-WASP and WAVE2, with Arp2/3 complex. Competition between actin-WCA and glia maturation factor (GMF) for binding to Arp2/3 complex suggests that during activation the first actin monomer binds at the barbed end of Arp2. Based on distance constrains obtained by time-resolved fluorescence resonance energy transfer, we define the relative position of the two actin-WCAs on Arp2/3 complex and propose an atomic model of the 11-subunit transitional complex. PMID:24518936

  19. Enhanced Positioning Algorithm of ARPS for Improving Accuracy and Expanding Service Coverage

    PubMed Central

    Lee, Kyuman; Baek, Hoki; Lim, Jaesung

    2016-01-01

    The airborne relay-based positioning system (ARPS), which employs the relaying of navigation signals, was proposed as an alternative positioning system. However, the ARPS has limitations, such as relatively large vertical error and service restrictions, because firstly, the user position is estimated based on airborne relays that are located in one direction, and secondly, the positioning is processed using only relayed navigation signals. In this paper, we propose an enhanced positioning algorithm to improve the performance of the ARPS. The main idea of the enhanced algorithm is the adaptable use of either virtual or direct measurements of reference stations in the calculation process based on the structural features of the ARPS. Unlike the existing two-step algorithm for airborne relay and user positioning, the enhanced algorithm is divided into two cases based on whether the required number of navigation signals for user positioning is met. In the first case, where the number of signals is greater than four, the user first estimates the positions of the airborne relays and its own initial position. Then, the user position is re-estimated by integrating a virtual measurement of a reference station that is calculated using the initial estimated user position and known reference positions. To prevent performance degradation, the re-estimation is performed after determining its requirement through comparing the expected position errors. If the navigation signals are insufficient, such as when the user is outside of airborne relay coverage, the user position is estimated by additionally using direct signal measurements of the reference stations in place of absent relayed signals. The simulation results demonstrate that a higher accuracy level can be achieved because the user position is estimated based on the measurements of airborne relays and a ground station. Furthermore, the service coverage is expanded by using direct measurements of reference stations for user

  20. Serendipitous discovery of the long-sought active galactic nucleus in Arp 299-A

    NASA Astrophysics Data System (ADS)

    Pérez-Torres, M. A.; Alberdi, A.; Romero-Cañizales, C.; Bondi, M.

    2010-09-01

    Context. The dusty nuclear regions of luminous infra-red galaxies (LIRGs) are heated by either an intense burst of massive star formation, an active galactic nucleus (AGN), or a combination of both. Disentangling the contribution of each of those putative dust-heating agents is a challenging task, and direct imaging of the innermost few pc can only be accomplished at radio wavelengths, using very high-angular resolution observations. Aims: We observed the nucleus A of the interacting starburst galaxy Arp 299, using very long baseline interferometry (VLBI) radio observations at 1.7 and 5.0 GHz. Our aim was to characterize the compact sources in the innermost few pc region of Arp 299-A, as well as to detect recently exploded core-collapse supernovae. Methods: We used the European VLBI Network (EVN) to image the 1.7 and 5.0 GHz compact radio emission of the parsec-scale structure in the nucleus of Arp 299-A with milliarcsecond resolution. Results: Our EVN observations show that one of the compact VLBI sources, A1, previously detected at 5.0 GHz, has a flat spectrum between 1.7 and 5.0 GHz and is the brightest source at both frequencies. Our 1.7 GHz EVN image shows also diffuse, low-surface brightness emission extending westwards from A1 and displays a prominent core-jet structure. Conclusions: The morphology, radio luminosity, spectral index and ratio of radio-to-X-ray emission of the A1-A5 region is consistent with a low-luminosity AGN (LLAGN), and rules out the possibility that it is a chain of young radio supernovae (RSNe) and supernova remnants (SNRs). We therefore conclude that A1-A5 is the long-sought AGN in Arp 299-A. This finding may suggest that both starburst and AGN are frequently associated phenomena in mergers.

  1. ALMA IMAGING OF HCN, CS, AND DUST IN ARP 220 AND NGC 6240

    SciTech Connect

    Scoville, Nick; Manohar, Swarnima; Murchikova, Lena; Sheth, Kartik; Walter, Fabian; Zschaechner, Laura; Yun, Min; Koda, Jin; Sanders, David; Barnes, Joshua; Thompson, Todd; Robertson, Brant; Tacconi, Linda; Narayanan, Desika; Genzel, Reinhard; Davies, Richard; Hernquist, Lars; Brown, Robert; Hayward, Christopher C.; Kartaltepe, Jeyhan; and others

    2015-02-10

    We report ALMA Band 7 (350 GHz) imaging at 0.''4-0.''6 resolution and Band 9 (696 GHz) at ∼0.''25 resolution of the luminous IR galaxies Arp 220 and NGC 6240. The long wavelength dust continuum is used to estimate interstellar medium masses for Arp 220 east and west and NGC 6240 of 1.9, 4.2, and 1.6 × 10{sup 9} M {sub ☉}within radii of 69, 65, and 190 pc. The HCN emission was modeled to derive the emissivity distribution as a function of radius and the kinematics of each nuclear disk, yielding dynamical masses consistent with the masses and sizes derived from the dust emission. In Arp 220, the major dust and gas concentrations are at radii less than 50 pc in both counter-rotating nuclear disks. The thickness of the disks in Arp 220 estimated from the velocity dispersion and rotation velocities are 10-20 pc and the mean gas densities are n{sub H{sub 2}}∼10{sup 5} cm{sup –3} at R <50 pc. We develop an analytic treatment for the molecular excitation (including photon trapping), yielding volume densities for both the HCN and CS emission with n {sub H2} ∼ 2 × 10{sup 5} cm{sup –3}. The agreement of the mean density from the total mass and size with that required for excitation suggests that the volume is essentially filled with dense gas, i.e., it is not cloudy or like swiss cheese.

  2. Sludge Batch 4 Simulant Flowsheet Studies with ARP and MCU: Impact of MCU Organics

    SciTech Connect

    Baich, M. A.; Herman, C. C.; Eibling, R. E.; Williams, M. F.; Smith, F. G.

    2005-07-01

    Two facilities for treating the salt currently being stored in the High Level Waste (HLW) tanks are currently planned to begin operations during the processing of Sludge Batch 4 (SB4). The Immobilization Technology Section (ITS) of the Savannah River National Laboratory (SRNL) was requested by the Defense Waste Processing Facility (DWPF) via Technical Task Request (TTR) HLW/DWPF/TTR-2004-0031 (Washburn, 2004) to evaluate the impacts on DWPF processing for streams from the Actinide Removal Process (ARP) and the Modular Caustic Side Solvent Side Extraction (CSSX) Unit (MCU). In particular, the TTR requests SRNL to validate the existing process flowsheet and establish a coupled operations flowsheet for use with SB4. The flowsheet runs are required so an evaluation of potential chemical processing issues, quantification of the potential hydrogen generation rates, and estimation of the required acid stoichiometry can be made. Previous testing (Baich et. al., 2003) was performed for incorporating ARP/MST in Sludge Batch 3 (SB3) and recommendations were made to DWPF on possible flowsheet options. However, since that time, some changes have occurred to the ARP facility processing strategy, and material balances have been revised (Subosits, 2004). Thus, testing with updated compositions was necessary. Since the MCU is a new design and project, no CPC flowsheet studies have been performed for this stream. This testing will validate the previously recommended ARP stream addition methods based on the new information and based on the need to also incorporate the MCU stream. The basic principle of solvent extraction is to use a sparingly soluble diluent material that carries an extractant that will complex with the cesium ions in the caustic HLW solution. The decontaminated aqueous stream (raffinate) is then sent to Saltstone for disposal. The cesium contained in the organic phase (solvent) can then be stripped into an aqueous phase ready for transfer to the DWPF. The solvent is

  3. A deep Chandra observation of the interacting star-forming galaxy Arp 299

    NASA Astrophysics Data System (ADS)

    Anastasopoulou, K.; Zezas, A.; Ballo, L.; Della Ceca, R.

    2016-08-01

    We present results from a 90 ks Chandra ACIS-S observation of the X-ray luminous interacting galaxy system Arp 299 (NGC 3690/IC 694). We detect 25 discrete X-ray sources with luminosities above ˜4.0 × 1038 erg s-1 covering the entire Ultra Luminous X-ray source (ULX) regime. Based on the hard X-ray spectra of the non-nuclear discrete sources identified in Arp 299, and their association with young, actively star-forming region of Arp 299 we identify them as HMXBs. We find in total 20 off-nuclear sources with luminosities above the ULX limit, 14 of which are point-like sources. Furthermore we observe a marginally significant deficit in the number of ULXs, with respect to the number expected from scaling relations of X-ray binaries with the star formation rate (SFR). Although the high metallicity of the galaxy could result in lower ULX numbers, the good agreement between the observed total X-ray luminosity of ULXs, and that expected from the relevant scaling relation indicates that this deficit could be the result of confusion effects. The integrated spectrum of the galaxy shows the presence of a hot gaseous component with kT = 0.72 ± 0.03 keV, contributing ˜20 per cent of the soft (0.1-2.0 keV) unabsorbed luminosity of the galaxy. A plume of soft X-ray emission in the west of the galaxy indicates a large scale outflow. We find that the AGN in NGC 3690 contributes only 22 per cent of the observed broad-band X-ray luminosity of Arp 299.

  4. Enhanced Positioning Algorithm of ARPS for Improving Accuracy and Expanding Service Coverage.

    PubMed

    Lee, Kyuman; Baek, Hoki; Lim, Jaesung

    2016-01-01

    The airborne relay-based positioning system (ARPS), which employs the relaying of navigation signals, was proposed as an alternative positioning system. However, the ARPS has limitations, such as relatively large vertical error and service restrictions, because firstly, the user position is estimated based on airborne relays that are located in one direction, and secondly, the positioning is processed using only relayed navigation signals. In this paper, we propose an enhanced positioning algorithm to improve the performance of the ARPS. The main idea of the enhanced algorithm is the adaptable use of either virtual or direct measurements of reference stations in the calculation process based on the structural features of the ARPS. Unlike the existing two-step algorithm for airborne relay and user positioning, the enhanced algorithm is divided into two cases based on whether the required number of navigation signals for user positioning is met. In the first case, where the number of signals is greater than four, the user first estimates the positions of the airborne relays and its own initial position. Then, the user position is re-estimated by integrating a virtual measurement of a reference station that is calculated using the initial estimated user position and known reference positions. To prevent performance degradation, the re-estimation is performed after determining its requirement through comparing the expected position errors. If the navigation signals are insufficient, such as when the user is outside of airborne relay coverage, the user position is estimated by additionally using direct signal measurements of the reference stations in place of absent relayed signals. The simulation results demonstrate that a higher accuracy level can be achieved because the user position is estimated based on the measurements of airborne relays and a ground station. Furthermore, the service coverage is expanded by using direct measurements of reference stations for user

  5. IR and dc magneto-transport and ARPES compared: n-type cuprates

    NASA Astrophysics Data System (ADS)

    Drew, H. D.; Jenkins, G. S.; Schmadel, D. C.; Bach, P. L.; Greene, R.; Kontani, H.; Béchamp-Laganière, X.; Roberge, G.; Fournier, P.

    2010-03-01

    IR Hall angle measurements were performed on under- and overdoped Pr2-xCexCuO4 (PCCO) samples at sufficiently low optical excitation energies (below 10meV) to directly probe the Fermi-surface (FS) properties. In the underdoped samples, a rapid reduction of the Hall mass with decreasing doping indicating formation of FS pockets will be discussed in terms of ARPES measured arcs. In the overdoped samples, the low temperature finite-frequency Hall coefficient RH is severely suppressed below the low temperature dc RH as well as the value predicted by ARPES data analyzed within the relaxation time approximation. This suppression with frequency is similar to the dc suppression observed at temperature T˜φ. The addition of electronlike contributions to the ac σxy, even at T=0, directly implicates inelastic scattering as the causal mechanism of the anomalous Hall effect in PCCO. These results will be discussed in terms of Fermi liquid theories utilizing the ARPES measured Fermi surfaces.

  6. The Quasiparticle Puzzle: Reconciling ARPES and FTSTS Studies of Bi2212

    SciTech Connect

    Vishik, I.M.; Nowadnick, E.A.; Lee, W.S.; Shen, Z.X.; Moritz, B.; Devereaux, T.P.; Tanaka, K.; Sasagawa, T.; Fujii, T.; /Tokyo U.

    2009-12-17

    Angle Resolved Photoemission Spectroscopy (ARPES) probes the momentum-space electronic structure of materials, and provides invaluable information about the high-temperature superconducting cuprates. Likewise, cuprates real-space, inhomogeneous electronic structure is elucidated by Scanning Tunneling Spectroscopy (STS). Recently, STS has exploited quasiparticle interference (QPI) - wave-like electrons scattering off impurities to produce periodic interference patterns - to infer properties of the QP in momentum-space. Surprisingly, some interference peaks in Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+{delta}} (Bi-2212) are absent beyond the antiferromagnetic (AF) zone boundary, implying the dominance of particular scattering process. Here, we show that ARPES sees no evidence of quasiparticle (QP) extinction: QP-like peaks are measured everywhere on the Fermi surface, evolving smoothly across the AF zone boundary. This apparent contradiction stems from different natures of single-particle (ARPES) and two-particle (STS) processes underlying these probes. Using a simple model, we demonstrate extinction of QPI without implying the loss of QP beyond the AF zone boundary.

  7. Stellar velocity dispersion in ARP 220 and NGC 6240: Elliptical galaxies in formation

    NASA Astrophysics Data System (ADS)

    Doyon, Rene; Wells, M.; Wright, G. S.; Joseph, R. D.; Nadeau, D.; James, P. A.

    1994-12-01

    We present high-resolution (R is approximately 7000) spectra of the 2.3 micron CO absorption bandhead of two luminous merging galaxies, NGC 6240 and Arp 220, obtained with CGS4 on the United Kingdom Infrared Telescope. We have also secured subarcsecond images of NGC 6240 at 2.2 micron using the Montreal Infrared Camera (MONICA) on the Canada-France-Hawaii Telescope (CFHT). The velocity dispersion (sigmaobs = FWHM/2.354) inferred from the broadening of the CO bandhead in the central 2 sec of the brightest nucleus of NGC 6240 is 359 +/- 21 km/s, which is among the highest values ever found in the center of a galaxy. Arp 220 shows a velocity dispersion of 150 +/- 21 km/s. The infrared light profile of NGC 6240 beyond a radius of 0.7 sec is well fitted by an r1/4 law, but the overall brightness distribution is best represented by a shallower profile such as a King (1966) profile with a core radius of 0.20 kpc. Both Arp 220 and NGC 6240 have mass densities, velocity dispersions, and central surface brightnesses consistent with the fundamental parameter plane of elliptical galaxies.

  8. α5β1 integrin recycling promotes Arp2/3-independent cancer cell invasion via the formin FHOD3

    PubMed Central

    Paul, Nikki R.; Allen, Jennifer L.; Chapman, Anna; Morlan-Mairal, Maria; Zindy, Egor; Jacquemet, Guillaume; Fernandez del Ama, Laura; Ferizovic, Nermina; Green, David M.; Howe, Jonathan D.; Ehler, Elisabeth; Hurlstone, Adam

    2015-01-01

    Invasive migration in 3D extracellular matrix (ECM) is crucial to cancer metastasis, yet little is known of the molecular mechanisms that drive reorganization of the cytoskeleton as cancer cells disseminate in vivo. 2D Rac-driven lamellipodial migration is well understood, but how these features apply to 3D migration is not clear. We find that lamellipodia-like protrusions and retrograde actin flow are indeed observed in cells moving in 3D ECM. However, Rab-coupling protein (RCP)-driven endocytic recycling of α5β1 integrin enhances invasive migration of cancer cells into fibronectin-rich 3D ECM, driven by RhoA and filopodial spike-based protrusions, not lamellipodia. Furthermore, we show that actin spike protrusions are Arp2/3-independent. Dynamic actin spike assembly in cells invading in vitro and in vivo is regulated by Formin homology-2 domain containing 3 (FHOD3), which is activated by RhoA/ROCK, establishing a novel mechanism through which the RCP–α5β1 pathway reprograms the actin cytoskeleton to promote invasive migration and local invasion in vivo. PMID:26370503

  9. Phosphorylation of CRN2 by CK2 regulates F-actin and Arp2/3 interaction and inhibits cell migration

    PubMed Central

    Xavier, Charles-Peter; Rastetter, Raphael H.; Blömacher, Margit; Stumpf, Maria; Himmel, Mirko; Morgan, Reginald O.; Fernandez, Maria-Pilar; Wang, Conan; Osman, Asiah; Miyata, Yoshihiko; Gjerset, Ruth A.; Eichinger, Ludwig; Hofmann, Andreas; Linder, Stefan; Noegel, Angelika A.; Clemen, Christoph S.

    2012-01-01

    CRN2 (synonyms: coronin 1C, coronin 3) functions in the re-organization of the actin network and is implicated in cellular processes like protrusion formation, secretion, migration and invasion. We demonstrate that CRN2 is a binding partner and substrate of protein kinase CK2, which phosphorylates CRN2 at S463 in its C-terminal coiled coil domain. Phosphomimetic S463D CRN2 loses the wild-type CRN2 ability to inhibit actin polymerization, to bundle F-actin, and to bind to the Arp2/3 complex. As a consequence, S463D mutant CRN2 changes the morphology of the F-actin network in the front of lamellipodia. Our data imply that CK2-dependent phosphorylation of CRN2 is involved in the modulation of the local morphology of complex actin structures and thereby inhibits cell migration. PMID:22355754

  10. Expression of PDGFRα Is a Determinant of the PVR Potential of ARPE19 Cells

    PubMed Central

    Lei, Hetian; Rhéaume, Marc-André; Velez, Gisela; Mukai, Shizuo

    2011-01-01

    Purpose. Previous studies indicate that the expression of platelet-derived growth factor (PDGF) receptor α (PDGFRα) dramatically increases the ability of fibroblasts to induce experimental proliferative vitreoretinopathy (PVR). The purpose of this study was to determine whether PDGFRα contributed to the PVR potential of retinal pigment epithelial (RPE) cells, one of the most abundant cell types in PVR membranes. Methods. PDGFRα expression in human ARPE19 cells was increased or decreased by stably expressing the PDGFRα cDNA or short hairpin (sh) RNA directed at PDGFRα, respectively. The level of PDGFRα expression in the resulting panel of cell lines was either barely detectable (KD), standard (similar to the level of primary RPE cells), or overexpressed approximately 80-fold. Western blot analysis was used to assess the level of p53 and the activation state of PDGFRα and Akt. The following cellular responses were monitored: proliferation, apoptosis, and contraction. The PVR potential of cells was tested in a rabbit model of PVR in which cells were coinjected with platelet-rich plasma into the vitreous. Results. Comparison of KD and overexpressing cells indicated that high-level expression of PDGFRα dramatically augmented signaling events, cellular responses, and the PVR potential of ARPE19 cells. However, all these outcomes were also significantly increased, albeit not as robustly, by PDGFRα expression to the level typically present in RPE cells. Conclusions. Even though RPE cells express substantially less PDGFRα than fibroblasts, it significantly boosts PVR-related signaling events, cellular responses, and the PVR potential of ARPE19 cells. These studies suggest that inhibiting activation, signaling, or both by PDGFRα has the potential to prevent the development of PVR. PMID:21642621

  11. Near-infrared (Fe II) and Pa Beta imaging and spectroscopy of Arp 220

    NASA Technical Reports Server (NTRS)

    Armus, L.; Shupe, D. L.; Matthews, K.; Soifer, B. T.; Neugebauer, G.

    1995-01-01

    We have imaged the ultraluminous infrared galaxy Arp 220 in light of the near-infrared (Fe II) 1.257 micron and Pa-beta lines, and have obtained spectra in the J- and H-band atmospheric windows. Arp 220 is a strong source of (Fe II) and Pa-beta emission, with luminosities of 1.3 x 10(exp 41) and 9.2 x 10(exp 40) ergs/s, respectively. The (Fe II) and Pa-beta emission are both extended over the central 2 sec-3 sec, but with different morphologies. We suggest that the extended (Fe II) emission is produced through the interaction of fast shocks with ambient gas in the interstellar medium (ISM) at the base of the outflowing, supernovae-driven superwind mapped by Heckman et al. (1987). The bolometric luminosity of the starburst required to power this wind is estimated to be at least 2 x 10(exp 11) solar luminosity. If the spatially unresolved (Fe II) emission is produced via a large number of supernova remnants, the implied rate is approximately 0.6/yr. The overall luminosity of such a starburst could account for a large fraction (1/2-1/3) of the Arp 220 energy budget, but the large deficit of ionizing photons (as counted by the Pa-beta luminosity) requires that the starburst be rapidly declining and/or have a low upper mass cutoff. Alternatively, dust may effectively compete with the gas for ionizing photons, or much of the ionizing radiation may escape through 'holes' in the ISM. It is also possible that a buried active galactic nuclei (AGN) produces a large fraction of the unresolved (Fe II) and Pa-beta emission. We briefly discuss these possibilities in light of these new imaging and spectroscopic data.

  12. EXTREME DUST DISKS IN Arp 220 AS REVEALED BY ALMA

    SciTech Connect

    Wilson, C. D.; Rangwala, N.; Glenn, J.; Maloney, P. R.; Spinoglio, L.; Pereira-Santaella, M.

    2014-07-10

    We present new images of Arp 220 from the Atacama Large Millimeter/submillimeter Array with the highest combination of frequency (691 GHz) and resolution (0.''36 × 0.''20) ever obtained for this prototypical ultraluminous infrared galaxy. The western nucleus is revealed to contain warm (200 K) dust that is optically thick (τ{sub 434} {sub μm} = 5.3), while the eastern nucleus is cooler (80 K) and somewhat less opaque (τ{sub 434} {sub μm} = 1.7). We derive full width at half-maximum diameters of 76 × ≤ 70 pc and 123 × 79 pc for the western and eastern nucleus, respectively. The two nuclei combined account for (83{sub −38}{sup +65} (calibration) {sub −34}{sup +0} (systematic))% of the total infrared luminosity of Arp 220. The luminosity surface density of the western nucleus (log (σT{sup 4})=14.3±0.2{sub −0.7}{sup +0} in units of L {sub ☉} kpc{sup –2}) appears sufficiently high to require the presence of an active galactic nucleus (AGN) or a ''hot starburst'', although the exact value depends sensitively on the brightness distribution adopted for the source. Although the role of any central AGN remains open, the inferred mean gas column densities of (0.6-1.8) × 10{sup 25} cm{sup –2} mean that any AGN in Arp 220 must be Compton-thick.

  13. Star Formation Rate and Gas Relations in the Arp 299 Merger from the VIXENS Survey

    NASA Astrophysics Data System (ADS)

    Heiderman, Amanda L.; Evans, N. J.; Gebhardt, K.; Blanc, G. A.; Davis, T.; Papovich, C. J.; van den Bosch, R.; Iono, D.; Yun, M.; VIXENS Team

    2014-01-01

    We investigate the relationship between star formation and gas content in late interaction phase merger Arp 299 from the VIRUS-P Investigation of the eXtreme ENvironments of Starbursts (VIXENS) integral field unit survey. By comparing H-alpha, Pa-alpha and 24um data to CO(1-0), CO(2-1), HCN(1-0), HCO+(1-0), and HI maps, we explore the relation between the star formation rate and gas surface densities on spatially resolved ~kpc scales. We find discrepancies from known extragalactic spatially resolved relations in nearby spiral galaxies and disk-averaged relations in high-z mergers.

  14. The genesis of the ring galaxy Arp 144 (NGC 7828/29)

    NASA Technical Reports Server (NTRS)

    Joy, Marshall; Ellis, H. B., Jr.; Tollestrup, E. V.; Brock, D.; Higdon, J. L.

    1988-01-01

    Multicolor near-infrared images have been obtained for the 'folded ring' galaxy Arp 144 (NGC 7828/29). About 10 to the 10th solar mass stellar nuclei associated with both NGC 7828 and NGC 7829 are found, indicating that this system is the result of an interaction between two similarly massive galaxies. The galaxy/intergalactic H I cloud collision model proposed by Freeman and de Vaucouleurs (1974) appears to be untenable, since it unequivocally predicts the existence of a single evolved stellar nucleus.

  15. ARPES studies on FeTe1-x Se x iron chalcogenides epitaxial thin films

    NASA Astrophysics Data System (ADS)

    Innocenti, Davide; Moreschini, Luca; Chang, Young Jun; Walter, Andrew; Bostwick, Aaron; di Castro, Daniele; Tebano, Antonello; Medaglia, Pier Gianni; Bellingeri, Emilio; Pallecchi, Ilaria; Ferdeghini, Carlo; Balestrino, Giuseppe; Rotenberg, Eli

    2011-03-01

    The physics of iron-based chalcogenides raises fundamental questions on the interplay of magnetic order and electron pairing at the origin of the superconducting state. We have performed angle-resolved photemission spectroscopy (ARPES) studies on high-quality epitaxial thin films of FeTe 1-x Se x , grown by in situ pulsed laser deposition (PLD) on beamline 7.0.1 at the ALS. Specifically, we are able to show the evolution of the band structure as a function of x. We discuss our experimental results in comparison to the available theoretical band calculations.

  16. HST Ultraviolet Spectrum of ARP 102B, the Prototypical Double-Peaked Emission-Line AGN

    NASA Astrophysics Data System (ADS)

    Eracleous, M.; Filippenko, A. V.; Halpern, J. P.; Chen, K.

    1995-12-01

    UV spectra of the nucleus of the elliptical galaxy Arp 102B were obtained with the HST's Faint Object Spectrograph in order to investigate the UV emission-line counterparts of its unusual double-peaked Balmer lines. Broad Mg II lambda 2798 is present with nearly the same profile as the Balmer lines (peaks separated by ~ 12,000 km s(-1) ), and a typical Mg II/Hβ ratio of 1. But there is little, if any C III] lambda 1909 or C IV lambda 1550 emission corresponding to the displaced Balmer-line peaks. Most important, there is no double-peaked component detected in Lyalpha ; the Lyalpha /Hβ ratio is < 0.12 in the displaced peaks. However, there is an ``ordinary,'' non-displaced broad-line component with FWHM ~ 3500 km s(-1) in all of the permitted lines, demonstrating the need to invoke different locations and different physical conditions for double-peaked and single-peaked line components in the same object. The striking absence of displaced peaks in Lyalpha cannot be explained solely by reddening. Rather, it indicates that high density and large optical depth in Lyalpha are required to destroy the line photons by collisional deexcitation and possibly by bound-free absorption out of the n=2 level of hydrogen. These results strongly support the application, at least to Arp 102B, of the accretion-disk model of Dumont and Collin-Souffrin, in which the disk produces only low-ionization lines and a Lyalpha /Hβ ratio that agrees with our upper limit. Also present is an extraordinary system of absorption lines at the systemic redshift of Arp 102B, in which metastable levels of Fe II up to 1.1 eV above the ground state participate in addition to the more common resonance transitions. Absorption from metastable levels has been seen previously only in two unusual, low-ionization BALQSOs, Q0059--2735 and Mrk 231. Why they are seen in absorption in Arp 102B, a relatively unobscured AGN, but in no other appropriately observed Seyfert or radio galaxy, is a mystery.

  17. The Arp2/3 activator WASH regulates α5β1-integrin-mediated invasive migration

    PubMed Central

    Zech, Tobias; Calaminus, Simon D. J.; Caswell, Patrick; Spence, Heather J.; Carnell, Michael; Insall, Robert H.; Norman, Jim; Machesky, Laura M.

    2011-01-01

    The actin cytoskeleton provides scaffolding and physical force to effect fundamental processes such as motility, cytokinesis and vesicle trafficking. The Arp2/3 complex nucleates actin structures and contributes to endocytic vesicle invagination and trafficking away from the plasma membrane. Internalisation and directed recycling of integrins are major driving forces for invasive cell motility and potentially for cancer metastasis. Here, we describe a direct requirement for WASH and Arp2/3-mediated actin polymerisation on the endosomal membrane system for α5β1 integrin recycling. WASH regulates the trafficking of endosomal α5β1 integrin to the plasma membrane and is fundamental for integrin-driven cell morphology changes and integrin-mediated cancer cell invasion. Thus, we implicate WASH and Arp2/3-driven actin nucleation in receptor recycling leading to invasive motility. PMID:22114305

  18. ARPES measurements of the superconducting gap of Fe-based superconductors and their implications to the pairing mechanism.

    PubMed

    Richard, P; Qian, T; Ding, H

    2015-07-29

    Its direct momentum sensitivity confers to angle-resolved photoemission spectroscopy (ARPES) a unique perspective in investigating the superconducting gap of multi-band systems. In this review we discuss ARPES studies on the superconducting gap of high-temperature Fe-based superconductors. We show that while Fermi-surface-driven pairing mechanisms fail to provide a universal scheme for the Fe-based superconductors, theoretical approaches based on short-range interactions lead to a more robust and universal description of superconductivity in these materials. Our findings are also discussed in the broader context of unconventional superconductivity. PMID:26153847

  19. PWR ENDF/B-VII cross-section libraries for ORIGEN-ARP

    SciTech Connect

    McGraw, C.; Ilas, G.

    2012-07-01

    New pressurized water reactor (PWR) cross-section libraries were generated for use with the ORIGEN-ARP depletion sequence in the SCALE nuclear analysis code system. These libraries are based on ENDF/B-VII nuclear data and were generated using the two-dimensional depletion sequence, TRITON/NEWT, in SCALE 6.1. The libraries contain multiple burnup-dependent cross-sections for seven PWR fuel designs, with enrichments ranging from 1.5 to 6 wt% {sup 235}U. The burnup range has been extended from the 72 GWd/MTU used in previous versions of the libraries to 90 GWd/MTU. Validation of the libraries using radiochemical assay measurements and decay heat measurements for PWR spent fuel showed good agreement between calculated and experimental data. Verification against detailed TRITON simulations for the considered assembly designs showed that depletion calculations performed in ORIGEN-ARP with the pre-generated libraries provide similar results as obtained with direct TRITON depletion, while greatly reducing the computation time. (authors)

  20. Chandra Observations of Extended X-Ray Emission in ARP 220

    NASA Technical Reports Server (NTRS)

    McDowell, J. C.; Clements, D. L.; Lamb, S. A.; Shaked, S.; Hearn, N. C.; Colina, L.; Mundell, C.; Borne, K.; Baker, A. C.; Arribas, S.

    2003-01-01

    We resolve the extended X-ray emission from the prototypical ultraluminous infrared galaxy Arp 220. Extended, faint, edge-brightened, soft X-ray lobes outside the optical galaxy are observed to a distance of 1CL 15 kpc on each side of the nuclear region. Bright plumes inside the optical isophotes coincide with the optical line emission and extend 1 1 kpc from end to end across the nucleus. The data for the plumes cannot be fitted by a single-temperature plasma and display a range of temperatures from 0.2 to 1 keV. The plumes emerge from bright, diffuse circumnuclear emission in the inner 3 kpc centered on the Ha peak, which is displaced from the radio nuclei. There is a close morphological correspondence between the Ha and soft X-ray emission on all spatial scales. We interpret the plumes as a starburst-driven superwind and discuss two interpretations of the emission from the lobes in the context of simulations of the merger dynamics of Arp 220.

  1. ULTRAVIOLET/OPTICAL/INFRARED COLOR SEQUENCES ALONG THE TIDAL RING/ARM OF Arp 107

    SciTech Connect

    Lapham, Ryen C.; Smith, Beverly J.; Struck, Curtis E-mail: smithbj@etsu.edu

    2013-05-15

    We construct UV/optical/IR spectral energy distributions for 29 star forming regions in the interacting galaxy Arp 107, using GALEX UV, Sloan Digitized Sky Survey optical, and Spitzer infrared images. In an earlier study utilizing only the Spitzer data, we found a sequence in the mid-infrared colors of star-forming knots along the strong tidal arm in this system. In the current study, we find sequences in the UV/optical colors along the tidal arm that mirror those in the mid-infrared, with blue UV/optical colors found for regions that are red in the mid-infrared, and vice versa. With single-burst stellar population synthesis models, we find a sequence in the average stellar age along this arm, with younger stars preferentially located further out in the arm. Models that allow two populations of different ages and dust attenuations suggest that there may be both a young component and an older population present in these regions. Thus the observed color sequences may be better interpreted as a sequence in the relative proportion of young and old stars along the arm, with a larger fraction of young stars near the end. Comparison with star forming regions in other interacting galaxies shows that the Arp 107 regions are relatively quiescent, with less intense star formation than in many other systems.

  2. ARPES-parameterized Hubbard approach to d-wave cuprate superconductors

    SciTech Connect

    Pérez, Luis A.; Galván, César G.; Wang, Chumin

    2014-01-27

    In the last decade, the Angle Resolved Photoemission Spectroscopy (ARPES) has achieved important advances in both energy and angular resolutions, providing a direct measurement of the single-particle dispersion relation and superconducting gap. These dispersion relation data allow a full determination of the self-energy, first and second neighbor parameters in the Hubbard model. This model and its generalizations offer a simple and general way to describe the electronic correlation in solids. In particular, the parameters of correlated hopping interactions, responsible of the d-wave superconductivity in the generalized Hubbard model, are determined from ARPES data and the critical temperature within the mean-field approximation. In this work, we determine the model parameters for Bi{sub 2}Sr{sub 2−x}La{sub x}CuO{sub 6+δ} and study its d-wave superconducting gap as a function of temperature by solving numerically two coupled integral equations. Finally, the calculated electronic specific heat is compared with experimental results.

  3. Polarization of Line Emission from an Accretion Disk and Application to ARP 102B

    NASA Technical Reports Server (NTRS)

    Chen, Kaiyou; Halpern, Jules P.; Titarchuk, Lev G.

    1997-01-01

    We model the polarization properties of line emission from an accretion disk under a range of assumptions about the source function and electron-scattering optical depth tau(sub es). For small values of tau(sub es) and modest viewing angles, polarization can be in excess of the Chandrasekhar result for tau(sub es) = infinity. The polarization vector can be either parallel or perpendicular to the projected direction of the disk axis. The polarization properties of the double-peaked H-alpha emission line of the broad-line radio galaxy Arp 102B observed by Antonucci, Hurt, and Agol can be understood in terms of electron scattering and line broadening within the line-emitting region if tau(sub es) is of order unity, and if the position angle of polarization is parallel to the projected disk axis. The required small tau(sub es) is consistent with the hypothesis that the Balmer lines in Arp 102B are produced by photoionization of the disk atmosphere.

  4. Application of iterative phase-retrieval algorithms to ARPES orbital tomography

    NASA Astrophysics Data System (ADS)

    Kliuiev, P.; Latychevskaia, T.; Osterwalder, J.; Hengsberger, M.; Castiglioni, L.

    2016-09-01

    Electronic wave functions of planar molecules can be reconstructed via inverse Fourier transform of angle-resolved photoelectron spectroscopy (ARPES) data, provided the phase of the electron wave in the detector plane is known. Since the recorded intensity is proportional to the absolute square of the Fourier transform of the initial state wave function, information about the phase distribution is lost in the measurement. It was shown that the phase can be retrieved in some cases by iterative algorithms using a priori information about the object such as its size and symmetry. We suggest a more generalized and robust approach for the reconstruction of molecular orbitals based on state-of-the-art phase-retrieval algorithms currently used in coherent diffraction imaging (CDI). We draw an analogy between the phase problem in molecular orbital imaging by ARPES and of that in optical CDI by performing an optical analogue experiment on micrometer-sized structures. We successfully reconstruct amplitude and phase of both the micrometer-sized objects and a molecular orbital from the optical and photoelectron far-field intensity distributions, respectively, without any prior information about the shape of the objects.

  5. Molecular Gas in Starburts ARP 220 & NGC 6240: Understanding Mergers using High Density Gas Tracers

    NASA Astrophysics Data System (ADS)

    Manohar, Swarnima; Scoville, Nicholas; Sheth, Kartik

    2015-01-01

    NGC 6240 and Arp 220 can be considered the founding members of a very active class of objects called Ultraluminous Infrared Galaxies or ULIRGs. They are in different stages of mergers and hence are excellent case studies to enhance our knowledge about the merging process. We have imaged the dense star-forming regions of these galaxies at sub-arcsec resolution with ALMA and CARMA. Multi-band imaging allows multilevel excitation analysis of HCN, HCO+ and CS transitions which will constrain the properties of the gas as a function of position and velocity (across line profiles). We are doing an extensive multilevel excitation analysis of the merger as a function of radius which enables in depth understanding of the gas dynamics and gas properties such as temperature and density. This in turn probes the homogeneity of the gas in the merging system and hence the regions that facilitate high star formation rates. This tandem use of CARMA with ALMA to map these systems at different merger stages will assemble a more integrated picture of the merger process. We are probing the distribution and dynamics of star forming gas and star formation activity in the dense disk structures to enable new theoretical understanding of the physics, dynamics, star formation activity and associated feedback in the most active and rapidly evolving galactic nuclei. Here we present our observations of Arp 220 and NGC 6240 from ALMA and CARMA.

  6. Structure and Dynamics of an Arp2/3 Complex-independent Component of the Lamellipodial Actin Network

    PubMed Central

    Henson, John H.; Cheung, David; Fried, Christopher A.; Shuster, Charles B.; McClellan, Mary K.; Voss, Meagen K.; Sheridan, John T.; Oldenbourg, Rudolf

    2010-01-01

    Sea urchin coelomocytes contain an unusually broad lamellipodial region and have served as a useful model experimental system for studying the process of actin-based retrograde/centripetal flow. In the current study the small molecule drug 2,3-butanedione monoxime (BDM) was employed as a means of delocalizing the Arp2/3 complex from the cell edge in an effort to investigate the Arp2/3 complex-independent aspects of retrograde flow. Digitally-enhanced phase contrast, fluorescence and polarization light microscopy, along with rotary shadow TEM methods demonstrated that BDM treatment resulted in the centripetal displacement of the Arp2/3 complex and the associated dendritic lamellipodial (LP) actin network from the cell edge. In its wake there remained an array of elongate actin filaments organized into concave arcs that displayed retrograde flow at approximately one quarter the normal rate. Actin polymerization inhibitor experiments indicated that these arcs were generated by polymerization at the cell edge, while active myosin-based contraction in BDM treated cells was demonstrated by localization with anti-phospho-MRLC antibody, the retraction of the cytoskeleton in the presence of BDM, and the response of the BDM arcs to laser-based severing. The results suggest that BDM treatment reveals an Arp2/3 complex-independent actin structure in coelomocytes consisting of elongate filaments integrated into the LP network and that these filaments represent a potential connection between the LP network and the central cytoskeleton. PMID:19530177

  7. Disruption of Arp2/3 Results in Asymmetric Structural Plasticity of Dendritic Spines and Progressive Synaptic and Behavioral Abnormalities

    PubMed Central

    Kim, Il Hwan; Racz, Bence; Wang, Hong; Burianek, Lauren; Weinberg, Richard; Yasuda, Ryohei; Wetsel, William C.; Soderling, Scott H.

    2013-01-01

    Despite evidence for a strong genetic contribution to several major psychiatric disorders, individual candidate genes account for only a small fraction of these disorders, leading to the suggestion that multigenetic pathways may be involved. Several known genetic risk factors for psychiatric disease are related to the regulation of actin polymerization, which plays a key role in synaptic plasticity. To gain insight into and test the possible pathogenetic role of this pathway, we designed a conditional knockout of the Arp2/3 complex, a conserved final output for actin signaling pathways that orchestrates de novo actin polymerization. Here we report that postnatal loss of the Arp2/3 subunit ArpC3 in forebrain excitatory neurons leads to an asymmetric structural plasticity of dendritic spines, followed by a progressive loss of spine synapses. This progression of synaptic deficits corresponds with an evolution of distinct cognitive, psychomotor, and social disturbances as the mice age. Together these results point to the dysfunction of actin signaling, specifically that which converges to regulate Arp2/3, as an important cellular pathway that may contribute to the etiology of complex psychiatric disorders. PMID:23554489

  8. Electronic structure of NaFeAs superconductor: LDA+DMFT calculations compared to the ARPES experiment

    NASA Astrophysics Data System (ADS)

    Nekrasov, I. A.; Pavlov, N. S.; Sadovskii, M. V.

    2015-07-01

    We present the results of extended theoretical LDA+DMFT calculations for a new iron-pnictide high temperature superconductor NaFeAs compared with the recent high quality angle-resolved photoemission (ARPES) experiments on this system (see arXiv:1409.1537). The universal manifestation of correlation effects in iron-pnictides is narrowing of conducting bands near the Fermi level. Our calculations demonstrate that for NaFeAs the effective mass is renormalized on average by a factor of the order of 3, in good agreement with ARPES data. This is essentially due to correlation effects on Fe-3 d orbitals only and no additional interactions with any kind of Boson modes, as suggested in the work mentioned, are necessary to describe the experiment. In addition, we show that ARPES data taken at about 160 eV beam energy most probably corresponds to k z = π Brillouin zone boundary, while ARPES data measured at about 80 eV beam energy rather represents k z = 0. Contributions of different Fe-3 d orbitals into spectral function map are also discussed.

  9. Disruption of Arp2/3 results in asymmetric structural plasticity of dendritic spines and progressive synaptic and behavioral abnormalities.

    PubMed

    Kim, Il Hwan; Racz, Bence; Wang, Hong; Burianek, Lauren; Weinberg, Richard; Yasuda, Ryohei; Wetsel, William C; Soderling, Scott H

    2013-04-01

    Despite evidence for a strong genetic contribution to several major psychiatric disorders, individual candidate genes account for only a small fraction of these disorders, leading to the suggestion that multigenetic pathways may be involved. Several known genetic risk factors for psychiatric disease are related to the regulation of actin polymerization, which plays a key role in synaptic plasticity. To gain insight into and test the possible pathogenetic role of this pathway, we designed a conditional knock-out of the Arp2/3 complex, a conserved final output for actin signaling pathways that orchestrates de novo actin polymerization. Here we report that postnatal loss of the Arp2/3 subunit ArpC3 in forebrain excitatory neurons leads to an asymmetric structural plasticity of dendritic spines, followed by a progressive loss of spine synapses. This progression of synaptic deficits corresponds with an evolution of distinct cognitive, psychomotor, and social disturbances as the mice age. Together, these results point to the dysfunction of actin signaling, specifically that which converges to regulate Arp2/3, as an important cellular pathway that may contribute to the etiology of complex psychiatric disorders.

  10. KEY FACTORS THAT INFLUENCE THE PERFORMANCE PROPERTIES OF ARP/MCU SALTSTONE MIXES

    SciTech Connect

    Harbour, J.; Edwards, T.; Williams, V.

    2009-10-05

    At the Saltstone Production Facility (SPF), decontaminated salt solution (DSS) is combined with premix (a cementitious mixture of portland cement (PC), blast furnace slag (BFS) and Class F fly ash (FA)) in a Readco mixer to produce fresh (uncured) Saltstone. After transfer to the Saltstone Disposal Facility (SDF) the hydration reactions initiated during the contact of the premix and salt solution continue during the curing period to produce the hardened waste form product. The amount of heat generated from hydration and the resultant temperature increase in the vaults depend on the composition of the decontaminated salt solution being dispositioned as well as the grout formulation (mix design). This report details the results from Task 3 of the Saltstone Variability Study for FY09 which was performed to identify, and quantify when possible, those factors that drive the performance properties of the projected ARP/MCU Batches. A baseline ARP/MCU mix (at 0.60 water to cementitious materials (w/cm) ratio) was established and consisted of the normal premix composition and a salt solution that was an average of the projected compositions of the last three ARP/MCU batches developed by T. A. Le. This task introduced significant variation in (1) wt % slag, w/cm ratio, and wt % portland cement about the baseline mix and (2) the temperature of curing in order to better assess the dependence of the performance properties on these factors. Two separate campaigns, designated Phase 10 and Phase 11, were carried out under Task 3. Experimental designs and statistical analyses were used to search for correlation among properties and to develop linear models to predict property values based on factors such as w/cm ratio, slag concentration, and portland cement concentration. It turns out that the projected salt compositions contained relatively high amounts of aluminate (0.22 M) even though no aluminate was introduced due to caustic aluminate removal from High Level Waste. Previous

  11. Arp 65 interaction debris: massive H I displacement and star formation

    NASA Astrophysics Data System (ADS)

    Sengupta, C.; Scott, T. C.; Paudel, S.; Saikia, D. J.; Dwarakanath, K. S.; Sohn, B. W.

    2015-12-01

    Context. Pre-merger tidal interactions between pairs of galaxies are known to induce significant changes in the morphologies and kinematics of the stellar and interstellar medium components. Large amounts of gas and stars are often found to be disturbed or displaced as tidal debris. This debris then evolves, sometimes forming stars and occasionally forming tidal dwarf galaxies. Here we present results from our H i study of Arp 65, an interacting pair hosting extended H i tidal debris. Aims: In an effort to understand the evolution of tidal debris produced by interacting pairs of galaxies, including in situ star and tidal dwarf galaxy formation, we are mapping H i in a sample of interacting galaxy pairs. The Arp 65 pair is the latest member of this sample to be mapped. Methods: Our resolved H i 21 cm line survey is being carried out using the Giant Metrewave Radio Telescope. We used our H i survey data as well as available SDSS optical, Spitzer infra-red and GALEX UV data to study the evolution of the tidal debris and the correlation of H i with the star-forming regions within it. Results: In Arp 65 we see a high impact pre-merger tidal interaction involving a pair of massive galaxies (NGC 90 and NGC 93) that have a stellar mass ratio of ~1:3. The interaction, which probably occurred ~1.0-2.5 × 108 yr ago, appears to have displaced a large fraction of the H i in NGC 90 (including the highest column density H i) beyond its optical disk. We also find extended on-going star formation in the outer disk of NGC 90. In the major star-forming regions, we find the H i column densities to be ~4.7 × 1020 cm-2 or lower. But no signature of star formation was found in the highest column density H i debris SE of NGC 90. This indicates conditions within the highest density H i debris remain hostile to star formation and it reaffirms that high H i column densities may be a necessary but not sufficient criterion for star formation.

  12. Tissue factor induces VEGF expression via activation of the Wnt/β-catenin signaling pathway in ARPE-19 cells

    PubMed Central

    Wang, Ying; Sang, Aimin; Zhu, Manhui; Zhang, Guowei; Guan, Huaijin; Ji, Min

    2016-01-01

    Purpose The purpose of the present study was to investigate the potential signal mechanism of tissue factor (TF) in the regulation of the expression of vascular endothelial growth factor (VEGF) in human retinal pigment epithelial (ARPE-19) cells. Methods An in vitro RPE cell chemical hypoxia model was established by adding cobalt chloride (CoCl2) in the culture medium. The irritative concentration of CoCl2 was determined with a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay kit. VEGF production in ARPE-19 cells was measured with enzyme-linked immunosorbent assay (ELISA) and western blotting. The Wnt signaling pathway–associated molecules, including phospho-glycogen synthase kinase 3β (p-GSK3β), GSK3β, p-β-catenin and β-catenin, were detected with western blotting. pEGFP-N3-hTF was constructed and verified with digestion of the restriction enzyme and sequencing analysis. Human TF overexpression and silencing plasmids were transfected into the ARPE-19 cells to clarify the causal relationship between TF and VEGF expression. The Transwell coculture system of ARPE-19 cells and RF/6A rhesus macaque choroid–retinal endothelial cells was performed to evaluate cell invasion and tube formation ability. Results Our anoxic model of ARPE-19 cells showed that TF expression was upregulated in accordance with variations in hypoxia-inducible factor 1-alpha (HIF-1α) and VEGF levels. Silencing and overexpression of TF decreased and increased VEGF expression, respectively. The Wnt/β-catenin signaling pathway played an important role in this effect. Results from the ARPE-19 cell and RF/6A cell coculture system showed that the enhancement of TF expression in the ARPE-19 cells led to significantly faster invasion and stronger tube-forming ability of the RF/6A cells, while siRNA-mediated TF silencing caused the opposite effects. Pharmacological disruption of Wnt signaling IWR-1-endo inhibited the effects compared to the TF-overexpressing group

  13. Arp2/3 Inhibition Induces Amoeboid-Like Protrusions in MCF10A Epithelial Cells by Reduced Cytoskeletal-Membrane Coupling and Focal Adhesion Assembly

    PubMed Central

    Stricker, Jonathan; Sayegh, Kareem; Campillo, Clement; Gardel, Margaret L.

    2014-01-01

    Here we demonstrate that Arp2/3 regulates a transition between mesenchymal and amoeboid protrusions in MCF10A epithelial cells. Using genetic and pharmacological means, we first show Arp2/3 inhibition impairs directed cell migration. Arp2/3 inhibition results in a dramatically impaired cell adhesion, causing deficient cell attachment and spreading to ECM as well as an 8-fold decrease in nascent adhesion assembly at the leading edge. While Arp2/3 does not play a significant role in myosin-dependent adhesion growth, mature focal adhesions undergo large scale movements against the ECM suggesting reduced coupling to the ECM. Cell edge protrusions occur at similar rates when Arp2/3 is inhibited but their morphology is dramatically altered. Persistent lamellipodia are abrogated and we observe a markedly increased incidence of blebbing and unstable pseuodopods. Micropipette-aspiration assays indicate that Arp2/3-inhibited cells have a weak coupling between the cell cortex and the plasma membrane, and suggest a potential mechanism for increased pseudopod and bleb formation. Pseudopods are not sensitive to reduced in formin or myosin II activity. Collectively, these results indicate that Arp2/3 is not necessary for rapid protrusion of the cell edge but plays a crucial role in assembling focal adhesions required for its stabilization. PMID:24967897

  14. Evidence for Charge-Density-Wave in Underdoped Bi2201 from ARPES and LEED

    NASA Astrophysics Data System (ADS)

    Rosen, J. A.; Comin, R.; Levy, G.; Fournier, D.; Zhu, Z.-H.; Ludbrook, B.; Veenstra, C. N.; Wong, D.; Dosanjh, P.; Yoshida, Y.; Eisaki, H.; Petaccia, L.; Damascelli, A.

    2012-02-01

    While there is mounting evidence for a broken symmetry in the pseudogap state of the high-Tc cuprates, the identification of a specific phase remains elusive. Through the combination of electronic (ARPES) and structural (LEED) probes, we uncover a temperature dependent evolution of the CuO2 plane band dispersion in highly-ordered Bi2201, which is directly associated with a hitherto-undetected evolution of the incommensurate superstructure. The quasilinear, continuous variation of the modulation wavelength 2π/Q2 from ˜ 6 to 43,elow a characteristic TQ2 30,, provides evidence for an electronically-driven charge-density-wave ordering. This points to a remarkable electron-lattice coupling, in which the footprint of the BiO-layer-induced superstructure is found in the modulated electronic structure of the CuO2 plane.

  15. HST/WFC3 OBSERVATIONS OF AN OFF-NUCLEAR SUPERBUBBLE IN ARP 220

    SciTech Connect

    Lockhart, Kelly E.; Lu, Jessica R.; Sanders, David B.; Kewley, Lisa J.; Dopita, Michael A.; Allen, Mark G.; Rupke, David; Calzetti, Daniela; Davies, Richard I.; Engel, Hauke; Heckman, Timothy M.; Leitherer, Claus

    2015-09-10

    We present a high spatial resolution optical and infrared study of the circumnuclear region in Arp 220, a late-stage galaxy merger. Narrowband imaging using Hubble Space Telescope/WFC3 has resolved the previously observed peak in Hα+[N ii] emission into a bubble-shaped feature. This feature measures 1.″6 in diameter, or 600 pc, and is only 1″ northwest of the western nucleus. The bubble is aligned with the western nucleus and the large-scale outflow axis seen in X-rays. We explore several possibilities for the bubble origin, including a jet or outflow from a hidden active galactic nucleus (AGN), outflows from high levels of star formation within the few hundred pc nuclear gas disk, or an ultraluminous X-ray source. An obscured AGN or high levels of star formation within the inner ∼100 pc of the nuclei are favored based on the alignment of the bubble and energetics arguments.

  16. HST/WFC3 Observations of an Off-nuclear Superbubble in Arp 220

    NASA Astrophysics Data System (ADS)

    Lockhart, Kelly E.; Kewley, Lisa J.; Lu, Jessica R.; Allen, Mark G.; Rupke, David; Calzetti, Daniela; Davies, Richard I.; Dopita, Michael A.; Engel, Hauke; Heckman, Timothy M.; Leitherer, Claus; Sanders, David B.

    2015-09-01

    We present a high spatial resolution optical and infrared study of the circumnuclear region in Arp 220, a late-stage galaxy merger. Narrowband imaging using Hubble Space Telescope/WFC3 has resolved the previously observed peak in Hα+[N ii] emission into a bubble-shaped feature. This feature measures 1.″6 in diameter, or 600 pc, and is only 1″ northwest of the western nucleus. The bubble is aligned with the western nucleus and the large-scale outflow axis seen in X-rays. We explore several possibilities for the bubble origin, including a jet or outflow from a hidden active galactic nucleus (AGN), outflows from high levels of star formation within the few hundred pc nuclear gas disk, or an ultraluminous X-ray source. An obscured AGN or high levels of star formation within the inner ∼100 pc of the nuclei are favored based on the alignment of the bubble and energetics arguments.

  17. Arp2/3-mediated F-actin formation controls regulated exocytosis in vivo

    PubMed Central

    Tran, Duy T.; Masedunskas, Andrius; Weigert, Roberto; Ten Hagen, Kelly G.

    2015-01-01

    The actin cytoskeleton plays crucial roles in many cellular processes, including regulated secretion. However, the mechanisms controlling F-actin dynamics in this process are largely unknown. Through 3D time-lapse imaging in a secreting organ, we show that F-actin is actively disassembled along the apical plasma membrane at the site of secretory vesicle fusion and re-assembled directionally on vesicle membranes. Moreover, we show that fusion pore formation and PIP2 redistribution precedes actin and myosin recruitment to secretory vesicle membranes. Finally, we show essential roles for the branched actin nucleators Arp2/3- and WASp in the process of secretory cargo expulsion and integration of vesicular membranes with the apical plasma membrane. Our results highlight previously unknown roles for branched actin in exocytosis and provide a genetically tractable system to image the temporal and spatial dynamics of polarized secretion in vivo. PMID:26639106

  18. Far-infrared spectroscopy of NGC 6946, IC 342, and Arp 299

    NASA Technical Reports Server (NTRS)

    Lord, Steven D.; Hollenbach, David J.; Colgan, Sean W. J.; Haas, Michael R.; Rubin, Robert H.; Erickson, Edwin F.

    1990-01-01

    Researchers investigated the physical conditions in the infrared bright galaxies NGC 6946, IC 342, and Arp 299 through measurements of far-infrared emission lines from Si II, O I, C II, and O III using the facility Cooled Grating Spectrometer on the Kuiper Airborne Observatory. These data are interpreted using our theoretical models for photodissociation regions and H II regions. For the central 45 inches of these galaxies, researchers determined that the dominant excitation mechanism for the far infrared radiation (FIR) lines is far ultraviolet radiation (FUR) radiation from young stars, and the authors derived the total mass, density, and temperature of the warm atomic gas and the typical sizes, number densities, and filling factors for the interstellar clouds.

  19. ARPES studies in LaTiO3/SrTiO3 heterostructures

    NASA Astrophysics Data System (ADS)

    Chang, Young Jun; Moreschini, Luca; Kim, Yong Su; Walter, Andrew L.; Innocenti, Davide; Bostwick, Aaron; Gaines, Geoffrey A.; Horn, Karsten; Rotenberg, Eli

    2011-03-01

    Electronic band structure of LaTiO3/SrTiO3 heterostructures was studied using angle resolved photoemission spectroscopy (ARPES). LaTiO3 films, grown by in situ pulsed laser deposition (PLD) on beamline 7.0.1 at Advanced Light Source, exhibit a thickness-dependent phase transition from the correlated metallic interface to Mott insulator. We observed the quasi-particle peak at the Fermi level explaining the metallic interface for ultrathin LaTiO3, and the band gap opened for thick LaTiO3 similar to the bulk. We compare the thickness dependent electronic structure with theoretically calculated phase diagram (S. Okamoto and A. J. Millis, Nature 428, 630 (2004)). Work supported by U.S. DOE (DE-AC02-05CH11231 for ALS), the Max Planck Society, and Swiss National Science Foundation (PBELP2-125484).

  20. the effect of electron doping in TiO2 assessed by ARPES

    NASA Astrophysics Data System (ADS)

    Moreschini, Luca; Moser, Simon; Jacimovic, Jacim; Barisic, Osor; Berger, Helmut; Magrez, Arnaud; Chang, Young Jun; Kim, Keun Su; Bostwick, Aaron; Forro, Laszlo; Rotenberg, Eli; Grioni, Marco

    2013-03-01

    The titanium oxide TiO2 has been object of extensive studies because of its suitability in many practical fields, ranging from photovoltaic applications, to catalysis, memristors, and others. As for many other transition metal oxides, great attention has been devoted to the impact on the electronic structure of different doping mechanisms, either extrinsic or due to the creation of oxygen vacancies. Here we report an angle-resolved photoemission (ARPES) work on TiO2 single crystals and epitaxial films grown wIth the in situ pulsed-laser-deposition (PLD) system available on beamline 7.0.1 at the Advanced Light Source. We show the evolution of the electronic structure as a function of the amount of oxygen vacancies induced by the photon beam.

  1. Arp2/3-mediated F-actin formation controls regulated exocytosis in vivo.

    PubMed

    Tran, Duy T; Masedunskas, Andrius; Weigert, Roberto; Ten Hagen, Kelly G

    2015-01-01

    The actin cytoskeleton plays crucial roles in many cellular processes, including regulated secretion. However, the mechanisms controlling F-actin dynamics in this process are largely unknown. Through 3D time-lapse imaging in a secreting organ, we show that F-actin is actively disassembled along the apical plasma membrane at the site of secretory vesicle fusion and re-assembled directionally on vesicle membranes. Moreover, we show that fusion pore formation and PIP2 redistribution precedes actin and myosin recruitment to secretory vesicle membranes. Finally, we show essential roles for the branched actin nucleators Arp2/3- and WASp in the process of secretory cargo expulsion and integration of vesicular membranes with the apical plasma membrane. Our results highlight previously unknown roles for branched actin in exocytosis and provide a genetically tractable system to image the temporal and spatial dynamics of polarized secretion in vivo.

  2. Arp2/3-mediated F-actin formation controls regulated exocytosis in vivo.

    PubMed

    Tran, Duy T; Masedunskas, Andrius; Weigert, Roberto; Ten Hagen, Kelly G

    2015-01-01

    The actin cytoskeleton plays crucial roles in many cellular processes, including regulated secretion. However, the mechanisms controlling F-actin dynamics in this process are largely unknown. Through 3D time-lapse imaging in a secreting organ, we show that F-actin is actively disassembled along the apical plasma membrane at the site of secretory vesicle fusion and re-assembled directionally on vesicle membranes. Moreover, we show that fusion pore formation and PIP2 redistribution precedes actin and myosin recruitment to secretory vesicle membranes. Finally, we show essential roles for the branched actin nucleators Arp2/3- and WASp in the process of secretory cargo expulsion and integration of vesicular membranes with the apical plasma membrane. Our results highlight previously unknown roles for branched actin in exocytosis and provide a genetically tractable system to image the temporal and spatial dynamics of polarized secretion in vivo. PMID:26639106

  3. Detecting the minimum gap locus in ARPES spectra of Bi2201

    NASA Astrophysics Data System (ADS)

    Hashimoto, Makoto; He, Ruihua; Moore, Rob; Lu, Donghui; Yoshida, Yoshiyuki; Ishikado, Motoyuki; Eisaki, Hiroshi; Hussain, Zahid; Devereaux, Tom; Shen, Zhi-Xun

    2012-02-01

    Recent angle-resolved photoemission (ARPES) studies have reported a direct evidence for the competing nature of the pseudogap by showing that the pseudogap dispersion is not tied to Fermi momentum (kF)[1,2]. In this study, to get more detailed information on how the competing pseudogap evolves across the pseudogap temperature (T*), we introduce a new analysis method for spectral weight. We found a clear indication that the pseudogap opens at T* with the minimum gap locus deviating from kF, which is completely different manner from the gap opening by simple superconductivity, and strongly supports that the pseudogap is another distinct order. [1] M. Hashimoto and R.-H. He et al., Nature Phys. 6, 14-418 (2010). [2] R.-H. He and M. Hashimoto et al., Science 331, 1579-1583 (2011).

  4. Chemically Distinct Nuclei and Outflowing Shocked Molecular Gas in Arp 220

    NASA Astrophysics Data System (ADS)

    Tunnard, R.; Greve, T. R.; Garcia-Burillo, S.; Graciá Carpio, J.; Fischer, J.; Fuente, A.; González-Alfonso, E.; Hailey-Dunsheath, S.; Neri, R.; Sturm, E.; Usero, A.; Planesas, P.

    2015-02-01

    We present the results of interferometric spectral line observations of Arp 220 at 3.5 mm and 1.2 mm from the Plateau de Bure Interferometer, imaging the two nuclear disks in H13CN(1-0) and (3-2), H13CO+(1-0) and (3-2), and HN13C(3-2) as well as SiO(2-1) and (6-5), HC15N(3-2), and SO(66-55). The gas traced by SiO(6-5) has a complex and extended kinematic signature including a prominent P Cygni profile, almost identical to previous observations of HCO+(3-2). Spatial offsets 0.''1 north and south of the continuum center in the emission and absorption of the SiO(6-5) P Cygni profile in the western nucleus (WN) imply a bipolar outflow, delineating the northern and southern edges of its disk and suggesting a disk radius of ~40 pc, consistent with that found by ALMA observations of Arp 220. We address the blending of SiO(6-5) and H13CO+(3-2) by considering two limiting cases with regards to the H13CO+ emission throughout our analysis. Large velocity gradient modeling is used to constrain the physical conditions of the gas and to infer abundance ratios in the two nuclei. Our most conservative lower limit on the [H13CN]/[H13CO+] abundance ratio is 11 in the WN, compared with 0.10 in the eastern nucleus (EN). Comparing these ratios to the literature we argue on chemical grounds for an energetically significant active galactic nucleus in the WN driving either X-ray or shock chemistry, and a dominant starburst in the EN.

  5. Structures and sites of nonenzymatic glucosylation of protein: characterization by carbon-13 nuclear magnetic resonance spectroscopy

    SciTech Connect

    Fisher, C.I.

    1985-01-01

    Products of nonenzymatic glucosylation of protein were studied by carbon-13 NMR spectroscopy at 100 MHz in phosphate buffer. The anomeric region of the spectrum of glycated cytochrome c (blocked amino terminus) showed three signals representing the C-2 carbon of the alpha and beta-furanose (101.7 and 99.2 ppm) and beta pyranose (95.8 ppm) anomers of the Amadori rearrangement products (ARP) at lysine epsilon amino groups. The spectrum of glycated poly-L-lysine showed two distinct sets of three resonances; the second set, resonating to lower shielding than the first, was assigned to C-2 of the anomers of ARP at the alpha amino terminus. A third set of peaks was observed on glucation of RNase A corresponding to the ARP at lysine residue 41. The anomeric region of RNase denatured with urea at pH 7.4 was similar to that of glycated poly-L-lysine, while at pH 4.0 it was indistinguishable from that of glycated cytochrome c. The anomeric spectum of glycated hemoglobin was comparable to that of poly-L-lysine, and distinct resonances were observed for the ARP at the alpha amino terminal valine and epsilon amino groups. Because of the differences in chemical shift of C-2 of the ARP, we conclude that the pKa of the amino group influences the electronic environment of the anomeric carbon of the ARP.

  6. Multiple A2E treatments lead to melanization of rod outer segment–challenged ARPE-19 cells

    PubMed Central

    Poliakov, Eugenia; Strunnikova, Natalya V.; Jiang, Jian-kang; Martinez, Bianca; Parikh, Toral; Lakkaraju, Aparna; Thomas, Craig; Brooks, Brian P.

    2014-01-01

    Purpose Daily phagocytosis of outer segments (OSs) and retinoid recycling by the RPE lead to the accumulation of storage bodies in the RPE containing autofluorescent lipofuscin, which consists of lipids and bisretinoids such as A2E and its oxidation products. Accumulation of A2E and its oxidation products is implicated in the pathogenesis of several retinal degenerative diseases. However, A2E accumulates in the RPE during normal aging. In this study, we used a cell model to determine the homeostatic mechanisms of RPE cells in response to A2E accumulation. Methods To distinguish between pathologic and normal responses of the RPE to A2E accumulation, we treated established ARPE-19 cells (cultured for 3 weeks after reaching confluence) with low micromolar amounts of A2E for several weeks. We compared the lysosomal function, lysosomal pH, degree of OS digestion, and melanization of the treated cells to untreated control cells in response to a challenge of purified rod OSs (ROSs). A2E was analyzed with high-performance liquid chromatography (HPLC); and A2E and melanin were identified with mass spectrometry. Results We found that post-confluent ARPE-19 cells took up and accumulated A2E under dim light conditions. Spectral analysis of the HPLC separations and mass spectrometry showed that A2E-fed cells contained A2E and oxidized A2E (furan-A2E). A2E accumulation led to a modest increase (up to 0.25 unit) in lysosomal pH in these cells. The specific activity of cathepsin D and lysosomal acid phosphatase was reduced in the A2E-treated cells, but ROS degradation was not impaired. We found that, upon challenge with ROSs, melanin pigment was induced in the lysosomal fraction of the A2E-treated ARPE-19 cells. Thus, the ARPE-19 cells responded to the A2E treatment and ROS challenge by producing a melanin-containing lysosome fraction. We speculate that this prevents them from becoming impaired in OS processing. Conclusions We used a modified ARPE-19 cell model in which

  7. Strategies of ARP application (Automatic Resistivity Profiling) for viticultural precision farming

    NASA Astrophysics Data System (ADS)

    Costantini, E. A. C.; Andrenelli, M. C.; Bucelli, P.; Magini, S.; Natarelli, L.; Pellegrini, S.; Perria, R.; Storchi, P.; Vignozzi, N.

    2009-04-01

    Introduction Viticultural precision farming needs detailed soil information, which can be obtained by means of remote as well as proximal sensors, besides traditional invasive soil survey. Nevertheless, the use of the new technologies is still in its infancy, because of their costs and the lack of knowledge about the detail actually needed for the viticultural husbandry. The main aim of this work was to test the sensitivity of the ARP methodology (Automatic Resistivity Profiling) in supporting soil survey for viticultural precision farming. In addition, we tried to optimize the detail of geoelectrical measurements and soil sampling to reduce the cost of the integrated survey, maintaining a significant information accuracy for viticulture. Materials and methods Two vineyards in coastal Tuscany (central Italy), about 3.5 ha each, were selected. Vineyard 1 was cultivated with Cabernet Sauvignon and Cabernet Franc, while vineyard 2 only had Cabernet Sauvignon. Soil survey and geoelectrical investigation were conducted in may 2007. The ARP methodology consists in the injection in soil of electric current through one pair of electrodes mounted on teeth wheels and measuring the resulting potential with other three pairs of electrodes, placed of the same mobile equipment. The electrical resistance of the soil (ER) is expressed as ohm per m. The depth of investigation is a function of the geometry of the electrodes and the soil being probed. Increasing the distance between electrodes will increase the depth while decreasing the measured potential. The innovative character of the ARP technique is represented by the passage of a mobile machinery, able to perform 30,000 measurements per hectare, with a measurement every 0.2 m. The ARP system, equipped with a digital encoder and DGPS system, is transported by a four-wheeled vehicle. It is fitted with three sensors that contemporaneously analyse three distinct levels of the soil, the values of which are represented by maps of

  8. OPERATIONAL AND COMPOSITIONAL FACTORS THAT AFFECT THE PERFORMANCE PROPERTIES OF ARP/MCU SALTSTONE GROUT

    SciTech Connect

    Reigel, M.; Edwards, T.; Pickenheim, B.

    2012-02-15

    The Saltstone Production Facility (SPF) receives low level waste (LLW) salt solution from Tank 50H for treatment and disposal. Tank 50H receives transfers from the Effluent Treatment Project (ETP), the H-Canyon General Purpose Evaporator, and the Actinide Removal Process/Modular Caustic Side Solvent Extraction Unit (ARP/MCU) Decontaminated Salt Solution Hold Tank (DSS-HT). At the SPF, the LLW is mixed with premix (a cementitious mixture of portland cement (PC), blast furnace slag (BFS) and Class F fly ash (FA)) in a Readco mixer to produce fresh (uncured) saltstone that is transferred to the Saltstone Disposal Facility (SDF) vaults. The saltstone formulation (mix design) must produce a grout waste form that meets both placement and performance properties. In previous simulated saltstone studies, multiple compositional factors were identified that drive the performance properties of saltstone made from the projected ARP/MCU salt solution. This composition was selected as salt solution simulant since ARP/MCU is the primary influent into Tank 50H. The primary performance property investigated was hydraulic conductivity since it is a variable input property to the saltstone Performance Assessment (PA) transport model. In addition, the porosity, also referred to as void structure, is another variable that impacts the PA response. In addition, Young's modulus and cured density are other performance properties analyzed in this report; however they are indicators of the performance of saltstone and not direct inputs into the PA. The data from previous studies showed that the largest impact on the performance properties of saltstone was due to curing temperature, followed by aluminate concentration in the salt solution, water to premix ratio and premix composition. However, due to the scope of the previous studies, only a few mixes were cured and analyzed at higher temperatures. The samples cured at 60 C had an increased hydraulic conductivity of approximately 600 times

  9. Ammonia as a Temperature Tracer in the Ultraluminous Galaxy Merger Arp 220

    NASA Astrophysics Data System (ADS)

    Ott, Jürgen; Henkel, Christian; Braatz, James A.; Weiß, Axel

    2011-12-01

    We present Australia Telescope Compact Array (ATCA) and Robert C. Byrd Green Bank Telescope (GBT) observations of ammonia (NH3) and the 1.2 cm radio continuum toward the ultraluminous infrared galaxy merger Arp 220. We detect the NH3(1,1), (2,2), (3,3), (4,4), (5,5), and (6,6) inversion lines in absorption against the unresolved, (62 ± 9) mJy continuum source at 1.2 cm. The peak apparent optical depths of the ammonia lines range from ~0.05 to 0.18. The absorption lines are well described by single-component Gaussians with central velocities in between the velocities of the eastern and western cores of Arp 220. Therefore, the ammonia likely traces gas that encompasses both cores. The absorption depth of the NH3(1,1) line is significantly shallower than expected based on the depths of the other transitions. The shallow (1,1) profile may be caused by contamination from emission by a hypothetical, cold (lsim 20 K) gas layer with an estimated column density of <~ 2 × 1014 cm-2. This layer would have to be located behind or away from the radio continuum sources to produce the contaminating emission. The widths of the ammonia absorption lines are ~120-430 km s-1, in agreement with those of other molecular tracers. We cannot confirm the extremely large line widths of up to ~1800 km s-1 previously reported for this galaxy. Using all of the ATCA detections except for the shallow (1,1) line, we determine a rotational temperature of (124 ± 19) K, corresponding to a kinetic temperature of T kin = (186 ± 55) K. Ammonia column densities depend on the excitation temperature. For excitation temperatures of 10 K and 50 K, we estimate N(NH3) = (1.7 ± 0.1) × 1016 cm-2 and (8.4 ± 0.5) × 1016 cm-2, respectively. The relation scales linearly for possible higher excitation temperatures. Our observations are consistent with an ortho-to-para-ammonia ratio of unity, implying that the ammonia formation temperature exceeds ~30 K. In the context of a model with a molecular ring that

  10. ORIGEN-ARP Cross-Section Libraries for Magnox, Advanced Gas-Cooled, and VVER Reactor Designs

    SciTech Connect

    Murphy, BD

    2004-03-10

    Cross-section libraries for the ORIGEN-ARP system were extended to include four non-U.S. reactor types: the Magnox reactor, the Advanced Gas-Cooled Reactor, the VVER-440, and the VVER-1000. Typical design and operational parameters for these four reactor types were determined by an examination of a variety of published information sources. Burnup simulation models of the reactors were then developed using the SAS2H sequence from the Oak Ridge National Laboratory SCALE code system. In turn, these models were used to prepare the burnup-dependent cross-section libraries suitable for use with ORIGEN-ARP. The reactor designs together with the development of the SAS2H models are described, and a small number of validation results using spent-fuel assay data are reported.

  11. Broadening the Spectrum of Actin-Based Protrusive Activity Mediated by Arp2/3 Complex-Facilitated Polymerization: Motility of Cytoplasmic Ridges and Tubular Projections

    PubMed Central

    Henson, John H.; Gianakas, Anastasia D.; Henson, Lauren H.; Lakin, Christina L.; Voss, Meagen K.; Bewersdorf, Joerg; Oldenbourg, Rudolf; Morris, Robert L.

    2014-01-01

    Arp2/3 complex-facilitated actin polymerization plays an essential role in a variety of cellular functions including motility, adherence, endocytosis and trafficking. In the present study we employ the sea urchin coelomocyte experimental model system to test the hypotheses that Arp2/3 complex-nucleated actin assembly mediates the motility of two unusual cellular protrusions; the cytoplasmic ridges present during coelomocyte spreading, and inducible, tubular-shaped, and neurite-like projections. Our investigations couple pharmacological manipulation employing inhibitors of actin polymerization and the Arp2/3 complex with a wide array of imaging methods including digitally enhanced phase contrast, DIC and polarization light microscopy of live cells; conventional, confocal and super-resolution light microscopy of fluorescently labeled cells; and scanning and transmission electron microscopy. Taken together, the results of this study indicate that Arp2/3 complex-facilitated actin polymerization underlies the motility of coelomocyte cytoplasmic ridges and tubular projections, that these processes are related to each other, and that they have been preliminarily identified in other cell types. The results also highlight the broad spectrum of actin-based protrusive activities dependent on the Arp2/3 complex and provide additional insights into the pervasive nature of this ubiquitous actin nucleator. Furthermore we provide the first evidence of a possible mechanistic difference between the impacts of the small molecule drugs BDM and CK666 on the Arp2/3 complex. PMID:25111797

  12. CHEMICALLY DISTINCT NUCLEI AND OUTFLOWING SHOCKED MOLECULAR GAS IN Arp 220

    SciTech Connect

    Tunnard, R.; Greve, T. R.; Garcia-Burillo, S.; Fuente, A.; Usero, A.; Planesas, P.; Carpio, J. Graciá; Hailey-Dunsheath, S.; Sturm, E.; Fischer, J.; González-Alfonso, E.; Neri, R.

    2015-02-10

    We present the results of interferometric spectral line observations of Arp 220 at 3.5 mm and 1.2 mm from the Plateau de Bure Interferometer, imaging the two nuclear disks in H{sup 13}CN(1-0) and (3-2), H{sup 13}CO{sup +}(1-0) and (3-2), and HN{sup 13}C(3-2) as well as SiO(2-1) and (6-5), HC{sup 15}N(3-2), and SO(6{sub 6}-5{sub 5}). The gas traced by SiO(6-5) has a complex and extended kinematic signature including a prominent P Cygni profile, almost identical to previous observations of HCO{sup +}(3-2). Spatial offsets 0.''1 north and south of the continuum center in the emission and absorption of the SiO(6-5) P Cygni profile in the western nucleus (WN) imply a bipolar outflow, delineating the northern and southern edges of its disk and suggesting a disk radius of ∼40 pc, consistent with that found by ALMA observations of Arp 220. We address the blending of SiO(6-5) and H{sup 13}CO{sup +}(3-2) by considering two limiting cases with regards to the H{sup 13}CO{sup +} emission throughout our analysis. Large velocity gradient modeling is used to constrain the physical conditions of the gas and to infer abundance ratios in the two nuclei. Our most conservative lower limit on the [H{sup 13}CN]/[H{sup 13}CO{sup +}] abundance ratio is 11 in the WN, compared with 0.10 in the eastern nucleus (EN). Comparing these ratios to the literature we argue on chemical grounds for an energetically significant active galactic nucleus in the WN driving either X-ray or shock chemistry, and a dominant starburst in the EN.

  13. Luminous Infrared Galaxies with the Submillimeter Array. III. The Dense Kiloparsec Molecular Concentrations of Arp 299

    NASA Astrophysics Data System (ADS)

    Sliwa, Kazimierz; Wilson, Christine D.; Petitpas, Glen R.; Armus, Lee; Juvela, Mika; Matsushita, Satoki; Peck, Alison B.; Yun, Min S.

    2012-07-01

    We have used high-resolution (~2farcs3) observations of the local (D L = 46 Mpc) luminous infrared galaxy Arp 299 to map out the physical properties of the molecular gas that provides the fuel for its extreme star formation activity. The 12CO J = 3-2, 12CO J = 2-1, and 13CO J = 2-1 lines were observed with the Submillimeter Array, and the short spacings of the 12CO J = 2-1 and J = 3-2 observations have been recovered using the James Clerk Maxwell Telescope single dish observations. We use the radiative transfer code RADEX to estimate the physical properties (density, column density, and temperature) of the different regions in this system. The RADEX solutions of the two galaxy nuclei, IC 694 and NGC 3690, are consistent with a wide range of gas components, from warm moderately dense gas with T kin > 30 K and n(H2) ~ 0.3-3 × 103 cm-3 to cold dense gas with T kin ~ 10-30 K and n(H2) > 3 × 103 cm-3. The overlap region is shown to have a better constrained solution with T kin ~ 10-50 K and n(H2) ~ 1-30 × 103 cm-3. We estimate the gas masses and star formation rates of each region in order to derive molecular gas depletion times. The depletion times of all regions (20-50 Myr) are found to be about two orders of magnitude lower than those of normal spiral galaxies. This rapid depletion time can probably be explained by a high fraction of dense gas on kiloparsec scales in Arp 299. We estimate the CO-to-H2 factor, αco to be 0.4 ± 0.3(3 × 10-4/x CO) M⊙ (K km s-1 pc2)-1 for the overlap region. This value agrees well with values determined previously for more advanced merger systems.

  14. LUMINOUS INFRARED GALAXIES WITH THE SUBMILLIMETER ARRAY. III. THE DENSE KILOPARSEC MOLECULAR CONCENTRATIONS OF Arp 299

    SciTech Connect

    Sliwa, Kazimierz; Wilson, Christine D.; Petitpas, Glen R.; Armus, Lee; Juvela, Mika; Matsushita, Satoki; Peck, Alison B.; Yun, Min S. E-mail: wilson@physics.mcmaster.ca E-mail: lee@ipac.caltech.edu E-mail: satoki@asiaa.sinica.edu.tw E-mail: myun@astro.umass.edu

    2012-07-01

    We have used high-resolution ({approx}2.''3) observations of the local (D{sub L} = 46 Mpc) luminous infrared galaxy Arp 299 to map out the physical properties of the molecular gas that provides the fuel for its extreme star formation activity. The {sup 12}CO J = 3-2, {sup 12}CO J = 2-1, and {sup 13}CO J = 2-1 lines were observed with the Submillimeter Array, and the short spacings of the {sup 12}CO J = 2-1 and J = 3-2 observations have been recovered using the James Clerk Maxwell Telescope single dish observations. We use the radiative transfer code RADEX to estimate the physical properties (density, column density, and temperature) of the different regions in this system. The RADEX solutions of the two galaxy nuclei, IC 694 and NGC 3690, are consistent with a wide range of gas components, from warm moderately dense gas with T{sub kin} > 30 K and n(H{sub 2}) {approx} 0.3-3 Multiplication-Sign 10{sup 3} cm{sup -3} to cold dense gas with T{sub kin} {approx} 10-30 K and n(H{sub 2}) > 3 Multiplication-Sign 10{sup 3} cm{sup -3}. The overlap region is shown to have a better constrained solution with T{sub kin} {approx} 10-50 K and n(H{sub 2}) {approx} 1-30 Multiplication-Sign 10{sup 3} cm{sup -3}. We estimate the gas masses and star formation rates of each region in order to derive molecular gas depletion times. The depletion times of all regions (20-50 Myr) are found to be about two orders of magnitude lower than those of normal spiral galaxies. This rapid depletion time can probably be explained by a high fraction of dense gas on kiloparsec scales in Arp 299. We estimate the CO-to-H{sub 2} factor, {alpha}{sub co} to be 0.4 {+-} 0.3(3 Multiplication-Sign 10{sup -4}/x{sub CO}) M{sub Sun} (K km s{sup -1} pc{sup 2}){sup -1} for the overlap region. This value agrees well with values determined previously for more advanced merger systems.

  15. UNCOVERING THE DEEPLY EMBEDDED ACTIVE GALACTIC NUCLEUS ACTIVITY IN THE NUCLEAR REGIONS OF THE INTERACTING GALAXY Arp 299

    SciTech Connect

    Alonso-Herrero, A.; Roche, P. F.; Esquej, P.; Colina, L.; González-Martín, O.; Ramos Almeida, C.; Asensio Ramos, A.; Rodríguez Espinosa, J. M.; Alvarez, C.; Pereira-Santaella, M.; Levenson, N. A.; Packham, C.; Mason, R. E.; Aretxaga, I.; Díaz-Santos, T.; Perlman, E.; Telesco, C. M.

    2013-12-10

    We present mid-infrared (MIR) 8-13 μm spectroscopy of the nuclear regions of the interacting galaxy Arp 299 (IC 694+NGC 3690) obtained with CanariCam (CC) on the 10.4 m Gran Telescopio Canarias (GTC). The high angular resolution (∼0.''3-0.''6) of the data allows us to probe nuclear physical scales between 60 and 120 pc, which is a factor of 10 improvement over previous MIR spectroscopic observations of this system. The GTC/CC spectroscopy displays evidence of deeply embedded active galactic nucleus (AGN) activity in both nuclei. The GTC/CC nuclear spectrum of NGC 3690/Arp 299-B1 can be explained as emission from AGN-heated dust in a clumpy torus with both a high covering factor and high extinction along the line of sight. The estimated bolometric luminosity of the AGN in NGC 3690 is 3.2 ± 0.6 × 10{sup 44} erg s{sup –1}. The nuclear GTC/CC spectrum of IC 694/Arp 299-A shows 11.3 μm polycyclic aromatic hydrocarbon emission stemming from a deeply embedded (A{sub V} ∼ 24 mag) region of less than 120 pc in size. There is also a continuum-emitting dust component. If associated with the putative AGN in IC 694, we estimate that it would be approximately five times less luminous than the AGN in NGC 3690. The presence of dual AGN activity makes Arp 299 a good example to study such phenomena in the early coalescence phase of interacting galaxies.

  16. Tolerance of ARPE 19 cells to organophosphorus pesticide chlorpyrifos is limited to concentration and time of exposure.

    PubMed

    Gomathy, Narayanan; Sumantran, Venil N; Shabna, A; Sulochana, K N

    2015-01-01

    Age related macular degeneration is a blinding disease common in elder adults. The prevalence of age related macular degeneration has been found to be 1.8% in the Indian population. Organophosphates are widely used insecticides with well documented neurological effects, and the persistent nature of these compounds in the body results in long term health effects. Farmers exposed to organophosphorus pesticides in USA had an earlier onset of age related macular degeneration when compared to unexposed controls. A recent study found significant levels of an organophosphate, termed chlorpyrifos, in the blood samples of Indian farmers. Therefore, in understanding the link between age related macular degeneration and chlorpyrifos, the need for investigation is important. Our data show that ARPE-19 (retinal pigment epithelial cells) exhibit a cytoprotective response to chlorpyrifos as measured by viability, mitochondrial membrane potential, superoxide dismutase activity, and increased levels of glutathione peroxidase and reduced glutathione, after 24 h exposure to chlorpyrifos. However, this cytoprotective response was absent in ARPE-19 cells exposed to the same range of concentrations of chlorpyrifos for 48 h. These results have physiological significance, since HPLC analysis showed that effects of chlorpyrifos were mediated through its entry into ARPE-19 cells. HPLC analysis also showed that chlorpyrifos remained stable, as we recovered up to 80% of the chlorpyrifos added to 6 different ocular tissues. PMID:25619908

  17. The INO80 Complex Requires the Arp5-Ies6 Subcomplex for Chromatin Remodeling and Metabolic Regulation

    PubMed Central

    Yao, Wei; King, Devin A.; Beckwith, Sean L.; Gowans, Graeme J.; Yen, Kuangyu; Zhou, Coral

    2016-01-01

    ATP-dependent chromatin remodeling complexes are essential for transcription regulation, and yet it is unclear how these multisubunit complexes coordinate their activities to facilitate diverse transcriptional responses. In this study, we found that the conserved Arp5 and Ies6 subunits of the Saccharomyces cerevisiae INO80 chromatin-remodeler form an abundant and distinct subcomplex in vivo and stimulate INO80-mediated activity in vitro. Moreover, our genomic studies reveal that the relative occupancy of Arp5-Ies6 correlates with nucleosome positioning at transcriptional start sites and expression levels of >1,000 INO80-regulated genes. Notably, these genes are significantly enriched in energy metabolism pathways. Specifically, arp5Δ, ies6Δ, and ino80Δ mutants demonstrate decreased expression of genes involved in glycolysis and increased expression of genes in the oxidative phosphorylation pathway. Deregulation of these metabolic pathways results in constitutively elevated mitochondrial potential and oxygen consumption. Our results illustrate the dynamic nature of the INO80 complex assembly and demonstrate for the first time that a chromatin remodeler regulates glycolytic and respiratory capacity, thereby maintaining metabolic stability. PMID:26755556

  18. The nature of supernovae 2010O and 2010P in Arp 299 - I. Near-infrared and optical evolution

    NASA Astrophysics Data System (ADS)

    Kankare, E.; Mattila, S.; Ryder, S.; Fraser, M.; Pastorello, A.; Elias-Rosa, N.; Romero-Cañizales, C.; Alberdi, A.; Hentunen, V.-P.; Herrero-Illana, R.; Kotilainen, J.; Pérez-Torres, M.-A.; Väisänen, P.

    2014-05-01

    We present near-infrared and optical photometry, plus optical spectroscopy of two stripped-envelope supernovae (SNe) 2010O and 2010P that exploded in two different components of an interacting luminous infrared galaxy Arp 299 within only a few days of one another. SN 2010O is found to be photometrically and spectroscopically similar to many normal Type Ib SNe and our multiwavelength observations of SN 2010P suggest it to be a Type IIb SN. No signs of clear hydrogen features or interaction with the circumstellar medium are evident in the optical spectrum of SN 2010P. We derive estimates for the host galaxy line-of-sight extinctions for both SNe, based on both light curve and spectroscopic comparison finding consistent results. These methods are also found to provide much more robust estimates of the SN host galaxy reddening than the commonly used empirical relations between extinction and equivalent width of Na I D absorption features. The SN observations also suggest that different extinction laws are present in different components of Arp 299. For completeness, we study high-resolution pre-explosion images of Arp 299 and find both SNe to be close to, but not coincident with, extended sources that are likely massive clusters. A very simple model applied to the bolometric light curve of SN 2010O implies a rough estimate for the explosion parameters of Ek ≈ 3 × 1051 erg, Mej ≈ 2.9 M⊙ and MNi ≈ 0.16 M⊙.

  19. Evaluation of an ARPS-based canopy flow modeling system for use in future operational smoke prediction efforts

    NASA Astrophysics Data System (ADS)

    Kiefer, M. T.; Zhong, S.; Heilman, W. E.; Charney, J. J.; Bian, X.

    2013-06-01

    Efforts to develop a canopy flow modeling system based on the Advanced Regional Prediction System (ARPS) model are discussed. The standard version of ARPS is modified to account for the effect of drag forces on mean and turbulent flow through a vegetation canopy, via production and sink terms in the momentum and subgrid-scale turbulent kinetic energy (TKE) equations. Additionally, a downward decaying net radiation profile inside the canopy is used to account for the attenuation of net radiation by vegetation elements. As a critical step in the model development process, simulations performed with the new canopy model, termed ARPS-CANOPY, are examined and compared to observations from the Canopy Horizontal Array Turbulence Study (CHATS) experiment. Comparisons of mean and turbulent flow properties in a statistically homogeneous atmosphere are presented for two cases, one when the trees are dormant without leaves and another when the trees are full of mature leaves. The model is shown to reproduce the shape of the vertical profiles of mean wind, temperature, and TKE observed during the CHATS experiment, with errors generally smaller in the afternoon and in the case with stronger mean flow. Sensitivity experiments with relatively coarse (90 m) horizontal grid spacing retain the overall mean profile shapes and diurnal trends seen in the finer-resolution simulations. The work described herein is part of a larger effort to develop predictive tools for close-range (on the order of 1 km from the source) smoke dispersion from low-intensity fires within forested areas.

  20. Perinuclear Arp2/3-driven actin polymerization enables nuclear deformation to facilitate cell migration through complex environments

    PubMed Central

    Thiam, Hawa-Racine; Vargas, Pablo; Carpi, Nicolas; Crespo, Carolina Lage; Raab, Matthew; Terriac, Emmanuel; King, Megan C.; Jacobelli, Jordan; Alberts, Arthur S.; Stradal, Theresia; Lennon-Dumenil, Ana-Maria; Piel, Matthieu

    2016-01-01

    Cell migration has two opposite faces: although necessary for physiological processes such as immune responses, it can also have detrimental effects by enabling metastatic cells to invade new organs. In vivo, migration occurs in complex environments and often requires a high cellular deformability, a property limited by the cell nucleus. Here we show that dendritic cells, the sentinels of the immune system, possess a mechanism to pass through micrometric constrictions. This mechanism is based on a rapid Arp2/3-dependent actin nucleation around the nucleus that disrupts the nuclear lamina, the main structure limiting nuclear deformability. The cells' requirement for Arp2/3 to pass through constrictions can be relieved when nuclear stiffness is decreased by suppressing lamin A/C expression. We propose a new role for Arp2/3 in three-dimensional cell migration, allowing fast-moving cells such as leukocytes to rapidly and efficiently migrate through narrow gaps, a process probably important for their function. PMID:26975831

  1. Perinuclear Arp2/3-driven actin polymerization enables nuclear deformation to facilitate cell migration through complex environments.

    PubMed

    Thiam, Hawa-Racine; Vargas, Pablo; Carpi, Nicolas; Crespo, Carolina Lage; Raab, Matthew; Terriac, Emmanuel; King, Megan C; Jacobelli, Jordan; Alberts, Arthur S; Stradal, Theresia; Lennon-Dumenil, Ana-Maria; Piel, Matthieu

    2016-01-01

    Cell migration has two opposite faces: although necessary for physiological processes such as immune responses, it can also have detrimental effects by enabling metastatic cells to invade new organs. In vivo, migration occurs in complex environments and often requires a high cellular deformability, a property limited by the cell nucleus. Here we show that dendritic cells, the sentinels of the immune system, possess a mechanism to pass through micrometric constrictions. This mechanism is based on a rapid Arp2/3-dependent actin nucleation around the nucleus that disrupts the nuclear lamina, the main structure limiting nuclear deformability. The cells' requirement for Arp2/3 to pass through constrictions can be relieved when nuclear stiffness is decreased by suppressing lamin A/C expression. We propose a new role for Arp2/3 in three-dimensional cell migration, allowing fast-moving cells such as leukocytes to rapidly and efficiently migrate through narrow gaps, a process probably important for their function. PMID:26975831

  2. Actin Interacts with Dengue Virus 2 and 4 Envelope Proteins.

    PubMed

    Jitoboam, Kunlakanya; Phaonakrop, Narumon; Libsittikul, Sirikwan; Thepparit, Chutima; Roytrakul, Sittiruk; Smith, Duncan R

    2016-01-01

    Dengue virus (DENV) remains a significant public health problem in many tropical and sub-tropical countries worldwide. The DENV envelope (E) protein is the major antigenic determinant and the protein that mediates receptor binding and endosomal fusion. In contrast to some other DENV proteins, relatively few cellular interacting proteins have been identified. To address this issue a co-immuoprecipitation strategy was employed. The predominant co-immunoprecipitating proteins identified were actin and actin related proteins, however the results suggested that actin was the only bona fide interacting partner. Actin was shown to interact with the E protein of DENV 2 and 4, and the interaction between actin and DENV E protein was shown to occur in a truncated DENV consisting of only domains I and II. Actin was shown to decrease during infection, but this was not associated with a decrease in gene transcription. Actin-related proteins also showed a decrease in expression during infection that was not transcriptionally regulated. Cytoskeletal reorganization was not observed during infection, suggesting that the interaction between actin and E protein has a cell type specific component. PMID:27010925

  3. Actin Interacts with Dengue Virus 2 and 4 Envelope Proteins

    PubMed Central

    Jitoboam, Kunlakanya; Phaonakrop, Narumon; Libsittikul, Sirikwan; Thepparit, Chutima; Roytrakul, Sittiruk; Smith, Duncan R.

    2016-01-01

    Dengue virus (DENV) remains a significant public health problem in many tropical and sub-tropical countries worldwide. The DENV envelope (E) protein is the major antigenic determinant and the protein that mediates receptor binding and endosomal fusion. In contrast to some other DENV proteins, relatively few cellular interacting proteins have been identified. To address this issue a co-immuoprecipitation strategy was employed. The predominant co-immunoprecipitating proteins identified were actin and actin related proteins, however the results suggested that actin was the only bona fide interacting partner. Actin was shown to interact with the E protein of DENV 2 and 4, and the interaction between actin and DENV E protein was shown to occur in a truncated DENV consisting of only domains I and II. Actin was shown to decrease during infection, but this was not associated with a decrease in gene transcription. Actin-related proteins also showed a decrease in expression during infection that was not transcriptionally regulated. Cytoskeletal reorganization was not observed during infection, suggesting that the interaction between actin and E protein has a cell type specific component. PMID:27010925

  4. The Unphosphorylated EIIANtr Protein Represses the Synthesis of Alkylresorcinols in Azotobacter vinelandii

    PubMed Central

    Muriel-Millán, Luis Felipe; Moreno, Soledad; Romero, Yanet; Bedoya-Pérez, Leidy Patricia; Castañeda, Miguel; Segura, Daniel; Espín, Guadalupe

    2015-01-01

    Upon encystment induction, Azotobacter vinelandii produces the phenolic lipids alkylresorcinols (ARs) that are structural components of the cysts. The enzymes responsible for the ARs synthesis are encoded in the arsABCD operon, whose expression is activated by ArpR. The transcription of arpR is initiated from an RpoS dependent promoter. The nitrogen-related phosphotransferase system (PTSNtr) is a global regulatory system present in Gram negative bacteria. It comprises the EINtr, NPr and EIIANtr proteins encoded by ptsP, ptsO and ptsN genes respectively. These proteins participate in a phosphoryl-group transfer from phosphoenolpyruvate to protein EIIANtr via the phosphotransferases EINtr and NPr. In A. vinelandii, the non-phosphorylated form of EIIANtr was previously shown to repress the synthesis of poly-ß-hydroxybutyrate. In this work, we show that PTSNtr also regulates the synthesis of ARs. In a strain that carries unphosphorylated EIIANtr, the expression of arpR was reduced, while synthesis of ARs and transcription of arsA were almost abrogated. The expression of arpR from an RpoS-independent promoter in this strain restored the ARs synthesis. Taken together these results indicate that unphosphorylated EIIANtr negatively affects activation of arpR transcription by RpoS. PMID:25642700

  5. The nature of supernovae 2010O and 2010P in Arp 299 - II. Radio emission

    NASA Astrophysics Data System (ADS)

    Romero-Cañizales, C.; Herrero-Illana, R.; Pérez-Torres, M. A.; Alberdi, A.; Kankare, E.; Bauer, F. E.; Ryder, S. D.; Mattila, S.; Conway, J. E.; Beswick, R. J.; Muxlow, T. W. B.

    2014-05-01

    We report radio observations of two stripped-envelope supernovae (SNe), 2010O and 2010P, which exploded within a few days of each other in the luminous infrared galaxy Arp 299. Whilst SN 2010O remains undetected at radio frequencies, SN 2010P was detected (with an astrometric accuracy better than 1 milli arcsec in position) in its optically thin phase in epochs ranging from ˜1 to ˜3 yr after its explosion date, indicating a very slow radio evolution and a strong interaction of the SN ejecta with the circumstellar medium. Our late-time radio observations towards SN 2010P probe the dense circumstellar envelope of this SN, and imply dot{M} [ {M_{⊙} yr^{-1}}] / v_{wind} [10 km s^{-1}] =(3.0-5.1) × 10-5, with a 5 GHz peak luminosity of ˜1.2 × 1027 erg s- 1 Hz- 1 on day ˜464 after explosion. This is consistent with a Type IIb classification for SN 2010P, making it the most distant and most slowly evolving Type IIb radio SN detected to date.

  6. Probing the magnetic field of the nearby galaxy pair Arp 269

    NASA Astrophysics Data System (ADS)

    Nikiel-Wroczyński, B.; Jamrozy, M.; Soida, M.; Urbanik, M.; Knapik, J.

    2016-06-01

    We present a multiwavelength radio study of the nearby galaxy pair Arp 269 (NGC 4490/85). High sensitivity to extended structures gained by using the merged interferometric and single-dish maps allowed us to reveal a previously undiscovered extension of the radio continuum emission. Its direction is significantly different from that of the neutral gas tail, suggesting that different physical processes might be involved in their creation. The population of radio-emitting electrons is generally young, signifying an ongoing, vigorous star formation - this claim is supported by strong magnetic fields (over 20 μG), similar to the ones found in much larger spiral galaxies. From the study of the spectral energy distribution, we conclude that the electron population in the intergalactic bridge between member galaxies originates from the disc areas, and therefore its age (approximately 3.7-16.9 Myr, depending on the model used) reflects the time-scale of the interaction. We have also discovered an angularly near compact steep source - which is a member of a different galaxy pair - at a redshift of approximately 0.125.

  7. Local Data Integration in East Central Florida Using the ARPS Data Analysis System

    NASA Technical Reports Server (NTRS)

    Case, Jonathan; Manobianco, John

    1998-01-01

    This paper describes the Applied Meteorology Unit's (AMU) efforts to configure, implement, and test a version of the Advanced Regional Prediction System (ARPS) Data Analysis System (ADAS; Brewster 1996) that assimilates all available data within 250 km of the Kennedy Space Center (KSC) and the Eastern Range at Cape Canaveral Air Station (CCAS). The objective for running a Local Data Integration System (LDIS) such as ADAS is to generate products which may enhance weather nowcasts and short-range (less than 6 h) forecasts issued in support of ground and aerospace operations at KSC/CCAS. A LDIS such as ADAS has the potential to provide added value because it combines observational data to produce gridded analyses of temperature, wind, and moisture (including clouds) and diagnostic quantities such as vorticity, divergence, etc. at specified temporal and spatial resolutions. In this regard, a LDTS along with suitable visualization tools may provide users with a ignore complete and comprehensive understanding of evolving weather than could be developed by individually examining the disparate data sets over the same area and time. The AMU implemented a working prototype of the ADAS which does not run in real-time. Instead, the AMU is evaluating ADAS through post-analyses of weather events for a warm and cool season case. The case studies were chosen to investigate the capabilities and limitations of a LDIS such as ADAS including the impact of non-incorporation of specific data sources on the utility of the subsequent analyses.

  8. THE MASS OF THE BLACK HOLE IN Arp 151 FROM BAYESIAN MODELING OF REVERBERATION MAPPING DATA

    SciTech Connect

    Brewer, Brendon J.; Treu, Tommaso; Pancoast, Anna; Bennert, Vardha N.; Barth, Aaron J.; Bentz, Misty C.; Filippenko, Alexei V.; Greene, Jenny E.; Malkan, Matthew A.; Woo, Jong-Hak

    2011-06-01

    Supermassive black holes are believed to be ubiquitous at the centers of galaxies. Measuring their masses is extremely challenging yet essential for understanding their role in the formation and evolution of cosmic structure. We present a direct measurement of the mass of a black hole in an active galactic nucleus (Arp 151) based on the motion of the gas responsible for the broad emission lines. By analyzing and modeling spectroscopic and photometric time series, we find that the gas is well described by a disk or torus with an average radius of 3.99 {+-} 1.25 light days and an opening angle of 68.9{sup +21.4}{sub -17.2} deg, viewed at an inclination angle of 67.8 {+-} 7.8 deg (that is, closer to face-on than edge-on). The black hole mass is inferred to be 10{sup 6.51{+-}0.28} M{sub sun}. The method is fully general and can be used to determine the masses of black holes at arbitrary distances, enabling studies of their evolution over cosmic time.

  9. Long-term Failure Prediction based on an ARP Model of Global Risk Network

    NASA Astrophysics Data System (ADS)

    Lin, Xin; Moussawi, Alaa; Szymanski, Boleslaw; Korniss, Gyorgy

    Risks that threaten modern societies form an intricately interconnected network. Hence, it is important to understand how risk materializations in distinct domains influence each other. In the paper, we study the global risks network defined by World Economic Forum experts in the form of Stochastic Block Model. We model risks as Alternating Renewal Processes with variable intensities driven by hidden values of exogenous and endogenous failure probabilities. Based on the expert assessments and historical status of each risk, we use Maximum Likelihood Evaluation to find the optimal model parameters and demonstrate that the model considering network effects significantly outperforms the others. In the talk, we discuss how the model can be used to provide quantitative means for measuring interdependencies and materialization of risks in the network. We also present recent results of long-term predictions in the form of predicated distributions of materializations over various time periods. Finally we show how the simulation of ARP's enables us to probe limits of the predictability of the system parameters from historical data and ability to recover hidden variable. Supported in part by DTRA, ARL NS-CTA.

  10. DECONTAMINATION FACTORS AND FILTRATION FLUX IMPACT TO ARP AT REDUCED MST CONCENTRATION

    SciTech Connect

    Hobbs, D.

    2012-06-27

    Tank Farm and Closure Engineering is evaluating changes to the Actinide Removal Process facility operations to decrease the MST concentration from 0.4 g/L to 0.2 g/L and the contact time from 12 hours to between 6 and 8 hours. For this evaluation, SRNL reviewed previous datasets investigating the performance of MST at 0.2 g/L in salt solutions ranging from 4.5 to 7.5 M in sodium concentration. In general, reducing the MST concentration from 0.4 to 0.2 g/L and increasing the ionic strength from 4.5 to 7.5 M in sodium concentration will decrease the measured decontamination factors for plutonium, neptunium, uranium and strontium. The decontamination factors as well as single standard deviation values for each sorbate are reported. These values are applicable within the sorbate and sodium concentrations used in the experimental measurements. Decreasing the MST concentration in the ARP from 0.4 g/L to 0.2 g/L will produce an increase in the filter flux, and could lead to longer operating times between filter cleaning. The increase in flux is a function of a number of operating parameters, and is difficult to quantify. However, it is estimated that the reduction in MST could result in a reduction of filtration time of up to 20%.

  11. The zinc ionophore clioquinol reverses autophagy arrest in chloroquine-treated ARPE-19 cells and in APP/mutant presenilin-1-transfected Chinese hamster ovary cells.

    PubMed

    Seo, Bo-Ra; Lee, Sook-Jeong; Cho, Kyung Sook; Yoon, Young Hee; Koh, Jae-Young

    2015-12-01

    Arrested autophagy may contribute to the pathogenesis of Alzheimer's disease. Because we found that chloroquine (CQ) causes arrested autophagy but clioquinol (ClioQ), a zinc ionophore, activates autophagic flux, in the present study, we examined whether ClioQ can overcome arrested autophagy induced by CQ or mutant presenilin-1 (mPS1). CQ induced vacuole formation and cell death in adult retinal pigment epithelial (ARPE-19) cells, but co-treatment with ClioQ attenuated CQ-associated toxicity in a zinc-dependent manner. Increases in lysosome dilation and blockage of autophagic flux by CQ were also markedly attenuated by ClioQ treatment. Interestingly, CQ increased lysosomal pH in amyloid precursor protein (APP)/mPS1-expressing Chinese hamster ovary 7WΔE9 (CHO-7WΔE9) cell line, and ClioQ partially re-acidified lysosomes. Furthermore, accumulation of amyloid-β (Aβ) oligomers in CHO-7WΔE9 cells was markedly attenuated by ClioQ. Moreover, intracellular accumulation of exogenously applied fluorescein isothiocyanate-conjugated Aβ(1-42) was also increased by CQ but was returned to control levels by ClioQ. These results suggest that modulation of lysosomal functions by manipulating lysosomal zinc levels may be a useful strategy for clearing intracellular Aβ oligomers. PMID:26453000

  12. Paxillin, a novel controller in the signaling of estrogen to FAK/N-WASP/Arp2/3 complex in breast cancer cells.

    PubMed

    Shortrede, Jorge Eduardo; Uzair, Ivonne Denise; Neira, Flavia Judith; Flamini, Marina Inés; Sanchez, Angel Matías

    2016-07-15

    Breast cancer is the major cause of cancer-related death in women. Its treatment is particularly difficult when metastasis occurs. The ability of cancer cells to move and invade the surrounding environment is the basis of local and distant metastasis. Cancer cells are able to remodel the actin cytoskeleton, which requires the recruitment of numerous structural and regulatory proteins that modulate actin filaments dynamics, including Paxillin or the Neural Wiskott-Aldrich Syndrome Protein (N-WASP). We show that 17-β estradiol (E2) induces phosphorylation of Paxillin and its translocation toward membrane sites where focal adhesion complexes are assembled. This cascade is triggered by a Gαi1/Gβ protein-dependent signaling of estrogen receptor α (ERα) to c-Src, focal adhesion kinase (FAK) and Paxillin. Within this complex, activated Paxillin recruits the small GTPase Cdc42, which triggers N-WASP phosphorylation. This results in the redistribution of Arp2/3 complexes at sites where membrane structures related to cell movement are formed. Recruitment of Paxillin, Cdc42 and N-WASP is necessary for cell adhesion, migration and invasion induced by E2 in breast cancer cells. In parallel, we investigated whether Raloxifene (RAL), a selective estrogen receptor modulator (SERMs), could inhibit or revert the effects of E2 in breast cancer cell movement. We found that, in the presence of E2, RAL acts as an ER antagonist and displays an inhibitory effect on estrogen-promoted cell adhesion and migration via FAK/Paxillin/N-WASP. Our findings identify an original mechanism through which estrogen regulates breast cancer cell motility and invasion via Paxillin. These results may have clinical relevance for the development of new therapeutic strategies for cancer treatment. PMID:27095481

  13. HIGH-RESOLUTION RADIO CONTINUUM MEASUREMENTS OF THE NUCLEAR DISKS OF Arp 220

    SciTech Connect

    Barcos-Muñoz, L.; Evans, A. S.; Privon, G. C.; Stierwalt, S.; Leroy, A. K.; Condon, J.; Reichardt, A.; Armus, L.; Mazzarella, J. M.; Murphy, E. J.; Meier, D. S.; Momjian, E.; Ott, J.; Sakamoto, K.; Sanders, D. B.; Schinnerer, E.; Walter, F.; Surace, J. A.; Thompson, T. A.

    2015-01-20

    We present new Karl G. Jansky Very Large Array radio continuum images of the nuclei of Arp 220, the nearest ultra-luminous infrared galaxy. These new images have both the angular resolution to study the detailed morphologies of the two nuclei that power the galaxy merger and sensitivity to a wide range of spatial scales. At 33 GHz, we achieve a resolution of 0.''081 × 0.''063 (29.9 × 23.3 pc) and resolve the radio emission surrounding both nuclei. We conclude from the decomposition of the radio spectral energy distribution that a majority of the 33 GHz emission is synchrotron radiation. The spatial distributions of radio emission in both nuclei are well described by exponential profiles. These have deconvolved half-light radii (R {sub 50d}) of 51 and 35 pc for the eastern and western nuclei, respectively, and they match the number density profile of radio supernovae observed with very long baseline interferometry. This similarity might be due to the fast cooling of cosmic rays electrons caused by the presence of a strong (∼mG) magnetic field in this system. We estimate extremely high molecular gas surface densities of 2.2{sub −1.0}{sup +2.1}×10{sup 5} (east) and 4.5{sub −1.9}{sup +4.5}×10{sup 5} (west) M {sub ☉} pc{sup –2}, corresponding to total hydrogen column densities of N {sub H} = 2.7{sub −1.2}{sup +2.7}×10{sup 25} (east) and 5.6{sub −2.4}{sup +5.5}×10{sup 25} cm{sup –2} (west). The implied gas volume densities are similarly high, n{sub H{sub {sub 2}}}∼3.8{sub −1.6}{sup +3.8}×10{sup 4} (east) and ∼11{sub −4.5}{sup +12}×10{sup 4} cm{sup –3} (west). We also estimate very high luminosity surface densities of Σ{sub IR}∼4.2{sub −0.7}{sup +1.6}×10{sup 13} (east) and Σ{sub IR}∼9.7{sub −2.4}{sup +3.7}×10{sup 13} (west) L{sub ⊙} kpc{sup −2}, and star formation rate surface densities of Σ{sub SFR} ∼ 10{sup 3.7} {sup ±} {sup 0.1} (east) and Σ{sub SFR} ∼ 10{sup 4.1} {sup ±} {sup 0.1}(west) M {sub ☉} yr{sup

  14. ARPES Study on the Strongly Correlated Iron Chalcogenides Fe1+ySexTe1-x

    NASA Astrophysics Data System (ADS)

    Liu, Zhongkai

    2014-03-01

    The level of electronic correlation has been one of the key questions in understanding the nature of iron-based superconductivity. Using Angle Resolved Photoemission Spectroscopy (ARPES), we systematically investigated the correlation level in the iron chalcogenide family Fe1+ySexTe1-x. For the parent compound Fe1.02Te, we discovered ``peak-dip-hump'' spectra with heavily renormalized quasiparticles in the low temperature antiferromagnetic (AFM) state, characteristic of coherent polarons seen in other correlated materials with complex electronic and lattice interactions. As the temperature (or Se ratio x) increases and Fe1.02SexTe1-x is in the paramagnetic (PM) phase, we observed dissociation behavior of polarons, suggestive of connection between the weakening electron-phonon coupling and AFM. Further increase of x leads to an incoherent to coherent crossover in the electronic structure, indicating a reduction in the electronic correlation as the superconductivity emerges. Furthermore, the reduction of the electronic correlation in Fe1+ySexTe1-x evolves in an orbital-dependent way, where the dxy orbital is influenced most significantly. At the other end of the phase diagram (FeSe) where the single crystal is not stable, we have studied the MBE-grown thin film which also reveals orbital-dependent strong correlation in the electronic structure. Our findings provide a quantitative comprehension on the correlation level and its evolution on the phase diagram of Fe1+ySexTe1-x. We discuss the physical scenarios leading to strong correlations and its connection to superconductivity.

  15. Inhibition of phagocytic activity of ARPE-19 cells by free radical mediated oxidative stress.

    PubMed

    Olchawa, Magdalena M; Pilat, Anna K; Szewczyk, Grzegorz M; Sarna, Tadeusz Jan

    2016-08-01

    Oxidative stress is a main factor responsible for key changes leading to the onset of age-related macular degeneration (ARMD) that occur in the retinal pigment epithelium (RPE), which is involved in phagocytosis of photoreceptor outer segments (POS). In this study, hydrogen peroxide (H2O2), H2O2 and iron ions (Fe) or rose Bengal (RB) in the presence of NADH and Fe were used to model free radical mediated oxidative stress to test if free radicals and singlet oxygen have different efficiency to inhibit phagocytosis of ARPE-19 cells. Free radical mediated oxidative stress was confirmed by HPLC-EC(Hg) measurements of cholesterol hydroperoxides in treated cells. Electron paramagnetic resonance (EPR) spin trapping was employed to detect superoxide anion. Cell survival was analyzed by the MTT assay. Specific phagocytosis of fluorescein-5-isothiocyanate-labeled POS and non-specific phagocytosis of fluorescent beads were measured by flow cytometry. HPLC analysis of cells photosensitized with RB in the presence of NADH and Fe indicated substantial increase in formation of free radical-dependent 7α/7β-hydroperoxides. EPR spin trapping confirmed the photogeneration of superoxide anion in samples enriched with RB, NADH and Fe. For all three protocols sub-lethal oxidative stress induced significant inhibition of the specific phagocytosis of POS. In contrast, non-specific phagocytosis was inhibited only by H2O2 or H2O2 and Fe treatment. Inhibition of phagocytosis was transient and recoverable by 24 h. These results suggest that free radicals may exert similar to singlet oxygen efficiency in inhibiting phagocytosis of RPE cells, and that the effect depends on the location where initial reactive species are formed. PMID:27225587

  16. Tidal bridge and tidal dwarf candidates in the interacting system Arp194

    NASA Astrophysics Data System (ADS)

    Zasov, Anatoly V.; Saburova, Anna S.; Egorov, Oleg V.; Afanasiev, Viktor L.

    2016-11-01

    Arp194 is a system of recently collided galaxies, where the southern galaxy (S) passed through the gaseous disc of the northern galaxy (N) which in turn consists of two close components. This system is of special interest due to the presence of regions of active star formation in the bridge between galaxies, the brightest of which (the region A) has a size of at least 4 kpc. We obtained three spectral slices of the system for different slit positions at the 6-m telescope of SAO RAS. We estimated the radial distribution of line-of-sight velocity and velocity dispersion as well as the intensities of emission lines and oxygen abundance 12 + log (O/H). The gas in the bridge is only partially mixed chemically and spatially: we observe the O/H gradient with the galactocentric distances both from S and N galaxies and a high dispersion of O/H in the outskirts of N-galaxy. Velocity dispersion of the emission-line gas is the lowest in the star-forming sites of the bridge and exceeds 50-70 km s-1 in the disturbed region of N-galaxy. Based on the SDSS photometrical data and our kinematical profiles we measured the masses of stellar population and the dynamical masses of individual objects. We confirm that the region A is the gravitationally bound tidal dwarf with the age of 107-108 yr, which is falling on to the parent S-galaxy. There is no evidence of the significant amount of dark matter in this dwarf galaxy.

  17. Dynamics of H2O2 Availability to ARPE-19 Cultures in Models of Oxidative Stress

    PubMed Central

    Kaczara, Patrycja; Sarna, Tadeusz; Burke, Janice M.

    2010-01-01

    Oxidative injury to cells such as the retinal pigment epithelium (RPE) is often modeled using H2O2-treated cultures, but H2O2 concentrations are not sustained in culture medium. Here medium levels of H2O2 and cytotoxicity were analyzed in ARPE-19 cultures following H2O2 delivery as a single pulse or with continuous generation using glucose oxidase (GOx). When added as a pulse, H2O2 is rapidly depleted (within 2 hr); cytotoxicity at 24, determined by the MTT assay for mitochondrial function, is unaffected by medium replacement at 2 hr. Continuous generation of H2O2 produces complex outcomes. At low GOx concentrations, H2O2 levels are sustained by conditions in which generation matches depletion, but when GOx concentrations produce cytotoxic levels of H2O2, oxidant depletion accelerates. Acceleration results partly from the release of contents from oxidant damaged cells as indicated by testing depletion after controlled membrane disruption with detergents. Cytotoxicity analyses show that cells can tolerate short exposure to high H2O2 doses delivered as a pulse but are susceptible to lower chronic doses. The results provide broadly applicable guidance for using GOx to produce sustained H2O2 levels in cultured cells. This approach will be specifically useful for modeling chronic stress relevant for RPE aging and have wider value for studying cellular effects of sub-lethal oxidant injury and for evaluating antioxidants that may protect significantly against mild but not lethal stress. PMID:20100568

  18. Afatinib Reduces STAT6 Signaling of Host ARPE-19 Cells Infected with Toxoplasma gondii

    PubMed Central

    Yang, Zhaoshou; Ahn, Hye-Jin; Park, Young-Hoon; Nam, Ho-Woo

    2016-01-01

    Specific gene expressions of host cells by spontaneous STAT6 phosphorylation are major strategy for the survival of intracellular Toxoplasma gondii against parasiticidal events through STAT1 phosphorylation by infection provoked IFN-γ. We determined the effects of small molecules of tyrosine kinase inhibitors (TKIs) on the growth of T. gondii and on the relationship with STAT1 and STAT6 phosphorylation in ARPE-19 cells. We counted the number of T. gondii RH tachyzoites per parasitophorous vacuolar membrane (PVM) after treatment with TKIs at 12-hr intervals for 72 hr. The change of STAT6 phosphorylation was assessed via western blot and immunofluorescence assay. Among the tested TKIs, Afatinib (pan ErbB/EGFR inhibitor, 5 µM) inhibited 98.0% of the growth of T. gondii, which was comparable to pyrimethamine (5 µM) at 96.9% and followed by Erlotinib (ErbB1/EGFR inhibitor, 20 µM) at 33.8% and Sunitinib (PDGFR or c-Kit inhibitor, 10 µM) at 21.3%. In the early stage of the infection (2, 4, and 8 hr after T. gondii challenge), Afatinib inhibited the phosphorylation of STAT6 in western blot and immunofluorescence assay. Both JAK1 and JAK3, the upper hierarchical kinases of cytokine signaling, were strongly phosphorylated at 2 hr and then disappeared entirely after 4 hr. Some TKIs, especially the EGFR inhibitors, might play an important role in the inhibition of intracellular replication of T. gondii through the inhibition of the direct phosphorylation of STAT6 by T. gondii. PMID:26951976

  19. The Formin Diaphanous Regulates Myoblast Fusion through Actin Polymerization and Arp2/3 Regulation.

    PubMed

    Deng, Su; Bothe, Ingo; Baylies, Mary K

    2015-08-01

    The formation of multinucleated muscle cells through cell-cell fusion is a conserved process from fruit flies to humans. Numerous studies have shown the importance of Arp2/3, its regulators, and branched actin for the formation of an actin structure, the F-actin focus, at the fusion site. This F-actin focus forms the core of an invasive podosome-like structure that is required for myoblast fusion. In this study, we find that the formin Diaphanous (Dia), which nucleates and facilitates the elongation of actin filaments, is essential for Drosophila myoblast fusion. Following cell recognition and adhesion, Dia is enriched at the myoblast fusion site, concomitant with, and having the same dynamics as, the F-actin focus. Through analysis of Dia loss-of-function conditions using mutant alleles but particularly a dominant negative Dia transgene, we demonstrate that reduction in Dia activity in myoblasts leads to a fusion block. Significantly, no actin focus is detected, and neither branched actin regulators, SCAR or WASp, accumulate at the fusion site when Dia levels are reduced. Expression of constitutively active Dia also causes a fusion block that is associated with an increase in highly dynamic filopodia, altered actin turnover rates and F-actin distribution, and mislocalization of SCAR and WASp at the fusion site. Together our data indicate that Dia plays two roles during invasive podosome formation at the fusion site: it dictates the level of linear F-actin polymerization, and it is required for appropriate branched actin polymerization via localization of SCAR and WASp. These studies provide new insight to the mechanisms of cell-cell fusion, the relationship between different regulators of actin polymerization, and invasive podosome formation that occurs in normal development and in disease.

  20. Reduction of cellular stress by TolC-dependent efflux pumps in Escherichia coli indicated by BaeSR and CpxARP activation of spy in efflux mutants.

    PubMed

    Rosner, Judah L; Martin, Robert G

    2013-03-01

    Escherichia coli has nine inner membrane efflux pumps which complex with the outer membrane protein TolC and cognate membrane fusion proteins to form tripartite transperiplasmic pumps with diverse functions, including the expulsion of antibiotics. We recently observed that tolC mutants have elevated activities for three stress response regulators, MarA, SoxS, and Rob, and we suggested that TolC-dependent efflux is required to prevent the accumulation of stressful cellular metabolites. Here, we used spy::lacZ fusions to show that two systems for sensing/repairing extracytoplasmic stress, BaeRS and CpxARP, are activated in the absence of TolC-dependent efflux. In either tolC mutants or bacteria with mutations in the genes for four TolC-dependent efflux pumps, spy expression was increased 6- to 8-fold. spy encodes a periplasmic chaperone regulated by the BaeRS and CpxARP stress response systems. The overexpression of spy in tolC or multiple efflux pump mutants also depended on these systems. spy overexpression was not due to acetate, ethanol, or indole accumulation, since external acetate had only a minor effect on wild-type cells, ethanol had a large effect that was not CpxA dependent, and a tolC tnaA mutant which cannot accumulate internal indole overexpressed spy. We propose that, unless TolC-dependent pumps excrete certain metabolites, the metabolites accumulate and activate at least five different stress response systems.

  1. CO J = 6-5 IN Arp 220: STRONG EFFECTS OF DUST ON HIGH-J CO LINES

    SciTech Connect

    Papadopoulos, Padeli P.; Isaak, Kate; Van der Werf, Paul E-mail: Kate.Isaak@astro.cf.ac.u

    2010-03-10

    We report new single dish CO J = 6-5 line observations for the archetypal Ultra Luminous Infrared Galaxy (ULIRG) Arp 220 with the James Clerk Maxwell Telescope atop Mauna Kea in Hawaii. The J = 6-5 line is found to be faint, with brightness temperature ratios (6-5)/(1-0), (6-5)/(3-2) of R{sub 65/10} = 0.080 +- 0.017 and R{sub 65/32} = 0.082 +- 0.019, suggesting very low excitation conditions that cannot be reconciled with the warm and very dense molecular gas present in one of the most extreme starbursts in the local universe. We find that an optically thick dust continuum, with tau(nu {approx}> 350 GHz) {approx}> 1 for the bulk of the warm dust and gas in Arp 220, submerges this line to an almost black body curve, reducing its flux, and affecting its CO spectral line energy distribution at high frequencies. This also resolves the C{sup +} line deficiency in this object, first observed by Infrared Space Observatory: the near absence of that line is a dust optical depth effect, not a dense photodissociation region phenomenon. Finally, we briefly comment on the possibility of such extreme interstellar medium (ISM) states in other ULIRGs in the distant universe, and their consequences for the diagnostic utility of high frequency molecular and atomic ISM lines in such systems. In the case of Arp 220, we anticipate that the now spaceborne Herschel Space Observatory will find faint high-J CO lines at nu {approx}> 690 GHz that would appear as sub-thermally excited with respect to the low-J ones as a result of the effects of dust absorption.

  2. Molecular gas heating mechanisms, and star formation feedback in merger/starbursts: NGC 6240 and Arp 193 as case studies

    SciTech Connect

    Papadopoulos, Padelis P.; Zhang, Zhi-Yu; Weiss, Axel; Van der Werf, Paul; Israel, F. P.; Greve, T. R.; Isaak, Kate G.; Gao, Y. E-mail: zyzhang@pmo.ac.cn E-mail: aweiss@mpifr-bonn.mpg.de E-mail: israel@strw.leidenuniv.nl E-mail: kisaak@rssd.esa.int

    2014-06-20

    We used the SPIRE/FTS instrument aboard the Herschel Space Observatory to obtain the Spectral Line Energy Distributions (SLEDs) of CO from J = 4-3 to J = 13-12 of Arp 193 and NGC 6240, two classical merger/starbursts selected from our molecular line survey of local Luminous Infrared Galaxies (L {sub IR} ≥ 10{sup 11} L {sub ☉}). The high-J CO SLEDs are then combined with ground-based low-J CO, {sup 13}CO, HCN, HCO{sup +}, CS line data and used to probe the thermal and dynamical states of their large molecular gas reservoirs. We find the two CO SLEDs strongly diverging from J = 4-3 onward, with NGC 6240 having a much higher CO line excitation than Arp 193, despite their similar low-J CO SLEDs and L {sub FIR}/L {sub CO,} {sub 1} {sub –0}, L {sub HCN}/L {sub CO} (J = 1-0) ratios (proxies of star formation efficiency and dense gas mass fraction). In Arp 193, one of the three most extreme starbursts in the local universe, the molecular SLEDs indicate a small amount (∼5%-15%) of dense gas (n ≥ 10{sup 4} cm{sup –3}) unlike NGC 6240 where most of the molecular gas (∼60%-70%) is dense (n ∼ (10{sup 4}-10{sup 5}) cm{sup –3}). Strong star-formation feedback can drive this disparity in their dense gas mass fractions, and also induce extreme thermal and dynamical states for the molecular gas. In NGC 6240, and to a lesser degree in Arp 193, we find large molecular gas masses whose thermal states cannot be maintained by FUV photons from Photon-Dominated Regions. We argue that this may happen often in metal-rich merger/starbursts, strongly altering the initial conditions of star formation. ALMA can now directly probe these conditions across cosmic epoch, and even probe their deeply dust-enshrouded outcome, the stellar initial mass function averaged over galactic evolution.

  3. Hubble Space Telescope Ultraviolet Spectrum of ARP 102B, the Prototypical Double-peaked Emission-Line AGN

    NASA Astrophysics Data System (ADS)

    Halpern, Jules P.; Eracleous, Michael; Filippenko, Alexei V.; Chen, Kaiyou

    1996-06-01

    UV spectra of the nucleus of the elliptical galaxy Arp 102B were obtained with the HST's Faint Object Spectrograph in order to investigate the UV emission-line counterparts of its unusual double-peaked Balmer lines. Broad Mg II λ2798 is present with nearly the same profile as the Balmer lines (peaks separated by ~12,000 km s^-1^), and a typical Mg II/Hβ ratio of 1. But there is little, if any C III] λ 1909 or C IV λ1550 emission corresponding to the displaced Balmer- line peaks. Most important, there is no double-peaked component detected in Lyα; the Lyα/Hβ ratio is less than 0.12 in the displaced peaks. However, there is an "ordinary," non-displaced broad-line component with FWHM ~3500 km s^-1^ in all of the permitted lines, demonstrating the need to invoke different locations and different physical conditions for double-peaked and single-peaked line components in the same object. The. striking absence of displaced peaks In Lyα probably cannot be explained solely by reddening. Rather, It indicates that high density and large optical depth in Lyα are required to destroy the line photons by collisional de-excitation and possibly by bound-free absorption out of the n = 2 level of hydrogen. These results strongly support the application, at least to Arp 102B, of the accretion- disk model of Dumont & Collin-Souffrin, in which the disk produces only low-ionization lines and a Lyα/Hβ ratio that agrees with our observed upper limit. Also present is an extraordinary system of absorption lines at the systemic redshift of Arp 102B, in which metastable levels of Fe II up to 1.1 eV above the ground state participate in addition to the more common resonance transitions. Absorption from metastable levels of Fe II have been seen previously only in two unusual, low-ionization broad absorption-line QSOs, Q0059 - 2735 and Mrk 231. Temperatures and densities needed to excite these levels are similar to narrow-line region conditions. Why they are seen in absorption in Arp

  4. ARPES lineshapes, coherent to incoherent ratios, and the waterfall self-energy of Bi2212 cuprate superconductors

    NASA Astrophysics Data System (ADS)

    Wang, Qiang; Sun, Zhe; Das, Tanmoy; Balatsky, Alexander; Rotenberg, Eli; Berger, Helmuth; Eisaki, Hiroshi; Aiura, Yoshihiro; Dessau, Daniel

    2011-03-01

    We report a detailed lineshape analysis of ARPES data on Bi2212 in which we separate out the sharp coherent peaks from the higher energy incoherent ``background'' portions, which includes and makes up the famous waterfall regions. We find that the ratio of the incoherent to coherent weights scales quadratically with the peak energy of the coherent portion of the spectra over a very wide energy range. We show that this behavior, including the waterfalls, can be understood with a simple model electron self-energy, giving a new and powerful experimental tool for determining self-energy effects in correlated electron systems.

  5. Isolation of a Novel Family of C2H2 Zinc Finger Proteins Implicated in Transcriptional Repression Mediated by Chicken Ovalbumin Upstream Promoter Transcription Factor (COUP-TF) Orphan Nuclear Receptors*

    PubMed Central

    Avram, Dorina; Fields, Andrew; Top, Karen Pretty On; Nevrivy, Daniel J.; Ishmael, Jane E.; Leid, Mark

    2010-01-01

    Two novel and related C2H2 zinc finger proteins that are highly expressed in the brain, CTIP1 and CTIP2 (COUP TF-interacting proteins 1 and 2, respectively), were isolated and shown to interact with all members of the chicken ovalbumin upstream promoter transcription factor (COUP-TF) subfamily of orphan nuclear receptors. The interaction of CTIP1 with ARP1 was studied in detail, and CTIP1 was found to harbor two independent ARP1 interaction domains, ID1 and ID2, whereas the putative AF-2 of ARP1 was required for interaction with CTIP1. CTIP1, which exhibited a punctate staining pattern within the nucleus of transfected cells, recruited cotransfected ARP1 to these foci and potentiated ARP1-mediated transcriptional repression of a reporter construct. However, transcriptional repression mediated by ARP1 acting through CTIP1 did not appear to involve recruitment of a trichostatin A-sensitive histone deacetylase(s) to the template, suggesting that this repression pathway may be distinct from that utilized by several other nuclear receptors. PMID:10744719

  6. Formation of a Tidal Dwarf Galaxy in the Interacting System Arp 245 (NGC 2992/93)

    NASA Astrophysics Data System (ADS)

    Duc, P.-A.; Brinks, E.; Springel, V.; Pichardo, B.; Weilbacher, P.; Mirabel, I. F.

    2000-09-01

    Among the various phenomena observed in interacting galaxies is the ejection due to tidal forces of stellar and gaseous material into the intergalactic medium and its subsequent rearranging which can lead to the formation of self-gravitating tidal dwarf galaxies (TDGs). We investigate this process with a detailed multiwavelength study of the interacting system Arp 245 and a numerical model of the collision computed with a Tree-SPH code. Our observations consist of optical/near-infrared broadband imaging, Hα imaging, optical spectroscopy, H I VLA cartography and CO line mapping. The system, composed of the two spiral galaxies NGC 2992 and NGC 2993, is observed at an early stage of the interaction, about 100 Myr after perigalacticon, though at a time when tidal tails have already developed. The VLA observations disclose a third partner to the interaction: an edge-on, flat galaxy, FGC 0938, which looks strikingly undisturbed and might just be falling toward the NGC 2992/93 system. Our H I map shows prominent counterparts to the optical tails. Whereas the stellar and gaseous components of the plume that originates from NGC 2992 match, the stellar and H I tails emanating from NGC 2993 have a different morphology. In particular, the H I forms a ring, a feature that has been successfully reproduced by our numerical simulations. The H I emission in the system as a whole peaks at the tip of the NGC 2992 tail where a gas reservoir of about 109 Msolar, about 60% of the H I toward NGC 2992, coincides with a star-forming optical condensation, A245N. The latter tidal object exhibits properties ranging between those of dwarf irregular galaxies (structural parameters, gas content, star formation rate) and those of spiral disks (metallicity, star formation efficiency, stellar population). Although it is likely, based on our analysis of the H I and model data cube, that A245N might become an independent dwarf galaxy, the dynamical evidence is still open to debate. Prompted by the

  7. Low energy kink in the band dispersions of Sr2 RuO 4 studied by ARPES

    NASA Astrophysics Data System (ADS)

    Kim, Chul; Kim, Choonghyun; Koh, Y. Y.; Yu, Jaejun; Arita, M.; Shimada, K.; Yoshida, Y.; Kim, C.

    2011-03-01

    In Sr 2 Ru O4 , incommensurate antiferromagnetic fluctuations (IAF) were reported to have 4 - 10 meV energy with {q} = (0.6 π , 0.6 π) while the lowest optical phonon is at 12meV. If an electron is coupled to AIF in Sr 2 Ru O4 , the electronic band dispersions will kink below 10meV. Then, one can attribute the low energy kinks below 10meV to the electron-IAF coupling. In spite of the fact that multiple kink energies were recently reported in Sr 2 Ru O4 , kinks below 10meV has not been observed. To look for the so far unobserved electron-IAF coupling in Sr 2 Ru O4 , we performed ultra high resolution angle resolved photoemission (ARPES) experiments on Sr 2 Ru O4 with clean surfaces. In the results, we observe kinks in the band dispersions at energies below 10 meV which show strong momentum dependence. To elucidate the origin of these new kinks, we compare ARPES results with inelastic neutron scattering and band calculation results.

  8. Panax ginseng Fraction F3 Extracted by Supercritical Carbon Dioxide Protects against Oxidative Stress in ARPE-19 Cells

    PubMed Central

    Yang, Chao-Chin; Chen, Chiu-Yuan; Wu, Chun-Chi; Koo, Malcolm; Yu, Zer-Ran; Wang, Be-Jen

    2016-01-01

    In our previous work, the ethanolic extract of Panax ginseng C. A. Meyer was successively partitioned using supercritical carbon dioxide at pressures in series to yield residue (R), F1, F2, and F3 fractions. Among them, F3 contained the highest deglycosylated ginsenosides and exerted the strongest antioxidant and anti-inflammatory activities. The aim of this study was to investigate the protective effects of P. ginseng fractions against cellular oxidative stress induced by hydrogen peroxide (H2O2). Viability of adult retinal pigment epithelium-19 (ARPE-19) cells was examined after treatments of different concentrations of fractions followed by exposure to H2O2. Oxidative levels (malondialdehyde (MDA), 8-hydroxydeoxyguanosine (8-OHdG), and reactive oxygen species (ROS)) and levels of activity of antioxidant enzymes were assessed. Results showed that F3 could dose-dependently protected ARPE-19 cells against oxidative injury induced by H2O2. F3 at a level of 1 mg/mL could restore the cell death induced by H2O2 of up to 60% and could alleviate the increase in cellular oxidation (MDA, 8-OHdG, and ROS) induced by H2O2. Moreover, F3 could restore the activities of antioxidant enzymes suppressed by H2O2. In conclusion, F3 obtained using supercritical carbon dioxide fractionation could significantly increase the antioxidant capacity of P. ginseng extract. The antioxidant capacity was highly correlated with the concentration of F3. PMID:27754362

  9. Depth-resolved ARPES of buried layers and interfaces via soft x-ray standing-wave excited photoemission

    NASA Astrophysics Data System (ADS)

    Gray, Alexander; Minar, Jan; Plucinski, Lukasz; Huijben, Mark; Bostwick, Aaron; Rotenberg, Eli; Yang, See-Hun; Schneider, Claus; Ebert, Hubert; Fadley, Charles

    2012-02-01

    We introduce a new depth-selective photoemission technique, achieved by combining soft x-ray ARPES with standing-wave (SW) excited photoelectron spectroscopy, wherein the intensity profile of the exciting x-ray radiation is tailored within the sample. This effect is accomplished by setting-up an x-ray standing-wave field within the sample by growing it on a synthetic periodic multilayer mirror substrate, which in first-order Bragg reflection acts as the standing-wave generator. The antinodes of the standing wave function as epicenters for photoemission and can be moved vertically through the buried layers and interfaces by scanning the x-ray incidence angle. The new SW-ARPES technique is then applied to the investigation of the electronic properties of the buried interface within a magnetic tunnel junction La0.7Sr0.3MnO3/SrTiO3. The experimental results are compared to the state-of-art one-step photoemission theory including matrix element effects.

  10. The Formation of Tidal Dwarf Galaxies in Interacting Systems: the Case of Arp 245 (NGC 2992/93)

    NASA Astrophysics Data System (ADS)

    Brinks, Elias; Duc, Pierre-Alain; Springel, Volker; Pichardo, Barbara; Weilbacher, Peter; Mirabel, Felix

    We present some highlights of our multi-wavelength study, which involves optical broad- and narrow-band imaging, long-slit spectroscopy, high-resolution HI and CO observations, of the interacting system Arp 245. This object consists of the galaxies NGC 2992 and NGC 2993. Based on a numerical model of the collision, which was computed with a Tree-SPH code, we derive that Arp 245 is observed at an early stage of the interaction, about 100 Myr after perigalacticon, though at a time when tidal tails have already developed. At the tip of the NGC 2992 tail we find a gas reservoir of about 10^9M_odot, or about 60% of the HI which is seen towards NGC 2992, which coincides with what appears to be a star-forming tidal dwarf galaxy, A245N. The TDG A245N exhibits properties ranging between those of dwarf irregular galaxies (structural parameters, gas content, star formation rate) and those of spiral disks (metallicity, star formation efficiency, stellar population). We speculate what the required conditions are to form a TDG, and how they can be distinguished from field dwarf irregulars.

  11. DETERMINATION OF THE IMPACT OF GLYCOLATE ON ARP AND MCU OPERATIONS

    SciTech Connect

    Taylor-Pashow, K.; Peters, T.; Shehee, T.

    2012-06-04

    Savannah River Remediation (SRR) is evaluating an alternate flowsheet for the Defense Waste Processing Facility (DWPF) using glycolic acid as a reductant. An important aspect of the development of the glycolic acid flowsheet is determining if glycolate has any detrimental downstream impacts. Testing was performed to determine if there is any impact to the strontium and actinide sorption by monosodium titanate (MST) and modified monosodium titanate (mMST) or if there is an impact to the cesium removal at the Modular Caustic-Side Solvent Extraction Processing Unit (MCU). Sorption testing was performed using both MST and modified MST (mMST) in the presence of 5,000 and 10,000 ppm (mass basis) glycolate. 10,000 ppm is the estimated bounding concentration expected in the DWPF recycle stream based on DWPF melter flammable gas model results. The presence of glycolate was found to slow the removal of Sr and Pu by MST, while increasing the removal rate of Np. Results indicate that the impact is a kinetic effect, and the overall capacity of the material is not affected. There was no measurable effect on U removal at either glycolate concentration. The slower removal rates for Sr and Pu at 5,000 and 10,000 ppm glycolate could result in lower DF values for these sorbates in ARP based on the current (12 hours) and proposed (8 hours) contact times. For the highest glycolate concentration used in this study, the percentage of Sr removed at 6 hours of contact decreased by 1% and the percentage of Pu removed decreased by nearly 7%. The impact may prove insignificant if the concentration of glycolate that is returned to the tank farm is well below the concentrations tested in this study. The presence of glycolate also decreased the removal rates for all three sorbates (Sr, Pu, and Np) by mMST. Similarly to MST, the results for mMST indicate that the impact is a kinetic effect, and the overall capacity of the material is not affected. The presence of glycolate did not change the lack

  12. Spin-label CW microwave power saturation and rapid passage with triangular non-adiabatic rapid sweep (NARS) and adiabatic rapid passage (ARP) EPR spectroscopy.

    PubMed

    Kittell, Aaron W; Hyde, James S

    2015-06-01

    Non-adiabatic rapid passage (NARS) electron paramagnetic resonance (EPR) spectroscopy was introduced by Kittell et al. (2011) as a general purpose technique to collect the pure absorption response. The technique has been used to improve sensitivity relative to sinusoidal magnetic field modulation, increase the range of inter-spin distances that can be measured under near physiological conditions (Kittell et al., 2012), and enhance spectral resolution in copper (II) spectra (Hyde et al., 2013). In the present work, the method is extended to CW microwave power saturation of spin-labeled T4 Lysozyme (T4L). As in the cited papers, rapid triangular sweep of the polarizing magnetic field was superimposed on slow sweep across the spectrum. Adiabatic rapid passage (ARP) effects were encountered in samples undergoing very slow rotational diffusion as the triangular magnetic field sweep rate was increased. The paper reports results of variation of experimental parameters at the interface of adiabatic and non-adiabatic rapid sweep conditions. Comparison of the forward (up) and reverse (down) triangular sweeps is shown to be a good indicator of the presence of rapid passage effects. Spectral turning points can be distinguished from spectral regions between turning points in two ways: differential microwave power saturation and differential passage effects. Oxygen accessibility data are shown under NARS conditions that appear similar to conventional field modulation data. However, the sensitivity is much higher, permitting, in principle, experiments at substantially lower protein concentrations. Spectral displays were obtained that appear sensitive to rotational diffusion in the range of rotational correlation times of 10(-3) to 10(-7) s in a manner that is analogous to saturation transfer spectroscopy.

  13. Spin-label CW microwave power saturation and rapid passage with triangular non-adiabatic rapid sweep (NARS) and adiabatic rapid passage (ARP) EPR spectroscopy

    NASA Astrophysics Data System (ADS)

    Kittell, Aaron W.; Hyde, James S.

    2015-06-01

    Non-adiabatic rapid passage (NARS) electron paramagnetic resonance (EPR) spectroscopy was introduced by Kittell et al. (2011) as a general purpose technique to collect the pure absorption response. The technique has been used to improve sensitivity relative to sinusoidal magnetic field modulation, increase the range of inter-spin distances that can be measured under near physiological conditions (Kittell et al., 2012), and enhance spectral resolution in copper (II) spectra (Hyde et al., 2013). In the present work, the method is extended to CW microwave power saturation of spin-labeled T4 Lysozyme (T4L). As in the cited papers, rapid triangular sweep of the polarizing magnetic field was superimposed on slow sweep across the spectrum. Adiabatic rapid passage (ARP) effects were encountered in samples undergoing very slow rotational diffusion as the triangular magnetic field sweep rate was increased. The paper reports results of variation of experimental parameters at the interface of adiabatic and non-adiabatic rapid sweep conditions. Comparison of the forward (up) and reverse (down) triangular sweeps is shown to be a good indicator of the presence of rapid passage effects. Spectral turning points can be distinguished from spectral regions between turning points in two ways: differential microwave power saturation and differential passage effects. Oxygen accessibility data are shown under NARS conditions that appear similar to conventional field modulation data. However, the sensitivity is much higher, permitting, in principle, experiments at substantially lower protein concentrations. Spectral displays were obtained that appear sensitive to rotational diffusion in the range of rotational correlation times of 10-3 to 10-7 s in a manner that is analogous to saturation transfer spectroscopy.

  14. Spin-label CW microwave power saturation and rapid passage with triangular non-adiabatic rapid sweep (NARS) and adiabatic rapid passage (ARP) EPR spectroscopy.

    PubMed

    Kittell, Aaron W; Hyde, James S

    2015-06-01

    Non-adiabatic rapid passage (NARS) electron paramagnetic resonance (EPR) spectroscopy was introduced by Kittell et al. (2011) as a general purpose technique to collect the pure absorption response. The technique has been used to improve sensitivity relative to sinusoidal magnetic field modulation, increase the range of inter-spin distances that can be measured under near physiological conditions (Kittell et al., 2012), and enhance spectral resolution in copper (II) spectra (Hyde et al., 2013). In the present work, the method is extended to CW microwave power saturation of spin-labeled T4 Lysozyme (T4L). As in the cited papers, rapid triangular sweep of the polarizing magnetic field was superimposed on slow sweep across the spectrum. Adiabatic rapid passage (ARP) effects were encountered in samples undergoing very slow rotational diffusion as the triangular magnetic field sweep rate was increased. The paper reports results of variation of experimental parameters at the interface of adiabatic and non-adiabatic rapid sweep conditions. Comparison of the forward (up) and reverse (down) triangular sweeps is shown to be a good indicator of the presence of rapid passage effects. Spectral turning points can be distinguished from spectral regions between turning points in two ways: differential microwave power saturation and differential passage effects. Oxygen accessibility data are shown under NARS conditions that appear similar to conventional field modulation data. However, the sensitivity is much higher, permitting, in principle, experiments at substantially lower protein concentrations. Spectral displays were obtained that appear sensitive to rotational diffusion in the range of rotational correlation times of 10(-3) to 10(-7) s in a manner that is analogous to saturation transfer spectroscopy. PMID:25917132

  15. Proteins.

    ERIC Educational Resources Information Center

    Doolittle, Russell F.

    1985-01-01

    Examines proteins which give rise to structure and, by virtue of selective binding to other molecules, make genes. Binding sites, amino acids, protein evolution, and molecular paleontology are discussed. Work with encoding segments of deoxyribonucleic acid (exons) and noncoding stretches (introns) provides new information for hypotheses. (DH)

  16. Protein

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Proteins are the major structural and functional components of all cells in the body. They are macromolecules that comprise 1 or more chains of amino acids that vary in their sequence and length and are folded into specific 3-dimensional structures. The sizes and conformations of proteins, therefor...

  17. Determination of the Impact of Glycolate on ARP and MCU Operations

    SciTech Connect

    Taylor-Pashow, K. M.L.; Peters, T. B.; Fondeur, F. F.; Shehee, T. C.; Washington, A. L.

    2012-12-13

    Savannah River Remediation (SRR) is evaluating an alternate flowsheet for the Defense Waste Processing Facility (DWPF) using glycolic acid as a reductant. An important aspect of the development of the glycolic acid flowsheet is determining if glycolate has any detrimental downstream impacts. Testing was performed to determine if there is any impact to the strontium and actinide sorption by monosodium titanate (MST) and modified monosodium titanate (mMST) or if there is an impact to the cesium removal, phase separation, or coalescer performance at the Modular Caustic-Side Solvent Extraction Processing Unit (MCU). Sorption testing was performed using both MST and modified MST (mMST) in the presence of 5000 and 10,000 ppm (mass basis) glycolate. 10,000 ppm is the estimated bounding concentration expected in the DWPF recycle stream based on DWPF melter flammable gas model results. The presence of glycolate was found to slow the removal of Sr and Pu by MST, while increasing the removal rate of Np. Results indicate that the impact is a kinetic effect, and the overall capacity of the material is not affected. There was no measurable effect on U removal at either glycolate concentration. The slower removal rates for Sr and Pu at 5000 and 10,000 ppm glycolate could result in lower DF values for these sorbates in ARP based on the current (12 hours) and proposed (8 hours) contact times. For the highest glycolate concentration used in this study, the percentage of Sr removed at 6 hours of contact decreased by 1% and the percentage of Pu removed decreased by nearly 7%. The impact may prove insignificant if the concentration of glycolate that is returned to the tank farm is well below the concentrations tested in this study. The presence of glycolate also decreased the removal rates for all three sorbates (Sr, Pu, and Np) by mMST. Similar to MST, the results for mMST indicate that the impact is a kinetic effect, and the overall capacity of the material is not affected. The

  18. The FAK–Arp2/3 interaction promotes leading edge advance and haptosensing by coupling nascent adhesions to lamellipodia actin

    PubMed Central

    Swaminathan, Vinay; Fischer, R. S.; Waterman, Clare M.

    2016-01-01

    Cell migration is initiated in response to biochemical or physical cues in the environment that promote actin-mediated lamellipodial protrusion followed by the formation of nascent integrin adhesions (NAs) within the protrusion to drive leading edge advance. Although FAK is known to be required for cell migration through effects on focal adhesions, its role in NA formation and lamellipodial dynamics is unclear. Live-cell microscopy of FAK−/− cells with expression of phosphorylation deficient or a FERM-domain mutant deficient in Arp2/3 binding revealed a requirement for FAK in promoting the dense formation, transient stabilization, and timely turnover of NA within lamellipodia to couple actin-driven protrusion to adhesion and advance of the leading edge. Phosphorylation on Y397 of FAK promotes dense NA formation but is dispensable for transient NA stabilization and leading edge advance. In contrast, transient NA stabilization and advance of the cell edge requires FAK–Arp2/3 interaction, which promotes Arp2/3 localization to NA and reduces FAK activity. Haptosensing of extracellular matrix (ECM) concentration during migration requires the interaction between FAK and Arp2/3, whereas FAK phosphorylation modulates mechanosensing of ECM stiffness during spreading. Taken together, our results show that mechanistically separable functions of FAK in NA are required for cells to distinguish distinct properties of their environment during migration. PMID:26842895

  19. Soft-X-ray ARPES facility at the ADRESS beamline of the SLS: concepts, technical realisation and scientific applications.

    PubMed

    Strocov, V N; Wang, X; Shi, M; Kobayashi, M; Krempasky, J; Hess, C; Schmitt, T; Patthey, L

    2014-01-01

    Soft-X-ray angle-resolved photoelectron spectroscopy (ARPES) with photon energies around 1 keV combines the momentum space resolution with increasing probing depth. The concepts and technical realisation of the new soft-X-ray ARPES endstation at the ADRESS beamline of SLS are described. The experimental geometry of the endstation is characterized by grazing X-ray incidence on the sample to increase the photoyield and vertical orientation of the measurement plane. The vacuum chambers adopt a radial layout allowing most efficient sample transfer. High accuracy of the angular resolution is ensured by alignment strategies focused on precise matching of the X-ray beam and optical axis of the analyzer. The high photon flux of up to 10(13) photons s(-1) (0.01% bandwidth)(-1) delivered by the beamline combined with the optimized experimental geometry break through the dramatic loss of the valence band photoexcitation cross section at soft-X-ray energies. ARPES images with energy resolution up to a few tens of meV are typically acquired on the time scale of minutes. A few application examples illustrate the power of our advanced soft-X-ray ARPES instrumentation to explore the electronic structure of bulk crystals with resolution in three-dimensional momentum, access buried heterostructures and study elemental composition of the valence states using resonant excitation.

  20. Mechanism of riboflavin uptake by cultured human retinal pigment epithelial ARPE-19 cells: possible regulation by an intracellular Ca2+-calmodulin-mediated pathway.

    PubMed

    Said, Hamid M; Wang, Shuling; Ma, Thomas Y

    2005-07-15

    In mammalian cells (including those of the ocular system), the water-soluble vitamin B2 (riboflavin, RF) assumes an essential role in a variety of metabolic reactions and is critical for normal cellular functions, growth and development. Cells of the human retinal pigment epithelium (hRPE) play an important role in providing a sufficient supply of RF to the retina, but nothing is known about the mechanism of the vitamin uptake by these cells and its regulation. Our aim in the present study was to address this issue using the hRPE ARPE-19 cells as the retinal epithelial model. Our results show RF uptake in the hRPE to be: (1) energy and temperature dependent and occurring without metabolic alteration in the transported substrate, (2) pH but not Na+ dependent, (3) saturable as a function of concentration with an apparent Km of 80 +/- 14 nM, (4) trans-stimulated by unlabelled RF and its structural analogue lumiflavine, (5) cis-inhibited by the RF structural analogues lumiflavine and lumichrome but not by unrelated compounds, and (6) inhibited by the anion transport inhibitors 4,4'-diisothiocyanatostilbene-2,2'-disulphonic acid (DIDS) and 4-acetamido-4'-isothiocyanatostilbene-2,2'-disulphonic acid (SITS) as well as by the Na+ -H+ exchange inhibitor amiloride and the sulfhydryl group inhibitor p-chloromercuriphenylsulphonate (p-CMPS). Maintaining the hRPE cells in a RF-deficient medium led to a specific and significant up-regulation in RF uptake which was mediated via changes in the number and affinity of the RF uptake carriers. While modulating the activities of intracellular protein kinase A (PKA)-, protein kinase C (PKC)-, protein tyrosine kinase (PTK)-, and nitric oxide (NO)-mediated pathways were found to have no role in regulating RF uptake, a role for the Ca2+ -calmodulin-mediated pathway was observed. These studies demonstrate for the first time the involvement of a specialized carrier-mediated mechanism for RF uptake by hRPE cells and show that the process is

  1. Constraining Gamma-Ray Emission from Luminous Infrared Galaxies with Fermi-LAT; Tentative Detection of Arp 220

    NASA Astrophysics Data System (ADS)

    Griffin, Rhiannon D.; Dai, Xinyu; Thompson, Todd A.

    2016-05-01

    Star-forming galaxies produce gamma-rays primarily via pion production, resulting from inelastic collisions between cosmic-ray protons and the interstellar medium (ISM). The dense ISM and high star formation rates of luminous and ultra-luminous infrared galaxies (LIRGs and ULIRGs) imply that they should be strong gamma-ray emitters, but so far only two LIRGs have been detected. Theoretical models for their emission depend on the unknown fraction of cosmic-ray protons that escape these galaxies before interacting. We analyze Fermi-LAT data for 82 of the brightest Infrared Astronomical Satellite LIRGs and ULIRGs. We examine each system individually and carry out a stacking analysis to constrain their gamma-ray fluxes. We report the detection of the nearest ULIRG Arp 220 (˜4.6σ). We observe a gamma-ray flux (0.8-100 GeV) of 2.4 × 10-10 phot cm-2 s-1 with a photon index of 2.23 (8.2 × 1041 erg s-1 at 77 Mpc). We also derive upper limits (ULs) for the stacked LIRGs and ULIRGs. The gamma-ray luminosity of Arp 220 and the stacked ULs agree with calorimetric predictions for dense star-forming galaxies. With the detection of Arp 220, we extend the gamma-ray-IR luminosity correlation to the high-luminosity regime with {log}{L}0.1-100{GeV}=1.25× {log}{L}8-1000μ {{m}}+26.7 as well as the gamma-ray-radio continuum luminosity correlation with {log}{L}0.1-100{GeV}=1.22× {log}{L}1.4{GHz}+13.3. The current survey of Fermi-LAT is on the verge of detecting more LIRGs/ULIRGs in the local universe, and we expect even more detections with deeper Fermi-LAT observations or the next generation of gamma-ray detectors.

  2. Constraining Gamma-Ray Emission from Luminous Infrared Galaxies with Fermi-LAT; Tentative Detection of Arp 220

    NASA Astrophysics Data System (ADS)

    Griffin, Rhiannon D.; Dai, Xinyu; Thompson, Todd A.

    2016-05-01

    Star-forming galaxies produce gamma-rays primarily via pion production, resulting from inelastic collisions between cosmic-ray protons and the interstellar medium (ISM). The dense ISM and high star formation rates of luminous and ultra-luminous infrared galaxies (LIRGs and ULIRGs) imply that they should be strong gamma-ray emitters, but so far only two LIRGs have been detected. Theoretical models for their emission depend on the unknown fraction of cosmic-ray protons that escape these galaxies before interacting. We analyze Fermi-LAT data for 82 of the brightest Infrared Astronomical Satellite LIRGs and ULIRGs. We examine each system individually and carry out a stacking analysis to constrain their gamma-ray fluxes. We report the detection of the nearest ULIRG Arp 220 (˜4.6σ). We observe a gamma-ray flux (0.8–100 GeV) of 2.4 × 10‑10 phot cm‑2 s‑1 with a photon index of 2.23 (8.2 × 1041 erg s‑1 at 77 Mpc). We also derive upper limits (ULs) for the stacked LIRGs and ULIRGs. The gamma-ray luminosity of Arp 220 and the stacked ULs agree with calorimetric predictions for dense star-forming galaxies. With the detection of Arp 220, we extend the gamma-ray–IR luminosity correlation to the high-luminosity regime with {log}{L}0.1-100{GeV}=1.25× {log}{L}8-1000μ {{m}}+26.7 as well as the gamma-ray–radio continuum luminosity correlation with {log}{L}0.1-100{GeV}=1.22× {log}{L}1.4{GHz}+13.3. The current survey of Fermi-LAT is on the verge of detecting more LIRGs/ULIRGs in the local universe, and we expect even more detections with deeper Fermi-LAT observations or the next generation of gamma-ray detectors.

  3. Proteins

    NASA Astrophysics Data System (ADS)

    Regnier, Fred E.; Gooding, Karen M.

    Because of the complexity of cellular material and body fluids, it is seldom possible to analyze a natural product directly. Qualitative and quantitative analyses must often be preceded by some purification step that separates the molecular species being examined from interfering materials. In the case of proteins, column liquid chromatography has been used extensively for these fractionations. With the advent of gel permeation, cation exchange, anion exchange, hydrophobic, and affinity chromatography, it became possible to resolve proteins through their fundamental properties of size, charge, hydrophobicity, and biological affinity. The chromatographic separations used in the early isolation and characterization of many proteins later became analytical tools in their routine analysis. Unfortunately, these inherently simple and versatile column chromatographic techniques introduced in the 50s and 60s have a severe limitation in routine analysis-separation time. It is common to encounter 1-24 h separation times with the classical gel-type supports.

  4. Electronic structure of transferred graphene/h-BN van der Waals heterostructures with nonzero stacking angles by nano-ARPES.

    PubMed

    Wang, Eryin; Chen, Guorui; Wan, Guoliang; Lu, Xiaobo; Chen, Chaoyu; Avila, Jose; Fedorov, Alexei V; Zhang, Guangyu; Asensio, Maria C; Zhang, Yuanbo; Zhou, Shuyun

    2016-11-01

    In van der Waals heterostructures, the periodic potential from the Moiré superlattice can be used as a control knob to modulate the electronic structure of the constituent materials. Here we present a nanoscale angle-resolved photoemission spectroscopy (nano-ARPES) study of transferred graphene/h-BN heterostructures with two different stacking angles of 2.4° and 4.3° respectively. Our measurements reveal six replicas of graphene Dirac cones at the superlattice Brillouin zone (SBZ) centers. The size of the SBZ and its relative rotation angle to the graphene BZ are in good agreement with Moiré superlattice period extracted from atomic force microscopy (AFM) measurements. Comparison to the epitaxial graphene/h-BN with 0° stacking angles suggests that the interaction between graphene and h-BN decreases with increasing stacking angle. PMID:27604538

  5. Electronic structure of transferred graphene/h-BN van der Waals heterostructures with nonzero stacking angles by nano-ARPES

    NASA Astrophysics Data System (ADS)

    Wang, Eryin; Chen, Guorui; Wan, Guoliang; Lu, Xiaobo; Chen, Chaoyu; Avila, Jose; Fedorov, Alexei V.; Zhang, Guangyu; Asensio, Maria C.; Zhang, Yuanbo; Zhou, Shuyun

    2016-11-01

    In van der Waals heterostructures, the periodic potential from the Moiré superlattice can be used as a control knob to modulate the electronic structure of the constituent materials. Here we present a nanoscale angle-resolved photoemission spectroscopy (nano-ARPES) study of transferred graphene/h-BN heterostructures with two different stacking angles of 2.4° and 4.3° respectively. Our measurements reveal six replicas of graphene Dirac cones at the superlattice Brillouin zone (SBZ) centers. The size of the SBZ and its relative rotation angle to the graphene BZ are in good agreement with Moiré superlattice period extracted from atomic force microscopy (AFM) measurements. Comparison to the epitaxial graphene/h-BN with 0° stacking angles suggests that the interaction between graphene and h-BN decreases with increasing stacking angle.

  6. THE LICK AGN MONITORING PROJECT: VELOCITY-DELAY MAPS FROM THE MAXIMUM-ENTROPY METHOD FOR Arp 151

    SciTech Connect

    Bentz, Misty C.; Barth, Aaron J.; Walsh, Jonelle L.; Horne, Keith; Bennert, Vardha Nicola; Treu, Tommaso; Canalizo, Gabriela; Filippenko, Alexei V.; Gates, Elinor L.; Malkan, Matthew A.; Minezaki, Takeo; Woo, Jong-Hak

    2010-09-01

    We present velocity-delay maps for optical H I, He I, and He II recombination lines in Arp 151, recovered by fitting a reverberation model to spectrophotometric monitoring data using the maximum-entropy method. H I response is detected over the range 0-15 days, with the response confined within the virial envelope. The Balmer-line maps have similar morphologies but exhibit radial stratification, with progressively longer delays for H{gamma} to H{beta} to H{alpha}. The He I and He II response is confined within 1-2 days. There is a deficit of prompt response in the Balmer-line cores but strong prompt response in the red wings. Comparison with simple models identifies two classes that reproduce these features: free-falling gas and a half-illuminated disk with a hot spot at small radius on the receding lune. Symmetrically illuminated models with gas orbiting in an inclined disk or an isotropic distribution of randomly inclined circular orbits can reproduce the virial structure but not the observed asymmetry. Radial outflows are also largely ruled out by the observed asymmetry. A warped-disk geometry provides a physically plausible mechanism for the asymmetric illumination and hot spot features. Simple estimates show that a disk in the broad-line region of Arp 151 could be unstable to warping induced by radiation pressure. Our results demonstrate the potential power of detailed modeling combined with monitoring campaigns at higher cadence to characterize the gas kinematics and physical processes that give rise to the broad emission lines in active galactic nuclei.

  7. The Lick AGN Monitoring Project: Velocity-delay Maps from the Maximum-entropy Method for Arp 151

    NASA Astrophysics Data System (ADS)

    Bentz, Misty C.; Horne, Keith; Barth, Aaron J.; Bennert, Vardha Nicola; Canalizo, Gabriela; Filippenko, Alexei V.; Gates, Elinor L.; Malkan, Matthew A.; Minezaki, Takeo; Treu, Tommaso; Woo, Jong-Hak; Walsh, Jonelle L.

    2010-09-01

    We present velocity-delay maps for optical H I, He I, and He II recombination lines in Arp 151, recovered by fitting a reverberation model to spectrophotometric monitoring data using the maximum-entropy method. H I response is detected over the range 0-15 days, with the response confined within the virial envelope. The Balmer-line maps have similar morphologies but exhibit radial stratification, with progressively longer delays for Hγ to Hβ to Hα. The He I and He II response is confined within 1-2 days. There is a deficit of prompt response in the Balmer-line cores but strong prompt response in the red wings. Comparison with simple models identifies two classes that reproduce these features: free-falling gas and a half-illuminated disk with a hot spot at small radius on the receding lune. Symmetrically illuminated models with gas orbiting in an inclined disk or an isotropic distribution of randomly inclined circular orbits can reproduce the virial structure but not the observed asymmetry. Radial outflows are also largely ruled out by the observed asymmetry. A warped-disk geometry provides a physically plausible mechanism for the asymmetric illumination and hot spot features. Simple estimates show that a disk in the broad-line region of Arp 151 could be unstable to warping induced by radiation pressure. Our results demonstrate the potential power of detailed modeling combined with monitoring campaigns at higher cadence to characterize the gas kinematics and physical processes that give rise to the broad emission lines in active galactic nuclei.

  8. IMPACT OF SB4 TANK 40 DECANT AND ARP/MCU ADDITIONS WITH/WITHOUT ADDED CAUSTIC ON DWPF CPC PERFORMANCE

    SciTech Connect

    Koopman, D; David Best, D; Frances Williams, F

    2008-04-18

    The Savannah River National Laboratory (SRNL) was requested to investigate the impact of decanting supernate from the Sludge Batch four (SB4) feed in Tank 40. The specific questions concerned the potential impact on the stoichiometric acid window determined for SB4 with respect to overall hydrogen generation rates, nitrite destruction in the Sludge Receipt and Adjustment Tank (SRAT) and the rheology of the sludge, SRAT product, and Slurry Mix Evaporator (SME) product slurries. The scope included considering an addition of sodium hydroxide to Tank 40 to partially offset the sodium lost during decanting as well as considering the impact of bounding quantities of Actinide Removal Process (ARP) feed and Modular Caustic-Side Solvent Extraction Unit (MCU) feed on these same parameters. Simulated SB4 waste was first adjusted to match the dilution that has occurred in Tank 40 during the initial period of SB4 operations in the DWPF. The adjusted simulant was decanted an equivalent of 100,000 gallons relative to 413,740 gallons projected supernate volume. The decanted simulant was divided into two equal parts. One part received an addition of sodium hydroxide to increase the Na{sub 2}O content of the calcined sludge solids by about 3%. The baseline decanted simulant and caustic adjusted simulant were each tested in three pairs of DWPF process simulations of the SRAT and SME cycles. The simulations were at the nominal SB4 acid stoichiometry of 130% with and without bounding ARP/MCU additions and at 170% of acid without ARP/MCU. The 170% case without ARP/MCU was considered bounding relative to 170% with ARP/MCU based on calculated acid requirements. No significant negative impacts on the proposed acid operating window for the SRAT and SME cycles were noted in the simulations. Nitrite was successfully destroyed and mercury reduced in all six SRAT cycles. Hydrogen was produced in all six SRAT and SME cycles, but the levels were below the DWPF SRAT and SME cycle limits in all

  9. Formation of filopodia-like bundles in vitro from a dendritic network.

    PubMed

    Vignjevic, Danijela; Yarar, Defne; Welch, Matthew D; Peloquin, John; Svitkina, Tatyana; Borisy, Gary G

    2003-03-17

    We report the development and characterization of an in vitro system for the formation of filopodia-like bundles. Beads coated with actin-related protein 2/3 (Arp2/3)-activating proteins can induce two distinct types of actin organization in cytoplasmic extracts: (1) comet tails or clouds displaying a dendritic array of actin filaments and (2) stars with filament bundles radiating from the bead. Actin filaments in these bundles, like those in filopodia, are long, unbranched, aligned, uniformly polar, and grow at the barbed end. Like filopodia, star bundles are enriched in fascin and lack Arp2/3 complex and capping protein. Transition from dendritic to bundled organization was induced by depletion of capping protein, and add-back of this protein restored the dendritic mode. Depletion experiments demonstrated that star formation is dependent on Arp2/3 complex. This poses the paradox of how Arp2/3 complex can be involved in the formation of both branched (lamellipodia-like) and unbranched (filopodia-like) actin structures. Using purified proteins, we showed that a small number of components are sufficient for the assembly of filopodia-like bundles: Wiskott-Aldrich syndrome protein (WASP)-coated beads, actin, Arp2/3 complex, and fascin. We propose a model for filopodial formation in which actin filaments of a preexisting dendritic network are elongated by inhibition of capping and subsequently cross-linked into bundles by fascin.

  10. Herschel/PACS spectroscopy of NGC 4418 and Arp 220: H2O, H218O, OH, 18OH, O I, HCN, and NH3

    NASA Astrophysics Data System (ADS)

    González-Alfonso, E.; Fischer, J.; Graciá-Carpio, J.; Sturm, E.; Hailey-Dunsheath, S.; Lutz, D.; Poglitsch, A.; Contursi, A.; Feuchtgruber, H.; Veilleux, S.; Spoon, H. W. W.; Verma, A.; Christopher, N.; Davies, R.; Sternberg, A.; Genzel, R.; Tacconi, L.

    2012-05-01

    Full range Herschel/PACS spectroscopy of the (ultra)luminous infrared galaxies NGC 4418 and Arp 220, observed as part of the SHINING key programme, reveals high excitation in H2O, OH, HCN, and NH3. In NGC 4418, absorption lines were detected with Elower > 800 K (H2O), 600 K (OH), 1075 K (HCN), and 600 K (NH3), while in Arp 220 the excitation is somewhat lower. While outflow signatures in moderate excitation lines are seen in Arp 220 as have been seen in previous studies, in NGC 4418 the lines tracing its outer regions are redshifted relative to the nucleus, suggesting an inflow with Ṁ ≲ 12 M⊙ yr-1. Both galaxies have compact and warm (Tdust ≳ 100 K) nuclear continuum components, together with a more extended and colder component that is much more prominent and massive in Arp 220. A chemical dichotomy is found in both sources: on the one hand, the nuclear regions have high H2O abundances, ~10-5, and high HCN/H2O and HCN/NH3 column density ratios of 0.1-0.4 and 2-5, respectively, indicating a chemistry typical of evolved hot cores where grain mantle evaporation has occurred. On the other hand, the high OH abundance, with OH/H2O ratios of ~0.5, indicates the effects of X-rays and/or cosmic rays. The nuclear media have high surface brightnesses (≳1013 L⊙/kpc2) and are estimated to be very thick (NH ≳ 1025 cm-2). While NGC 4418 shows weak absorption in H218O and 18OH, with a 16O-to-18O ratio of ≳250-500, the relatively strong absorption of the rare isotopologues in Arp 220 indicates 18O enhancement, with 16O-to-18O of 70-130. Further away from the nuclear regions, the H2O abundance decreases to ≲10-7 and the OH/H2O ratio is reversed relative to the nuclear region to 2.5-10. Despite the different scales and morphologies of NGC 4418, Arp 220, and Mrk 231, preliminary evidence is found for an evolutionary sequence from infall, hot-core like chemistry, and solar oxygen isotope ratio to high velocity outflow, disruption of the hot core chemistry and

  11. Prehistoric spatial patterning and subsistence studies: Archaeological investigations at Sample Unit U19arP4, Nevada Test Site, Nye County, Nevada

    SciTech Connect

    Johnson, W.G.; DuBarton, A.; Edwards, S.; Drollinger, H.

    1992-12-31

    This report documents the methods and results of archaeological investigations at Sample Unit U19arP4 on Pahute Mesa at the Nevada Test Site (NTS). Eight sites were located there: four lithic artifact scatters (26NY1370, 26NY1372, 26NY3666 and 26NY3667), two temporary camps (26NY3665 and 26NY5418), one artifact locality (26NY5419), and one quarry (26NY3664). One of the lithic scatters, 26NY3667, incorporated a previously recorded rock ring, 26NY1371, that could not be relocated during subsequent investigations. Surface artifacts were collected from all but two of the sites, 26NY1370 and 26NY1372. The data retrieved from these investigations include over one thousand artifacts, such as projectile points, bifaces, debitage, groundstone, and pottery. The temporally diagnostic materials indicate periodic use of Sample Unit U19arP4 from the Middle Archaic to the Shoshonean period.

  12. Prehistoric spatial patterning and subsistence studies: Archaeological investigations at Sample Unit U19arP4, Nevada Test Site, Nye County, Nevada

    SciTech Connect

    Johnson, W.G.; DuBarton, A.; Edwards, S.; Drollinger, H.

    1992-01-01

    This report documents the methods and results of archaeological investigations at Sample Unit U19arP4 on Pahute Mesa at the Nevada Test Site (NTS). Eight sites were located there: four lithic artifact scatters (26NY1370, 26NY1372, 26NY3666 and 26NY3667), two temporary camps (26NY3665 and 26NY5418), one artifact locality (26NY5419), and one quarry (26NY3664). One of the lithic scatters, 26NY3667, incorporated a previously recorded rock ring, 26NY1371, that could not be relocated during subsequent investigations. Surface artifacts were collected from all but two of the sites, 26NY1370 and 26NY1372. The data retrieved from these investigations include over one thousand artifacts, such as projectile points, bifaces, debitage, groundstone, and pottery. The temporally diagnostic materials indicate periodic use of Sample Unit U19arP4 from the Middle Archaic to the Shoshonean period.

  13. COMMIX-1AR/P: A three-dimensional transient single-phase computer program for thermal hydraulic analysis of single and multicomponent systems

    SciTech Connect

    Garner, P.L.; Blomquist, R.N.; Gelbard, E.M.

    1992-09-01

    The COMMIX-1AR/P computer program is designed for analyzing the steady-state and transient aspects of single-phase fluid flow and heat transfer in three spatial dimensions. This version is an extension of the modeling in COMMIX-1A to include multiple fluids in physically separate regions of the computational domain, modeling descriptions for pumps, radiation heat transfer between surfaces of the solids which are embedded in or surround the fluid, a k-[var epsilon] model for fluid turbulence, and improved numerical techniques. The porous-medium formulation in COMMIX allows the program to be applied to a wide range of problems involving both simple and complex geometrical arrangements. The input preparation and execution procedures are presented for the COMMIX-1AR/P program and several postprocessor programs which produce graphical displays of the calculated results.

  14. Comparison of CDC and sequence-based molecular typing of syphilis treponemes: tpr and arp loci are variable in multiple samples from the same patient

    PubMed Central

    2013-01-01

    Background Molecular typing of syphilis-causing strains provides important epidemiologic data. We tested whether identified molecular subtypes were identical in PCR-positive parallel samples taken from the same patient at a same time. We also tested whether subtype prevalence differs in skin and blood samples. Results Eighteen syphilis positive patients (showing both positive serology and PCR), with two PCR-typeable parallel samples taken at the same time, were tested with both CDC (Centers for Disease Control and Prevention) and sequence-based typing. Samples taken from 9 of 18 patients were completely typed for TP0136, TP0548, 23S rDNA, arp, and tpr loci. The CDC typing revealed 11 distinct genotypes while the sequence-based typing identified 6 genotypes. When results from molecular typing of TP0136, TP0548, and 23S rDNA were analyzed in samples taken from the same patient, no discrepancies in the identified genotypes were found; however, there were discrepancies in 11 of 18 patients (61.1%) samples relative to the arp and tpr loci. In addition to the above described typing, 127 PCR-positive swabs and whole blood samples were tested for individual genotype frequencies. The repetition number for the arp gene was lower in whole blood (WB) samples compared to swab samples. Similarly, the most common tpr RFLP type “d” was found to have lower occurrence rates in WB samples while type “e” had an increased occurrence in these samples. Conclusions Differences in the CDC subtypes identified in parallel samples indicated genetic instability of the arp and tpr loci and suggested limited applicability of the CDC typing system in epidemiological studies. Differences in treponemal genotypes detected in whole blood and swab samples suggested important differences between both compartments and/or differences in adherence of treponeme variants to human cells. PMID:23898829

  15. The Entamoeba histolytica, Arp2/3 Complex Is Recruited to Phagocytic Cups through an Atypical Kinase EhAK1

    PubMed Central

    Babuta, Mrigya; Mansuri, M Shahid; Bhattacharya, Sudha; Bhattacharya, Alok

    2015-01-01

    The parasite Entamoeba histolytica is the etiological agent of amoebiasis and phagocytosis plays a key role in virulence of this organism. Signaling pathways involved in activation of cytoskeletal dynamics required for phagocytosis remain to be elucidated. Phagocytosis is initiated with sequential recruitment of EhC2PK, EhCaBP1, EhCaBP3 and an atypical kinase EhAK1 after particle attachment. Here we show that EhARPC1, an essential subunit of the actin branching complex Arp 2/3 is recruited to the phagocytic initiation sites by EhAK1. Imaging, expression knockdown of different molecules and pull down experiments suggest that EhARPC1 interacts with EhAK1 and that it is required during initiation of phagocytosis and phagosome formation. Moreover, recruitment of EhARPC2 at the phagocytosis initiation by EhAK1 is also observed, indicating that the Arp 2/3 complex is recruited. In conclusion, these results suggests a novel mechanism of recruitment of Arp 2/3 complex during phagocytosis in E. histolytica. PMID:26646565

  16. High harmonic generation based time resolved ARPES at 30 eV with 50 meV energy resolution

    NASA Astrophysics Data System (ADS)

    Rohwer, Timm; Sie, Edbert J.; Mahmood, Fahad; Gedik, Nuh

    Angle-resolved photoelectron spectroscopy (ARPES) has emerged as a leading technique in identifying equilibrium properties of complex electronic systems as well as their correlated dynamics. By using femtosecond high harmonic generation (HHG) pulses, this technique can be extended to monitor ultrafast changes in the electronic structure in response to an optical excitation. However, the broad bandwidth of the HHG pulses has been a major experimental limitation. In this contribution, we combine the HHG source with an off-axis Czerny-Turner XUV monochromator and a three-dimensional ``ARTOF'' photoelectron detector to achieve an unrivaled overall energy resolution of 50 meV in multiple harmonic energies. Moreover, the use of a stack of different gratings enables us to fine control both the photon energy and time vs. energy resolution to its particular needs. The performance of our setup is demonstrated by studies on the transition metal dichalcogenide IrTe2 which undergoes a first-order structural transition and accompanied reconstruction of the band structure upon cooling without the characteristic opening of an energy gap.

  17. Quantifying electronic correlation strength in a complex oxide: A combined DMFT and ARPES study of LaNiO3

    NASA Astrophysics Data System (ADS)

    Nowadnick, E. A.; Ruf, J. P.; Park, H.; King, P. D. C.; Schlom, D. G.; Shen, K. M.; Millis, A. J.

    2015-12-01

    The electronic correlation strength is a basic quantity that characterizes the physical properties of materials such as transition metal oxides. Determining correlation strengths requires both precise definitions and a careful comparison between experiment and theory. In this paper, we define the correlation strength via the magnitude of the electron self-energy near the Fermi level. For the case of LaNiO3, we obtain both the experimental and theoretical mass enhancements m⊙/m by considering high resolution angle-resolved photoemission spectroscopy (ARPES) measurements and density functional + dynamical mean field theory (DFT + DMFT) calculations. We use valence-band photoemission data to constrain the free parameters in the theory and demonstrate a quantitative agreement between the experiment and theory when both the realistic crystal structure and strong electronic correlations are taken into account. In addition, by considering DFT + DMFT calculations on epitaxially strained LaNiO3, we find a strain-induced evolution of m⊙/m in qualitative agreement with trends derived from optics experiments. These results provide a benchmark for the accuracy of the DFT + DMFT theoretical approach, and can serve as a test case when considering other complex materials. By establishing the level of accuracy of the theory, this work also will enable better quantitative predictions when engineering new emergent properties in nickelate heterostructures.

  18. ARPES view on surface and bulk hybridization phenomena in the antiferromagnetic Kondo lattice CeRh2Si2.

    PubMed

    Patil, S; Generalov, A; Güttler, M; Kushwaha, P; Chikina, A; Kummer, K; Rödel, T C; Santander-Syro, A F; Caroca-Canales, N; Geibel, C; Danzenbächer, S; Kucherenko, Yu; Laubschat, C; Allen, J W; Vyalikh, D V

    2016-01-01

    The hybridization between localized 4f electrons and itinerant electrons in rare-earth-based materials gives rise to their exotic properties like valence fluctuations, Kondo behaviour, heavy-fermions, or unconventional superconductivity. Here we present an angle-resolved photoemission spectroscopy (ARPES) study of the Kondo lattice antiferromagnet CeRh2Si2, where the surface and bulk Ce-4f spectral responses were clearly resolved. The pronounced 4f (0) peak seen for the Ce terminated surface gets strongly suppressed in the bulk Ce-4f spectra taken from a Si-terminated crystal due to much larger f-d hybridization. Most interestingly, the bulk Ce-4f spectra reveal a fine structure near the Fermi edge reflecting the crystal electric field splitting of the bulk magnetic 4f (1)5/2 state. This structure presents a clear dispersion upon crossing valence states, providing direct evidence of f-d hybridization. Our findings give precise insight into f-d hybridization penomena and highlight their importance in the antiferromagnetic phases of Kondo lattices. PMID:26987899

  19. ARPES view on surface and bulk hybridization phenomena in the antiferromagnetic Kondo lattice CeRh2Si2

    PubMed Central

    Patil, S.; Generalov, A.; Güttler, M.; Kushwaha, P.; Chikina, A.; Kummer, K.; Rödel, T. C.; Santander-Syro, A. F.; Caroca-Canales, N.; Geibel, C.; Danzenbächer, S.; Kucherenko, Yu.; Laubschat, C.; Allen, J. W.; Vyalikh, D. V.

    2016-01-01

    The hybridization between localized 4f electrons and itinerant electrons in rare-earth-based materials gives rise to their exotic properties like valence fluctuations, Kondo behaviour, heavy-fermions, or unconventional superconductivity. Here we present an angle-resolved photoemission spectroscopy (ARPES) study of the Kondo lattice antiferromagnet CeRh2Si2, where the surface and bulk Ce-4f spectral responses were clearly resolved. The pronounced 4f 0 peak seen for the Ce terminated surface gets strongly suppressed in the bulk Ce-4f spectra taken from a Si-terminated crystal due to much larger f-d hybridization. Most interestingly, the bulk Ce-4f spectra reveal a fine structure near the Fermi edge reflecting the crystal electric field splitting of the bulk magnetic 4f 15/2 state. This structure presents a clear dispersion upon crossing valence states, providing direct evidence of f-d hybridization. Our findings give precise insight into f-d hybridization penomena and highlight their importance in the antiferromagnetic phases of Kondo lattices. PMID:26987899

  20. Subarcsecond international LOFAR radio images of Arp 220 at 150 MHz. A kpc-scale star forming disk surrounding nuclei with shocked outflows

    NASA Astrophysics Data System (ADS)

    Varenius, E.; Conway, J. E.; Martí-Vidal, I.; Aalto, S.; Barcos-Muñoz, L.; König, S.; Pérez-Torres, M. A.; Deller, A. T.; Moldón, J.; Gallagher, J. S.; Yoast-Hull, T. M.; Horellou, C.; Morabito, L. K.; Alberdi, A.; Jackson, N.; Beswick, R.; Carozzi, T. D.; Wucknitz, O.; Ramírez-Olivencia, N.

    2016-09-01

    Context. Arp 220 is the prototypical ultra luminous infrared galaxy (ULIRG). Despite extensive studies, the structure at MHz-frequencies has remained unknown because of limits in spatial resolution. Aims: This work aims to constrain the flux and shape of radio emission from Arp 220 at MHz frequencies. Methods: We analyse new observations with the International Low Frequency Array (LOFAR) telescope, and archival data from the Multi-Element Radio Linked Interferometer Network (MERLIN) and the Karl G. Jansky Very Large Array (VLA). We model the spatially resolved radio spectrum of Arp 220 from 150 MHz to 33 GHz. Results: We present an image of Arp 220 at 150 MHz with resolution 0.̋65 × 0.̋35, sensitivity 0.15 mJy beam-1, and integrated flux density 394 ± 59 mJy. More than 80% of the detected flux comes from extended (6''≈ 2.2 kpc) steep spectrum (α = -0.7) emission, likely from star formation in the molecular disk surrounding the two nuclei. We find elongated features extending 0.3'' (110 pc) and 0.9'' (330 pc) from the eastern and western nucleus respectively, which we interpret as evidence for outflows. The extent of radio emission requires acceleration of cosmic rays far outside the nuclei. We find that a simple three component model can explain most of the observed radio spectrum of the galaxy. When accounting for absorption at 1.4 GHz, Arp 220 follows the FIR/radio correlation with q = 2.36, and we estimate a star formation rate of 220 M⊙ yr-1. We derive thermal fractions at 1 GHz of less than 1% for the nuclei, which indicates that a major part of the UV-photons are absorbed by dust. Conclusions: International LOFAR observations shows great promise to detect steep spectrum outflows and probe regions of thermal absorption. However, in LIRGs the emission detected at 150 MHz does not necessarily come from the main regions of star formation. This implies that high spatial resolution is crucial for accurate estimates of star formation rates for such galaxies

  1. The nuclear starburst in Arp 299-A: from the 5.0 GHz VLBI radio light-curves to its core-collapse supernova rate

    NASA Astrophysics Data System (ADS)

    Bondi, M.; Pérez-Torres, M. A.; Herrero-Illana, R.; Alberdi, A.

    2012-03-01

    Context. The nuclear region of the luminous infrared galaxy (LIRG) Arp 299-A hosts a recent ( ≃ 10 Myr) intense burst of massive star formation that is expected to lead to numerous core-collapse supernovae (CCSNe). Previous VLBI observations, carried out with the European VLBI Network (EVN) at 5.0 GHz and with the VLBA at 2.3 and 8.4 GHz, resulted in the detection of many compact, bright, non-thermal sources in a region ≲ 150 pc in size. Aims: We aim to establish the nature of all non-thermal compact components in Arp 299-A, as well as to estimate its core-collapse supernova rate. While the majority of the compact components are expected to be young radio supernovae (RSNe) and supernova remnants (SNRs), a definitive classification is still lacking. Yet, this is very relevant for eventually establishing the CCSN rate, as well as the star formation rate, for this galaxy. Methods: We used multi-epoch EVN observations taken at 5.0 GHz to image the compact radio sources in the nuclear region of Arp 299-A with milliarcsecond resolution. We also used one single-epoch 5.0 GHz Multi-Element Radio Linked Interferometer Network (MERLIN) observation to image the extended emission in which these compact radio sources are embedded. Results: We present the first 5.0 GHz radio light-curve (spanning ~2.5 yr) of all compact components in the nuclear starburst of Arp 299-A. Twenty-six compact sources are detected, eight of which are new objects. The properties of all detected objects are consistent with them being a mixed population of CCSNe and SNRs. We find clear evidence for at least two new CCSNe, implying a lower limit to the CCSN rate of νSN ≳ 0.80 SN/yr, indicating that the bulk of the current star formation in Arp 299-A is taking place in the innermost ~150 pc.A few more objects show variability consistent with them being recently exploded SNe, but only future observations will clarify this point. Our MERLIN observations trace a region of diffuse extended emission that

  2. Secretory proteins characteristic of environmental changes in cellular signal transduction: Expression in oral fluid

    NASA Astrophysics Data System (ADS)

    Mednieks, M. I.; Burke, J. C.; Sivakumar, T. P.; Hand, A. R.; Grindeland, R. E.

    2000-01-01

    Past studies have shown that both hypo- and hyper-gravity have significant consequences on a variety of tissues and organ systems. It is not known if the effects of environmental stimuli such as altered gravity are beneficial or detrimental, and if the effects can be prevented or reversed. Animal experiments from the Space Lab and Cosmos missions indicate that events that are mediated by cyclic AMP, such as cellular responses to catecholamine and peptide hormone action, are significantly altered in a number of tissues as a consequence of space flight. A secretory cyclic AMP-receptor protein (cARP), is present in saliva, and can serve as an indicator of individual responses to physiologic and environmental stress. Animal experiments have shown that the hypergravity component of space flight is a significant stress factor. In humans, cARP levels in each individual are constant under normal conditions, but elevated after acute stress. Additionally, the levels of cARP in secreted saliva can be compared to those in gingival crevicular fluid (GCF), which reflects the protein composition of serum. The ratio of cARP in saliva to that in GCF can be used as a measure of basal compared to hyper-or hypo-gravity values. An ultimate goal is to test hyper and zero G responses in human saliva to determine if cARP is a suitable index of acute and chronic stress. A miniaturized test kit for saliva collection has been designed. Samples can be collected and stored till analyses are carried out that will distinguish the effects of increased gravity from those of one and zero G. Such tests can serve as an individualized monitoring system for physiologic responses either in space or on earth. .

  3. Reconstitution of actin-based motility of Listeria and Shigella using pure proteins

    NASA Astrophysics Data System (ADS)

    Loisel, Thomas P.; Boujemaa, Rajaa; Pantaloni, Dominique; Carlier, Marie-France

    1999-10-01

    Actin polymerization is essential for cell locomotion and is thought to generate the force responsible for cellular protrusions. The Arp2/3 complex is required to stimulate actin assembly at the leading edge in response to signalling. The bacteria Listeria and Shigella bypass the signalling pathway and harness the Arp2/3 complex to induce actin assembly and to propel themselves in living cells. However, the Arp2/3 complex alone is insufficient to promote movement. Here we have used pure components of the actin cytoskeleton to reconstitute sustained movement in Listeria and Shigella in vitro. Actin-based propulsion is driven by the free energy released by ATP hydrolysis linked to actin polymerization, and does not require myosin. In addition to actin and activated Arp2/3 complex, actin depolymerizing factor (ADF, or cofilin) and capping protein are also required for motility as they maintain a high steady-state level of G-actin, which controls the rate of unidirectional growth of actin filaments at the surface of the bacterium. The movement is more effective when profilin, α-actinin and VASP (for Listeria) are also included. These results have implications for our understanding of the mechanism of actin-based motility in cells.

  4. Ankyrin-repeat proteins from sponge symbionts modulate amoebal phagocytosis.

    PubMed

    Nguyen, Mary T H D; Liu, Michael; Thomas, Torsten

    2014-03-01

    Bacteria-eukaryote symbiosis occurs in all stages of evolution, from simple amoebae to mammals, and from facultative to obligate associations. Sponges are ancient metazoans that form intimate symbiotic interactions with complex communities of bacteria. The basic nutritional requirements of the sponge are in part satisfied by the phagocytosis of bacterial food particles from the surrounding water. How bacterial symbionts, which are permanently associated with the sponge, survive in the presence of phagocytic cells is largely unknown. Here, we present the discovery of a genomic fragment from an uncultured gamma-proteobacterial sponge symbiont that encodes for four proteins, whose closest known relatives are found in a sponge genome. Through recombinant approaches, we show that these four eukaryotic-like, ankyrin-repeat proteins (ARP) when expressed in Eschericha coli can modulate phagocytosis of amoebal cells and lead to accumulation of bacteria in the phagosome. Mechanistically, two ARPs appear to interfere with phagosome development in a similar way to reduced vacuole acidification, by blocking the fusion of the early phagosome with the lysosome and its digestive enzymes. Our results show that ARP from sponge symbionts can function to interfere with phagocytosis, and we postulate that this might be one mechanism by which symbionts can escape digestion in a sponge host.

  5. An Operational Configuration of the ARPS Data Analysis System to Initialize WRF in the NM'S Environmental Modeling System

    NASA Technical Reports Server (NTRS)

    Case, Jonathan; Blottman, Pete; Hoeth, Brian; Oram, Timothy

    2006-01-01

    The Weather Research and Forecasting (WRF) model is the next generation community mesoscale model designed to enhance collaboration between the research and operational sectors. The NM'S as a whole has begun a transition toward WRF as the mesoscale model of choice to use as a tool in making local forecasts. Currently, both the National Weather Service in Melbourne, FL (NWS MLB) and the Spaceflight Meteorology Group (SMG) are running the Advanced Regional Prediction System (AIRPS) Data Analysis System (ADAS) every 15 minutes over the Florida peninsula to produce high-resolution diagnostics supporting their daily operations. In addition, the NWS MLB and SMG have used ADAS to provide initial conditions for short-range forecasts from the ARPS numerical weather prediction (NWP) model. Both NM'S MLB and SMG have derived great benefit from the maturity of ADAS, and would like to use ADAS for providing initial conditions to WRF. In order to assist in this WRF transition effort, the Applied Meteorology Unit (AMU) was tasked to configure and implement an operational version of WRF that uses output from ADAS for the model initial conditions. Both agencies asked the AMU to develop a framework that allows the ADAS initial conditions to be incorporated into the WRF Environmental Modeling System (EMS) software. Developed by the NM'S Science Operations Officer (S00) Science and Training Resource Center (STRC), the EMS is a complete, full physics, NWP package that incorporates dynamical cores from both the National Center for Atmospheric Research's Advanced Research WRF (ARW) and the National Centers for Environmental Prediction's Non-Hydrostatic Mesoscale Model (NMM) into a single end-to-end forecasting system. The EMS performs nearly all pre- and postprocessing and can be run automatically to obtain external grid data for WRF boundary conditions, run the model, and convert the data into a format that can be readily viewed within the Advanced Weather Interactive Processing System

  6. An HST Search for the Progenitor of the Type Ib Supernova 2010O in NGC 3690/Arp 299

    NASA Astrophysics Data System (ADS)

    Bond, Howard E.; Aloisi, A.; Garmany, C.; James, B.; Newton, J.; Puckett, T.; Sohn, S. T.; van der Marel, R. P.; Nelemans, G.; Voss, R.; Nielsen, M.

    2011-01-01

    Several progenitor stars of Type II supernovae (SNe) have been identified in archival pre-explosion HST images. All of them are consistent with being red supergiants, as had been expected but never actually confirmed until the advent of HST imaging. The hydrogen-deficient Type Ib and Ic SNe are in a less satisfactory state. They are believed to be core-collapse SNe arising from massive stars that have lost their H envelopes. Unfortunately, however, there has never been an identified progenitor of an SN Ib or Ic, so it remains uncertain whether they are massive Wolf-Rayet stars, or less-massive stars in interacting binaries. The Type Ib SN 2010O was discovered by the amateur members of our team. It appeared in the starburst interacting galaxy NGC 3690 (Arp 299). It offers a tantalizing new opportunity, because NGC 3690 has been the subject of very extensive HST observations, ranging from the UV and optical to the near-IR, obtained before the outburst. SN 2010O is also interesting because of its close proximity to a variable X-ray source discovered by our team in pre-explosion Chandra images, which may support the interacting-binary scenario. We imaged SN 2010O with the HST's Wide Field Planetary Camera 3 in June 2010. We find that it lies close to, but not within, a young compact cluster. There is no conspicuous optical progenitor star in the pre-outburst HST images. We will discuss the implications for the progenitor objects of Type Ib supernovae. Funding from STScI is gratefully acknowledged.

  7. Protective effects of resveratrol against UVA-induced damage in ARPE19 cells.

    PubMed

    Chan, Chi-Ming; Huang, Cheng-Hua; Li, Hsin-Ju; Hsiao, Chien-Yu; Su, Ching-Chieh; Lee, Pei-Lan; Hung, Chi-Feng

    2015-01-01

    Ultraviolet radiation, especially UVA, can penetrate the lens, reach the retina, and induce oxidative stress to retinal pigment epithelial (RPE) cells. Even though it is weakly absorbed by protein and DNA, it may trigger the production of reactive oxygen species (ROS) and generate oxidative injury; oxidative injury to the retinal pigment epithelium has been implicated to play a contributory role in age-related macular degeneration (AMD). Studies showed that resveratrol, an abundant and active component of red grapes, can protect several cell types from oxidative stress. In this study, adult RPE cells being treated with different concentrations of resveratrol were used to evaluate the protective effect of resveratrol on RPE cells against UVA-induced damage. Cell viability assay showed that resveratrol reduced the UVA-induced decrease in RPE cell viability. Through flow cytometry analysis, we found that the generation of intracellular H2O2 induced by UVA irradiation in RPE cells could be suppressed by resveratrol in a concentration-dependent manner. Results of Western blot analysis demonstrated that resveratrol lowered the activation of UVA-induced extracellular signal-regulated kinase, c-jun-NH2 terminal kinase and p38 kinase in RPE cells. In addition, there was also a reduction in UVA-induced cyclooxygenase-2 (COX-2) expression in RPE cells pretreated with resveratrol. Our observations suggest that resveratrol is effective in preventing RPE cells from being damaged by UVA radiation, and is worth considering for further development as a chemoprotective agent for the prevention of early AMD. PMID:25775159

  8. Electronic structure of (In,Mn)As quantum dots buried in GaAs investigated by soft-x-ray ARPES

    NASA Astrophysics Data System (ADS)

    Bouravleuv, A. D.; Lev, L. L.; Piamonteze, C.; Wang, X.; Schmitt, T.; Khrebtov, A. I.; Samsonenko, Yu B.; Kanski, J.; Cirlin, G. E.; Strocov, V. N.

    2016-10-01

    Electronic structure of a molecular beam epitaxy-grown system of (In,Mn)As quantum dots (QDs) buried in GaAs is explored with soft-x-ray angle-resolved photoelectron spectroscopy (ARPES) using photon energies around 1 keV. This technique, ideally suited for buried systems, extends the momentum-resolving capabilities of conventional ARPES with enhanced probing depth as well as elemental and chemical state specificity achieved with resonant photoexcitation. The experimental results resolve the dispersive energy bands of the GaAs substrate buried in ∼2 nm below the surface, and the impurity states (ISs) derived from the substitutional Mn atoms in the (In,Mn)As QDs and oxidized Mn atoms distributed near the surface. An energy shift of the Mn ISs in the QDs compared to (In,Mn)As DMS is attributed to the band offset and proximity effect at the interface with the surrounding GaAs. The absence of any ISs in the vicinity of the VBM relates the electron transport in (In,Mn)As QDs to the prototype (In,Mn)As diluted magnetic semiconductor. The SX-ARPES results are supported by measurements of the shallow core levels under variation of probing depth through photon energy. X-ray absorption measurements identify significant diffusion of interstitial Mn atoms out of the QDs towards the surface, and the role of magnetic circular dichroism is to block the ferromagnetic response of the (In,Mn)As QDs. Possible routes are drawn to tune the growth procedure aiming at practical applications of the (In,Mn)As based systems.

  9. ARPES study of the evolution of band structure and charge density wave properties in RTe3 ( R=Y , La, Ce, Sm, Gd, Tb, and Dy)

    SciTech Connect

    Hussain, Zahid; Brouet, Veronique; Yang, Wanli; Zhou, Xingjiang; Hussain, Zahid; Moore, R.G.; He, R.; Lu, D. H.; Shen, Z.X.; Laverock, J.; Dugdale, S.B.; Ru, N.; Fisher, R.

    2008-01-16

    We present a detailed angle-resolved photoemission spectroscopy (ARPES) investigation of the RTe3 family, which sets this system as an ideal"textbook" example for the formation of a nesting driven charge density wave (CDW). This family indeed exhibits the full range of phenomena that can be associated to CDWinstabilities, from the opening of large gaps on the best nested parts of Fermi surface (up to 0.4 eV), to the existence of residual metallic pockets. ARPES is the best suited technique to characterize these features, thanks to its unique ability to resolve the electronic structure in k space. An additional advantage of RTe3 is that theband structure can be very accurately described by a simple two dimensional tight-binding (TB) model, which allows one to understand and easily reproduce many characteristics of the CDW. In this paper, we first establish the main features of the electronic structure by comparing our ARPES measurements with the linear muffin-tinorbital band calculations. We use this to define the validity and limits of the TB model. We then present a complete description of the CDW properties and of their strong evolution as a function of R. Using simple models, we are able to reproduce perfectly the evolution of gaps in k space, the evolution of the CDW wave vector with R, and the shape of the residual metallic pockets. Finally, we give an estimation of the CDWinteraction parameters and find that the change in the electronic density of states n (EF), due to lattice expansion when different R ions are inserted, has the correct order of magnitude to explain the evolution of the CDW properties.

  10. Electronic structure of (In,Mn)As quantum dots buried in GaAs investigated by soft-x-ray ARPES.

    PubMed

    Bouravleuv, A D; Lev, L L; Piamonteze, C; Wang, X; Schmitt, T; Khrebtov, A I; Samsonenko, Yu B; Kanski, J; Cirlin, G E; Strocov, V N

    2016-10-21

    Electronic structure of a molecular beam epitaxy-grown system of (In,Mn)As quantum dots (QDs) buried in GaAs is explored with soft-x-ray angle-resolved photoelectron spectroscopy (ARPES) using photon energies around 1 keV. This technique, ideally suited for buried systems, extends the momentum-resolving capabilities of conventional ARPES with enhanced probing depth as well as elemental and chemical state specificity achieved with resonant photoexcitation. The experimental results resolve the dispersive energy bands of the GaAs substrate buried in ∼2 nm below the surface, and the impurity states (ISs) derived from the substitutional Mn atoms in the (In,Mn)As QDs and oxidized Mn atoms distributed near the surface. An energy shift of the Mn ISs in the QDs compared to (In,Mn)As DMS is attributed to the band offset and proximity effect at the interface with the surrounding GaAs. The absence of any ISs in the vicinity of the VBM relates the electron transport in (In,Mn)As QDs to the prototype (In,Mn)As diluted magnetic semiconductor. The SX-ARPES results are supported by measurements of the shallow core levels under variation of probing depth through photon energy. X-ray absorption measurements identify significant diffusion of interstitial Mn atoms out of the QDs towards the surface, and the role of magnetic circular dichroism is to block the ferromagnetic response of the (In,Mn)As QDs. Possible routes are drawn to tune the growth procedure aiming at practical applications of the (In,Mn)As based systems. PMID:27631689

  11. Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method.

    PubMed

    Oshikawa, Mio; Tsutsui, Chihiro; Ikegami, Tomoko; Fuchida, Yuki; Matsubara, Maki; Toyama, Shigeru; Usami, Ron; Ohtoko, Kuniyo; Kato, Seishi

    2011-08-01

    PURPOSE. To collect an entire set of full-length cDNA clones derived from human retina-derived cell lines and to identify full-length transcripts for retinal preferentially expressed genes. METHODS. The full-length cDNA libraries were constructed from a retinoblastoma cell line, Y79, and a retinal pigment epithelium cell line, ARPE-19, using the vector-capping method, which generates a genuine full-length cDNA. By single-pass sequencing of the 5'-end of cDNA clones and subsequent mapping to the human genome, the authors determined their transcriptional start sites and annotated the cDNA clones. RESULTS. Of the 23,616 clones isolated from Y79-derived cDNA libraries, 19,229 full-length cDNA clones were identified and classified into 4808 genes, including genes of >10 kbp. Of the 7067 genes obtained from the Y79 and ARPE-19 libraries, the authors selected 72 genes that were preferentially expressed in the eye, of which 131 clones corresponding to 57 genes were fully sequenced. As a result, we discovered many variants that were produced by different transcriptional start sites, alternative splicing, and alternative polyadenylation. CONCLUSIONS. The bias-free, full-length cDNA libraries constructed using the vector-capping method were shown to be useful for collecting an entire set of full-length cDNA clones for these retinal cell lines. Full-length transcriptome analysis of these cDNA libraries revealed that there were, unexpectedly, many transcript variants for each gene, indicating that obtaining the full-length cDNA for each variant is indispensable for analyzing its function. The full-length cDNA clones (approximately 80,000 clones each for ARPE-19 and Y79) will be useful as a resource for investigating the human retina. PMID:21697133

  12. Development and Deployment of an Aerospace Recommended Practice (ARP) Compliant Measurement System for nvPM Certification Measurements of Aircraft Engines - Current Status.

    NASA Astrophysics Data System (ADS)

    Whitefield, P. D.; Hagen, D. E.; Lobo, P.; Miake-Lye, R. C.

    2015-12-01

    The Society of Automotive Engineers (SAE) Aircraft Exhaust Emissions Measurement Committee (E-31) has published an Aerospace Information Report (AIR) 6241 detailing the sampling system for the measurement of non-volatile particulate matter (nvPM) from aircraft engines (SAE 2013). The system is designed to operate in parallel with existing International Civil Aviation Organization (ICAO) Annex 16 compliant combustion gas sampling systems used for emissions certification from aircraft engines captured by conventional (Annex 16) gas sampling rakes (ICAO, 2008). The SAE E-31 committee is also working to ballot an Aerospace Recommended Practice (ARP) that will provide the methodology and system specification to measure nvPM from aircraft engines. The ARP is currently in preparation and is expected to be ready for ballot in 2015. A prototype AIR-compliant nvPM measurement system - The North American Reference System (NARS) has been built and evaluated at the MSTCOE under the joint sponsorship of the FAA, EPA and Transport Canada. It has been used to validate the performance characteristics of OEM AIR-compliant systems and is being used in engine certification type testing at OEM facilities to obtain data from a set of representative engines in the fleet. The data collected during these tests will be used by ICAO/CAEP/WG3/PMTG to develop a metric on which on the regulation for nvPM emissions will be based. This paper will review the salient features of the NARS including: (1) emissions sample transport from probe tip to the key diagnostic tools, (2) the mass and number-based diagnostic tools for nvPM mass and number concentration measurement and (3) methods employed to assess the extent of nvPM loss throughout the sampling system. This paper will conclude with a discussion of the recent results from inter-comparison studies conducted with other US - based systems that gives credence to the ARP's readiness for ballot.

  13. Electronic structure of (In,Mn)As quantum dots buried in GaAs investigated by soft-x-ray ARPES.

    PubMed

    Bouravleuv, A D; Lev, L L; Piamonteze, C; Wang, X; Schmitt, T; Khrebtov, A I; Samsonenko, Yu B; Kanski, J; Cirlin, G E; Strocov, V N

    2016-10-21

    Electronic structure of a molecular beam epitaxy-grown system of (In,Mn)As quantum dots (QDs) buried in GaAs is explored with soft-x-ray angle-resolved photoelectron spectroscopy (ARPES) using photon energies around 1 keV. This technique, ideally suited for buried systems, extends the momentum-resolving capabilities of conventional ARPES with enhanced probing depth as well as elemental and chemical state specificity achieved with resonant photoexcitation. The experimental results resolve the dispersive energy bands of the GaAs substrate buried in ∼2 nm below the surface, and the impurity states (ISs) derived from the substitutional Mn atoms in the (In,Mn)As QDs and oxidized Mn atoms distributed near the surface. An energy shift of the Mn ISs in the QDs compared to (In,Mn)As DMS is attributed to the band offset and proximity effect at the interface with the surrounding GaAs. The absence of any ISs in the vicinity of the VBM relates the electron transport in (In,Mn)As QDs to the prototype (In,Mn)As diluted magnetic semiconductor. The SX-ARPES results are supported by measurements of the shallow core levels under variation of probing depth through photon energy. X-ray absorption measurements identify significant diffusion of interstitial Mn atoms out of the QDs towards the surface, and the role of magnetic circular dichroism is to block the ferromagnetic response of the (In,Mn)As QDs. Possible routes are drawn to tune the growth procedure aiming at practical applications of the (In,Mn)As based systems.

  14. A Modification of the Isotope Generation and Depletion Code System ORIGEN. CCC-702/ORIGEN-ARP is recommended for new ORIGEN users.

    1984-05-04

    Version 00 KORIGEN is a modification of the isotope generation and depletion code system CCC-217/ORIGEN. ORIGEN solved the equations of radioactive growth and decay allowing continuous first order chemical processing and a neutron flux described by a three-region spectrum. Complex decay and transmutation schemes were treated. Note that this package has not been updated in many years; and all new ORIGEN users are advised to request the CCC-702/ORIGEN-ARP package, which is a PC application formore » Windows 95/NT or later.« less

  15. ARPES EVIDENCE FOR A QUASIPARTICLE LIQUID IN OVERDOPED Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+delta}.

    SciTech Connect

    WELLS,B.O.; YUSOF,Z.; VALLA,T.; FEDOROV,A.V.; JOHNSON,P.; KENDZIORA,C.; JIAN,S.; HINKS,D.

    2001-07-23

    High resolution angle-resolved photoemission spectroscopy of highly overdoped Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+{delta}} with a T{sub c} = 51K indicates that the basic transport processes in this material are fundamentally different from both the lesser doped cuprates as well as model metallic compounds. The overdoped sample has sharp ARPES peaks at the Fermi energy throughout the Brillouin zone even in the normal state, unlike the lesser-doped compounds. In particular, the spectra near ({pi},0) point show the presence of a sharp peak well above T{sub c}. The ARPES lineshapes, and thus the self energy, at a given energy are almost independent of k. Further, the quasiparticle scattering rate at the Fermi energy seems to be closely tied to direct resistivity measurements. This leads us to the conclusion that overdoped Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+{delta}} is best described as a quasiparticle liquid. However, the energy dependence of the scattering rates is quite similar to that found in the lesser-doped compounds and quite different from that seen in a typical metal.

  16. Water, methanol and dense gas tracers in the local ULIRG Arp 220: results from the new SEPIA Band 5 Science Verification campaign

    NASA Astrophysics Data System (ADS)

    Galametz, M.; Zhang, Z.-Y.; Immer, K.; Humphreys, E.; Aladro, R.; De Breuck, C.; Ginsburg, A.; Madden, S. C.; Møller, P.; Arumugam, V.

    2016-10-01

    We present a line survey of the ultraluminous infrared galaxy Arp 220, taken with the newly installed SEPIA (Swedish-European Southern Observatory PI receiver for APEX) Band 5 instrument on APEX (Atacama Pathfinder Experiment). We illustrate the capacity of SEPIA to detect the 183.3 GHz H2O 31,3-22,0 line against the atmospheric H2O absorption feature. We confirm the previous detection of the HCN(2-1) line, and detect new transitions of standard dense gas tracers such as HNC(2-1), HCO+(2-1), CS(4-3), C34S(4-3) and HC3N(20-19). We also detect HCN(2-1) v2 = 1 and the 193.5 GHz methanol (4-3) group for the first time. The absence of time variations in the megamaser water line compared to previous observations seems to rule out an AGN nuclear origin for the line. It could, on the contrary, favour a thermal origin instead, but also possibly be a sign that the megamaser emission is associated with star-forming cores washed out in the beam. We finally discuss how the new transitions of HCN, HNC and HCO+ refine our knowledge of the interstellar medium physical conditions in Arp 220.

  17. Tuning the electronic structure of bulk FeSe with chemical pressure using quantum oscillations and angle resolved photoemission spectroscopy (ARPES)

    NASA Astrophysics Data System (ADS)

    Coldea, Amalia

    FeSe is a unique and intriguing superconductor which can be tuned into a high temperature superconducting state using applied pressure, chemical intercalation and surface doping. In the absence of magnetism, the structural transition in FeSe is believed to be electronically driven, with the orbital degrees of freedom playing an important part. This scenario supports the stabilization of a nematic state in FeSe, which manifests as a Fermi surface deformation in the presence of strong interactions, as detected by ARPES. Another manifestation of the nematicity is the enhanced nematic susceptibility determined from elastoresistance measurements under applied strain. Isovalent Sulphur substitution onto the Selenium site constitutes a chemical pressure, which subtly modifies the electronic structure of FeSe, suppressing the structural transition without inducing high temperature superconductivity. I will present the evolution of the electronic structure with chemical pressure in FeSe, as determined from quantum oscillations and ARPES studies and I will discuss the suppression of the nematic electronic state and the role of electronic correlations. Experiments were performed at high magnetic field facilities in Tallahassee, Nijmegen and Toulouse and Diamond Light Source, UK. This work is mainly supported by EPSRC, UK (EP/I004475/1, EP/I017836/1) and I acknowledge my collaborators from Refs. .

  18. All-Trans Retinoic Acid Modulates DNA Damage Response and the Expression of the VEGF-A and MKI67 Genes in ARPE-19 Cells Subjected to Oxidative Stress.

    PubMed

    Tokarz, Paulina; Piastowska-Ciesielska, Agnieszka Wanda; Kaarniranta, Kai; Blasiak, Janusz

    2016-01-01

    Age-related macular degeneration (AMD) is characterized by the progressive degradation of photoreceptors and retinal pigment epithelium (RPE) cells. ARPE-19 is an RPE cell line established as an in vitro model for the study of AMD pathogenesis. Oxidative stress is an AMD pathogenesis factor that induces DNA damage. Thus, the oxidative stress-mediated DNA damage response (DDR) of ARPE-19 cells can be important in AMD pathogenesis. The metabolism of retinoids-which regulates cell proliferation, differentiation, and the visual cycle in the retina-was reported to be disturbed in AMD patients. In the present work, we studied the effect of all-trans retinoic acid (ATRA, a retinoid) on DDR in ARPE-19 cells subjected to oxidative stress. We observed that ATRA increased the level of reactive oxygen species (ROS), alkali-labile sites in DNA, DNA single-strand breaks, and cell death evoked by oxidative stress. ATRA did not modulate DNA repair or the distribution of cells in cell cycle in the response of ARPE-19 cells to oxidative stress. ATRA induced autophagy in the absence of oxidative stress, but had no effect on this process in the stress. ATRA induced over-expression of proliferation marker MKI67 and neovascularization marker VEGF-A. In conclusion, ATRA increased oxidative stress in ARPE-19 cells, resulting in more lesions to their DNA and cell death. Moreover, ATRA can modulate some properties of these cells, including neovascularization, which is associated with the exudative form of AMD. Therefore, ATRA can be important in the prevention, diagnosis, and therapy of AMD.

  19. All-Trans Retinoic Acid Modulates DNA Damage Response and the Expression of the VEGF-A and MKI67 Genes in ARPE-19 Cells Subjected to Oxidative Stress

    PubMed Central

    Tokarz, Paulina; Piastowska-Ciesielska, Agnieszka Wanda; Kaarniranta, Kai; Blasiak, Janusz

    2016-01-01

    Age-related macular degeneration (AMD) is characterized by the progressive degradation of photoreceptors and retinal pigment epithelium (RPE) cells. ARPE-19 is an RPE cell line established as an in vitro model for the study of AMD pathogenesis. Oxidative stress is an AMD pathogenesis factor that induces DNA damage. Thus, the oxidative stress-mediated DNA damage response (DDR) of ARPE-19 cells can be important in AMD pathogenesis. The metabolism of retinoids—which regulates cell proliferation, differentiation, and the visual cycle in the retina—was reported to be disturbed in AMD patients. In the present work, we studied the effect of all-trans retinoic acid (ATRA, a retinoid) on DDR in ARPE-19 cells subjected to oxidative stress. We observed that ATRA increased the level of reactive oxygen species (ROS), alkali-labile sites in DNA, DNA single-strand breaks, and cell death evoked by oxidative stress. ATRA did not modulate DNA repair or the distribution of cells in cell cycle in the response of ARPE-19 cells to oxidative stress. ATRA induced autophagy in the absence of oxidative stress, but had no effect on this process in the stress. ATRA induced over-expression of proliferation marker MKI67 and neovascularization marker VEGF-A. In conclusion, ATRA increased oxidative stress in ARPE-19 cells, resulting in more lesions to their DNA and cell death. Moreover, ATRA can modulate some properties of these cells, including neovascularization, which is associated with the exudative form of AMD. Therefore, ATRA can be important in the prevention, diagnosis, and therapy of AMD. PMID:27314326

  20. Common Origin of the Circular-dichroism Pattern in ARPES of SrTiO3 and CuxBi2Se3

    SciTech Connect

    Bell, Christopher

    2011-08-19

    We investigate circular dichroism in the angular distribution (CDAD) of photoelectrons from SrTiO{sub 3}:Nb and Cu{sub x}Bi{sub 2}Se{sub 3} recorded by 7-eV laser ARPES. In addition to the well-known node that occurs in CDAD when the incidence plane matches the mirror plane of the crystal, we show that another type of node occurs when the mirror plane of the crystal is vertical to the incidence plane and the electronic state is two dimensional. The flower-shaped CDAD's occurring around the Fermi level of SrTiO{sub 3}:Nb and around the Dirac point of Cu{sub x}Bi{sub 2}Se{sub 3} are explained on equal footings. A surface-state-to-surface-resonance transition is indicated for the topological state of Cu{sub x}Bi{sub 2}Se{sub 3}.

  1. Arpes study of the superconducting gap and pseudogap in Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+x}.

    SciTech Connect

    Campuzano, J. C.; Ding, H.; Norman, M. R.; Randeria, M.; Yokoya, T.; Takahashi, T.; Takeuchi, T.; Mochiku, T.; Kadowaki, K.; Guptasarma, P.; Hinks, D. G.; Materials Science Division; Univ. of Illinois at Chicago; Tata Inst. for Fundamental Research; Tohoku Univ.; Nagoya Univ.; National Research Inst. for Metals; Univ. of Tsukuba

    1998-01-01

    In this paper, we review some of our ARPES results on the superconducting and pseudogaps in Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+x}. We find that optimally and overdoped samples exhibit a d-wave gap, which closes at the same temperature, T{sub c}, for all k points. In underdoped samples, a leading edge gap is found up to a temperature T*>T{sub c}. We find that T* scales with the maximum low temperature gap, increasing as the doping is reduced. The momentum dependence of the pseudogap is similar to that of the superconducting gap; however, the pseudogap closes at different temperatures for different k points.

  2. Assimilation of coastal Doppler radar data with the ARPS 3DVAR and cloud analysis for the prediction of Hurricane Ike (2008)

    NASA Astrophysics Data System (ADS)

    Zhao, Kun; Xue, Ming

    2009-06-01

    The impact of radar data on the analysis and prediction of the structure, intensity, and track of landfalling Hurricane Ike (2008), at a cloud-resolving resolution, is examined. Radial velocity (Vr) and reflectivity (Z) data from coastal radars are assimilated over a 6-h period before Ike landfall, using the ARPS 3DVAR and cloud analysis package through 30-min assimilation cycles. Eighteen-hour predictions were made. All 4 experiments that assimilate radar data produce better structure, intensity and precipitation forecasts than that from operational GFS analysis. The improvement to the track forecast lasts for the entire 18 hours while that to intensity prediction lasts about 12 hours. The Vr data help improve the track forecast more while reflectivity data help improve intensity forecast most. Best results are obtained when both Z and Vr data are assimilated.

  3. OBSERVATIONS OF Arp 220 USING HERSCHEL-SPIRE: AN UNPRECEDENTED VIEW OF THE MOLECULAR GAS IN AN EXTREME STAR FORMATION ENVIRONMENT

    SciTech Connect

    Rangwala, Naseem; Maloney, Philip R.; Glenn, Jason; Kamenetzky, Julia; Wilson, Christine D.; Mentuch, Erin; Schirm, Maximilien R. P.; Rykala, Adam; Isaak, Kate; Baes, Maarten; Bendo, George J.; Boselli, Alessandro; Bradford, Charles M.; Clements, D. L.; Cooray, Asantha; Fulton, Trevor; Imhof, Peter; Madden, Suzanne C.; Sauvage, Marc; and others

    2011-12-10

    We present Herschel Spectral and Photometric Imaging Receiver Fourier Transform Spectrometer (Herschel SPIRE-FTS) observations of Arp 220, a nearby ultra-luminous infrared galaxy. The FTS provides continuous spectral coverage from 190 to 670 {mu}m, a wavelength region that is either very difficult to observe or completely inaccessible from the ground. The spectrum provides a good measurement of the continuum and detection of several molecular and atomic species. We detect luminous CO (J = 4-3 to 13-12) and water rotational transitions with comparable total luminosity {approx}2 Multiplication-Sign 10{sup 8} L{sub Sun }; very high-J transitions of HCN (J = 12-11 to 17-16) in absorption; strong absorption features of rare species such as OH{sup +}, H{sub 2}O{sup +}, and HF; and atomic lines of [C I] and [N II]. The modeling of the continuum shows that the dust is warm, with T = 66 K, and has an unusually large optical depth, with {tau}{sub dust} {approx} 5 at 100 {mu}m. The total far-infrared luminosity of Arp 220 is L{sub FIR} {approx} 2 Multiplication-Sign 10{sup 12} L{sub Sun }. Non-LTE modeling of the extinction corrected CO rotational transitions shows that the spectral line energy distribution of CO is fit well by two temperature components: cold molecular gas at T {approx} 50 K and warm molecular gas at T {approx} 1350{sup +280}{sub -100} K (the inferred temperatures are much lower if CO line fluxes are not corrected for dust extinction). These two components are not in pressure equilibrium. The mass of the warm gas is 10% of the cold gas, but it dominates the CO luminosity. The ratio of total CO luminosity to the total FIR luminosity is L{sub CO}/L{sub FIR} {approx} 10{sup -4} (the most luminous lines, such as J = 6-5, have L{sub CO,J=6-5}/L{sub FIR} {approx} 10{sup -5}). The temperature of the warm gas is in excellent agreement with the observations of H{sub 2} rotational lines. At 1350 K, H{sub 2} dominates the cooling ({approx}20 L{sub Sun} M{sup -1}{sub

  4. Observations of Arp 220 Using Herschel-SPIRE: An Unprecedented View of the Molecular Gas in an Extreme Star Formation Environment

    NASA Astrophysics Data System (ADS)

    Rangwala, Naseem; Maloney, Philip R.; Glenn, Jason; Wilson, Christine D.; Rykala, Adam; Isaak, Kate; Baes, Maarten; Bendo, George J.; Boselli, Alessandro; Bradford, Charles M.; Clements, D. L.; Cooray, Asantha; Fulton, Trevor; Imhof, Peter; Kamenetzky, Julia; Madden, Suzanne C.; Mentuch, Erin; Sacchi, Nicola; Sauvage, Marc; Schirm, Maximilien R. P.; Smith, M. W. L.; Spinoglio, Luigi; Wolfire, Mark

    2011-12-01

    We present Herschel Spectral and Photometric Imaging Receiver Fourier Transform Spectrometer (Herschel SPIRE-FTS) observations of Arp 220, a nearby ultra-luminous infrared galaxy. The FTS provides continuous spectral coverage from 190 to 670 μm, a wavelength region that is either very difficult to observe or completely inaccessible from the ground. The spectrum provides a good measurement of the continuum and detection of several molecular and atomic species. We detect luminous CO (J = 4-3 to 13-12) and water rotational transitions with comparable total luminosity ~2 × 108 L ⊙ very high-J transitions of HCN (J = 12-11 to 17-16) in absorption; strong absorption features of rare species such as OH+, H2O+, and HF; and atomic lines of [C I] and [N II]. The modeling of the continuum shows that the dust is warm, with T = 66 K, and has an unusually large optical depth, with τdust ~ 5 at 100 μm. The total far-infrared luminosity of Arp 220 is L FIR ~ 2 × 1012 L ⊙. Non-LTE modeling of the extinction corrected CO rotational transitions shows that the spectral line energy distribution of CO is fit well by two temperature components: cold molecular gas at T ~ 50 K and warm molecular gas at T ~ 1350+280 - 100 K (the inferred temperatures are much lower if CO line fluxes are not corrected for dust extinction). These two components are not in pressure equilibrium. The mass of the warm gas is 10% of the cold gas, but it dominates the CO luminosity. The ratio of total CO luminosity to the total FIR luminosity is L CO/L FIR ~ 10-4 (the most luminous lines, such as J = 6-5, have L CO, J = 6-5/L FIR ~ 10-5). The temperature of the warm gas is in excellent agreement with the observations of H2 rotational lines. At 1350 K, H2 dominates the cooling (~20 L ⊙ M -1 ⊙) in the interstellar medium compared to CO (~0.4 L ⊙ M -1 ⊙). We have ruled out photodissociation regions, X-ray-dominated regions, and cosmic rays as likely sources of excitation of this warm molecular gas

  5. Human Lyme arthritis and the immunoglobulin G antibody response to the 37-kilodalton arthritis-related protein of Borrelia burgdorferi.

    PubMed

    Salazar, Carlos A; Rothemich, Monika; Drouin, Elise E; Glickstein, Lisa; Steere, Allen C

    2005-05-01

    In Borrelia burgdorferi-infected C3H-scid mice, antiserum to a differentially expressed, 37-kDa spirochetal outer-surface protein, termed arthritis-related protein (Arp), has been shown to prevent or reduce the severity of arthritis. In this study, we determined the immunoglobulin G (IgG) antibody responses to this spirochetal protein in single serum samples from 124 antibiotic-treated human patients with early or late manifestations of Lyme disease and in serial serum samples from 20 historic, untreated patients who were followed longitudinally from early infection through the period of arthritis. These 20 patients were representative of the spectrum of the severity and duration of Lyme arthritis. Among the 124 antibiotic-treated patients, 53% with culture-proven erythema migrans (EM) had IgG responses to recombinant glutathione S-transferase (GST)-Arp, as did 59% of the patients with facial palsy and 68% of those with Lyme arthritis. In addition, 75 to 80% of the 20 past, untreated patients had reactivity with this protein when EM was present, during initial episodes of joint pain, or during the maximal period of arthritis. There was no association at any of these three time points between GST-Arp antibody levels and the severity of the maximal attack of arthritis or the total duration of arthritis. Thus, after the first several weeks of infection, 60 to 80% of patients had IgG antibody responses to GST-Arp, but this response did not correlate with the severity or duration of Lyme arthritis.

  6. Human Lyme Arthritis and the Immunoglobulin G Antibody Response to the 37-Kilodalton Arthritis-Related Protein of Borrelia burgdorferi

    PubMed Central

    Salazar, Carlos A.; Rothemich, Monika; Drouin, Elise E.; Glickstein, Lisa; Steere, Allen C.

    2005-01-01

    In Borrelia burgdorferi-infected C3H-scid mice, antiserum to a differentially expressed, 37-kDa spirochetal outer-surface protein, termed arthritis-related protein (Arp), has been shown to prevent or reduce the severity of arthritis. In this study, we determined the immunoglobulin G (IgG) antibody responses to this spirochetal protein in single serum samples from 124 antibiotic-treated human patients with early or late manifestations of Lyme disease and in serial serum samples from 20 historic, untreated patients who were followed longitudinally from early infection through the period of arthritis. These 20 patients were representative of the spectrum of the severity and duration of Lyme arthritis. Among the 124 antibiotic-treated patients, 53% with culture-proven erythema migrans (EM) had IgG responses to recombinant glutathione S-transferase (GST)-Arp, as did 59% of the patients with facial palsy and 68% of those with Lyme arthritis. In addition, 75 to 80% of the 20 past, untreated patients had reactivity with this protein when EM was present, during initial episodes of joint pain, or during the maximal period of arthritis. There was no association at any of these three time points between GST-Arp antibody levels and the severity of the maximal attack of arthritis or the total duration of arthritis. Thus, after the first several weeks of infection, 60 to 80% of patients had IgG antibody responses to GST-Arp, but this response did not correlate with the severity or duration of Lyme arthritis. PMID:15845501

  7. Analysis and implementation of PM sampling methodology protocols to aid in the development of an ARP (aerospace recommended practice) for aircraft non-volatile PM measurements

    NASA Astrophysics Data System (ADS)

    Catron, Brian Lowell

    Due to the growing concerns that particulate matter (PM) have on health and the environment, there is a need to include mass and number non-volatile PM measurements to current jet engine certification. This thesis looks at the necessary work required to help produce recommendations and perform background research to aid in the creation of an improved Aerospace Recommended Practice (ARP) (by the SAE E-31 Committee). This work addressed the following issues. The investigation began in the Missouri S&T Center of Excellence for Aerospace Particulate Emissions Reduction Research (COE) laboratory with an examination of the jet engine surrogate used, the miniCAST, as well as integrating it into the COE's PM measurement system. A clean PM sample line was aged by running a PM source through it until a steady state signal was measured by the instruments in order to make a recommended procedure for line conditioning as well as reconditioning. Several eductors were studied for their performance characteristics and compared against desired characteristics, which suggested a need to include a pressure relief valve to cap the sample pressure at the eductor entrance. A volatile particle remover (VPR) was studied for penetration and ability to remove volatile material. A prototype E-31 system was setup at the second alternative aviation fuel experiment (AAFEX II), which provided a direct comparison of probe tip dilution and downstream dilution and found comparable results when line loss was taken into account. Also performed at AAFEX II was a study that compared measured sample line penetration with theoretical calculations finding that theoretical calculations were an accurate alternative of measuring line loss. Two PM sampling systems were setup at an ARP demonstration and both system had similar results for both number and mass measurement. An instrument comparison was also performed that included an examination of condensation particle counter (CPC) cutoff size. It was also

  8. Mitochondrial "movement" and lens optics following oxidative stress from UV-B irradiation: cultured bovine lenses and human retinal pigment epithelial cells (ARPE-19) as examples.

    PubMed

    Bantseev, Vladimir; Youn, Hyun-Yi

    2006-12-01

    Mitochondria provide energy generated by oxidative phosphorylation and at the same time play a central role in apoptosis and aging. As a byproduct of respiration, the electron transport chain is known to be the major intracellular site for the generation of reactive oxygen species (ROS). Exposure to solar and occupational ultraviolet (UV) radiation, and thus production of ROS and subsequent cell death, has been implicated in a large spectrum of skin and ocular pathologies, including cataract. Retinal pigment epithelial cell apoptosis generates photoreceptor dysfunction and ultimately visual impairment. The purpose of this article was to characterize in vitro changes following oxidative stress with UV-B radiation in (a) ocular lens optics and cellular function in terms of mitochondrial dynamics of bovine lens epithelium and superficial cortical fiber cells and (b) human retinal pigment epithelial (ARPE-19) cells. Cultured bovine lenses and confluent cultures of ARPE-19 cells were irradiated with broadband UV-B radiation at energy levels of 0.5 and 1.0 J/cm(2). Lens optical function (spherical aberration) was monitored daily up to 14 days using an automated laser scanning system that was developed at the University of Waterloo. This system consists of a single collimated scanning helium-neon laser source that projects a thin (0.05 mm) laser beam onto a plain mirror mounted at 45 degrees on a carriage assembly. This mirror reflects the laser beam directly up through the scanner table surface and through the lens under examination. A digital camera captures the actual position and slope of the laser beam at each step. When all steps have been made, the captured data for each step position is used to calculate the back vertex distance for each position and the difference in that measurement between beams. To investigate mitochondrial movement, the mitochondria-specific fluorescent dye Rhodamine 123 was used. Time series were acquired with a Zeiss 510 (configuration Meta

  9. COMMIX-1AR/P: A three-dimensional transient single-phase computer program for thermal hydraulic analysis of single and multicomponent systems. Volume 2, User`s guide

    SciTech Connect

    Garner, P.L.; Blomquist, R.N.; Gelbard, E.M.

    1992-09-01

    The COMMIX-1AR/P computer program is designed for analyzing the steady-state and transient aspects of single-phase fluid flow and heat transfer in three spatial dimensions. This version is an extension of the modeling in COMMIX-1A to include multiple fluids in physically separate regions of the computational domain, modeling descriptions for pumps, radiation heat transfer between surfaces of the solids which are embedded in or surround the fluid, a k-{var_epsilon} model for fluid turbulence, and improved numerical techniques. The porous-medium formulation in COMMIX allows the program to be applied to a wide range of problems involving both simple and complex geometrical arrangements. The input preparation and execution procedures are presented for the COMMIX-1AR/P program and several postprocessor programs which produce graphical displays of the calculated results.

  10. Regulation of DNA Translocation Efficiency within the Chromatin Remodeler RSC/Sth1 Potentiates Nucleosome Sliding and Ejection.

    PubMed

    Clapier, Cedric R; Kasten, Margaret M; Parnell, Timothy J; Viswanathan, Ramya; Szerlong, Heather; Sirinakis, George; Zhang, Yongli; Cairns, Bradley R

    2016-05-01

    The RSC chromatin remodeler slides and ejects nucleosomes, utilizing a catalytic subunit (Sth1) with DNA translocation activity, which can pump DNA around the nucleosome. A central question is whether and how DNA translocation is regulated to achieve sliding versus ejection. Here, we report the regulation of DNA translocation efficiency by two domains residing on Sth1 (Post-HSA and Protrusion 1) and by actin-related proteins (ARPs) that bind Sth1. ARPs facilitated sliding and ejection by improving "coupling"-the amount of DNA translocation by Sth1 relative to ATP hydrolysis. We also identified and characterized Protrusion 1 mutations that promote "coupling," and Post-HSA mutations that improve ATP hydrolysis; notably, the strongest mutations conferred efficient nucleosome ejection without ARPs. Taken together, sliding-to-ejection involves a continuum of DNA translocation efficiency, consistent with higher magnitudes of ATPase and coupling activities (involving ARPs and Sth1 domains), enabling the simultaneous rupture of multiple histone-DNA contacts facilitating ejection.

  11. Arabidopsis CROOKED encodes for the smallest subunit of the ARP2/3 complex and controls cell shape by region specific fine F-actin formation.

    PubMed

    Mathur, Jaideep; Mathur, Neeta; Kirik, Victor; Kernebeck, Birgit; Srinivas, Bhylahalli Purushottam; Hülskamp, Martin

    2003-07-01

    The generation of a specific cell shape requires differential growth, whereby specific regions of the cell expand more relative to others. The Arabidopsis crooked mutant exhibits aberrant cell shapes that develop because of mis-directed expansion, especially during a rapid growth phase. GFP-aided visualization of the F-actin cytoskeleton and the behavior of subcellular organelles in different cell-types in crooked and wild-type Arabidopsis revealed that localized expansion is promoted in cellular regions with fine F-actin arrays but is restricted in areas that maintain dense F-actin. This suggested that a spatiotemporal distinction between fine versus dense F-actin in a growing cell could determine the final shape of the cell. CROOKED was molecularly identified as the plant homolog of ARPC5, the smallest sub-unit of the ARP2/3 complex that in other organisms is renowned for its role in creating dendritic arrays of fine F-actin. Rescue of crooked phenotype by the human ortholog provides the first molecular evidence for the presence and functional conservation of the complex in higher plants. Our cell-biological and molecular characterization of CROOKED suggests a general actin-based mechanism for regulating differential growth and generating cell shape diversity. PMID:12783786

  12. Degradation of vinyl chloride (VC) by the sulfite/UV advanced reduction process (ARP): effects of process variables and a kinetic model.

    PubMed

    Liu, Xu; Yoon, Sunhee; Batchelor, Bill; Abdel-Wahab, Ahmed

    2013-06-01

    Vinyl chloride (VC) poses a threat to humans and environment due to its toxicity and carcinogenicity. In this study, an advanced reduction process (ARP) that combines sulfite with UV light was developed to destroy VC. The degradation of VC followed pseudo-first-order decay kinetics and the effects of several experimental factors on the degradation rate constant were investigated. The largest rate constant was observed at pH9, but complete dechlorination was obtained at pH11. Higher sulfite dose and light intensity were found to increase the rate constant linearly. The rate constant had a little drop when the initial VC concentration was below 1.5mg/L and then was approximately constant between 1.5mg/L and 3.1mg/L. A degradation mechanism was proposed to describe reactions between VC and the reactive species that were produced by the photolysis of sulfite. A kinetic model that described major reactions in the system was developed and was able to explain the dependence of the rate constant on the experimental factors examined. This study may provide a new treatment technology for the removal of a variety of halogenated contaminants.

  13. Downregulating p22phox ameliorates inflammatory response in Angiotensin II-induced oxidative stress by regulating MAPK and NF-κB pathways in ARPE-19 cells.

    PubMed

    Qiu, Yiguo; Tao, Lifei; Lei, Chunyan; Wang, Jiaming; Yang, Peizeng; Li, Qiuhong; Lei, Bo

    2015-01-01

    Oxidative stress and inflammation are two interrelated biological events implicated in the pathogenesis of many diseases. Reactive oxygen species (ROS) produced under oxidative stress play a key role in pathological conditions. Inhibition of p22phox, an indispensable component of the NADPH oxidase (NOX) complex comprising the main source of ROS, plays a protective role in many ocular conditions by inhibiting the activation of NOXs and the generation of ROS. However, little is understood regarding the role of p22phox in oxidative stress-related inflammation in the eye. We used a p22phox small interfering RNA (siRNA) to transfect the retinal pigment epithelium (RPE)-derived cell line ARPE-19, and human primary RPE (hRPE) cells, then stimulated with Ang II. We observed a potent anti-inflammatory effect and studied the underlying mechanism. Downregulating p22phox resulted in decreased ROS generation, a reduction of NOXs (NOX1, 2, 4) and a decrease in inflammatory cytokine. In addition, p22phox downregulation reduced the activation of the MAPK and NF-κB signaling pathways. We conclude that inhibition of p22phox has an anti-inflammatory effect in Ang II-induced oxidative stress. Suppressing the MAPK and NF-κB pathways is involved in this protective effect. These results suggest that p22phox may provide a promising therapeutic target for oxidative stress-induced ocular inflammation.

  14. Selective activation of p120ctn-Kaiso signaling to unlock contact inhibition of ARPE-19 cells without epithelial-mesenchymal transition.

    PubMed

    Chen, Hung-Chi; Zhu, Ying-Ting; Chen, Szu-Yu; Tseng, Scheffer C G

    2012-01-01

    Contact-inhibition ubiquitously exists in non-transformed cells and explains the poor regenerative capacity of in vivo human retinal pigment epithelial cells (RPE) during aging, injury and diseases. RPE injury or degeneration may unlock mitotic block mediated by contact inhibition but may also promote epithelial-mesenchymal transition (EMT) contributing to retinal blindness. Herein, we confirmed that EMT ensued in post-confluent ARPE-19 cells when contact inhibition was disrupted with EGTA followed by addition of EGF and FGF-2 because of activation of canonical Wnt and Smad/ZEB signaling. In contrast, knockdown of p120-catenin (p120) unlocked such mitotic block by activating p120/Kaiso, but not activating canonical Wnt and Smad/ZEB signaling, thus avoiding EMT. Nuclear BrdU labeling was correlated with nuclear release of Kaiso through p120 nuclear translocation, which was associated with activation of RhoA-ROCK signaling, destabilization of microtubules. Prolonged p120 siRNA knockdown followed by withdrawal further expanded RPE into more compact monolayers with a normal phenotype and a higher density. This new strategy based on selective activation of p120/Kaiso but not Wnt/β-catenin signaling obviates the need of using single cells and the risk of EMT, and may be deployed to engineer surgical grafts containing RPE and other tissues. PMID:22590627

  15. Quantifying electronic correlation strength in a complex oxide: a combined DMFT and ARPES study of LaNiO{sub 3}

    SciTech Connect

    Nowadnick, E. A.; Ruf, J. P.; Park, H.; King, P. D. C.; Schlom, D. G.; Shen, K. M.; Millis, A. J.

    2015-12-07

    The electronic correlation strength is a basic quantity that characterizes the physical properties of materials such as transition metal oxides. Determining correlation strengths requires both precise definitions and a careful comparison between experiment and theory. In this paper, we define the correlation strength via the magnitude of the electron self-energy near the Fermi level. For the case of LaNiO3, we obtain both the experimental and theoretical mass enhancements m/m by considering high resolution angle-resolved photoemission spectroscopy (ARPES) measurements and density functional+dynamical mean field theory (DFT+DMFT) calculations.We use valence-band photoemission data to constrain the free parameters in the theory and demonstrate a quantitative agreement between the experiment and theory when both the realistic crystal structure and strong electronic correlations are taken into account. In addition, by considering DFT+DMFT calculations on epitaxially strained LaNiO3, we find a strain-induced evolution of m/m in qualitative agreement with trends derived from optics experiments. These results provide a benchmark for the accuracy of the DFT+DMFT theoretical approach, and can serve as a test case when considering other complex materials. By establishing the level of accuracy of the theory, this work also will enable better quantitative predictions when engineering new emergent properties in nickelate heterostructures.

  16. Wiskott-Aldrich syndrome proteins in the nucleus: aWASH with possibilities.

    PubMed

    Verboon, Jeffrey M; Sugumar, Bina; Parkhurst, Susan M

    2015-01-01

    Actin and proteins that regulate its dynamics or interactions have well-established roles in the cytoplasm where they function as key components of the cytoskeleton to control diverse processes, including cellular infrastructure, cellular motility, cell signaling, and vesicle transport. Recent work has also uncovered roles for actin and its regulatory proteins in the nucleus, primarily in mechanisms governing gene expression. The Wiskott Aldrich Syndrome (WAS) family of proteins, comprising the WASP/N-WASP, SCAR/WAVE, WHAMM/JMY/WHAMY, and WASH subfamilies, function in the cytoplasm where they activate the Arp2/3 complex to form branched actin filaments. WAS proteins are present in the nucleus and have been implicated as transcriptional regulators. We found that Drosophila Wash, in addition to transcriptional effects, is involved in global nuclear architecture. Here we summarize the regulation and function of nuclear WAS proteins, and highlight how our work with Wash expands the possibilities for the functions of these proteins in the nucleus.

  17. Systematic mutational analysis of the amino-terminal domain of the Listeria monocytogenes ActA protein reveals novel functions in actin-based motility.

    PubMed

    Lauer, P; Theriot, J A; Skoble, J; Welch, M D; Portnoy, D A

    2001-12-01

    The Listeria monocytogenes ActA protein acts as a scaffold to assemble and activate host cell actin cytoskeletal factors at the bacterial surface, resulting in directional actin polymerization and propulsion of the bacterium through the cytoplasm. We have constructed 20 clustered charged-to-alanine mutations in the NH2-terminal domain of ActA and replaced the endogenous actA gene with these molecular variants. These 20 clones were evaluated in several biological assays for phenotypes associated with particular amino acid changes. Additionally, each protein variant was purified and tested for stimulation of the Arp2/3 complex, and a subset was tested for actin monomer binding. These specific mutations refined the two regions involved in Arp2/3 activation and suggest that the actin-binding sequence of ActA spans 40 amino acids. We also identified a 'motility rate and cloud-to-tail transition' region in which nine contiguous mutations spanning amino acids 165-260 caused motility rate defects and changed the ratio of intracellular bacteria associated with actin clouds and comet tails without affecting Arp2/3 activation. Several unusual motility phenotypes were associated with amino acid changes in this region, including altered paths through the cytoplasm, discontinuous actin tails in host cells and the tendency to 'skid' or dramatically change direction while moving. These unusual phenotypes illustrate the complexity of ActA functions that control the actin-based motility of L. monocytogenes.

  18. The PCH family protein, Cdc15p, recruits two F-actin nucleation pathways to coordinate cytokinetic actin ring formation in Schizosaccharomyces pombe.

    PubMed

    Carnahan, Robert H; Gould, Kathleen L

    2003-09-01

    Cytokinetic actin ring (CAR) formation in Schizosaccharomyces pombe requires two independent actin nucleation pathways, one dependent on the Arp2/3 complex and another involving the formin Cdc12p. Here we investigate the role of the S. pombe Cdc15 homology family protein, Cdc15p, in CAR assembly and find that it interacts with proteins from both of these nucleation pathways. Cdc15p binds directly to the Arp2/3 complex activator Myo1p, which likely explains why actin patches and the Arp2/3 complex fail to be medially recruited during mitosis in cdc15 mutants. Cdc15p also binds directly to Cdc12p. Cdc15p and Cdc12p not only display mutual dependence for CAR localization, but also exist together in a ring-nucleating structure before CAR formation. The disruption of these interactions in cdc15 null cells is likely to be the reason for their complete lack of CARs. We propose a model in which Cdc15p plays a critical role in recruiting and coordinating the pathways essential for the assembly of medially located F-actin filaments and construction of the CAR.

  19. Systematic mutational analysis of the amino-terminal domain of the Listeria monocytogenes ActA protein reveals novel functions in actin-based motility.

    PubMed

    Lauer, P; Theriot, J A; Skoble, J; Welch, M D; Portnoy, D A

    2001-12-01

    The Listeria monocytogenes ActA protein acts as a scaffold to assemble and activate host cell actin cytoskeletal factors at the bacterial surface, resulting in directional actin polymerization and propulsion of the bacterium through the cytoplasm. We have constructed 20 clustered charged-to-alanine mutations in the NH2-terminal domain of ActA and replaced the endogenous actA gene with these molecular variants. These 20 clones were evaluated in several biological assays for phenotypes associated with particular amino acid changes. Additionally, each protein variant was purified and tested for stimulation of the Arp2/3 complex, and a subset was tested for actin monomer binding. These specific mutations refined the two regions involved in Arp2/3 activation and suggest that the actin-binding sequence of ActA spans 40 amino acids. We also identified a 'motility rate and cloud-to-tail transition' region in which nine contiguous mutations spanning amino acids 165-260 caused motility rate defects and changed the ratio of intracellular bacteria associated with actin clouds and comet tails without affecting Arp2/3 activation. Several unusual motility phenotypes were associated with amino acid changes in this region, including altered paths through the cytoplasm, discontinuous actin tails in host cells and the tendency to 'skid' or dramatically change direction while moving. These unusual phenotypes illustrate the complexity of ActA functions that control the actin-based motility of L. monocytogenes. PMID:11886549

  20. Co-Expression of Anti-Rotavirus Proteins (Llama VHH Antibody Fragments) in Lactobacillus: Development and Functionality of Vectors Containing Two Expression Cassettes in Tandem

    PubMed Central

    Günaydın, Gökçe; Álvarez, Beatriz; Lin, Yin; Hammarström, Lennart; Marcotte, Harold

    2014-01-01

    Rotavirus is an important pediatric pathogen, causing severe diarrhea and being associated with a high mortality rate causing approximately 500 000 deaths annually worldwide. Even though some vaccines are currently available, their efficacy is lower in the developing world, as compared to developed countries. Therefore, alternative or complementary treatment options are needed in the developing countries where the disease burden is the largest. The effect of Lactobacillus in promoting health and its use as a vehicle for delivery of protein and antibody fragments was previously shown. In this study, we have developed co-expression vectors enabling Lactobacillus paracasei BL23 to produce two VHH fragments against rotavirus (referred to as anti-rotavirus proteins 1 and 3, ARP1 and ARP3) as secreted and/or surface displayed products. ARP1 and ARP3 fragments were successfully co-expressed as shown by Western blot and flow cytometry. In addition, engineered Lactobacillus produced VHH antibody fragments were shown to bind to a broad range of rotavirus serotypes (including the human rotavirus strains 69M, Va70, F45, DS1, Wa and ST3 and simian rotavirus strains including RRV and SA11), by flow cytometry and ELISA. Hereby, we have demonstrated for the first time that when RRV was captured by one VHH displayed on the surface of co-expressor Lactobacillus, targeting other epitope was possible with another VHH secreted from the same bacterium. Therefore, Lactobacillus producing two VHH antibody fragments may potentially serve as treatment against rotavirus with a reduced risk of development of escape mutants. This co-expression and delivery platform can also be used for delivery of VHH fragments against a variety of mucosal pathogens or production of other therapeutic molecules. PMID:24781086

  1. Impact of assimilating airborne Doppler radar velocity data using the ARPS 3DVAR on the analysis and prediction of Hurricane Ike (2008)

    NASA Astrophysics Data System (ADS)

    Du, Ningzhu; Xue, Ming; Zhao, Kun; Min, Jinzhong

    2012-09-01

    The ARPS 3DVAR data assimilation system is enhanced and used for the first time to assimilate airborne Doppler radar wind observations. It is applied to Hurricane Ike (2008), where radar observations taken along four flight legs through the hurricane vortex 14 to 18 h before it made landfall are assimilated. An optimal horizontal de-correlation scale for the background error is determined through sensitivity experiments. A comparison is made between assimilating retrieved winds and assimilating radial velocity data directly. The effect of the number of assimilation cycles, each analyzing data from one flight leg, is also examined. The assimilation of retrieved wind data and of radial velocity data produces similar results. However, direct assimilation of radial velocity data is recommended for both theoretical and practical reasons. In both cases, velocity data assimilation improves the analyzed hurricane structure and intensity as well as leads to better prediction of the intensity. Improvement to the track forecasting is also found. The assimilation of radial velocity observations from all four flight legs through intermittent assimilation cycles produces the best analyses and forecasts. The first analysis in the first cycle tends to produce the largest analysis increment. It is through the mutual adjustments among model variables during the forecast periods that a balanced vortex with lowered central pressure is established. The wind speeds extracted from the assimilated model state agree very well with independent surface wind measurements by the stepped-frequency microwave radiometer onboard the aircraft, and with independent flight-level wind speeds detected by the NOAA P-3 aircraft in-flight measurements. Twenty-four hour accumulated precipitation is noticeably improved over the case without radar data assimilation.

  2. The CARMA Paired Antenna Calibration System: Atmospheric Phase Correction for Millimeter Wave Interferometry and Its Application to Mapping the Ultraluminous Galaxy Arp 193

    NASA Astrophysics Data System (ADS)

    Zauderer, B. Ashley; Bolatto, Alberto D.; Vogel, Stuart N.; Carpenter, John M.; Peréz, Laura M.; Lamb, James W.; Woody, David P.; Bock, Douglas C.-J.; Carlstrom, John E.; Culverhouse, Thomas L.; Curley, Roger; Leitch, Erik M.; Plambeck, Richard L.; Pound, Marc W.; Marrone, Daniel P.; Muchovej, Stephen J.; Mundy, Lee G.; Teng, Stacy H.; Teuben, Peter J.; Volgenau, Nikolaus H.; Wright, Melvyn C. H.; Wu, Dalton

    2016-01-01

    Phase fluctuations introduced by the atmosphere are the main limiting factor in attaining diffraction limited performance in extended interferometric arrays at millimeter and submillimeter wavelengths. We report the results of C-PACS, the Combined Array for Research in Millimeter-Wave Astronomy Paired Antenna Calibration System. We present a systematic study of several hundred test observations taken during the 2009–2010 winter observing season where we utilize CARMA's eight 3.5 m antennas to monitor an atmospheric calibrator while simultaneously acquiring science observations with 6.1 and 10.4 m antennas on baselines ranging from a few hundred meters to ∼2 km. We find that C-PACS is systematically successful at improving coherence on long baselines under a variety of atmospheric conditions. We find that the angular separation between the atmospheric calibrator and target source is the most important consideration, with consistently successful phase correction at CARMA requiring a suitable calibrator located ≲6° away from the science target. We show that cloud cover does not affect the success of C-PACS. We demonstrate C-PACS in typical use by applying it to the observations of the nearby very luminous infrared galaxy Arp 193 in 12CO(2-1) at a linear resolution of ≈70 pc (0.″12 × 0.″18), 3 times better than previously published molecular maps of this galaxy. We resolve the molecular disk rotation kinematics and the molecular gas distribution and measure the gas surface densities and masses on 90 pc scales. We find that molecular gas constitutes ∼30% of the dynamical mass in the inner 700 pc of this object with a surface density ∼104 M⊙ pc‑2 we compare these properties to those of the starburst region of NGC 253.

  3. CALIFA spectroscopy of the interacting galaxy NGC 5394 (Arp 84): starbursts, enhanced [N II]6584 and signs of outflows and shocks

    NASA Astrophysics Data System (ADS)

    Roche, Nathan; Humphrey, Andrew; Gomes, Jean Michel; Papaderos, Polychronis; Lagos, Patricio; Sánchez, Sebastián F.

    2015-11-01

    We investigate the spiral galaxy NGC 5394, which is strongly interacting with the larger spiral NGC 5395 (the pair is Arp 84), using optical integral-field spectroscopy from the CALIFA (Calar Alto Legacy Integral Field Area) survey. Spatially resolved equivalent widths, emission-line ratios and kinematics reveal many features related to the interaction, which has reshaped the galaxy. H α maps (with other diagnostic emission lines) show a concentrated central (r < 1 kpc) starburst and three less luminous star-forming regions (one knot far out in the northern arm), and we estimate the dust-corrected total star-formation rate as 3.39 M⊙ yr- 1. However, much of the galaxy, especially the outer tidal arms, has a post-starburst spectrum, evidence of a more extensive episode of star formation a few ×108 yr ago, triggered by the previous perigalacticon. The [N II]6584/H α ratio is high in the nucleus, reaching 0.63 at the centre, which we interpret as related to high electron density (ne ≃ 750 cm- 3 from the [S II]{6717over 6731} ratio). We find a central region of strong and blueshifted Na I(5890,5896) absorption, indicative of a starburst-driven outflow from the nucleus at an estimated velocity ˜223 km s- 1. The CALIFA data also show an annular region at radii 2.25-4 kpc from the nucleus, with elevated ratios of [N II], [O I]6300 etc. to the Balmer lines - this is evidence of shock excitation, which might be the result of interaction-triggered gas inflow.

  4. Theoretical Modelling of the Diffuse Emission of (gamma)-rays From Extreme Regions of Star Formation: The Case of Arp 220

    SciTech Connect

    Torres, D F

    2004-07-09

    Our current understanding of ultraluminous infrared galaxies suggest that they are recent galaxy mergers in which much of the gas in the former spiral disks, particularly that located at distances less than 5 kpc from each of the pre-merger nuclei, has fallen into a common center, triggering a huge starburst phenomenon. This large nuclear concentration of molecular gas has been detected by many groups, and estimates of molecular mass and density have been made. Not surprisingly, these estimates were found to be orders of magnitude larger than the corresponding values found in our Galaxy. In this paper, a self-consistent model of the high energy emission of the super-starburst galaxy Arp 220 is presented. The model also provides an estimate of the radio emission from each of the components of the central region of the galaxy (western and eastern extreme starbursts, and molecular disk). The predicted radio spectrum is found as a result of the synchrotron and free-free emission, and absorption, of the primary and secondary steady population of electrons and positrons. The latter is output of charged pion decay and knock-on leptonic production, subject to a full set of losses in the interstellar medium. The resulting radio spectrum is in agreement with sub-arcsec radio observations, what allows to estimate the magnetic field. In addition, the FIR emission is modeled with dust emissivity, and the computed FIR photon density is used as a target for inverse Compton process as well as to give account of losses in the {gamma}-ray scape. Bremsstrahlung emission and neutral pion decay are also computed, and the {gamma}-ray spectrum is finally predicted. Future possible observations with GLAST, and the ground based Cherenkov telescopes are discussed.

  5. Salivary Proteins Associated with Periodontitis in Patients with Type 2 Diabetes Mellitus

    PubMed Central

    Chan, Hang Haw; Rahim, Zubaidah H. A.; Jessie, Kala; Hashim, Onn H.; Taiyeb-Ali, Tara B.

    2012-01-01

    The objective of this study was to investigate the salivary proteins that are associated with periodontitis in patients with Type 2 diabetes mellitus (T2DM). Volunteers for the study were patients from the Diabetic Unit, University of Malaya Medical Centre, whose periodontal status was determined. The diabetic volunteers were divided into two groups, i.e., patients with periodontitis and those who were periodontally healthy. Saliva samples were collected and treated with 10% TCA/acetone/20 mM DTT to precipitate the proteins, which were then separated using two-dimensional polyacrylamide gel electrophoresis. Gel images were scanned using the GS-800TM Calibrated Densitometer. The protein spots were analyzed and expressed in percentage volumes. The percentage volume of each protein spot was subjected to Mann-Whitney statistical analysis using SPSS software and false discovery rate correction. When the expression of the salivary proteins was compared between the T2DM patients with periodontitis with those who were periodontally healthy, seven proteins, including polymeric immunoglobulin receptor, plastin-2, actin related protein 3, leukocyte elastase inhibitor, carbonic anhydrases 6, immunoglobulin J and interleukin-1 receptor antagonist, were found to be differentially expressed (p < 0.01304). This implies that the proteins may have the potential to be used as biomarkers for the prediction of T2DM patients who may be prone to periodontitis. PMID:22606001

  6. Exploration of the dynamic properties of protein complexes predicted from spatially constrained protein-protein interaction networks.

    PubMed

    Yen, Eric A; Tsay, Aaron; Waldispuhl, Jerome; Vogel, Jackie

    2014-05-01

    Protein complexes are not static, but rather highly dynamic with subunits that undergo 1-dimensional diffusion with respect to each other. Interactions within protein complexes are modulated through regulatory inputs that alter interactions and introduce new components and deplete existing components through exchange. While it is clear that the structure and function of any given protein complex is coupled to its dynamical properties, it remains a challenge to predict the possible conformations that complexes can adopt. Protein-fragment Complementation Assays detect physical interactions between protein pairs constrained to ≤8 nm from each other in living cells. This method has been used to build networks composed of 1000s of pair-wise interactions. Significantly, these networks contain a wealth of dynamic information, as the assay is fully reversible and the proteins are expressed in their natural context. In this study, we describe a method that extracts this valuable information in the form of predicted conformations, allowing the user to explore the conformational landscape, to search for structures that correlate with an activity state, and estimate the abundance of conformations in the living cell. The generator is based on a Markov Chain Monte Carlo simulation that uses the interaction dataset as input and is constrained by the physical resolution of the assay. We applied this method to an 18-member protein complex composed of the seven core proteins of the budding yeast Arp2/3 complex and 11 associated regulators and effector proteins. We generated 20,480 output structures and identified conformational states using principle component analysis. We interrogated the conformation landscape and found evidence of symmetry breaking, a mixture of likely active and inactive conformational states and dynamic exchange of the core protein Arc15 between core and regulatory components. Our method provides a novel tool for prediction and visualization of the hidden

  7. Actin-interacting and flagellar proteins in Leishmania spp.: Bioinformatics predictions to functional assignments in phagosome formation

    PubMed Central

    2009-01-01

    Several motile processes are responsible for the movement of proteins into and within the flagellar membrane, but little is known about the process by which specific proteins (either actin-associated or not) are targeted to protozoan flagellar membranes. Actin is a major cytoskeleton protein, while polymerization and depolymerization of parasite actin and actin-interacting proteins (AIPs) during both processes of motility and host cell entry might be key events for successful infection. For a better understanding the eukaryotic flagellar dynamics, we have surveyed genomes, transcriptomes and proteomes of pathogenic Leishmania spp. to identify pertinent genes/proteins and to build in silico models to properly address their putative roles in trypanosomatid virulence. In a search for AIPs involved in flagellar activities, we applied computational biology and proteomic tools to infer from the biological meaning of coronins and Arp2/3, two important elements in phagosome formation after parasite phagocytosis by macrophages. Results presented here provide the first report of Leishmania coronin and Arp2/3 as flagellar proteins that also might be involved in phagosome formation through actin polymerization within the flagellar environment. This is an issue worthy of further in vitro examination that remains now as a direct, positive bioinformatics-derived inference to be presented. PMID:21637533

  8. Actin-interacting and flagellar proteins in Leishmania spp.: Bioinformatics predictions to functional assignments in phagosome formation.

    PubMed

    Diniz, Michely C; Costa, Marcília P; Pacheco, Ana C L; Kamimura, Michel T; Silva, Samara C; Carneiro, Laura D G; Sousa, Ana P L; Soares, Carlos E A; Souza, Celeste S F; de Oliveira, Diana Magalhães

    2009-07-01

    Several motile processes are responsible for the movement of proteins into and within the flagellar membrane, but little is known about the process by which specific proteins (either actin-associated or not) are targeted to protozoan flagellar membranes. Actin is a major cytoskeleton protein, while polymerization and depolymerization of parasite actin and actin-interacting proteins (AIPs) during both processes of motility and host cell entry might be key events for successful infection. For a better understanding the eukaryotic flagellar dynamics, we have surveyed genomes, transcriptomes and proteomes of pathogenic Leishmania spp. to identify pertinent genes/proteins and to build in silico models to properly address their putative roles in trypanosomatid virulence. In a search for AIPs involved in flagellar activities, we applied computational biology and proteomic tools to infer from the biological meaning of coronins and Arp2/3, two important elements in phagosome formation after parasite phagocytosis by macrophages. Results presented here provide the first report of Leishmania coronin and Arp2/3 as flagellar proteins that also might be involved in phagosome formation through actin polymerization within the flagellar environment. This is an issue worthy of further in vitro examination that remains now as a direct, positive bioinformatics-derived inference to be presented. PMID:21637533

  9. Creating Protein Models from Electron-Density Maps using Particle-Filtering Methods

    PubMed Central

    Kondrashov, Dmitry A.; Bitto, Eduard; Soni, Ameet; Bingman, Craig A.; Phillips, George N.; Shavlik, Jude W.

    2008-01-01

    Motivation One bottleneck in high-throughput protein crystallography is interpreting an electron-density map; that is, fitting a molecular model to the 3D picture crystallography produces. Previously, we developed Acmi, an algorithm that uses a probabilistic model to infer an accurate protein backbone layout. Here we use a sampling method known as particle filtering to produce a set of all-atom protein models. We use the output of Acmi to guide the particle filter's sampling, producing an accurate, physically feasible set of structures. Results We test our algorithm on ten poor-quality experimental density maps. We show that particle filtering produces accurate all-atom models, resulting in fewer chains, lower sidechain RMS error, and reduced R factor, compared to simply placing the best-matching sidechains on Acmi's trace. We show that our approach produces a more accurate model than three leading methods – Textal, Resolve, and ARP/wARP – in terms of main chain completeness, sidechain identification, and crystallographic R factor. PMID:17933855

  10. High energy resolution ARPES measurements of the normal and superconducting states of Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+{delta}}

    SciTech Connect

    Dessau, D.S.; King, D.M.; Shen, Z.X.

    1993-08-01

    The near-E{sub F} electronic structure and Fermi surface of Bi2212 has been mapped out with ARPES. A key feature of our measured bandstructure is the existence of an extended region of flat CuO{sub 2}-derived bands at E{sub F}. Comparative analysis of this data with that from NdCeCuO and YBCO{sub 7} suggests that many of the anomalous (normal) physical properties of Bi2212 and YBCO{sub 7} (NdCeCuO) may be related to the existence (absence) of such bands at E{sub F}. Superconducting gap anisotropy at least an order of magnitude larger than that of the conventional superconductors has been observed in the a-b plane of Bi2212 in ARPES. For samples with {Tc} of 88K, the gap size reaches a maximum of approximately 20 MeV along the Cu-O bond direction, and a minimum of much smaller or vanishing magnitude 450 away. The experimental data is discussed within the context of various theoretical models. In particular, a detailed comparison with what is expected from a superconductor with a d{sub x2-y2} order parameter is carried out, yielding a consistent picture.

  11. Capping protein regulatory cycle driven by CARMIL and V-1 may promote actin network assembly at protruding edges

    PubMed Central

    Fujiwara, Ikuko; Remmert, Kirsten; Piszczek, Grzegorz; Hammer, John A.

    2014-01-01

    Although capping protein (CP) terminates actin filament elongation, it promotes Arp2/3-dependent actin network assembly and accelerates actin-based motility both in vitro and in vivo. In vitro, capping protein Arp2/3 myosin I linker (CARMIL) antagonizes CP by reducing its affinity for the barbed end and by uncapping CP-capped filaments, whereas the protein V-1/myotrophin sequesters CP in an inactive complex. Previous work showed that CARMIL can readily retrieve CP from the CP:V-1 complex, thereby converting inactive CP into a version with moderate affinity for the barbed end. Here we further clarify the mechanism of this exchange reaction, and we demonstrate that the CP:CARMIL complex created by complex exchange slows the rate of barbed-end elongation by rapidly associating with, and dissociating from, the barbed end. Importantly, the cellular concentrations of V-1 and CP determined here argue that most CP is sequestered by V-1 at steady state in vivo. Finally, we show that CARMIL is recruited to the plasma membrane and only at cell edges undergoing active protrusion. Assuming that CARMIL is active only at this location, our data argue that a large pool of freely diffusing, inactive CP (CP:V-1) feeds, via CARMIL-driven complex exchange, the formation of weak-capping complexes (CP:CARMIL) at the plasma membrane of protruding edges. In vivo, therefore, CARMIL should promote Arp2/3-dependent actin network assembly at the leading edge by promoting barbed-end capping there. PMID:24778263

  12. Molecular characterization of neurally expressing genes in the para sodium channel gene cluster of Drosophila

    SciTech Connect

    Hong, Chang-Sook; Ganetzky, B.

    1996-03-01

    To elucidate the mechanisms regulating expression of para, which encodes the major class of sodium channels in the Drosophila nervous system, we have tried to locate upstream cis-acting regulatory elements by mapping the transcriptional start site and analyzing the region immediately upstream of para in region 14D of the polytene chromosomes. From these studies, we have discovered that the region contains a cluster of neurally expressing genes. Here we report the molecular characterization of the genomic organization of the 14D region and the genes within this region, which are: calnexin (Cnx), actin related protein 14D (Arp14D), calcineurin A 14D (CnnA14D), and chromosome associated protein (Cap). The tight clustering of these genes, their neuronal expression patterns, and their potential functions related to expression, modulation, or regulation of sodium channels raise the possibility that these genes represent a functionally related group sharing some coordinate regulatory mechanism. 76 refs., 11 figs.

  13. Molecular Characterization of Neurally Expressing Genes in the Para Sodium Channel Gene Cluster of Drosophila

    PubMed Central

    Hong, C. S.; Ganetzky, B.

    1996-01-01

    To elucidate the mechanisms regulating expression of para, which encodes the major class of sodium channels in the Drosophila nervous system, we have tried to locate upstream cis-acting regulatory elements by mapping the transcriptional start site and analyzing the region immediately upstream of para in region 14D of the polytene chromosomes. From these studies, we have discovered that the region contains a cluster of neurally expressing genes. Here we report the molecular characterization of the genomic organization of the 14D region and the genes within this region, which are: calnexin (Cnx), actin related protein 14D (Arp14D), calcineurin A 14D (CnnA14D), and chromosome associated protein (Cap). The tight clustering of these genes, their neuronal expression patterns, and their potential functions related to expression, modulation, or regulation of sodium channels raise the possibility that these genes represent a functionally related group sharing some coordinate regulatory mechanism. PMID:8849894

  14. The Disruption of the Cytoskeleton during Semaphorin 3A induced Growth Cone Collapse Correlates with Differences in Actin Organization and Associated Binding Proteins

    PubMed Central

    Brown, Jacquelyn A; Bridgman, Paul C

    2010-01-01

    Repulsive guidance cues induce growth cone collapse or collapse and retraction. Collapse results from disruption and loss of the actin cytoskeleton. Actin rich regions of growth cones contain binding proteins that influence filament organization, such as Arp2/3, cortactin, and fascin, but little is known about the role that these proteins play in collapse. Here we show that Semaphorin 3A (Sema 3A), which is repulsive to mouse dorsal root ganglion neurons, has unequal effects on actin binding proteins and their associated filaments. The immunofluorescence staining intensity of Arp-2 and cortactin decreases relative to total protein, while in unextracted growth cones fascin increases. Fascin and myosin IIB staining redistribute and show increased overlap. The degree of actin filament loss during collapse correlates with filament superstructures detected by rotary shadow electron microscopy. Collapse results in the loss of branched f-actin meshworks, while actin bundles are partially retained to varying degrees. Taken together with the known affects of Sema 3A on actin, this suggests a model for collapse that follows a sequence; depolymerization of actin meshworks followed by partial depolymerization of fascin associated actin bundles and their movement to the neurite to complete collapse. The relocated fascin associated actin bundles may provide the substrate for actomyosin contractions that produce retraction. PMID:19513995

  15. The Recent De Novo Origin of Protein C-Termini

    PubMed Central

    Andreatta, Matthew E.; Levine, Joshua A.; Foy, Scott G.; Guzman, Lynette D.; Kosinski, Luke J.; Cordes, Matthew H.J.; Masel, Joanna

    2015-01-01

    Protein-coding sequences can arise either from duplication and divergence of existing sequences, or de novo from noncoding DNA. Unfortunately, recently evolved de novo genes can be hard to distinguish from false positives, making their study difficult. Here, we study a more tractable version of the process of conversion of noncoding sequence into coding: the co-option of short segments of noncoding sequence into the C-termini of existing proteins via the loss of a stop codon. Because we study recent additions to potentially old genes, we are able to apply a variety of stringent quality filters to our annotations of what is a true protein-coding gene, discarding the putative proteins of unknown function that are typical of recent fully de novo genes. We identify 54 examples of C-terminal extensions in Saccharomyces and 28 in Drosophila, all of them recent enough to still be polymorphic. We find one putative gene fusion that turns out, on close inspection, to be the product of replicated assembly errors, further highlighting the issue of false positives in the study of rare events. Four of the Saccharomyces C-terminal extensions (to ADH1, ARP8, TPM2, and PIS1) that survived our quality filters are predicted to lead to significant modification of a protein domain structure. PMID:26002864

  16. Proteins modified by the lipid peroxidation aldehyde DODE in MCF7 breast cancer cells

    PubMed Central

    Slade, Peter G.; Williams, Michelle V.; Brahmbatt, Viral; Dash, Ajit; Wishnok, John S.; Tannenbaum, Steven R.

    2010-01-01

    The hydroperoxide of linoleic acid (13-HPODE) degrades to 9,12-dioxo-10(E)-dodecenoic acid (DODE) which readily modifies proteins. This study identified the major proteins in MCF7 cells modified by DODE. To reduce false positives, three methods were use to identify DODE-modified proteins. First, cells were treated with a synthetically biotinylated 13-HPODE (13-HPODE-biotin). Modified proteins were enriched by neutravidin affinity and identified by 2D-LC-MS/MS. Second, cells were treated with native 13-HPODE. Protein-carbonyls were biotinylated with an aldehyde reactive probe (ARP) and modified proteins enriched by neutravidin affinity and identified by 2D-LC-MS/MS. Third, using a newly developed DODE antibody, DODE modified proteins were located by 2D-SDS-PAGE and Western blot and identified by in-gel digestion and LC-MS/MS. Analysis of the proteins characterized by all three methods revealed a significant overlap and identified 32 primary proteins modified by DODE in MCF7 cells. These results demonstrated the feasibility for the cellular formation of DODE protein-carbonyl adducts that may be future indicators of oxidative stress. PMID:20131800

  17. The F-BAR protein Cip4/Toca-1 antagonizes the formin Diaphanous in membrane stabilization and compartmentalization

    PubMed Central

    Yan, Shuling; Lv, Zhiyi; Winterhoff, Moritz; Wenzl, Christian; Zobel, Thomas; Faix, Jan; Bogdan, Sven; Grosshans, Jörg

    2013-01-01

    Summary During Drosophila embryogenesis, the first epithelium with defined cortical compartments is established during cellularization. Actin polymerization is required for the separation of lateral and basal domains as well as suppression of tubular extensions in the basal domain. The actin nucleator mediating this function is unknown. We found that the formin Diaphanous (Dia) is required for establishing and maintaining distinct lateral and basal domains during cellularization. In dia mutant embryos lateral marker proteins, such as Discs-large and Armadillo/β-Catenin spread into the basal compartment. Furthermore, high-resolution and live-imaging analysis of dia mutant embryos revealed an increased number of membrane extensions and endocytic activity at the basal domain, indicating a suppressing function of dia on membrane invaginations. Dia function might be based on an antagonistic interaction with the F-BAR protein Cip4/Toca-1, a known activator of the WASP/WAVE-Arp2/3 pathway. Dia and Cip4 physically and functionally interact and overexpression of Cip4 phenocopies dia loss-of-function. In vitro, Cip4 inhibits mainly actin nucleation by Dia. Thus, our data support a model in which linear actin filaments induced by Dia stabilize cortical compartmentalization by antagonizing membrane turnover induced by WASP/WAVE-Arp2/3. PMID:23424199

  18. Phosphoproteome Profiling of SH-SY5y Neuroblastoma Cells Treated with Anesthetics: Sevoflurane and Isoflurane Affect the Phosphorylation of Proteins Involved in Cytoskeletal Regulation

    PubMed Central

    Lee, Joomin; Ahn, Eunsook; Park, Wyun Kon; Park, Seyeon

    2016-01-01

    Inhalation anesthetics are used to decrease the spinal cord transmission of painful stimuli. However, the molecular or biochemical processes within cells that regulate anesthetic-induced responses at the cellular level are largely unknown. Here, we report the phosphoproteome profile of SH-SY5y human neuroblastoma cells treated with sevoflurane, a clinically used anesthetic. Phosphoproteins were isolated from cell lysates and analyzed using two-dimensional gel electrophoresis. The phosphorylation of putative anesthetic-responsive marker proteins was validated using western blot analysis in cells treated with both sevoflurane and isoflurane. A total of 25 phosphoproteins were identified as differentially phosphorylated proteins. These included key regulators that signal cytoskeletal remodeling steps in pathways related to vesicle trafficking, axonal growth, and cell migration. These proteins included the Rho GTPase, Ras-GAP SH3 binding protein, Rho GTPase activating protein, actin-related protein, and actin. Sevoflurane and isoflurane also resulted in the dissolution of F-actin fibers in SH-SY5y cells. Our results show that anesthetics affect the phosphorylation of proteins involved in cytoskeletal remodeling pathways. PMID:27611435

  19. Phosphoproteome Profiling of SH-SY5y Neuroblastoma Cells Treated with Anesthetics: Sevoflurane and Isoflurane Affect the Phosphorylation of Proteins Involved in Cytoskeletal Regulation.

    PubMed

    Lee, Joomin; Ahn, Eunsook; Park, Wyun Kon; Park, Seyeon

    2016-01-01

    Inhalation anesthetics are used to decrease the spinal cord transmission of painful stimuli. However, the molecular or biochemical processes within cells that regulate anesthetic-induced responses at the cellular level are largely unknown. Here, we report the phosphoproteome profile of SH-SY5y human neuroblastoma cells treated with sevoflurane, a clinically used anesthetic. Phosphoproteins were isolated from cell lysates and analyzed using two-dimensional gel electrophoresis. The phosphorylation of putative anesthetic-responsive marker proteins was validated using western blot analysis in cells treated with both sevoflurane and isoflurane. A total of 25 phosphoproteins were identified as differentially phosphorylated proteins. These included key regulators that signal cytoskeletal remodeling steps in pathways related to vesicle trafficking, axonal growth, and cell migration. These proteins included the Rho GTPase, Ras-GAP SH3 binding protein, Rho GTPase activating protein, actin-related protein, and actin. Sevoflurane and isoflurane also resulted in the dissolution of F-actin fibers in SH-SY5y cells. Our results show that anesthetics affect the phosphorylation of proteins involved in cytoskeletal remodeling pathways.

  20. Phosphoproteome Profiling of SH-SY5y Neuroblastoma Cells Treated with Anesthetics: Sevoflurane and Isoflurane Affect the Phosphorylation of Proteins Involved in Cytoskeletal Regulation.

    PubMed

    Lee, Joomin; Ahn, Eunsook; Park, Wyun Kon; Park, Seyeon

    2016-01-01

    Inhalation anesthetics are used to decrease the spinal cord transmission of painful stimuli. However, the molecular or biochemical processes within cells that regulate anesthetic-induced responses at the cellular level are largely unknown. Here, we report the phosphoproteome profile of SH-SY5y human neuroblastoma cells treated with sevoflurane, a clinically used anesthetic. Phosphoproteins were isolated from cell lysates and analyzed using two-dimensional gel electrophoresis. The phosphorylation of putative anesthetic-responsive marker proteins was validated using western blot analysis in cells treated with both sevoflurane and isoflurane. A total of 25 phosphoproteins were identified as differentially phosphorylated proteins. These included key regulators that signal cytoskeletal remodeling steps in pathways related to vesicle trafficking, axonal growth, and cell migration. These proteins included the Rho GTPase, Ras-GAP SH3 binding protein, Rho GTPase activating protein, actin-related protein, and actin. Sevoflurane and isoflurane also resulted in the dissolution of F-actin fibers in SH-SY5y cells. Our results show that anesthetics affect the phosphorylation of proteins involved in cytoskeletal remodeling pathways. PMID:27611435

  1. Spine pruning drives antipsychotic-sensitive locomotion via circuit control of striatal dopamine.

    PubMed

    Kim, Il Hwan; Rossi, Mark A; Aryal, Dipendra K; Racz, Bence; Kim, Namsoo; Uezu, Akiyoshi; Wang, Fan; Wetsel, William C; Weinberg, Richard J; Yin, Henry; Soderling, Scott H

    2015-06-01

    Psychiatric and neurodevelopmental disorders may arise from anomalies in long-range neuronal connectivity downstream of pathologies in dendritic spines. However, the mechanisms that may link spine pathology to circuit abnormalities relevant to atypical behavior remain unknown. Using a mouse model to conditionally disrupt a critical regulator of the dendritic spine cytoskeleton, the actin-related protein 2/3 complex (Arp2/3), we report here a molecular mechanism that unexpectedly reveals the inter-relationship of progressive spine pruning, elevated frontal cortical excitation of pyramidal neurons and striatal hyperdopaminergia in a cortical-to-midbrain circuit abnormality. The main symptomatic manifestations of this circuit abnormality are psychomotor agitation and stereotypical behaviors, which are relieved by antipsychotics. Moreover, this antipsychotic-responsive locomotion can be mimicked in wild-type mice by optogenetic activation of this circuit. Collectively these results reveal molecular and neural-circuit mechanisms, illustrating how diverse pathologies may converge to drive behaviors relevant to psychiatric disorders.

  2. Retinal proteins modified by 4-hydroxynonenal: identification of molecular targets.

    PubMed

    Kapphahn, Rebecca J; Giwa, Babatomiwa M; Berg, Kristin M; Roehrich, Heidi; Feng, Xiao; Olsen, Timothy W; Ferrington, Deborah A

    2006-07-01

    The reactive aldehyde, 4-hydroxynonenal (HNE), is a product of lipid peroxidation that can covalently modify and inactivate proteins. Previously, we reported increased HNE modification of select retinal proteins resolved by one-dimensional gel electrophoresis in aged Fisher 344 x Brown Norway rats (Louie, J.L., Kapphahn, R.J., Ferrington, D.A., 2002. Proteasome function and protein oxidation in the aged retina. Exp. Eye Res. 75, 271-284). In the current study, quantitative assessment of HNE molar content using slot blot immunoassays showed HNE content is increased 30% in aged rat retina. In contrast, there was no age-related difference in HNE content in individual spots resolved by 2D gel electrophoresis suggesting the increased modification is likely on membrane proteins that are missing on 2D gels. The HNE-immunoreactive proteins resolved by 2D gel electrophoresis were identified by MALDI-TOF mass spectrometry. These proteins are involved in metabolism, chaperone function, and fatty acid transport. Proteins that were frequently modified and had the highest molar content of HNE included triosephosphate isomerase, alpha enolase, heat shock cognate 70 and betaB2 crystallin. Immunochemical detection of HNE adducts on retinal sections showed greater immune reaction in ganglion cells, photoreceptor inner segment, and the inner plexiform layer. Identification of HNE modified proteins in two alternative model systems, human retinal pigment epithelial cells in culture (ARPE19) and human donor eyes, indicated that triosephosphate isomerase and alpha enolase are generally modified. These results identify a common subset of proteins that contain HNE adducts and suggest that select retinal proteins are molecular targets for HNE modification. PMID:16530755

  3. Pan1 is an intrinsically disordered protein with homotypic interactions

    PubMed Central

    Pierce, B. D.; Toptygin, D.; Wendland, B.

    2013-01-01

    The yeast scaffold protein Pan1 contains two EH domains at its N-terminus, a predicted coiled-coil central region, and a C-terminal proline-rich domain. Pan1 is also predicted to contain regions of intrinsic disorder, characteristic of proteins that have many binding partners. In vitro biochemical data suggest that Pan1 exists as a dimer, and we have identified amino acids 705–848 as critical for this homotypic interaction. Tryptophan fluorescence was used to further characterize Pan1 conformational states. Pan1 contains four endogenous tryptophans, each in a distinct region of the protein: Trp312 and Trp642 are each in an EH domain, Trp957 is in the central region, and Trp1280 is a critical residue in the Arp2/3 activation domain. To examine the local environment of each of these tryptophans, three of the four tryptophans were mutagenized to phenylalanine to create four proteins, each with only one tryptophan residue. When quenched with acrylamide, these single tryptophan mutants appeared to undergo collisional quenching exclusively and were moderately accessible to the acrylamide molecule. Quenching with iodide or cesium, however, revealed different Stern-Volmer constants due to unique electrostatic environments of the tryptophan residues. Time-resolved fluorescence anisotropy data confirmed structural and disorder predictions of Pan1. Further experimentation to fully develop a model of Pan1 conformational dynamics will assist in a deeper understanding of the mechanisms of endocytosis. PMID:23801378

  4. Curcumin analog 1, 5-bis (2-trifluoromethylphenyl)-1, 4-pentadien-3-one exhibits enhanced ability on Nrf2 activation and protection against acrolein-induced ARPE-19 cell toxicity

    SciTech Connect

    Li, Yuan; Zou, Xuan; Cao, Ke; Xu, Jie; Yue, Tingting; Dai, Fang; Zhou, Bo; Lu, Wuyuan; Feng, Zhihui; Liu, Jiankang

    2013-11-01

    Curcumin, a phytochemical agent in the spice turmeric, has received increasing attention for its anticancer, anti-inflammatory and antioxidant properties. However, application of curcumin has been limited due to its insolubility in water and poor bioavailability both clinically and experimentally. In addition, the protective effects and mechanisms of curcumin in eye diseases have been poorly studied. In the present study, we synthesized a curcumin analog, 1, 5-bis (2-trifluoromethylphenyl)-1, 4-pentadien-3-one (C3), which displayed improved protective effect against acrolein-induced toxicity in a human retinal pigment epithelial cell line (ARPE-19). At 5 μM, curcumin completely protected against acrolein-induced cell oxidative damage and preserved GSH levels and mitochondrial function. Surprisingly, C3 displayed a complete protective effect at 0.5 μM, which was much more efficient than curcumin. Both 0.5 μM C3 and 5 μM curcumin induced Nrf2 nuclear translocation and Nrf2 target genes transcription similarly. Experiments using Nrf2 siRNA showed that the protective effects of curcumin and C3 were eliminated by Nrf2 knockdown. Additionally, both curcumin and C3 activated the PI3/Akt pathway, however, Nrf2 activation was independent of this pathway, and therefore, we hypothesized that both curcumin and C3 activated phase II enzymes via directly disrupting the Nrf2/Keap1 complex and promoting Nrf2's nuclear translocation. Since acrolein challenge of ARPE-19 cells has been used as a model of smoking and age-related macular degeneration (AMD), we concluded that the curcumin analog, C3, may be a more promising drug candidate for its potential application for the prevention and treatment of eye diseases, such as AMD. - Highlights: • We examine toxicity effects of cigarette smoking component acrolein in retina cells. • We report a more efficient curcumin analog (C3) protecting cellular function. • Mitochondrial function and phase II enzyme activation are the major

  5. Lotus japonicus ARPC1 is required for rhizobial infection.

    PubMed

    Hossain, Md Shakhawat; Liao, Jinqiu; James, Euan K; Sato, Shusei; Tabata, Satoshi; Jurkiewicz, Anna; Madsen, Lene H; Stougaard, Jens; Ross, Loretta; Szczyglowski, Krzysztof

    2012-10-01

    Remodeling of the plant cell cytoskeleton precedes symbiotic entry of nitrogen-fixing bacteria within the host plant roots. Here we identify a Lotus japonicus gene encoding a predicted ACTIN-RELATED PROTEIN COMPONENT1 (ARPC1) as essential for rhizobial infection but not for arbuscular mycorrhiza symbiosis. In other organisms ARPC1 constitutes a subunit of the ARP2/3 complex, the major nucleator of Y-branched actin filaments. The L. japonicus arpc1 mutant showed a distorted trichome phenotype and was defective in epidermal infection thread formation, producing mostly empty nodules. A few partially colonized nodules that did form in arpc1 contained abnormal infections. Together with previously described L. japonicus Nck-associated protein1 and 121F-specific p53 inducible RNA mutants, which are also impaired in the accommodation of rhizobia, our data indicate that ARPC1 and, by inference a suppressor of cAMP receptor/WASP-family verpolin homologous protein-ARP2/3 pathway, must have been coopted during evolution of nitrogen-fixing symbiosis to specifically mediate bacterial entry.

  6. Helicobacter pylori CagA Induces AGS Cell Elongation through a Cell Retraction Defect That Is Independent of Cdc42, Rac1, and Arp2/3▿ †

    PubMed Central

    Bourzac, Kevin M.; Botham, Crystal M.; Guillemin, Karen

    2007-01-01

    Helicobacter pylori, which infects over one-half the world's population, is a significant risk factor in a spectrum of gastric diseases, including peptic ulcers and gastric cancer. Strains of H. pylori that deliver the effector molecule CagA into host cells via a type IV secretion system are associated with more severe disease outcomes. In a tissue culture model of infection, CagA delivery results in a dramatic cellular elongation referred to as the “hummingbird” phenotype, which is characterized by long, thin cellular extensions. These actin-based cytoskeletal rearrangements are reminiscent of structures that are regulated by Rho GTPases and the Arp2/3 complex. We tested whether these signaling pathways were important in the H. pylori-induced cell elongation phenotype. Contrary to our expectations, we found that these molecules are dispensable for cell elongation. Instead, time-lapse video microscopy revealed that cells infected by cagA+ H. pylori become elongated because they fail to release their back ends during cell locomotion. Consistent with a model in which CagA causes cell elongation by inhibiting the disassembly of adhesive cell contacts at migrating cells' lagging ends, immunohistochemical analysis revealed that focal adhesion complexes persist at the distal tips of elongated cell projections. Thus, our data implicate a set of signaling molecules in the hummingbird phenotype that are different than the molecules previously suspected. PMID:17194805

  7. Site-specific protein adducts of 4-hydroxy-2(E)-nonenal in human THP-1 monocytic cells: Protein carbonylation is diminished by ascorbic acid

    PubMed Central

    Chavez, Juan; Chung, Woon-Gye; Miranda, Cristobal L.; Singhal, Mudita; Stevens, Jan F.; Maier, Claudia S.

    2010-01-01

    The protein targets and sites of modification by 4-hydroxy-2(E)-nonenal (HNE) in human monocytic THP-1 cells after exogenous exposure to HNE were examined using a multi-pronged proteomic approach involving electrophoretic, immunoblotting and mass spectrometric methods. Immunoblot analysis using monoclonal anti-HNE antibodies showed several proteins as targets of HNE adduction. Pretreatment of THP-1 cells with ascorbic acid resulted in reduced levels of HNE-protein adducts. Biotinylation of Michael-type HNE adducts using an aldehyde-reactive hydroxylamine-functionalized probe (aldehyde-reactive probe, ARP) and subsequent enrichment facilitated the identification and site-specific assignment of the modifications by LC-MS/MS analysis. Sixteen proteins were unequivocally identified as targets of HNE adduction and eighteen sites of HNE modification at Cys and His residues were assigned. HNE exposure of THP-1 cells resulted in the modification of proteins involved in cytoskeleton organization and regulation, proteins associated with stress responses and enzymes of the glycolytic and other metabolic pathways. This study yielded the first evidence of site-specific adduction of HNE to Cys-295 in tubulin α-1B chain, Cys-351 and Cys-499 in α-actinin-4, Cys-328 in vimentin, Cys-369 in D-3-phosphoglycerate dehydrogenase and His-246 in aldolase A. PMID:20043646

  8. Site-Specific Protein Adducts of 4-Hydroxy-2(E)-Nonenal in Human THP-1 Monocytic Cells: Protein Carbonylation Is Diminished by Ascorbic Acid

    SciTech Connect

    Chavez, Juan; Chung, Woon-Gye; Miranda, Cristobal L.; Singhal, Mudita; Stevens, Jan F.; Maier, Claudia S.

    2010-01-18

    The protein targets and sites of modification by 4-hydroxy-2(E)-nonenal (HNE) in human monocytic THP-1 cells after exogenous exposure to HNE were examined using a multipronged proteomic approach involving electrophoretic, immunoblotting, and mass spectrometric methods. Immunoblot analysis using monoclonal anti-HNE antibodies showed several proteins as targets of HNE adduction. Pretreatment of THP-1 cells with ascorbic acid resulted in reduced levels of HNE-protein adducts. Biotinylation of Michael-type HNE adducts using an aldehyde-reactive hydroxylamine-functionalized probe (aldehyde-reactive probe, ARP) and subsequent enrichment facilitated the identification and site-specific assignment of the modifications by LC-MS/MS analysis. Sixteen proteins were unequivocally identified as targets of HNE adduction, and eighteen sites of HNE modification at Cys and His residues were assigned. HNE exposure of THP-1 cells resulted in the modification of proteins involved in cytoskeleton organization and regulation, proteins associated with stress responses, and enzymes of the glycolytic and other metabolic pathways. Finally, this study yielded the first evidence of site-specific adduction of HNE to Cys-295 in tubulin α-1B chain, Cys-351 and Cys-499 in α-actinin-4, Cys-328 in vimentin, Cys-369 in d-3-phosphoglycerate dehydrogenase, and His-246 in aldolase A.

  9. Secondary Reactions and Strategies to Improve Quantitative Protein Footprinting

    SciTech Connect

    Xu,G.; Kiselar, J.; He, Q.; Chance, M.

    2005-01-01

    Hydroxyl radical-mediated footprinting permits detailed examination of structure and dynamic processes of proteins and large biological assemblies, as changes in the rate of reaction of radicals with target peptides are governed by changes in the solvent accessibility of the side-chain probe residues. The precise and accurate determination of peptide reaction rates is essential to successfully probing protein structure using footprinting. In this study, we specifically examine the magnitude and mechanisms of secondary oxidation occurring after radiolytic exposure and prior to mass spectrometric analysis. Secondary oxidation results from hydrogen peroxide and other oxidative species generated during radiolysis, significantly impacting the oxidation of Met and Cys but not aromatic or other reactive residues. Secondary oxidation of Met with formation of sulfoxide degrades data reproducibility and inflates the perceived solvent accessibility of Met-containing peptides. It can be suppressed by adding trace amounts of catalase or millimolar Met-NH{sub 2} (or Met-OH) buffer immediately after irradiation; this leads to greatly improved adherence to first-order kinetics and more precise observed oxidation rates. The strategy is shown to suppress secondary oxidation in model peptides and improve data quality in examining the reactivity of peptides within the Arp2/3 protein complex. Cysteine is also subject to secondary oxidation generating disulfide as the principal product. The disulfides can be reduced before mass spectrometric analysis by reducing agents such as TCEP, while methionine sulfoxide is refractory to reduction by this reagent under typical reducing conditions.

  10. Phase transitions in the assembly of multivalent signalling proteins

    SciTech Connect

    Li, Pilong; Banjade, Sudeep; Cheng, Hui-Chun; Kim, Soyeon; Chen, Baoyu; Guo, Liang; Llaguno, Marc; Hollingsworth, Javoris V.; King, David S.; Banani, Salman F.; Russo, Paul S.; Jiang, Qiu-Xing; Nixon, B. Tracy; Rosen, Michael K.

    2013-04-08

    Cells are organized on length scales ranging from angstrom to micrometers. However, the mechanisms by which angstrom-scale molecular properties are translated to micrometer-scale macroscopic properties are not well understood. Here we show that interactions between diverse synthetic, multivalent macromolecules (including multi-domain proteins and RNA) produce sharp liquid-liquid-demixing phase separations, generating micrometer-sized liquid droplets in aqueous solution. This macroscopic transition corresponds to a molecular transition between small complexes and large, dynamic supramolecular polymers. The concentrations needed for phase transition are directly related to the valency of the interacting species. In the case of the actin-regulatory protein called neural Wiskott-Aldrich syndrome protein (N-WASP) interacting with its established biological partners NCK and phosphorylated nephrin1, the phase transition corresponds to a sharp increase in activity towards an actin nucleation factor, the Arp2/3 complex. The transition is governed by the degree of phosphorylation of nephrin, explaining how this property of the system can be controlled to regulatory effect by kinases. The widespread occurrence of multivalent systems suggests that phase transitions may be used to spatially organize and biochemically regulate information throughout biology.

  11. The bacterial cell division proteins FtsA and FtsZ self-organize into dynamic cytoskeletal patterns

    PubMed Central

    Loose, Martin; Mitchison, Timothy J.

    2014-01-01

    Bacterial cytokinesis is commonly initiated by the Z-ring, a cytoskeletal structure assembling at the site of division. Its primary component is FtsZ, a tubulin superfamily GTPase, which is recruited to the membrane by the actin-related protein FtsA. Both proteins are required for the formation of the Z-ring, but if and how they influence each other’s assembly dynamics is not known. Here, we reconstituted FtsA-dependent recruitment of FtsZ polymers to supported membranes, where both proteins self-organize into complex patterns, such as fast-moving filament bundles and chirally rotating rings. Using fluorescence microscopy and biochemical perturbations, we found that these large-scale rearrangements of FtsZ emerge from its polymerization dynamics and a dual, antagonistic role of FtsA: recruitment of FtsZ filaments to the membrane and a negative regulation on FtsZ organization. Our findings provide a model for the initial steps of bacterial cell division and illustrate how dynamic polymers can self-organize into large-scale structures. PMID:24316672

  12. Protein Condensation

    NASA Astrophysics Data System (ADS)

    Gunton, James D.; Shiryayev, Andrey; Pagan, Daniel L.

    2007-09-01

    Preface; 1. Introduction; 2. Globular protein structure; 3. Experimental methods; 4. Thermodynamics and statistical mechanics; 5. Protein-protein interactions; 6. Theoretical studies of equilibrium; 7. Nucleation theory; 8. Experimental studies of nucleation; 9. Lysozyme; 10. Some other globular proteins; 11. Membrane proteins; 12. Crystallins and cataracts; 13. Sickle hemoglobin and sickle cell anemia; 14, Alzheimer's disease; Index.

  13. Protein Condensation

    NASA Astrophysics Data System (ADS)

    Gunton, James D.; Shiryayev, Andrey; Pagan, Daniel L.

    2014-07-01

    Preface; 1. Introduction; 2. Globular protein structure; 3. Experimental methods; 4. Thermodynamics and statistical mechanics; 5. Protein-protein interactions; 6. Theoretical studies of equilibrium; 7. Nucleation theory; 8. Experimental studies of nucleation; 9. Lysozyme; 10. Some other globular proteins; 11. Membrane proteins; 12. Crystallins and cataracts; 13. Sickle hemoglobin and sickle cell anemia; 14, Alzheimer's disease; Index.

  14. Expression of early and late cellular damage markers by ARPE-19 cells following prolonged treatment with UV-A radiation.

    PubMed

    Tringali, Giuseppe; Sampaolese, Beatrice; Clementi, Maria Elisabetta

    2016-10-01

    Pathological alterations to the retinal pigment epithelium underlie several eye diseases, which lead to visual impairment and even blindness. Exposure to ultraviolet (UV) radiation is associated with some skin and ocular pathologies; UV radiation may induce DNA breakdown and cause cellular damage through the production of reactive oxygen species (ROS), thus leading to programmed cell death. The present study aimed to investigate the production of ROS and the gene expression levels of anti‑ and proapoptotic proteins [B‑cell lymphoma 2 (Bcl‑2), Bcl‑2‑associated X protein (Bax) and caspase‑3] in human retinal pigment epithelial cells (ARPE‑19) treated with UV‑A for 5 h consecutively. The results demonstrated that prolonged exposure to UV‑A induced: i) Cell death, the decrease in cell viability was time‑dependent and reached statistical significance after 3 h; ii) a significant and substantial increase in ROS levels that remained constant for the duration of the experiment, the levels were significantly increased after 1 h of exposure; iii) an activation of apoptotic genes (Bax and caspase‑3) after 1 h of treatment, which was accompanied by a decrease in the anti‑apoptotic gene Bcl‑2; and iv) a loss of apoptotic signals and a rapid decrease in cellular viability after 3 h of consecutive treatment. These processes may trigger necrosis, which was observed in the cells following treatment with UV‑A for 5 consecutive hours. In conclusion, the present study is the first, to the best of our knowledge, to provide in vitro evidence regarding the sequence of events that underlie the cellular damage induced by prolonged UV‑A radiation, starting from the first 30 min of treatment. UV‑A radiation resulted in the activation of apoptotic events, and subsequently led to irreversible cell necrosis. PMID:27573029

  15. Expression of early and late cellular damage markers by ARPE-19 cells following prolonged treatment with UV-A radiation.

    PubMed

    Tringali, Giuseppe; Sampaolese, Beatrice; Clementi, Maria Elisabetta

    2016-10-01

    Pathological alterations to the retinal pigment epithelium underlie several eye diseases, which lead to visual impairment and even blindness. Exposure to ultraviolet (UV) radiation is associated with some skin and ocular pathologies; UV radiation may induce DNA breakdown and cause cellular damage through the production of reactive oxygen species (ROS), thus leading to programmed cell death. The present study aimed to investigate the production of ROS and the gene expression levels of anti‑ and proapoptotic proteins [B‑cell lymphoma 2 (Bcl‑2), Bcl‑2‑associated X protein (Bax) and caspase‑3] in human retinal pigment epithelial cells (ARPE‑19) treated with UV‑A for 5 h consecutively. The results demonstrated that prolonged exposure to UV‑A induced: i) Cell death, the decrease in cell viability was time‑dependent and reached statistical significance after 3 h; ii) a significant and substantial increase in ROS levels that remained constant for the duration of the experiment, the levels were significantly increased after 1 h of exposure; iii) an activation of apoptotic genes (Bax and caspase‑3) after 1 h of treatment, which was accompanied by a decrease in the anti‑apoptotic gene Bcl‑2; and iv) a loss of apoptotic signals and a rapid decrease in cellular viability after 3 h of consecutive treatment. These processes may trigger necrosis, which was observed in the cells following treatment with UV‑A for 5 consecutive hours. In conclusion, the present study is the first, to the best of our knowledge, to provide in vitro evidence regarding the sequence of events that underlie the cellular damage induced by prolonged UV‑A radiation, starting from the first 30 min of treatment. UV‑A radiation resulted in the activation of apoptotic events, and subsequently led to irreversible cell necrosis.

  16. Fucoidan protects ARPE-19 cells from oxidative stress via normalization of reactive oxygen species generation through the Ca²⁺-dependent ERK signaling pathway.

    PubMed

    Li, Xiaoxia; Zhao, Haiyan; Wang, Qingfa; Liang, Hongyan; Jiang, Xiaofeng

    2015-05-01

    Diabetic retinopathy (DR) is a common complication of diabetes mellitus (DM) and it is the main cause of loss of vision. In previous years, interest in the biological activities of marine organisms has intensified. The effect of fucoidan from the seaweed Fucus vesiculosus on the molecular mechanisms of numerous diseases has been studied, while to date, its effect on DR was yet to be investigated. Therefore, the aim of the present study was to evaluate the role of fucoidan in DR. The human retinal pigment epithelial cell line ARPE‑19 was exposed to high D‑glucose in the presence or absence of fucoidan. Cell viability was monitored using MTT and lactate dehydrogenase assays. The intracellular reactive oxygen species (ROS) generation was measured using fluorescence spectrophotometry. Cell apoptosis was measured by flow cytometry using Annexin V‑fluorescein isothiocyanate staining. Ca2+ influx was measured with a calcium imaging system and the activation of the extracellular signal‑regulated kinase (ERK) protein was evaluated using western blot analysis. The non‑toxic fucoidan protected ARPE‑19 cells from high glucose‑induced cell death and normalized high glucose‑induced generation of ROS. Fucoidan also inhibited high glucose‑induced cell apoptosis, as well as the Ca2+ influx and ERK1/2 phosphorylation in ARPE‑19 cells. Taken together, these findings indicated that fucoidan protects ARPE‑19 cells against high glucose‑induced oxidative damage via normalization of ROS generation through the Ca2+‑dependent ERK signaling pathway.

  17. Crystal structure of a nuclear actin ternary complex.

    PubMed

    Cao, Tingting; Sun, Lingfei; Jiang, Yuxiang; Huang, Shanjin; Wang, Jiawei; Chen, Zhucheng

    2016-08-01

    Actin polymerizes and forms filamentous structures (F-actin) in the cytoplasm of eukaryotic cells. It also exists in the nucleus and regulates various nucleic acid transactions, particularly through its incorporation into multiple chromatin-remodeling complexes. However, the specific structure of actin and the mechanisms that regulate its polymeric nature inside the nucleus remain unknown. Here, we report the crystal structure of nuclear actin (N-actin) complexed with actin-related protein 4 (Arp4) and the helicase-SANT-associated (HSA) domain of the chromatin remodeler Swr1. The inner face and barbed end of N-actin are sequestered by interactions with Arp4 and the HSA domain, respectively, which prevents N-actin from polymerization and binding to many actin regulators. The two major domains of N-actin are more twisted than those of globular actin (G-actin), and its nucleotide-binding pocket is occluded, freeing N-actin from binding to and regulation by ATP. These findings revealed the salient structural features of N-actin that distinguish it from its cytoplasmic counterpart and provide a rational basis for its functions and regulation inside the nucleus. PMID:27457955

  18. Diffusion of GPI-anchored proteins is influenced by the activity of dynamic cortical actin.

    PubMed

    Saha, Suvrajit; Lee, Il-Hyung; Polley, Anirban; Groves, Jay T; Rao, Madan; Mayor, Satyajit

    2015-11-01

    Molecular diffusion at the surface of living cells is believed to be predominantly driven by thermal kicks. However, there is growing evidence that certain cell surface molecules are driven by the fluctuating dynamics of cortical cytoskeleton. Using fluorescence correlation spectroscopy, we measure the diffusion coefficient of a variety of cell surface molecules over a temperature range of 24-37 °C. Exogenously incorporated fluorescent lipids with short acyl chains exhibit the expected increase of diffusion coefficient over this temperature range. In contrast, we find that GPI-anchored proteins exhibit temperature-independent diffusion over this range and revert to temperature-dependent diffusion on cell membrane blebs, in cells depleted of cholesterol, and upon acute perturbation of actin dynamics and myosin activity. A model transmembrane protein with a cytosolic actin-binding domain also exhibits the temperature-independent behavior, directly implicating the role of cortical actin. We show that diffusion of GPI-anchored proteins also becomes temperature dependent when the filamentous dynamic actin nucleator formin is inhibited. However, changes in cortical actin mesh size or perturbation of branched actin nucleator Arp2/3 do not affect this behavior. Thus cell surface diffusion of GPI-anchored proteins and transmembrane proteins that associate with actin is driven by active fluctuations of dynamic cortical actin filaments in addition to thermal fluctuations, consistent with expectations from an "active actin-membrane composite" cell surface.

  19. Diffusion of GPI-anchored proteins is influenced by the activity of dynamic cortical actin

    PubMed Central

    Saha, Suvrajit; Lee, Il-Hyung; Polley, Anirban; Groves, Jay T.; Rao, Madan; Mayor, Satyajit

    2015-01-01

    Molecular diffusion at the surface of living cells is believed to be predominantly driven by thermal kicks. However, there is growing evidence that certain cell surface molecules are driven by the fluctuating dynamics of cortical cytoskeleton. Using fluorescence correlation spectroscopy, we measure the diffusion coefficient of a variety of cell surface molecules over a temperature range of 24–37°C. Exogenously incorporated fluorescent lipids with short acyl chains exhibit the expected increase of diffusion coefficient over this temperature range. In contrast, we find that GPI-anchored proteins exhibit temperature-independent diffusion over this range and revert to temperature-dependent diffusion on cell membrane blebs, in cells depleted of cholesterol, and upon acute perturbation of actin dynamics and myosin activity. A model transmembrane protein with a cytosolic actin-binding domain also exhibits the temperature-independent behavior, directly implicating the role of cortical actin. We show that diffusion of GPI-anchored proteins also becomes temperature dependent when the filamentous dynamic actin nucleator formin is inhibited. However, changes in cortical actin mesh size or perturbation of branched actin nucleator Arp2/3 do not affect this behavior. Thus cell surface diffusion of GPI-anchored proteins and transmembrane proteins that associate with actin is driven by active fluctuations of dynamic cortical actin filaments in addition to thermal fluctuations, consistent with expectations from an “active actin-membrane composite” cell surface. PMID:26378258

  20. Phase transitions of multivalent proteins can promote clustering of membrane receptors

    PubMed Central

    Banjade, Sudeep; Rosen, Michael K

    2014-01-01

    Clustering of proteins into micrometer-sized structures at membranes is observed in many signaling pathways. Most models of clustering are specific to particular systems, and relationships between physical properties of the clusters and their molecular components are not well understood. We report biochemical reconstitution on supported lipid bilayers of protein clusters containing the adhesion receptor Nephrin and its cytoplasmic partners, Nck and N-WASP. With Nephrin attached to the bilayer, multivalent interactions enable these proteins to polymerize on the membrane surface and undergo two-dimensional phase separation, producing micrometer-sized clusters. Dynamics and thermodynamics of the clusters are modulated by the valencies and affinities of the interacting species. In the presence of the Arp2/3 complex, the clusters assemble actin filaments, suggesting that clustering of regulatory factors could promote local actin assembly at membranes. Interactions between multivalent proteins could be a general mechanism for cytoplasmic adaptor proteins to organize membrane receptors into micrometer-scale signaling zones. DOI: http://dx.doi.org/10.7554/eLife.04123.001 PMID:25321392

  1. Phylogenetic Analysis Identifies Many Uncharacterized Actin-like Proteins (Alps) in Bacteria: Regulated Polymerization, Dynamic Instability, and Treadmilling in Alp7A

    PubMed Central

    Derman, Alan I.; Becker, Eric C.; Truong, Bao D.; Fujioka, Akina; Tucey, Timothy M.; Erb, Marcella L.; Patterson, Paula C.; Pogliano, Joe

    2010-01-01

    Summary Actin, one of the most abundant proteins in the eukaryotic cell, also has an abundance of relatives in the eukaryotic proteome. To date though, only five families of actins have been characterized in bacteria. We have conducted a phylogenetic search and uncovered more than 35 highly divergent families of actin-like proteins (Alps) in bacteria. Their genes are found primarily on phage genomes, on plasmids, and on integrating conjugative elements, and are likely to be involved in a variety of functions. We characterize three Alps and find that all form filaments in the cell. The filaments of Alp7A, a plasmid partitioning protein and one of the most divergent of the Alps, display dynamic instability and also treadmill. Alp7A requires other elements from the plasmid to assemble into dynamic polymers in the cell. Our findings suggest that most if not all of the Alps are indeed actin relatives, and that actin is very well represented in bacteria. PMID:19602153

  2. Total protein

    MedlinePlus

    ... page: //medlineplus.gov/ency/article/003483.htm Total protein To use the sharing features on this page, please enable JavaScript. The total protein test measures the total amount of two classes ...

  3. Epithelial Membrane Protein-2 (EMP2) and Experimental Proliferative Vitreoretinopathy (PVR)

    PubMed Central

    Telander, David G.; Morales, Shawn A.; Mareninov, Sergey; Forward, Krisztina; Gordon, Lynn K.

    2014-01-01

    Purpose Proliferative vitreoretinopathy (PVR) is believed to result in part from de-differentiation of retinal pigment epithelium (RPE) with cellular migration in the vitreous cavity, membrane formation, and contraction in an aberrant wound-healing strategy. In an in vitro collagen-gel contraction assay, epithelial membrane protein 2 (EMP2) controls contraction through activation of focal adhesion kinase (FAK) in a RPE cell line (ARPE-19). The purpose of this study was to investigate how blocking or altering the level of EMP2 expression changed clinical PVR in an in vivo model. Methods Using the ARPE-19 cell line, the levels of EMP2 modulated through stable transfections of an EMP2 overexpressing construct, EMP2 ribozyme, or vector alone. These transfected cell lines were used in a rabbit model of PVR. The severity of PVR was classified by two masked observers. An EMP2 blocking antibody was also used to decrease functional EMP2 in the PVR model. Immunohistochemistry was used to evaluate EMP2 expression in vivo. Results The transfectants with lower levels of EMP2 had significantly less PVR severity than the degree of PVR induced by wild-type cells (p = 0.05). Also, the transfectants with a low-level of EMP2 expression showed a strong trend of less PVR severity than the high-levels EMP2 transfectants (p = 0.06). Blocking EMP2 with a specific polyclonal antibody significantly decreased the level of PVR severity (p = 0.02). PVR membranes were found to be positive for EMP2 expression. Conclusions These in vivo studies support a direct correlation between EMP2 expression and severity of PVR. These results validate the potential for controlling RPE biology through a change in EMP2 expression, and provide a potential therapeutic target for this disease. PMID:21591864

  4. Protein Microarrays

    NASA Astrophysics Data System (ADS)

    Ricard-Blum, S.

    Proteins are key actors in the life of the cell, involved in many physiological and pathological processes. Since variations in the expression of messenger RNA are not systematically correlated with variations in the protein levels, the latter better reflect the way a cell functions. Protein microarrays thus supply complementary information to DNA chips. They are used in particular to analyse protein expression profiles, to detect proteins within complex biological media, and to study protein-protein interactions, which give information about the functions of those proteins [3-9]. They have the same advantages as DNA microarrays for high-throughput analysis, miniaturisation, and the possibility of automation. Section 18.1 gives a brief overview of proteins. Following this, Sect. 18.2 describes how protein microarrays can be made on flat supports, explaining how proteins can be produced and immobilised on a solid support, and discussing the different kinds of substrate and detection method. Section 18.3 discusses the particular format of protein microarrays in suspension. The diversity of protein microarrays and their applications are then reported in Sect. 18.4, with applications to therapeutics (protein-drug interactions) and diagnostics. The prospects for future developments of protein microarrays are then outlined in the conclusion. The bibliography provides an extensive list of reviews and detailed references for those readers who wish to go further in this area. Indeed, the aim of the present chapter is not to give an exhaustive or detailed analysis of the state of the art, but rather to provide the reader with the basic elements needed to understand how proteins are designed and used.

  5. Dietary Proteins

    MedlinePlus

    ... meat, dairy products, nuts, and certain grains and beans. Proteins from meat and other animal products are complete proteins. This means they supply all of the amino acids the body can't make on its own. Most plant proteins are incomplete. You should eat different types ...

  6. Protein Structure

    ERIC Educational Resources Information Center

    Asmus, Elaine Garbarino

    2007-01-01

    Individual students model specific amino acids and then, through dehydration synthesis, a class of students models a protein. The students clearly learn amino acid structure, primary, secondary, tertiary, and quaternary structure in proteins and the nature of the bonds maintaining a protein's shape. This activity is fun, concrete, inexpensive and…

  7. The complement regulator C4b-binding protein analyzed by molecular modeling, bioinformatics and computer-aided experimental design.

    PubMed

    Villoutreix, B O; Blom, A M; Webb, J; Dahlbäck, B

    1999-05-01

    Molecular modeling and bioinformatics have gained recognition as scientific disciplines of importance in the field of biomedical research. Molecular modeling not only allows to predict the three-dimensional structure of a protein but also helps to define its function. Careful incorporation of the experimental findings in the structural/theoretical data provides means to understand molecular mechanisms for highly complex biological systems. C4b-binding protein (C4BP) is composed of one beta-chain and seven alpha-chains essentially built from three- and eight-complement control protein (CCP) modules, respectively, followed by a non-repeat carboxy-terminal region involved in polymerization of the chains. C4BP is involved in the regulation of the complement system and interacts with many molecules such as C4b, Arp, protein S and heparin. Here, we report experimental and computer data obtained for C4BP. Protein modeling together with site directed mutagenesis indicate that R39, R64 and R66 from the C4BP alpha-chain form a key binding site for heparin, suggesting that this region could be of major importance for interaction with C4b. We also propose that the first CCP of the C4BP beta-chain displays a key hydrophobic surface of major importance for the interaction with the coagulation cofactor protein S. PMID:10408373

  8. Are cobaltates conventional? An ARPES viewpoint

    SciTech Connect

    Hasan, M.Z. . E-mail: mzhasan@Princeton.edu; Qian, D.; Foo, M.L.; Cava, R.J.

    2006-07-15

    Recently discovered class of cobaltate superconductors (Na{sub 0.3}CoO{sub 2}.nH{sub 2}O) is a novel realization of interacting quantum electron system in a triangular network with low-energy degrees of freedom. We employ angle-resolved photoemission spectroscopy to study the quasiparticle parameters in the parent superconductors. Results reveal a large hole-like Fermi surface generated by the crossing of heavy quasiparticles. The measured quasiparticle parameters collectively suggest two orders of magnitude departure from the conventional weak coupling (such as Al) Bardeen-Cooper-Schrieffer electron dynamics paradigm and unveils cobaltates as a rather hidden class of relatively high temperature superconductors. These parameters also form the basis for a microscopic Hamiltonian of the system.

  9. Actin-associated protein palladin is required for migration behavior and differentiation potential of C2C12 myoblast cells

    SciTech Connect

    Nguyen, Ngoc Uyen Nhi; Liang, Vincent Roderick; Wang, Hao-Ven

    2014-09-26

    Highlights: • Palladin is involved in myogenesis in vitro. • Palladin knockdown by siRNA increases myoblast proliferation, viability and differentiation. • Palladin knockdown decreases C2C12 myoblast migration ability. - Abstract: The actin-associated protein palladin has been shown to be involved in differentiation processes in non-muscle tissues. However, but its function in skeletal muscle has rarely been studied. Palladin plays important roles in the regulation of diverse actin-related signaling in a number of cell types. Since intact actin-cytoskeletal remodeling is necessary for myogenesis, in the present study, we pursue to investigate the role of actin-associated palladin in skeletal muscle differentiation. Palladin in C2C12 myoblasts is knocked-down using specific small interfering RNA (siRNA). The results show that down-regulation of palladin decreased migratory activity of mouse skeletal muscle C2C12 myoblasts. Furthermore, the depletion of palladin enhances C2C12 vitality and proliferation. Of note, the loss of palladin promotes C2C12 to express the myosin heavy chain, suggesting that palladin has a role in the modulation of C2C12 differentiation. It is thus proposed that palladin is required for normal C2C12 myogenesis in vitro.

  10. Large scale systematic proteomic quantification from non-metastatic to metastatic colorectal cancer

    NASA Astrophysics Data System (ADS)

    Yin, Xuefei; Zhang, Yang; Guo, Shaowen; Jin, Hong; Wang, Wenhai; Yang, Pengyuan

    2015-07-01

    A systematic proteomic quantification of formalin-fixed, paraffin-embedded (FFPE) colorectal cancer tissues from stage I to stage IIIC was performed in large scale. 1017 proteins were identified with 338 proteins in quantitative changes by label free method, while 341 proteins were quantified with significant expression changes among 6294 proteins by iTRAQ method. We found that proteins related to migration expression increased and those for binding and adherent decreased during the colorectal cancer development according to the gene ontology (GO) annotation and ingenuity pathway analysis (IPA). The integrin alpha 5 (ITA5) in integrin family was focused, which was consistent with the metastasis related pathway. The expression level of ITA5 decreased in metastasis tissues and the result has been further verified by Western blotting. Another two cell migration related proteins vitronectin (VTN) and actin-related protein (ARP3) were also proved to be up-regulated by both mass spectrometry (MS) based quantification results and Western blotting. Up to now, our result shows one of the largest dataset in colorectal cancer proteomics research. Our strategy reveals a disease driven omics-pattern for the metastasis colorectal cancer.

  11. Transport proteins.

    PubMed

    Thatcher, Jack D

    2013-04-16

    This Teaching Resource provides and describes two animated lessons that illustrate general properties of transport proteins. The lesson called "transport protein classes" depicts major classes and subclasses of transport proteins. The "transporters, mechanism of action" lesson explains how transporters and P class ATPase (adenosine triphosphatase) pumps function. These animations serve as valuable resources for any collegiate-level course that describes these important factors. Courses that might use them include introductory biology, biochemistry, cell biology, physiology, and biophysics.

  12. Proteins wriggle.

    PubMed Central

    Cahill, Michael; Cahill, Sean; Cahill, Kevin

    2002-01-01

    We propose an algorithmic strategy for improving the efficiency of Monte Carlo searches for the low-energy states of proteins. Our strategy is motivated by a model of how proteins alter their shapes. In our model, when proteins fold under physiological conditions, their backbone dihedral angles change synchronously in groups of four or more to avoid steric clashes and respect the kinematic conservation laws. They wriggle; they do not thrash. We describe a simple algorithm that can be used to incorporate wriggling in Monte Carlo simulations of protein folding. We have tested this wriggling algorithm against a code in which the dihedral angles are varied independently (thrashing). Our standard of success is the average root-mean-square distance (rmsd) between the alpha-carbons of the folding protein and those of its native structure. After 100,000 Monte Carlo sweeps, the relative decrease in the mean rmsd, as one switches from thrashing to wriggling, rises from 11% for the protein 3LZM with 164 amino acids (aa) to 40% for the protein 1A1S with 313 aa and 47% for the protein 16PK with 415 aa. These results suggest that wriggling is useful and that its utility increases with the size of the protein. One may implement wriggling on a parallel computer or a computer farm. PMID:11964253

  13. Deoxyhypusine Modification of Eukaryotic Translation Initiation Factor 5A (eIF5A) Is Essential for Trypanosoma brucei Growth and for Expression of Polyprolyl-containing Proteins.

    PubMed

    Nguyen, Suong; Leija, Chrisopher; Kinch, Lisa; Regmi, Sandesh; Li, Qiong; Grishin, Nick V; Phillips, Margaret A

    2015-08-01

    The eukaryotic protozoan parasite Trypanosoma brucei is the causative agent of human African trypanosomiasis. Polyamine biosynthesis is essential in T. brucei, and the polyamine spermidine is required for synthesis of a novel cofactor called trypanothione and for deoxyhypusine modification of eukaryotic translation initiation factor 5A (eIF5A). eIF5A promotes translation of proteins containing polyprolyl tracts in mammals and yeast. To evaluate the function of eIF5A in T. brucei, we used RNA interference (RNAi) to knock down eIF5A levels and found that it is essential for T. brucei growth. The RNAi-induced growth defect was complemented by expression of wild-type human eIF5A but not by a Lys-50 mutant that blocks modification by deoxyhypusine. Bioinformatics analysis showed that 15% of the T. brucei proteome contains 3 or more consecutive prolines and that actin-related proteins and cysteine proteases were highly enriched in the group. Steady-state protein levels of representative proteins containing 9 consecutive prolines that are involved in actin assembly (formin and CAP/Srv2p) were significantly reduced by knockdown of eIF5A. Several T. brucei polyprolyl proteins are involved in flagellar assembly. Knockdown of TbeIF5A led to abnormal cell morphologies and detached flagella, suggesting that eIF5A is important for translation of proteins needed for these processes. Potential specialized functions for eIF5A in T. brucei in translation of variable surface glycoproteins were also uncovered. Inhibitors of deoxyhypusination would be expected to cause a pleomorphic effect on multiple cell processes, suggesting that deoxyhypusine/hypusine biosynthesis could be a promising drug target in not just T. brucei but in other eukaryotic pathogens.

  14. Deoxyhypusine Modification of Eukaryotic Translation Initiation Factor 5A (eIF5A) Is Essential for Trypanosoma brucei Growth and for Expression of Polyprolyl-containing Proteins*

    PubMed Central

    Nguyen, Suong; Leija, Chrisopher; Kinch, Lisa; Regmi, Sandesh; Li, Qiong; Grishin, Nick V.; Phillips, Margaret A.

    2015-01-01

    The eukaryotic protozoan parasite Trypanosoma brucei is the causative agent of human African trypanosomiasis. Polyamine biosynthesis is essential in T. brucei, and the polyamine spermidine is required for synthesis of a novel cofactor called trypanothione and for deoxyhypusine modification of eukaryotic translation initiation factor 5A (eIF5A). eIF5A promotes translation of proteins containing polyprolyl tracts in mammals and yeast. To evaluate the function of eIF5A in T. brucei, we used RNA interference (RNAi) to knock down eIF5A levels and found that it is essential for T. brucei growth. The RNAi-induced growth defect was complemented by expression of wild-type human eIF5A but not by a Lys-50 mutant that blocks modification by deoxyhypusine. Bioinformatics analysis showed that 15% of the T. brucei proteome contains 3 or more consecutive prolines and that actin-related proteins and cysteine proteases were highly enriched in the group. Steady-state protein levels of representative proteins containing 9 consecutive prolines that are involved in actin assembly (formin and CAP/Srv2p) were significantly reduced by knockdown of eIF5A. Several T. brucei polyprolyl proteins are involved in flagellar assembly. Knockdown of TbeIF5A led to abnormal cell morphologies and detached flagella, suggesting that eIF5A is important for translation of proteins needed for these processes. Potential specialized functions for eIF5A in T. brucei in translation of variable surface glycoproteins were also uncovered. Inhibitors of deoxyhypusination would be expected to cause a pleomorphic effect on multiple cell processes, suggesting that deoxyhypusine/hypusine biosynthesis could be a promising drug target in not just T. brucei but in other eukaryotic pathogens. PMID:26082486

  15. Polarity protein Crumbs homolog-3 (CRB3) regulates ectoplasmic specialization dynamics through its action on F-actin organization in Sertoli cells

    PubMed Central

    Gao, Ying; Lui, Wing-yee; Lee, Will M.; Cheng, C. Yan

    2016-01-01

    Crumbs homolog 3 (or Crumbs3, CRB3) is a polarity protein expressed by Sertoli and germ cells at the basal compartment in the seminiferous epithelium. CRB3 also expressed at the blood-testis barrier (BTB), co-localized with F-actin, TJ proteins occludin/ZO-1 and basal ES (ectoplasmic specialization) proteins N-cadherin/β-catenin at stages IV-VII only. The binding partners of CRB3 in the testis were the branched actin polymerization protein Arp3, and the barbed end-capping and bundling protein Eps8, illustrating its possible role in actin organization. CRB3 knockdown (KD) by RNAi in Sertoli cells with an established tight junction (TJ)-permeability barrier perturbed the TJ-barrier via changes in the distribution of TJ- and basal ES-proteins at the cell-cell interface. These changes were the result of CRB3 KD-induced re-organization of actin microfilaments, in which actin microfilaments were truncated, and extensively branched, thereby destabilizing F-actin-based adhesion protein complexes at the BTB. Using Polyplus in vivo-jetPEI as a transfection medium with high efficiency for CRB3 KD in the testis, the CRB3 KD testes displayed defects in spermatid and phagosome transport, and also spermatid polarity due to a disruption of F-actin organization. In summary, CRB3 is an actin microfilament regulator, playing a pivotal role in organizing actin filament bundles at the ES. PMID:27358069

  16. Mechanical force-induced polymerization and depolymerization of F-actin at water/solid interfaces

    NASA Astrophysics Data System (ADS)

    Zhang, Xueqiang; Hu, Xiuyuan; Lei, Haozhi; Hu, Jun; Zhang, Yi

    2016-03-01

    Actin molecules are among the three main cytoskeleton proteins of cells and undergo rapid cycling to regulate critical processes such as endocytosis, cytokinesis, cell polarity, and cell morphogenesis. Although extensive studies have been carried out on the dynamics as well as biological functions of actin polymerization and depolymerization both in vivo and in vitro, the molecular mechanisms by which cells sense and respond to mechanical signals are not fully understood. In particular, little attention has been paid to the effect of a physical force that is exerted directly on the actin cytoskeleton. In this paper, we have explored how the mechanical force affects the actin polymerization and depolymerization behaviors at water/solid interfaces using an atomic force microscope (AFM) operated in liquid. By raster scanning an AFM probe on a substrate surface with a certain load, it was found that actin monomers could polymerize into filaments without the help of actin related proteins (ARPs). Further study indicated that actin monomers were inclined to form filaments only under a small scanning load. The polymerized actin filaments would be depolymerized when the mechanical force was stronger. A possible mechanism has been suggested to explain the mechanical force induced actin polymerization.Actin molecules are among the three main cytoskeleton proteins of cells and undergo rapid cycling to regulate critical processes such as endocytosis, cytokinesis, cell polarity, and cell morphogenesis. Although extensive studies have been carried out on the dynamics as well as biological functions of actin polymerization and depolymerization both in vivo and in vitro, the molecular mechanisms by which cells sense and respond to mechanical signals are not fully understood. In particular, little attention has been paid to the effect of a physical force that is exerted directly on the actin cytoskeleton. In this paper, we have explored how the mechanical force affects the actin

  17. Formin 1 Regulates Ectoplasmic Specialization in the Rat Testis Through Its Actin Nucleation and Bundling Activity.

    PubMed

    Li, Nan; Mruk, Dolores D; Wong, Chris K C; Han, Daishu; Lee, Will M; Cheng, C Yan

    2015-08-01

    During spermatogenesis, developing spermatids and preleptotene spermatocytes are transported across the adluminal compartment and the blood-testis barrier (BTB), respectively, so that spermatids line up near the luminal edge to prepare for spermiation, whereas preleptotene spermatocytes enter the adluminal compartment to differentiate into late spermatocytes to prepare for meiosis I/II. These cellular events involve actin microfilament reorganization at the testis-specific, actin-rich Sertoli-spermatid and Sertoli-Sertoli cell junction called apical and basal ectoplasmic specialization (ES). Formin 1, an actin nucleation protein known to promote actin microfilament elongation and bundling, was expressed at the apical ES but limited to stage VII of the epithelial cycle, whereas its expression at the basal ES/BTB stretched from stage III to stage VI, diminished in stage VII, and was undetectable in stage VIII tubules. Using an in vitro model of studying Sertoli cell BTB function by RNA interference and biochemical assays to monitor actin bundling and polymerization activity, a knockdown of formin 1 in Sertoli cells by approximately 70% impeded the tight junction-permeability function. This disruptive effect on the tight junction barrier was mediated by a loss of actin microfilament bundling and actin polymerization capability mediated by changes in the localization of branched actin-inducing protein Arp3 (actin-related protein 3), and actin bundling proteins Eps8 (epidermal growth factor receptor pathway substrate 8) and palladin, thereby disrupting cell adhesion. Formin 1 knockdown in vivo was found to impede spermatid adhesion, transport, and polarity, causing defects in spermiation in which elongated spermatids remained embedded into the epithelium in stage IX tubules, mediated by changes in the spatiotemporal expression of Arp3, Eps8, and palladin. In summary, formin 1 is a regulator of ES dynamics.

  18. Protein Crystallization

    NASA Technical Reports Server (NTRS)

    Chernov, Alexander A.

    2005-01-01

    Nucleation, growth and perfection of protein crystals will be overviewed along with crystal mechanical properties. The knowledge is based on experiments using optical and force crystals behave similar to inorganic crystals, though with a difference in orders of magnitude in growing parameters. For example, the low incorporation rate of large biomolecules requires up to 100 times larger supersaturation to grow protein, rather than inorganic crystals. Nucleation is often poorly reproducible, partly because of turbulence accompanying the mixing of precipitant with protein solution. Light scattering reveals fluctuations of molecular cluster size, its growth, surface energies and increased clustering as protein ages. Growth most often occurs layer-by-layer resulting in faceted crystals. New molecular layer on crystal face is terminated by a step where molecular incorporation occurs. Quantitative data on the incorporation rate will be discussed. Rounded crystals with molecularly disordered interfaces will be explained. Defects in crystals compromise the x-ray diffraction resolution crucially needed to find the 3D atomic structure of biomolecules. The defects are immobile so that birth defects stay forever. All lattice defects known for inorganics are revealed in protein crystals. Contribution of molecular conformations to lattice disorder is important, but not studied. This contribution may be enhanced by stress field from other defects. Homologous impurities (e.g., dimers, acetylated molecules) are trapped more willingly by a growing crystal than foreign protein impurities. The trapped impurities induce internal stress eliminated in crystals exceeding a critical size (part of mni for ferritin, lysozyme). Lesser impurities are trapped from stagnant, as compared to the flowing, solution. Freezing may induce much more defects unless quickly amorphysizing intracrystalline water.

  19. Bacteriophage protein-protein interactions.

    PubMed

    Häuser, Roman; Blasche, Sonja; Dokland, Terje; Haggård-Ljungquist, Elisabeth; von Brunn, Albrecht; Salas, Margarita; Casjens, Sherwood; Molineux, Ian; Uetz, Peter

    2012-01-01

    Bacteriophages T7, λ, P22, and P2/P4 (from Escherichia coli), as well as ϕ29 (from Bacillus subtilis), are among the best-studied bacterial viruses. This chapter summarizes published protein interaction data of intraviral protein interactions, as well as known phage-host protein interactions of these phages retrieved from the literature. We also review the published results of comprehensive protein interaction analyses of Pneumococcus phages Dp-1 and Cp-1, as well as coliphages λ and T7. For example, the ≈55 proteins encoded by the T7 genome are connected by ≈43 interactions with another ≈15 between the phage and its host. The chapter compiles published interactions for the well-studied phages λ (33 intra-phage/22 phage-host), P22 (38/9), P2/P4 (14/3), and ϕ29 (20/2). We discuss whether different interaction patterns reflect different phage lifestyles or whether they may be artifacts of sampling. Phages that infect the same host can interact with different host target proteins, as exemplified by E. coli phage λ and T7. Despite decades of intensive investigation, only a fraction of these phage interactomes are known. Technical limitations and a lack of depth in many studies explain the gaps in our knowledge. Strategies to complete current interactome maps are described. Although limited space precludes detailed overviews of phage molecular biology, this compilation will allow future studies to put interaction data into the context of phage biology. PMID:22748812

  20. Recombinant protein production technology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recombinant protein production is an important technology for antibody production, biochemical activity study, and structural determination during the post-genomic era. Limiting factors in recombinant protein production include low-level protein expression, protein precipitation, and loss of protein...

  1. Anti-inflammatory mechanisms of the annexin A1 protein and its mimetic peptide Ac2-26 in models of ocular inflammation in vivo and in vitro.

    PubMed

    Girol, Ana P; Mimura, Kallyne K O; Drewes, Carine C; Bolonheis, Simone M; Solito, Egle; Farsky, Sandra H P; Gil, Cristiane D; Oliani, Sonia M

    2013-06-01

    Annexin A1 (AnxA1) is a protein that displays potent anti-inflammatory properties, but its expression in eye tissue and its role in ocular inflammatory diseases have not been well studied. We investigated the mechanism of action and potential uses of AnxA1 and its mimetic peptide (Ac2-26) in the endotoxin-induced uveitis (EIU) rodent model and in human ARPE-19 cells activated by LPS. In rats, analysis of untreated EIU after 24 and 48 h or EIU treated with topical applications or with a single s.c. injection of Ac2-26 revealed the anti-inflammatory actions of Ac2-26 on leukocyte infiltration and on the release of inflammatory mediators; the systemic administration of Boc2, a formylated peptide receptor (fpr) antagonist, abrogated the peptide's protective effects. Moreover, AnxA1(-/-) mice exhibited exacerbated EIU compared with wild-type animals. Immunohistochemical studies of ocular tissue showed a specific AnxA1 posttranslational modification in EIU and indicated that the fpr2 receptor mediated the anti-inflammatory actions of AnxA1. In vitro studies confirmed the roles of AnxA1 and fpr2 and the protective effects of Ac2-26 on the release of chemical mediators in ARPE-19 cells. Molecular analysis of NF-κB translocation and IL-6, IL-8, and cyclooxygenase-2 gene expression indicated that the protective effects of AnxA1 occur independently of the NF-κB signaling pathway and possibly in a posttranscriptional manner. Together, our data highlight the role of AnxA1 in ocular inflammation, especially uveitis, and suggest the use of AnxA1 or its mimetic peptide Ac2-26 as a therapeutic approach.

  2. Protein electrophoresis - serum

    MedlinePlus

    ... of protein and fat, called lipoproteins (such as LDL cholesterol). ... globulin proteins may indicate: Abnormally low level of LDL cholesterol Malnutrition Increased gamma globulin proteins may indicate: Bone ...

  3. Ena/VASP proteins cooperate with the WAVE complex to regulate the actin cytoskeleton.

    PubMed

    Chen, Xing Judy; Squarr, Anna Julia; Stephan, Raiko; Chen, Baoyu; Higgins, Theresa E; Barry, David J; Martin, Morag C; Rosen, Michael K; Bogdan, Sven; Way, Michael

    2014-09-01

    Ena/VASP proteins and the WAVE regulatory complex (WRC) regulate cell motility by virtue of their ability to independently promote actin polymerization. We demonstrate that Ena/VASP and the WRC control actin polymerization in a cooperative manner through the interaction of the Ena/VASP EVH1 domain with an extended proline rich motif in Abi. This interaction increases cell migration and enables VASP to cooperatively enhance WRC stimulation of Arp2/3 complex-mediated actin assembly in vitro in the presence of Rac. Loss of this interaction in Drosophila macrophages results in defects in lamellipodia formation, cell spreading, and redistribution of Ena to the tips of filopodia-like extensions. Rescue experiments of abi mutants also reveals a physiological requirement for the Abi:Ena interaction in photoreceptor axon targeting and oogenesis. Our data demonstrate that the activities of Ena/VASP and the WRC are intimately linked to ensure optimal control of actin polymerization during cell migration and development.

  4. A chemical inhibitor of N-WASP reveals a new mechanism for targeting protein interactions

    PubMed Central

    Peterson, Jeffrey R.; Lokey, R. Scott; Mitchison, Timothy J.; Kirschner, Marc W.

    2001-01-01

    Cell morphology and motility are governed largely by complex signaling networks that ultimately engage the actin cytoskeleton. Understanding how individual circuits contribute to the process of forming cellular structures would be aided greatly by the availability of specific chemical inhibitors. We have used a novel chemical screen in Xenopus cell-free extracts to identify compounds that inhibit signaling pathways regulating actin polymerization. Here we report the results of a high-throughput screen for compounds that inhibit phosphatidylinositol 4,5-bisphosphate (PIP2)-induced actin assembly and the identification of the first compound, a cyclic peptide, known to block actin assembly by inhibiting an upstream signaling component. We identify the target of this compound as N-WASP, a protein that has been investigated for its role as a node interconnecting various actin signaling networks. We show that this compound prevents activation of the Arp2/3 complex by N-WASP by allosterically stabilizing the autoinhibited conformation of N-WASP. PMID:11553809

  5. How capping protein enhances actin filament growth and nucleation on biomimetic beads

    NASA Astrophysics Data System (ADS)

    Wang, Ruizhe; Carlsson, Anders E.

    2015-12-01

    Capping protein (CP), which caps the growing ends of actin filaments, accelerates actin-based motility. Recent experiments on biomimetic beads have shown that CP also enhances the rate of actin filament nucleation. Proposed explanations for these phenomena include (i) the actin funneling hypothesis (AFH), in which the presence of CP increases the free-actin concentration, and (ii) the monomer gating model, in which CP binding to actin filament barbed ends makes more monomers available for filament nucleation. To establish how CP increases the rates of filament elongation and nucleation on biomimetic beads, we perform a quantitative modeling analysis of actin polymerization, using rate equations that include actin filament nucleation, polymerization and capping, as modified by monomer depletion near the surface of the bead. With one adjustable parameter, our simulation results match previously measured time courses of polymerized actin and filament number. The results support a version of the AFH where CP increases the local actin monomer concentration at the bead surface, but leaves the global free-actin concentration nearly constant. Because the rate of filament nucleation increases with the monomer concentration, the increased local monomer concentration enhances actin filament nucleation. We derive a closed-form formula for the characteristic CP concentration where the local free-actin concentration reaches half the bulk value, and find it to be comparable to the global Arp2/3 complex concentration. We also propose an experimental protocol for distinguishing branching nucleation of filaments from spontaneous nucleation.

  6. Treatment of proteins with dietary polyphenols lowers the formation of AGEs and AGE-induced toxicity.

    PubMed

    Zhang, Xinchen; Hu, Shuting; Chen, Feng; Wang, Mingfu

    2014-10-01

    Advanced glycation endproducts (AGEs) are a group of harmful compounds produced either endogenously or during thermal food processing. Once absorbed by humans via food intake, AGEs can cause oxidative cell damage and contribute to pathological development of various diseases. The AGE-inhibitory activity of dietary polyphenols in vitro has been extensively reported before, but the current study is pioneering in examining the antiglycation activity of five selected dietary polyphenols (phloretin, naringenin, epicatechin, chlorogenic acid, and rosmarinic acid) during the thermal protein glycation process. When added into the glucose-casein glycation model heated at 120 °C for 2 h, these polyphenols were capable of inhibiting the formation of both total fluorescent AGEs and nonfluorescent carboxymethyllysine (CML). The thermal stability and transformation of polyphenols are likely important factors affecting their antioxidant activity and inhibitory efficacy of reactive carbonyl species formation. Treatment with epicatechin would lower not only AGE formation but also AGE-induced cytotoxicity and oxidative stress to human retinal pigment epithelial (ARPE-19) cells. PMID:25208810

  7. Screening a yeast library of temperature-sensitive mutants reveals a role for actin in tombusvirus RNA recombination.

    PubMed

    Prasanth, K Reddisiva; Kovalev, Nikolay; de Castro Martín, Isabel Fernández; Baker, Jannine; Nagy, Peter D

    2016-02-01

    Genetic recombination in RNA viruses drives the evolutionary arms race with host's antiviral strategies and recombination also facilitates adaptation of viruses to new hosts. In this paper, the authors used tombusvirus and a temperature-sensitive (ts) mutant library of yeast to identify 40 host proteins affecting viral recombination in yeast model host. Subsequent detailed analysis with two identified actin-related proteins, Act1p and Arp3p, has revealed that the wt actin network helps TBSV to maintain low level viral recombination. Pharmacological inhibition of actin in plant protoplasts confirmed the role of the actin network in tombusvirus recombination. An in vitro approach revealed the altered activity of the tombusvirus replicase in the presence of mutated Act1p. The authors show more efficient recruitment of a cellular DEAD-box helicase, which enhances tombusvirus recombination, into the membrane-bound replicase in Act1p mutant yeast. Overall, this work shows that the actin network affects tombusvirus recombination in yeast and plant cells.

  8. Mechanical force-induced polymerization and depolymerization of F-actin at water/solid interfaces.

    PubMed

    Zhang, Xueqiang; Hu, Xiuyuan; Lei, Haozhi; Hu, Jun; Zhang, Yi

    2016-03-21

    Actin molecules are among the three main cytoskeleton proteins of cells and undergo rapid cycling to regulate critical processes such as endocytosis, cytokinesis, cell polarity, and cell morphogenesis. Although extensive studies have been carried out on the dynamics as well as biological functions of actin polymerization and depolymerization both in vivo and in vitro, the molecular mechanisms by which cells sense and respond to mechanical signals are not fully understood. In particular, little attention has been paid to the effect of a physical force that is exerted directly on the actin cytoskeleton. In this paper, we have explored how the mechanical force affects the actin polymerization and depolymerization behaviors at water/solid interfaces using an atomic force microscope (AFM) operated in liquid. By raster scanning an AFM probe on a substrate surface with a certain load, it was found that actin monomers could polymerize into filaments without the help of actin related proteins (ARPs). Further study indicated that actin monomers were inclined to form filaments only under a small scanning load. The polymerized actin filaments would be depolymerized when the mechanical force was stronger. A possible mechanism has been suggested to explain the mechanical force induced actin polymerization.

  9. Protein sulfhydration.

    PubMed

    Paul, Bindu D; Snyder, Solomon H

    2015-01-01

    Hydrogen sulfide (H2S) is one of the gasotransmitters that modulates various biological processes and participates in multiple signaling pathways. H2S signals by a process termed sulfhydration. Sulfhydration has recently been recognized as a posttranslational modification similar to nitrosylation. Sulfhydration occurs at reactive cysteine residues in proteins and results in the conversion of an -SH group of cysteine to an -SSH or a persulfide group. Sulfhydration is highly prevalent in vivo, and aberrant sulfhydration patterns have been observed under several pathological conditions ranging from heart disease to neurodegenerative diseases such as Parkinson's disease. The biotin switch assay, originally developed to detect nitrosylation, has been modified to detect sulfhydration. In this chapter, we discuss the physiological roles of sulfhydration and the methodologies used to detect this modification.

  10. Drosophila comes of age as a model system for understanding the function of cytoskeletal proteins in cells, tissues, and organisms.

    PubMed

    Rodal, Avital A; Del Signore, Steven J; Martin, Adam C

    2015-05-01

    For the last 100 years, Drosophila melanogaster has been a powerhouse genetic system for understanding mechanisms of inheritance, development, and behavior in animals. In recent years, advances in imaging and genetic tools have led to Drosophila becoming one of the most effective systems for unlocking the subcellular functions of proteins (and particularly cytoskeletal proteins) in complex developmental settings. In this review, written for non-Drosophila experts, we will discuss critical technical advances that have enabled these cell biological insights, highlighting three examples of cytoskeletal discoveries that have arisen as a result: (1) regulation of Arp2/3 complex in myoblast fusion, (2) cooperation of the actin filament nucleators Spire and Cappuccino in establishment of oocyte polarity, and (3) coordination of supracellular myosin cables. These specific examples illustrate the unique power of Drosophila both to uncover new cytoskeletal structures and functions, and to place these discoveries in a broader in vivo context, providing insights that would have been impossible in a cell culture model or in vitro. Many of the cellular structures identified in Drosophila have clear counterparts in mammalian cells and tissues, and therefore elucidating cytoskeletal functions in Drosophila will be broadly applicable to other organisms.

  11. EspF Interacts with Nucleation-Promoting Factors To Recruit Junctional Proteins into Pedestals for Pedestal Maturation and Disruption of Paracellular Permeability ▿

    PubMed Central

    Peralta-Ramírez, Janneth; Hernandez, J. Manuel; Manning-Cela, Rebeca; Luna-Muñoz, José; Garcia-Tovar, Carlos; Nougayréde, Jean-Philippe; Oswald, Eric; Navarro-Garcia, Fernando

    2008-01-01

    Many pathogenic bacteria subvert normal host cell processes by delivering effector proteins which mimic eukaryotic functions directly into target cells. EspF is a multifunctional protein injected into host cells by attaching and effacing pathogens, but its mechanism of action is not understood completely. In silico analyses of EspF revealed two key motifs: proline-rich domains and PDZ domain binding motifs. Such functional domains may allow EspF to act as an actin nucleation-promoting factor by mimicking host proteins. In agreement with these predictions, we found that EspF from rabbit enteropathogenic Escherichia coli (E22) participates in the regulation of actin polymerization by binding to a complex of proteins at the tight junctions (TJ). EspF bound to actin and profilin throughout the course of infection. However, after 2 h of infection, EspF also bound to the neural Wiskott-Aldrich syndrome protein and to the Arp2/3, zonula occludens-1 (ZO-1), and ZO-2 proteins. Moreover, EspF caused occludin, claudin, ZO-1, and ZO-2 redistribution and loss of transepithelial electrical resistance, suggesting that actin sequestration by EspF may cause local actin depolymerization leading to EspF-induced TJ disruption. Furthermore, EspF caused recruitment of these TJ proteins into the pedestals. An E22 strain lacking EspF did not cause TJ disruption and pedestals were smaller than those induced by the wild-type strain. Additionally, the pedestals were located mainly in the TJ. The overexpression of EspF caused bigger pedestals located along the length of the cells. Thus, actin sequestration by EspF allows the recruitment of junctional proteins into the pedestals, leading to the maturation of actin pedestals and the disruption of paracellular permeability. PMID:18559425

  12. Fusion-protein-assisted protein crystallization.

    PubMed

    Kobe, Bostjan; Ve, Thomas; Williams, Simon J

    2015-07-01

    Fusion proteins can be used directly in protein crystallization to assist crystallization in at least two different ways. In one approach, the `heterologous fusion-protein approach', the fusion partner can provide additional surface area to promote crystal contact formation. In another approach, the `fusion of interacting proteins approach', protein assemblies can be stabilized by covalently linking the interacting partners. The linker connecting the proteins plays different roles in the two applications: in the first approach a rigid linker is required to reduce conformational heterogeneity; in the second, conversely, a flexible linker is required that allows the native interaction between the fused proteins. The two approaches can also be combined. The recent applications of fusion-protein technology in protein crystallization from the work of our own and other laboratories are briefly reviewed.

  13. Tonicity-responsive enhancer binding protein regulates the expression of aldose reductase and protein kinase C δ in a mouse model of diabetic retinopathy.

    PubMed

    Park, Jeongsook; Kim, Hwajin; Park, So Yun; Lim, Sun Woo; Kim, Yoon Sook; Lee, Dong Hoon; Roh, Gu Seob; Kim, Hyun Joon; Kang, Sang Soo; Cho, Gyeong Jae; Jeong, Bo-Young; Kwon, H Moo; Choi, Wan Sung

    2014-05-01

    Recent studies revealed that Tonicity-responsive enhancer binding protein (TonEBP) directly regulates the transcription of aldose reductase (AR), which catalyzes the first step of the polyol pathway of glucose metabolism. Activation of protein kinase C δ (PKCδ) is dependent on AR and it has been linked to diabetic complications. However, whether TonEBP affects expressions of AR and PKCδ in diabetic retinopathy was not clearly shown. In this study, we used TonEBP heterozygote mice to study the role of TonEBP in streptozotocin (STZ)-induced diabetic retinopathy. We performed immunofluorescence staining and found that retinal expressions of AR and PKCδ were significantly reduced in the heterozygotes compared to wild type littermates, particularly in ganglion cell layer. To examine further the effect of TonEBP reduction in retinal tissues, we performed intravitreal injection of TonEBP siRNA and confirmed the decrease in AR and PKCδ levels. In addition, we found that a proapoptotic factor, Bax level was reduced and a survival factor, Bcl2 level was increased after injection of TonEBP siRNA, indicating that TonEBP mediates apoptotic cell death. In parallel, TonEBP siRNA was applied to the in vitro human retinal pigment epithelial (ARPE-19) cells cultured in high glucose media. We have consistently found the decrease in AR and PKCδ levels and changes in apoptotic factors for survival. Together, these results clearly demonstrated that hyperglycemia-induced TonEBP plays a crucial role in increasing AR and PKCδ levels and leading to apoptotic death. Our findings suggest that TonEBP reduction is an effective therapeutic strategy for diabetic retinopathy. PMID:24631337

  14. EDITORIAL: Precision proteins Precision proteins

    NASA Astrophysics Data System (ADS)

    Demming, Anna

    2010-06-01

    Since the birth of modern day medicine, during the times of Hippocrates in ancient Greece, the profession has developed from the rudimentary classification of disease into a rigorous science with an inspiring capability to treat and cure. Scientific methodology has distilled clinical diagnostic tools from the early arts of prognosis, which used to rely as much on revelation and prophecy, as intuition and judgement [1]. Over the past decade, research into the interactions between proteins and nanosystems has provided some ingenious and apt techniques for delving into the intricacies of anatomical systems. In vivo biosensing has emerged as a vibrant field of research, as much of medical diagnosis relies on the detection of substances or an imbalance in the chemicals in the body. The inherent properties of nanoscale structures, such as cantilevers, make them well suited to biosensing applications that demand the detection of molecules at very low concentrations. Measurable deflections in cantilevers functionalised with antibodies provide quantitative indicators of the presence of specific antigens when the two react. Such developments have roused mounting interest in the interactions of proteins with nanostructures, such as carbon nanotubes [3], which have demonstrated great potential as generic biomarkers. Plasmonic properties are also being exploited in sensing applications, such as the molecular sentinel recently devised by researchers in the US. The device uses the plasmonic properties of a silver nanoparticle linked to a Raman labelled hairpin DNA probe to signal changes in the probe geometry resulting from interactions with substances in the environment. Success stories so far include the detection of two specific genes associated with breast cancer [4]. A greater understanding of how RNA interference regulates gene expression has highlighted the potential of using this natural process as another agent for combating disease in personalized medicine. However, the

  15. EDITORIAL: Precision proteins Precision proteins

    NASA Astrophysics Data System (ADS)

    Demming, Anna

    2010-06-01

    Since the birth of modern day medicine, during the times of Hippocrates in ancient Greece, the profession has developed from the rudimentary classification of disease into a rigorous science with an inspiring capability to treat and cure. Scientific methodology has distilled clinical diagnostic tools from the early arts of prognosis, which used to rely as much on revelation and prophecy, as intuition and judgement [1]. Over the past decade, research into the interactions between proteins and nanosystems has provided some ingenious and apt techniques for delving into the intricacies of anatomical systems. In vivo biosensing has emerged as a vibrant field of research, as much of medical diagnosis relies on the detection of substances or an imbalance in the chemicals in the body. The inherent properties of nanoscale structures, such as cantilevers, make them well suited to biosensing applications that demand the detection of molecules at very low concentrations. Measurable deflections in cantilevers functionalised with antibodies provide quantitative indicators of the presence of specific antigens when the two react. Such developments have roused mounting interest in the interactions of proteins with nanostructures, such as carbon nanotubes [3], which have demonstrated great potential as generic biomarkers. Plasmonic properties are also being exploited in sensing applications, such as the molecular sentinel recently devised by researchers in the US. The device uses the plasmonic properties of a silver nanoparticle linked to a Raman labelled hairpin DNA probe to signal changes in the probe geometry resulting from interactions with substances in the environment. Success stories so far include the detection of two specific genes associated with breast cancer [4]. A greater understanding of how RNA interference regulates gene expression has highlighted the potential of using this natural process as another agent for combating disease in personalized medicine. However, the

  16. Protein Crystal Based Nanomaterials

    NASA Technical Reports Server (NTRS)

    Bell, Jeffrey A.; VanRoey, Patrick

    2001-01-01

    This is the final report on a NASA Grant. It concerns a description of work done, which includes: (1) Protein crystals cross-linked to form fibers; (2) Engineering of protein to favor crystallization; (3) Better knowledge-based potentials for protein-protein contacts; (4) Simulation of protein crystallization.

  17. Shotgun protein sequencing.

    SciTech Connect

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  18. Actin dynamics regulated by the balance of neuronal Wiskott-Aldrich syndrome protein (N-WASP) and cofilin activities determines the biphasic response of glucose-induced insulin secretion.

    PubMed

    Uenishi, Eita; Shibasaki, Tadao; Takahashi, Harumi; Seki, Chihiro; Hamaguchi, Hitomi; Yasuda, Takao; Tatebe, Masao; Oiso, Yutaka; Takenawa, Tadaomi; Seino, Susumu

    2013-09-01

    Actin dynamics in pancreatic β-cells is involved in insulin secretion. However, the molecular mechanisms of the regulation of actin dynamics by intracellular signals in pancreatic β-cells and its role in phasic insulin secretion are largely unknown. In this study, we elucidate the regulation of actin dynamics by neuronal Wiskott-Aldrich syndrome protein (N-WASP) and cofilin in pancreatic β-cells and demonstrate its role in glucose-induced insulin secretion (GIIS). N-WASP, which promotes actin polymerization through activation of the actin nucleation factor Arp2/3 complex, was found to be activated by glucose stimulation in insulin-secreting clonal pancreatic β-cells (MIN6-K8 β-cells). Introduction of a dominant-negative mutant of N-WASP, which lacks G-actin and Arp2/3 complex-binding region VCA, into MIN6-K8 β-cells or knockdown of N-WASP suppressed GIIS, especially the second phase. We also found that cofilin, which severs F-actin in its dephosphorylated (active) form, is converted to the phosphorylated (inactive) form by glucose stimulation in MIN6-K8 β-cells, thereby promoting F-actin remodeling. In addition, the dominant-negative mutant of cofilin, which inhibits activation of endogenous cofilin, or knockdown of cofilin reduced the second phase of GIIS. However, the first phase of GIIS occurs in the G-actin predominant state, in which cofilin activity predominates over N-WASP activity. Thus, actin dynamics regulated by the balance of N-WASP and cofilin activities determines the biphasic response of GIIS.

  19. Protein immobilization strategies for protein biochips.

    PubMed

    Rusmini, Federica; Zhong, Zhiyuan; Feijen, Jan

    2007-06-01

    In the past few years, protein biochips have emerged as promising proteomic and diagnostic tools for obtaining information about protein functions and interactions. Important technological innovations have been made. However, considerable development is still required, especially regarding protein immobilization, in order to fully realize the potential of protein biochips. In fact, protein immobilization is the key to the success of microarray technology. Proteins need to be immobilized onto surfaces with high density in order to allow the usage of small amount of sample solution. Nonspecific protein adsorption needs to be avoided or at least minimized in order to improve detection performances. Moreover, full retention of protein conformation and activity is a challenging task to be accomplished. Although a large number of review papers on protein biochips have been published in recent years, few have focused on protein immobilization technology. In this review, current protein immobilization strategies, including physical, covalent, and bioaffinity immobilization for the fabrication of protein biochips, are described. Particular consideration has been given to oriented immobilization, also referred to as site-specific immobilization, which is believed will improve homogeneous surface covering and accessibility of the active site.

  20. Protein-losing enteropathy

    MedlinePlus

    ... this page: //medlineplus.gov/ency/article/007338.htm Protein-losing enteropathy To use the sharing features on this page, please enable JavaScript. Protein-losing enteropathy is an abnormal loss of protein ...

  1. Protein in diet

    MedlinePlus

    ... basic structure of protein is a chain of amino acids. You need protein in your diet to help ... Protein foods are broken down into parts called amino acids during digestion. The human body needs a number ...

  2. Localization and role of MYO-1, an endocytic protein in hyphae of Neurospora crassa.

    PubMed

    Lara-Rojas, Fernando; Bartnicki-García, Salomón; Mouriño-Pérez, Rosa R

    2016-03-01

    The subapical endocytic collar is a prominent feature of hyphae of Neurospora crassa. It comprises a dynamic collection of actin patches associated with a number of proteins required for endocytosis, namely, ARP-2/3 complex, fimbrin, coronin, etc. We presently show that MYO-1 is another key component of this endocytic collar. A myo-1 sequence was identified in the genome of N. crassa and used it to generate a strain with a myo-1-sgfp allele under the ccg1 promoter. Examination of living hyphae by confocal microscopy, revealed MYO-1-GFP located mainly as a dynamic collection of small patches arranged in collar-like fashion in the hyphal subapex. Dual tagging showed MYO-1-GFP partially colocalized with two other endocytic proteins, fimbrin and coronin. MYO-1 was also present during septum formation. By recovering a viable strain, albeit severely inhibited, after deletion of myo-1, it was possible to investigate the phenotypic consequences of the elimination of MYO-1. Deletion of myo-1 caused a severe reduction in growth rate (95%), near absence of aerial mycelium and no conidiation. A reduced uptake of the lipophilic dye FM4-64 indicated a deficiency in endocytosis in the Δmyo-1 mutant. Hyphae were produced by the Δmyo-1 mutant but their morphogenesis was severely affected; hyphal morphology was distorted displaying irregular periods of isotropic and polarized growth. The morphological alterations were accompanied, and presumably caused, by a disruption in the organization and dynamics of a myosin-deprived actin cytoskeleton that, ultimately, compromised the stability and function of the Spitzenkörper as a vesicle supply center.

  3. Novel Thermosensitive Pentablock Copolymers for Sustained Delivery of Proteins in the Treatment of Posterior Segment Diseases

    PubMed Central

    Patel, Sulabh P.; Vaishya, Ravi; Yang, Xiaoyan; Pal, Dhananjay; Mitra, Ashim K.

    2015-01-01

    Biodegradable and injectable in situ thermosensitive hydrogels were investigated for sustained delivery of protein therapeutics in the treatment of ocular posterior segment neovascular diseases. A series of triblock (TB, polycaprolac-tone-polyethylene glycol-polycaprolactone (PCL-PEG-PCL), B-A-B) and pentablock copolymers (PBCs) (polylactic acid (PLA)-PCL-PEG-PCL-PLA (C-B-A-B-C) and PEG-PCL-PLA-PCL-PEG (A-B-C-B-A)) were synthesized and evaluated for their thermosensitive behavior. Effects of molecular weight, hydrophobicity and block arrangement on polymer crystallinity, sol-gel transition, micelle size, viscosity and in vitro drug release were examined. Results from sol-gel transition studies demonstrated that aqueous solutions of block copolymers can immediately transform to hydrogel upon exposure to physiological temperature. PBC provide significantly longer sustained release (more than 20 days) of IgG relative to TB copolymers. Moreover, kinematic viscosity of aqueous solution at 25°C for A-B-C-B-A type of PBCs was noticeably lower than the TB (B-A-B) copolymers and other PBCs with C-B-A-B-C block arrangements suggesting desired syringeability. The presence of PLA blocks in PBCs (C-B-A-B-C and A-B-C-B-A) significantly reduces crystallinity. Hence, it is anticipated that PBCs will have a faster rate of degradation relative to PCL-PEG-PCL based TB copolymers. PBCs also exhibited excellent cell viability and biocompatibility on ARPE-19 (human retinal pigment epithelial cell line) and RAW-264.7 (mouse macrophage cells), likely rendering it safe for ocular applications. Owing to biodegradability, thermosensitivity, ease of handling and biocompatibility PBC hydrogels can be considered as promising biomaterial for sustained delivery of protein therapeutics to the back of the eye. PMID:25315374

  4. Nanotechnologies in protein microarrays.

    PubMed

    Krizkova, Sona; Heger, Zbynek; Zalewska, Marta; Moulick, Amitava; Adam, Vojtech; Kizek, Rene

    2015-01-01

    Protein microarray technology became an important research tool for study and detection of proteins, protein-protein interactions and a number of other applications. The utilization of nanoparticle-based materials and nanotechnology-based techniques for immobilization allows us not only to extend the surface for biomolecule immobilization resulting in enhanced substrate binding properties, decreased background signals and enhanced reporter systems for more sensitive assays. Generally in contemporarily developed microarray systems, multiple nanotechnology-based techniques are combined. In this review, applications of nanoparticles and nanotechnologies in creating protein microarrays, proteins immobilization and detection are summarized. We anticipate that advanced nanotechnologies can be exploited to expand promising fields of proteins identification, monitoring of protein-protein or drug-protein interactions, or proteins structures. PMID:26039143

  5. Protein domain architectures.

    PubMed

    Mulder, Nicola J

    2010-01-01

    Proteins are composed of functional units, or domains, that can be found alone or in combination with other domains. Analysis of protein domain architectures and the movement of protein domains within and across different genomes provide clues about the evolution of protein function. The classification of proteins into families and domains is provided through publicly available tools and databases that use known protein domains to predict other members in new proteins sequences. Currently at least 80% of the main protein sequence databases can be classified using these tools, thus providing a large data set to work from for analyzing protein domain architectures. Each of the protein domain databases provide intuitive web interfaces for viewing and analyzing their domain classifications and provide their data freely for downloading. Some of the main protein family and domain databases are described here, along with their Web-based tools for analyzing domain architectures.

  6. PREFACE: Protein protein interactions: principles and predictions

    NASA Astrophysics Data System (ADS)

    Nussinov, Ruth; Tsai, Chung-Jung

    2005-06-01

    Proteins are the `workhorses' of the cell. Their roles span functions as diverse as being molecular machines and signalling. They carry out catalytic reactions, transport, form viral capsids, traverse membranes and form regulated channels, transmit information from DNA to RNA, making possible the synthesis of new proteins, and they are responsible for the degradation of unnecessary proteins and nucleic acids. They are the vehicles of the immune response and are responsible for viral entry into the cell. Given their importance, considerable effort has been centered on the prediction of protein function. A prime way to do this is through identification of binding partners. If the function of at least one of the components with which the protein interacts is known, that should let us assign its function(s) and the pathway(s) in which it plays a role. This holds since the vast majority of their chores in the living cell involve protein-protein interactions. Hence, through the intricate network of these interactions we can map cellular pathways, their interconnectivities and their dynamic regulation. Their identification is at the heart of functional genomics; their prediction is crucial for drug discovery. Knowledge of the pathway, its topology, length, and dynamics may provide useful information for forecasting side effects. The goal of predicting protein-protein interactions is daunting. Some associations are obligatory, others are continuously forming and dissociating. In principle, from the physical standpoint, any two proteins can interact, but under what conditions and at which strength? The principles of protein-protein interactions are general: the non-covalent interactions of two proteins are largely the outcome of the hydrophobic effect, which drives the interactions. In addition, hydrogen bonds and electrostatic interactions play important roles. Thus, many of the interactions observed in vitro are the outcome of experimental overexpression. Protein disorder

  7. Protein sequence comparison and protein evolution

    SciTech Connect

    Pearson, W.R.

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. This tutorial examines how the information conserved during the evolution of a protein molecule can be used to infer reliably homology, and thus a shared proteinfold and possibly a shared active site or function. The authors start by reviewing a geological/evolutionary time scale. Next they look at the evolution of several protein families. During the tutorial, these families will be used to demonstrate that homologous protein ancestry can be inferred with confidence. They also examine different modes of protein evolution and consider some hypotheses that have been presented to explain the very earliest events in protein evolution. The next part of the tutorial will examine the technical aspects of protein sequence comparison. Both optimal and heuristic algorithms and their associated parameters that are used to characterize protein sequence similarities are discussed. Perhaps more importantly, they survey the statistics of local similarity scores, and how these statistics can both be used to improve the selectivity of a search and to evaluate the significance of a match. They them examine distantly related members of three protein families, the serine proteases, the glutathione transferases, and the G-protein-coupled receptors (GCRs). Finally, the discuss how sequence similarity can be used to examine internal repeated or mosaic structures in proteins.

  8. Inferring Protein Associations Using Protein Pulldown Assays

    SciTech Connect

    Sharp, Julia L.; Anderson, Kevin K.; Daly, Don S.; Auberry, Deanna L.; Borkowski, John J.; Cannon, William R.

    2007-02-01

    Background: One method to infer protein-protein associations is through a “bait-prey pulldown” assay using a protein affinity agent and an LC-MS (liquid chromatography-mass spectrometry)-based protein identification method. False positive and negative protein identifications are not uncommon, however, leading to incorrect inferences. Methods: A pulldown experiment generates a protein association matrix wherein each column represents a sample from one bait protein, each row represents one prey protein and each cell contains a presence/absence association indicator. Our method evaluates the presence/absence pattern across a prey protein (row) with a Likelihood Ratio Test (LRT), computing its p-value with simulated LRT test statistic distributions after a check with simulated binomial random variates disqualified the large sample 2 test. A pulldown experiment often involves hundreds of tests so we apply the false discovery rate method to control the false positive rate. Based on the p-value, each prey protein is assigned a category (specific association, non-specific association, or not associated) and appraised with respect to the pulldown experiment’s goal and design. The method is illustrated using a pulldown experiment investigating the protein complexes of Shewanella oneidensis MR-1. Results: The Monte Carlo simulated LRT p-values objectively reveal specific and ubiquitous prey, as well as potential systematic errors. The example analysis shows the results to be biologically sensible and more realistic than the ad hoc screening methods previously utilized. Conclusions: The method presented appears to be informative for screening for protein-protein associations.

  9. NPF motifs in the vaccinia virus protein A36 recruit intersectin-1 to promote Cdc42:N-WASP-mediated viral release from infected cells.

    PubMed

    Snetkov, Xenia; Weisswange, Ina; Pfanzelter, Julia; Humphries, Ashley C; Way, Michael

    2016-01-01

    During its egress, vaccinia virus transiently recruits AP-2 and clathrin after fusion with the plasma membrane. This recruitment polarizes the viral protein A36 beneath the virus, enhancing actin polymerization and the spread of infection. We now demonstrate that three NPF motifs in the C-terminus of A36 recruit AP-2 and clathrin by interacting directly with the Epsin15 homology domains of Eps15 and intersectin-1. A36 is the first identified viral NPF motif containing protein shown to interact with endocytic machinery. Vaccinia still induces actin tails in the absence of the A36 NPF motifs. Their loss, however, reduces the cell-to-cell spread of vaccinia. This is due to a significant reduction in virus release from infected cells, as the lack of intersectin-1 recruitment leads to a loss of Cdc42 activation, impairing N-WASP-driven Arp2/3-mediated actin polymerization. Our results suggest that initial A36-mediated virus release plays a more important role than A36-driven super-repulsion in promoting the cell-to-cell spread of vaccinia. PMID:27670116

  10. Mirror image proteins.

    PubMed

    Zhao, Le; Lu, Wuyuan

    2014-10-01

    Proteins composed entirely of unnatural d-amino acids and the achiral amino acid glycine are mirror image forms of their native l-protein counterparts. Recent advances in chemical protein synthesis afford unique and facile synthetic access to domain-sized mirror image d-proteins, enabling protein research to be conducted through 'the looking glass' and in a way previously unattainable. d-Proteins can facilitate structure determination of their native l-forms that are difficult to crystallize (racemic X-ray crystallography); d-proteins can serve as the bait for library screening to ultimately yield pharmacologically superior d-peptide/d-protein therapeutics (mirror-image phage display); d-proteins can also be used as a powerful mechanistic tool for probing molecular events in biology. This review examines recent progress in the application of mirror image proteins to structural biology, drug discovery, and immunology.

  11. High-throughput and multiplexed protein array technology: protein-DNA and protein-protein interactions.

    PubMed

    Sakanyan, Vehary

    2005-02-01

    Miniaturized protein arrays address protein interactions with various types of molecules in a high-throughput and multiplexed fashion. This review focuses on achievements in the analysis of protein-DNA and protein-protein interactions. The technological feasibility of protein arrays depends on the different factors that enable the arrayed proteins to recognize molecular partners and on the specificity of the interactions involved. Proteome-scale studies of molecular interactions require high-throughput approaches for both the production and purification of functionally active proteins. Various solutions have been proposed to avoid non-specific protein interactions on array supports and to monitor low-abundance molecules. The data accumulated indicate that this emerging technology is perfectly suited to resolve networks of protein interactions involved in complex physiological and pathological phenomena in different organisms and to develop sensitive tools for biomedical applications.

  12. Protein- protein interaction detection system using fluorescent protein microdomains

    DOEpatents

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2010-02-23

    The invention provides a protein labeling and interaction detection system based on engineered fragments of fluorescent and chromophoric proteins that require fused interacting polypeptides to drive the association of the fragments, and further are soluble and stable, and do not change the solubility of polypeptides to which they are fused. In one embodiment, a test protein X is fused to a sixteen amino acid fragment of GFP (.beta.-strand 10, amino acids 198-214), engineered to not perturb fusion protein solubility. A second test protein Y is fused to a sixteen amino acid fragment of GFP (.beta.-strand 11, amino acids 215-230), engineered to not perturb fusion protein solubility. When X and Y interact, they bring the GFP strands into proximity, and are detected by complementation with a third GFP fragment consisting of GFP amino acids 1-198 (strands 1-9). When GFP strands 10 and 11 are held together by interaction of protein X and Y, they spontaneous association with GFP strands 1-9, resulting in structural complementation, folding, and concomitant GFP fluorescence.

  13. [Protein expression and purification].

    PubMed

    Růčková, E; Müller, P; Vojtěšek, B

    2014-01-01

    Production of recombinant proteins is essential for many applications in both basic research and also in medicine, where recombinant proteins are used as pharmaceuticals. This review summarizes procedures involved in recombinant protein expression and purification, including molecular cloning of target genes into expression vectors, selection of the appropriate expression system, and protein purification techniques. Recombinant DNA technology allows protein engineering to modify protein stability, activity and function or to facilitate protein purification by affinity tag fusions. A wide range of cloning systems enabling fast and effective design of expression vectors is currently available. A first choice of protein expression system is usually the bacteria Escherichia coli. The main advantages of this prokaryotic expression system are low cost and simplicity; on the other hand this system is often unsuitable for production of complex mammalian proteins. Protein expression mediated by eukaryotic cells (yeast, insect and mammalian cells) usually produces properly folded and posttranslationally modified proteins. How-ever, cultivation of insect and, especially, mammalian cells is time consuming and expensive. Affinity tagged recombinant proteins are purified efficiently using affinity chromatography. An affinity tag is a protein or peptide that mediates specific binding to a chromatography column, unbound proteins are removed during a washing step and pure protein is subsequently eluted. PMID:24945544

  14. Nck adaptors, besides promoting N-WASP mediated actin-nucleation activity at pedestals, influence the cellular levels of enteropathogenic Escherichia coli Tir effector.

    PubMed

    Nieto-Pelegrin, Elvira; Kenny, Brendan; Martinez-Quiles, Narcisa

    2014-01-01

    Enteropathogenic Escherichia coli (EPEC) binding to human intestinal cells triggers the formation of disease-associated actin rich structures called pedestals. The latter process requires the delivery, via a Type 3 secretion system, of the translocated Intimin receptor (Tir) protein into the host plasma membrane where binding of a host kinase-modified form to the bacterial surface protein Intimin triggers pedestal formation. Tir-Intimin interaction recruits the Nck adaptor to a Tir tyrosine phosphorylated residue where it activates neural Wiskott-Aldrich syndrome protein (N-WASP); initiating the major pathway to actin polymerization mediated by the actin-related protein (Arp) 2/3 complex. Previous studies with Nck-deficient mouse embryonic fibroblasts (MEFs) identified a key role for Nck in pedestal formation, presumed to reflect a lack of N-WASP activation. Here, we show the defect relates to reduced amounts of Tir within Nck-deficient cells. Indeed, Tir delivery and, thus, pedestal formation defects were much greater for MEFs than HeLa (human epithelial) cells. Crucially, the levels of two other effectors (EspB/EspF) within Nck-deficient MEFs were not reduced unlike that of Map (Mitochondrial associated protein) which, like Tir, requires CesT chaperone function for efficient delivery. Interestingly, drugs blocking various host protein degradation pathways failed to increase Tir cellular levels unlike an inhibitor of deacetylase activity (Trichostatin A; TSA). Treatments with TSA resulted in significant recovery of Tir levels, potentiation of actin polymerization and improvement in bacterial attachment to cells. Our findings have important implications for the current model of Tir-mediated actin polymerization and opens new lines of research in this area. PMID:25482634

  15. Urine Protein and Urine Protein to Creatinine Ratio

    MedlinePlus

    ... limited. Home Visit Global Sites Search Help? Urine Protein and Urine Protein to Creatinine Ratio Share this page: Was this page helpful? Also known as: 24-Hour Urine Protein; Urine Total Protein; Urine Protein to Creatinine Ratio; ...

  16. Designing Fluorinated Proteins.

    PubMed

    Marsh, E N G

    2016-01-01

    As methods to incorporate noncanonical amino acid residues into proteins have become more powerful, interest in their use to modify the physical and biological properties of proteins and enzymes has increased. This chapter discusses the use of highly fluorinated analogs of hydrophobic amino acids, for example, hexafluoroleucine, in protein design. In particular, fluorinated residues have proven to be generally effective in increasing the thermodynamic stability of proteins. The chapter provides an overview of the different fluorinated amino acids that have been used in protein design and the various methods available for producing fluorinated proteins. It discusses model proteins systems into which highly fluorinated amino acids have been introduced and the reasons why fluorinated residues are generally stabilizing, with particular reference to thermodynamic and structural studies from our laboratory. Lastly, details of the methodology we have developed to measure the thermodynamic stability of oligomeric fluorinated proteins are presented, as this may be generally applicable to many proteins. PMID:27586337

  17. DNA mimicry by proteins.

    PubMed

    Dryden, D T F; Tock, M R

    2006-04-01

    It has been discovered recently, via structural and biophysical analyses, that proteins can mimic DNA structures in order to inhibit proteins that would normally bind to DNA. Mimicry of the phosphate backbone of DNA, the hydrogen-bonding properties of the nucleotide bases and the bending and twisting of the DNA double helix are all present in the mimics discovered to date. These mimics target a range of proteins and enzymes such as DNA restriction enzymes, DNA repair enzymes, DNA gyrase and nucleosomal and nucleoid-associated proteins. The unusual properties of these protein DNA mimics may provide a foundation for the design of targeted inhibitors of DNA-binding proteins. PMID:16545103

  18. Physics of protein motility and motor proteins

    NASA Astrophysics Data System (ADS)

    Kolomeisky, Anatoly B.

    2013-09-01

    Motor proteins are enzymatic molecules that transform chemical energy into mechanical motion and work. They are critically important for supporting various cellular activities and functions. In the last 15 years significant progress in understanding the functioning of motor proteins has been achieved due to revolutionary breakthroughs in single-molecule experimental techniques and strong advances in theoretical modelling. However, microscopic mechanisms of protein motility are still not well explained, and the collective efforts of many scientists are needed in order to solve these complex problems. In this special section the reader will find the latest advances on the difficult road to mapping motor proteins dynamics in various systems. Recent experimental developments have allowed researchers to monitor and to influence the activity of single motor proteins with a high spatial and temporal resolution. It has stimulated significant theoretical efforts to understand the non-equilibrium nature of protein motility phenomena. The latest results from all these advances are presented and discussed in this special section. We would like to thank the scientists from all over the world who have reported their latest research results for this special section. We are also grateful to the staff and editors of Journal of Physics: Condensed Matter for their invaluable help in handling all the administrative and refereeing activities. The field of motor proteins and protein motility is fast moving, and we hope that this collection of articles will be a useful source of information in this highly interdisciplinary area. Physics of protein motility and motor proteins contents Physics of protein motility and motor proteinsAnatoly B Kolomeisky Identification of unique interactions between the flexible linker and the RecA-like domains of DEAD-box helicase Mss116 Yuan Zhang, Mirkó Palla, Andrew Sun and Jung-Chi Liao The load dependence of the physical properties of a molecular motor

  19. Protein and protein hydrolysates in sports nutrition.

    PubMed

    van Loon, Luc J C; Kies, Arie K; Saris, Wim H M

    2007-08-01

    With the increasing knowledge about the role of nutrition in increasing exercise performance, it has become clear over the last 2 decades that amino acids, protein, and protein hydrolysates can play an important role. Most of the attention has been focused on their effects at a muscular level. As these nutrients are ingested, however, it also means that gastrointestinal digestibility and absorption can modulate their efficacy significantly. Therefore, discussing the role of amino acids, protein, and protein hydrolysates in sports nutrition entails holding a discussion on all levels of the metabolic route. On May 28-29, 2007, a small group of researchers active in the field of exercise science and protein metabolism presented an overview of the different aspects of the application of protein and protein hydrolysates in sports nutrition. In addition, they were asked to share their opinions on the future progress in their fields of research. In this overview, an introduction to the workshop and a short summary of its outcome is provided.

  20. Engineering fluorescent proteins.

    PubMed

    Miyawaki, Atsushi; Nagai, Takeharu; Mizuno, Hideaki

    2005-01-01

    Green fluorescent protein from the jellyfish Aequorea victora (GFP) and GFP-like proteins from Anthozoa species encode light-absorbing chromophores intrinsically within their respective protein sequences. Recent studies have made progress in obtaining bright variants of these proteins which develop chromophores quickly and efficiently, as well as novel fluorescent proteins that photoactivate or photoconvert, i.e., become fluorescent or change colors upon illumination at specific wavelengths. Also, monomeric versions of these proteins have been engineered for fusion protein applications. Simple GFP variants and circularly permuted GFP variants have been used to develop fluorescent probes that sense physiological signals such as membrane potential and concentrations of free calcium. Further molecular characterization of the structure and maturation of these proteins is in progress, aimed at providing information for rational design of variants with desired fluorescence properties.

  1. Learning about Proteins

    MedlinePlus

    ... body, and protecting you from disease. All About Amino Acids When you eat foods that contain protein, the ... called amino (say: uh-MEE-no) acids. The amino acids then can be reused to make the proteins ...

  2. Protein S blood test

    MedlinePlus

    ... a normal substance in your body that prevents blood clotting. A blood test can be done to see ... family history of blood clots. Protein S helps control blood clotting. A lack of this protein or problem with ...

  3. Protein C blood test

    MedlinePlus

    ... a normal substance in the body that prevents blood clotting. A blood test can be done to see ... history of blood clots. Protein C helps control blood clotting. A lack of this protein or problem with ...

  4. [Protein-losing enteropathy].

    PubMed

    Amiot, A

    2015-07-01

    Protein-losing enteropathy is a rare syndrome of gastrointestinal protein loss. The primary causes can be classified into lymphatic leakage due to increased interstitial pressure and increased leakage of protein-rich fluids due to erosive or non-erosive gastrointestinal disorders. The diagnosis of protein-losing enteropathy should be considered in patients with chronic diarrhea and peripheral oedema. The diagnosis of protein-losing enteropathy is most commonly based on the determination of fecal alpha-1 antitrypsin clearance. Most protein-losing enteropathy cases are the result of either lymphatic obstruction or a variety of gastrointestinal disorders and cardiac diseases, while primary intestinal lymphangiectasia (Waldmann's disease) is less common. Treatment of protein-losing enteropathy targets the underlying disease but also includes dietary modification, such as high-protein and low-fat diet along with medium-chain triglyceride supplementation. PMID:25618488

  5. Protein and older adults.

    PubMed

    Chernoff, Ronni

    2004-12-01

    Body composition changes as people get older. One of the noteworthy alterations is the reduction in total body protein. A decrease in skeletal muscle is the most noticeable manifestation of this change but there is also a reduction in other physiologic proteins such as organ tissue, blood components, and immune bodies as well as declines in total body potassium and water. This contributes to impaired wound healing, loss of skin elasticity, and an inability to fight infection. The recommended dietary allowance (RDA) for adults for protein is 0.8 grams of protein per kilogram of body weight. Protein tissue accounts for 30% of whole-body protein turnover but that rate declines to 20% or less by age 70. The result of this phenomenon is that older adults require more protein/kilogram body weight than do younger adults. Recently, it has become clear that the requirement for exogenous protein is at least 1.0 gram/kilogram body weight. Adequate dietary intake of protein may be more difficult for older adults to obtain. Dietary animal protein is the primary source of high biological value protein, iron, vitamin B(12), folic acid, biotin and other essential nutrients. In fact, egg protein is the standard against which all other proteins are compared. Compared to other high-quality protein sources like meat, poultry and seafood, eggs are the least expensive. The importance of dietary protein cannot be underestimated in the diets of older adults; inadequate protein intake contributes to a decrease in reserve capacity, increased skin fragility, decreased immune function, poorer healing, and longer recuperation from illness.

  6. Texturized dairy proteins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dairy proteins are amenable to structural modifications induced by high temperature, shear and moisture; in particular, whey proteins can change conformation to new unfolded states. The change in protein state is a basis for creating new foods. The dairy products, nonfat dried milk (NDM), whey prote...

  7. Modeling Protein Self Assembly

    ERIC Educational Resources Information Center

    Baker, William P.; Jones, Carleton Buck; Hull, Elizabeth

    2004-01-01

    Understanding the structure and function of proteins is an important part of the standards-based science curriculum. Proteins serve vital roles within the cell and malfunctions in protein self assembly are implicated in degenerative diseases. Experience indicates that this topic is a difficult one for many students. We have found that the concept…

  8. Destabilized bioluminescent proteins

    DOEpatents

    Allen, Michael S.; Rakesh, Gupta; Gary, Sayler S.

    2007-07-31

    Purified nucleic acids, vectors and cells containing a gene cassette encoding at least one modified bioluminescent protein, wherein the modification includes the addition of a peptide sequence. The duration of bioluminescence emitted by the modified bioluminescent protein is shorter than the duration of bioluminescence emitted by an unmodified form of the bioluminescent protein.

  9. Modeling Protein Domain Function

    ERIC Educational Resources Information Center

    Baker, William P.; Jones, Carleton "Buck"; Hull, Elizabeth

    2007-01-01

    This simple but effective laboratory exercise helps students understand the concept of protein domain function. They use foam beads, Styrofoam craft balls, and pipe cleaners to explore how domains within protein active sites interact to form a functional protein. The activity allows students to gain content mastery and an understanding of the…

  10. CSF total protein

    MedlinePlus

    CSF total protein is a test to determine the amount of protein in your spinal fluid, also called cerebrospinal fluid (CSF). ... The normal protein range varies from lab to lab, but is typically about 15 to 60 mg/dL. Note: mg/dL = ...

  11. Protopia: a protein-protein interaction tool

    PubMed Central

    Real-Chicharro, Alejandro; Ruiz-Mostazo, Iván; Navas-Delgado, Ismael; Kerzazi, Amine; Chniber, Othmane; Sánchez-Jiménez, Francisca; Medina, Miguel Ángel; Aldana-Montes, José F

    2009-01-01

    Background Protein-protein interactions can be considered the basic skeleton for living organism self-organization and homeostasis. Impressive quantities of experimental data are being obtained and computational tools are essential to integrate and to organize this information. This paper presents Protopia, a biological tool that offers a way of searching for proteins and their interactions in different Protein Interaction Web Databases, as a part of a multidisciplinary initiative of our institution for the integration of biological data . Results The tool accesses the different Databases (at present, the free version of Transfac, DIP, Hprd, Int-Act and iHop), and results are expressed with biological protein names or databases codes and can be depicted as a vector or a matrix. They can be represented and handled interactively as an organic graph. Comparison among databases is carried out using the Uniprot codes annotated for each protein. Conclusion The tool locates and integrates the current information stored in the aforementioned databases, and redundancies among them are detected. Results are compatible with the most important network analysers, so that they can be compared and analysed by other world-wide known tools and platforms. The visualization possibilities help to attain this goal and they are especially interesting for handling multiple-step or complex networks. PMID:19828077

  12. Viral complement regulatory proteins.

    PubMed

    Rosengard, A M; Ahearn, J M

    1999-05-01

    The inactivation of complement provides cells and tissues critical protection from complement-mediated attack and decreases the associated recruitment of other inflammatory mediators. In an attempt to evade the host immune response, viruses have evolved two mechanisms to acquire complement regulatory proteins. They can directly seize the host cell complement regulators onto their outer envelope and/or they can produce their own proteins which are either secreted into the neighboring intercellular space or expressed as membrane-bound proteins on the infected host cell. The following review will concentrate on the viral homologues of the mammalian complement regulatory proteins, specifically those containing complement control protein (CCP) repeats. PMID:10408371

  13. Highly thermostable fluorescent proteins

    DOEpatents

    Bradbury, Andrew M.; Waldo, Geoffrey S.; Kiss, Csaba

    2011-03-22

    Thermostable fluorescent proteins (TSFPs), methods for generating these and other stability-enhanced proteins, polynucleotides encoding such proteins, and assays and method for using the TSFPs and TSFP-encoding nucleic acid molecules are provided. The TSFPs of the invention show extremely enhanced levels of stability and thermotolerance. In one case, for example, a TSFP of the invention is so stable it can be heated to 99.degree. C. for short periods of time without denaturing, and retains 85% of its fluorescence when heated to 80.degree. C. for several minutes. The invention also provides a method for generating stability-enhanced variants of a protein, including but not limited to fluorescent proteins.

  14. Highly thermostable fluorescent proteins

    DOEpatents

    Bradbury, Andrew M.; Waldo, Geoffrey S.; Kiss, Csaba

    2012-05-01

    Thermostable fluorescent proteins (TSFPs), methods for generating these and other stability-enhanced proteins, polynucleotides encoding such proteins, and assays and method for using the TSFPs and TSFP-encoding nucleic acid molecules are provided. The TSFPs of the invention show extremely enhanced levels of stability and thermotolerance. In one case, for example, a TSFP of the invention is so stable it can be heated to 99.degree. C. for short periods of time without denaturing, and retains 85% of its fluorescence when heated to 80.degree. C. for several minutes. The invention also provides a method for generating stability-enhanced variants of a protein, including but not limited to fluorescent proteins.

  15. Highly thermostable fluorescent proteins

    DOEpatents

    Bradbury, Andrew M.; Waldo, Geoffrey S.; Kiss, Csaba

    2011-11-29

    Thermostable fluorescent proteins (TSFPs), methods for generating these and other stability-enhanced proteins, polynucleotides encoding such proteins, and assays and method for using the TSFPs and TSFP-encoding nucleic acid molecules are provided. The TSFPs of the invention show extremely enhanced levels of stability and thermotolerance. In one case, for example, a TSFP of the invention is so stable it can be heated to 99.degree. C. for short periods of time without denaturing, and retains 85% of its fluorescence when heated to 80.degree. C. for several minutes. The invention also provides a method for generating stability-enhanced variants of a protein, including but not limited to fluorescent proteins.

  16. Selective Precipitation of Proteins.

    PubMed

    Matulis, Daumantas

    2016-01-01

    Selective precipitation of proteins can be used as a bulk method to recover the majority of proteins from a crude lysate, as a selective method to fractionate a subset of proteins from a protein solution, or as a very specific method to recover a single protein of interest from a purification step. This unit describes a number of methods suitable for selective precipitation. In each of the protocols that are outlined, the physical or chemical basis of the precipitation process, the parameters that can be varied for optimization, and the basic steps for developing an optimized precipitation are described.

  17. Protein crystallization with paper

    NASA Astrophysics Data System (ADS)

    Matsuoka, Miki; Kakinouchi, Keisuke; Adachi, Hiroaki; Maruyama, Mihoko; Sugiyama, Shigeru; Sano, Satoshi; Yoshikawa, Hiroshi Y.; Takahashi, Yoshinori; Yoshimura, Masashi; Matsumura, Hiroyoshi; Murakami, Satoshi; Inoue, Tsuyoshi; Mori, Yusuke; Takano, Kazufumi

    2016-05-01

    We developed a new protein crystallization method that incorporates paper. A small piece of paper, such as facial tissue or KimWipes, was added to a drop of protein solution in the traditional sitting drop vapor diffusion technique, and protein crystals grew by incorporating paper. By this method, we achieved the growth of protein crystals with reducing osmotic shock. Because the technique is very simple and the materials are easy to obtain, this method will come into wide use for protein crystallization. In the future, it could be applied to nanoliter-scale crystallization screening on a paper sheet such as in inkjet printing.

  18. Forces stabilizing proteins.

    PubMed

    Nick Pace, C; Scholtz, J Martin; Grimsley, Gerald R

    2014-06-27

    The goal of this article is to summarize what has been learned about the major forces stabilizing proteins since the late 1980s when site-directed mutagenesis became possible. The following conclusions are derived from experimental studies of hydrophobic and hydrogen bonding variants. (1) Based on studies of 138 hydrophobic interaction variants in 11 proteins, burying a -CH2- group on folding contributes 1.1±0.5 kcal/mol to protein stability. (2) The burial of non-polar side chains contributes to protein stability in two ways: first, a term that depends on the removal of the side chains from water and, more importantly, the enhanced London dispersion forces that result from the tight packing in the protein interior. (3) Based on studies of 151 hydrogen bonding variants in 15 proteins, forming a hydrogen bond on folding contributes 1.1±0.8 kcal/mol to protein stability. (4) The contribution of hydrogen bonds to protein stability is strongly context dependent. (5) Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. (6) Polar group burial can make a favorable contribution to protein stability even if the polar group is not hydrogen bonded. (7) Hydrophobic interactions and hydrogen bonds both make large contributions to protein stability.

  19. Clinical protein mass spectrometry.

    PubMed

    Scherl, Alexander

    2015-06-15

    Quantitative protein analysis is routinely performed in clinical chemistry laboratories for diagnosis, therapeutic monitoring, and prognosis. Today, protein assays are mostly performed either with non-specific detection methods or immunoassays. Mass spectrometry (MS) is a very specific analytical method potentially very well suited for clinical laboratories. Its unique advantage relies in the high specificity of the detection. Any protein sequence variant, the presence of a post-translational modification or degradation will differ in mass and structure, and these differences will appear in the mass spectrum of the protein. On the other hand, protein MS is a relatively young technique, demanding specialized personnel and expensive instrumentation. Many scientists and opinion leaders predict MS to replace immunoassays for routine protein analysis, but there are only few protein MS applications routinely used in clinical chemistry laboratories today. The present review consists of a didactical introduction summarizing the pros and cons of MS assays compared to immunoassays, the different instrumentations, and various MS protein assays that have been proposed and/or are used in clinical laboratories. An important distinction is made between full length protein analysis (top-down method) and peptide analysis after enzymatic digestion of the proteins (bottom-up method) and its implication for the protein assay. The document ends with an outlook on what type of analyses could be used in the future, and for what type of applications MS has a clear advantage compared to immunoassays.

  20. Forces Stabilizing Proteins

    PubMed Central

    Pace, C. Nick; Scholtz, J. Martin; Grimsley, Gerald R.

    2014-01-01

    The goal of this article is to summarize what has been learned about the major forces stabilizing proteins since the late 1980s when site-directed mutagenesis became possible. The following conclusions are derived from experimental studies of hydrophobic and hydrogen bonding variants. 1. Based on studies of 138 hydrophobic interaction variants in 11 proteins, burying a –CH2– group on folding contributes 1.1 ± 0.5 kcal/mol to protein stability. 2. The burial of nonpolar side chains contributes to protein stability in two ways: first, a term that depends on the removal of the side chains from water and, more importantly, the enhanced London dispersion forces that result from the tight packing in the protein interior. 3. Based on studies of 151 hydrogen bonding variants in 15 proteins, forming a hydrogen bond on folding contributes 1.1 ± 0.8 kcal/mol to protein stability. 4. The contribution of hydrogen bonds to protein stability is strongly context dependent. 5. Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. 6. Polar group burial can make a favorable contribution to protein stability even if the polar group is not hydrogen bonded. 7. Hydrophobic interactions and hydrogen bonds both make large contributions to protein stability. PMID:24846139

  1. Protein Complexes in Bacteria

    PubMed Central

    Caufield, J. Harry; Abreu, Marco; Wimble, Christopher; Uetz, Peter

    2015-01-01

    Large-scale analyses of protein complexes have recently become available for Escherichia coli and Mycoplasma pneumoniae, yielding 443 and 116 heteromultimeric soluble protein complexes, respectively. We have coupled the results of these mass spectrometry-characterized protein complexes with the 285 “gold standard” protein complexes identified by EcoCyc. A comparison with databases of gene orthology, conservation, and essentiality identified proteins conserved or lost in complexes of other species. For instance, of 285 “gold standard” protein complexes in E. coli, less than 10% are fully conserved among a set of 7 distantly-related bacterial “model” species. Complex conservation follows one of three models: well-conserved complexes, complexes with a conserved core, and complexes with partial conservation but no conserved core. Expanding the comparison to 894 distinct bacterial genomes illustrates fractional conservation and the limits of co-conservation among components of protein complexes: just 14 out of 285 model protein complexes are perfectly conserved across 95% of the genomes used, yet we predict more than 180 may be partially conserved across at least half of the genomes. No clear relationship between gene essentiality and protein complex conservation is observed, as even poorly conserved complexes contain a significant number of essential proteins. Finally, we identify 183 complexes containing well-conserved components and uncharacterized proteins which will be interesting targets for future experimental studies. PMID:25723151

  2. Protein solubility modeling

    NASA Technical Reports Server (NTRS)

    Agena, S. M.; Pusey, M. L.; Bogle, I. D.

    1999-01-01

    A thermodynamic framework (UNIQUAC model with temperature dependent parameters) is applied to model the salt-induced protein crystallization equilibrium, i.e., protein solubility. The framework introduces a term for the solubility product describing protein transfer between the liquid and solid phase and a term for the solution behavior describing deviation from ideal solution. Protein solubility is modeled as a function of salt concentration and temperature for a four-component system consisting of a protein, pseudo solvent (water and buffer), cation, and anion (salt). Two different systems, lysozyme with sodium chloride and concanavalin A with ammonium sulfate, are investigated. Comparison of the modeled and experimental protein solubility data results in an average root mean square deviation of 5.8%, demonstrating that the model closely follows the experimental behavior. Model calculations and model parameters are reviewed to examine the model and protein crystallization process. Copyright 1999 John Wiley & Sons, Inc.

  3. Protein and vegetarian diets.

    PubMed

    Marsh, Kate A; Munn, Elizabeth A; Baines, Surinder K

    2013-08-19

    A vegetarian diet can easily meet human dietary protein requirements as long as energy needs are met and a variety of foods are eaten. Vegetarians should obtain protein from a variety of plant sources, including legumes, soy products, grains, nuts and seeds. Eggs and dairy products also provide protein for those following a lacto-ovo-vegetarian diet. There is no need to consciously combine different plant proteins at each meal as long as a variety of foods are eaten from day to day, because the human body maintains a pool of amino acids which can be used to complement dietary protein. The consumption of plant proteins rather than animal proteins by vegetarians may contribute to their reduced risk of chronic diseases such as diabetes and heart disease.

  4. Racemic protein crystallography.

    PubMed

    Yeates, Todd O; Kent, Stephen B H

    2012-01-01

    Although natural proteins are chiral and are all of one "handedness," their mirror image forms can be prepared by chemical synthesis. This opens up new opportunities for protein crystallography. A racemic mixture of the enantiomeric forms of a protein molecule can crystallize in ways that natural proteins cannot. Recent experimental data support a theoretical prediction that this should make racemic protein mixtures highly amenable to crystallization. Crystals obtained from racemic mixtures also offer advantages in structure determination strategies. The relevance of these potential advantages is heightened by advances in synthetic methods, which are extending the size limit for proteins that can be prepared by chemical synthesis. Recent ideas and results in the area of racemic protein crystallography are reviewed.

  5. Pigment-protein complexes

    SciTech Connect

    Siegelman, H W

    1980-01-01

    The photosynthetically-active pigment protein complexes of procaryotes and eucaryotes include chlorophyll proteins, carotenochlorophyll proteins, and biliproteins. They are either integral components or attached to photosynthetic membranes. Detergents are frequently required to solubilize the pigment-protein complexes. The membrane localization and detergent solubilization strongly suggest that the pigment-protein complexes are bound to the membranes by hydrophobic interactions. Hydrophobic interactions of proteins are characterized by an increase in entropy. Their bonding energy is directly related to temperature and ionic strength. Hydrophobic-interaction chromatography, a relatively new separation procedure, can furnish an important method for the purification of pigment-protein complexes. Phycobilisome purification and properties provide an example of the need to maintain hydrophobic interactions to preserve structure and function.

  6. Insights on the Cuprate High Energy Anomaly Observed in ARPES

    SciTech Connect

    Moritz, Brian

    2011-08-16

    Recently, angle-resolved photoemission spectroscopy has been used to highlight an anomalously large band renormalization at high binding energies in cuprate superconductors: the high energy 'waterfall' or high energy anomaly (HEA). The anomaly is present for both hole- and electron-doped cuprates as well as the half-filled parent insulators with different energy scales arising on either side of the phase diagram. While photoemission matrix elements clearly play a role in changing the aesthetic appearance of the band dispersion, i.e. creating a 'waterfall'-like appearance, they provide an inadequate description for the physics that underlies the strong band renormalization giving rise to the HEA. Model calculations of the single-band Hubbard Hamiltonian showcase the role played by correlations in the formation of the HEA and uncover significant differences in the HEA energy scale for hole- and electron-doped cuprates. In addition, this approach properly captures the transfer of spectral weight accompanying doping in a correlated material and provides a unifying description of the HEA across both sides of the cuprate phase diagram. We find that the anomaly demarcates a transition, or cross-over, from a quasiparticle band at low binding energies near the Fermi level to valence bands at higher binding energy, assumed to be of strong oxygen character.

  7. Laser-ARPES studies of BSCCO-BASED cuprate superconductors

    NASA Astrophysics Data System (ADS)

    Douglas, J. F.; Koralek, J. D.; Sun, Z.; Plumb, N. C.; Wang, Q.; Reber, T. J.; Griffith, J. D.; Aiura, Y.; Oka, K.; Eisaki, H.; Dessau, D. S.; Devereaux, T. P.; Johnson, S. S.

    2007-03-01

    Utilizing 6 eV and 7 eV laser light, we have performed high-resolution ANGLE RESOLVED PHOTOEMISSION studies of the BSCCO family of superconductors. This higher resolution, in both energy and momentum, has allowed the observation of interesting new doping- and temperature-dependent features in the nodal and near nodal dispersions in these materials.

  8. ARPS Enabled Titan Rover Concept with Inflatable Wheels

    NASA Technical Reports Server (NTRS)

    Balint, Tibor S.; Schriener, Timothy M.; Shirley, James H.

    2006-01-01

    The Decadal Survey identified Titan as one of the top priority science destinations in the large moons category, while NASA's proposed Design Reference Mission Set ranked a Titan in-situ explorer second, after a recommended Europa Geophysical Observer mission. This paper discusses a Titan rover concept, enabled by a single advanced Radioisotope Power System that could provide about 110We (BOL). The concept targets the smaller Flagship or potentially the New Frontiers mission class. This MSL class rover would traverse on four 1.5 m diameter inflatable wheels during its 3 years mission duration and would use as much design and flight heritage as possible to reduce mission cost. Direct to Earth communication would remove the need for a relay orbiter. Details on the strawman instrument payload, and rover subsystems are given for this science driven mission concept. In addition, power system trades between Advanced RTG, TPV, and Advanced Stirling and Brayton Radioisotope Power Systems (RPS) are outlined. While many possible approaches exist for Titan in-situ exploration, the Titan rover concept presented here could provide a scientifically interesting and programmatically affordable solution.

  9. Protein kinesis: The dynamics of protein trafficking and stability

    SciTech Connect

    1995-12-31

    The purpose of this conference is to provide a multidisciplinary forum for exchange of state-of-the-art information on protein kinesis. This volume contains abstracts of papers in the following areas: protein folding and modification in the endoplasmic reticulum; protein trafficking; protein translocation and folding; protein degradation; polarity; nuclear trafficking; membrane dynamics; and protein import into organelles.

  10. Toxic proteins in plants.

    PubMed

    Dang, Liuyi; Van Damme, Els J M

    2015-09-01

    Plants have evolved to synthesize a variety of noxious compounds to cope with unfavorable circumstances, among which a large group of toxic proteins that play a critical role in plant defense against predators and microbes. Up to now, a wide range of harmful proteins have been discovered in different plants, including lectins, ribosome-inactivating proteins, protease inhibitors, ureases, arcelins, antimicrobial peptides and pore-forming toxins. To fulfill their role in plant defense, these proteins exhibit various degrees of toxicity towards animals, insects, bacteria or fungi. Numerous studies have been carried out to investigate the toxic effects and mode of action of these plant proteins in order to explore their possible applications. Indeed, because of their biological activities, toxic plant proteins are also considered as potentially useful tools in crop protection and in biomedical applications, such as cancer treatment. Genes encoding toxic plant proteins have been introduced into crop genomes using genetic engineering technology in order to increase the plant's resistance against pathogens and diseases. Despite the availability of ample information on toxic plant proteins, very few publications have attempted to summarize the research progress made during the last decades. This review focuses on the diversity of toxic plant proteins in view of their toxicity as well as their mode of action. Furthermore, an outlook towards the biological role(s) of these proteins and their potential applications is discussed.

  11. Ect2/Pbl Acts via Rho and Polarity Proteins to Direct the Assembly of an Isotropic Actomyosin Cortex upon Mitotic Entry

    PubMed Central

    Rosa, André; Vlassaks, Evi; Pichaud, Franck; Baum, Buzz

    2015-01-01

    Summary Entry into mitosis is accompanied by profound changes in cortical actomyosin organization. Here, we delineate a pathway downstream of the RhoGEF Pbl/Ect2 that directs this process in a model epithelium. Our data suggest that the release of Pbl/Ect2 from the nucleus at mitotic entry drives Rho-dependent activation of Myosin-II and, in parallel, induces a switch from Arp2/3 to Diaphanous-mediated cortical actin nucleation that depends on Cdc42, aPKC, and Par6. At the same time, the mitotic relocalization of these apical protein complexes to more lateral cell surfaces enables Cdc42/aPKC/Par6 to take on a mitosis-specific function—aiding the assembly of a relatively isotropic metaphase cortex. Together, these data reveal how the repolarization and remodeling of the actomyosin cortex are coordinated upon entry into mitosis to provide cells with the isotropic and rigid form they need to undergo faithful chromosome segregation and division in a crowded tissue environment. PMID:25703349

  12. Modeling Protein Expression and Protein Signaling Pathways

    PubMed Central

    Telesca, Donatello; Müller, Peter; Kornblau, Steven M.; Suchard, Marc A.; Ji, Yuan

    2015-01-01

    High-throughput functional proteomic technologies provide a way to quantify the expression of proteins of interest. Statistical inference centers on identifying the activation state of proteins and their patterns of molecular interaction formalized as dependence structure. Inference on dependence structure is particularly important when proteins are selected because they are part of a common molecular pathway. In that case, inference on dependence structure reveals properties of the underlying pathway. We propose a probability model that represents molecular interactions at the level of hidden binary latent variables that can be interpreted as indicators for active versus inactive states of the proteins. The proposed approach exploits available expert knowledge about the target pathway to define an informative prior on the hidden conditional dependence structure. An important feature of this prior is that it provides an instrument to explicitly anchor the model space to a set of interactions of interest, favoring a local search approach to model determination. We apply our model to reverse-phase protein array data from a study on acute myeloid leukemia. Our inference identifies relevant subpathways in relation to the unfolding of the biological process under study. PMID:26246646

  13. Energy design for protein-protein interactions

    PubMed Central

    Ravikant, D. V. S.; Elber, Ron

    2011-01-01

    Proteins bind to other proteins efficiently and specifically to carry on many cell functions such as signaling, activation, transport, enzymatic reactions, and more. To determine the geometry and strength of binding of a protein pair, an energy function is required. An algorithm to design an optimal energy function, based on empirical data of protein complexes, is proposed and applied. Emphasis is made on negative design in which incorrect geometries are presented to the algorithm that learns to avoid them. For the docking problem the search for plausible geometries can be performed exhaustively. The possible geometries of the complex are generated on a grid with the help of a fast Fourier transform algorithm. A novel formulation of negative design makes it possible to investigate iteratively hundreds of millions of negative examples while monotonically improving the quality of the potential. Experimental structures for 640 protein complexes are used to generate positive and negative examples for learning parameters. The algorithm designed in this work finds the correct binding structure as the lowest energy minimum in 318 cases of the 640 examples. Further benchmarks on independent sets confirm the significant capacity of the scoring function to recognize correct modes of interactions. PMID:21842951

  14. Principles of Flexible Protein-Protein Docking

    PubMed Central

    Andrusier, Nelly; Mashiach, Efrat; Nussinov, Ruth; Wolfson, Haim J.

    2008-01-01

    Treating flexibility in molecular docking is a major challenge in cell biology research. Here we describe the background and the principles of existing flexible protein-protein docking methods, focusing on the algorithms and their rational. We describe how protein flexibility is treated in different stages of the docking process: in the preprocessing stage, rigid and flexible parts are identified and their possible conformations are modeled. This preprocessing provides information for the subsequent docking and refinement stages. In the docking stage, an ensemble of pre-generated conformations or the identified rigid domains may be docked separately. In the refinement stage, small-scale movements of the backbone and side-chains are modeled and the binding orientation is improved by rigid-body adjustments. For clarity of presentation, we divide the different methods into categories. This should allow the reader to focus on the most suitable method for a particular docking problem. PMID:18655061

  15. Antimicrobial proteins: From old proteins, new tricks.

    PubMed

    Smith, Valerie J; Dyrynda, Elisabeth A

    2015-12-01

    This review describes the main types of antimicrobial peptides (AMPs) synthesised by crustaceans, primarily those identified in shrimp, crayfish, crab and lobster. It includes an overview of their range of microbicidal activities and the current landscape of our understanding of their gene expression patterns in different body tissues. It further summarises how their expression might change following various types of immune challenges. The review further considers proteins or protein fragments from crustaceans that have antimicrobial properties but are more usually associated with other biological functions, or are derived from such proteins. It discusses how these unconventional AMPs might be generated at, or delivered to, sites of infection and how they might contribute to crustacean host defence in vivo. It also highlights recent work that is starting to reveal the extent of multi-functionality displayed by some decapod AMPs, particularly their participation in other aspects of host protection. Examples of such activities include proteinase inhibition, phagocytosis, antiviral activity and haematopoiesis. PMID:26320628

  16. Electrophoretic separation of proteins.

    PubMed

    Chakavarti, Bulbul; Chakavarti, Deb

    2008-01-01

    Electrophoresis is used to separate complex mixtures of proteins (e.g., from cells, subcellular fractions, column fractions, or immunoprecipitates), to investigate subunit compositions, and to verify homogeneity of protein samples. It can also serve to purify proteins for use in further applications. In polyacrylamide gel electrophoresis, proteins migrate in response to an electrical field through pores in a polyacrylamide gel matrix; pore size decreases with increasing acrylamide concentration. The combination of pore size and protein charge, size, and shape determines the migration rate of the protein. In this unit, the standard Laemmli method is described for discontinuous gel electrophoresis under denaturing conditions, i.e., in the presence of sodium dodecyl sulfate (SDS). PMID:19066548

  17. Functional Protein Microarray Technology

    PubMed Central

    Hu, Shaohui; Xie, Zhi; Qian, Jiang; Blackshaw, Seth; Zhu, Heng

    2010-01-01

    Functional protein microarrays are emerging as a promising new tool for large-scale and high-throughput studies. In this article, we will review their applications in basic proteomics research, where various types of assays have been developed to probe binding activities to other biomolecules, such as proteins, DNA, RNA, small molecules, and glycans. We will also report recent progress of using functional protein microarrays in profiling protein posttranslational modifications, including phosphorylation, ubiquitylation, acetylation, and nitrosylation. Finally, we will discuss potential of functional protein microarrays in biomarker identification and clinical diagnostics. We strongly believe that functional protein microarrays will soon become an indispensible and invaluable tool in proteomics research and systems biology. PMID:20872749

  18. Biofilm Matrix Proteins

    PubMed Central

    Fong, Jiunn N. C.; Yildiz, Fitnat H.

    2015-01-01

    Proteinaceous components of the biofilm matrix include secreted extracellular proteins, cell surface adhesins and protein subunits of cell appendages such as flagella and pili. Biofilm matrix proteins play diverse roles in biofilm formation and dissolution. They are involved in attaching cells to surfaces, stabilizing the biofilm matrix via interactions with exopolysaccharide and nucleic acid components, developing three-dimensional biofilm architectures, and dissolving biofilm matrix via enzymatic degradation of polysaccharides, proteins, and nucleic acids. In this chapter, we will review functions of matrix proteins in a selected set of microorganisms, studies of the matrix proteomes of Vibrio cholerae and Pseudomonas aeruginosa, and roles of outer membrane vesicles and of nucleoid-binding proteins in biofilm formation. PMID:26104709

  19. Protein Crystal Quality Studies

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Eddie Snell, Post-Doctoral Fellow the National Research Council (NRC) uses a reciprocal space mapping diffractometer for macromolecular crystal quality studies. The diffractometer is used in mapping the structure of macromolecules such as proteins to determine their structure and thus understand how they function with other proteins in the body. This is one of several analytical tools used on proteins crystallized on Earth and in space experiments. Photo credit: NASA/Marshall Space Flight Center (MSFC)

  20. Computer Models of Proteins

    NASA Technical Reports Server (NTRS)

    2000-01-01

    Dr. Marc Pusey (seated) and Dr. Craig Kundrot use computers to analyze x-ray maps and generate three-dimensional models of protein structures. With this information, scientists at Marshall Space Flight Center can learn how proteins are made and how they work. The computer screen depicts a proten structure as a ball-and-stick model. Other models depict the actual volume occupied by the atoms, or the ribbon-like structures that are crucial to a protein's function.

  1. Protein oxidation and peroxidation.

    PubMed

    Davies, Michael J

    2016-04-01

    Proteins are major targets for radicals and two-electron oxidants in biological systems due to their abundance and high rate constants for reaction. With highly reactive radicals damage occurs at multiple side-chain and backbone sites. Less reactive species show greater selectivity with regard to the residues targeted and their spatial location. Modification can result in increased side-chain hydrophilicity, side-chain and backbone fragmentation, aggregation via covalent cross-linking or hydrophobic interactions, protein unfolding and altered conformation, altered interactions with biological partners and modified turnover. In the presence of O2, high yields of peroxyl radicals and peroxides (protein peroxidation) are formed; the latter account for up to 70% of the initial oxidant flux. Protein peroxides can oxidize both proteins and other targets. One-electron reduction results in additional radicals and chain reactions with alcohols and carbonyls as major products; the latter are commonly used markers of protein damage. Direct oxidation of cysteine (and less commonly) methionine residues is a major reaction; this is typically faster than with H2O2, and results in altered protein activity and function. Unlike H2O2, which is rapidly removed by protective enzymes, protein peroxides are only slowly removed, and catabolism is a major fate. Although turnover of modified proteins by proteasomal and lysosomal enzymes, and other proteases (e.g. mitochondrial Lon), can be efficient, protein hydroperoxides inhibit these pathways and this may contribute to the accumulation of modified proteins in cells. Available evidence supports an association between protein oxidation and multiple human pathologies, but whether this link is causal remains to be established.

  2. Protein oxidation and peroxidation

    PubMed Central

    Davies, Michael J.

    2016-01-01

    Proteins are major targets for radicals and two-electron oxidants in biological systems due to their abundance and high rate constants for reaction. With highly reactive radicals damage occurs at multiple side-chain and backbone sites. Less reactive species show greater selectivity with regard to the residues targeted and their spatial location. Modification can result in increased side-chain hydrophilicity, side-chain and backbone fragmentation, aggregation via covalent cross-linking or hydrophobic interactions, protein unfolding and altered conformation, altered interactions with biological partners and modified turnover. In the presence of O2, high yields of peroxyl radicals and peroxides (protein peroxidation) are formed; the latter account for up to 70% of the initial oxidant flux. Protein peroxides can oxidize both proteins and other targets. One-electron reduction results in additional radicals and chain reactions with alcohols and carbonyls as major products; the latter are commonly used markers of protein damage. Direct oxidation of cysteine (and less commonly) methionine residues is a major reaction; this is typically faster than with H2O2, and results in altered protein activity and function. Unlike H2O2, which is rapidly removed by protective enzymes, protein peroxides are only slowly removed, and catabolism is a major fate. Although turnover of modified proteins by proteasomal and lysosomal enzymes, and other proteases (e.g. mitochondrial Lon), can be efficient, protein hydroperoxides inhibit these pathways and this may contribute to the accumulation of modified proteins in cells. Available evidence supports an association between protein oxidation and multiple human pathologies, but whether this link is causal remains to be established. PMID:27026395

  3. Pressure cryocooling protein crystals

    DOEpatents

    Kim, Chae Un; Gruner, Sol M.

    2011-10-04

    Preparation of cryocooled protein crystal is provided by use of helium pressurizing and cryocooling to obtain cryocooled protein crystal allowing collection of high resolution data and by heavier noble gas (krypton or xenon) binding followed by helium pressurizing and cryocooling to obtain cryocooled protein crystal for collection of high resolution data and SAD phasing simultaneously. The helium pressurizing is carried out on crystal coated to prevent dehydration or on crystal grown in aqueous solution in a capillary.

  4. Protein-Losing Gastroenteropathy

    PubMed Central

    Pops, Martin A.

    1966-01-01

    In the past 10 years with the development of improved methods, particularly radioisotope techniques, it has been demonstrated that a number of patients with gastrointestinal disease and depletion of plasma proteins become hypoproteinemic because of actual leakage of albumin and other plasma proteins into the lumen of the gastrointestinal tract. The site of protein leakage is variable depending on the underlying pathological state but the loss of protein-containing lymph through the gastrointestinal lymphatic channels seems to be the major mechanism for hypoproteinemia. It has become apparent that there exists a normal mechanism for secretion of plasma proteins into the gastrointestinal tract as part of the overall metabolism of the plasma proteins. When the process is exaggerated so that resynthesis of plasma protein cannot keep pace with its degradation, sometimes severe hypoproteinemia is the result. Such a pathological process has now been described in approximately 40 disease states. A review of all the techniques which can demonstrate gastroenteric protein loss reveals that there are no widely available quantitative tests but that accurate quantitation is not necessary for the diagnosis of protein losing gastroenteropathy. PMID:18730025

  5. Human Mitochondrial Protein Database

    National Institute of Standards and Technology Data Gateway

    SRD 131 Human Mitochondrial Protein Database (Web, free access)   The Human Mitochondrial Protein Database (HMPDb) provides comprehensive data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases. This database is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases.

  6. Acanthamoeba castellanii STAT protein.

    PubMed

    Kicinska, Anna; Leluk, Jacek; Jarmuszkiewicz, Wieslawa

    2014-01-01

    STAT (signal transducers and activators of transcription) proteins are one of the important mediators of phosphotyrosine-regulated signaling in metazoan cells. We described the presence of STAT protein in a unicellular, free-living amoebae with a simple life cycle, Acanthamoeba castellanii. A. castellanii is the only, studied to date, Amoebozoan that does not belong to Mycetozoa but possesses STATs. A sequence of the A. castellanii STAT protein includes domains similar to those of the Dictyostelium STAT proteins: a coiled coil (characteristic for Dictyostelium STAT coiled coil), a STAT DNA-binding domain and a Src-homology domain. The search for protein sequences homologous to A. castellanii STAT revealed 17 additional sequences from lower eukaryotes. Interestingly, all of these sequences come from Amoebozoa organisms that belong to either Mycetozoa (slime molds) or Centramoebida. We showed that there are four separated clades within the slime mold STAT proteins. The A. castellanii STAT protein branches next to a group of STATc proteins from Mycetozoa. We also demonstrate that Amoebozoa form a distinct monophyletic lineage within the STAT protein world that is well separated from the other groups. PMID:25338074

  7. The Halophile protein database.

    PubMed

    Sharma, Naveen; Farooqi, Mohammad Samir; Chaturvedi, Krishna Kumar; Lal, Shashi Bhushan; Grover, Monendra; Rai, Anil; Pandey, Pankaj

    2014-01-01

    Halophilic archaea/bacteria adapt to different salt concentration, namely extreme, moderate and low. These type of adaptations may occur as a result of modification of protein structure and other changes in different cell organelles. Thus proteins may play an important role in the adaptation of halophilic archaea/bacteria to saline conditions. The Halophile protein database (HProtDB) is a systematic attempt to document the biochemical and biophysical properties of proteins from halophilic archaea/bacteria which may be involved in adaptation of these organisms to saline conditions. In this database, various physicochemical properties such as molecular weight, theoretical pI, amino acid composition, atomic composition, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (Gravy) have been listed. These physicochemical properties play an important role in identifying the protein structure, bonding pattern and function of the specific proteins. This database is comprehensive, manually curated, non-redundant catalogue of proteins. The database currently contains 59 897 proteins properties extracted from 21 different strains of halophilic archaea/bacteria. The database can be accessed through link. Database URL: http://webapp.cabgrid.res.in/protein/

  8. Moonlighting proteins in cancer.

    PubMed

    Min, Kyung-Won; Lee, Seong-Ho; Baek, Seung Joon

    2016-01-01

    Since the 1980s, growing evidence suggested that the cellular localization of proteins determined their activity and biological functions. In a classical view, a protein is characterized by the single cellular compartment where it primarily resides and functions. It is now believed that when proteins appear in different subcellular locations, the cells surpass the expected activity of proteins given the same genomic information to fulfill complex biological behavior. Many proteins are recognized for having the potential to exist in multiple locations in cells. Dysregulation of translocation may cause cancer or contribute to poorer cancer prognosis. Thus, quantitative and comprehensive assessment of dynamic proteins and associated protein movements could be a promising indicator in determining cancer prognosis and efficiency of cancer treatment and therapy. This review will summarize these so-called moonlighting proteins, in terms of a coupled intracellular cancer signaling pathway. Determination of the detailed biological intracellular and extracellular transit and regulatory activity of moonlighting proteins permits a better understanding of cancer and identification of potential means of molecular intervention.

  9. Biomolecular membrane protein crystallization

    NASA Astrophysics Data System (ADS)

    Reddy Bolla, Jani; Su, Chih-Chia; Yu, Edward W.

    2012-07-01

    Integral membrane proteins comprise approximately 30% of the sequenced genomes, and there is an immediate need for their high-resolution structural information. Currently, the most reliable approach to obtain these structures is X-ray crystallography. However, obtaining crystals of membrane proteins that diffract to high resolution appears to be quite challenging, and remains a major obstacle in structural determination. This brief review summarizes a variety of methodologies for use in crystallizing these membrane proteins. Hopefully, by introducing the available methods, techniques, and providing a general understanding of membrane proteins, a rational decision can be made about now to crystallize these complex materials.

  10. Glycolipid transfer proteins

    PubMed Central

    Brown, Rhoderick E.; Mattjus, Peter

    2007-01-01

    Glycolipid transfer proteins (GLTPs) are small (24 kD), soluble, ubiquitous proteins characterized by their ability to accelerate the intermembrane transfer of glycolipids in vitro. GLTP specificity encompasses both sphingoid- and glycerol-based glycolipids, but with a strict requirement that the initial sugar residue be beta-linked to the hydrophobic lipid backbone. The 3D protein structures of GLTP reveal liganded structures with unique lipid binding modes. The biochemical properties of GLTP action at the membrane surface have been studied rather comprehensively, but the biological role of GLTP remains enigmatic. What is clear is that GLTP differs distinctly from other known glycolipid-binding proteins, such as nonspecific lipid transfer proteins, lysosomal sphingolipid activator proteins, lectins, lung surfactant proteins as well as other lipid binding/transfer proteins. Based on the unique conformational architecture that targets GLTP to membranes and enables glycolipid binding, GLTP is now considered the prototypical and founding member of a new protein superfamily in eukaryotes. PMID:17320476

  11. Consensus protein design

    PubMed Central

    Porebski, Benjamin T.; Buckle, Ashley M.

    2016-01-01

    A popular and successful strategy in semi-rational design of protein stability is the use of evolutionary information encapsulated in homologous protein sequences. Consensus design is based on the hypothesis that at a given position, the respective consensus amino acid contributes more than average to the stability of the protein than non-conserved amino acids. Here, we review the consensus design approach, its theoretical underpinnings, successes, limitations and challenges, as well as providing a detailed guide to its application in protein engineering. PMID:27274091

  12. Chemical Synthesis of Proteins

    PubMed Central

    Nilsson, Bradley L.; Soellner, Matthew B.; Raines, Ronald T.

    2010-01-01

    Proteins have become accessible targets for chemical synthesis. The basic strategy is to use native chemical ligation, Staudinger ligation, or other orthogonal chemical reactions to couple synthetic peptides. The ligation reactions are compatible with a variety of solvents and proceed in solution or on a solid support. Chemical synthesis enables a level of control on protein composition that greatly exceeds that attainable with ribosome-mediated biosynthesis. Accordingly, the chemical synthesis of proteins is providing previously unattainable insight into the structure and function of proteins. PMID:15869385

  13. Self assembling proteins

    DOEpatents

    Yeates, Todd O.; Padilla, Jennifer; Colovos, Chris

    2004-06-29

    Novel fusion proteins capable of self-assembling into regular structures, as well as nucleic acids encoding the same, are provided. The subject fusion proteins comprise at least two oligomerization domains rigidly linked together, e.g. through an alpha helical linking group. Also provided are regular structures comprising a plurality of self-assembled fusion proteins of the subject invention, and methods for producing the same. The subject fusion proteins find use in the preparation of a variety of nanostructures, where such structures include: cages, shells, double-layer rings, two-dimensional layers, three-dimensional crystals, filaments, and tubes.

  14. Comparative genome analysis of cortactin and HS1: the significance of the F-actin binding repeat domain

    PubMed Central

    van Rossum, Agnes GSH; Schuuring-Scholtes, Ellen; Seggelen, Vera van Buuren-van; Kluin, Philip M; Schuuring, Ed

    2005-01-01

    Background In human carcinomas, overexpression of cortactin correlates with poor prognosis. Cortactin is an F-actin-binding protein involved in cytoskeletal rearrangements and cell migration by promoting actin-related protein (Arp)2/3 mediated actin polymerization. It shares a high amino acid sequence and structural similarity to hematopoietic lineage cell-specific protein 1 (HS1) although their functions differ considerable. In this manuscript we describe the genomic organization of these two genes in a variety of species by a combination of cloning and database searches. Based on our analysis, we predict the genesis of the actin-binding repeat domain during evolution. Results Cortactin homologues exist in sponges, worms, shrimps, insects, urochordates, fishes, amphibians, birds and mammalians, whereas HS1 exists in vertebrates only, suggesting that both genes have been derived from an ancestor cortactin gene by duplication. In agreement with this, comparative genome analysis revealed very similar exon-intron structures and sequence homologies, especially over the regions that encode the characteristic highly conserved F-actin-binding repeat domain. Cortactin splice variants affecting this F-actin-binding domain were identified not only in mammalians, but also in amphibians, fishes and birds. In mammalians, cortactin is ubiquitously expressed except in hematopoietic cells, whereas HS1 is mainly expressed in hematopoietic cells. In accordance with their distinct tissue specificity, the putative promoter region of cortactin is different from HS1. Conclusions Comparative analysis of the genomic organization and amino acid sequences of cortactin and HS1 provides inside into their origin and evolution. Our analysis shows that both genes originated from a gene duplication event and subsequently HS1 lost two repeats, whereas cortactin gained one repeat. Our analysis genetically underscores the significance of the F-actin binding domain in cytoskeletal remodeling, which

  15. Protein metabolism and requirements.

    PubMed

    Biolo, Gianni

    2013-01-01

    Skeletal muscle adaptation to critical illness includes insulin resistance, accelerated proteolysis, and increased release of glutamine and the other amino acids. Such amino acid efflux from skeletal muscle provides precursors for protein synthesis and energy fuel to the liver and to the rapidly dividing cells of the intestinal mucosa and the immune system. From these adaptation mechanisms, severe muscle wasting, glutamine depletion, and hyperglycemia, with increased patient morbidity and mortality, may ensue. Protein/amino acid nutrition, through either enteral or parenteral routes, plays a pivotal role in treatment of metabolic abnormalities in critical illness. In contrast to energy requirement, which can be accurately assessed by indirect calorimetry, methods to determine individual protein/amino acid needs are not currently available. In critical illness, a decreased ability of protein/amino acid intake to promote body protein synthesis is defined as anabolic resistance. This abnormality leads to increased protein/amino acid requirement and relative inefficiency of nutritional interventions. In addition to stress mediators, immobility and physical inactivity are key determinants of anabolic resistance. The development of mobility protocols in the intensive care unit should be encouraged to enhance the efficacy of nutrition. In critical illness, protein/amino acid requirement has been defined as the intake level associated with the lowest rate of catabolism. The optimal protein-sparing effects in patients receiving adequate energy are achieved when protein/amino acids are administered at rates between 1.3 and 1.5 g/kg/day. Extra glutamine supplementation is required in conditions of severe systemic inflammatory response. Protein requirement increases during hypocaloric feeding and in patients with acute renal failure on continuous renal replacement therapy. Evidence suggests that receiving adequate protein/amino acid intake may be more important than achieving

  16. Human Plasma Protein C

    PubMed Central

    Kisiel, Walter

    1979-01-01

    Protein C is a vitamin K-dependent protein, which exists in bovine plasma as a precursor of a serine protease. In this study, protein C was isolated to homogeneity from human plasma by barium citrate adsorption and elution, ammonium sulfate fractionation, DEAE-Sephadex chromatography, dextran sulfate agarose chromatography, and preparative polyacrylamide gel electrophoresis. Human protein C (Mr = 62,000) contains 23% carbohydrate and is composed of a light chain (Mr = 21,000) and a heavy chain (Mr = 41,000) held together by a disulfide bond(s). The light chain has an amino-terminal sequence of Ala-Asn-Ser-Phe-Leu- and the heavy chain has an aminoterminal sequence of Asp-Pro-Glu-Asp-Gln. The residues that are identical to bovine protein C are underlined. Incubation of human protein C with human α-thrombin at an enzyme to substrate weight ratio of 1:50 resulted in the formation of activated protein C, an enzyme with serine amidase activity. In the activation reaction, the apparent molecular weight of the heavy chain decreased from 41,000 to 40,000 as determined by gel electrophoresis in the presence of sodium dodecyl sulfate. No apparent change in the molecular weight of the light chain was observed in the activation process. The heavy chain of human activated protein C also contains the active-site serine residue as evidenced by its ability to react with radiolabeled diisopropyl fluorophosphate. Human activated protein C markedly prolongs the kaolin-cephalin clotting time of human plasma, but not that of bovine plasma. The amidolytic and anticoagulant activities of human activated protein C were completely obviated by prior incubation of the enzyme with diisopropyl fluorophosphate. These results indicate that human protein C, like its bovine counterpart, exists in plasma as a zymogen and is converted to a serine protease by limited proteolysis with attendant anticoagulant activity. Images PMID:468991

  17. Interolog interfaces in protein-protein docking.

    PubMed

    Alsop, James D; Mitchell, Julie C

    2015-11-01

    Proteins are essential elements of biological systems, and their function typically relies on their ability to successfully bind to specific partners. Recently, an emphasis of study into protein interactions has been on hot spots, or residues in the binding interface that make a significant contribution to the binding energetics. In this study, we investigate how conservation of hot spots can be used to guide docking prediction. We show that the use of evolutionary data combined with hot spot prediction highlights near-native structures across a range of benchmark examples. Our approach explores various strategies for using hot spots and evolutionary data to score protein complexes, using both absolute and chemical definitions of conservation along with refinements to these strategies that look at windowed conservation and filtering to ensure a minimum number of hot spots in each binding partner. Finally, structure-based models of orthologs were generated for comparison with sequence-based scoring. Using two data sets of 22 and 85 examples, a high rate of top 10 and top 1 predictions are observed, with up to 82% of examples returning a top 10 hit and 35% returning top 1 hit depending on the data set and strategy applied; upon inclusion of the native structure among the decoys, up to 55% of examples yielded a top 1 hit. The 20 common examples between data sets show that more carefully curated interolog data yields better predictions, particularly in achieving top 1 hits. Proteins 2015; 83:1940-1946. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

  18. The folate binding proteins.

    PubMed

    Corrocher, R; Olivieri, O; Pacor, M L

    1991-01-01

    Folates are essential molecules for cell life and, not surprisingly, their transport in biological fluids and their transfer to cells are finely regulated. Folate binding proteins play a major role in this regulation. This paper will review our knowledge on these proteins and examine the most recent advances in this field. PMID:1820987

  19. Poxviral Ankyrin Proteins

    PubMed Central

    Herbert, Michael H.; Squire, Christopher J.; Mercer, Andrew A

    2015-01-01

    Multiple repeats of the ankyrin motif (ANK) are ubiquitous throughout the kingdoms of life but are absent from most viruses. The main exception to this is the poxvirus family, and specifically the chordopoxviruses, with ANK repeat proteins present in all but three species from separate genera. The poxviral ANK repeat proteins belong to distinct orthologue groups spread over different species, and align well with the phylogeny of their genera. This distribution throughout the chordopoxviruses indicates these proteins were present in an ancestral vertebrate poxvirus, and have since undergone numerous duplication events. Most poxviral ANK repeat proteins contain an unusual topology of multiple ANK motifs starting at the N-terminus with a C-terminal poxviral homologue of the cellular F-box enabling interaction with the cellular SCF ubiquitin ligase complex. The subtle variations between ANK repeat proteins of individual poxviruses suggest an array of different substrates may be bound by these protein-protein interaction domains and, via the F-box, potentially directed to cellular ubiquitination pathways and possible degradation. Known interaction partners of several of these proteins indicate that the NF-κB coordinated anti-viral response is a key target, whilst some poxviral ANK repeat domains also have an F-box independent affect on viral host-range. PMID:25690795

  20. Protein Unfolding and Alzheimer's

    NASA Astrophysics Data System (ADS)

    Cheng, Kelvin

    2012-10-01

    Early interaction events of beta-amyloid (Aβ) proteins with neurons have been associated with the pathogenesis of Alzheimer's disease. Knowledge pertaining to the role of lipid molecules, particularly cholesterol, in modulating the single Aβ interactions with neurons at the atomic length and picosecond time resolutions, remains unclear. In our research, we have used atomistic molecular dynamics simulations to explore early molecular events including protein insertion kinetics, protein unfolding, and protein-induced membrane disruption of Aβ in lipid domains that mimic the nanoscopic raft and non-raft regions of the neural membrane. In this talk, I will summarize our current work on investigating the role of cholesterol in regulating the Aβ interaction events with membranes at the molecular level. I will also explain how our results will provide new insights into understanding the pathogenesis of Alzheimer's disease associated with the Aβ proteins.

  1. Structures of membrane proteins

    PubMed Central

    Vinothkumar, Kutti R.; Henderson, Richard

    2010-01-01

    In reviewing the structures of membrane proteins determined up to the end of 2009, we present in words and pictures the most informative examples from each family. We group the structures together according to their function and architecture to provide an overview of the major principles and variations on the most common themes. The first structures, determined 20 years ago, were those of naturally abundant proteins with limited conformational variability, and each membrane protein structure determined was a major landmark. With the advent of complete genome sequences and efficient expression systems, there has been an explosion in the rate of membrane protein structure determination, with many classes represented. New structures are published every month and more than 150 unique membrane protein structures have been determined. This review analyses the reasons for this success, discusses the challenges that still lie ahead, and presents a concise summary of the key achievements with illustrated examples selected from each class. PMID:20667175

  2. Protein disulfide engineering.

    PubMed

    Dombkowski, Alan A; Sultana, Kazi Zakia; Craig, Douglas B

    2014-01-21

    Improving the stability of proteins is an important goal in many biomedical and industrial applications. A logical approach is to emulate stabilizing molecular interactions found in nature. Disulfide bonds are covalent interactions that provide substantial stability to many proteins and conform to well-defined geometric conformations, thus making them appealing candidates in protein engineering efforts. Disulfide engineering is the directed design of novel disulfide bonds into target proteins. This important biotechnological tool has achieved considerable success in a wide range of applications, yet the rules that govern the stabilizing effects of disulfide bonds are not fully characterized. Contrary to expectations, many designed disulfide bonds have resulted in decreased stability of the modified protein. We review progress in disulfide engineering, with an emphasis on the issue of stability and computational methods that facilitate engineering efforts.

  3. Proteins, fluctuations and complexity

    SciTech Connect

    Frauenfelder, Hans; Chen, Guo; Fenimore, Paul W

    2008-01-01

    Glasses, supercooled liquids, and proteins share common properties, in particular the existence of two different types of fluctuations, {alpha} and {beta}. While the effect of the {alpha} fluctuations on proteins has been known for a few years, the effect of {beta} fluctuations has not been understood. By comparing neutron scattering data on the protein myoglobin with the {beta} fluctuations in the hydration shell measured by dielectric spectroscopy we show that the internal protein motions are slaved to these fluctuations. We also show that there is no 'dynamic transition' in proteins near 200 K. The rapid increase in the mean square displacement with temperature in many neutron scattering experiments is quantitatively predicted by the {beta} fluctuations in the hydration shell.

  4. Junin virus structural proteins.

    PubMed Central

    De Martínez Segovia, Z M; De Mitri, M I

    1977-01-01

    Polyacrylamide gel electrophoresis of purified Junin virus revealed six distinct structural polypeptides, two major and four minor ones. Four of these polypeptides appeared to be covalently linked with carbohydrate. The molecular weights of the six proteins, estimated by coelectrophoresis with marker proteins, ranged from 25,000 to 91,000. One of the two major components (number 3) was identified as a nucleoprotein and had a molecular weight of 64,000. It was the most prominent protein and was nonglycosylated. The other major protein (number 5), with a molecular weight of 38,000, was a glucoprotein and a component of the viral envelope. The location on the virion of three additional glycopeptides with molecular weights of 91,000, 72,000, and 52,000, together with a protein with a molecular weight of 25,000, was not well defined. PMID:189088

  5. Drugging Membrane Protein Interactions

    PubMed Central

    Yin, Hang; Flynn, Aaron D.

    2016-01-01

    The majority of therapeutics target membrane proteins, accessible on the surface of cells, to alter cellular signaling. Cells use membrane proteins to transduce signals into cells, transport ions and molecules, bind the cell to a surface or substrate, and catalyze reactions. Newly devised technologies allow us to drug conventionally “undruggable” regions of membrane proteins, enabling modulation of protein–protein, protein–lipid, and protein–nucleic acid interactions. In this review, we survey the state of the art in high-throughput screening and rational design in drug discovery, and we evaluate the advances in biological understanding and technological capacity that will drive pharmacotherapy forward against unorthodox membrane protein targets. PMID:26863923

  6. Proteins in unexpected locations.

    PubMed Central

    Smalheiser, N R

    1996-01-01

    Members of all classes of proteins--cytoskeletal components, secreted growth factors, glycolytic enzymes, kinases, transcription factors, chaperones, transmembrane proteins, and extracellular matrix proteins--have been identified in cellular compartments other than their conventional sites of action. Some of these proteins are expressed as distinct compartment-specific isoforms, have novel mechanisms for intercompartmental translocation, have distinct endogenous biological actions within each compartment, and are regulated in a compartment-specific manner as a function of physiologic state. The possibility that many, if not most, proteins have distinct roles in more than one cellular compartment has implications for the evolution of cell organization and may be important for understanding pathological conditions such as Alzheimer's disease and cancer. PMID:8862516

  7. Protein crystallization in microgravity.

    PubMed

    Aibara, S; Shibata, K; Morita, Y

    1997-12-01

    A space experiment involving protein crystallization was conducted in a microgravity environment using the space shuttle "Endeavour" of STS-47, on a 9-day mission from September 12th to 20th in 1992. The crystallization was carried out according to a batch method, and 5 proteins were selected as flight samples for crystallization. Two of these proteins: hen egg-white lysozyme and co-amino acid: pyruvate aminotransferase from Pseudomonas sp. F-126, were obtained as single crystals of good diffraction quality. Since 1992 we have carried out several space experiments for protein crystallization aboard space shuttles and the space station MIR. Our experimental results obtained mainly from hen egg-white lysozyme are described below, focusing on the effects of microgravity on protein crystal growth.

  8. Manipulating and Visualizing Proteins

    SciTech Connect

    Simon, Horst D.

    2003-12-05

    ProteinShop Gives Researchers a Hands-On Tool for Manipulating, Visualizing Protein Structures. The Human Genome Project and other biological research efforts are creating an avalanche of new data about the chemical makeup and genetic codes of living organisms. But in order to make sense of this raw data, researchers need software tools which let them explore and model data in a more intuitive fashion. With this in mind, researchers at Lawrence Berkeley National Laboratory and the University of California, Davis, have developed ProteinShop, a visualization and modeling program which allows researchers to manipulate protein structures with pinpoint control, guided in large part by their own biological and experimental instincts. Biologists have spent the last half century trying to unravel the ''protein folding problem,'' which refers to the way chains of amino acids physically fold themselves into three-dimensional proteins. This final shape, which resembles a crumpled ribbon or piece of origami, is what determines how the protein functions and translates genetic information. Understanding and modeling this geometrically complex formation is no easy matter. ProteinShop takes a given sequence of amino acids and uses visualization guides to help generate predictions about the secondary structures, identifying alpha helices and flat beta strands, and the coil regions that bind them. Once secondary structures are in place, researchers can twist and turn these pre-configurations until they come up with a number of possible tertiary structure conformations. In turn, these are fed into a computationally intensive optimization procedure that tries to find the final, three-dimensional protein structure. Most importantly, ProteinShop allows users to add human knowledge and intuition to the protein structure prediction process, thus bypassing bad configurations that would otherwise be fruitless for optimization. This saves compute cycles and accelerates the entire process, so

  9. Regulation of protein turnover by heat shock proteins.

    PubMed

    Bozaykut, Perinur; Ozer, Nesrin Kartal; Karademir, Betul

    2014-12-01

    Protein turnover reflects the balance between synthesis and degradation of proteins, and it is a crucial process for the maintenance of the cellular protein pool. The folding of proteins, refolding of misfolded proteins, and also degradation of misfolded and damaged proteins are involved in the protein quality control (PQC) system. Correct protein folding and degradation are controlled by many different factors, one of the most important of which is the heat shock protein family. Heat shock proteins (HSPs) are in the class of molecular chaperones, which may prevent the inappropriate interaction of proteins and induce correct folding. On the other hand, these proteins play significant roles in the degradation pathways, including endoplasmic reticulum-associated degradation (ERAD), the ubiquitin-proteasome system, and autophagy. This review focuses on the emerging role of HSPs in the regulation