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Sample records for promoting dna ejection

  1. Polarized DNA Ejection from the Herpesvirus Capsid

    Newcomb, William W.; Cockrell, Shelley K.; Homa, Fred L.; Brown, Jay C.

    2009-01-01

    Ejection of DNA from the capsid is an early step in infection by all herpesviruses. Ejection or DNA uncoating occurs after a parental capsid has entered the host cell cytoplasm, migrated to the nucleus and bound to a nuclear pore. DNA exits the capsid through the portal vertex and proceeds by way of the nuclear pore complex into the nucleoplasm where it is transcribed and replicated. Here we describe use of an in vitro uncoating system to determine which genome end exits first from the herpes simplex virus (HSV-1) capsid. Purified DNA-containing capsids were bound to a solid surface and warmed under conditions in which some, but not all, of the DNA was ejected. Restriction endonuclease digestion was then used to identify the genomic origin of the ejected DNA. The results support the view that the S segment end exits the capsid first. Preferential release at the S end demonstrates that herpesvirus DNA uncoating conforms to the paradigm in dsDNA bacteriophage where the last end packaged is the first to be ejected. Release of HSV-1 DNA beginning at the S end causes the first gene to enter the host cell nucleus to be α4, a transcription factor required for expression of early genes. PMID:19631662

  2. A study on interaction of DNA molecules and carbon nanotubes for an effective ejection of the molecules

    Wu, N.; Wang, Q.

    2012-01-01

    The ejection of DNA molecules from carbon nanotubes is reported from interaction energy perspectives by molecular dynamics simulations. The critical ejection energy, which is to be applied to a DNA molecule for a successful ejection from a carbon nanotube, is investigated based on a study on the friction and binding energy between the DNA molecule and the tube. An effective ejection is realized by subjecting a kinetic energy on the DNA molecule that is larger than the solved critical ejection energy. In addition, the relationship between ejection energies and sizes of DNA molecules and carbon nanotubes is investigated. -- Highlights: ► Report the ejection of DNA molecules from CNTs from interaction energy perspectives. ► Develop a methodology for the critical energy of an effective ejection of a DNA molecule from a CNT. ► Present the relationship between critical ejection energies and sizes of DNA molecules and CNTs. ► Provide a general guidance on the ejection of encapsulated molecules from CNTs.

  3. The mechanism of DNA ejection in the Bacillus anthracis spore-binding phage 8a revealed by cryo-electron tomography

    Fu, Xiaofeng [Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030 (United States); Walter, Michael H. [Department of Biology, University of Northern Iowa, Cedar Falls, IA 50614 (United States); Paredes, Angel [Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030 (United States); Morais, Marc C., E-mail: mcmorais@utmb.edu [Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555 (United States); Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555 (United States); Liu, Jun, E-mail: Jun.Liu.1@uth.tmc.edu [Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030 (United States)

    2011-12-20

    The structure of the Bacillus anthracis spore-binding phage 8a was determined by cryo-electron tomography. The phage capsid forms a T = 16 icosahedron attached to a contractile tail via a head-tail connector protein. The tail consists of a six-start helical sheath surrounding a central tail tube, and a structurally novel baseplate at the distal end of the tail that recognizes and attaches to host cells. The parameters of the icosahedral capsid lattice and the helical tail sheath suggest protein folds for the capsid and tail-sheath proteins, respectively, and indicate evolutionary relationships to other dsDNA viruses. Analysis of 2518 intact phage particles show four distinct conformations that likely correspond to four sequential states of the DNA ejection process during infection. Comparison of the four observed conformations suggests a mechanism for DNA ejection, including the molecular basis underlying coordination of tail sheath contraction and genome release from the capsid.

  4. Compilation and analysis of Escherichia coli promoter DNA sequences.

    Hawley, D K; McClure, W R

    1983-01-01

    The DNA sequence of 168 promoter regions (-50 to +10) for Escherichia coli RNA polymerase were compiled. The complete listing was divided into two groups depending upon whether or not the promoter had been defined by genetic (promoter mutations) or biochemical (5' end determination) criteria. A consensus promoter sequence based on homologies among 112 well-defined promoters was determined that was in substantial agreement with previous compilations. In addition, we have tabulated 98 promoter ...

  5. Intrinsically bent DNA in replication origins and gene promoters.

    Gimenes, F; Takeda, K I; Fiorini, A; Gouveia, F S; Fernandez, M A

    2008-06-24

    Intrinsically bent DNA is an alternative conformation of the DNA molecule caused by the presence of dA/dT tracts, 2 to 6 bp long, in a helical turn phase DNA or with multiple intervals of 10 to 11 bp. Other than flexibility, intrinsic bending sites induce DNA curvature in particular chromosome regions such as replication origins and promoters. Intrinsically bent DNA sites are important in initiating DNA replication, and are sometimes found near to regions associated with the nuclear matrix. Many methods have been developed to localize bent sites, for example, circular permutation, computational analysis, and atomic force microscopy. This review discusses intrinsically bent DNA sites associated with replication origins and gene promoter regions in prokaryote and eukaryote cells. We also describe methods for identifying bent DNA sites for circular permutation and computational analysis.

  6. Gadd45a promotes DNA demethylation through TDG

    Li, Zheng; Gu, Tian-Peng; Weber, Alain R.; Shen, Jia-Zhen; Li, Bin-Zhong; Xie, Zhi-Guo; Yin, Ruichuan; Guo, Fan; Liu, Xiaomeng; Tang, Fuchou; Wang, Hailin; Sch?r, Primo; Xu, Guo-Liang

    2015-01-01

    Growth arrest and DNA-damage-inducible protein 45 (Gadd45) family members have been implicated in DNA demethylation in vertebrates. However, it remained unclear how they contribute to the demethylation process. Here, we demonstrate that Gadd45a promotes active DNA demethylation through thymine DNA glycosylase (TDG) which has recently been shown to excise 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) generated in Ten-eleven-translocation (Tet)?initiated oxidative demethylation. The conn...

  7. Unveiling DNA structural properties of promoter regions of ...

    Aditya Kumar

    Unveiling DNA structural properties of promoter regions of prokaryotic transcriptome and their role in gene expression. Aditya Kumar. Assistant Professor. Molecular Biology & Biotechnology. Tezpur University. Tezpur – 784028, Assam ...

  8. DNA structure in human RNA polymerase II promoters

    Pedersen, Anders Gorm; Baldi, Pierre; Chauvin, Yves

    1998-01-01

    with a very low level of sequence similarity. The sequences, which include both TATA-containing and TATA-less promoters, are aligned by hidden Markov models. Using three different models of sequence-derived DNA bendability, the aligned promoters display a common structural profile with bendability being low...... protein in a manner reminiscent of DNA in a nucleosome. This notion is further supported by the finding that the periodic bendability is caused mainly by the complementary triplet pairs CAG/CTG and GGC/GCC, which previously have been found to correlate with nucleosome positioning. We present models where......The fact that DNA three-dimensional structure is important for transcriptional regulation begs the question of whether eukaryotic promoters contain general structural features independently of what genes they control. We present an analysis of a large set of human RNA polymerase II promoters...

  9. Equilibrious Strand Exchange Promoted by DNA Conformational Switching

    Wu, Zhiguo; Xie, Xiao; Li, Puzhen; Zhao, Jiayi; Huang, Lili; Zhou, Xiang

    2013-01-01

    Most of DNA strand exchange reactions in vitro are based on toehold strategy which is generally nonequilibrium, and intracellular strand exchange mediated by proteins shows little sequence specificity. Herein, a new strand exchange promoted by equilibrious DNA conformational switching is verified. Duplexes containing c-myc sequence which is potentially converted into G-quadruplex are designed in this strategy. The dynamic equilibrium between duplex and G4-DNA is response to the specific exchange of homologous single-stranded DNA (ssDNA). The SER is enzyme free and sequence specific. No ATP is needed and the displaced ssDNAs are identical to the homologous ssDNAs. The SER products and exchange kenetics are analyzed by PAGE and the RecA mediated SER is performed as the contrast. This SER is a new feature of G4-DNAs and a novel strategy to utilize the dynamic equilibrium of DNA conformations.

  10. The two faces of endogenous DNA editing enzymes: Promoting ...

    The two faces of endogenous DNA editing enzymes: Promoting gene mutations as well as genome repair. Type B lymphocytes are a specific type of white blood cell within our immune system. They produce and export antibodies which seek out, attach to, and neutralize microbes and toxins. A unique way that B ...

  11. Promoter DNA hypermethylation and gene repression in undifferentiated Arabidopsis cells.

    María Berdasco

    Full Text Available Maintaining and acquiring the pluripotent cell state in plants is critical to tissue regeneration and vegetative multiplication. Histone-based epigenetic mechanisms are important for regulating this undifferentiated state. Here we report the use of genetic and pharmacological experimental approaches to show that Arabidopsis cell suspensions and calluses specifically repress some genes as a result of promoter DNA hypermethylation. We found that promoters of the MAPK12, GSTU10 and BXL1 genes become hypermethylated in callus cells and that hypermethylation also affects the TTG1, GSTF5, SUVH8, fimbrin and CCD7 genes in cell suspensions. Promoter hypermethylation in undifferentiated cells was associated with histone hypoacetylation and primarily occurred at CpG sites. Accordingly, we found that the process specifically depends on MET1 and DRM2 methyltransferases, as demonstrated with DNA methyltransferase mutants. Our results suggest that promoter DNA methylation may be another important epigenetic mechanism for the establishment and/or maintenance of the undifferentiated state in plant cells.

  12. Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining

    Kukshal, Vandna; Kim, In-Kwon; Hura, Gregory L.; Tomkinson, Alan E.; Tainer, John A.; Ellenberger, Tom

    2015-01-01

    Mammalian DNA ligase III (LigIII) functions in both nuclear and mitochondrial DNA metabolism. In the nucleus, LigIII has functional redundancy with DNA ligase I whereas LigIII is the only mitochondrial DNA ligase and is essential for the survival of cells dependent upon oxidative respiration. The unique LigIII zinc finger (ZnF) domain is not required for catalytic activity but senses DNA strand breaks and stimulates intermolecular ligation of two DNAs by an unknown mechanism. Consistent with this activity, LigIII acts in an alternative pathway of DNA double strand break repair that buttresses canonical non-homologous end joining (NHEJ) and is manifest in NHEJ-defective cancer cells, but how LigIII acts in joining intermolecular DNA ends versus nick ligation is unclear. To investigate how LigIII efficiently joins two DNAs, we developed a real-time, fluorescence-based assay of DNA bridging suitable for high-throughput screening. On a nicked duplex DNA substrate, the results reveal binding competition between the ZnF and the oligonucleotide/oligosaccharide-binding domain, one of three domains constituting the LigIII catalytic core. In contrast, these domains collaborate and are essential for formation of a DNA-bridging intermediate by adenylated LigIII that positions a pair of blunt-ended duplex DNAs for efficient and specific intermolecular ligation. PMID:26130724

  13. Human Fanconi anemia monoubiquitination pathway promotes homologous DNA repair.

    Nakanishi, Koji; Yang, Yun-Gui; Pierce, Andrew J; Taniguchi, Toshiyasu; Digweed, Martin; D'Andrea, Alan D; Wang, Zhao-Qi; Jasin, Maria

    2005-01-25

    Fanconi anemia (FA) is a recessive disorder characterized by congenital abnormalities, progressive bone-marrow failure, and cancer susceptibility. Cells from FA patients are hypersensitive to agents that produce DNA crosslinks and, after treatment with these agents, have pronounced chromosome breakage and other cytogenetic abnormalities. Eight FANC genes have been cloned, and the encoded proteins interact in a common cellular pathway. DNA-damaging agents activate the monoubiquitination of FANCD2, resulting in its targeting to nuclear foci that also contain BRCA1 and BRCA2/FANCD1, proteins involved in homology-directed DNA repair. Given the interaction of the FANC proteins with BRCA1 and BRCA2, we tested whether cells from FA patients (groups A, G, and D2) and mouse Fanca-/- cells with a targeted mutation are impaired for this repair pathway. We find that both the upstream (FANCA and FANCG) and downstream (FANCD2) FA pathway components promote homology-directed repair of chromosomal double-strand breaks (DSBs). The FANCD2 monoubiquitination site is critical for normal levels of repair, whereas the ATM phosphorylation site is not. The defect in these cells, however, is mild, differentiating them from BRCA1 and BRCA2 mutant cells. Surprisingly, we provide evidence that these proteins, like BRCA1 but unlike BRCA2, promote a second DSB repair pathway involving homology, i.e., single-strand annealing. These results suggest an early role for the FANC proteins in homologous DSB repair pathway choice.

  14. SAMHD1 Promotes DNA End Resection to Facilitate DNA Repair by Homologous Recombination

    Waaqo Daddacha

    2017-08-01

    Full Text Available DNA double-strand break (DSB repair by homologous recombination (HR is initiated by CtIP/MRN-mediated DNA end resection to maintain genome integrity. SAMHD1 is a dNTP triphosphohydrolase, which restricts HIV-1 infection, and mutations are associated with Aicardi-Goutières syndrome and cancer. We show that SAMHD1 has a dNTPase-independent function in promoting DNA end resection to facilitate DSB repair by HR. SAMHD1 deficiency or Vpx-mediated degradation causes hypersensitivity to DSB-inducing agents, and SAMHD1 is recruited to DSBs. SAMHD1 complexes with CtIP via a conserved C-terminal domain and recruits CtIP to DSBs to facilitate end resection and HR. Significantly, a cancer-associated mutant with impaired CtIP interaction, but not dNTPase-inactive SAMHD1, fails to rescue the end resection impairment of SAMHD1 depletion. Our findings define a dNTPase-independent function for SAMHD1 in HR-mediated DSB repair by facilitating CtIP accrual to promote DNA end resection, providing insight into how SAMHD1 promotes genome integrity.

  15. Senataxin Mutation Reveals How R-Loops Promote Transcription by Blocking DNA Methylation at Gene Promoters.

    Grunseich, Christopher; Wang, Isabel X; Watts, Jason A; Burdick, Joshua T; Guber, Robert D; Zhu, Zhengwei; Bruzel, Alan; Lanman, Tyler; Chen, Kelian; Schindler, Alice B; Edwards, Nancy; Ray-Chaudhury, Abhik; Yao, Jianhua; Lehky, Tanya; Piszczek, Grzegorz; Crain, Barbara; Fischbeck, Kenneth H; Cheung, Vivian G

    2018-02-01

    R-loops are three-stranded nucleic acid structures found abundantly and yet often viewed as by-products of transcription. Studying cells from patients with a motor neuron disease (amyotrophic lateral sclerosis 4 [ALS4]) caused by a mutation in senataxin, we uncovered how R-loops promote transcription. In ALS4 patients, the senataxin mutation depletes R-loops with a consequent effect on gene expression. With fewer R-loops in ALS4 cells, the expression of BAMBI, a negative regulator of transforming growth factor β (TGF-β), is reduced; that then leads to the activation of the TGF-β pathway. We uncovered that genome-wide R-loops influence promoter methylation of over 1,200 human genes. DNA methyl-transferase 1 favors binding to double-stranded DNA over R-loops. Thus, in forming R-loops, nascent RNA blocks DNA methylation and promotes further transcription. Hence, our results show that nucleic acid structures, in addition to sequences, influence the binding and activity of regulatory proteins. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. The regulation of transactivator of transcription on the activity of DNA-PKcs promoter

    Yang Tianyi; Zhang Shimeng; Qin Xia; Li Bing; Liu Xiaodan; Zhou Pingkun

    2012-01-01

    Objective: To explore the influence of human immunodeficiency virus transactivator of transcription (TAT) on the promoter activity of DNA dependent protein kinase catalytic subunit (DNA-PKcs). Methods: The truncated promoters of DNA-PKcs were cloned by PCR from the template DNA from HeLa genomic DNA, and the pGL3-basic-DNA-PKcs promoter reporter plasmids were constructed. The activity of DNA-PKcs promoters was detected by dual-luciferase reporter assay system. A Lac-repressor and Lacoperator based green fluorescent protein imaging system was used to assay the chromatin remodeling activity. Results: A series of reporter plasmids harboring the truncated promoters of DNA-PKcs from -939 bp to -1 bp were constructed. The sequence of -64 bp to-1 bp was identified as a critical element for the activity of DNA-PKes promoter. TAT can suppress the activity of DNA-PKcs promoter. TAT participates in the regulation of the large scale chromatin relaxation. Ionizing radiation attenuates the activity of TAT played in the chromatin remodeling. Conclusion: TAT represses the promoter activity of DNA repair protein DNA-PKcs, and also play a role of large scale chromatin remodeling which can te attenuated by ionizing radiation. (authors)

  17. RADX interacts with single-stranded DNA to promote replication fork stability

    Schubert, Lisa; Ho, Teresa; Hoffmann, Saskia

    2017-01-01

    Single-stranded DNA (ssDNA) regions form as an intermediate in many DNA-associated transactions. Multiple cellular proteins interact with ssDNA via the oligonucleotide/oligosaccharide-binding (OB) fold domain. The heterotrimeric, multi-OB fold domain-containing Replication Protein A (RPA) complex...... ssDNA-binding activities is critical for avoiding these defects. Our findings establish RADX as an important component of cellular pathways that promote DNA replication integrity under basal and stressful conditions by means of multiple ssDNA-binding proteins....

  18. Ejection Tower Lab

    Federal Laboratory Consortium — The Ejection Tower Facility's mission is to test and evaluate new ejection seat technology being researched and developed for future defense forces. The captive and...

  19. DNA methylation of PTEN gene promoter region is not correlated ...

    Yomi

    2012-02-23

    Feb 23, 2012 ... of Shandong, Qingdao Agricultural University, Qingdao, 266109, China. 2Daping ... (Kang et al., 2002), glioblastoma (Baeza et al., 2003), breast cancer ... DNA isolation by using micro DNA isolation kit (Tiangen, Beijing,. China) .... Asano T, Yao Y, Zhu J, Li D, Abbruzzese JL, Reddy SA (2004). The PI.

  20. DnaA protein DNA-binding domain binds to Hda protein to promote inter-AAA+ domain interaction involved in regulatory inactivation of DnaA.

    Keyamura, Kenji; Katayama, Tsutomu

    2011-08-19

    Chromosomal replication is initiated from the replication origin oriC in Escherichia coli by the active ATP-bound form of DnaA protein. The regulatory inactivation of DnaA (RIDA) system, a complex of the ADP-bound Hda and the DNA-loaded replicase clamp, represses extra initiations by facilitating DnaA-bound ATP hydrolysis, yielding the inactive ADP-bound form of DnaA. However, the mechanisms involved in promoting the DnaA-Hda interaction have not been determined except for the involvement of an interaction between the AAA+ domains of the two. This study revealed that DnaA Leu-422 and Pro-423 residues within DnaA domain IV, including a typical DNA-binding HTH motif, are specifically required for RIDA-dependent ATP hydrolysis in vitro and that these residues support efficient interaction with the DNA-loaded clamp·Hda complex and with Hda in vitro. Consistently, substitutions of these residues caused accumulation of ATP-bound DnaA in vivo and oriC-dependent inhibition of cell growth. Leu-422 plays a more important role in these activities than Pro-423. By contrast, neither of these residues is crucial for DNA replication from oriC, although they are highly conserved in DnaA orthologues. Structural analysis of a DnaA·Hda complex model suggested that these residues make contact with residues in the vicinity of the Hda AAA+ sensor I that participates in formation of a nucleotide-interacting surface. Together, the results show that functional DnaA-Hda interactions require a second interaction site within DnaA domain IV in addition to the AAA+ domain and suggest that these interactions are crucial for the formation of RIDA complexes that are active for DnaA-ATP hydrolysis.

  1. DnaA Protein DNA-binding Domain Binds to Hda Protein to Promote Inter-AAA+ Domain Interaction Involved in Regulatory Inactivation of DnaA*

    Keyamura, Kenji; Katayama, Tsutomu

    2011-01-01

    Chromosomal replication is initiated from the replication origin oriC in Escherichia coli by the active ATP-bound form of DnaA protein. The regulatory inactivation of DnaA (RIDA) system, a complex of the ADP-bound Hda and the DNA-loaded replicase clamp, represses extra initiations by facilitating DnaA-bound ATP hydrolysis, yielding the inactive ADP-bound form of DnaA. However, the mechanisms involved in promoting the DnaA-Hda interaction have not been determined except for the involvement of an interaction between the AAA+ domains of the two. This study revealed that DnaA Leu-422 and Pro-423 residues within DnaA domain IV, including a typical DNA-binding HTH motif, are specifically required for RIDA-dependent ATP hydrolysis in vitro and that these residues support efficient interaction with the DNA-loaded clamp·Hda complex and with Hda in vitro. Consistently, substitutions of these residues caused accumulation of ATP-bound DnaA in vivo and oriC-dependent inhibition of cell growth. Leu-422 plays a more important role in these activities than Pro-423. By contrast, neither of these residues is crucial for DNA replication from oriC, although they are highly conserved in DnaA orthologues. Structural analysis of a DnaA·Hda complex model suggested that these residues make contact with residues in the vicinity of the Hda AAA+ sensor I that participates in formation of a nucleotide-interacting surface. Together, the results show that functional DnaA-Hda interactions require a second interaction site within DnaA domain IV in addition to the AAA+ domain and suggest that these interactions are crucial for the formation of RIDA complexes that are active for DnaA-ATP hydrolysis. PMID:21708944

  2. Luciferase assay to study the activity of a cloned promoter DNA fragment.

    Solberg, Nina; Krauss, Stefan

    2013-01-01

    Luciferase based assays have become an invaluable tool for the analysis of cloned promoter DNA fragments, both for verifying the ability of a potential promoter fragment to drive the expression of a luciferase reporter gene in various cellular contexts, and for dissecting binding elements in the promoter. Here, we describe the use of the Dual-Luciferase(®) Reporter Assay System created by Promega (Promega Corporation, Wisconsin, USA) to study the cloned 6.7 kilobases (kb) mouse (m) Tcf3 promoter DNA fragment in mouse embryonic derived neural stem cells (NSC). In this system, the expression of the firefly luciferase driven by the cloned mTcf3 promoter DNA fragment (including transcription initiation sites) is correlated with a co-transfected control reporter expressing Renilla luciferase from the herpes simplex virus (HSV) thymidine kinase promoter. Using an internal control reporter allows to normalize the activity of the experimental reporter to the internal control, which minimizes experimental variability.

  3. N-terminal domains of human DNA polymerase lambda promote primer realignment during translesion DNA synthesis

    Taggart, David J.; Dayeh, Daniel M.; Fredrickson, Saul W.; Suo, Zucai

    2014-01-01

    The X-family DNA polymerases λ (Polλ) and β (Polβ) possess similar 5′-2-deoxyribose-5-phosphatelyase (dRPase) and polymerase domains. Besides these domains, Polλ also possesses a BRCA1 C-terminal (BRCT) domain and a proline-rich domain at its N terminus. However, it is unclear how these non-enzymatic domains contribute to the unique biological functions of Polλ. Here, we used primer extension assays and a newly developed high-throughput short oligonucleotide sequencing assay (HT-SOSA) to compare the efficiency of lesion bypass and fidelity of human Polβ, Polλ and two N-terminal deletion constructs of Polλ during the bypass of either an abasic site or a 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodG) lesion. We demonstrate that the BRCT domain of Polλ enhances the efficiency of abasic site bypass by approximately 1.6-fold. In contrast, deletion of the N-terminal domains of Polλ did not affect the efficiency of 8-oxodG bypass relative to nucleotide incorporations opposite undamaged dG. HT-SOSA analysis demonstrated that Polλ and Polβ preferentially generated −1 or −2 frameshift mutations when bypassing an abasic site and the single or double base deletion frequency was highly sequence dependent. Interestingly, the BRCT and proline-rich domains of Polλ cooperatively promoted the generation of −2 frameshift mutations when the abasic site was situated within a sequence context that was susceptible to homology-driven primer realignment. Furthermore, both N-terminal domains of Polλ increased the generation of −1 frameshift mutations during 8-oxodG bypass and influenced the frequency of substitution mutations produced by Polλ opposite the 8-oxodG lesion. Overall, our data support a model wherein the BRCT and proline-rich domains of Polλ act cooperatively to promote primer/template realignment between DNA strands of limited sequence homology. This function of the N-terminal domains may facilitate the role of Polλ as a gap-filling polymerase

  4. Genistein promotes DNA demethylation of the steroidogenic factor 1 (SF-1) promoter in endometrial stromal cells

    Matsukura, Hiroshi; Aisaki, Ken-ichi; Igarashi, Katsuhide; Matsushima, Yuko; Kanno, Jun; Muramatsu, Masaaki; Sudo, Katsuko; Sato, Noriko

    2011-01-01

    Highlights: → Genistein (GEN) is a phytoestrogen found in soy products. → GEN demethylated/unsilenced the steroidogenic factor 1 gene in endometrial tissue. → GEN thus altered mRNA expression in uteri of ovariectomized (OVX) mice. → A high-resolution melting assay was used to screen for epigenetic change. → We isolated an endometrial cell clone that was epigenetically modulated by GEN. -- Abstract: It has recently been demonstrated that genistein (GEN), a phytoestrogen in soy products, is an epigenetic modulator in various types of cells; but its effect on endometrium has not yet been determined. We investigated the effects of GEN on mouse uterine cells, in vivo and in vitro. Oral administration of GEN for 1 week induced mild proliferation of the endometrium in ovariectomized (OVX) mice, which was accompanied by the induction of steroidogenic factor 1 (SF-1) gene expression. GEN administration induced demethylation of multiple CpG sites in the SF-1 promoter; these sites are extensively methylated and thus silenced in normal endometrium. The GEN-mediated promoter demethylation occurred predominantly on the luminal side, as opposed to myometrium side, indicating that the epigenetic change was mainly shown in regenerated cells. Primary cultures of endometrial stromal cell colonies were screened for GEN-mediated alterations of DNA methylation by a high-resolution melting (HRM) method. One out of 20 colony-forming cell clones showed GEN-induced demethylation of SF-1. This clone exhibited a high proliferation capacity with continuous colony formation activity through multiple serial clonings. We propose that only a portion of endometrial cells are capable of receiving epigenetic modulation by GEN.

  5. Genistein promotes DNA demethylation of the steroidogenic factor 1 (SF-1) promoter in endometrial stromal cells

    Matsukura, Hiroshi, E-mail: hmatsukura.epi@mri.tmd.ac.jp [Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 2-3-10 Kanda-surugadai, Chiyoda-ku, Tokyo 101-0062 (Japan); Aisaki, Ken-ichi; Igarashi, Katsuhide; Matsushima, Yuko; Kanno, Jun [Division of Cellular and Molecular Toxicology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501 (Japan); Muramatsu, Masaaki [Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 2-3-10 Kanda-surugadai, Chiyoda-ku, Tokyo 101-0062 (Japan); Sudo, Katsuko [Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 2-3-10 Kanda-surugadai, Chiyoda-ku, Tokyo 101-0062 (Japan); Animal Research Center, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402 (Japan); Sato, Noriko, E-mail: nsato.epi@tmd.ac.jp [Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 2-3-10 Kanda-surugadai, Chiyoda-ku, Tokyo 101-0062 (Japan)

    2011-08-26

    Highlights: {yields} Genistein (GEN) is a phytoestrogen found in soy products. {yields} GEN demethylated/unsilenced the steroidogenic factor 1 gene in endometrial tissue. {yields} GEN thus altered mRNA expression in uteri of ovariectomized (OVX) mice. {yields} A high-resolution melting assay was used to screen for epigenetic change. {yields} We isolated an endometrial cell clone that was epigenetically modulated by GEN. -- Abstract: It has recently been demonstrated that genistein (GEN), a phytoestrogen in soy products, is an epigenetic modulator in various types of cells; but its effect on endometrium has not yet been determined. We investigated the effects of GEN on mouse uterine cells, in vivo and in vitro. Oral administration of GEN for 1 week induced mild proliferation of the endometrium in ovariectomized (OVX) mice, which was accompanied by the induction of steroidogenic factor 1 (SF-1) gene expression. GEN administration induced demethylation of multiple CpG sites in the SF-1 promoter; these sites are extensively methylated and thus silenced in normal endometrium. The GEN-mediated promoter demethylation occurred predominantly on the luminal side, as opposed to myometrium side, indicating that the epigenetic change was mainly shown in regenerated cells. Primary cultures of endometrial stromal cell colonies were screened for GEN-mediated alterations of DNA methylation by a high-resolution melting (HRM) method. One out of 20 colony-forming cell clones showed GEN-induced demethylation of SF-1. This clone exhibited a high proliferation capacity with continuous colony formation activity through multiple serial clonings. We propose that only a portion of endometrial cells are capable of receiving epigenetic modulation by GEN.

  6. Histone modification alteration coordinated with acquisition of promoter DNA methylation during Epstein-Barr virus infection.

    Funata, Sayaka; Matsusaka, Keisuke; Yamanaka, Ryota; Yamamoto, Shogo; Okabe, Atsushi; Fukuyo, Masaki; Aburatani, Hiroyuki; Fukayama, Masashi; Kaneda, Atsushi

    2017-08-15

    Aberrant DNA hypermethylation is a major epigenetic mechanism to inactivate tumor suppressor genes in cancer. Epstein-Barr virus positive gastric cancer is the most frequently hypermethylated tumor among human malignancies. Herein, we performed comprehensive analysis of epigenomic alteration during EBV infection, by Infinium HumanMethylation 450K BeadChip for DNA methylation and ChIP-sequencing for histone modification alteration during EBV infection into gastric cancer cell line MKN7. Among 7,775 genes with increased DNA methylation in promoter regions, roughly half were "DNA methylation-sensitive" genes, which acquired DNA methylation in the whole promoter regions and thus were repressed. These included anti-oncogenic genes, e.g. CDKN2A . The other half were "DNA methylation-resistant" genes, where DNA methylation is acquired in the surrounding of promoter regions, but unmethylated status is protected in the vicinity of transcription start site. These genes thereby retained gene expression, and included DNA repair genes. Histone modification was altered dynamically and coordinately with DNA methylation alteration. DNA methylation-sensitive genes significantly correlated with loss of H3K27me3 pre-marks or decrease of active histone marks, H3K4me3 and H3K27ac. Apoptosis-related genes were significantly enriched in these epigenetically repressed genes. Gain of active histone marks significantly correlated with DNA methylation-resistant genes. Genes related to mitotic cell cycle and DNA repair were significantly enriched in these epigenetically activated genes. Our data show that orchestrated epigenetic alterations are important in gene regulation during EBV infection, and histone modification status in promoter regions significantly associated with acquisition of de novo DNA methylation or protection of unmethylated status at transcription start site.

  7. Human SIRT6 promotes DNA end resection through CtIP deacetylation

    Kaidi, Abderrahmane; Weinert, Brian T; Choudhary, Chunaram

    2010-01-01

    SIRT6 belongs to the sirtuin family of protein lysine deacetylases, which regulate aging and genome stability. We found that human SIRT6 has a role in promoting DNA end resection, a crucial step in DNA double-strand break (DSB) repair by homologous recombination. SIRT6 depletion impaired the accu...

  8. Promoter analysis of the Chilo iridescent virus DNA polymerase and major capsid protein genes

    Nalcacioglu, R.; Marks, H.; Vlak, J.M.; Demirbag, Z.; Oers, van M.M.

    2003-01-01

    The DNA polymerase (DNApol) and major capsid protein (MCP) genes were used as models to study promoter activity in Chilo iridescent virus (CIV). Infection of Bombyx mori SPC-BM-36 cells in the presence of inhibitors of DNA or protein synthesis showed that DNApol, as well as helicase, is an

  9. Human FAN1 promotes strand incision in 5'-flapped DNA complexed with RPA.

    Takahashi, Daisuke; Sato, Koichi; Hirayama, Emiko; Takata, Minoru; Kurumizaka, Hitoshi

    2015-09-01

    Fanconi anaemia (FA) is a human infantile recessive disorder. Seventeen FA causal proteins cooperatively function in the DNA interstrand crosslink (ICL) repair pathway. Dual DNA strand incisions around the crosslink are critical steps in ICL repair. FA-associated nuclease 1 (FAN1) is a DNA structure-specific endonuclease that is considered to be involved in DNA incision at the stalled replication fork. Replication protein A (RPA) rapidly assembles on the single-stranded DNA region of the stalled fork. However, the effect of RPA on the FAN1-mediated DNA incision has not been determined. In this study, we purified human FAN1, as a bacterially expressed recombinant protein. FAN1 exhibited robust endonuclease activity with 5'-flapped DNA, which is formed at the stalled replication fork. We found that FAN1 efficiently promoted DNA incision at the proper site of RPA-coated 5'-flapped DNA. Therefore, FAN1 possesses the ability to promote the ICL repair of 5'-flapped DNA covered by RPA. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

  10. DNA entropy reveals a significant difference in complexity between housekeeping and tissue specific gene promoters.

    Thomas, David; Finan, Chris; Newport, Melanie J; Jones, Susan

    2015-10-01

    The complexity of DNA can be quantified using estimates of entropy. Variation in DNA complexity is expected between the promoters of genes with different transcriptional mechanisms; namely housekeeping (HK) and tissue specific (TS). The former are transcribed constitutively to maintain general cellular functions, and the latter are transcribed in restricted tissue and cells types for specific molecular events. It is known that promoter features in the human genome are related to tissue specificity, but this has been difficult to quantify on a genomic scale. If entropy effectively quantifies DNA complexity, calculating the entropies of HK and TS gene promoters as profiles may reveal significant differences. Entropy profiles were calculated for a total dataset of 12,003 human gene promoters and for 501 housekeeping (HK) and 587 tissue specific (TS) human gene promoters. The mean profiles show the TS promoters have a significantly lower entropy (pentropy distributions for the 3 datasets show that promoter entropies could be used to identify novel HK genes. Functional features comprise DNA sequence patterns that are non-random and hence they have lower entropies. The lower entropy of TS gene promoters can be explained by a higher density of positive and negative regulatory elements, required for genes with complex spatial and temporary expression. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Evolutionary Transition of Promoter and Gene Body DNA Methylation across Invertebrate-Vertebrate Boundary.

    Keller, Thomas E; Han, Priscilla; Yi, Soojin V

    2016-04-01

    Genomes of invertebrates and vertebrates exhibit highly divergent patterns of DNA methylation. Invertebrate genomes tend to be sparsely methylated, and DNA methylation is mostly targeted to a subset of transcription units (gene bodies). In a drastic contrast, vertebrate genomes are generally globally and heavily methylated, punctuated by the limited local hypo-methylation of putative regulatory regions such as promoters. These genomic differences also translate into functional differences in DNA methylation and gene regulation. Although promoter DNA methylation is an important regulatory component of vertebrate gene expression, its role in invertebrate gene regulation has been little explored. Instead, gene body DNA methylation is associated with expression of invertebrate genes. However, the evolutionary steps leading to the differentiation of invertebrate and vertebrate genomic DNA methylation remain unresolved. Here we analyzed experimentally determined DNA methylation maps of several species across the invertebrate-vertebrate boundary, to elucidate how vertebrate gene methylation has evolved. We show that, in contrast to the prevailing idea, a substantial number of promoters in an invertebrate basal chordate Ciona intestinalis are methylated. Moreover, gene expression data indicate significant, epigenomic context-dependent associations between promoter methylation and expression in C. intestinalis. However, there is no evidence that promoter methylation in invertebrate chordate has been evolutionarily maintained across the invertebrate-vertebrate boundary. Rather, body-methylated invertebrate genes preferentially obtain hypo-methylated promoters among vertebrates. Conversely, promoter methylation is preferentially found in lineage- and tissue-specific vertebrate genes. These results provide important insights into the evolutionary origin of epigenetic regulation of vertebrate gene expression. © The Author(s) 2015. Published by Oxford University Press on behalf

  12. Gene assembly via one-pot chemical ligation of DNA promoted by DNA nanostructures

    Manuguerra, Ilenia; Croce, Stefano; El-Sagheer, Afaf H.

    2018-01-01

    Current gene synthesis methods are driven by enzymatic reactions. Here we report the one-pot synthesis of a chemically-ligated gene from 14 oligonucleotides. The chemical ligation benefits from the highly efficient click chemistry approach templated by DNA nanostructures, and produces modified DNA...

  13. The G-quadruplex DNA stabilizing drug pyridostatin promotes DNA damage and downregulates transcription of Brca1 in neurons.

    Moruno-Manchon, Jose F; Koellhoffer, Edward C; Gopakumar, Jayakrishnan; Hambarde, Shashank; Kim, Nayun; McCullough, Louise D; Tsvetkov, Andrey S

    2017-09-12

    The G-quadruplex is a non-canonical DNA secondary structure formed by four DNA strands containing multiple runs of guanines. G-quadruplexes play important roles in DNA recombination, replication, telomere maintenance, and regulation of transcription. Small molecules that stabilize the G-quadruplexes alter gene expression in cancer cells. Here, we hypothesized that the G-quadruplexes regulate transcription in neurons. We discovered that pyridostatin, a small molecule that specifically stabilizes G-quadruplex DNA complexes, induced neurotoxicity and promoted the formation of DNA double-strand breaks (DSBs) in cultured neurons. We also found that pyridostatin downregulated transcription of the Brca1 gene, a gene that is critical for DSB repair. Importantly, in an in vitro gel shift assay, we discovered that an antibody specific to the G-quadruplex structure binds to a synthetic oligonucleotide, which corresponds to the first putative G-quadruplex in the Brca1 gene promoter. Our results suggest that the G-quadruplex complexes regulate transcription in neurons. Studying the G-quadruplexes could represent a new avenue for neurodegeneration and brain aging research.

  14. DNA methylation of PTEN gene promoter region is not correlated ...

    Tumor suppressor gene PTEN plays an important role in cell cycle. Disorder of PTEN protein can cause cell growth and division in an uncontrolled way, which can lead to the formation of tumors. It has been proven that epigenetic mechanisms, such as promoter hypermethylation, may account for inactivation of PTEN in a ...

  15. Promoter analysis of the Chilo iridescent virus DNA polymerase and major capsid protein genes

    Nalcacioglu, Remziye; Marks, Hendrik; Vlak, Just M.; Demirbag, Zihni; Oers, Monique M. van

    2003-01-01

    The DNA polymerase (DNApol) and major capsid protein (MCP) genes were used as models to study promoter activity in Chilo iridescent virus (CIV). Infection of Bombyx mori SPC-BM-36 cells in the presence of inhibitors of DNA or protein synthesis showed that DNApol, as well as helicase, is an immediate-early gene and confirmed that the major capsid protein (MCP) is a late gene. Transcription of DNApol initiated 35 nt upstream and that of MCP 14 nt upstream of the translational start site. In a luciferase reporter gene assay both promoters were active only when cells were infected with CIV. For DNApol sequences between position -27 and -6, relative to the transcriptional start site, were essential for promoter activity. Furthermore, mutation of a G within the sequence TTGTTTT located just upstream of the DNApol transcription initiation site reduced the promoter activity by 25%. Sequences crucial for MCP promoter activity are located between positions -53 and -29

  16. Gene promoter methylation and DNA repair capacity in monozygotic twins with discordant smoking habits.

    Ottini, Laura; Rizzolo, Piera; Siniscalchi, Ester; Zijno, Andrea; Silvestri, Valentina; Crebelli, Riccardo; Marcon, Francesca

    2015-02-01

    The influence of DNA repair capacity, plasma nutrients and tobacco smoke exposure on DNA methylation was investigated in blood cells of twenty-one couples of monozygotic twins with discordant smoking habits. All study subjects had previously been characterized for mutagen sensitivity with challenge assays with ionizing radiation in peripheral blood lymphocytes. Plasma levels of folic acid, vitamin B12 and homocysteine were also available from a previous investigation. In this work DNA methylation in the promoter region of a panel of ten genes involved in cell cycle control, differentiation, apoptosis and DNA repair (p16, FHIT, RAR, CDH1, DAPK1, hTERT, RASSF1A, MGMT, BRCA1 and PALB2) was assessed in the same batches of cells isolated for previous studies, using the methylation-sensitive high-resolution melting technique. Fairly similar profiles of gene promoter methylation were observed within co-twins compared to unrelated subjects (p= 1.23 × 10(-7)), with no significant difference related to smoking habits (p = 0.23). In a regression analysis the methylation index of study subjects, used as synthetic descriptor of overall promoter methylation, displayed a significant inverse correlation with radiation-induced micronuclei (p = 0.021) and plasma folic acid level (p = 0.007) both in smokers and in non-smokers. The observed association between repair of radiation-induced DNA damage and promoter methylation suggests the involvement of the DNA repair machinery in DNA modification. Data also highlight the possible modulating effect of folate deficiency on DNA methylation and the strong influence of familiarity on the individual epigenetic profile. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. APOBEC3 cytidine deaminases in double-strand DNA break repair and cancer promotion.

    Nowarski, Roni; Kotler, Moshe

    2013-06-15

    High frequency of cytidine to thymidine conversions was identified in the genome of several types of cancer cells. In breast cancer cells, these mutations are clustered in long DNA regions associated with single-strand DNA (ssDNA), double-strand DNA breaks (DSB), and genomic rearrangements. The observed mutational pattern resembles the deamination signature of cytidine to uridine carried out by members of the APOBEC3 family of cellular deaminases. Consistently, APOBEC3B (A3B) was recently identified as the mutational source in breast cancer cells. A3G is another member of the cytidine deaminases family predominantly expressed in lymphoma cells, where it is involved in mutational DSB repair following ionizing radiation treatments. This activity provides us with a new paradigm for cancer cell survival and tumor promotion and a mechanistic link between ssDNA, DSBs, and clustered mutations. Cancer Res; 73(12); 3494-8. ©2013 AACR. ©2013 AACR.

  18. Evaluation of oxidative DNA damage promoted by storage in sperm from sex-reversed rainbow trout.

    Pérez-Cerezales, S; Martínez-Páramo, S; Cabrita, E; Martínez-Pastor, F; de Paz, P; Herráez, M P

    2009-03-01

    Short-term storage and cryopreservation of sperm are two common procedures in aquaculture, used for routine practices in artificial insemination reproduction and gene banking, respectively. Nevertheless, both procedures cause injuries affecting sperm motility, viability, cell structure and DNA stability, which diminish reproductive success. DNA modification is considered extremely important, especially when sperm storage is carried out with gene banking purposes. DNA damage caused by sperm storage is not well characterized and previous studies have reported simple and double strand breaks that have been attributed to oxidative events promoted by the generation of free radicals during storage. The objective of this study was to reveal DNA fragmentation and to explore the presence of oxidized bases that could be produced by oxidative events during short-term storage and cryopreservation in sex-reversed rainbow trout (Oncorhynchus mykiss) spermatozoa. Sperm from six males was analyzed separately. Different aliquots of the samples were stored 2h (fresh) or 5 days at 4 degrees C or were cryopreserved. Then spermatozoa were analyzed using the Comet assay, as well as combining this method with digestion with two endonucleases from Escherichia coli (Endonuclease III, that cut in oxidized cytosines, and FPG, cutting in oxidized guanosines). Both storage procedures yielded DNA fragmentation, but only short-term storage oxidative events were clearly detected, showing that oxidative processes affect guanosines rather than cytosines. Cryopreservation increases DNA fragmentation but the presence of oxidized bases was not noticed, suggesting that mechanisms other than oxidative stress could be involved in DNA fragmentation promoted by freezing.

  19. DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis.

    Le, Tuan-Ngoc; Schumann, Ulrike; Smith, Neil A; Tiwari, Sameer; Au, Phil Chi Khang; Zhu, Qian-Hao; Taylor, Jennifer M; Kazan, Kemal; Llewellyn, Danny J; Zhang, Ren; Dennis, Elizabeth S; Wang, Ming-Bo

    2014-09-17

    DNA demethylases regulate DNA methylation levels in eukaryotes. Arabidopsis encodes four DNA demethylases, DEMETER (DME), REPRESSOR OF SILENCING 1 (ROS1), DEMETER-LIKE 2 (DML2), and DML3. While DME is involved in maternal specific gene expression during seed development, the biological function of the remaining DNA demethylases remains unclear. We show that ROS1, DML2, and DML3 play a role in fungal disease resistance in Arabidopsis. A triple DNA demethylase mutant, rdd (ros1 dml2 dml3), shows increased susceptibility to the fungal pathogen Fusarium oxysporum. We identify 348 genes differentially expressed in rdd relative to wild type, and a significant proportion of these genes are downregulated in rdd and have functions in stress response, suggesting that DNA demethylases maintain or positively regulate the expression of stress response genes required for F. oxysporum resistance. The rdd-downregulated stress response genes are enriched for short transposable element sequences in their promoters. Many of these transposable elements and their surrounding sequences show localized DNA methylation changes in rdd, and a general reduction in CHH methylation, suggesting that RNA-directed DNA methylation (RdDM), responsible for CHH methylation, may participate in DNA demethylase-mediated regulation of stress response genes. Many of the rdd-downregulated stress response genes are downregulated in the RdDM mutants nrpd1 and nrpe1, and the RdDM mutants nrpe1 and ago4 show enhanced susceptibility to F. oxysporum infection. Our results suggest that a primary function of DNA demethylases in plants is to regulate the expression of stress response genes by targeting promoter transposable element sequences.

  20. Hda monomerization by ADP binding promotes replicase clamp-mediated DnaA-ATP hydrolysis.

    Su'etsugu, Masayuki; Nakamura, Kenta; Keyamura, Kenji; Kudo, Yuka; Katayama, Tsutomu

    2008-12-26

    ATP-DnaA is the initiator of chromosomal replication in Escherichia coli, and the activity of DnaA is regulated by the regulatory inactivation of the DnaA (RIDA) system. In this system, the Hda protein promotes DnaA-ATP hydrolysis to produce inactive ADP-DnaA in a mechanism that is mediated by the DNA-loaded form of the replicase sliding clamp. In this study, we first revealed that hda translation uses an unusual initiation codon, CUG, located downstream of the annotated initiation codon. The CUG initiation codon could be used for restricting the Hda level, as this initiation codon has a low translation efficiency, and the cellular Hda level is only approximately 100 molecules per cell. Hda translated using the correct reading frame was purified and found to have a high RIDA activity in vitro. Moreover, we found that Hda has a high affinity for ADP but not for other nucleotides, including ATP. ADP-Hda was active in the RIDA system in vitro and stable in a monomeric state, whereas apo-Hda formed inactive homomultimers. Both ADP-Hda and apo-Hda could form complexes with the DNA-loaded clamp; however, only ADP-Hda-DNA-clamp complexes were highly functional in the following interaction with DnaA. Formation of ADP-Hda was also observed in vivo, and mutant analysis suggested that ADP binding is crucial for cellular Hda activity. Thus, we propose that ADP is a crucial Hda ligand that promotes the activated conformation of the protein. ADP-dependent monomerization might enable the arginine finger of the Hda AAA+ domain to be accessible to ATP bound to the DnaA AAA+ domain.

  1. Mechanisms of DNA damage by the tumor promoter and progressor benzoyl peroxide

    Swauger, J.E.; Dolan, P.M.; Zweier, J.L.; Kensler, T.W.

    1990-01-01

    Benzoyl peroxide (BzPO), a tumor promoter and progressor in mouse skin, produces strand breaks in DNA of exposed cells. Previously we have reported that the metabolism of BzPO in keratinocytes proceeds via the initial cleavage of the peroxide bond, yielding benzoyloxyl radicals which, in turn, can fragment to form phenyl radicals and carbon dioxide. Benzoic acid, the product of hydrogen abstraction by the benzoyloxyl radical, is the major stable metabolite of BzPO produced by keratinocytes. In the present study we have examined the capacity of BzPO to generate strand scissions in φX-174 plasmid DNA. DNA damage was dose-dependent over a concentration range of 10-1000 μM BzPO and was dependent on the presence of copper but not other transition state metals. By contrast, benzoic acid did not produce DNA damage in this system. The inclusion of spin trapping agents (PBN, DBNBS), radical scavenging agents (Nal, GSH), or the copper chelator o-phenanthroline in incubations was found to significantly reduce the extent of DNA damage. Electron paramagnetic resonance spectroscopy studies suggested that the primary radical trapped was the benzoyloxyl radical, implying a role for this radical in the generation of the observed DNA damage. Collectively these observations suggest BzPO may be activated to DNA damaging intermediates in keratinocytes via metal-catalyzed cleavage of the peroxide bond resulting in the formation of the benzoyloxyl radical. Covalent modification of DNA was not observed when [ 14 C]BzPO was incubated with calf thymus DNA in the presence of copper. Overall, these results suggest that BzPO induces DNA damage via benzoyloxyl radical mediated proton abstraction from the DNA strand and the adduct formation with DNA is unlikely to occur

  2. Identification of functional DNA variants in the constitutive promoter region of MDM2

    Lalonde Marie-Eve

    2012-09-01

    Full Text Available Abstract Although mutations in the oncoprotein murine double minute 2 (MDM2 are rare, MDM2 gene overexpression has been observed in several human tumors. Given that even modest changes in MDM2 levels might influence the p53 tumor suppressor signaling pathway, we postulated that sequence variation in the promoter region of MDM2 could lead to disregulated expression and variation in gene dosage. Two promoters have been reported for MDM2; an internal promoter (P2, which is located near the end of intron 1 and is p53-responsive, and an upstream constitutive promoter (P1, which is p53-independent. Both promoter regions contain DNA variants that could influence the expression levels of MDM2, including the well-studied single nucleotide polymorphism (SNP SNP309, which is located in the promoter P2; i.e., upstream of exon 2. In this report, we screened the promoter P1 for DNA variants and assessed the functional impact of the corresponding SNPs. Using the dbSNP database and genotyping validation in individuals of European descent, we identified three common SNPs (−1494 G > A; indel 40 bp; and −182 C > G. Three major promoter haplotypes were inferred by using these three promoter SNPs together with rs2279744 (SNP309. Following subcloning into a gene reporter system, we found that two of the haplotypes significantly influenced MDM2 promoter activity in a haplotype-specific manner. Site-directed mutagenesis experiments indicated that the 40 bp insertion/deletion variation is causing the observed allelic promoter activity. This study suggests that part of the variability in the MDM2 expression levels could be explained by allelic p53-independent P1 promoter activity.

  3. The mitochondrial outer membrane protein MDI promotes local protein synthesis and mtDNA replication.

    Zhang, Yi; Chen, Yong; Gucek, Marjan; Xu, Hong

    2016-05-17

    Early embryonic development features rapid nuclear DNA replication cycles, but lacks mtDNA replication. To meet the high-energy demands of embryogenesis, mature oocytes are furnished with vast amounts of mitochondria and mtDNA However, the cellular machinery driving massive mtDNA replication in ovaries remains unknown. Here, we describe a Drosophila AKAP protein, MDI that recruits a translation stimulator, La-related protein (Larp), to the mitochondrial outer membrane in ovaries. The MDI-Larp complex promotes the synthesis of a subset of nuclear-encoded mitochondrial proteins by cytosolic ribosomes on the mitochondrial surface. MDI-Larp's targets include mtDNA replication factors, mitochondrial ribosomal proteins, and electron-transport chain subunits. Lack of MDI abolishes mtDNA replication in ovaries, which leads to mtDNA deficiency in mature eggs. Targeting Larp to the mitochondrial outer membrane independently of MDI restores local protein synthesis and rescues the phenotypes of mdi mutant flies. Our work suggests that a selective translational boost by the MDI-Larp complex on the outer mitochondrial membrane might be essential for mtDNA replication and mitochondrial biogenesis during oogenesis. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

  4. The Chilo iridescent virus DNA polymerase promoter contains an essential AAAAT motif

    Nalcacioglu, R.; Ince, I.A.; Vlak, J.M.; Demirbag, Z.; Oers, van M.M.

    2007-01-01

    The delayed-early DNA polymerase promoter of Chilo iridescent virus (CIV), officially known as Invertebrate iridescent virus, was fine mapped by constructing a series of increasing deletions and by introducing point mutations. The effects of these mutations were examined in a luciferase reporter

  5. ATM-Dependent Phosphorylation of MEF2D Promotes Neuronal Survival after DNA Damage

    Chan, Shing Fai; Sances, Sam; Brill, Laurence M.; Okamoto, Shu-ichi; Zaidi, Rameez; McKercher, Scott R.; Akhtar, Mohd W.; Nakanishi, Nobuki

    2014-01-01

    Mutations in the ataxia telangiectasia mutated (ATM) gene, which encodes a kinase critical for the normal DNA damage response, cause the neurodegenerative disorder ataxia-telangiectasia (AT). The substrates of ATM in the brain are poorly understood. Here we demonstrate that ATM phosphorylates and activates the transcription factor myocyte enhancer factor 2D (MEF2D), which plays a critical role in promoting survival of cerebellar granule cells. ATM associates with MEF2D after DNA damage and phosphorylates the transcription factor at four ATM consensus sites. Knockdown of endogenous MEF2D with a short-hairpin RNA (shRNA) increases sensitivity to etoposide-induced DNA damage and neuronal cell death. Interestingly, substitution of endogenous MEF2D with an shRNA-resistant phosphomimetic MEF2D mutant protects cerebellar granule cells from cell death after DNA damage, whereas an shRNA-resistant nonphosphorylatable MEF2D mutant does not. In vivo, cerebella in Mef2d knock-out mice manifest increased susceptibility to DNA damage. Together, our results show that MEF2D is a substrate for phosphorylation by ATM, thus promoting survival in response to DNA damage. Moreover, dysregulation of the ATM–MEF2D pathway may contribute to neurodegeneration in AT. PMID:24672010

  6. DAF-16/FOXO and EGL-27/GATA promote developmental growth in response to persistent somatic DNA damage.

    Mueller, Michael M; Castells-Roca, Laia; Babu, Vipin; Ermolaeva, Maria A; Müller, Roman-Ulrich; Frommolt, Peter; Williams, Ashley B; Greiss, Sebastian; Schneider, Jennifer I; Benzing, Thomas; Schermer, Bernhard; Schumacher, Björn

    2014-12-01

    Genome maintenance defects cause complex disease phenotypes characterized by developmental failure, cancer susceptibility and premature ageing. It remains poorly understood how DNA damage responses function during organismal development and maintain tissue functionality when DNA damage accumulates with ageing. Here we show that the FOXO transcription factor DAF-16 is activated in response to DNA damage during development, whereas the DNA damage responsiveness of DAF-16 declines with ageing. We find that in contrast to its established role in mediating starvation arrest, DAF-16 alleviates DNA-damage-induced developmental arrest and even in the absence of DNA repair promotes developmental growth and enhances somatic tissue functionality. We demonstrate that the GATA transcription factor EGL-27 co-regulates DAF-16 target genes in response to DNA damage and together with DAF-16 promotes developmental growth. We propose that EGL-27/GATA activity specifies DAF-16-mediated DNA damage responses to enable developmental progression and to prolong tissue functioning when DNA damage persists.

  7. Architecture of the bacteriophage T4 activator MotA/promoter DNA interaction during sigma appropriation.

    Hsieh, Meng-Lun; James, Tamara D; Knipling, Leslie; Waddell, M Brett; White, Stephen; Hinton, Deborah M

    2013-09-20

    Gene expression can be regulated through factors that direct RNA polymerase to the correct promoter sequence at the correct time. Bacteriophage T4 controls its development in this way using phage proteins that interact with host RNA polymerase. Using a process called σ appropriation, the T4 co-activator AsiA structurally remodels the σ(70) subunit of host RNA polymerase, while a T4 activator, MotA, engages the C terminus of σ(70) and binds to a DNA promoter element, the MotA box. Structures for the N-terminal (NTD) and C-terminal (CTD) domains of MotA are available, but no structure exists for MotA with or without DNA. We report the first molecular map of the MotA/DNA interaction within the σ-appropriated complex, which we obtained by using the cleaving reagent, iron bromoacetamidobenzyl-EDTA (FeBABE). We conjugated surface-exposed, single cysteines in MotA with FeBABE and performed cleavage reactions in the context of stable transcription complexes. The DNA cleavage sites were analyzed using ICM Molsoft software and three-dimensional physical models of MotA(NTD), MotA(CTD), and the DNA to investigate shape complementarity between the protein and the DNA and to position MotA on the DNA. We found that the unusual "double wing" motif present within MotA(CTD) resides in the major groove of the MotA box. In addition, we have used surface plasmon resonance to show that MotA alone is in a very dynamic equilibrium with the MotA element. Our results demonstrate the utility of fine resolution FeBABE mapping to determine the architecture of protein-DNA complexes that have been recalcitrant to traditional structure analyses.

  8. The Conjugative Relaxase TrwC Promotes Integration of Foreign DNA in the Human Genome.

    González-Prieto, Coral; Gabriel, Richard; Dehio, Christoph; Schmidt, Manfred; Llosa, Matxalen

    2017-06-15

    -specific integrase activity in bacteria, as an integrase in human cells. Although it is not efficient as a site-specific integrase, we found that TrwC is active in human cells and promotes random integration of the transferred DNA in the human genome, probably acting as a DNA chaperone until it is integrated by host mechanisms. TrwC-DNA complexes can be delivered to human cells through a type IV secretion system involved in pathogenesis. Thus, TrwC could be used in vivo to transfer the DNA of interest into the appropriate cell and promote its integration. If used in combination with a site-specific nuclease, it could lead to site-specific integration of the incoming DNA by homologous recombination. Copyright © 2017 American Society for Microbiology.

  9. DNA polymerase iota (Pol ι) promotes invasion and metastasis of esophageal squamous cell carcinoma.

    Zou, Shitao; Shang, Zeng-Fu; Liu, Biao; Zhang, Shuyu; Wu, Jinchang; Huang, Min; Ding, Wei-Qun; Zhou, Jundong

    2016-05-31

    DNA polymerase iota (Pol ι) is an error-prone DNA polymerase involved in translesion DNA synthesis (TLS) that contributes to the accumulation of DNA mutations. We recently showed that Pol ι is overexpressed in human esophageal squamous cell cancer (ESCC) tissues which promotes ESCC' progression. The present study was aimed at investigating the molecular mechanisms by which Pol ι enhances the invasiveness and metastasis of ESCC cells. We found that the expression of Pol ι is significantly higher in ESCCs with lymph node metastasis compared to those without lymph node metastasis. Kaplan-Meier analysis revealed an inverse correlation between Pol ι expression and patient prognosis. The expression levels of matrix metalloproteinase-2 (MMP-2) and matrix metalloproteinase-9 (MMP-9), two essential regulators of cells' invasiveness, were positively associated with Pol ι expression in ESCC tissues. Ectopic expression of Pol ι enhanced the motility and invasiveness of ESCC cells as evaluated by wound-healing and transwell assays, respectively. A xenograft nude mouse model showed that Pol ι promotes the colonization of ESCC cells in the liver, lung and kidney. Signaling pathway analysis identified the JNK-AP-1 cascade as a mediator of the Pol ι-induced increase in the expression of MMP-2/9 and enhancement of ESCC progression. These data demonstrate the underlying mechanism by which Pol ι promotes ESCC progression, suggesting that Pol ι is a potential novel prognostic biomarker and therapeutic target for ESCC.

  10. Hda Monomerization by ADP Binding Promotes Replicase Clamp-mediated DnaA-ATP Hydrolysis*S⃞

    Su'etsugu, Masayuki; Nakamura, Kenta; Keyamura, Kenji; Kudo, Yuka; Katayama, Tsutomu

    2008-01-01

    ATP-DnaA is the initiator of chromosomal replication in Escherichia coli, and the activity of DnaA is regulated by the regulatory inactivation of the DnaA (RIDA) system. In this system, the Hda protein promotes DnaA-ATP hydrolysis to produce inactive ADP-DnaA in a mechanism that is mediated by the DNA-loaded form of the replicase sliding clamp. In this study, we first revealed that hda translation uses an unusual initiation codon, CUG, located downstream of the annotat...

  11. The RAB2B-GARIL5 Complex Promotes Cytosolic DNA-Induced Innate Immune Responses.

    Takahama, Michihiro; Fukuda, Mitsunori; Ohbayashi, Norihiko; Kozaki, Tatsuya; Misawa, Takuma; Okamoto, Toru; Matsuura, Yoshiharu; Akira, Shizuo; Saitoh, Tatsuya

    2017-09-19

    Cyclic GMP-AMP synthase (cGAS) is a cytosolic DNA sensor that induces the IFN antiviral response. However, the regulatory mechanisms that mediate cGAS-triggered signaling have not been fully explored. Here, we show the involvement of a small GTPase, RAB2B, and its effector protein, Golgi-associated RAB2B interactor-like 5 (GARIL5), in the cGAS-mediated IFN response. RAB2B-deficiency affects the IFN response induced by cytosolic DNA. Consistent with this, RAB2B deficiency enhances replication of vaccinia virus, a DNA virus. After DNA stimulation, RAB2B colocalizes with stimulator of interferon genes (STING), the downstream signal mediator of cGAS, on the Golgi apparatus. The GTP-binding activity of RAB2B is required for its localization on the Golgi apparatus and for recruitment of GARIL5. GARIL5 deficiency also affects the IFN response induced by cytosolic DNA and enhances replication of vaccinia virus. These findings indicate that the RAB2B-GARIL5 complex promotes IFN responses against DNA viruses by regulating the cGAS-STING signaling axis. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  12. The RAB2B-GARIL5 Complex Promotes Cytosolic DNA-Induced Innate Immune Responses

    Michihiro Takahama

    2017-09-01

    Full Text Available Cyclic GMP-AMP synthase (cGAS is a cytosolic DNA sensor that induces the IFN antiviral response. However, the regulatory mechanisms that mediate cGAS-triggered signaling have not been fully explored. Here, we show the involvement of a small GTPase, RAB2B, and its effector protein, Golgi-associated RAB2B interactor-like 5 (GARIL5, in the cGAS-mediated IFN response. RAB2B-deficiency affects the IFN response induced by cytosolic DNA. Consistent with this, RAB2B deficiency enhances replication of vaccinia virus, a DNA virus. After DNA stimulation, RAB2B colocalizes with stimulator of interferon genes (STING, the downstream signal mediator of cGAS, on the Golgi apparatus. The GTP-binding activity of RAB2B is required for its localization on the Golgi apparatus and for recruitment of GARIL5. GARIL5 deficiency also affects the IFN response induced by cytosolic DNA and enhances replication of vaccinia virus. These findings indicate that the RAB2B-GARIL5 complex promotes IFN responses against DNA viruses by regulating the cGAS-STING signaling axis.

  13. Coronal Mass Ejections

    Kunow, H; Linker, J. A; Schwenn, R; Steiger, R

    2006-01-01

    It is well known that the Sun gravitationally controls the orbits of planets and minor bodies. Much less known, however, is the domain of plasma fields and charged particles in which the Sun governs a heliosphere out to a distance of about 15 billion kilometers. What forces activates the Sun to maintain this power? Coronal Mass Ejections (CMEs) and their descendants are the troops serving the Sun during high solar activity periods. This volume offers a comprehensive and integrated overview of our present knowledge and understanding of Coronal Mass Ejections (CMEs) and their descendants, Interplanetary CMEs (ICMEs). It results from a series of workshops held between 2000 and 2004. An international team of about sixty experimenters involved e.g. in the SOHO, ULYSSES, VOYAGER, PIONEER, HELIOS, WIND, IMP, and ACE missions, ground observers, and theoreticians worked jointly on interpreting the observations and developing new models for CME initiations, development, and interplanetary propagation. The book provides...

  14. CaMV-35S promoter sequence-specific DNA methylation in lettuce.

    Okumura, Azusa; Shimada, Asahi; Yamasaki, Satoshi; Horino, Takuya; Iwata, Yuji; Koizumi, Nozomu; Nishihara, Masahiro; Mishiba, Kei-ichiro

    2016-01-01

    We found 35S promoter sequence-specific DNA methylation in lettuce. Additionally, transgenic lettuce plants having a modified 35S promoter lost methylation, suggesting the modified sequence is subjected to the methylation machinery. We previously reported that cauliflower mosaic virus 35S promoter-specific DNA methylation in transgenic gentian (Gentiana triflora × G. scabra) plants occurs irrespective of the copy number and the genomic location of T-DNA, and causes strong gene silencing. To confirm whether 35S-specific methylation can occur in other plant species, transgenic lettuce (Lactuca sativa L.) plants with a single copy of the 35S promoter-driven sGFP gene were produced and analyzed. Among 10 lines of transgenic plants, 3, 4, and 3 lines showed strong, weak, and no expression of sGFP mRNA, respectively. Bisulfite genomic sequencing of the 35S promoter region showed hypermethylation at CpG and CpWpG (where W is A or T) sites in 9 of 10 lines. Gentian-type de novo methylation pattern, consisting of methylated cytosines at CpHpH (where H is A, C, or T) sites, was also observed in the transgenic lettuce lines, suggesting that lettuce and gentian share similar methylation machinery. Four of five transgenic lettuce lines having a single copy of a modified 35S promoter, which was modified in the proposed core target of de novo methylation in gentian, exhibited 35S hypomethylation, indicating that the modified sequence may be the target of the 35S-specific methylation machinery.

  15. Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

    Fauteux, François; Strömvik, Martina V

    2009-01-01

    Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP) gene promoters from three plant families, namely Brassicaceae (mustards), Fabaceae (legumes) and Poaceae (grasses) using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L.) Heynh.), soybean (Glycine max (L.) Merr.) and rice (Oryza sativa L.) respectively. We have identified three conserved motifs (two RY-like and one ACGT-like) in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination of conserved motifs

  16. Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

    Fauteux François

    2009-10-01

    Full Text Available Abstract Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP gene promoters from three plant families, namely Brassicaceae (mustards, Fabaceae (legumes and Poaceae (grasses using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L. Heynh., soybean (Glycine max (L. Merr. and rice (Oryza sativa L. respectively. We have identified three conserved motifs (two RY-like and one ACGT-like in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination

  17. MGMT DNA repair gene promoter/enhancer haplotypes alter transcription factor binding and gene expression.

    Xu, Meixiang; Cross, Courtney E; Speidel, Jordan T; Abdel-Rahman, Sherif Z

    2016-10-01

    The O 6 -methylguanine-DNA methyltransferase (MGMT) protein removes O 6 -alkyl-guanine adducts from DNA. MGMT expression can thus alter the sensitivity of cells and tissues to environmental and chemotherapeutic alkylating agents. Previously, we defined the haplotype structure encompassing single nucleotide polymorphisms (SNPs) in the MGMT promoter/enhancer (P/E) region and found that haplotypes, rather than individual SNPs, alter MGMT promoter activity. The exact mechanism(s) by which these haplotypes exert their effect on MGMT promoter activity is currently unknown, but we noted that many of the SNPs comprising the MGMT P/E haplotypes are located within or in close proximity to putative transcription factor binding sites. Thus, these haplotypes could potentially affect transcription factor binding and, subsequently, alter MGMT promoter activity. In this study, we test the hypothesis that MGMT P/E haplotypes affect MGMT promoter activity by altering transcription factor (TF) binding to the P/E region. We used a promoter binding TF profiling array and a reporter assay to evaluate the effect of different P/E haplotypes on TF binding and MGMT expression, respectively. Our data revealed a significant difference in TF binding profiles between the different haplotypes evaluated. We identified TFs that consistently showed significant haplotype-dependent binding alterations (p ≤ 0.01) and revealed their role in regulating MGMT expression using siRNAs and a dual-luciferase reporter assay system. The data generated support our hypothesis that promoter haplotypes alter the binding of TFs to the MGMT P/E and, subsequently, affect their regulatory function on MGMT promoter activity and expression level.

  18. Transgelin gene is frequently downregulated by promoter DNA hypermethylation in breast cancer.

    Sayar, Nilufer; Karahan, Gurbet; Konu, Ozlen; Bozkurt, Betul; Bozdogan, Onder; Yulug, Isik G

    2015-01-01

    CpG hypermethylation in gene promoters is a frequent mechanism of tumor suppressor gene silencing in various types of cancers. It usually occurs at early steps of cancer progression and can be detected easily, giving rise to development of promising biomarkers for both detection and progression of cancer, including breast cancer. 5-aza-2'-deoxycytidine (AZA) is a DNA demethylating and anti-cancer agent resulting in induction of genes suppressed via DNA hypermethylation. Using microarray expression profiling of AZA- or DMSO-treated breast cancer and non-tumorigenic breast (NTB) cells, we identified for the first time TAGLN gene as a target of DNA hypermethylation in breast cancer. TAGLN expression was significantly and frequently downregulated via promoter DNA hypermethylation in breast cancer cells compared to NTB cells, and also in 13/21 (61.9 %) of breast tumors compared to matched normal tissues. Analyses of public microarray methylation data showed that TAGLN was also hypermethylated in 63.02 % of tumors compared to normal tissues; relapse-free survival of patients was worse with higher TAGLN methylation; and methylation levels could discriminate between tumors and healthy tissues with 83.14 % sensitivity and 100 % specificity. Additionally, qRT-PCR and immunohistochemistry experiments showed that TAGLN expression was significantly downregulated in two more independent sets of breast tumors compared to normal tissues and was lower in tumors with poor prognosis. Colony formation was increased in TAGLN silenced NTB cells, while decreased in overexpressing BC cells. TAGLN gene is frequently downregulated by DNA hypermethylation, and TAGLN promoter methylation profiles could serve as a future diagnostic biomarker, with possible clinical impact regarding the prognosis in breast cancer.

  19. Recombination Promoted by DNA Viruses: Phage λ to Herpes Simplex Virus

    Weller, Sandra K.; Sawitzke, James A.

    2015-01-01

    The purpose of this review is to explore recombination strategies in DNA viruses. Homologous recombination is a universal genetic process that plays multiple roles in the biology of all organisms, including viruses. Recombination and DNA replication are interconnected, with recombination being essential for repairing DNA damage and supporting replication of the viral genome. Recombination also creates genetic diversity, and viral recombination mechanisms have important implications for understanding viral origins as well as the dynamic nature of viral-host interactions. Both bacteriophage λ and herpes simplex virus (HSV) display high rates of recombination, both utilizing their own proteins and commandeering cellular proteins to promote recombination reactions. We focus primarily on λ and HSV, as they have proven amenable to both genetic and biochemical analysis and have recently been shown to exhibit some surprising similarities that will guide future studies. PMID:25002096

  20. Fasting protects mice from lethal DNA damage by promoting small intestinal epithelial stem cell survival.

    Tinkum, Kelsey L; Stemler, Kristina M; White, Lynn S; Loza, Andrew J; Jeter-Jones, Sabrina; Michalski, Basia M; Kuzmicki, Catherine; Pless, Robert; Stappenbeck, Thaddeus S; Piwnica-Worms, David; Piwnica-Worms, Helen

    2015-12-22

    Short-term fasting protects mice from lethal doses of chemotherapy through undetermined mechanisms. Herein, we demonstrate that fasting preserves small intestinal (SI) architecture by maintaining SI stem cell viability and SI barrier function following exposure to high-dose etoposide. Nearly all SI stem cells were lost in fed mice, whereas fasting promoted sufficient SI stem cell survival to preserve SI integrity after etoposide treatment. Lineage tracing demonstrated that multiple SI stem cell populations, marked by Lgr5, Bmi1, or HopX expression, contributed to fasting-induced survival. DNA repair and DNA damage response genes were elevated in SI stem/progenitor cells of fasted etoposide-treated mice, which importantly correlated with faster resolution of DNA double-strand breaks and less apoptosis. Thus, fasting preserved SI stem cell viability as well as SI architecture and barrier function suggesting that fasting may reduce host toxicity in patients undergoing dose intensive chemotherapy.

  1. TH17 cells promote microbial killing and innate immune sensing of DNA via interleukin 26

    Meller, Stephan; Di Domizio, Jeremy; Voo, Kui S; Friedrich, Heike C; Chamilos, Georgios; Ganguly, Dipyaman; Conrad, Curdin; Gregorio, Josh; Le Roy, Didier; Roger, Thierry; Ladbury, John E; Homey, Bernhard; Watowich, Stanley; Modlin, Robert L; Kontoyiannis, Dimitrios P; Liu, Yong-Jun; Arold, Stefan T.; Gilliet, Michel

    2015-01-01

    Interleukin 17-producing helper T cells (TH 17 cells) have a major role in protection against infections and in mediating autoimmune diseases, yet the mechanisms involved are incompletely understood. We found that interleukin 26 (IL-26), a human TH17 cell-derived cytokine, is a cationic amphipathic protein that kills extracellular bacteria via membrane-pore formation. Furthermore, TH17 cell-derived IL-26 formed complexes with bacterial DNA and self-DNA released by dying bacteria and host cells. The resulting IL-26-DNA complexes triggered the production of type I interferon by plasmacytoid dendritic cells via activation of Toll-like receptor 9, but independently of the IL-26 receptor. These findings provide insights into the potent antimicrobial and proinflammatory function of TH17 cells by showing that IL-26 is a natural human antimicrobial that promotes immune sensing of bacterial and host cell death. © 2015 Nature America, Inc.

  2. FAN1 acts with FANCI-FANCD2 to promote DNA interstrand cross-link repair.

    Liu, Ting; Ghosal, Gargi; Yuan, Jingsong; Chen, Junjie; Huang, Jun

    2010-08-06

    Fanconi anemia (FA) is caused by mutations in 13 Fanc genes and renders cells hypersensitive to DNA interstrand cross-linking (ICL) agents. A central event in the FA pathway is mono-ubiquitylation of the FANCI-FANCD2 (ID) protein complex. Here, we characterize a previously unrecognized nuclease, Fanconi anemia-associated nuclease 1 (FAN1), that promotes ICL repair in a manner strictly dependent on its ability to accumulate at or near sites of DNA damage and that relies on mono-ubiquitylation of the ID complex. Thus, the mono-ubiquitylated ID complex recruits the downstream repair protein FAN1 and facilitates the repair of DNA interstrand cross-links.

  3. TH17 cells promote microbial killing and innate immune sensing of DNA via interleukin 26

    Meller, Stephan

    2015-07-13

    Interleukin 17-producing helper T cells (TH 17 cells) have a major role in protection against infections and in mediating autoimmune diseases, yet the mechanisms involved are incompletely understood. We found that interleukin 26 (IL-26), a human TH17 cell-derived cytokine, is a cationic amphipathic protein that kills extracellular bacteria via membrane-pore formation. Furthermore, TH17 cell-derived IL-26 formed complexes with bacterial DNA and self-DNA released by dying bacteria and host cells. The resulting IL-26-DNA complexes triggered the production of type I interferon by plasmacytoid dendritic cells via activation of Toll-like receptor 9, but independently of the IL-26 receptor. These findings provide insights into the potent antimicrobial and proinflammatory function of TH17 cells by showing that IL-26 is a natural human antimicrobial that promotes immune sensing of bacterial and host cell death. © 2015 Nature America, Inc.

  4. DNA methylation dynamics in the rat EGF gene promoter after partial hepatectomy

    Deming Li

    2014-06-01

    Full Text Available Epidermal growth factor (EGF, a multifunctional growth factor, is a regulator in a wide variety of physiological processes. EGF plays an important role in the regulation of liver regeneration. This study was aimed at investigating the methylation level of EGF gene throughout liver regeneration. DNA of liver tissue from control rats and partial hepatectomy (PH rats at 10 time points was extracted and a 354 bp fragment including 10 CpG sites from the transcription start was amplified after DNA was modified by sodium bisulfate. The result of sequencing suggested that methylation ratio of four CpG sites was found to be significantly changed when PH group was compared to control group, in particular two of them were extremely striking. mRNA expression of EGF was down-regulated in total during liver regeneration. We think that the rat EGF promoter region is regulated by variation in DNA methylation during liver regeneration.

  5. G9a coordinates with the RPA complex to promote DNA damage repair and cell survival.

    Yang, Qiaoyan; Zhu, Qian; Lu, Xiaopeng; Du, Yipeng; Cao, Linlin; Shen, Changchun; Hou, Tianyun; Li, Meiting; Li, Zhiming; Liu, Chaohua; Wu, Di; Xu, Xingzhi; Wang, Lina; Wang, Haiying; Zhao, Ying; Yang, Yang; Zhu, Wei-Guo

    2017-07-25

    Histone methyltransferase G9a has critical roles in promoting cancer-cell growth and gene suppression, but whether it is also associated with the DNA damage response is rarely studied. Here, we report that loss of G9a impairs DNA damage repair and enhances the sensitivity of cancer cells to radiation and chemotherapeutics. In response to DNA double-strand breaks (DSBs), G9a is phosphorylated at serine 211 by casein kinase 2 (CK2) and recruited to chromatin. The chromatin-enriched G9a can then directly interact with replication protein A (RPA) and promote loading of the RPA and Rad51 recombinase to DSBs. This mechanism facilitates homologous recombination (HR) and cell survival. We confirmed the interaction between RPA and G9a to be critical for RPA foci formation and HR upon DNA damage. Collectively, our findings demonstrate a regulatory pathway based on CK2-G9a-RPA that permits HR in cancer cells and provide further rationale for the use of G9a inhibitors as a cancer therapeutic.

  6. Set2 Methyltransferase Facilitates DNA Replication and Promotes Genotoxic Stress Responses through MBF-Dependent Transcription.

    Pai, Chen-Chun; Kishkevich, Anastasiya; Deegan, Rachel S; Keszthelyi, Andrea; Folkes, Lisa; Kearsey, Stephen E; De León, Nagore; Soriano, Ignacio; de Bruin, Robertus Antonius Maria; Carr, Antony M; Humphrey, Timothy C

    2017-09-12

    Chromatin modification through histone H3 lysine 36 methylation by the SETD2 tumor suppressor plays a key role in maintaining genome stability. Here, we describe a role for Set2-dependent H3K36 methylation in facilitating DNA replication and the transcriptional responses to both replication stress and DNA damage through promoting MluI cell-cycle box (MCB) binding factor (MBF)-complex-dependent transcription in fission yeast. Set2 loss leads to reduced MBF-dependent ribonucleotide reductase (RNR) expression, reduced deoxyribonucleoside triphosphate (dNTP) synthesis, altered replication origin firing, and a checkpoint-dependent S-phase delay. Accordingly, prolonged S phase in the absence of Set2 is suppressed by increasing dNTP synthesis. Furthermore, H3K36 is di- and tri-methylated at these MBF gene promoters, and Set2 loss leads to reduced MBF binding and transcription in response to genotoxic stress. Together, these findings provide new insights into how H3K36 methylation facilitates DNA replication and promotes genotoxic stress responses in fission yeast. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  7. Set2 Methyltransferase Facilitates DNA Replication and Promotes Genotoxic Stress Responses through MBF-Dependent Transcription

    Chen-Chun Pai

    2017-09-01

    Full Text Available Chromatin modification through histone H3 lysine 36 methylation by the SETD2 tumor suppressor plays a key role in maintaining genome stability. Here, we describe a role for Set2-dependent H3K36 methylation in facilitating DNA replication and the transcriptional responses to both replication stress and DNA damage through promoting MluI cell-cycle box (MCB binding factor (MBF-complex-dependent transcription in fission yeast. Set2 loss leads to reduced MBF-dependent ribonucleotide reductase (RNR expression, reduced deoxyribonucleoside triphosphate (dNTP synthesis, altered replication origin firing, and a checkpoint-dependent S-phase delay. Accordingly, prolonged S phase in the absence of Set2 is suppressed by increasing dNTP synthesis. Furthermore, H3K36 is di- and tri-methylated at these MBF gene promoters, and Set2 loss leads to reduced MBF binding and transcription in response to genotoxic stress. Together, these findings provide new insights into how H3K36 methylation facilitates DNA replication and promotes genotoxic stress responses in fission yeast.

  8. Osteoponin Promoter Controlled by DNA Methylation: Aberrant Methylation in Cloned Porcine Genome

    Chih-Jie Shen

    2014-01-01

    Full Text Available Cloned animals usually exhibited many defects in physical characteristics or aberrant epigenetic reprogramming, especially in some important organ development. Osteoponin (OPN is an extracellular-matrix protein involved in heart and bone development and diseases. In this study, we investigated the correlation between OPN mRNA and its promoter methylation changes by the 5-aza-dc treatment in fibroblast cell and promoter assay. Aberrant methylation of porcine OPN was frequently found in different tissues of somatic nuclear transferred cloning pigs, and bisulfite sequence data suggested that the OPN promoter region −2615 to −2239 nucleotides (nt may be a crucial regulation DNA element. In pig ear fibroblast cell culture study, the demethylation of OPN promoter was found in dose-dependent response of 5-aza-dc treatment and followed the OPN mRNA reexpression. In cloned pig study, discrepant expression pattern was identified in several cloned pig tissues, especially in brain, heart, and ear. Promoter assay data revealed that four methylated CpG sites presenting in the −2615 to −2239 nt region cause significant downregulation of OPN promoter activity. These data suggested that methylation in the OPN promoter plays a crucial role in the regulation of OPN expression that we found in cloned pigs genome.

  9. HMGB1-mediated DNA bending: Distinct roles in increasing p53 binding to DNA and the transactivation of p53-responsive gene promoters.

    Štros, Michal; Kučírek, Martin; Sani, Soodabeh Abbasi; Polanská, Eva

    2018-03-01

    HMGB1 is a chromatin-associated protein that has been implicated in many important biological processes such as transcription, recombination, DNA repair, and genome stability. These functions include the enhancement of binding of a number of transcription factors, including the tumor suppressor protein p53, to their specific DNA-binding sites. HMGB1 is composed of two highly conserved HMG boxes, linked to an intrinsically disordered acidic C-terminal tail. Previous reports have suggested that the ability of HMGB1 to bend DNA may explain the in vitro HMGB1-mediated increase in sequence-specific DNA binding by p53. The aim of this study was to reinvestigate the importance of HMGB1-induced DNA bending in relationship to the ability of the protein to promote the specific binding of p53 to short DNA duplexes in vitro, and to transactivate two major p53-regulated human genes: Mdm2 and p21/WAF1. Using a number of HMGB1 mutants, we report that the HMGB1-mediated increase in sequence-specific p53 binding to DNA duplexes in vitro depends very little on HMGB1-mediated DNA bending. The presence of the acidic C-terminal tail of HMGB1 and/or the oxidation of the protein can reduce the HMGB1-mediated p53 binding. Interestingly, the induction of transactivation of p53-responsive gene promoters by HMGB1 requires both the ability of the protein to bend DNA and the acidic C-terminal tail, and is promoter-specific. We propose that the efficient transactivation of p53-responsive gene promoters by HMGB1 depends on complex events, rather than solely on the promotion of p53 binding to its DNA cognate sites. Copyright © 2018 Elsevier B.V. All rights reserved.

  10. DNA Methylation Analysis of BRD1 Promoter Regions and the Schizophrenia rs138880 Risk Allele.

    Mads Dyrvig

    Full Text Available The bromodomain containing 1 gene, BRD1 is essential for embryogenesis and CNS development. It encodes a protein that participates in histone modifying complexes and thereby regulates the expression of a large number of genes. Genetic variants in the BRD1 locus show association with schizophrenia and bipolar disorder and risk alleles in the promoter region correlate with reduced BRD1 expression. Insights into the transcriptional regulation of BRD1 and the pathogenic mechanisms associated with BRD1 risk variants, however, remain sparse. By studying transcripts in human HeLa and SH-SY5Y cells we provide evidence for differences in relative expression of BRD1 transcripts with three alternative 5' UTRs (exon 1C, 1B, and 1A. We further show that expression of these transcript variants covaries negatively with DNA methylation proportions in their upstream promoter regions suggesting that promoter usage might be regulated by DNA methylation. In line with findings that the risk allele of the rs138880 SNP in the BRD1 promoter region correlates with reduced BRD1 expression, we find that it is also associated with moderate regional BRD1 promoter hypermethylation in both adipose tissue and blood. Importantly, we demonstrate by inspecting available DNA methylation and expression data that these regions undergo changes in methylation during fetal brain development and that differences in their methylation proportions in fetal compared to postnatal frontal cortex correlate significantly with BRD1 expression. These findings suggest that BRD1 may be dysregulated in both the developing and mature brain of risk allele carriers. Finally, we demonstrate that commonly used mood stabilizers Lithium, Valproate, and Carbamazepine affect the expression of BRD1 in SH-SY5Y cells. Altogether this study indicates a link between genetic risk and epigenetic dysregulation of BRD1 which raises interesting perspectives for targeting the mechanisms pharmacologically.

  11. Viral DNA Replication Orientation and hnRNPs Regulate Transcription of the Human Papillomavirus 18 Late Promoter.

    Wang, Xiaohong; Liu, Haibin; Ge, Hui; Ajiro, Masahiko; Sharma, Nishi R; Meyers, Craig; Morozov, Pavel; Tuschl, Thomas; Klar, Amar; Court, Donald; Zheng, Zhi-Ming

    2017-05-30

    The life cycle of human papillomaviruses (HPVs) is tightly linked to keratinocyte differentiation. Although expression of viral early genes is initiated immediately upon virus infection of undifferentiated basal cells, viral DNA amplification and late gene expression occur only in the mid to upper strata of the keratinocytes undergoing terminal differentiation. In this report, we show that the relative activity of HPV18 TATA-less late promoter P 811 depends on its orientation relative to that of the origin (Ori) of viral DNA replication and is sensitive to the eukaryotic DNA polymerase inhibitor aphidicolin. Additionally, transfected 70-nucleotide (nt)-long single-strand DNA oligonucleotides that are homologous to the region near Ori induce late promoter activity. We also found that promoter activation in raft cultures leads to production of the late promoter-associated, sense-strand transcription initiation RNAs (tiRNAs) and splice-site small RNAs (spliRNAs). Finally, a cis -acting AAGTATGCA core element that functions as a repressor to the promoter was identified. This element interacts with hnRNP D0B and hnRNP A/B factors. Point mutations in the core prevented binding of hnRNPs and increased the promoter activity. Confirming this result, knocking down the expression of both hnRNPs in keratinocytes led to increased promoter activity. Taking the data together, our study revealed the mechanism of how the HPV18 late promoter is regulated by DNA replication and host factors. IMPORTANCE It has been known for decades that the activity of viral late promoters is associated with viral DNA replication among almost all DNA viruses. However, the mechanism of how DNA replication activates the viral late promoter and what components of the replication machinery are involved remain largely unknown. In this study, we characterized the P 811 promoter region of HPV18 and demonstrated that its activation depends on the orientation of DNA replication. Using single

  12. Two-Stage Dynamics of In Vivo Bacteriophage Genome Ejection

    Chen, Yi-Ju; Wu, David; Gelbart, William; Knobler, Charles M.; Phillips, Rob; Kegel, Willem K.

    2018-04-01

    Biopolymer translocation is a key step in viral infection processes. The transfer of information-encoding genomes allows viruses to reprogram the cell fate of their hosts. Constituting 96% of all known bacterial viruses [A. Fokine and M. G. Rossmann, Molecular architecture of tailed double-stranded DNA phages, Bacteriophage 4, e28281 (2014)], the tailed bacteriophages deliver their DNA into host cells via an "ejection" process, leaving their protein shells outside of the bacteria; a similar scenario occurs for mammalian viruses like herpes, where the DNA genome is ejected into the nucleus of host cells, while the viral capsid remains bound outside to a nuclear-pore complex. In light of previous experimental measurements of in vivo bacteriophage λ ejection, we analyze here the physical processes that give rise to the observed dynamics. We propose that, after an initial phase driven by self-repulsion of DNA in the capsid, the ejection is driven by anomalous diffusion of phage DNA in the crowded bacterial cytoplasm. We expect that this two-step mechanism is general for phages that operate by pressure-driven ejection, and we discuss predictions of our theory to be tested in future experiments.

  13. Sirt6 Promotes DNA End Joining in iPSCs Derived from Old Mice

    Wen Chen

    2017-03-01

    Full Text Available Induced pluripotent stem cells (iPSCs have great potential for treating age-related diseases, but the genome integrity of iPSCs is critically important. Here, we demonstrate that non-homologous end joining (NHEJ, rather than homologous recombination (HR, is less efficient in iPSCs from old mice than young mice. We further find that Sirt6 is downregulated in iPSCs from old mice. Sirt6 directly binds to Ku80 and facilitates the Ku80/DNA-PKcs interaction, thus promoting DNA-PKcs phosphorylation at residue S2056, leading to efficient NHEJ. Rescue experiments show that introducing a combination of Sirt6 and the Yamanaka factors during reprogramming significantly promotes DNA double-strand break (DSB repair by activating NHEJ in iPSCs derived from old mice. Thus, our study suggests a strategy to improve the quality of iPSCs derived from old donors by activating NHEJ and stabilizing the genome.

  14. Alpha-Lipoic acid counteracts the promoted oxidative DNA damage in the liver of septic rats

    Abd-Allah, Adel R.A.

    2006-01-01

    Viral, parasitic infections and chemical carcinogens are among the etiological factors of liver cancer. It seems important to study the initiating and promoting agents to evaluate the etiology and prevention of such life threatening disease. Intestine-derived bacteria product, lipopolysaccharide (LPS), is mainly detoxified by the liver. It has shown to induce a state of oxidative DNA damage is not fully investigated. Increased oxidative DNA damage and rate of cell proliferation may initiate or even promote cancer. In the present work, the capability of LPS to induce 8-hydroxydeoxyguanosine (8-HDG), a specific DNA adduct for oxidative DNA damage, in rat livers is tested. Furthermore, a possible protective effect of alpha lipoic acid (ALA) is also assessed. Investigated parameters are liver contents of glutathione (GSH), lipid peroxides (MDA), nitric oxide (NO) and 8-HDG in the liver-extracted DNA. Serum activities of ALT, AST and GGT as liver-function markers as well as IL2 are assessed. Moreover, liver histology is examined. LPS was given doses of 1, 3, 5, 7 and 9 mg/kg once i.p. while, the rat mortality was examined 24 hours later. ALA was given in doses of 50, 100 and 200 mg/kg once i.p. 3h before LPS is found to be 5mg/kg. LPS increased the level of 8-HDG, MDA and NO in the liver. It also induced acute liver necrosis and inflammatory cell infiltration as shown in liver-histopathology and in the significant increase in the activities of ALT, AST and GGT. LPS increased the serum level of IL2 as well. The dose 200mg/kg of ALA revealed a 100% protection against LPS-induced lethality. It also, prevented the LPS-induced increase in 8-HDG in liver extracted DNA, the liver contents of MDA and NO. ALA also rescued the LPS-induced GSH depletion. It corrected the liver function as shown by the prevention of increases in the activity of ALT, AST and GGT with a remarkable improvement in the liver histology. Moreover, it prevented the increase in serum level of IL2. These

  15. P-body proteins regulate transcriptional rewiring to promote DNA replication stress resistance.

    Loll-Krippleber, Raphael; Brown, Grant W

    2017-09-15

    mRNA-processing (P-) bodies are cytoplasmic granules that form in eukaryotic cells in response to numerous stresses to serve as sites of degradation and storage of mRNAs. Functional P-bodies are critical for the DNA replication stress response in yeast, yet the repertoire of P-body targets and the mechanisms by which P-bodies promote replication stress resistance are unknown. In this study we identify the complete complement of mRNA targets of P-bodies during replication stress induced by hydroxyurea treatment. The key P-body protein Lsm1 controls the abundance of HHT1, ACF4, ARL3, TMA16, RRS1 and YOX1 mRNAs to prevent their toxic accumulation during replication stress. Accumulation of YOX1 mRNA causes aberrant downregulation of a network of genes critical for DNA replication stress resistance and leads to toxic acetaldehyde accumulation. Our data reveal the scope and the targets of regulation by P-body proteins during the DNA replication stress response.P-bodies form in response to stress and act as sites of mRNA storage and degradation. Here the authors identify the mRNA targets of P-bodies during DNA replication stress, and show that P-body proteins act to prevent toxic accumulation of these target transcripts.

  16. Proton ejection project for Saturne

    Bronca, G.; Gendreau, G.

    1959-01-01

    The reasons for choosing the ejection system are given. The characteristics required for the ejected beam are followed by a description of the ejection process, in chronological order from the viewpoint of the protons: movement of the particles, taking into account the various elements which make up the system (internal magnet, external magnet, quadrupoles, ejection correction coils, thin and thick cables,...) and specification of these elements. Then follows an estimation of the delay in manufacture and the cost of the project. Finally, the characteristics of the magnets and quadrupoles are listed in an appendix. (author) [fr

  17. DNA of HeLa cells during caffeine-promoted recovery from X-ray induced G2 arrest

    Bases, R.; Mendez, F.; Liebeskind, D.; Elequin, F.; Neubort, S.

    1980-01-01

    Progression of X-irradiated HeLa cells from G2 arrest through mitosis was promoted by 1mM caffeine. Caffeine promoted the return from abnormally high levels of radiation-induced immunoreactivity to antinucleoside antibodies, which indicates persistent DNA strand separation, to the low levels normally found in G2. With caffeine, the irradiated cells progressed through mitosis, producing daughter cells with the normal G1 content of DNA. Without caffeine, the DNA content of individual radiation-arrested cells retained G2 values and the abnormally high levels of immunoreactivity to antinucleoside antibodies. (author)

  18. A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice

    La, Honggui; Ding, Bo; Mishra, Gyan Prakash; Zhou, Bo; Yang, Hongmei; Bellizzi, Maria Del Rosario; Chen, Songbiao; Meyers, Blake C.; Peng, Zhaohua; Zhu, Jian-Kang; Wang, Guoliang

    2011-01-01

    DNA 5-methylcytosine (5-meC) is an important epigenetic mark for transcriptional gene silencing in many eukaryotes. In Arabidopsis, 5-meC DNA glycosylase/lyases actively remove 5-meC to counter-act transcriptional gene silencing in a locus-specific manner, and have been suggested to maintain the expression of transposons. However, it is unclear whether plant DNA demethylases can promote the transposition of transposons. Here we report the functional characterization of the DNA glycosylase/lyase DNG701 in rice. DNG701 encodes a large (1,812 amino acid residues) DNA glycosylase domain protein. Recombinant DNG701 protein showed 5-meC DNA glycosylase and lyase activities in vitro. Knockout or knockdown of DNG701 in rice plants led to DNA hypermethylation and reduced expression of the retrotransposon Tos17. Tos17 showed less transposition in calli derived from dng701 knockout mutant seeds compared with that in wild-type calli. Overexpression of DNG701 in both rice calli and transgenic plants substantially reduced DNA methylation levels of Tos17 and enhanced its expression. The overexpression also led to more frequent transposition of Tos17 in calli. Our results demonstrate that rice DNG701 is a 5-meC DNA glycosylase/lyase responsible for the demethylation of Tos17 and this DNA demethylase plays a critical role in promoting Tos17 transposition in rice calli.

  19. A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice

    La, Honggui

    2011-09-06

    DNA 5-methylcytosine (5-meC) is an important epigenetic mark for transcriptional gene silencing in many eukaryotes. In Arabidopsis, 5-meC DNA glycosylase/lyases actively remove 5-meC to counter-act transcriptional gene silencing in a locus-specific manner, and have been suggested to maintain the expression of transposons. However, it is unclear whether plant DNA demethylases can promote the transposition of transposons. Here we report the functional characterization of the DNA glycosylase/lyase DNG701 in rice. DNG701 encodes a large (1,812 amino acid residues) DNA glycosylase domain protein. Recombinant DNG701 protein showed 5-meC DNA glycosylase and lyase activities in vitro. Knockout or knockdown of DNG701 in rice plants led to DNA hypermethylation and reduced expression of the retrotransposon Tos17. Tos17 showed less transposition in calli derived from dng701 knockout mutant seeds compared with that in wild-type calli. Overexpression of DNG701 in both rice calli and transgenic plants substantially reduced DNA methylation levels of Tos17 and enhanced its expression. The overexpression also led to more frequent transposition of Tos17 in calli. Our results demonstrate that rice DNG701 is a 5-meC DNA glycosylase/lyase responsible for the demethylation of Tos17 and this DNA demethylase plays a critical role in promoting Tos17 transposition in rice calli.

  20. DNA Topoisomerases Maintain Promoters in a State Competent for Transcriptional Activation in Saccharomyces cerevisiae

    Pedersen, Jakob Madsen; Fredsøe, Jacob Christian; Rødgaard, Morten Terpager

    2012-01-01

    To investigate the role of DNA topoisomerases in transcription, we have studied global gene expression in Saccharomyces cerevisiae cells deficient for topoisomerases I and II and performed single-gene analyses to support our findings. The genome-wide studies show a general transcriptional down......-regulation upon lack of the enzymes, which correlates with gene activity but not gene length. Furthermore, our data reveal a distinct subclass of genes with a strong requirement for topoisomerases. These genes are characterized by high transcriptional plasticity, chromatin regulation, TATA box presence......-depth analysis of the inducible PHO5 gene reveals that topoisomerases are essential for binding of the Pho4p transcription factor to the PHO5 promoter, which is required for promoter nucleosome removal during activation. In contrast, topoisomerases are dispensable for constitutive transcription initiation...

  1. Mutations in BALB mitochondrial DNA induce CCL20 up-regulation promoting tumorigenic phenotypes

    Sligh, James [Department of Medicine—Dermatology Division, University of Arizona, Tucson, AZ 857 24 (United States); University of Arizona Cancer Center, Tucson, AZ 85724 (United States); Janda, Jaroslav [University of Arizona Cancer Center, Tucson, AZ 85724 (United States); Jandova, Jana, E-mail: jjandova@email.arizona.edu [Department of Medicine—Dermatology Division, University of Arizona, Tucson, AZ 857 24 (United States); University of Arizona Cancer Center, Tucson, AZ 85724 (United States)

    2014-11-15

    -κB activation inhibited CCL20 expression in mtBALB cybrids and decreased their migratory capabilities. Thus, acquired mtDNA mutations may promote tumorigenic phenotypes through up-regulation of chemokine CCL20.

  2. Gain of DNA methylation is enhanced in the absence of CTCF at the human retinoblastoma gene promoter

    Dávalos-Salas, Mercedes; Furlan-Magaril, Mayra; González-Buendía, Edgar; Valdes-Quezada, Christian; Ayala-Ortega, Erandi; Recillas-Targa, Félix

    2011-01-01

    Long-term gene silencing throughout cell division is generally achieved by DNA methylation and other epigenetic processes. Aberrant DNA methylation is now widely recognized to be associated with cancer and other human diseases. Here we addressed the contribution of the multifunctional nuclear factor CTCF to the epigenetic regulation of the human retinoblastoma (Rb) gene promoter in different tumoral cell lines. To assess the DNA methylation status of the Rb promoter, genomic DNA from stably transfected human erythroleukemic K562 cells expressing a GFP reporter transgene was transformed with sodium bisulfite, and then PCR-amplified with modified primers and sequenced. Single- and multi-copy integrants with the CTCF binding site mutated were isolated and characterized by Southern blotting. Silenced transgenes were reactivated using 5-aza-2'-deoxycytidine and Trichostatin-A, and their expression was monitored by fluorescent cytometry. Rb gene expression and protein abundance were assessed by RT-PCR and Western blotting in three different glioma cell lines, and DNA methylation of the promoter region was determined by sodium bisulfite sequencing, together with CTCF dissociation and methyl-CpG-binding protein incorporation by chromatin immunoprecipitation assays. We found that the inability of CTCF to bind to the Rb promoter causes a dramatic loss of gene expression and a progressive gain of DNA methylation. This study indicates that CTCF plays an important role in maintaining the Rb promoter in an optimal chromatin configuration. The absence of CTCF induces a rapid epigenetic silencing through a progressive gain of DNA methylation. Consequently, CTCF can now be seen as one of the epigenetic components that allows the proper configuration of tumor suppressor gene promoters. Its aberrant dissociation can then predispose key genes in cancer cells to acquire DNA methylation and epigenetic silencing

  3. A composite method based on formal grammar and DNA structural features in detecting human polymerase II promoter region.

    Sutapa Datta

    Full Text Available An important step in understanding gene regulation is to identify the promoter regions where the transcription factor binding takes place. Predicting a promoter region de novo has been a theoretical goal for many researchers for a long time. There exists a number of in silico methods to predict the promoter region de novo but most of these methods are still suffering from various shortcomings, a major one being the selection of appropriate features of promoter region distinguishing them from non-promoters. In this communication, we have proposed a new composite method that predicts promoter sequences based on the interrelationship between structural profiles of DNA and primary sequence elements of the promoter regions. We have shown that a Context Free Grammar (CFG can formalize the relationships between different primary sequence features and by utilizing the CFG, we demonstrate that an efficient parser can be constructed for extracting these relationships from DNA sequences to distinguish the true promoter sequences from non-promoter sequences. Along with CFG, we have extracted the structural features of the promoter region to improve upon the efficiency of our prediction system. Extensive experiments performed on different datasets reveals that our method is effective in predicting promoter sequences on a genome-wide scale and performs satisfactorily as compared to other promoter prediction techniques.

  4. A Composite Method Based on Formal Grammar and DNA Structural Features in Detecting Human Polymerase II Promoter Region

    Datta, Sutapa; Mukhopadhyay, Subhasis

    2013-01-01

    An important step in understanding gene regulation is to identify the promoter regions where the transcription factor binding takes place. Predicting a promoter region de novo has been a theoretical goal for many researchers for a long time. There exists a number of in silico methods to predict the promoter region de novo but most of these methods are still suffering from various shortcomings, a major one being the selection of appropriate features of promoter region distinguishing them from non-promoters. In this communication, we have proposed a new composite method that predicts promoter sequences based on the interrelationship between structural profiles of DNA and primary sequence elements of the promoter regions. We have shown that a Context Free Grammar (CFG) can formalize the relationships between different primary sequence features and by utilizing the CFG, we demonstrate that an efficient parser can be constructed for extracting these relationships from DNA sequences to distinguish the true promoter sequences from non-promoter sequences. Along with CFG, we have extracted the structural features of the promoter region to improve upon the efficiency of our prediction system. Extensive experiments performed on different datasets reveals that our method is effective in predicting promoter sequences on a genome-wide scale and performs satisfactorily as compared to other promoter prediction techniques. PMID:23437045

  5. The N-terminus of TDP-43 promotes its oligomerization and enhances DNA binding affinity

    Chang, Chung-ke [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Wu, Tzong-Huah [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China); Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biochemistry, Academia Sinica, Taipei 115, Taiwan (China); Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan (China); Wu, Chu-Ya [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China); Graduate Institute of Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan (China); Chiang, Ming-hui; Toh, Elsie Khai-Woon [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Hsu, Yin-Chih; Lin, Ku-Feng [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China); Liao, Yu-heng [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Huang, Tai-huang, E-mail: bmthh@gate.sinica.edu.tw [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Department of Physics, National Taiwan Normal University, Taipei 106, Taiwan (China); Huang, Joseph Jen-Tse, E-mail: jthuang@chem.sinica.edu.tw [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China)

    2012-08-24

    Highlights: Black-Right-Pointing-Pointer The N-terminus of TDP-43 contains an independently folded structural domain (NTD). Black-Right-Pointing-Pointer The structural domains of TDP-43 are arranged in a beads-on-a-string fashion. Black-Right-Pointing-Pointer The NTD promotes TDP-43 oligomerization in a concentration-dependent manner. Black-Right-Pointing-Pointer The NTD may assist nucleic acid-binding activity of TDP-43. -- Abstract: TDP-43 is a DNA/RNA-binding protein associated with different neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD-U). Here, the structural and physical properties of the N-terminus on TDP-43 have been carefully characterized through a combination of nuclear magnetic resonance (NMR), circular dichroism (CD) and fluorescence anisotropy studies. We demonstrate for the first time the importance of the N-terminus in promoting TDP-43 oligomerization and enhancing its DNA-binding affinity. An unidentified structural domain in the N-terminus is also disclosed. Our findings provide insights into the N-terminal domain function of TDP-43.

  6. Promoter DNA methylation pattern identifies prognostic subgroups in childhood T-cell acute lymphoblastic leukemia.

    Magnus Borssén

    Full Text Available BACKGROUND: Treatment of pediatric T-cell acute lymphoblastic leukemia (T-ALL has improved, but there is a considerable fraction of patients experiencing a poor outcome. There is a need for better prognostic markers and aberrant DNA methylation is a candidate in other malignancies, but its potential prognostic significance in T-ALL is hitherto undecided. DESIGN AND METHODS: Genome wide promoter DNA methylation analysis was performed in pediatric T-ALL samples (n = 43 using arrays covering >27000 CpG sites. Clinical outcome was evaluated in relation to methylation status and compared with a contemporary T-ALL group not tested for methylation (n = 32. RESULTS: Based on CpG island methylator phenotype (CIMP, T-ALL samples were subgrouped as CIMP+ (high methylation and CIMP- (low methylation. CIMP- T-ALL patients had significantly worse overall and event free survival (p = 0.02 and p = 0.001, respectively compared to CIMP+ cases. CIMP status was an independent factor for survival in multivariate analysis including age, gender and white blood cell count. Analysis of differently methylated genes in the CIMP subgroups showed an overrepresentation of transcription factors, ligands and polycomb target genes. CONCLUSIONS: We identified global promoter methylation profiling as being of relevance for subgrouping and prognostication of pediatric T-ALL.

  7. HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae.

    Guillen-Ahlers, Hector; Rao, Prahlad K; Levenstein, Mark E; Kennedy-Darling, Julia; Perumalla, Danu S; Jadhav, Avinash Y L; Glenn, Jeremy P; Ludwig-Kubinski, Amy; Drigalenko, Eugene; Montoya, Maria J; Göring, Harald H; Anderson, Corianna D; Scalf, Mark; Gildersleeve, Heidi I S; Cole, Regina; Greene, Alexandra M; Oduro, Akua K; Lazarova, Katarina; Cesnik, Anthony J; Barfknecht, Jared; Cirillo, Lisa A; Gasch, Audrey P; Shortreed, Michael R; Smith, Lloyd M; Olivier, Michael

    2016-06-01

    Currently available methods for interrogating DNA-protein interactions at individual genomic loci have significant limitations, and make it difficult to work with unmodified cells or examine single-copy regions without specific antibodies. In this study, we describe a physiological application of the Hybridization Capture of Chromatin-Associated Proteins for Proteomics (HyCCAPP) methodology we have developed. Both novel and known locus-specific DNA-protein interactions were identified at the ENO2 and GAL1 promoter regions of Saccharomyces cerevisiae, and revealed subgroups of proteins present in significantly different levels at the loci in cells grown on glucose versus galactose as the carbon source. Results were validated using chromatin immunoprecipitation. Overall, our analysis demonstrates that HyCCAPP is an effective and flexible technology that does not require specific antibodies nor prior knowledge of locally occurring DNA-protein interactions and can now be used to identify changes in protein interactions at target regions in the genome in response to physiological challenges. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Mouse Rad9b is essential for embryonic development and promotes resistance to DNA damage

    Leloup, Corinne; Hopkins, Kevin M.; Wang, Xiangyuan; Zhu, Aiping; Wolgemuth, Debra J.; Lieberman, Howard B.

    2010-01-01

    RAD9 participates in promoting resistance to DNA damage, cell cycle checkpoint control, DNA repair, apoptosis, embryogenesis, and regulation of transcription. A paralogue of RAD9 (named RAD9B) has been identified. To define the function of mouse Rad9b (Mrad9b), embryonic stem (ES) cells with a targeted gene deletion were constructed and used to generate Mrad9b mutant mice. Mrad9b−/− embryos are resorbed after E7.5 while some of the heterozygotes die between E12.5 and a few days after birth. Mrad9b is expressed in embryonic brain and Mrad9b+/− embryos exhibit abnormal neural tube closure. Mrad9b−/− mouse embryonic fibroblasts are not viable. Mrad9b−/− ES cells are more sensitive to gamma rays and mitomycin C than Mrad9b+/+ controls, but show normal gamma-ray-induced G2/M checkpoint control. There is no evidence of spontaneous genomic instability in Mrad9b−/− cells. Our findings thus indicate that Mrad9b is essential for embryonic development and mediates resistance to certain DNA damaging agents. PMID:20842695

  9. Asymmetric Arginine dimethylation of Epstein-Barr virus nuclear antigen 2 promotes DNA targeting

    Gross, Henrik; Barth, Stephanie; Palermo, Richard D.; Mamiani, Alfredo; Hennard, Christine; Zimber-Strobl, Ursula; West, Michelle J.; Kremmer, Elisabeth; Graesser, Friedrich A.

    2010-01-01

    The Epstein-Barr virus (EBV) growth-transforms B-lymphocytes. The virus-encoded nuclear antigen 2 (EBNA2) is essential for transformation and activates gene expression by association with DNA-bound transcription factors such as RBPJκ (CSL/CBF1). We have previously shown that EBNA2 contains symmetrically dimethylated Arginine (sDMA) residues. Deletion of the RG-repeat results in a reduced ability of the virus to immortalise B-cells. We now show that the RG repeat also contains asymmetrically dimethylated Arginines (aDMA) but neither non-methylated (NMA) Arginines nor citrulline residues. We demonstrate that only aDMA-containing EBNA2 is found in a complex with DNA-bound RBPJκ in vitro and preferentially associates with the EBNA2-responsive EBV C, LMP1 and LMP2A promoters in vivo. Inhibition of methylation in EBV-infected cells results in reduced expression of the EBNA2-regulated viral gene LMP1, providing additional evidence that methylation is a prerequisite for DNA-binding by EBNA2 via association with the transcription factor RBPJκ.

  10. Infrared A radiation promotes survival of human melanocytes carrying ultraviolet radiation-induced DNA damage.

    Kimeswenger, Susanne; Schwarz, Agatha; Födinger, Dagmar; Müller, Susanne; Pehamberger, Hubert; Schwarz, Thomas; Jantschitsch, Christian

    2016-06-01

    The link between solar radiation and melanoma is still elusive. Although infrared radiation (IR) accounts for over 50% of terrestrial solar energy, its influence on human skin is not well explored. There is increasing evidence that IR influences the expression patterns of several molecules independently of heat. A previous in vivo study revealed that pretreatment with IR might promote the development of UVR-induced non-epithelial skin cancer and possibly of melanoma in mice. To expand on this, the aim of the present study was to evaluate the impact of IR on UVR-induced apoptosis and DNA repair in normal human epidermal melanocytes. The balance between these two effects is a key factor of malignant transformation. Human melanocytes were exposed to physiologic doses of IR and UVR. Compared to cells irradiated with UVR only, simultaneous exposure to IR significantly reduced the apoptotic rate. However, IR did not influence the repair of UVR-induced DNA damage. IR partly reversed the pro-apoptotic effects of UVR via modification of the expression and activity of proteins mainly of the extrinsic apoptotic pathway. In conclusion, IR enhances the survival of melanocytes carrying UVR-induced DNA damage and thereby might contribute to melanomagenesis. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  11. Two-Stage Dynamics of In Vivo Bacteriophage Genome Ejection

    Yi-Ju Chen

    2018-05-01

    Full Text Available Biopolymer translocation is a key step in viral infection processes. The transfer of information-encoding genomes allows viruses to reprogram the cell fate of their hosts. Constituting 96% of all known bacterial viruses [A. Fokine and M. G. Rossmann, Molecular architecture of tailed double-stranded DNA phages, Bacteriophage 4, e28281 (2014], the tailed bacteriophages deliver their DNA into host cells via an “ejection” process, leaving their protein shells outside of the bacteria; a similar scenario occurs for mammalian viruses like herpes, where the DNA genome is ejected into the nucleus of host cells, while the viral capsid remains bound outside to a nuclear-pore complex. In light of previous experimental measurements of in vivo bacteriophage λ ejection, we analyze here the physical processes that give rise to the observed dynamics. We propose that, after an initial phase driven by self-repulsion of DNA in the capsid, the ejection is driven by anomalous diffusion of phage DNA in the crowded bacterial cytoplasm. We expect that this two-step mechanism is general for phages that operate by pressure-driven ejection, and we discuss predictions of our theory to be tested in future experiments.

  12. RNA Pol II promotes transcription of centromeric satellite DNA in beetles.

    Zeljka Pezer

    Full Text Available Transcripts of centromeric satellite DNAs are known to play a role in heterochromatin formation as well as in establishment of the kinetochore. However, little is known about basic mechanisms of satellite DNA expression within constitutive heterochromatin and its regulation. Here we present comprehensive analysis of transcription of abundant centromeric satellite DNA, PRAT from beetle Palorus ratzeburgii (Coleoptera. This satellite is characterized by preservation and extreme sequence conservation among evolutionarily distant insect species. PRAT is expressed in all three developmental stages: larvae, pupae and adults at similar level. Transcripts are abundant comprising 0.033% of total RNA and are heterogeneous in size ranging from 0.5 kb up to more than 5 kb. Transcription proceeds from both strands but with 10 fold different expression intensity and transcripts are not processed into siRNAs. Most of the transcripts (80% are not polyadenylated and remain in the nucleus while a small portion is exported to the cytoplasm. Multiple, irregularly distributed transcription initiation sites as well as termination sites have been mapped within the PRAT sequence using primer extension and RLM-RACE. The presence of cap structure as well as poly(A tails in a portion of the transcripts indicate RNA polymerase II-dependent transcription and a putative polymerase II promoter site overlaps the most conserved part of the PRAT sequence. The treatment of larvae with alpha-amanitin decreases the level of PRAT transcripts at concentrations that selectively inhibit pol II activity. In conclusion, stable, RNA polymerase II dependant transcripts of abundant centromeric satellite DNA, not regulated by RNAi, have been identified and characterized. This study offers a basic understanding of expression of highly abundant heterochromatic DNA which in beetle species constitutes up to 50% of the genome.

  13. Chronic exposure to trichloroethylene increases DNA methylation of the Ifng promoter in CD4+ T cells.

    Gilbert, Kathleen M; Blossom, Sarah J; Erickson, Stephen W; Broadfoot, Brannon; West, Kirk; Bai, Shasha; Li, Jingyun; Cooney, Craig A

    2016-10-17

    CD4 + T cells in female MRL+/+ mice exposed to solvent and water pollutant trichloroethylene (TCE) skew toward effector/memory CD4 + T cells, and demonstrate seemingly non-monotonic alterations in IFN-γ production. In the current study we examined the mechanism for this immunotoxicity using effector/memory and naïve CD4 + T cells isolated every 6 weeks during a 40 week exposure to TCE (0.5mg/ml in drinking water). A time-dependent effect of TCE exposure on both Ifng gene expression and IFN-γ protein production was observed in effector/memory CD4 + T cells, with an increase after 22 weeks of exposure and a decrease after 40 weeks of exposure. No such effect of TCE was observed in naïve CD4 + T cells. A cumulative increase in DNA methylation in the CpG sites of the promoter of the Ifng gene was observed in effector/memory, but not naïve, CD4 + T cells over time. Also unique to the Ifng promoter was an increase in methylation variance in effector/memory compared to naïve CD4 + T cells. Taken together, the CpG sites of the Ifng promoter in effector/memory CD4 + T cells were especially sensitive to the effects of TCE exposure, which may help explain the regulatory effect of the chemical on this gene. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  14. Targets of DNA-binding proteins in bacterial promoter regions present enhanced probabilities for spontaneous thermal openings

    Apostolaki, Angeliki; Kalosakas, George

    2011-01-01

    We mapped promoter regions of double-stranded DNA with respect to the probabilities of appearance of relatively large bubble openings exclusively due to thermal fluctuations at physiological temperatures. We analyzed five well-studied promoter regions of procaryotic type and found a spatial correlation between the binding sites of transcription factors and the position of peaks in the probability pattern of large thermal openings. Other distinct peaks of the calculated patterns correlate with potential binding sites of DNA-binding proteins. These results suggest that a DNA molecule would more frequently expose the bases that participate in contacts with proteins, which would probably enhance the probability of the latter to reach their targets. It also stands for using this method as a means to analyze DNA sequences based on their intrinsic thermal properties

  15. Popping the cork: mechanisms of phage genome ejection

    Molineux, I.J.; Panja, D.

    2013-01-01

    Sixty years after Hershey and Chase showed that nucleic acid is the major component of phage particles that is ejected into cells, we still do not fully understand how the process occurs. Advances in electron microscopy have revealed the structure of the condensed DNA confined in a phage capsid, and

  16. Construction of recombinant adenovirus with Egr-1 promoter and Smad7 cDNA and study of the Egr-1 promoter's biological activity

    Cai Xuwei; Fu Xiaolong; Yang Jian; Song Houyan

    2005-01-01

    Objective: To construct a recombinant replication-defective adenovirus containing Egr-1 promoter and Smad7 cDNA, then to evaluate the biological activity of Egr-1 promoter. Methods: Based on Adeno- X TM expression system, CMV promoter of the pShuttle vector was replaced by Egr-1 promoter, and the Smad7 cDNA was subcloned into the MCS(multiple cloning site) of pShuttle. The recombinant pShuttle was then sub-cloned into the Adeno-X TM genome, which was transformed into E. coli to get recombinant Adeno-X TM plasmid DNA. The recombinant adenovirus was packaged and amplified in the transfected HEK293 cells before it was purified and tested for viral titer. The fibroblasts (3T6 cells) infected by the recombinant adenovirus were irradiated , and the activity of Egr-1 promoter was quantitively determined by the amount of Smad7 protein expressed in the 3T6 cells using Western blot. Results: Identified by restriction endonuclease analysis and PCR, the recombinant adenovirus containing Egr-1 promoter and Smad7 cDNA was constructed successfully, with a viral titer of 1.0 x 10 11 TCID 50 /ml. The expressed amount of Smad7 protein varied at different dose levels and different time points post-irradiation in the 3T6 cells infected with the recombinant adenovirus. The amount of Smad7 protein increased along with the rising of the irradiation dose, and remained at a high expression level from 8 Gy to 15 Gy. The amount of Smad7 protein started to increase at 2 hours post-irradiation, and maintained a relatively high level for the next 5 hours before it descended, which was not observed in the control 3T6 cells. Conclusions: With the aid of Adeno-X TM expression system and molecular cloning techniques, construction of recombinant adenovirus could be quick and efficient. The recombined Egr-1 promoter has the activity of regulating the expression of downstream Smad7 cDNA. The increase in Smad7 expression under control of Egr-1 promoter induced by ionizing radiation is time- and dose

  17. Hda Monomerization by ADP Binding Promotes Replicase Clamp-mediated DnaA-ATP Hydrolysis*S⃞

    Su'etsugu, Masayuki; Nakamura, Kenta; Keyamura, Kenji; Kudo, Yuka; Katayama, Tsutomu

    2008-01-01

    ATP-DnaA is the initiator of chromosomal replication in Escherichia coli, and the activity of DnaA is regulated by the regulatory inactivation of the DnaA (RIDA) system. In this system, the Hda protein promotes DnaA-ATP hydrolysis to produce inactive ADP-DnaA in a mechanism that is mediated by the DNA-loaded form of the replicase sliding clamp. In this study, we first revealed that hda translation uses an unusual initiation codon, CUG, located downstream of the annotated initiation codon. The CUG initiation codon could be used for restricting the Hda level, as this initiation codon has a low translation efficiency, and the cellular Hda level is only ∼100 molecules per cell. Hda translated using the correct reading frame was purified and found to have a high RIDA activity in vitro. Moreover, we found that Hda has a high affinity for ADP but not for other nucleotides, including ATP. ADP-Hda was active in the RIDA system in vitro and stable in a monomeric state, whereas apo-Hda formed inactive homomultimers. Both ADP-Hda and apo-Hda could form complexes with the DNA-loaded clamp; however, only ADP-Hda-DNA-clamp complexes were highly functional in the following interaction with DnaA. Formation of ADP-Hda was also observed in vivo, and mutant analysis suggested that ADP binding is crucial for cellular Hda activity. Thus, we propose that ADP is a crucial Hda ligand that promotes the activated conformation of the protein. ADP-dependent monomerization might enable the arginine finger of the Hda AAA+ domain to be accessible to ATP bound to the DnaA AAA+ domain. PMID:18977760

  18. Expression and promoter DNA methylation of MLH1 in colorectal cancer and lung cancer.

    Ma, Yunxia; Chen, Yuan; Petersen, Iver

    2017-04-01

    Aberrant DNA methylation is a common molecular feature in human cancer. The aims of this study were to analyze the methylation status of MLH1, one of the DNA mismatch repair (MMR) genes, in human colorectal and lung cancer and to evaluate its clinical relevance. The expression of MLH1 was analyzed in 8 colorectal cancer (CRC) and 8 lung cancer cell lines by real-time RT-PCR and western blotting. The MLH1 protein expression was evaluated by immunohistochemistry on tissue microarrays including 121 primary CRC and 90 lung cancer patient samples. In cancer cell lines, the methylation status of MLH1 promoter and exon 2 was investigated by bisulfite sequencing (BS). Methylation-specific-PCR (MSP) was used to evaluate methylation status of MLH1. The expression of MLH1 mRNA was detected in 8 CRC cell lines as well as normal colonic fibroblast cells CCD-33Co. At protein levels, MLH1 was lost in one CRC cell line HCT-116 and normal cells CCD-33Co. No methylation was found in the promoter and exon 2 of MLH1 in CRC cell lines. MLH1 was expressed in 8 lung cancer cell lines at both mRNA and protein levels. Compared to cancer cells, normal bronchial epithelial cells (HBEC) had lower expression of MLH1 protein. In primary CRC, 54.5% of cases exhibited positive staining, while 47.8% of lung tumors were positive for MLH1 protein. MSP analysis showed that 58 out of 92 (63.0%) CRC and 41 out of 73 (56.2%) lung cancer exhibited MLH1 methylation. In CRC, the MLH1 methylation was significantly associated with tumor invasion in veins (P=0.012). However, no significant links were found between MLH1 expression and promoter methylation in both tumor entities. MLH1 methylation is a frequent molecular event in CRC and lung cancer patients. In CRC, methylation of MLH1 could be linked to vascular invasiveness. Copyright © 2017 Elsevier GmbH. All rights reserved.

  19. Overexpression of DNA damage-induced 45 α gene contributes to esophageal squamous cell cancer by promoter hypomethylation

    Wang Bao xiang

    2012-02-01

    Full Text Available Abstract Background Environmental factors-induced dysfunction of esophageal squamous epithelium, including genomic DNA impairment and apoptosis, play an important role in the pathogenesis of esophageal squamous cell cancer. DNA damage-induced 45α (GADD45α has been found promoting DNA repair and removing methylation marker, Therefore, in this study we will investigate whether GADD45α expression is induced and its mechanism in esophageal squamous cell cancer. Methods Two human esophageal squamous cell lines (ESCC, ECA109 and KYSE510 were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS. Lipofectamine 2000 was used to transfect cells. mRNA level of GADD45α was measured by reverse transcription-quantitive PCR (RT-qPCR, protein level of GADD45α was detected by western blot and Immunohistochemistry. Global DNA methylation of tissue sample was measured using the Methylamp Global DNA Methylation Quantification Ultra kit (Epigentek Group and promoter methylation was measured by bisulfite sequencing. Results GADD45a mRNA and protein levels were increased significantly in tumor tissue than that in adjacent normal tissue. Hypomethylation of global genomic DNA and GADD45α promoter were found in ESCC. The cell sensitivity to Cisplatin DDP was decreased significantly in Eca109 and Kyse510 cells, in which GADD45α expression was down-regulated by RNA interference (RNAi. In addition, silence of GADD45a expression in ESCC cells inhibited proliferation and promoted apoptosis. Conclusion Overexpression of GADD45α gene is due to DNA hypomethylation in ESCC. GADD45α may be a protective factor in DDP chemotherapy for esophageal squamous cell carcinoma.

  20. Stimulation of ribosomal RNA gene promoter by transcription factor Sp1 involves active DNA demethylation by Gadd45-NER pathway.

    Rajput, Pallavi; Pandey, Vijaya; Kumar, Vijay

    2016-08-01

    The well-studied Pol II transcription factor Sp1 has not been investigated for its regulatory role in rDNA transcription. Here, we show that Sp1 bound to specific sites on rDNA and localized into the nucleoli during the G1 phase of cell cycle to activate rDNA transcription. It facilitated the recruitment of Pol I pre-initiation complex and impeded the binding of nucleolar remodeling complex (NoRC) to rDNA resulting in the formation of euchromatin active state. More importantly, Sp1 also orchestrated the site-specific binding of Gadd45a-nucleotide excision repair (NER) complex resulting in active demethylation and transcriptional activation of rDNA. Interestingly, knockdown of Sp1 impaired rDNA transcription due to reduced engagement of the Gadd45a-NER complex and hypermethylation of rDNA. Thus, the present study unveils a novel role of Sp1 in rDNA transcription involving promoter demethylation. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Lyn tyrosine kinase promotes silencing of ATM-dependent checkpoint signaling during recovery from DNA double-strand breaks

    Fukumoto, Yasunori; Kuki, Kazumasa; Morii, Mariko; Miura, Takahito; Honda, Takuya; Ishibashi, Kenichi; Hasegawa, Hitomi; Kubota, Sho; Ide, Yudai; Yamaguchi, Noritaka; Nakayama, Yuji; Yamaguchi, Naoto

    2014-01-01

    Highlights: • Inhibition of Src family kinases decreased γ-H2AX signal. • Inhibition of Src family increased ATM-dependent phosphorylation of Chk2 and Kap1. • shRNA-mediated knockdown of Lyn increased phosphorylation of Kap1 by ATM. • Ectopic expression of Src family kinase suppressed ATM-mediated Kap1 phosphorylation. • Src is involved in upstream signaling for inactivation of ATM signaling. - Abstract: DNA damage activates the DNA damage checkpoint and the DNA repair machinery. After initial activation of DNA damage responses, cells recover to their original states through completion of DNA repair and termination of checkpoint signaling. Currently, little is known about the process by which cells recover from the DNA damage checkpoint, a process called checkpoint recovery. Here, we show that Src family kinases promote inactivation of ataxia telangiectasia mutated (ATM)-dependent checkpoint signaling during recovery from DNA double-strand breaks. Inhibition of Src activity increased ATM-dependent phosphorylation of Chk2 and Kap1. Src inhibition increased ATM signaling both in G2 phase and during asynchronous growth. shRNA knockdown of Lyn increased ATM signaling. Src-dependent nuclear tyrosine phosphorylation suppressed ATM-mediated Kap1 phosphorylation. These results suggest that Src family kinases are involved in upstream signaling that leads to inactivation of the ATM-dependent DNA damage checkpoint

  2. Allele-Specific DNA Methylation and Its Interplay with Repressive Histone Marks at Promoter-Mutant TERT Genes

    Josh Lewis Stern

    2017-12-01

    Full Text Available A mutation in the promoter of the Telomerase Reverse Transcriptase (TERT gene is the most frequent noncoding mutation in cancer. The mutation drives unusual monoallelic expression of TERT, allowing immortalization. Here, we find that DNA methylation of the TERT CpG island (CGI is also allele-specific in multiple cancers. The expressed allele is hypomethylated, which is opposite to cancers without TERT promoter mutations. The continued presence of Polycomb repressive complex 2 (PRC2 on the inactive allele suggests that histone marks of repressed chromatin may be causally linked to high DNA methylation. Consistent with this hypothesis, TERT promoter DNA containing 5-methyl-CpG has much increased affinity for PRC2 in vitro. Thus, CpG methylation and histone marks appear to collaborate to maintain the two TERT alleles in different epigenetic states in TERT promoter mutant cancers. Finally, in several cancers, DNA methylation levels at the TERT CGI correlate with altered patient survival.

  3. Allele-Specific DNA Methylation and Its Interplay with Repressive Histone Marks at Promoter-Mutant TERT Genes.

    Stern, Josh Lewis; Paucek, Richard D; Huang, Franklin W; Ghandi, Mahmoud; Nwumeh, Ronald; Costello, James C; Cech, Thomas R

    2017-12-26

    A mutation in the promoter of the Telomerase Reverse Transcriptase (TERT) gene is the most frequent noncoding mutation in cancer. The mutation drives unusual monoallelic expression of TERT, allowing immortalization. Here, we find that DNA methylation of the TERT CpG island (CGI) is also allele-specific in multiple cancers. The expressed allele is hypomethylated, which is opposite to cancers without TERT promoter mutations. The continued presence of Polycomb repressive complex 2 (PRC2) on the inactive allele suggests that histone marks of repressed chromatin may be causally linked to high DNA methylation. Consistent with this hypothesis, TERT promoter DNA containing 5-methyl-CpG has much increased affinity for PRC2 in vitro. Thus, CpG methylation and histone marks appear to collaborate to maintain the two TERT alleles in different epigenetic states in TERT promoter mutant cancers. Finally, in several cancers, DNA methylation levels at the TERT CGI correlate with altered patient survival. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  4. Exploring DNA methylation changes in promoter, intragenic, and intergenic regions as early and late events in breast cancer formation

    Rauscher, Garth H.; Kresovich, Jacob K.; Poulin, Matthew; Yan, Liying; Macias, Virgilia; Mahmoud, Abeer M.; Al-Alem, Umaima; Kajdacsy-Balla, Andre; Wiley, Elizabeth L.; Tonetti, Debra; Ehrlich, Melanie

    2015-01-01

    Breast cancer formation is associated with frequent changes in DNA methylation but the extent of very early alterations in DNA methylation and the biological significance of cancer-associated epigenetic changes need further elucidation. Pyrosequencing was done on bisulfite-treated DNA from formalin-fixed, paraffin-embedded sections containing invasive tumor and paired samples of histologically normal tissue adjacent to the cancers as well as control reduction mammoplasty samples from unaffected women. The DNA regions studied were promoters (BRCA1, CD44, ESR1, GSTM2, GSTP1, MAGEA1, MSI1, NFE2L3, RASSF1A, RUNX3, SIX3 and TFF1), far-upstream regions (EN1, PAX3, PITX2, and SGK1), introns (APC, EGFR, LHX2, RFX1 and SOX9) and the LINE-1 and satellite 2 DNA repeats. These choices were based upon previous literature or publicly available DNA methylome profiles. The percent methylation was averaged across neighboring CpG sites. Most of the assayed gene regions displayed hypermethylation in cancer vs. adjacent tissue but the TFF1 and MAGEA1 regions were significantly hypomethylated (p ≤0.001). Importantly, six of the 16 regions examined in a large collection of patients (105 – 129) and in 15-18 reduction mammoplasty samples were already aberrantly methylated in adjacent, histologically normal tissue vs. non-cancerous mammoplasty samples (p ≤0.01). In addition, examination of transcriptome and DNA methylation databases indicated that methylation at three non-promoter regions (far-upstream EN1 and PITX2 and intronic LHX2) was associated with higher gene expression, unlike the inverse associations between cancer DNA hypermethylation and cancer-altered gene expression usually reported. These three non-promoter regions also exhibited normal tissue-specific hypermethylation positively associated with differentiation-related gene expression (in muscle progenitor cells vs. many other types of normal cells). The importance of considering the exact DNA region analyzed and the

  5. DNA Mismatch Repair Deficiency Promotes Genomic Instability in a Subset of Papillary Thyroid Cancers.

    Javid, Mahsa; Sasanakietkul, Thanyawat; Nicolson, Norman G; Gibson, Courtney E; Callender, Glenda G; Korah, Reju; Carling, Tobias

    2018-02-01

    Efficient DNA damage repair by MutL-homolog DNA mismatch repair (MMR) enzymes, MLH1, MLH3, PMS1 and PMS2, are required to maintain thyrocyte genomic integrity. We hypothesized that persistent oxidative stress and consequent transcriptional dysregulation observed in thyroid follicles will lead to MMR deficiency and potentiate papillary thyroid tumorigenesis. MMR gene expression was analyzed by targeted microarray in 18 papillary thyroid cancer (PTC), 9 paracarcinoma normal thyroid (PCNT) and 10 normal thyroid (NT) samples. The findings were validated by qRT-PCR, and in follicular thyroid cancers (FTC) and follicular thyroid adenomas (FTA) for comparison. FOXO transcription factor expression was also analyzed. Protein expression was assessed by immunohistochemistry. Genomic integrity was evaluated by whole-exome sequencing-derived read-depth analysis and Mann-Whitney U test. Clinical correlations were assessed using Fisher's exact and t tests. Microarray and qRT-PCR revealed reduced expression of all four MMR genes in PTC compared with PCNT and of PMS2 compared with NT. FTC and FTA showed upregulation in MLH1, MLH3 and PMS2. PMS2 protein expression correlated with the mRNA expression pattern. FOXO1 showed lower expression in PMS2-deficient PTCs (log2-fold change -1.72 vs. -0.55, U = 11, p clinical characteristics. MMR deficiency, potentially promoted by FOXO1 suppression, may explain the etiology for PTC development in some patients. FTC and FTA retain MMR activity and are likely caused by a different tumorigenic pathway.

  6. Identification of a cryptic prokaryotic promoter within the cDNA encoding the 5' end of dengue virus RNA genome.

    Dongsheng Li

    Full Text Available Infectious cDNA clones of RNA viruses are important research tools, but flavivirus cDNA clones have proven difficult to assemble and propagate in bacteria. This has been attributed to genetic instability and/or host cell toxicity, however the mechanism leading to these difficulties has not been fully elucidated. Here we identify and characterize an efficient cryptic bacterial promoter in the cDNA encoding the dengue virus (DENV 5' UTR. Following cryptic transcription in E. coli, protein expression initiated at a conserved in-frame AUG that is downstream from the authentic DENV initiation codon, yielding a DENV polyprotein fragment that was truncated at the N-terminus. A more complete understanding of constitutive viral protein expression in E. coli might help explain the cloning and propagation difficulties generally observed with flavivirus cDNA.

  7. Photon-induced cell migration and integrin expression promoted by DNA integration of HPV16 genome

    Rieken, Stefan; Simon, Florian; Habermehl, Daniel; Dittmar, Jan Oliver; Combs, Stephanie E.; Weber, Klaus; Debus, Juergen; Lindel, Katja

    2014-01-01

    Persistent human papilloma virus 16 (HPV16) infections are a major cause of cervical cancer. The integration of the viral DNA into the host genome causes E2 gene disruption which prevents apoptosis and increases host cell motility. In cervical cancer patients, survival is limited by local infiltration and systemic dissemination. Surgical control rates are poor in cases of parametrial infiltration. In these patients, radiotherapy (RT) is administered to enhance local control. However, photon irradiation itself has been reported to increase cell motility. In cases of E2-disrupted cervical cancers, this phenomenon would impose an additional risk of enhanced tumor cell motility. Here, we analyze mechanisms underlying photon-increased migration in keratinocytes with differential E2 gene status. Isogenic W12 (intact E2 gene status) and S12 (disrupted E2 gene status) keratinocytes were analyzed in fibronectin-based and serum-stimulated migration experiments following single photon doses of 0, 2, and 10 Gy. Quantitative FACS analyses of integrin expression were performed. Migration and adhesion are increased in E2 gene-disrupted keratinocytes. E2 gene disruption promotes attractability by serum components, therefore, effectuating the risk of local infiltration and systemic dissemination. In S12 cells, migration is further increased by photon RT which leads to enhanced expression of fibronectin receptor integrins. HPV16-associated E2 gene disruption is a main predictor of treatment-refractory cancer virulence. E2 gene disruption promotes cell motility. Following photon RT, E2-disrupted tumors bear the risk of integrin-related infiltration and dissemination. (orig.) [de

  8. Coronal Mass Ejections An Introduction

    Howard, Timothy

    2011-01-01

    In times of growing technological sophistication and of our dependence on electronic technology, we are all affected by space weather. In its most extreme form, space weather can disrupt communications, damage and destroy spacecraft and power stations, and increase radiation exposure to astronauts and airline passengers. Major space weather events, called geomagnetic storms, are large disruptions in the Earth’s magnetic field brought about by the arrival of enormous magnetized plasma clouds from the Sun. Coronal mass ejections (CMEs) contain billions of tons of plasma and hurtle through space at speeds of several million miles per hour. Understanding coronal mass ejections and their impact on the Earth is of great interest to both the scientific and technological communities. This book provides an introduction to coronal mass ejections, including a history of their observation and scientific revelations, instruments and theory behind their detection and measurement, and the status quo of theories describing...

  9. DNA topoisomerase 1α promotes transcriptional silencing of transposable elements through DNA methylation and histone lysine 9 dimethylation in Arabidopsis.

    Thanh Theresa Dinh

    2014-07-01

    Full Text Available RNA-directed DNA methylation (RdDM and histone H3 lysine 9 dimethylation (H3K9me2 are related transcriptional silencing mechanisms that target transposable elements (TEs and repeats to maintain genome stability in plants. RdDM is mediated by small and long noncoding RNAs produced by the plant-specific RNA polymerases Pol IV and Pol V, respectively. Through a chemical genetics screen with a luciferase-based DNA methylation reporter, LUCL, we found that camptothecin, a compound with anti-cancer properties that targets DNA topoisomerase 1α (TOP1α was able to de-repress LUCL by reducing its DNA methylation and H3K9me2 levels. Further studies with Arabidopsis top1α mutants showed that TOP1α silences endogenous RdDM loci by facilitating the production of Pol V-dependent long non-coding RNAs, AGONAUTE4 recruitment and H3K9me2 deposition at TEs and repeats. This study assigned a new role in epigenetic silencing to an enzyme that affects DNA topology.

  10. Prognostic Significance of Promoter DNA Hypermethylation of cysteine dioxygenase 1 (CDO1 Gene in Primary Breast Cancer.

    Naoko Minatani

    Full Text Available Using pharmacological unmasking microarray, we identified promoter DNA methylation of cysteine dioxygenase 1 (CDO1 gene in human cancer. In this study, we assessed the clinicopathological significance of CDO1 methylation in primary breast cancer (BC with no prior chemotherapy. The CDO1 DNA methylation was quantified by TaqMan methylation specific PCR (Q-MSP in 7 BC cell lines and 172 primary BC patients with no prior chemotherapy. Promoter DNA of the CDO1 gene was hypermethylated in 6 BC cell lines except SK-BR3, and CDO1 gene expression was all silenced at mRNA level in the 7 BC cell lines. Quantification of CDO1 methylation was developed using Q-MSP, and assessed in primary BC. Among the clinicopathologic factors, CDO1 methylation level was not statistically significantly associated with any prognostic factors. The log-rank plot analysis elucidated that the higher methylation the tumors harbored, the poorer prognosis the patients exhibited. Using the median value of 58.0 as a cut-off one, disease specific survival in BC patients with CDO1 hypermethylation showed significantly poorer prognosis than those with hypomethylation (p = 0.004. Multivariate Cox proportional hazards model identified that CDO1 hypermethylation was prognostic factor as well as Ki-67 and hormone receptor status. The most intriguingly, CDO1 hypermethylation was of robust prognostic relevance in triple negative BC (p = 0.007. Promoter DNA methylation of CDO1 gene was robust prognostic indicator in primary BC patients with no prior chemotherapy. Prognostic relevance of the CDO1 promoter DNA methylation is worthy of being paid attention in triple negative BC cancer.

  11. 5-azacytidine promotes microspore embryogenesis initiation by decreasing global DNA methylation, but prevents subsequent embryo development in rapeseed and barley

    María-Teresa eSolís

    2015-06-01

    Full Text Available Microspores are reprogrammed by stress in vitro towards embryogenesis. This process is an important tool in breeding to obtain double-haploid plants. DNA methylation is a major epigenetic modification that changes in differentiation and proliferation. We have shown changes in global DNA methylation during microspore reprogramming. 5-Azacytidine (AzaC cannot be methylated and leads to DNA hypomethylation. AzaC is a useful demethylating agent to study DNA dynamics, with a potential application in microspore embryogenesis. This work analyzes the effects of short and long AzaC treatments on microspore embryogenesis initiation and progression in two species, the dicot Brassica napus and the monocot Hordeum vulgare. This involved the quantitative analyses of proembryo and embryo production, the quantification of DNA methylation, 5mdC immunofluorescence and confocal microscopy, and the analysis of chromatin organization (condensation/ decondensation by light and electron microscopy. Four days of AzaC treatments (2.5 µM increased embryo induction, response associated with a decrease of DNA methylation, modified 5mdC and heterochromatin patterns compared to untreated embryos. By contrast, longer AzaC treatments diminished embryo production. Similar effects were found in both species, indicating that DNA demethylation promotes microspore reprogramming, totipotency acquisition and embryogenesis initiation, while embryo differentiation requires de novo DNA methylation and is prevented by AzaC. This suggests a role for DNA methylation in the repression of microspore reprogramming and possibly totipotency acquisition.Results provide new insights into the role of epigenetic modifications in microspore embryogenesis and suggest a potential benefit of inhibitors, such as AzaC, to improve the process efficiency in biotechnology and breeding programs.

  12. The DnaK Chaperone Uses Different Mechanisms To Promote and Inhibit Replication of Vibrio cholerae Chromosome 2

    Jyoti K. Jha

    2017-04-01

    Full Text Available Replication of Vibrio cholerae chromosome 2 (Chr2 depends on molecular chaperone DnaK to facilitate binding of the initiator (RctB to the replication origin. The binding occurs at two kinds of site, 12-mers and 39-mers, which promote and inhibit replication, respectively. Here we show that DnaK employs different mechanisms to enhance the two kinds of binding. We found that mutations in rctB that reduce DnaK binding also reduce 12-mer binding and initiation. The initiation defect is suppressed by second-site mutations that increase 12-mer binding only marginally. Instead, they reduce replication inhibitory mechanisms: RctB dimerization and 39-mer binding. One suppressing change was in a dimerization domain which is folded similarly to the initiator of an iteron plasmid—the presumed progenitor of Chr2. In plasmids, DnaK promotes initiation by reducing dimerization. A different mutation was in the 39-mer binding domain of RctB and inactivated it, indicating an alternative suppression mechanism. Paradoxically, although DnaK increases 39-mer binding, the increase was also achieved by inactivating the DnaK binding site of RctB. This result suggests that the site inhibits the 39-mer binding domain (via autoinhibition when prevented from binding DnaK. Taken together, our results reveal an important feature of the transition from plasmid to chromosome: the Chr2 initiator retains the plasmid-like dimerization domain and its control by chaperones but uses the chaperones in an unprecedented way to control the inhibitory 39-mer binding.

  13. Translesion synthesis DNA polymerases promote error-free replication through the minor-groove DNA adduct 3-deaza-3-methyladenine.

    Yoon, Jung-Hoon; Roy Choudhury, Jayati; Park, Jeseong; Prakash, Satya; Prakash, Louise

    2017-11-10

    N3-Methyladenine (3-MeA) is formed in DNA by reaction with S -adenosylmethionine, the reactive methyl donor, and by reaction with alkylating agents. 3-MeA protrudes into the DNA minor groove and strongly blocks synthesis by replicative DNA polymerases (Pols). However, the mechanisms for replicating through this lesion in human cells remain unidentified. Here we analyzed the roles of translesion synthesis (TLS) Pols in the replication of 3-MeA-damaged DNA in human cells. Because 3-MeA has a short half-life in vitro , we used the stable 3-deaza analog, 3-deaza-3-methyladenine (3-dMeA), which blocks the DNA minor groove similarly to 3-MeA. We found that replication through the 3-dMeA adduct is mediated via three different pathways, dependent upon Polι/Polκ, Polθ, and Polζ. As inferred from biochemical studies, in the Polι/Polκ pathway, Polι inserts a nucleotide (nt) opposite 3-dMeA and Polκ extends synthesis from the inserted nt. In the Polθ pathway, Polθ carries out both the insertion and extension steps of TLS opposite 3-dMeA, and in the Polζ pathway, Polζ extends synthesis following nt insertion by an as yet unidentified Pol. Steady-state kinetic analyses indicated that Polι and Polθ insert the correct nt T opposite 3-dMeA with a much reduced catalytic efficiency and that both Pols exhibit a high propensity for inserting a wrong nt opposite this adduct. However, despite their low fidelity of synthesis opposite 3-dMeA, TLS opposite this lesion replicates DNA in a highly error-free manner in human cells. We discuss the implications of these observations for TLS mechanisms in human cells. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. RNA-processing proteins regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA.

    Manfrini, Nicola; Trovesi, Camilla; Wery, Maxime; Martina, Marina; Cesena, Daniele; Descrimes, Marc; Morillon, Antonin; d'Adda di Fagagna, Fabrizio; Longhese, Maria Pia

    2015-02-01

    Eukaryotic cells respond to DNA double-strand breaks (DSBs) by activating a checkpoint that depends on the protein kinases Tel1/ATM and Mec1/ATR. Mec1/ATR is activated by RPA-coated single-stranded DNA (ssDNA), which arises upon nucleolytic degradation (resection) of the DSB. Emerging evidences indicate that RNA-processing factors play critical, yet poorly understood, roles in genomic stability. Here, we provide evidence that the Saccharomyces cerevisiae RNA decay factors Xrn1, Rrp6 and Trf4 regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA. The lack of Xrn1 inhibits ssDNA generation at the DSB by preventing the loading of the MRX complex. By contrast, DSB resection is not affected in the absence of Rrp6 or Trf4, but their lack impairs the recruitment of RPA, and therefore of Mec1, to the DSB. Rrp6 and Trf4 inactivation affects neither Rad51/Rad52 association nor DSB repair by homologous recombination (HR), suggesting that full Mec1 activation requires higher amount of RPA-coated ssDNA than HR-mediated repair. Noteworthy, deep transcriptome analyses do not identify common misregulated gene expression that could explain the observed phenotypes. Our results provide a novel link between RNA processing and genome stability. © 2014 The Authors.

  15. StpA and Hha stimulate pausing by RNA polymerase by promoting DNA-DNA bridging of H-NS filaments.

    Boudreau, Beth A; Hron, Daniel R; Qin, Liang; van der Valk, Ramon A; Kotlajich, Matthew V; Dame, Remus T; Landick, Robert

    2018-06-20

    In enterobacteria, AT-rich horizontally acquired genes, including virulence genes, are silenced through the actions of at least three nucleoid-associated proteins (NAPs): H-NS, StpA and Hha. These proteins form gene-silencing nucleoprotein filaments through direct DNA binding by H-NS and StpA homodimers or heterodimers. Both linear and bridged filaments, in which NAPs bind one or two DNA segments, respectively, have been observed. Hha can interact with H-NS or StpA filaments, but itself lacks a DNA-binding domain. Filaments composed of H-NS alone can inhibit transcription initiation and, in the bridged conformation, slow elongating RNA polymerase (RNAP) by promoting backtracking at pause sites. How the other NAPs modulate these effects of H-NS is unknown, despite evidence that they help regulate subsets of silenced genes in vivo (e.g. in pathogenicity islands). Here we report that Hha and StpA greatly enhance H-NS-stimulated pausing by RNAP at 20°C. StpA:H-NS or StpA-only filaments also stimulate pausing at 37°C, a temperature at which Hha:H-NS or H-NS-only filaments have much less effect. In addition, we report that both Hha and StpA greatly stimulate DNA-DNA bridging by H-NS filaments. Together, these observations indicate that Hha and StpA can affect H-NS-mediated gene regulation by stimulating bridging of H-NS/DNA filaments.

  16. Ca2+ promoted the low transformation efficiency of plasmid DNA exposed to PAH contaminants.

    Fuxing Kang

    Full Text Available The effects of interactions between genetic materials and polycyclic aromatic hydrocarbons (PAHs on gene expression in the extracellular environment remain to be elucidated and little information is currently available on the effect of ionic strength on the transformation of plasmid DNA exposed to PAHs. Phenanthrene and pyrene were used as representative PAHs to evaluate the transformation of plasmid DNA after PAH exposure and to determine the role of Ca(2+ during the transformation. Plasmid DNA exposed to the test PAHs demonstrated low transformation efficiency. In the absence of PAHs, the transformation efficiency was 4.7 log units; however, the efficiency decreased to 3.72-3.14 log units with phenanthrene/pyrene exposures of 50 µg · L(-1. The addition of Ca(2+ enhanced the low transformation efficiency of DNA exposed to PAHs. Based on the co-sorption of Ca(2+ and phenanthrene/pyrene by DNA, we employed Fourier-transform infrared spectroscopy (FTIR, X-ray photoelectron spectroscopy (XPS, and mass spectrometry (MS to determine the mechanisms involved in PAH-induced DNA transformation. The observed low transformation efficiency of DNA exposed to either phenanthrene or pyrene can be attributed to a broken hydrogen bond in the double helix caused by planar PAHs. Added Ca(2+ formed strong electrovalent bonds with "-POO(--" groups in the DNA, weakening the interaction between PAHs and DNA based on weak molecular forces. This decreased the damage of PAHs to hydrogen bonds in double-stranded DNA by isolating DNA molecules from PAHs and consequently enhanced the transformation efficiency of DNA exposed to PAH contaminants. The findings provide insight into the effects of anthropogenic trace PAHs on DNA transfer in natural environments.

  17. DNA Methyltransferase 3B Gene Promoter and Interleukin-1 Receptor Antagonist Polymorphisms in Childhood Immune Thrombocytopenia

    Margarita Pesmatzoglou

    2012-01-01

    Full Text Available Primary immune thrombocytopenia (ITP is one of the most common blood diseases as well as the commonest acquired bleeding disorder in childhood. Although the etiology of ITP is unclear, in the pathogenesis of the disease, both environmental and genetic factors including polymorphisms of TNF-a, IL-10, and IL-4 genes have been suggested to be involved. In this study, we investigated the rs2424913 single-nucleotide polymorphism (SNP (C46359T in DNA methyltransferase 3B (DNMT3B gene promoter and the VNTR polymorphism of IL-1 receptor antagonist (IL-1 Ra intron-2 in 32 children (17 boys with the diagnosis of ITP and 64 healthy individuals. No significant differences were found in the genotype distribution of DNMT3B polymorphism between the children with ITP and the control group, whereas the frequency of allele T appeared significantly increased in children with ITP (P = 0.03, OR = 2, 95% CI: 1.06–3.94. In case of IL-1 Ra polymorphism, children with ITP had a significantly higher frequency of genotype I/II, compared to control group (P = 0.043, OR = 2.60, 95% CI: 1.02–6.50. Moreover, genotype I/I as well as allele I was overrepresented in the control group, suggesting that allele I may have a decreased risk for development of ITP. Our findings suggest that rs2424913 DNMT3B SNP as well as IL-1 Ra VNTR polymorphism may contribute to the susceptibility to ITP.

  18. Putative DNA G-quadruplex formation within the promoters of Plasmodium falciparum var genes

    Rowe J

    2009-08-01

    Full Text Available Abstract Background Guanine-rich nucleic acid sequences are capable of folding into an intramolecular four-stranded structure called a G-quadruplex. When found in gene promoter regions, G-quadruplexes can downregulate gene expression, possibly by blocking the transcriptional machinery. Here we have used a genome-wide bioinformatic approach to identify Putative G-Quadruplex Sequences (PQS in the Plasmodium falciparum genome, along with biophysical techniques to examine the physiological stability of P. falciparum PQS in vitro. Results We identified 63 PQS in the non-telomeric regions of the P. falciparum clone 3D7. Interestingly, 16 of these PQS occurred in the upstream region of a subset of the P. falciparum var genes (group B var genes. The var gene family encodes PfEMP1, the parasite's major variant antigen and adhesin expressed at the surface of infected erythrocytes, that plays a key role in malaria pathogenesis and immune evasion. The ability of the PQS found in the upstream regions of group B var genes (UpsB-Q to form stable G-quadruplex structures in vitro was confirmed using 1H NMR, circular dichroism, UV spectroscopy, and thermal denaturation experiments. Moreover, the synthetic compound BOQ1 that shows a higher affinity for DNA forming quadruplex rather than duplex structures was found to bind with high affinity to the UpsB-Q. Conclusion This is the first demonstration of non-telomeric PQS in the genome of P. falciparum that form stable G-quadruplexes under physiological conditions in vitro. These results allow the generation of a novel hypothesis that the G-quadruplex sequences in the upstream regions of var genes have the potential to play a role in the transcriptional control of this major virulence-associated multi-gene family.

  19. Examining a DNA Replication Requirement for Bacteriophage λ Red- and Rac Prophage RecET-Promoted Recombination in Escherichia coli.

    Thomason, Lynn C; Costantino, Nina; Court, Donald L

    2016-09-13

    -strand regions may be created during DNA replication or by single-strand exonuclease digestion of linear duplex DNA. Previously, in vitro studies reported that these recombinases promote the single-strand annealing of two complementary DNAs and also strand invasion of a single DNA strand into duplex DNA to create a three-stranded region. Here, in vivo experiments show that recombinase-mediated annealing of complementary single-stranded DNA is the predominant recombination pathway in E. coli. Copyright © 2016 Thomason et al.

  20. Doxorubicin hinders DNA condensation promoted by the protein bovine serum albumin (BSA).

    Lima, C H M; de Paula, H M C; da Silva, L H M; Rocha, M S

    2017-12-01

    In this work, we have studied the interaction between the anticancer drug doxorubicin (doxo) and condensed DNA, using optical tweezers. To perform this task, we use the protein bovine serum albumin (BSA) in the working buffer to mimic two key conditions present in the real intracellular environment: the condensed state of the DNA and the abundant presence of charged macromolecules in the surrounding medium. In particular, we have found that, when doxo is previously intercalated in disperse DNA, the drug hinders the DNA condensation process upon the addition of BSA in the buffer. On the other hand, when bare DNA is firstly condensed by BSA, doxo is capable to intercalate and to unfold the DNA condensates at relatively high concentrations. In addition, a specific interaction between BSA and doxo was verified, which significantly changes the chemical equilibrium of the DNA-doxo interaction. Finally, the presence of BSA in the buffer stabilizes the double-helix structure of the DNA-doxo complexes, preventing partial DNA denaturation induced by the stretching forces. © 2017 Wiley Periodicals, Inc.

  1. Sirtuin 7 promotes cellular survival following genomic stress by attenuation of DNA damage, SAPK activation and p53 response

    Kiran, Shashi; Oddi, Vineesha [Laboratory of Cancer Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500001 (India); Ramakrishna, Gayatri, E-mail: gayatrirama1@gmail.com [Laboratory of Cancer Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500001 (India); Laboratory of Cancer Cell Biology, Department of Research, Institute of Liver and Biliary Sciences, Delhi 110070 (India)

    2015-02-01

    Maintaining the genomic integrity is a constant challenge in proliferating cells. Amongst various proteins involved in this process, Sirtuins play a key role in DNA damage repair mechanisms in yeast as well as mammals. In the present work we report the role of one of the least explored Sirtuin viz., SIRT7, under conditions of genomic stress when treated with doxorubicin. Knockdown of SIRT7 sensitized osteosarcoma (U2OS) cells to DNA damage induced cell death by doxorubicin. SIRT7 overexpression in NIH3T3 delayed cell cycle progression by causing delay in G1 to S transition. SIRT7 overexpressing cells when treated with low dose of doxorubicin (0.25 µM) showed delayed onset of senescence, lesser accumulation of DNA damage marker γH2AX and lowered levels of growth arrest markers viz., p53 and p21 when compared to doxorubicin treated control GFP expressing cells. Resistance to DNA damage following SIRT7 overexpression was also evident by EdU incorporation studies where cellular growth arrest was significantly delayed. When treated with higher dose of doxorubicin (>1 µM), SIRT7 conferred resistance to apoptosis by attenuating stress activated kinases (SAPK viz., p38 and JNK) and p53 response thereby shifting the cellular fate towards senescence. Interestingly, relocalization of SIRT7 from nucleolus to nucleoplasm together with its co-localization with SAPK was an important feature associated with DNA damage. SIRT7 mediated resistance to doxorubicin induced apoptosis and senescence was lost when p53 level was restored by nutlin treatment. Overall, we propose SIRT7 attenuates DNA damage, SAPK activation and p53 response thereby promoting cellular survival under conditions of genomic stress. - Highlights: • Knockdown of SIRT7 sensitized cells to DNA damage induced apoptosis. • SIRT7 delayed onset of premature senescence by attenuating DNA damage response. • Overexpression of SIRT7 delayed cell cycle progression by delaying G1/S transition. • Upon DNA damage SIRT

  2. DNA methylation of specific CpG sites in the promoter region regulates the transcription of the mouse oxytocin receptor.

    Shimrat Mamrut

    Full Text Available Oxytocin is a peptide hormone, well known for its role in labor and suckling, and most recently for its involvement in mammalian social behavior. All central and peripheral actions of oxytocin are mediated through the oxytocin receptor, which is the product of a single gene. Transcription of the oxytocin receptor is subject to regulation by gonadal steroid hormones, and is profoundly elevated in the uterus and mammary glands during parturition. DNA methylation is a major epigenetic mechanism that regulates gene transcription, and has been linked to reduced expression of the oxytocin receptor in individuals with autism. Here, we hypothesized that transcription of the mouse oxytocin receptor is regulated by DNA methylation of specific sites in its promoter, in a tissue-specific manner. Hypothalamus-derived GT1-7, and mammary-derived 4T1 murine cell lines displayed negative correlations between oxytocin receptor transcription and methylation of the gene promoter, and demethylation caused a significant enhancement of oxytocin receptor transcription in 4T1 cells. Using a reporter gene assay, we showed that methylation of specific sites in the gene promoter, including an estrogen response element, significantly inhibits transcription. Furthermore, methylation of the oxytocin receptor promoter was found to be differentially correlated with oxytocin receptor expression in mammary glands and the uterus of virgin and post-partum mice, suggesting that it plays a distinct role in oxytocin receptor transcription among tissues and under different physiological conditions. Together, these results support the hypothesis that the expression of the mouse oxytocin receptor gene is epigenetically regulated by DNA methylation of its promoter.

  3. Tousled-like kinases phosphorylate Asf1 to promote histone supply during DNA replication

    Klimovskaia, Ilnaz M; Young, Clifford; Strømme, Caroline B

    2014-01-01

    During DNA replication, nucleosomes are rapidly assembled on newly synthesized DNA to restore chromatin organization. Asf1, a key histone H3-H4 chaperone required for this process, is phosphorylated by Tousled-like kinases (TLKs). Here, we identify TLK phosphorylation sites by mass spectrometry...

  4. COMPOSITION OF CORONAL MASS EJECTIONS

    Zurbuchen, T. H.; Weberg, M.; Lepri, S. T. [Department of Climate and Space Sciences and Engineering, University of Michigan, Ann Arbor, MI (United States); Von Steiger, R. [International Space Science Institute, Bern (Switzerland); Mewaldt, R. A. [California Institute of Technology, Pasadena, CA (United States); Antiochos, S. K. [Heliophysics Science Division, NASA Goddard Space Flight Center, Greenbelt, MD (United States)

    2016-07-20

    We analyze the physical origin of plasmas that are ejected from the solar corona. To address this issue, we perform a comprehensive analysis of the elemental composition of interplanetary coronal mass ejections (ICMEs) using recently released elemental composition data for Fe, Mg, Si, S, C, N, Ne, and He as compared to O and H. We find that ICMEs exhibit a systematic abundance increase of elements with first ionization potential (FIP) < 10 eV, as well as a significant increase of Ne as compared to quasi-stationary solar wind. ICME plasmas have a stronger FIP effect than slow wind, which indicates either that an FIP process is active during the ICME ejection or that a different type of solar plasma is injected into ICMEs. The observed FIP fractionation is largest during times when the Fe ionic charge states are elevated above Q {sub Fe} > 12.0. For ICMEs with elevated charge states, the FIP effect is enhanced by 70% over that of the slow wind. We argue that the compositionally hot parts of ICMEs are active region loops that do not normally have access to the heliosphere through the processes that give rise to solar wind. We also discuss the implications of this result for solar energetic particles accelerated during solar eruptions and for the origin of the slow wind itself.

  5. TRAIP promotes DNA damage response during genome replication and is mutated in primordial dwarfism.

    Harley, Margaret E; Murina, Olga; Leitch, Andrea; Higgs, Martin R; Bicknell, Louise S; Yigit, Gökhan; Blackford, Andrew N; Zlatanou, Anastasia; Mackenzie, Karen J; Reddy, Kaalak; Halachev, Mihail; McGlasson, Sarah; Reijns, Martin A M; Fluteau, Adeline; Martin, Carol-Anne; Sabbioneda, Simone; Elcioglu, Nursel H; Altmüller, Janine; Thiele, Holger; Greenhalgh, Lynn; Chessa, Luciana; Maghnie, Mohamad; Salim, Mahmoud; Bober, Michael B; Nürnberg, Peter; Jackson, Stephen P; Hurles, Matthew E; Wollnik, Bernd; Stewart, Grant S; Jackson, Andrew P

    2016-01-01

    DNA lesions encountered by replicative polymerases threaten genome stability and cell cycle progression. Here we report the identification of mutations in TRAIP, encoding an E3 RING ubiquitin ligase, in patients with microcephalic primordial dwarfism. We establish that TRAIP relocalizes to sites of DNA damage, where it is required for optimal phosphorylation of H2AX and RPA2 during S-phase in response to ultraviolet (UV) irradiation, as well as fork progression through UV-induced DNA lesions. TRAIP is necessary for efficient cell cycle progression and mutations in TRAIP therefore limit cellular proliferation, providing a potential mechanism for microcephaly and dwarfism phenotypes. Human genetics thus identifies TRAIP as a component of the DNA damage response to replication-blocking DNA lesions.

  6. Identification of Fic-1 as an enzyme that inhibits bacterial DNA replication by AMPylating GyrB, promoting filament formation.

    Lu, Canhua; Nakayasu, Ernesto S; Zhang, Li-Qun; Luo, Zhao-Qing

    2016-01-26

    The morphology of bacterial cells is important for virulence, evasion of the host immune system, and coping with environmental stresses. The widely distributed Fic proteins (filamentation induced by cAMP) are annotated as proteins involved in cell division because of the presence of the HPFx[D/E]GN[G/K]R motif. We showed that the presence of Fic-1 from Pseudomonas fluorescens significantly reduced the yield of plasmid DNA when expressed in Escherichia coli or P. fluorescens. Fic-1 interacted with GyrB, a subunit of DNA gyrase, which is essential for bacterial DNA replication. Fic-1 catalyzed the AMPylation of GyrB at Tyr(109), a residue critical for binding ATP, and exhibited auto-AMPylation activity. Mutation of the Fic-1 auto-AMPylated site greatly reduced AMPylation activity toward itself and toward GyrB. Fic-1-dependent AMPylation of GyrB triggered the SOS response, indicative of DNA replication stress or DNA damage. Fic-1 also promoted the formation of elongated cells when the SOS response was blocked. We identified an α-inhibitor protein that we named anti-Fic-1 (AntF), encoded by a gene immediately upstream of Fic-1. AntF interacted with Fic-1, inhibited the AMPylation activity of Fic-1 for GyrB in vitro, and blocked Fic-1-mediated inhibition of DNA replication in bacteria, suggesting that Fic-1 and AntF comprise a toxin-antitoxin module. Our work establishes Fic-1 as an AMPylating enzyme that targets GyrB to inhibit DNA replication and may target other proteins to regulate bacterial morphology. Copyright © 2016, American Association for the Advancement of Science.

  7. Placental promoter methylation of DNA repair genes and prenatal exposure to particulate air pollution: an ENVIRONAGE cohort study

    Kristof Y Neven, MSc

    2018-04-01

    Full Text Available Summary: Background: Exposure to particulate air pollution has been linked with risk of carcinogenesis. Damage to repair pathways might have long-term adverse health effects. We aimed to investigate the association of prenatal exposure to air pollution with placental mutation rate and the DNA methylation of key placental DNA repair genes. Methods: This cohort study used data from the ongoing ENVironmental Influence ON early AGEing (ENVIRONAGE birth cohort, which enrols pairs of mothers and neonates (singleton births only at the East-Limburg Hospital (Genk, Belgium. Placental DNA samples were collected after birth. We used bisulfite-PCR-pyrosequencing to investigate the mutation rate of Alu (a marker for overall DNA mutation and DNA methylation in the promoter genes of key DNA repair and tumour suppressor genes (APEX1, OGG1, PARP1, ERCC1, ERCC4, p53, and DAPK1. We used a high-resolution air pollution model to estimate exposure to particulate matter with a diameter less than 2·5 μm (PM2·5, black carbon, and NO2 over the entire pregnancy on the basis of maternal address. Alu mutation was analysed with a linear regression model, and methylation values of the selected genes were analysed in mixed-effects models. Effect estimates are presented as the relative percentage change in methylation for an ambient air pollution increment of one IQR (ie, the difference between the first and third quartiles of exposure in the entire cohort. Findings: 500 biobanked placental DNA samples were randomly selected from 814 pairs of mothers and neonates who were recruited to the cohort between Feb 1, 2010, and Dec 31, 2014, of which 463 samples met the pyrosequencing quality control criteria. IQR exposure increments were 3·84 μg/m3 for PM2·5, 0·36 μg/m3 for black carbon, and 5·34 μg/m3 for NO2. Among these samples, increased Alu mutation rate was associated with greater exposure to PM2·5 (r=0·26, p<0·0001 and black carbon (r=0·33, p<0·0001, but not NO2

  8. Photon-induced cell migration and integrin expression promoted by DNA integration of HPV16 genome

    Rieken, Stefan; Simon, Florian; Habermehl, Daniel; Dittmar, Jan Oliver; Combs, Stephanie E.; Weber, Klaus; Debus, Juergen; Lindel, Katja [University Hospital of Heidelberg, Department of Radiation Therapy and Radiation Oncology, Heidelberg (Germany)

    2014-10-15

    Persistent human papilloma virus 16 (HPV16) infections are a major cause of cervical cancer. The integration of the viral DNA into the host genome causes E2 gene disruption which prevents apoptosis and increases host cell motility. In cervical cancer patients, survival is limited by local infiltration and systemic dissemination. Surgical control rates are poor in cases of parametrial infiltration. In these patients, radiotherapy (RT) is administered to enhance local control. However, photon irradiation itself has been reported to increase cell motility. In cases of E2-disrupted cervical cancers, this phenomenon would impose an additional risk of enhanced tumor cell motility. Here, we analyze mechanisms underlying photon-increased migration in keratinocytes with differential E2 gene status. Isogenic W12 (intact E2 gene status) and S12 (disrupted E2 gene status) keratinocytes were analyzed in fibronectin-based and serum-stimulated migration experiments following single photon doses of 0, 2, and 10 Gy. Quantitative FACS analyses of integrin expression were performed. Migration and adhesion are increased in E2 gene-disrupted keratinocytes. E2 gene disruption promotes attractability by serum components, therefore, effectuating the risk of local infiltration and systemic dissemination. In S12 cells, migration is further increased by photon RT which leads to enhanced expression of fibronectin receptor integrins. HPV16-associated E2 gene disruption is a main predictor of treatment-refractory cancer virulence. E2 gene disruption promotes cell motility. Following photon RT, E2-disrupted tumors bear the risk of integrin-related infiltration and dissemination. (orig.) [German] Persistierende Infektionen mit humanen Papillomaviren 16 (HPV16) sind ein Hauptausloeser des Zervixkarzinoms. Die Integration der viralen DNS in das Wirtszellgenom fuehrt zum Integritaetsverlust des E2-Gens, wodurch in der Wirtszelle Apoptose verhindert und Motilitaet gesteigert werden. In

  9. High fructose consumption induces DNA methylation at PPARα and CPT1A promoter regions in the rat liver

    Ohashi, Koji [Department of Clinical Biochemistry, Fujita Health University School of Health Sciences, Toyoake (Japan); Munetsuna, Eiji [Department of Biochemistry, Fujita Health University School of Medicine, Toyoake (Japan); Yamada, Hiroya, E-mail: hyamada@fujita-hu.ac.jp [Department of Hygiene, Fujita Health University School of Medicine, Toyoake (Japan); Ando, Yoshitaka [Department of Joint Research Laboratory of Clinical Medicine, Fujita Health University Hospital, Toyoake (Japan); Yamazaki, Mirai; Taromaru, Nao; Nagura, Ayuri; Ishikawa, Hiroaki [Department of Clinical Biochemistry, Fujita Health University School of Health Sciences, Toyoake (Japan); Suzuki, Koji [Department of Public Health, Fujita Health University School of Health Sciences, Toyoake (Japan); Teradaira, Ryoji [Department of Clinical Biochemistry, Fujita Health University School of Health Sciences, Toyoake (Japan); Hashimoto, Shuji [Department of Hygiene, Fujita Health University School of Medicine, Toyoake (Japan)

    2015-12-04

    DNA methylation status is affected by environmental factors, including nutrition. Fructose consumption is considered a risk factor for the conditions that make up metabolic syndrome such as dyslipidemia. However, the pathogenetic mechanism by which fructose consumption leads to metabolic syndrome is unclear. Based on observations that epigenetic modifications are closely related to induction of metabolic syndrome, we hypothesized that fructose-induced metabolic syndrome is caused by epigenetic alterations. Male SD rats were designated to receive water or 20% fructose solution for 14 weeks. mRNA levels for peroxisome proliferator-activated receptor alpha (PPARα) and carnitine palmitoyltransferase 1A (CPT1A) was analyzed using Real-time PCR. Restriction digestion and real-time PCR (qAMP) was used for the analysis of DNA methylation status. Hepatic lipid accumulation was also observed by fructose intake. Fructose feeding also significantly decreased mRNA levels for PPARα and CPT1A. qAMP analysis demonstrated the hypermethylation of promoter regions of PPARα and CTP1A genes. Fructose-mediated attenuated gene expression may be mediated by alterations of DNA methylation status, and pathogenesis of metabolic syndrome induced by fructose relates to DNA methylation status. - Highlights: • No general consensus has been reached regarding the molecular mechanisms of the pathogenesis of fructose-induced diseases. • Significant increase in hepatic total methylation level was observed after fructose-supplemented feeding. • Fructose feeding significantly decreased mRNA levels for PPARα and CPT1A. • qAMP analysis demonstrated the hypermethylation of promoter regions of PPARα and CTP1A genes. • Fructose-mediated attenuated gene expression may be mediated by alterations of DNA methylation status in rat liver.

  10. High fructose consumption induces DNA methylation at PPARα and CPT1A promoter regions in the rat liver

    Ohashi, Koji; Munetsuna, Eiji; Yamada, Hiroya; Ando, Yoshitaka; Yamazaki, Mirai; Taromaru, Nao; Nagura, Ayuri; Ishikawa, Hiroaki; Suzuki, Koji; Teradaira, Ryoji; Hashimoto, Shuji

    2015-01-01

    DNA methylation status is affected by environmental factors, including nutrition. Fructose consumption is considered a risk factor for the conditions that make up metabolic syndrome such as dyslipidemia. However, the pathogenetic mechanism by which fructose consumption leads to metabolic syndrome is unclear. Based on observations that epigenetic modifications are closely related to induction of metabolic syndrome, we hypothesized that fructose-induced metabolic syndrome is caused by epigenetic alterations. Male SD rats were designated to receive water or 20% fructose solution for 14 weeks. mRNA levels for peroxisome proliferator-activated receptor alpha (PPARα) and carnitine palmitoyltransferase 1A (CPT1A) was analyzed using Real-time PCR. Restriction digestion and real-time PCR (qAMP) was used for the analysis of DNA methylation status. Hepatic lipid accumulation was also observed by fructose intake. Fructose feeding also significantly decreased mRNA levels for PPARα and CPT1A. qAMP analysis demonstrated the hypermethylation of promoter regions of PPARα and CTP1A genes. Fructose-mediated attenuated gene expression may be mediated by alterations of DNA methylation status, and pathogenesis of metabolic syndrome induced by fructose relates to DNA methylation status. - Highlights: • No general consensus has been reached regarding the molecular mechanisms of the pathogenesis of fructose-induced diseases. • Significant increase in hepatic total methylation level was observed after fructose-supplemented feeding. • Fructose feeding significantly decreased mRNA levels for PPARα and CPT1A. • qAMP analysis demonstrated the hypermethylation of promoter regions of PPARα and CTP1A genes. • Fructose-mediated attenuated gene expression may be mediated by alterations of DNA methylation status in rat liver.

  11. Bisphenol a promotes cell survival following oxidative DNA damage in mouse fibroblasts.

    Natalie R Gassman

    Full Text Available Bisphenol A (BPA is a biologically active industrial chemical used in production of consumer products. BPA has become a target of intense public scrutiny following concerns about its association with human diseases such as obesity, diabetes, reproductive disorders, and cancer. Recent studies link BPA with the generation of reactive oxygen species, and base excision repair (BER is responsible for removing oxidatively induced DNA lesions. Yet, the relationship between BPA and BER has yet to be examined. Further, the ubiquitous nature of BPA allows continuous exposure of the human genome concurrent with the normal endogenous and exogenous insults to the genome, and this co-exposure may impact the DNA damage response and repair. To determine the effect of BPA exposure on base excision repair of oxidatively induced DNA damage, cells compromised in double-strand break repair were treated with BPA alone or co-exposed with either potassium bromate (KBrO3 or laser irradiation as oxidative damaging agents. In experiments with KBrO3, co-treatment with BPA partially reversed the KBrO3-induced cytotoxicity observed in these cells, and this was coincident with an increase in guanine base lesions in genomic DNA. The improvement in cell survival and the increase in oxidatively induced DNA base lesions were reminiscent of previous results with alkyl adenine DNA glycosylase-deficient cells, suggesting that BPA may prevent initiation of repair of oxidized base lesions. With laser irradiation-induced DNA damage, treatment with BPA suppressed DNA repair as revealed by several indicators. These results are consistent with the hypothesis that BPA can induce a suppression of oxidized base lesion DNA repair by the base excision repair pathway.

  12. Achaete-scute complex homolog-1 promotes DNA repair in the lung carcinogenesis through matrix metalloproteinase-7 and O(6-methylguanine-DNA methyltransferase.

    Xiao-Yang Wang

    Full Text Available Lung cancer is the leading cause of cancer-related deaths in the world. Achaete-scute complex homolog-1 (Ascl1 is a member of the basic helix-loop-helix (bHLH transcription factor family that has multiple functions in the normal and neoplastic lung such as the regulation of neuroendocrine differentiation, prevention of apoptosis and promotion of tumor-initiating cells. We now show that Ascl1 directly regulates matrix metalloproteinase-7 (MMP-7 and O(6-methylguanine-DNA methyltransferase (MGMT. Loss- and gain-of-function experiments in human bronchial epithelial and lung carcinoma cell lines revealed that Ascl1, MMP-7 and MGMT are able to protect cells from the tobacco-specific nitrosamine NNK-induced DNA damage and the alkylating agent cisplatin-induced apoptosis. We also examined the role of Ascl1 in NNK-induced lung tumorigenesis in vivo. Using transgenic mice which constitutively expressed human Ascl1 in airway lining cells, we found that there was a delay in lung tumorigenesis. We conclude that Ascl1 potentially enhances DNA repair through activation of MMP-7 and MGMT which may impact lung carcinogenesis and chemoresistance. The study has uncovered a novel and unexpected function of Ascl1 which will contribute to better understanding of lung carcinogenesis and the broad implications of transcription factors in tobacco-related carcinogenesis.

  13. Lamin A/C-dependent interaction with 53BP1 promotes cellular responses to DNA damage

    Gibbs-Seymour, Ian; Markiewicz, Ewa; Bekker-Jensen, Simon

    2015-01-01

    Lamins A/C have been implicated in DNA damage response pathways. We show that the DNA repair protein 53BP1 is a lamin A/C binding protein. In undamaged human dermal fibroblasts (HDF), 53BP1 is a nucleoskeleton protein. 53BP1 binds to lamins A/C via its Tudor domain, and this is abrogated by DNA...... damage. Lamins A/C regulate 53BP1 levels and consequently lamin A/C-null HDF display a 53BP1 null-like phenotype. Our data favour a model in which lamins A/C maintain a nucleoplasmic pool of 53BP1 in order to facilitate its rapid recruitment to sites of DNA damage and could explain why an absence...

  14. Analysis of in vivo binding of yeast heat shock factor to promoter DNA

    SERVER

    2008-04-17

    Apr 17, 2008 ... The baker's yeast, Saccharomyces cerevisiae, harbors only a single HSF ... ethanol. The resulting DNA was dissolved in 20 µl TE. PCR. 3% of each .... tolerance oxidant stress, and involve in other biochemical pathways.

  15. DNA-binding determinants promoting NHEJ by human Polμ.

    Martin, Maria Jose; Juarez, Raquel; Blanco, Luis

    2012-12-01

    Non-homologous end-joining (NHEJ), the preferred pathway to repair double-strand breaks (DSBs) in higher eukaryotes, relies on a collection of molecular tools to process the broken ends, including specific DNA polymerases. Among them, Polµ is unique as it can catalyze DNA synthesis upon connection of two non-complementary ends. Here, we demonstrate that this capacity is intrinsic to Polµ, not conferred by other NHEJ factors. To understand the molecular determinants of its specific function in NHEJ, the interaction of human Polµ with DNA has been directly visualized by electromobility shift assay and footprinting assays. Stable interaction with a DNA gap requires the presence of a recessive 5'-P, thus orienting the catalytic domain for primer and nucleotide binding. Accordingly, recognition of the 5'-P is crucial to align the two DNA substrates of the NHEJ reaction. Site-directed mutagenesis demonstrates the relevance of three specific residues (Lys(249), Arg(253) and Arg(416)) in stabilizing the primer strand during end synapsis, allowing a range of microhomology-induced distortions beneficial for NHEJ. Moreover, our results suggest that the Polµ BRCT domain, thought to be exclusively involved in interaction with NHEJ core factors, has a direct role in binding the DNA region neighbor to the 5'-P, thus boosting Polµ-mediated NHEJ reactions.

  16. Prophage spontaneous activation promotes DNA release enhancing biofilm formation in Streptococcus pneumoniae.

    Margarida Carrolo

    Full Text Available Streptococcus pneumoniae (pneumococcus is able to form biofilms in vivo and previous studies propose that pneumococcal biofilms play a relevant role both in colonization and infection. Additionally, pneumococci recovered from human infections are characterized by a high prevalence of lysogenic bacteriophages (phages residing quiescently in their host chromosome. We investigated a possible link between lysogeny and biofilm formation. Considering that extracellular DNA (eDNA is a key factor in the biofilm matrix, we reasoned that prophage spontaneous activation with the consequent bacterial host lysis could provide a source of eDNA, enhancing pneumococcal biofilm development. Monitoring biofilm growth of lysogenic and non-lysogenic pneumococcal strains indicated that phage-infected bacteria are more proficient at forming biofilms, that is their biofilms are characterized by a higher biomass and cell viability. The presence of phage particles throughout the lysogenic strains biofilm development implicated prophage spontaneous induction in this effect. Analysis of lysogens deficient for phage lysin and the bacterial major autolysin revealed that the absence of either lytic activity impaired biofilm development and the addition of DNA restored the ability of mutant strains to form robust biofilms. These findings establish that limited phage-mediated host lysis of a fraction of the bacterial population, due to spontaneous phage induction, constitutes an important source of eDNA for the S. pneumoniae biofilm matrix and that this localized release of eDNA favors biofilm formation by the remaining bacterial population.

  17. APOBEC3G enhances lymphoma cell radioresistance by promoting cytidine deaminase-dependent DNA repair.

    Nowarski, Roni; Wilner, Ofer I; Cheshin, Ori; Shahar, Or D; Kenig, Edan; Baraz, Leah; Britan-Rosich, Elena; Nagler, Arnon; Harris, Reuben S; Goldberg, Michal; Willner, Itamar; Kotler, Moshe

    2012-07-12

    APOBEC3 proteins catalyze deamination of cytidines in single-stranded DNA (ssDNA), providing innate protection against retroviral replication by inducing deleterious dC > dU hypermutation of replication intermediates. APOBEC3G expression is induced in mitogen-activated lymphocytes; however, no physiologic role related to lymphoid cell proliferation has yet to be determined. Moreover, whether APOBEC3G cytidine deaminase activity transcends to processing cellular genomic DNA is unknown. Here we show that lymphoma cells expressing high APOBEC3G levels display efficient repair of genomic DNA double-strand breaks (DSBs) induced by ionizing radiation and enhanced survival of irradiated cells. APOBEC3G transiently accumulated in the nucleus in response to ionizing radiation and was recruited to DSB repair foci. Consistent with a direct role in DSB repair, inhibition of APOBEC3G expression or deaminase activity resulted in deficient DSB repair, whereas reconstitution of APOBEC3G expression in leukemia cells enhanced DSB repair. APOBEC3G activity involved processing of DNA flanking a DSB in an integrated reporter cassette. Atomic force microscopy indicated that APOBEC3G multimers associate with ssDNA termini, triggering multimer disassembly to multiple catalytic units. These results identify APOBEC3G as a prosurvival factor in lymphoma cells, marking APOBEC3G as a potential target for sensitizing lymphoma to radiation therapy.

  18. PTSD and DNA Methylation in Select Immune Function Gene Promoter Regions: A Repeated Measures Case-control Study of U.S. Military Service Members

    2013-06-24

    other relevant exposures which may influ- ence DNA methylation , such as dietary factors ( folate , vitamin B12 intake) (Fenech, 2001; Piyathilake and...ARTICLE published: 24 June 2013 doi: 10.3389/fpsyt.2013.00056 PTSD and DNA methylation in select immune function gene promoter regions: a repeated measures...largely unknown. Dis- tinct expression signatures for PTSD have been found, in particular for immune activation transcripts. DNA methylation may be

  19. FANCD2 Maintains Fork Stability in BRCA1/2-Deficient Tumors and Promotes Alternative End-Joining DNA Repair

    Zeina Kais

    2016-06-01

    Full Text Available BRCA1/2 proteins function in homologous recombination (HR-mediated DNA repair and cooperate with Fanconi anemia (FA proteins to maintain genomic integrity through replication fork stabilization. Loss of BRCA1/2 proteins results in DNA repair deficiency and replicative stress, leading to genomic instability and enhanced sensitivity to DNA-damaging agents. Recent studies have shown that BRCA1/2-deficient tumors upregulate Polθ-mediated alternative end-joining (alt-EJ repair as a survival mechanism. Whether other mechanisms maintain genomic integrity upon loss of BRCA1/2 proteins is currently unknown. Here we show that BRCA1/2-deficient tumors also upregulate FANCD2 activity. FANCD2 is required for fork protection and fork restart in BRCA1/2-deficient tumors. Moreover, FANCD2 promotes Polθ recruitment at sites of damage and alt-EJ repair. Finally, loss of FANCD2 in BRCA1/2-deficient tumors enhances cell death. These results reveal a synthetic lethal relationship between FANCD2 and BRCA1/2, and they identify FANCD2 as a central player orchestrating DNA repair pathway choice at the replication fork.

  20. Low-Dose Gene Therapy for Murine PKU Using Episomal Naked DNA Vectors Expressing PAH from Its Endogenous Liver Promoter

    Hiu Man Grisch-Chan

    2017-06-01

    Full Text Available Limited duration of transgene expression, insertional mutagenesis, and size limitations for transgene cassettes pose challenges and risk factors for many gene therapy vectors. Here, we report on physiological expression of liver phenylalanine hydroxylase (PAH by delivery of naked DNA/minicircle (MC-based vectors for correction of homozygous enu2 mice, a model of human phenylketonuria (PKU. Because MC vectors lack a defined size limit, we constructed a MC vector expressing a codon-optimized murine Pah cDNA that includes a truncated intron and is under the transcriptional control of a 3.6-kb native Pah promoter/enhancer sequence. This vector, delivered via hydrodynamic injection, yielded therapeutic liver PAH activity and sustained correction of blood phenylalanine comparable to viral or synthetic liver promoters. Therapeutic efficacy was seen with vector copy numbers of 95% loss of vector genomes and PAH activity in liver, demonstrating that MC vectors had not integrated into the liver genome. In conclusion, MC vectors, which do not have a defined size-limitation, offer a favorable safety profile for hepatic gene therapy due to their non-integration in combination with native promoters.

  1. Transcription of human 7S K DNA in vitro and in vivo is exclusively controlled by an upstream promoter

    Kleinert, H.; Benecke, B.J.

    1988-02-25

    The authors have analyzed the transcription of a recently isolated human 7S K RNA gene in vitro and in vivo. In contrast to hitherto characterized class III genes (genes transcribed by RNA polymerase III), the coding sequence of this gene is not required for faithful and efficient transcription by RNA polymerase III. In fact, a procaryotic vector DNA sequence was efficiently transcribed by RNA polymerase III under the control of the 7S K RNA gene upstream sequence in vitro and in vivo. S/sub 1/-nuclease protection analyses confirmed that the 7S K 5'flanking sequence was sufficient for accurate transcription initiation. These data demonstrate that 7S K DNA represents a novel class III gene, the promoter elements of which are located outside the coding sequence.

  2. Promotion of BRCA2-Dependent Homologous Recombination by DSS1 via RPA Targeting and DNA Mimicry.

    Zhao, Weixing; Vaithiyalingam, Sivaraja; San Filippo, Joseph; Maranon, David G; Jimenez-Sainz, Judit; Fontenay, Gerald V; Kwon, Youngho; Leung, Stanley G; Lu, Lucy; Jensen, Ryan B; Chazin, Walter J; Wiese, Claudia; Sung, Patrick

    2015-07-16

    The tumor suppressor BRCA2 is thought to facilitate the handoff of ssDNA from replication protein A (RPA) to the RAD51 recombinase during DNA break and replication fork repair by homologous recombination. However, we find that RPA-RAD51 exchange requires the BRCA2 partner DSS1. Biochemical, structural, and in vivo analyses reveal that DSS1 allows the BRCA2-DSS1 complex to physically and functionally interact with RPA. Mechanistically, DSS1 acts as a DNA mimic to attenuate the affinity of RPA for ssDNA. A mutation in the solvent-exposed acidic domain of DSS1 compromises the efficacy of RPA-RAD51 exchange. Thus, by targeting RPA and mimicking DNA, DSS1 functions with BRCA2 in a two-component homologous recombination mediator complex in genome maintenance and tumor suppression. Our findings may provide a paradigm for understanding the roles of DSS1 in other biological processes. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. HNRNPLL stabilizes mRNAs for DNA replication proteins and promotes cell cycle progression in colorectal cancer cells.

    Sakuma, Keiichiro; Sasaki, Eiichi; Kimura, Kenya; Komori, Koji; Shimizu, Yasuhiro; Yatabe, Yasushi; Aoki, Masahiro

    2018-06-05

    HNRNPLL (heterogeneous nuclear ribonucleoprotein L-like), an RNA-binding protein that regulates alternative splicing of pre-mRNAs, has been shown to regulate differentiation of lymphocytes, as well as metastasis of colorectal cancer cells. Here we show that HNRNPLL promotes cell cycle progression and hence proliferation of colorectal cancer cells. Functional annotation analysis of those genes whose expression levels were changed by three-fold or more in RNA sequencing analysis between SW480 cells overexpressing HNRNPLL and those knocked down for HNRNPLL revealed enrichment of DNA replication-related genes by HNRNPLL overexpression. Among 13 genes detected in the DNA replication pathway, PCNA, RFC3, and FEN1 showed reproducible upregulation by HNRNPLL overexpression both at mRNA and protein levels in SW480 and HT29 cells. Importantly, knockdown of any of these genes alone suppressed the proliferation promoting effect induced by HNRNPLL overexpression. RNA-immunoprecipitation assay presented a binding of FLAG-tagged HNRNPLL to mRNA of these genes, and HNRNPLL overexpression significantly suppressed the downregulation of these genes during 12 hours of actinomycin D treatment, suggesting a role of HNRNPLL in mRNA stability. Finally, analysis of a public RNA sequencing dataset of clinical samples suggested a link between overexpression of HNRNPLL and that of PCNA, RFC3, and FEN1. This link was further supported by immunohistochemistry of colorectal cancer clinical samples, whereas expression of CDKN1A, which is known to inhibit the cooperative function of PCNA, RFC3, and FEN1, was negatively associated with HNRNPLL expression. These results indicate that HNRNPLL stabilizes mRNAs encoding regulators of DNA replication and promotes colorectal cancer cell proliferation. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  4. Insufficient DNA methylation affects healthy aging and promotes age-related health problems.

    Liu, Liang; van Groen, Thomas; Kadish, Inga; Li, Yuanyuan; Wang, Deli; James, Smitha R; Karpf, Adam R; Tollefsbol, Trygve O

    2011-08-01

    DNA methylation plays an integral role in development and aging through epigenetic regulation of genome function. DNA methyltransferase 1 (Dnmt1) is the most prevalent DNA methyltransferase that maintains genomic methylation stability. To further elucidate the function of Dnmt1 in aging and age-related diseases, we exploited the Dnmt1+/- mouse model to investigate how Dnmt1 haploinsufficiency impacts the aging process by assessing the changes of several major aging phenotypes. We confirmed that Dnmt1 haploinsufficiency indeed decreases DNA methylation as a result of reduced Dnmt1 expression. To assess the effect of Dnmt1 haploinsufficiency on general body composition, we performed dual-energy X-ray absorptiometry analysis and showed that reduced Dnmt1 activity decreased bone mineral density and body weight, but with no significant impact on mortality or body fat content. Using behavioral tests, we demonstrated that Dnmt1 haploinsufficiency impairs learning and memory functions in an age-dependent manner. Taken together, our findings point to the interesting likelihood that reduced genomic methylation activity adversely affects the healthy aging process without altering survival and mortality. Our studies demonstrated that cognitive functions of the central nervous system are modulated by Dnmt1 activity and genomic methylation, highlighting the significance of the original epigenetic hypothesis underlying memory coding and function.

  5. Rad54 and Mus81 cooperation promotes DNA damage repair and restrains chromosome missegregation

    Ghamrasni, S El; Cardoso, R; Li, L

    2016-01-01

    . The inefficient repair of DNA double-strand breaks (DSBs) in Rad54(-/-)Mus81(-/-) cells was accompanied by elevated levels of chromosome missegregation and cell death. Perhaps as a consequence, tumor incidence in Rad54(-/-)Mus81(-/-) mice remained comparable to that in Mus81(-/-) mice. Our study highlights...

  6. Residual Cdk1/2 activity after DNA damage promotes senescence

    Müllers, E.; Cascales, H.S.; Burdová, Kamila; Macůrek, Libor; Lindqvist, A.

    2017-01-01

    Roč. 16, č. 3 (2017), s. 575-584 ISSN 1474-9726 R&D Projects: GA ČR GA13-18392S Institutional support: RVO:68378050 Keywords : Cdk1 * Cdk2 * cell cycle * checkpoint recovery * DNA damage response * G2phase * p21 * senescence Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemistry and molecular biology

  7. MMSET is dynamically regulated during cell-cycle progression and promotes normal DNA replication.

    Evans, Debra L; Zhang, Haoxing; Ham, Hyoungjun; Pei, Huadong; Lee, SeungBaek; Kim, JungJin; Billadeau, Daniel D; Lou, Zhenkun

    2016-01-01

    The timely and precise duplication of cellular DNA is essential for maintaining genome integrity and is thus tightly-regulated. During mitosis and G1, the Origin Recognition Complex (ORC) binds to future replication origins, coordinating with multiple factors to load the minichromosome maintenance (MCM) complex onto future replication origins as part of the pre-replication complex (pre-RC). The pre-RC machinery, in turn, remains inactive until the subsequent S phase when it is required for replication fork formation, thereby initiating DNA replication. Multiple myeloma SET domain-containing protein (MMSET, a.k.a. WHSC1, NSD2) is a histone methyltransferase that is frequently overexpressed in aggressive cancers and is essential for normal human development. Several studies have suggested a role for MMSET in cell-cycle regulation; however, whether MMSET is itself regulated during cell-cycle progression has not been examined. In this study, we report that MMSET is degraded during S phase in a cullin-ring ligase 4-Cdt2 (CRL4(Cdt2)) and proteasome-dependent manner. Notably, we also report defects in DNA replication and a decreased association of pre-RC factors with chromatin in MMSET-depleted cells. Taken together, our results suggest a dynamic regulation of MMSET levels throughout the cell cycle, and further characterize the role of MMSET in DNA replication and cell-cycle progression.

  8. Purification, crystallization and preliminary X-ray crystallographic analysis of the ETS domain of human Ergp55 in complex with the cfos promoter DNA sequence

    Gangwar, Shanti P.; Meena, Sita R.; Saxena, Ajay K.

    2012-01-01

    The ETS domain of human Ergp55 was purified and crystallized in native, complexes with E74, and cfos promoter DNA sequences. The X-ray intensity data set was collected on ETS–cfos promoter DNA complex crystal at 3.1 Å resolution to analyze the structure by molecular replacement technique. The Ergp55 protein belongs to the Ets family of transciption factors. The Ets transcription factors are involved in various developmental processes and the regulation of cancer metabolism. They contain a highly similar DNA-binding domain known as the ETS domain and have diverse functions in oncogenesis and physiology. The Ets transcription factors differ in their DNA-binding preference at the ETS site and the mechanisms by which they target genes are not clearly understood. To understand its DNA-binding mechanism, the ETS domain of Ergp55 was expressed and purified. The ETS domain was crystallized in the native form and in complex forms with DNA sequences from the E74 and cfos promoters. An X-ray diffraction data set was collected from an ETS–cfos DNA complex crystal at a wavelength of 0.9725 Å on the BM14 synchrotron beamline at the ESRF, France. The ETS–cfos DNA complex crystal belonged to space group C222 1 , with four molecules in the asymmetric unit. For structure analysis, initial phases for the ETS–cfos DNA complex were obtained by the molecular-replacement technique with Phaser in the CCP4 suite using the coordinates of Fli-1 protein and cfos DNA as search models. Structure analysis of the ETS–cfos DNA complex may possibly explain the DNA-binding specificity and its mechanism of interaction with the ETS domain of Ergp55

  9. Sumoylation Promotes the Stability of the DNA Sensor cGAS and the Adaptor STING to Regulate the Kinetics of Response to DNA Virus.

    Hu, Ming-Ming; Yang, Qing; Xie, Xue-Qin; Liao, Chen-Yang; Lin, Heng; Liu, Tian-Tian; Yin, Lei; Shu, Hong-Bing

    2016-09-20

    During viral infection, sensing of cytosolic DNA by the cyclic GMP-AMP synthase (cGAS) activates the adaptor protein STING and triggers an antiviral response. Little is known about the mechanisms that determine the kinetics of activation and deactivation of the cGAS-STING pathway, ensuring effective but controlled innate antiviral responses. Here we found that the ubiquitin ligase Trim38 targets cGas for sumoylation in uninfected cells and during the early phase of viral infection. Sumoylation of cGas prevented its polyubiquitination and degradation. Trim38 also sumoylated Sting during the early phase of viral infection, promoting both Sting activation and protein stability. In the late phase of infection, cGas and Sting were desumoylated by Senp2 and subsequently degraded via proteasomal and chaperone-mediated autophagy pathways, respectively. Our findings reveal an essential role for Trim38 in the innate immune response to DNA virus and provide insight into the mechanisms that ensure optimal activation and deactivation of the cGAS-STING pathway. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. A novel type of DNA-binding protein interacts with a conserved sequence in an early nodulin ENOD12 promoter

    Christiansen, H; Hansen, A C; Vijn, I

    1996-01-01

    The pea genes PsENOD12A and PsENOD12B are expressed in the root hairs shortly after infection with the nitrogen-fixing bacterium Rhizobium leguminosarum bv. viciae or after application of purified Nod factors. A 199 bp promoter fragment of the PsENOD12B gene contains sufficient information for Nod...... factor-induced tissue-specific expression. We have isolated a Vicia sativa cDNA encoding a 1641 amino acid protein, ENBP1, that interacts with the 199 bp ENOD12 promoter. Two different DNA-binding domains were identified in ENBP1. A domain containing six AT-hooks interacts specifically with an AT...... of the ENBP1 transcript in cells expressing ENOD12 strongly suggest that ENBP1 is a transcription factor involved in the regulation of ENOD12. Finally, the C-terminal region of ENBP1 shows strong homology to a protein from rat that is specifically expressed in testis tissue. Udgivelsesdato: 1996-Dec...

  11. The Fanconi anemia pathway promotes replication-dependent DNA interstrand cross-link repair.

    Knipscheer, Puck; Räschle, Markus; Smogorzewska, Agata; Enoiu, Milica; Ho, The Vinh; Schärer, Orlando D; Elledge, Stephen J; Walter, Johannes C

    2009-12-18

    Fanconi anemia is a human cancer predisposition syndrome caused by mutations in 13 Fanc genes. The disorder is characterized by genomic instability and cellular hypersensitivity to chemicals that generate DNA interstrand cross-links (ICLs). A central event in the activation of the Fanconi anemia pathway is the mono-ubiquitylation of the FANCI-FANCD2 complex, but how this complex confers ICL resistance remains enigmatic. Using a cell-free system, we showed that FANCI-FANCD2 is required for replication-coupled ICL repair in S phase. Removal of FANCD2 from extracts inhibits both nucleolytic incisions near the ICL and translesion DNA synthesis past the lesion. Reversal of these defects requires ubiquitylated FANCI-FANCD2. Our results show that multiple steps of the essential S-phase ICL repair mechanism fail when the Fanconi anemia pathway is compromised.

  12. A PHF8 homolog in C. elegans promotes DNA repair via homologous recombination.

    Changrim Lee

    Full Text Available PHF8 is a JmjC domain-containing histone demethylase, defects in which are associated with X-linked mental retardation. In this study, we examined the roles of two PHF8 homologs, JMJD-1.1 and JMJD-1.2, in the model organism C. elegans in response to DNA damage. A deletion mutation in either of the genes led to hypersensitivity to interstrand DNA crosslinks (ICLs, while only mutation of jmjd-1.1 resulted in hypersensitivity to double-strand DNA breaks (DSBs. In response to ICLs, JMJD-1.1 did not affect the focus formation of FCD-2, a homolog of FANCD2, a key protein in the Fanconi anemia pathway. However, the dynamic behavior of RPA-1 and RAD-51 was affected by the mutation: the accumulations of both proteins at ICLs appeared normal, but their subsequent disappearance was retarded, suggesting that later steps of homologous recombination were defective. Similar changes in the dynamic behavior of RPA-1 and RAD-51 were seen in response to DSBs, supporting a role of JMJD-1.1 in homologous recombination. Such a role was also supported by our finding that the hypersensitivity of jmjd-1.1 worms to ICLs was rescued by knockdown of lig-4, a homolog of Ligase 4 active in nonhomologous end-joining. The hypersensitivity of jmjd-1.1 worms to ICLs was increased by rad-54 knockdown, suggesting that JMJD-1.1 acts in parallel with RAD-54 in modulating chromatin structure. Indeed, the level of histone H3 Lys9 tri-methylation, a marker of heterochromatin, was higher in jmjd-1.1 cells than in wild-type cells. We conclude that the histone demethylase JMJD-1.1 influences homologous recombination either by relaxing heterochromatin structure or by indirectly regulating the expression of multiple genes affecting DNA repair.

  13. Mesotrione herbicide promotes biochemical changes and DNA damage in two fish species

    L.D.S. Piancini

    2015-01-01

    Full Text Available Mesotrione is one of the new herbicides that have emerged as an alternative after the ban of atrazine in the European Union. To our knowledge, any work using genetic or biochemical biomarkers was performed in any kind of fish evaluating the toxicity of this compound. The impact of acute (96 h exposure to environmentally relevant mesotrione concentrations (1.8, 7, 30, 115 e 460 μg L−1 were evaluated on the liver of Oreochorimis niloticus and Geophagus brasiliensis by assessing the activity of superoxide dismutase (SOD, glutathione peroxidase (GPx and glutathione-S- transferase (GST, the levels of reduced glutathione (GSH, carbonyl assays (PCO and lipid peroxide (LPO as well as the DNA damage to erithrocytes, liver and gills through the comet assay. We observed an increase in the concentration of GSH and the GPx activity in O. niloticus, and the GST and SOD activity in G. brasiliensis. We found significant increase in DNA damage in all tissues in both species. The results indicated that the acute exposure to mesotrione can induce oxidative stress and DNA damage in both species.

  14. Cyclin A2 promotes DNA repair in the brain during both development and aging.

    Gygli, Patrick E; Chang, Joshua C; Gokozan, Hamza N; Catacutan, Fay P; Schmidt, Theresa A; Kaya, Behiye; Goksel, Mustafa; Baig, Faisal S; Chen, Shannon; Griveau, Amelie; Michowski, Wojciech; Wong, Michael; Palanichamy, Kamalakannan; Sicinski, Piotr; Nelson, Randy J; Czeisler, Catherine; Otero, José J

    2016-07-01

    Various stem cell niches of the brain have differential requirements for Cyclin A2. Cyclin A2 loss results in marked cerebellar dysmorphia, whereas forebrain growth is retarded during early embryonic development yet achieves normal size at birth. To understand the differential requirements of distinct brain regions for Cyclin A2, we utilized neuroanatomical, transgenic mouse, and mathematical modeling techniques to generate testable hypotheses that provide insight into how Cyclin A2 loss results in compensatory forebrain growth during late embryonic development. Using unbiased measurements of the forebrain stem cell niche, we parameterized a mathematical model whereby logistic growth instructs progenitor cells as to the cell-types of their progeny. Our data was consistent with prior findings that progenitors proliferate along an auto-inhibitory growth curve. The growth retardation inCCNA2-null brains corresponded to cell cycle lengthening, imposing a developmental delay. We hypothesized that Cyclin A2 regulates DNA repair and that CCNA2-null progenitors thus experienced lengthened cell cycle. We demonstrate that CCNA2-null progenitors suffer abnormal DNA repair, and implicate Cyclin A2 in double-strand break repair. Cyclin A2's DNA repair functions are conserved among cell lines, neural progenitors, and hippocampal neurons. We further demonstrate that neuronal CCNA2 ablation results in learning and memory deficits in aged mice.

  15. Dual DNA binding property of ABA insensitive 3 like factors targeted to promoters responsive to ABA and auxin.

    Nag, Ronita; Maity, Manas Kanti; Dasgupta, Maitrayee

    2005-11-01

    The ABA responsive ABI3 and the auxin responsive ARF family of transcription factors bind the CATGCATG (Sph) and TGTCTC core motifs in ABA and auxin response elements (ABRE and AuxRE), respectively. Several evidences indicate ABI3s to act downstream to auxin too. Because DNA binding domain of ABI3s shows significant overlap with ARFs we enquired whether auxin responsiveness through ABI3s could be mediated by their binding to canonical AuxREs. Investigations were undertaken through in vitro gel mobility shift assays (GMSA) using the DNA binding domain B3 of PvAlf (Phaseolus vulgaris ABI3 like factor) and upstream regions of auxin responsive gene GH3 (-267 to -141) and ABA responsive gene Em (-316 to -146) harboring AuxRE and ABRE, respectively. We demonstrate that B3 domain of PvAlf could bind AuxRE only when B3 was associated with its flanking domain B2 (B2B3). Such strict requirement of B2 domain was not observed with ABRE, where B3 could bind with or without being associated with B2. This dual specificity in DNA binding of ABI3s was also demonstrated with nuclear extracts of cultured cells of Arachis hypogea. Supershift analysis of ABRE and AuxRE bound nuclear proteins with antibodies raised against B2B3 domains of PvAlf revealed that ABI3 associated complexes were detectable in association with both cis elements. Competition GMSA confirmed the same complexes to bind ABRE and AuxRE. This dual specificity of ABI3 like factors in DNA binding targeted to natural promoters responsive to ABA and auxin suggests them to have a potential role in conferring crosstalk between these two phytohormones.

  16. Induction and maintenance of DNA methylation in plant promoter sequences by apple latent spherical virus-induced transcriptional gene silencing

    Tatsuya eKon

    2014-11-01

    Full Text Available Apple latent spherical virus (ALSV is an efficient virus-induced gene silencing vector in functional genomics analyses of a broad range of plant species. Here, an Agrobacterium-mediated inoculation (agroinoculation system was developed for the ALSV vector, and virus-induced transcriptional gene silencing (VITGS is described in plants infected with the ALSV vector. The cDNAs of ALSV RNA1 and RNA2 were inserted between the CaMV 35S promoter and the NOS-T sequences in a binary vector pCAMBIA1300 to produce pCALSR1 and pCALSR2-XSB or pCALSR2-XSB/MN. When these vector constructs were agroinoculated into Nicotiana benthamiana plants with a construct expressing a viral silencing suppressor, the infection efficiency of the vectors was 100%. A recombinant ALSV vector carrying part of the 35S promoter sequence induced transcriptional gene silencing of the green fluorescent protein gene in a line of N. benthamiana plants, resulting in the disappearance of green fluorescence of infected plants. Bisulfite sequencing showed that cytosine residues at CG and CHG sites of the 35S promoter sequence were highly methylated in the silenced generation 0 plants infected with the ALSV carrying the promoter sequence as well as in progeny. The ALSV-mediated VITGS state was inherited by progeny for multiple generations. In addition, induction of VITGS of an endogenous gene (chalcone synthase-A was demonstrated in petunia plants infected with an ALSV vector carrying the native promoter sequence. These results suggest that ALSV-based vectors can be applied to study DNA methylation in plant genomes, and provide a useful tool for plant breeding via epigenetic modification.

  17. Electronic cigarette aerosols and copper nanoparticles induce mitochondrial stress and promote DNA fragmentation in lung fibroblasts

    Lerner, Chad A.; Rutagarama, Pierrot; Ahmad, Tanveer; Sundar, Isaac K.; Elder, Alison; Rahman, Irfan, E-mail: irfan_rahman@urmc.rochester.edu

    2016-09-02

    Oxidants or nanoparticles have recently been identified as constituents of aerosols released from various styles of electronic cigarettes (E-cigs). Cells in the lung may be directly exposed to these constituents and harbor reactive properties capable of incurring acute cell injury. Our results show mitochondria are sensitive to both E-cig aerosols and aerosol containing copper nanoparticles when exposed to human lung fibroblasts (HFL-1) using an Air-Liquid Interface culture system, evident by elevated levels of mitochondrial ROS (mtROS). Increased mtROS after aerosol exposure is associated with reduced stability of OxPhos electron transport chain (ETC) complex IV subunit and nuclear DNA fragmentation. Increased levels of IL-8 and IL-6 in HFL-1 conditioned media were also observed. These findings reveal both mitochondrial, genotoxic, and inflammatory stresses are features of direct cell exposure to E-cig aerosols which are ensued by inflammatory duress, raising a concern on deleterious effect of vaping. - Graphical abstract: Oxidants and possibly reactive properties of metal particles in E-cig aerosols impart mitochondrial oxidative stress and DNA damage. These biological effects accompany inflammatory response which may raise concern regarding long term E-cig use. Mitochondria may be particularly sensitive to reactive properties of E-cig aerosols in addition to the potential for them to induce genotoxic stress by generating increased ROS. - Highlights: • Mitochondria are sensitive to both E-cig aerosols and metal nanoparticles. • Increased mtROS by E-cig aerosol is associated with disrupted mitochondrial energy. • E-cig causes nuclear DNA fragmentation. • E-cig aerosols induce pro-inflammatory response in human fibroblasts.

  18. Electronic cigarette aerosols and copper nanoparticles induce mitochondrial stress and promote DNA fragmentation in lung fibroblasts

    Lerner, Chad A.; Rutagarama, Pierrot; Ahmad, Tanveer; Sundar, Isaac K.; Elder, Alison; Rahman, Irfan

    2016-01-01

    Oxidants or nanoparticles have recently been identified as constituents of aerosols released from various styles of electronic cigarettes (E-cigs). Cells in the lung may be directly exposed to these constituents and harbor reactive properties capable of incurring acute cell injury. Our results show mitochondria are sensitive to both E-cig aerosols and aerosol containing copper nanoparticles when exposed to human lung fibroblasts (HFL-1) using an Air-Liquid Interface culture system, evident by elevated levels of mitochondrial ROS (mtROS). Increased mtROS after aerosol exposure is associated with reduced stability of OxPhos electron transport chain (ETC) complex IV subunit and nuclear DNA fragmentation. Increased levels of IL-8 and IL-6 in HFL-1 conditioned media were also observed. These findings reveal both mitochondrial, genotoxic, and inflammatory stresses are features of direct cell exposure to E-cig aerosols which are ensued by inflammatory duress, raising a concern on deleterious effect of vaping. - Graphical abstract: Oxidants and possibly reactive properties of metal particles in E-cig aerosols impart mitochondrial oxidative stress and DNA damage. These biological effects accompany inflammatory response which may raise concern regarding long term E-cig use. Mitochondria may be particularly sensitive to reactive properties of E-cig aerosols in addition to the potential for them to induce genotoxic stress by generating increased ROS. - Highlights: • Mitochondria are sensitive to both E-cig aerosols and metal nanoparticles. • Increased mtROS by E-cig aerosol is associated with disrupted mitochondrial energy. • E-cig causes nuclear DNA fragmentation. • E-cig aerosols induce pro-inflammatory response in human fibroblasts.

  19. Human geminin promotes pre-RC formation and DNA replication by stabilizing CDT1 in mitosis

    Ballabeni, Andrea; Melixetian, Marina; Zamponi, Raffaella

    2004-01-01

    -mediated degradation by inhibiting its ubiquitination. In particular, Geminin ensures basal levels of CDT1 during S phase and its accumulation during mitosis. Consistently, inhibition of Geminin synthesis during M phase leads to impairment of pre-RC formation and DNA replication during the following cell cycle....... Moreover, we show that inhibition of CDK1 during mitosis, and not Geminin depletion, is sufficient for premature formation of pre-RCs, indicating that CDK activity is the major mitotic inhibitor of licensing in human cells. Taken together with recent data from our laboratory, our results demonstrate...

  20. Ultrasound - Aided ejection in micro injection molding

    Masato, D.; Sorgato, M.; Lucchetta, G.

    2018-05-01

    In this work, an ultrasound-aided ejection system was designed and tested for different polymers (PS, COC and POM) and mold topographies. The proposed solution aims at reducing the ejection friction by decreasing the adhesion component of the frictional force, which is controlled by the contact area developed during the filling stage of the injection molding process. The experimental results indicate a positive effect of ultrasound vibration on the friction force values, with a maximum reduction of 16. Moreover, it is demonstrated that the ultrasound effect is strictly related to both polymer selection and mold roughness. The combined effect on the ejection force of mold surface roughness, melt viscosity during filling and polymer elastic modulus at ejection was modeled to the experimental data, in order to demonstrate that the effect of ultrasound vibration on the ejection friction reduction is due to the heating of the contact interface and the consequent reduction of the polymer elastic modulus.

  1. The DnaK Chaperone Uses Different Mechanisms To Promote and Inhibit Replication of Vibrio cholerae Chromosome 2

    Jha, Jyoti K.; Li, Mi; Ghirlando, Rodolfo; Miller Jenkins, Lisa M.; Wlodawer, Alexander; Chattoraj, Dhruba; Dunny, Gary M.

    2017-04-18

    Replication of Vibrio cholerae chromosome 2 (Chr2) depends on molecular chaperone DnaK to facilitate binding of the initiator (RctB) to the replication origin. The binding occurs at two kinds of site, 12-mers and 39-mers, which promote and inhibit replication, respectively. Here we show that DnaK employs different mechanisms to enhance the two kinds of binding. We found that mutations inrctBthat reduce DnaK binding also reduce 12-mer binding and initiation. The initiation defect is suppressed by second-site mutations that increase 12-mer binding only marginally. Instead, they reduce replication inhibitory mechanisms: RctB dimerization and 39-mer binding. One suppressing change was in a dimerization domain which is folded similarly to the initiator of an iteron plasmid—the presumed progenitor of Chr2. In plasmids, DnaK promotes initiation by reducing dimerization. A different mutation was in the 39-mer binding domain of RctB and inactivated it, indicating an alternative suppression mechanism. Paradoxically, although DnaK increases 39-mer binding, the increase was also achieved by inactivating the DnaK binding site of RctB. This result suggests that the site inhibits the 39-mer binding domain (via autoinhibition) when prevented from binding DnaK. Taken together, our results reveal an important feature of the transition from plasmid to chromosome: the Chr2 initiator retains the plasmid-like dimerization domain and its control by chaperones but uses the chaperones in an unprecedented way to control the inhibitory 39-mer binding. IMPORTANCE The capacity of proteins to undergo remodeling provides opportunities to control their function. However, remodeling remains a poorly understood aspect of the structure-function paradigm due to its dynamic nature. Here we have studied remodeling of the initiator of replication ofVibrio choleraeChr2 by the molecular chaperone, DnaK. We show that DnaK binds to a site on the Chr2 initiator (RctB) that

  2. ATM regulates 3-methylpurine-DNA glycosylase and promotes therapeutic resistance to alkylating agents.

    Agnihotri, Sameer; Burrell, Kelly; Buczkowicz, Pawel; Remke, Marc; Golbourn, Brian; Chornenkyy, Yevgen; Gajadhar, Aaron; Fernandez, Nestor A; Clarke, Ian D; Barszczyk, Mark S; Pajovic, Sanja; Ternamian, Christian; Head, Renee; Sabha, Nesrin; Sobol, Robert W; Taylor, Michael D; Rutka, James T; Jones, Chris; Dirks, Peter B; Zadeh, Gelareh; Hawkins, Cynthia

    2014-10-01

    Alkylating agents are a first-line therapy for the treatment of several aggressive cancers, including pediatric glioblastoma, a lethal tumor in children. Unfortunately, many tumors are resistant to this therapy. We sought to identify ways of sensitizing tumor cells to alkylating agents while leaving normal cells unharmed, increasing therapeutic response while minimizing toxicity. Using an siRNA screen targeting over 240 DNA damage response genes, we identified novel sensitizers to alkylating agents. In particular, the base excision repair (BER) pathway, including 3-methylpurine-DNA glycosylase (MPG), as well as ataxia telangiectasia mutated (ATM), were identified in our screen. Interestingly, we identified MPG as a direct novel substrate of ATM. ATM-mediated phosphorylation of MPG was required for enhanced MPG function. Importantly, combined inhibition or loss of MPG and ATM resulted in increased alkylating agent-induced cytotoxicity in vitro and prolonged survival in vivo. The discovery of the ATM-MPG axis will lead to improved treatment of alkylating agent-resistant tumors. Inhibition of ATM and MPG-mediated BER cooperate to sensitize tumor cells to alkylating agents, impairing tumor growth in vitro and in vivo with no toxicity to normal cells, providing an ideal therapeutic window. ©2014 American Association for Cancer Research.

  3. Aag DNA glycosylase promotes alkylation-induced tissue damage mediated by Parp1.

    Calvo, Jennifer A; Moroski-Erkul, Catherine A; Lake, Annabelle; Eichinger, Lindsey W; Shah, Dharini; Jhun, Iny; Limsirichai, Prajit; Bronson, Roderick T; Christiani, David C; Meira, Lisiane B; Samson, Leona D

    2013-04-01

    Alkylating agents comprise a major class of front-line cancer chemotherapeutic compounds, and while these agents effectively kill tumor cells, they also damage healthy tissues. Although base excision repair (BER) is essential in repairing DNA alkylation damage, under certain conditions, initiation of BER can be detrimental. Here we illustrate that the alkyladenine DNA glycosylase (AAG) mediates alkylation-induced tissue damage and whole-animal lethality following exposure to alkylating agents. Aag-dependent tissue damage, as observed in cerebellar granule cells, splenocytes, thymocytes, bone marrow cells, pancreatic β-cells, and retinal photoreceptor cells, was detected in wild-type mice, exacerbated in Aag transgenic mice, and completely suppressed in Aag⁻/⁻ mice. Additional genetic experiments dissected the effects of modulating both BER and Parp1 on alkylation sensitivity in mice and determined that Aag acts upstream of Parp1 in alkylation-induced tissue damage; in fact, cytotoxicity in WT and Aag transgenic mice was abrogated in the absence of Parp1. These results provide in vivo evidence that Aag-initiated BER may play a critical role in determining the side-effects of alkylating agent chemotherapies and that Parp1 plays a crucial role in Aag-mediated tissue damage.

  4. Aag DNA glycosylase promotes alkylation-induced tissue damage mediated by Parp1.

    Jennifer A Calvo

    2013-04-01

    Full Text Available Alkylating agents comprise a major class of front-line cancer chemotherapeutic compounds, and while these agents effectively kill tumor cells, they also damage healthy tissues. Although base excision repair (BER is essential in repairing DNA alkylation damage, under certain conditions, initiation of BER can be detrimental. Here we illustrate that the alkyladenine DNA glycosylase (AAG mediates alkylation-induced tissue damage and whole-animal lethality following exposure to alkylating agents. Aag-dependent tissue damage, as observed in cerebellar granule cells, splenocytes, thymocytes, bone marrow cells, pancreatic β-cells, and retinal photoreceptor cells, was detected in wild-type mice, exacerbated in Aag transgenic mice, and completely suppressed in Aag⁻/⁻ mice. Additional genetic experiments dissected the effects of modulating both BER and Parp1 on alkylation sensitivity in mice and determined that Aag acts upstream of Parp1 in alkylation-induced tissue damage; in fact, cytotoxicity in WT and Aag transgenic mice was abrogated in the absence of Parp1. These results provide in vivo evidence that Aag-initiated BER may play a critical role in determining the side-effects of alkylating agent chemotherapies and that Parp1 plays a crucial role in Aag-mediated tissue damage.

  5. Differential effects of simple repeating DNA sequences on gene expression from the SV40 early promoter.

    Amirhaeri, S; Wohlrab, F; Wells, R D

    1995-02-17

    The influence of simple repeat sequences, cloned into different positions relative to the SV40 early promoter/enhancer, on the transient expression of the chloramphenicol acetyltransferase (CAT) gene was investigated. Insertion of (G)29.(C)29 in either orientation into the 5'-untranslated region of the CAT gene reduced expression in CV-1 cells 50-100 fold when compared with controls with random sequence inserts. Analysis of CAT-specific mRNA levels demonstrated that the effect was due to a reduction of CAT mRNA production rather than to posttranscriptional events. In contrast, insertion of the same insert in either orientation upstream of the promoter-enhancer or downstream of the gene stimulated gene expression 2-3-fold. These effects could be reversed by cotransfection of a competitor plasmid carrying (G)25.(C)25 sequences. The results suggest that a G.C-binding transcription factor modulates gene expression in this system and that promoter strength can be regulated by providing protein-binding sites in trans. Although constructs containing longer tracts of alternating (C-G), (T-G), or (A-T) sequences inhibited CAT expression when inserted in the 5'-untranslated region of the CAT gene, the amount of CAT mRNA was unaffected. Hence, these inhibitions must be due to posttranscriptional events, presumably at the level of translation. These effects of microsatellite sequences on gene expression are discussed with respect to recent data on related simple repeat sequences which cause several human genetic diseases.

  6. EWS Knockdown and Taxifolin Treatment Induced Differentiation and Removed DNA Methylation from p53 Promoter to Promote Expression of Puma and Noxa for Apoptosis in Ewing's Sarcoma.

    Hossain, Mohammad Motarab; Ray, Swapan Kumar

    2014-10-01

    Ewing's sarcoma is a pediatric tumor that mainly occurs in soft tissues and bones. Malignant characteristics of Ewing's sarcoma are correlated with expression of EWS oncogene. We achieved knockdown of EWS expression using a plasmid vector encoding EWS short hairpin RNA (shRNA) to increase anti-tumor mechanisms of taxifolin (TFL), a new flavonoid, in human Ewing's sarcoma cells in culture and animal models. Immunofluorescence microscopy and flow cytometric analysis showed high expression of EWS in human Ewing's sarcoma SK-N-MC and RD-ES cell lines. EWS shRNA plus TFL inhibited 80% cell viability and caused the highest decreases in EWS expression at mRNA and protein levels in both cell lines. Knockdown of EWS expression induced morphological features of differentiation. EWS shRNA plus TFL caused more alterations in molecular markers of differentiation than either agent alone. EWS shRNA plus TFL caused the highest decreases in cell migration with inhibition of survival, angiogenic and invasive factors. Knockdown of EWS expression was associated with removal of DNA methylation from p53 promoter, promoting expression of p53, Puma, and Noxa. EWS shRNA plus TFL induced the highest amounts of apoptosis with activation of extrinsic and intrinsic pathways in both cell lines in culture. EWS shRNA plus TFL also inhibited growth of Ewing's sarcoma tumors in animal models due to inhibition of differentiation inhibitors and angiogenic and invasive factors and also induction of activation of caspase-3 for apoptosis. Collectively, knockdown of EWS expression increased various anti-tumor mechanisms of TFL in human Ewing's sarcoma in cell culture and animal models.

  7. Evidence for direct geographic influences on linguistic sounds: the case of ejectives.

    Caleb Everett

    Full Text Available We present evidence that the geographic context in which a language is spoken may directly impact its phonological form. We examined the geographic coordinates and elevations of 567 language locations represented in a worldwide phonetic database. Languages with phonemic ejective consonants were found to occur closer to inhabitable regions of high elevation, when contrasted to languages without this class of sounds. In addition, the mean and median elevations of the locations of languages with ejectives were found to be comparatively high. The patterns uncovered surface on all major world landmasses, and are not the result of the influence of particular language families. They reflect a significant and positive worldwide correlation between elevation and the likelihood that a language employs ejective phonemes. In addition to documenting this correlation in detail, we offer two plausible motivations for its existence. We suggest that ejective sounds might be facilitated at higher elevations due to the associated decrease in ambient air pressure, which reduces the physiological effort required for the compression of air in the pharyngeal cavity--a unique articulatory component of ejective sounds. In addition, we hypothesize that ejective sounds may help to mitigate rates of water vapor loss through exhaled air. These explications demonstrate how a reduction of ambient air density could promote the usage of ejective phonemes in a given language. Our results reveal the direct influence of a geographic factor on the basic sound inventories of human languages.

  8. DBC1 promotes castration-resistant prostate cancer by positively regulating DNA binding and stability of AR-V7.

    Moon, Sue Jin; Jeong, Byong Chang; Kim, Hwa Jin; Lim, Joung Eun; Kwon, Ghee Young; Kim, Jeong Hoon

    2018-03-01

    Constitutively active AR-V7, one of the major androgen receptor (AR) splice variants lacking the ligand-binding domain, plays a key role in the development of castration-resistant prostate cancer (CRPC) and anti-androgen resistance. However, our understanding of the regulatory mechanisms of AR-V7-driven transcription is limited. Here we report DBC1 as a key regulator of AR-V7 transcriptional activity and stability in CRPC cells. DBC1 functions as a coactivator for AR-V7 and is required for the expression of AR-V7 target genes including CDH2, a mesenchymal marker linked to CRPC progression. DBC1 is required for recruitment of AR-V7 to its target enhancers and for long-range chromatin looping between the CDH2 enhancer and promoter. Mechanistically, DBC1 enhances DNA-binding activity of AR-V7 by direct interaction and inhibits CHIP E3 ligase-mediated ubiquitination and degradation of AR-V7 by competing with CHIP for AR-V7 binding, thereby stabilizing and activating AR-V7. Importantly, DBC1 depletion suppresses the tumorigenic and metastatic properties of CRPC cells. Our results firmly establish DBC1 as a critical AR-V7 coactivator that plays a key role in the regulation of DNA binding and stability of AR-V7 and has an important physiological role in CRPC progression.

  9. Analysis of RTEL1 and PCDHGB6 promoter methylation in circulating-free DNA of lung cancer patients using liquid biopsy: A pilot study.

    Powrózek, Tomasz; Krawczyk, Paweł; Kuźnar-Kamińska, Barbara; Batura-Gabryel, Halina; Milanowski, Janusz

    2016-08-01

    Analysis of epigenetic alterations such as methylation of circulating-free DNA (cf-DNA) expression significantly broadened perspectives of lung cancer (LC) screening. Moreover, methylation of tumor suppressor genes may be analyzed with non-invasive manner in patients' blood samples (liquid biopsy), what underline necessity of detailed investigation of tumor cf-DNA. The purpose of current study was to assess methylation of RTEL1 and PCDHGB6 promoter regions in cf-DNA of 70 LC patients and 80 healthy individuals using qMSP-PCR technique. Methylation status of both genes has not been investigated in cf-DNA of LC patients before. PCDHGB6 promoter methylation was found in 41.4% of LC patients and in 1.3% of healthy individuals, whereas promoter of RTEL1 was found methylated in 51.4% of LC patients and in 8.8% of healthy individuals. Combined analysis of two markers improved test sensitivity up to 62.9% and specificity up to 90% with area under the curve (AUC) in receiver operating curve (ROC) of 0.755. The evaluation of RTEL1 and PCDHGB6 promoter methylation may be an useful tool for non-invasive diagnosis of LC in liquid biopsy.

  10. DVC1 (C1orf124) is a DNA damage-targeting p97 adaptor that promotes ubiquitin-dependent responses to replication blocks

    Mosbech, Anna; Gibbs-Seymour, Ian; Kagias, Konstantinos

    2012-01-01

    Ubiquitin-mediated processes orchestrate critical DNA-damage signaling and repair pathways. We identify human DVC1 (C1orf124; Spartan) as a cell cycle-regulated anaphase-promoting complex (APC) substrate that accumulates at stalled replication forks. DVC1 recruitment to sites of replication stress...... synthesis (TLS) DNA polymerase η (Pol η) from monoubiquitylated PCNA. DVC1 knockdown enhances UV light-induced mutagenesis, and depletion of human DVC1 or the Caenorhabditis elegans ortholog DVC-1 causes hypersensitivity to replication stress-inducing agents. Our findings establish DVC1 as a DNA damage...

  11. Space weather and coronal mass ejections

    Howard, Tim

    2013-01-01

    Space weather has attracted a lot of attention in recent times. Severe space weather can disrupt spacecraft, and on Earth can be the cause of power outages and power station failure. It also presents a radiation hazard for airline passengers and astronauts. These ""magnetic storms"" are most commonly caused by coronal mass ejections, or CMES, which are large eruptions of plasma and magnetic field from the Sun that can reach speeds of several thousand km/s. In this SpringerBrief, Space Weather and Coronal Mass Ejections, author Timothy Howard briefly introduces the coronal mass ejection, its sc

  12. DNA methylation in Cosmc promoter region and aberrantly glycosylated IgA1 associated with pediatric IgA nephropathy.

    Qiang Sun

    Full Text Available IgA nephropathy (IgAN is one of the most common glomerular diseases leading to end-stage renal failure. Elevation of aberrantly glycosylated IgA1 is a key feature of it. The expression of the specific molecular chaperone of core1ß1, 3galactosyl transferase (Cosmc is known to be reduced in IgAN. We aimed to investigate whether the methylation of CpG islands of Cosmc gene promoter region could act as a possible mechanism responsible for down-regulation of Cosmc and related higher secretion of aberrantly glycosylated IgA1in lymphocytes from children with IgA nephropathy. Three groups were included: IgAN children (n = 26, other renal diseases (n = 11 and healthy children (n = 13. B-lymphocytes were isolated and cultured, treated or not with IL-4 or 5-Aza-2'-deoxycytidine (AZA. The levels of DNA methylation of Cosmc promotor region were not significantly different between the lymphocytes of the three children populations (P = 0.113, but there were significant differences between IgAN lymphocytes and lymphocytes of the other two children populations after IL-4 (P<0.0001 or AZA (P<0.0001. Cosmc mRNA expression was low in IgAN lymphocytes compared to the other two groups (P<0.0001. The level of aberrantly glycosylated IgA1 was markedly higher in IgAN group compared to the other groups (P<0.0001. After treatment with IL-4, the levels of Cosmc DNA methylation and aberrantly glycosylated IgA1 in IgAN lymphocytes were remarkably higher than the other two groups (P<0.0001 with more markedly decreased Cosmc mRNA content (P<0.0001. After treatment with AZA, the levels in IgAN lymphocytes were decreased, but was still remarkably higher than the other two groups (P<0.0001, while Cosmc mRNA content in IgAN lymphocytes were more markedly increased than the other two groups (P<0.0001. The alteration of DNA methylation by IL-4 or AZA specifically correlates in IgAN lymphocytes with alterations in Cosmc mRNA expression and with the level of aberrantly glycosylated

  13. Biallelic MLH1 SNP cDNA expression or constitutional promoter methylation can hide genomic rearrangements causing Lynch syndrome.

    Morak, Monika; Koehler, Udo; Schackert, Hans Konrad; Steinke, Verena; Royer-Pokora, Brigitte; Schulmann, Karsten; Kloor, Matthias; Höchter, Wilhelm; Weingart, Josef; Keiling, Cortina; Massdorf, Trisari; Holinski-Feder, Elke

    2011-08-01

    A positive family history, germline mutations in DNA mismatch repair genes, tumours with high microsatellite instability, and loss of mismatch repair protein expression are the hallmarks of hereditary non-polyposis colorectal cancer (Lynch syndrome). However, in ~10-15% of cases of suspected Lynch syndrome, no disease-causing mechanism can be detected. Oligo array analysis was performed to search for genomic imbalances in patients with suspected mutation-negative Lynch syndrome with MLH1 deficiency in their colorectal tumours. A deletion in the LRRFIP2 (leucine-rich repeat flightless-interacting protein 2) gene flanking the MLH1 gene was detected, which turned out to be a paracentric inversion on chromosome 3p22.2 creating two new stable fusion transcripts between MLH1 and LRRFIP2. A single-nucleotide polymorphism in MLH1 exon 8 was expressed from both alleles, initially pointing to appropriate MLH1 function at least in peripheral cells. In a second case, an inherited duplication of the MLH1 gene region resulted in constitutional MLH1 promoter methylation. Constitutional MLH1 promoter methylation may therefore in rare cases be a heritable disease mechanism and should not be overlooked in seemingly sporadic patients.

  14. SCAI promotes DNA double-strand break repair in distinct chromosomal contexts

    Hansen, Rebecca Kring; Mund, Andreas; Poulsen, Sara Lund

    2016-01-01

    cell invasion) as a 53BP1-interacting chromatin-associated protein that promotes the functionality of several DSB repair pathways in mammalian cells. SCAI undergoes prominent enrichment at DSB sites through dual mechanisms involving 53BP1-dependent recruitment to DSB-surrounding chromatin and 53BP1...... in repressive chromatin environments. Moreover, we establish an important role of SCAI in meiotic recombination, as SCAI deficiency in mice leads to germ cell loss and subfertility associated with impaired retention of the DMC1 recombinase on meiotic chromosomes. Collectively, our findings uncover SCAI...... as a physiologically important component of both NHEJ- and HR-mediated pathways that potentiates DSB repair efficiency in specific chromatin contexts....

  15. In Vitro and In Vivo Plant Growth Promoting Activities and DNA Fingerprinting of Antagonistic Endophytic Actinomycetes Associates with Medicinal Plants.

    Passari, Ajit Kumar; Mishra, Vineet Kumar; Gupta, Vijai Kumar; Yadav, Mukesh Kumar; Saikia, Ratul; Singh, Bhim Pratap

    2015-01-01

    Endophytic actinomycetes have shown unique plant growth promoting as well as antagonistic activity against fungal phytopathogens. In the present study forty-two endophytic actinomycetes recovered from medicinal plants were evaluated for their antagonistic potential and plant growth-promoting abilities. Twenty-two isolates which showed the inhibitory activity against at least one pathogen were subsequently tested for their plant-growth promoting activities and were compared genotypically using DNA based fingerprinting, including enterobacterial repetitive intergenic consensus (ERIC) and BOX repetitive elements. Genetic relatedness based on both ERIC and BOX-PCR generates specific patterns corresponding to particular genotypes. Exponentially grown antagonistic isolates were used to evaluate phosphate solubilization, siderophores, HCN, ammonia, chitinase, indole-3-acetic acid production, as well as antifungal activities. Out of 22 isolates, the amount of indole-3-acetic acid (IAA) ranging between 10-32 μg/ml was produced by 20 isolates and all isolates were positive for ammonia production ranging between 5.2 to 54 mg/ml. Among 22 isolates tested, the amount of hydroxamate-type siderophores were produced by 16 isolates ranging between 5.2 to 36.4 μg/ml, while catechols-type siderophores produced by 5 isolates ranging from 3.2 to 5.4 μg/ml. Fourteen isolates showed the solubilisation of inorganic phosphorous ranging from 3.2 to 32.6 mg/100ml. Chitinase and HCN production was shown by 19 and 15 different isolates, respectively. In addition, genes of indole acetic acid (iaaM) and chitinase (chiC) were successively amplified from 20 and 19 isolates respectively. The two potential strains Streptomyces sp. (BPSAC34) and Leifsonia xyli (BPSAC24) were tested in vivo and improved a range of growth parameters in chilli (Capsicum annuum L.) under greenhouse conditions. This study is the first published report that actinomycetes can be isolated as endophytes from within these

  16. Yeast Srs2 Helicase Promotes Redistribution of Single-Stranded DNA-Bound RPA and Rad52 in Homologous Recombination Regulation

    Luisina De Tullio

    2017-10-01

    Full Text Available Srs2 is a super-family 1 helicase that promotes genome stability by dismantling toxic DNA recombination intermediates. However, the mechanisms by which Srs2 remodels or resolves recombination intermediates remain poorly understood. Here, single-molecule imaging is used to visualize Srs2 in real time as it acts on single-stranded DNA (ssDNA bound by protein factors that function in recombination. We demonstrate that Srs2 is highly processive and translocates rapidly (∼170 nt per second in the 3′→5′ direction along ssDNA saturated with replication protein A (RPA. We show that RPA is evicted from DNA during the passage of Srs2. Remarkably, Srs2 also readily removes the recombination mediator Rad52 from RPA-ssDNA and, in doing so, promotes rapid redistribution of both Rad52 and RPA. These findings have important mechanistic implications for understanding how Srs2 and related nucleic acid motor proteins resolve potentially pathogenic nucleoprotein intermediates.

  17. Yeast Srs2 Helicase Promotes Redistribution of Single-Stranded DNA-Bound RPA and Rad52 in Homologous Recombination Regulation.

    De Tullio, Luisina; Kaniecki, Kyle; Kwon, Youngho; Crickard, J Brooks; Sung, Patrick; Greene, Eric C

    2017-10-17

    Srs2 is a super-family 1 helicase that promotes genome stability by dismantling toxic DNA recombination intermediates. However, the mechanisms by which Srs2 remodels or resolves recombination intermediates remain poorly understood. Here, single-molecule imaging is used to visualize Srs2 in real time as it acts on single-stranded DNA (ssDNA) bound by protein factors that function in recombination. We demonstrate that Srs2 is highly processive and translocates rapidly (∼170 nt per second) in the 3'→5' direction along ssDNA saturated with replication protein A (RPA). We show that RPA is evicted from DNA during the passage of Srs2. Remarkably, Srs2 also readily removes the recombination mediator Rad52 from RPA-ssDNA and, in doing so, promotes rapid redistribution of both Rad52 and RPA. These findings have important mechanistic implications for understanding how Srs2 and related nucleic acid motor proteins resolve potentially pathogenic nucleoprotein intermediates. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  18. Overexpression of transcription factor AP-2 stimulates the PA promoter of the human uracil-DNA glycosylase (UNG) gene through a mechanism involving derepression

    Aas, Per Arne; Pena Diaz, Javier; Liabakk, Nina Beate

    2009-01-01

    within the region of DNA marked by PA. Footprinting analysis and electrophoretic mobility shift assays of PA and putative AP-2 binding regions with HeLa cell nuclear extract and recombinant AP-2alpha protein indicate that AP-2 transcription factors are central in the regulated expression of UNG2 m......The PA promoter in the human uracil-DNA glycosylase gene (UNG) directs expression of the nuclear form (UNG2) of UNG proteins. Using a combination of promoter deletion and mutation analyses, and transient transfection of HeLa cells, we show that repressor and derepressor activities are contained......alpha, lacking the activation domain but retaining the DNA binding and dimerization domains, stimulated PA to a level approaching that of full-length AP-2, suggesting that AP-2 overexpression stimulates PA activity by a mechanism involving derepression rather than activation, possibly by neutralizing...

  19. An analysis of the binding of repressor protein ModE to modABCD (molybdate transport) operator/promoter DNA of Escherichia coli.

    Grunden, A M; Self, W T; Villain, M; Blalock, J E; Shanmugam, K T

    1999-08-20

    Expression of the modABCD operon in Escherichia coli, which codes for a molybdate-specific transporter, is repressed by ModE in vivo in a molybdate-dependent fashion. In vitro DNase I-footprinting experiments identified three distinct regions of protection by ModE-molybdate on the modA operator/promoter DNA, GTTATATT (-15 to -8; region 1), GCCTACAT (-4 to +4; region 2), and GTTACAT (+8 to +14; region 3). Within the three regions of the protected DNA, a pentamer sequence, TAYAT (Y = C or T), can be identified. DNA-electrophoretic mobility experiments showed that the protected regions 1 and 2 are essential for binding of ModE-molybdate to DNA, whereas the protected region 3 increases the affinity of the DNA to the repressor. The stoichiometry of this interaction was found to be two ModE-molybdate per modA operator DNA. ModE-molybdate at 5 nM completely protected the modABCD operator/promoter DNA from DNase I-catalyzed hydrolysis, whereas ModE alone failed to protect the DNA even at 100 nM. The apparent K(d) for the interaction between the modA operator DNA and ModE-molybdate was 0.3 nM, and the K(d) increased to 8 nM in the absence of molybdate. Among the various oxyanions tested, only tungstate replaced molybdate in the repression of modA by ModE, but the affinity of ModE-tungstate for modABCD operator DNA was 6 times lower than with ModE-molybdate. A mutant ModE(T125I) protein, which repressed modA-lac even in the absence of molybdate, protected the same region of modA operator DNA in the absence of molybdate. The apparent K(d) for the interaction between modA operator DNA and ModE(T125I) was 3 nM in the presence of molybdate and 4 nM without molybdate. The binding of molybdate to ModE resulted in a decrease in fluorescence emission, indicating a conformational change of the protein upon molybdate binding. The fluorescence emission spectra of mutant ModE proteins, ModE(T125I) and ModE(Q216*), were unaffected by molybdate. The molybdate-independent mutant Mod

  20. Promoter methylation and expression of MGMT and the DNA mismatch repair genes MLH1, MSH2, MSH6 and PMS2 in paired primary and recurrent glioblastomas.

    Felsberg, Jörg; Thon, Niklas; Eigenbrod, Sabina; Hentschel, Bettina; Sabel, Michael C; Westphal, Manfred; Schackert, Gabriele; Kreth, Friedrich Wilhelm; Pietsch, Torsten; Löffler, Markus; Weller, Michael; Reifenberger, Guido; Tonn, Jörg C

    2011-08-01

    Epigenetic silencing of the O(6) -methylguanine-DNA methyltransferase (MGMT) gene promoter is associated with prolonged survival in glioblastoma patients treated with temozolomide (TMZ). We investigated whether glioblastoma recurrence is associated with changes in the promoter methylation status and the expression of MGMT and the DNA mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2 in pairs of primary and recurrent glioblastomas of 80 patients, including 64 patients treated with radiotherapy and TMZ after the first operation. Among the primary tumors, the MGMT promoter was methylated in 31 patients and unmethylated in 49 patients. In 71 patients (89%), the MGMT promoter methylation status of the primary tumor was retained at recurrence. MGMT promoter methylation, but not MGMT protein expression, was associated with longer progression-free survival, overall survival and postrecurrence survival (PRS). Moreover, PRS was increased under salvage chemotherapy. Investigation of primary and recurrent glioblastomas of 43 patients did not identify promoter methylation in any of the four MMR genes. However, recurrent glioblastomas demonstrated significantly lower MSH2, MSH6 and PMS2 protein expression as detected by immunohistochemistry. In conclusion, reduced expression of MMR proteins, but not changes in MGMT promoter methylation, is characteristic of glioblastomas recurring after the current standards of care. Copyright © 2011 UICC.

  1. Heteroduplex DNA position defines the roles of the Sgs1, Srs2, and Mph1 helicases in promoting distinct recombination outcomes.

    Katrina Mitchel

    Full Text Available The contributions of the Sgs1, Mph1, and Srs2 DNA helicases during mitotic double-strand break (DSB repair in yeast were investigated using a gap-repair assay. A diverged chromosomal substrate was used as a repair template for the gapped plasmid, allowing mismatch-containing heteroduplex DNA (hDNA formed during recombination to be monitored. Overall DSB repair efficiencies and the proportions of crossovers (COs versus noncrossovers (NCOs were determined in wild-type and helicase-defective strains, allowing the efficiency of CO and NCO production in each background to be calculated. In addition, the products of individual NCO events were sequenced to determine the location of hDNA. Because hDNA position is expected to differ depending on whether a NCO is produced by synthesis-dependent-strand-annealing (SDSA or through a Holliday junction (HJ-containing intermediate, its position allows the underlying molecular mechanism to be inferred. Results demonstrate that each helicase reduces the proportion of CO recombinants, but that each does so in a fundamentally different way. Mph1 does not affect the overall efficiency of gap repair, and its loss alters the CO-NCO by promoting SDSA at the expense of HJ-containing intermediates. By contrast, Sgs1 and Srs2 are each required for efficient gap repair, strongly promoting NCO formation and having little effect on CO efficiency. hDNA analyses suggest that all three helicases promote SDSA, and that Sgs1 and Srs2 additionally dismantle HJ-containing intermediates. The hDNA data are consistent with the proposed role of Sgs1 in the dissolution of double HJs, and we propose that Srs2 dismantles nicked HJs.

  2. Prognostic role of APC and RASSF1A promoter methylation status in cell free circulating DNA of operable gastric cancer patients.

    Balgkouranidou, I; Matthaios, D; Karayiannakis, A; Bolanaki, H; Michailidis, P; Xenidis, N; Amarantidis, K; Chelis, L; Trypsianis, G; Chatzaki, E; Lianidou, E S; Kakolyris, S

    2015-08-01

    Gastric carcinogenesis is a multistep process including not only genetic mutations but also epigenetic alterations. The best known and more frequent epigenetic alteration is DNA methylation affecting tumor suppressor genes that may be involved in various carcinogenetic pathways. The aim of the present study was to investigate the methylation status of APC promoter 1A and RASSF1A promoter in cell free DNA of operable gastric cancer patients. Using methylation specific PCR, we examined the methylation status of APC promoter 1A and RASSF1A promoter in 73 blood samples obtained from patients with gastric cancer. APC and RASSF1A promoters were found to be methylated in 61 (83.6%) and 50 (68.5%) of the 73 gastric cancer samples examined, but in none of the healthy control samples (p APC promoter and elevated CEA (p = 0.033) as well as CA-19.9 (p = 0.032) levels, was noticed. The Kaplan-Meier estimates of survival, significantly favored patients with a non-methylated APC promoter status (p = 0.008). No other significant correlations between APC and RASSF1A methylation status and different tumor variables examined was observed. Serum RASSF1A and APC promoter hypermethylation is a frequent epigenetic event in patients with early operable gastric cancer. The observed correlations between APC promoter methylation status and survival as well as between a hypermethylated RASSF1A promoter and nodal positivity may be indicative of a prognostic role for those genes in early operable gastric cancer. Additional studies, in a larger cohort of patients are required to further explore whether these findings could serve as potential molecular biomarkers of survival and/or response to specific treatments. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Evaluation of folate receptor 1 (FOLR1) mRNA expression, its specific promoter methylation and global DNA hypomethylation in type I and type II ovarian cancers

    Notaro, Sara; Reimer, Daniel; Fiegl, Heidi; Schmid, Gabriel; Wiedemair, Annamarie; Rössler, Julia; Marth, Christian; Zeimet, Alain Gustave

    2016-01-01

    In this retrospective study we evaluated the respective correlations and clinical relevance of FOLR1 mRNA expression, FOLR1 promoter specific methylation and global DNA hypomethylation in type I and type II ovarian cancer. Two hundred fifty four ovarian cancers, 13 borderline tumours and 60 samples of healthy fallopian epithelium and normal ovarian epithelium were retrospectively analysed for FOLR1 expression with RT-PCR. FOLR1 DNA promoter methylation and global DNA hypomethylation (measured by means of LINE1 DNA hypomethylation) were evaluated with MethyLight technique. No correlation between FOLR1 mRNA expression and its specific promoter DNA methylation was found neither in type I nor in type II cancers, however, high FOLR1 mRNA expression was found to be correlated with global DNA hypomethylation in type II cancers (p = 0.033). Strong FOLR1 mRNA expression was revealed for Grades 2-3, FIGO stages III-IV, residual disease > 0, and serous histotype. High FOLR1 expression was found to predict increased platinum sensitivity in type I cancers (odds ratio = 3.288; 1.256-10.75; p = 0.020). One-year survival analysis showed in type I cancers an independent better outcome for strong expression of FOLR1 in FIGO stage III and IV. For the entire follow up period no significant independent outcome for FOLR1 expression was revealed. In type I cancers LINE 1 DNA hypomethylation was found to exhibit a worse PFS and OS which were confirmed to be independent in multivariate COX regression model for both PFS (p = 0.026) and OS (p = 0.012). No correlations were found between FOLR1 expression and its specific promoter methylation, however, high FOLR1 mRNA expression was associated with DNA hypomethylation in type II cancers. FOLR1 mRNA expression did not prove to predict clinical outcome in type II cancers, although strong FOLR1 expression generally denotes ovarian cancers with highly aggressive phenotype. In type I cancers, however, strong FOLR1 expression has been found to be a

  4. Validation of the use of an artificial mitochondrial reporter DNA vector containing a Cytomegalovirus promoter for mitochondrial transgene expression.

    Yamada, Yuma; Ishikawa, Takuya; Harashima, Hideyoshi

    2017-08-01

    Mitochondria have their own gene expression system that is independent of the nuclear system, and control cellular functions in cooperation with the nucleus. While a number of useful technologies for achieving nuclear transgene expression have been reported, only a few have focused on mitochondria. In this study, we validated the utility of an artificial mitochondrial DNA vector with a virus promoter on mitochondrial transgene expression. We designed and constructed pCMV-mtLuc (CGG) that contains a CMV promotor derived from Cytomegalovirus and an artificial mitochondrial genome with a NanoLuc (Nluc) luciferase gene that records adjustments to the mitochondrial codon system. Nluc luciferase activity measurements showed that the pCMV-mtLuc (CGG) efficiently produced the Nluc luciferase protein in human HeLa cells. Moreover, we optimized the mitochondrial transfection of pCMV-mtLuc (CGG) using a MITO-Porter system, a liposome-based carrier for mitochondrial delivery via membrane fusion. As a result, we found that transfection of pCMV-mtLuc (CGG) by MITO-Porter modified with the KALA peptide (cationic amphipathic cell-penetrating peptide) showed a high mitochondrial transgene expression. The developed mitochondrial transgene expression system represents a potentially useful tool for the fields of nanoscience and nanotechnology for controlling the intracellular microenvironment via the regulation of mitochondrial function and promises to open additional innovative research fields of study. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. SRSF1 Prevents DNA Damage and Promotes Tumorigenesis through Regulation of DBF4B Pre-mRNA Splicing

    Linlin Chen

    2017-12-01

    Full Text Available Dysregulated alternative splicing events have been implicated in many types of cancer, but the underlying molecular mechanisms remain unclear. Here, we observe that the splicing factor SRSF1 regulates DBF4B exon6 splicing by specifically binding and promoting its inclusion. Knockdown of the exon6-containing isoform (DBF4B-FL significantly inhibits the tumorigenic potential of colon cancer cells in vitro and in mice, and SRSF1 inactivation phenocopies DBF4B-FL depletion. DBF4B-FL and SRSF1 are required for cancer cell proliferation and for the maintenance of genomic stability. Overexpression of DBF4B-FL can protect against DNA damage induced by SRSF1 knockdown and rescues growth defects in SRSF1-depleted cells. Increased DBF4B exon6 inclusion parallels SRSF1 upregulation in clinical colorectal cancer samples. Taken together, our findings identify SRSF1 as a key regulator of DBF4B pre-mRNA splicing dysregulation in colon cancer, with possible clinical implications as candidate prognostic factors in cancer patients.

  6. Proton ejection project for Saturne; Projet d'ejection des protons de saturne

    Bronca, G; Gendreau, G

    1959-07-01

    The reasons for choosing the ejection system are given. The characteristics required for the ejected beam are followed by a description of the ejection process, in chronological order from the viewpoint of the protons: movement of the particles, taking into account the various elements which make up the system (internal magnet, external magnet, quadrupoles, ejection correction coils, thin and thick cables,...) and specification of these elements. Then follows an estimation of the delay in manufacture and the cost of the project. Finally, the characteristics of the magnets and quadrupoles are listed in an appendix. (author) [French] On donne d'abord les raisons du choix du systeme d'ejection, puis le principe. Apres les caracteristiques requises pour le faisceau ejecte, on decrit le processus d'ejection selon l'ordre chronologique vu par les protons: mouvement des particules compte tenu des divers elements composant le systeme (aimant interne, aimant externe, quadrupoles, enroulements correcteurs ejection, cibles mince et epaisse,. ..) et cahier de charge de ces elements. On estime, ensuite les delais de realisation et le cout du projet. Enfin, un resume des caracteristiques des aimants et quadrupoles est donne en appendice. (auteur)

  7. On the mass ejected by supernova explosions

    Bohigas, J.

    1984-01-01

    A simple model is developed in order to calculate the mass ejected by superonovae. We find that the 185, 1006, 1572 and 1604 AD events, all of them classified as either probable or possible type I supernovae, ejected between 0.1 and 0.4 solar masses with an expansion velocity of roughly 10,000 km s -1 . This range of masses suggests that a collapsed object is at the center of the remnants produced by these supernovae if the precursor was a white dwarf whose mass was closed to the Chandrasekhar limit. For the Crab we obtain an ejected mass of 0.45 Msub(sun) and point out that this value is not in contradiction with a proposal in which the moderate helium stars are good candidates for producing this kind of supernovae. Finally we obtain an ejected mass of 3.1 Msub(sun) for Cas A, indicating that a type II event produced this remnant. This ejected mass is closed to what would be expected for a progenitor like an OBN star. (author)

  8. DNA methylation of the gonadal aromatase (cyp19a promoter is involved in temperature-dependent sex ratio shifts in the European sea bass.

    Laia Navarro-Martín

    2011-12-01

    Full Text Available Sex ratio shifts in response to temperature are common in fish and reptiles. However, the mechanism linking temperature during early development and sex ratios has remained elusive. We show in the European sea bass (sb, a fish in which temperature effects on sex ratios are maximal before the gonads form, that juvenile males have double the DNA methylation levels of females in the promoter of gonadal aromatase (cyp19a, the enzyme that converts androgens into estrogens. Exposure to high temperature increased the cyp19a promoter methylation levels of females, indicating that induced-masculinization involves DNA methylation-mediated control of aromatase gene expression, with an observed inverse relationship between methylation levels and expression. Although different CpGs within the sb cyp19a promoter exhibited different sensitivity to temperature, we show that the increased methylation of the sb cyp19a promoter, which occurs in the gonads but not in the brain, is not a generalized effect of temperature. Importantly, these effects were also observed in sexually undifferentiated fish and were not altered by estrogen treatment. Thus, methylation of the sb cyp19a promoter is the cause of the lower expression of cyp19a in temperature-masculinized fish. In vitro, induced methylation of the sb cyp19a promoter suppressed the ability of SF-1 and Foxl2 to stimulate transcription. Finally, a CpG differentially methylated by temperature and adjacent to a Sox transcription factor binding site is conserved across species. Thus, DNA methylation of the aromatase promoter may be an essential component of the long-sought-after mechanism connecting environmental temperature and sex ratios in vertebrate species with temperature-dependent sex determination.

  9. The global DNA methylation surrogate LINE-1 methylation is correlated with MGMT promoter methylation and is a better prognostic factor for glioma.

    Fumiharu Ohka

    Full Text Available Gliomas are the most frequently occurring primary brain tumor in the central nervous system of adults. Glioblastoma multiformes (GBMs, WHO grade 4 have a dismal prognosis despite the use of the alkylating agent, temozolomide (TMZ, and even low grade gliomas (LGGs, WHO grade 2 eventually transform to malignant secondary GBMs. Although GBM patients benefit from promoter hypermethylation of the O(6-methylguanine-DNA methyltransferase (MGMT that is the main determinant of resistance to TMZ, recent studies suggested that MGMT promoter methylation is of prognostic as well as predictive significance for the efficacy of TMZ. Glioma-CpG island methylator phenotype (G-CIMP in the global genome was shown to be a significant predictor of improved survival in patients with GBM. Collectively, we hypothesized that MGMT promoter methylation might reflect global DNA methylation. Additionally in LGGs, the significance of MGMT promoter methylation is still undetermined. In the current study, we aimed to determine the correlation between clinical, genetic, and epigenetic profiles including LINE-1 and different cancer-related genes and the clinical outcome in newly diagnosed 57 LGG and 54 GBM patients. Here, we demonstrated that (1 IDH1/2 mutation is closely correlated with MGMT promoter methylation and 1p/19q codeletion in LGGs, (2 LINE-1 methylation levels in primary and secondary GBMs are lower than those in LGGs and normal brain tissues, (3 LINE-1 methylation is proportional to MGMT promoter methylation in gliomas, and (4 higher LINE-1 methylation is a favorable prognostic factor in primary GBMs, even compared to MGMT promoter methylation. As a global DNA methylation marker, LINE-1 may be a promising marker in gliomas.

  10. Hypoxia-induced DNA hypermethylation in human pulmonary fibroblasts is associated with Thy-1 promoter methylation and the development of a pro-fibrotic phenotype

    Robinson Claire M

    2012-08-01

    Full Text Available Abstract Background Pulmonary fibrosis is a debilitating and lethal disease with no effective treatment options. Understanding the pathological processes at play will direct the application of novel therapeutic avenues. Hypoxia has been implicated in the pathogenesis of pulmonary fibrosis yet the precise mechanism by which it contributes to disease progression remains to be fully elucidated. It has been shown that chronic hypoxia can alter DNA methylation patterns in tumour-derived cell lines. This epigenetic alteration can induce changes in cellular phenotype with promoter methylation being associated with gene silencing. Of particular relevance to idiopathic pulmonary fibrosis (IPF is the observation that Thy-1 promoter methylation is associated with a myofibroblast phenotype where loss of Thy-1 occurs alongside increased alpha smooth muscle actin (α-SMA expression. The initial aim of this study was to determine whether hypoxia regulates DNA methylation in normal human lung fibroblasts (CCD19Lu. As it has been reported that hypoxia suppresses Thy-1 expression during lung development we also studied the effect of hypoxia on Thy-1 promoter methylation and gene expression. Methods CCD19Lu were grown for up to 8 days in hypoxia and assessed for global changes in DNA methylation using flow cytometry. Real-time PCR was used to quantify expression of Thy-1, α-SMA, collagen I and III. Genomic DNA was bisulphite treated and methylation specific PCR (MSPCR was used to examine the methylation status of the Thy-1 promoter. Results Significant global hypermethylation was detected in hypoxic fibroblasts relative to normoxic controls and was accompanied by increased expression of myofibroblast markers. Thy-1 mRNA expression was suppressed in hypoxic cells, which was restored with the demethylating agent 5-aza-2′-deoxycytidine. MSPCR revealed that Thy-1 became methylated following fibroblast exposure to 1% O2. Conclusion These data suggest that global and

  11. Coronal mass ejections and coronal structures

    Hildner, E.; Bassi, J.; Bougeret, J.L.

    1986-01-01

    Research on coronal mass ejections (CMF) took a variety of forms, both observational and theoretical. On the observational side there were: case studies of individual events, in which it was attempted to provide the most complete descriptions possible, using correlative observations in diverse wavelengths; statistical studies of the properties of CMEs and their associated activity; observations which may tell us about the initiation of mass ejections; interplanetary observations of associated shocks and energetic particles; observations of CMEs traversing interplanetary space; and the beautiful synoptic charts which show to what degree mass ejections affect the background corona and how rapidly (if at all) the corona recovers its pre-disturbance form. These efforts are described in capsule form with an emphasis on presenting pictures, graphs, and tables so that the reader can form a personal appreciation of the work and its results

  12. Mycobacterium tuberculosis UvrD1 and UvrA proteins suppress DNA strand exchange promoted by cognate and noncognate RecA proteins.

    Singh, Pawan; Patil, K Neelakanteshwar; Khanduja, Jasbeer Singh; Kumar, P Sanjay; Williams, Alan; Rossi, Franca; Rizzi, Menico; Davis, Elaine O; Muniyappa, K

    2010-06-15

    DNA helicases are present in all kingdoms of life and play crucial roles in processes of DNA metabolism such as replication, repair, recombination, and transcription. To date, however, the role of DNA helicases during homologous recombination in mycobacteria remains unknown. In this study, we show that Mycobacterium tuberculosis UvrD1 more efficiently inhibited the strand exchange promoted by its cognate RecA, compared to noncognate Mycobacterium smegmatis or Escherichia coli RecA proteins. The M. tuberculosis UvrD1(Q276R) mutant lacking the helicase and ATPase activities was able to block strand exchange promoted by mycobacterial RecA proteins but not of E. coli RecA. We observed that M. tuberculosis UvrA by itself has no discernible effect on strand exchange promoted by E. coli RecA but impedes the reaction catalyzed by the mycobacterial RecA proteins. Our data also show that M. tuberculosis UvrA and UvrD1 can act together to inhibit strand exchange promoted by mycobacterial RecA proteins. Taken together, these findings raise the possibility that UvrD1 and UvrA might act together in vivo to counter the deleterious effects of RecA nucleoprotein filaments and/or facilitate the dissolution of recombination intermediates. Finally, we provide direct experimental evidence for a physical interaction between M. tuberculosis UvrD1 and RecA on one hand and RecA and UvrA on the other hand. These observations are consistent with a molecular mechanism, whereby M. tuberculosis UvrA and UvrD1, acting together, block DNA strand exchange promoted by cognate and noncognate RecA proteins.

  13. MMS exposure promotes increased MtDNA mutagenesis in the presence of replication-defective disease-associated DNA polymerase γ variants.

    Stumpf, Jeffrey D; Copeland, William C

    2014-10-01

    Mitochondrial DNA (mtDNA) encodes proteins essential for ATP production. Mutant variants of the mtDNA polymerase cause mutagenesis that contributes to aging, genetic diseases, and sensitivity to environmental agents. We interrogated mtDNA replication in Saccharomyces cerevisiae strains with disease-associated mutations affecting conserved regions of the mtDNA polymerase, Mip1, in the presence of the wild type Mip1. Mutant frequency arising from mtDNA base substitutions that confer erythromycin resistance and deletions between 21-nucleotide direct repeats was determined. Previously, increased mutagenesis was observed in strains encoding mutant variants that were insufficient to maintain mtDNA and that were not expected to reduce polymerase fidelity or exonuclease proofreading. Increased mutagenesis could be explained by mutant variants stalling the replication fork, thereby predisposing the template DNA to irreparable damage that is bypassed with poor fidelity. This hypothesis suggests that the exogenous base-alkylating agent, methyl methanesulfonate (MMS), would further increase mtDNA mutagenesis. Mitochondrial mutagenesis associated with MMS exposure was increased up to 30-fold in mip1 mutants containing disease-associated alterations that affect polymerase activity. Disrupting exonuclease activity of mutant variants was not associated with increased spontaneous mutagenesis compared with exonuclease-proficient alleles, suggesting that most or all of the mtDNA was replicated by wild type Mip1. A novel subset of C to G transversions was responsible for about half of the mutants arising after MMS exposure implicating error-prone bypass of methylated cytosines as the predominant mutational mechanism. Exposure to MMS does not disrupt exonuclease activity that suppresses deletions between 21-nucleotide direct repeats, suggesting the MMS-induce mutagenesis is not explained by inactivated exonuclease activity. Further, trace amounts of CdCl2 inhibit mtDNA replication but

  14. Ultrasonographic ejection fraction of normal gallbladder

    Park, Jin Hun; Kim, Seung Yup; Park, Yaung Hee; Kang, Ik Won; Yoon, Jong Sup [Hangang Sacred Heart Hospital, Halym College, Chuncheon (Korea, Republic of)

    1984-06-15

    Real-time ultrasonography is a simple, accurate, noninvasive and potentially valuable means of studying gallbladder size and emptying. The authors calculated ultrasonographically the ejection fraction of 80 cases of normally functioning gallbladder on oral cholecystography, from June 1983 to April 1984, at the department of radiology, Hangang Sacred Heart Hospital. The results were obtained as follows; 1. Ultrasonographic Ejection Fraction at 30 minutes after the fatty meal was 73.1{+-}16.85. 2. There was no significant difference in age and sex, statistically.

  15. Promoter hypermethylation of DNA repair genes MLH1 and MSH2 in adenocarcinomas and squamous cell carcinomas of the lung

    A. Gomes

    2014-01-01

    Full Text Available Five years survival of lung cancer is 16%, significantly lower than in prostate (99.9%, breast (88.5% and colon (64.1% carcinomas. When diagnosed in the surgical stage it increases to 50% but this group only comprises 14–16% of the cases. DNA methylation has emerged as a potential cancer-specific biomarker. Hypermethylation of CpG islands located in the promoter regions of tumour suppressor genes is now firmly established as an important mechanism for gene inactivation.This retrospective study included 40 squamous cell carcinomas and 40 adenocarcinomas in various surgical TNM stages to define methylation profile and possible silencing of DNA repair genes – MLH1 and MSH2 – using Methylation-Specific PCR and protein expression by immunohistochemistry in tumoural tissue, preneoplastic lesions and respiratory epithelium with normal histological features.The protein expression of MLH1 and MSH2 genes, in the available preneoplastic lesions and in normal cylindrical respiratory epithelium appeared reduced. The frequency of promoter hypermethylation found on these DNA repair genes was elevated, with a higher prevalence of methylation of MLH1 gene in 72% of squamous cell carcinoma. The differences are not so obvious for MSH2 promoter hypermethylation. No correlation was found among the status of methylation, the protein expression and the clinicopathological characteristics.With a larger study, a better characterization of the hypermethylation status of neoplastic and preneoplastic lesions in small biopsies would be achieved, inherent to tumour histology, heterogeneity and preservation, and finally differences in the study population to elucidate other possible mechanisms of altered expression of the hMLH1 and hMSH. Resumo: A sobrevivência aos cinco anos no cancro do pulmão é de 16%, significativamente inferior que nos carcinomas na próstata (99,9%, mama (88,5% e cólon (64,1%. Quando diagnosticado na fase cir

  16. Targeting human c-Myc promoter duplex DNA with actinomycin D by use of multi-way analysis of quantum-dot-mediated fluorescence resonance energy transfer

    Gholami, Somayeh; Kompany Zare, Mohsen

    2013-01-01

    Actinomycin D (Act D), an oncogenic c-Myc promoter binder, interferes with the action of RNA polymerase. There is great demand for high-throughput technology able to monitor the activity of DNA-binding drugs. To this end, binding of 7-aminoactinomycin D (7AAD) to the duplex c-Myc promoter...... pairs resulted in efficient energy transfer from drug to QD via fluorescence resonance energy transfer (FRET). Multi-way analysis of the three-way data array obtained from titration experiments was performed by use of restricted Tucker3 and hard trilinear decomposition (HTD). These techniques enable...... the important advantage over univariate classical methods of enabling us to investigate the source of variance in the fluorescence signal of the DNA-drug complex. It was established that hard trilinear decomposition analysis of FRET-measured data overcomes the problem of rank deficiency, enabling calculation...

  17. ESR1 gene promoter region methylation in free circulating DNA and its correlation with estrogen receptor protein expression in tumor tissue in breast cancer patients

    Martínez-Galán, Joaquina; Ríos, Sandra; Delgado, Juan Ramón; Torres-Torres, Blanca; Núñez, María Isabel; López-Peñalver, Jesús; Del Moral, Rosario; Ruiz De Almodóvar, José Mariano; Menjón, Salomón; Concha, Ángel; Chamorro, Clara

    2014-01-01

    Tumor expression of estrogen receptor (ER) is an important marker of prognosis, and is predictive of response to endocrine therapy in breast cancer. Several studies have observed that epigenetic events, such methylation of cytosines and deacetylation of histones, are involved in the complex mechanisms that regulate promoter transcription. However, the exact interplay of these factors in transcription activity is not well understood. In this study, we explored the relationship between ER expression status in tumor tissue samples and the methylation of the 5′ CpG promoter region of the estrogen receptor gene (ESR1) isolated from free circulating DNA (fcDNA) in plasma samples from breast cancer patients. Patients (n = 110) with non-metastatic breast cancer had analyses performed of ER expression (luminal phenotype in tumor tissue, by immunohistochemistry method), and the ESR1-DNA methylation status (fcDNA in plasma, by quantitative methylation specific PCR technique). Our results showed a significant association between presence of methylated ESR1 in patients with breast cancer and ER negative status in the tumor tissue (p = 0.0179). There was a trend towards a higher probability of ESR1-methylation in those phenotypes with poor prognosis i.e. 80% of triple negative patients, 60% of HER2 patients, compared to 28% and 5.9% of patients with better prognosis such as luminal A and luminal B, respectively. Silencing, by methylation, of the promoter region of the ESR1 affects the expression of the estrogen receptor protein in tumors of breast cancer patients; high methylation of ESR1-DNA is associated with estrogen receptor negative status which, in turn, may be implicated in the patient’s resistance to hormonal treatment in breast cancer. As such, epigenetic markers in plasma may be of interest as new targets for anticancer therapy, especially with respect to endocrine treatment

  18. DNA-binding site of major regulatory protein alpha 4 specifically associated with promoter-regulatory domains of alpha genes of herpes simplex virus type 1.

    Kristie, T M; Roizman, B

    1986-01-01

    Herpes simplex virus type 1 genes form at least five groups (alpha, beta 1, beta 2, gamma 1, and gamma 2) whose expression is coordinately regulated and sequentially ordered in a cascade fashion. Previous studies have shown that functional alpha 4 gene product is essential for the transition from alpha to beta protein synthesis and have suggested that alpha 4 gene expression is autoregulatory. We have previously reported that labeled DNA fragments containing promoter-regulatory domains of thr...

  19. Do centrioles generate a polar ejection force?

    Wells, Jonathan

    2005-01-01

    A microtubule-dependent polar ejection force that pushes chromosomes away from spindle poles during prometaphase is observed in animal cells but not in the cells of higher plants. Elongating microtubules and kinesin-like motor molecules have been proposed as possible causes, but neither accounts for all the data. In the hypothesis proposed here a polar ejection force is generated by centrioles, which are found in animals but not in higher plants. Centrioles consist of nine microtubule triplets arranged like the blades of a tiny turbine. Instead of viewing centrioles through the spectacles of molecular reductionism and neo-Darwinism, this hypothesis assumes that they are holistically designed to be turbines. Orthogonally oriented centriolar turbines could generate oscillations in spindle microtubules that resemble the motion produced by a laboratory vortexer. The result would be a microtubule-mediated ejection force tending to move chromosomes away from the spindle axis and the poles. A rise in intracellular calcium at the onset of anaphase could regulate the polar ejection force by shutting down the centriolar turbines, but defective regulation could result in an excessive force that contributes to the chromosomal instability characteristic of most cancer cells.

  20. The 3'-to-5' exonuclease activity of vaccinia virus DNA polymerase is essential and plays a role in promoting virus genetic recombination.

    Gammon, Don B; Evans, David H

    2009-05-01

    Poxviruses are subjected to extraordinarily high levels of genetic recombination during infection, although the enzymes catalyzing these reactions have never been identified. However, it is clear that virus-encoded DNA polymerases play some unknown yet critical role in virus recombination. Using a novel, antiviral-drug-based strategy to dissect recombination and replication reactions, we now show that the 3'-to-5' proofreading exonuclease activity of the viral DNA polymerase plays a key role in promoting recombination reactions. Linear DNA substrates were prepared containing the dCMP analog cidofovir (CDV) incorporated into the 3' ends of the molecules. The drug blocked the formation of concatemeric recombinant molecules in vitro in a process that was catalyzed by the proofreading activity of vaccinia virus DNA polymerase. Recombinant formation was also blocked when CDV-containing recombination substrates were transfected into cells infected with wild-type vaccinia virus. These inhibitory effects could be overcome if CDV-containing substrates were transfected into cells infected with CDV-resistant (CDV(r)) viruses, but only when resistance was linked to an A314T substitution mutation mapping within the 3'-to-5' exonuclease domain of the viral polymerase. Viruses encoding a CDV(r) mutation in the polymerase domain still exhibited a CDV-induced recombination deficiency. The A314T substitution also enhanced the enzyme's capacity to excise CDV molecules from the 3' ends of duplex DNA and to recombine these DNAs in vitro, as judged from experiments using purified mutant DNA polymerase. The 3'-to-5' exonuclease activity appears to be an essential virus function, and our results suggest that this might be because poxviruses use it to promote genetic exchange.

  1. A preliminary study of endocannabinoid system regulation in psychosis: Distinct alterations of CNR1 promoter DNA methylation in patients with schizophrenia.

    D'Addario, Claudio; Micale, Vincenzo; Di Bartolomeo, Martina; Stark, Tibor; Pucci, Mariangela; Sulcova, Alexandra; Palazzo, Mariacarlotta; Babinska, Zuzana; Cremaschi, Laura; Drago, Filippo; Carlo Altamura, A; Maccarrone, Mauro; Dell'Osso, Bernardo

    2017-10-01

    Compelling evidence supports the involvement of the endocannabinoid system (ECS) in psychosis vulnerability. We here evaluated the transcriptional regulation of ECS components in human peripheral blood mononuclear cells (PBMCs) obtained from subjects suffering from bipolar disorder, major depressive disorder and schizophrenia, focusing in particular on the effects of DNA methylation. We observed selective alterations of DNA methylation at the promoter of CNR1, the gene coding for the type-1 cannabinoid receptor, in schizophrenic patients (N=25) with no changes in any other disorder. We confirmed the regulation of CNR1 in a well-validated animal model of schizophrenia, induced by prenatal methylazoxymethanol (MAM) acetate exposure (N=7 per group) where we found, in the prefrontal cortex, a significant increase in CNR1 expression and a consistent reduction in DNA methylation at specific CpG sites of gene promoter. Overall, our findings suggest a selective dysregulation of ECS in psychosis, and highlight the evaluation of CNR1 DNA methylation levels in PBMCs as a potential biomarker for schizophrenia. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. The carboxyl terminus of FANCE recruits FANCD2 to the Fanconi Anemia (FA) E3 ligase complex to promote the FA DNA repair pathway.

    Polito, David; Cukras, Scott; Wang, Xiaozhe; Spence, Paige; Moreau, Lisa; D'Andrea, Alan D; Kee, Younghoon

    2014-03-07

    Fanconi anemia (FA) is a genome instability syndrome characterized by bone marrow failure and cellular hypersensitivity to DNA cross-linking agents. In response to DNA damage, the FA pathway is activated through the cooperation of 16 FA proteins. A central player in the pathway is a multisubunit E3 ubiquitin ligase complex or the FA core complex, which monoubiquitinates its substrates FANCD2 and FANCI. FANCE, a subunit of the FA core complex, plays an essential role by promoting the integrity of the complex and by directly recognizing FANCD2. To delineate its role in substrate ubiquitination from the core complex assembly, we analyzed a series of mutations within FANCE. We report that a phenylalanine located at the highly conserved extreme C terminus, referred to as Phe-522, is a critical residue for mediating the monoubiquitination of the FANCD2-FANCI complex. Using the FANCE mutant that specifically disrupts the FANCE-FANCD2 interaction as a tool, we found that the interaction-deficient mutant conferred cellular sensitivity in reconstituted FANCE-deficient cells to a similar degree as FANCE null cells, suggesting the significance of the FANCE-FANCD2 interaction in promoting cisplatin resistance. Intriguingly, ectopic expression of the FANCE C terminus fragment alone in FA normal cells disrupts DNA repair, consolidating the importance of the FANCE-FANCD2 interaction in the DNA cross-link repair.

  3. The Carboxyl Terminus of FANCE Recruits FANCD2 to the Fanconi Anemia (FA) E3 Ligase Complex to Promote the FA DNA Repair Pathway*

    Polito, David; Cukras, Scott; Wang, Xiaozhe; Spence, Paige; Moreau, Lisa; D'Andrea, Alan D.; Kee, Younghoon

    2014-01-01

    Fanconi anemia (FA) is a genome instability syndrome characterized by bone marrow failure and cellular hypersensitivity to DNA cross-linking agents. In response to DNA damage, the FA pathway is activated through the cooperation of 16 FA proteins. A central player in the pathway is a multisubunit E3 ubiquitin ligase complex or the FA core complex, which monoubiquitinates its substrates FANCD2 and FANCI. FANCE, a subunit of the FA core complex, plays an essential role by promoting the integrity of the complex and by directly recognizing FANCD2. To delineate its role in substrate ubiquitination from the core complex assembly, we analyzed a series of mutations within FANCE. We report that a phenylalanine located at the highly conserved extreme C terminus, referred to as Phe-522, is a critical residue for mediating the monoubiquitination of the FANCD2-FANCI complex. Using the FANCE mutant that specifically disrupts the FANCE-FANCD2 interaction as a tool, we found that the interaction-deficient mutant conferred cellular sensitivity in reconstituted FANCE-deficient cells to a similar degree as FANCE null cells, suggesting the significance of the FANCE-FANCD2 interaction in promoting cisplatin resistance. Intriguingly, ectopic expression of the FANCE C terminus fragment alone in FA normal cells disrupts DNA repair, consolidating the importance of the FANCE-FANCD2 interaction in the DNA cross-link repair. PMID:24451376

  4. Supernova mass ejection and core hydrodynamics

    Colgate, S.A.

    1978-01-01

    Simplifications that have emerged in the descriptions of stellar unstable collapse to a neutron star are discussed. The neutral current weak interaction leads to almost complete neutrino trapping in the collapse and to an electron fraction Y/sub e/ congruent to 0.35 in equilibrium with trapped electron neutrinos and ''iron'' nuclei. A soft equation of state (γ congruent to 1.30) leads to collapse, and bounce occurs on a hard core, γ = 2.5, at nuclear densities. Neutrino emission is predicted from a photosphere at r congruent to 2 x 10 7 cm and E/sub ν/ congruent to 10 MeV. The ejection of matter by an elastic core bounce and a subsequent escaping shock is marginal and may not be predicted for accurate values of the equation of state. A new concept of Rayleigh-Taylor driven core instabilities is invoked to predict an increased mass ejection either due to an increased flux and energy of neutrinos at second bounce time and, or, the rapid 0.1 to 0.4 second formation of a more energetically bound neutron star. The instability is caused by highly neutronized external matter from which neutrinos have escaped being supported by lighter matter of the lepton trapped core. An initial anisotropy of 10 -2 to 10 -3 should lead to adequately rapid (several milliseconds) overturn following several (2 to 4) bounces. Subsequent to the overturnwith or without a strong ejection shock, a weak ejection shock will allow an accretion shock to form on the ''cold'' neutron star core due to the reimplosion or rarefaction wave in the weakly ejected matter. The accretion shock forms at low enough mass accumulation rate, 1 / 2 M/sub solar/ sec -1 , such that a black body neutrino flux can escape from the shock front (kT congruent to 10 MeV, [E/sub ν/] congruent to 30 MeV). This strongly augments the weaker bounce ejection shock by heating the external matter in the mantle by electron neutrino scattering (congruent to 10 52 ergs) causing adequate mass ejection

  5. Virus-sized self-assembling lamellar complexes between plasmid DNA and cationic micelles promote gene transfer

    Pitard, Bruno; Aguerre, Olivier; Airiau, Marc; Lachagès, Anne-Marie; Boukhnikachvili, Tsiala; Byk, Gérardo; Dubertret, Catherine; Herviou, Christian; Scherman, Daniel; Mayaux, Jean-François; Crouzet, Joël

    1997-01-01

    Gene therapy is based on the vectorization of genes to target cells and their subsequent expression. Cationic amphiphile-mediated delivery of plasmid DNA is the nonviral gene transfer method most often used. We examined the supramolecular structure of lipopolyamine/plasmid DNA complexes under various condensing conditions. Plasmid DNA complexation with lipopolyamine micelles whose mean diameter was 5 nm revealed three domains, depending on the lipopolyamine/plasmid DNA ratio. These domains respectively corresponded to negatively, neutrally, and positively charged complexes. Transmission electron microscopy and x-ray scattering experiments on complexes originating from these three domains showed that although their morphology depends on the lipopolyamine/plasmid DNA ratio, their particle structure consists of ordered domains characterized by even spacing of 80 Å, irrespective of the lipid/DNA ratio. The most active lipopolyamine/DNA complexes for gene transfer were positively charged. They were characterized by fully condensed DNA inside spherical particles (diameter: 50 nm) sandwiched between lipid bilayers. These results show that supercoiled plasmid DNA is able to transform lipopolyamine micelles into a supramolecular organization characterized by ordered lamellar domains. PMID:9405626

  6. Structural organization of DNA in chlorella viruses.

    Timo Wulfmeyer

    Full Text Available Chlorella viruses have icosahedral capsids with an internal membrane enclosing their large dsDNA genomes and associated proteins. Their genomes are packaged in the particles with a predicted DNA density of ca. 0.2 bp nm(-3. Occasionally infection of an algal cell by an individual particle fails and the viral DNA is dynamically ejected from the capsid. This shows that the release of the DNA generates a force, which can aid in the transfer of the genome into the host in a successful infection. Imaging of ejected viral DNA indicates that it is intimately associated with proteins in a periodic fashion. The bulk of the protein particles detected by atomic force microscopy have a size of ∼60 kDa and two proteins (A278L and A282L of about this size are among 6 basic putative DNA binding proteins found in a proteomic analysis of DNA binding proteins packaged in the virion. A combination of fluorescence images of ejected DNA and a bioinformatics analysis of the DNA reveal periodic patterns in the viral DNA. The periodic distribution of GC rich regions in the genome provides potential binding sites for basic proteins. This DNA/protein aggregation could be responsible for the periodic concentration of fluorescently labeled DNA observed in ejected viral DNA. Collectively the data indicate that the large chlorella viruses have a DNA packaging strategy that differs from bacteriophages; it involves proteins and share similarities to that of chromatin structure in eukaryotes.

  7. Higher-speed coronal mass ejections and their geoeffectiveness

    Singh, A. K.; Bhargawa, Asheesh; Tonk, Apeksha

    2018-06-01

    We have attempted to examine the ability of coronal mass ejections to cause geoeffectiveness. To that end, we have investigated total 571 cases of higher-speed (> 1000 km/s) coronal mass ejection events observed during the years 1996-2012. On the basis of angular width (W) of observance, events of coronal mass ejection were further classified as front-side or halo coronal mass ejections (W = 360°); back-side halo coronal mass ejections (W = 360°); partial halo (120°mass ejections were much faster and more geoeffective in comparison of partial halo and non-halo coronal mass ejections. We also inferred that the front-sided halo coronal mass ejections were 67.1% geoeffective while geoeffectiveness of partial halo coronal mass ejections and non-halo coronal mass ejections were found to be 44.2% and 56.6% respectively. During the same period of observation, 43% of back-sided CMEs showed geoeffectiveness. We have also investigated some events of coronal mass ejections having speed > 2500 km/s as a case study. We have concluded that mere speed of coronal mass ejection and their association with solar flares or solar activity were not mere criterion for producing geoeffectiveness but angular width of coronal mass ejections and their originating position also played a key role.

  8. DNA vaccination in fish promotes an early chemokine-related recruitment of B cells to the muscle

    Castro, R.; Martínez-Alonso, S.; Fischer, U.

    2013-01-01

    might explain the recruitment of immune cells to the site of DNA injection. Our results suggest that B cells are involved in the initial phase of the immune response to intramuscular DNA vaccination against VHSV. This appears to be a major difference to what we know from mammalian models where T cells...

  9. Genome-wide DNA methylation profiling identifies ALDH1A3 promoter methylation as a prognostic predictor in G-CIMP- primary glioblastoma.

    Zhang, Wei; Yan, Wei; You, Gan; Bao, Zhaoshi; Wang, Yongzhi; Liu, Yanwei; You, Yongping; Jiang, Tao

    2013-01-01

    To date, the aberrations in the DNA methylation patterns that are associated with different prognoses of G-CIMP- primary GBMs remain to be elucidated. Here, DNA methylation profiling of primary GBM tissues from 13 long-term survivors (LTS; overall survival ⩾18months) and 20 short-term survivors (STS; overall survival ⩽9months) was performed. Then G-CIMP+ samples were excluded. The differentially expressed CpG loci were identified between residual 18 STS and 9 LTS G-CIMP- samples. Methylation levels of 11 CpG loci (10genes) were statistically significantly lower, and 43 CpG loci (40genes) were statistically significantly higher in the tumor tissues of LTS than those of STS G-CIMP- samples (PCIMP- samples, 3 CpG loci localized in the promoter of ALDH1A3. Furthermore, using an independent validation cohort containing 37 primary GBM samples without IDH1 mutation and MGMT promoter methylation, the hypermethylation status of ALDH1A3 promoter predicted a better prognosis with an accompanied low expression of ALDH1A3 protein. Taken together, our results defined prognosis-related methylation signatures systematically for the first time in G-CIMP- primary GBMs. ALDH1A3 promoter methylation conferred a favorable prognosis in G-CIMP- primary GBMs. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  10. DNA methylation induced changes in chromatin conformation of the promoter of the vitellogenin II gene of Japanese quail during aging.

    Gupta, Sanjay; Pathak, Rashmi U; Kanungo, Madhu S

    2006-08-01

    One approach to the understanding of the molecular basis of aging in higher organisms may be to use genes whose timing and rate of expression during the life span run parallel with specific functions that can be monitored. The genes for egg proteins, such as vitellogenin (VTG), which is expressed in the liver, and ovalbumin, lysozyme etc. that are expressed in the oviduct of birds, meet these requirements. Egg laying function is dependent on the production of these proteins, which, in turn, depends on the expression of their genes. In this communication we present the age-related studies on the VTG II gene of the bird, Japanese quail. The gene is expressed only in the liver and its expression is considerably lower in old birds that do not lay eggs. Comparison of the promoter region of the gene carrying the two important cis-acting elements, estrogen responsive element (ERE) and progesterone responsive element (PRE), shows it to be 100% homologous to the corresponding region of the chicken VTG II gene. Methylation of DNA and conformation of chromatin of this region were studied, as they are known to be important for regulation of expression of genes. Our studies show that in the liver of adult female quails which lay eggs, a -CCGG- sequence located in this region is hypomethylated, and the chromatin encompassing this region of the gene is relaxed. In the old, the -CCGG- sequence is hypermethylated and the chromatin is compact. This is correlated with a decrease in the expression of the gene and decrease in egg production. Further, electrophoretic mobility shift assay (EMSA) shows that the levels/affinity of specific trans-acting factors that bind to ERE and PRE present in the region, are not different in adult and old birds. Hence the methylation status of the -CCGG- sequence that is located in-between the ERE and the PRE may be crucial for the conformation of chromatin and availability of these two important cis-acting elements for the binding of the trans

  11. Aircrew ejection experience: questionnaire responses from 20 survivors.

    Taneja, Narinder; Pinto, Leslie J; Dogra, Manmohan

    2005-07-01

    Published studies on ejection have focused predominantly on the injuries sustained by aircrew and discussed their preventive measures from an aeromedical perspective. However, studies have not discussed aircrew experiences related to ejection or how they would like to advise other aircrew to successfully handle ejection as an event. Such information can assist in designing realistic indoctrination and training programs. This study was conducted to fill gaps in our understanding of aircrew perspectives of successful ejections. Aircrew reporting to the Institute of Aerospace Medicine (IAM), Indian Air Force, for post-ejection evaluation during the period of May 2003 to January 2005 completed a questionnaire that was designed for the study. A total of 20 aircrew completed this questionnaire. The mean age of the aircrew was 30.25 +/- 4.45 yr. Most of them had logged more than 500 flying hours. Some aircrew described their initial moments of ejection as "blacked out," "dazed, yet conscious," or as "a shock that gradually decreased." Practicing ejection drills on the ground, being prepared at all times, making a timely decision to eject, and assuming correct posture were identified as the most important factors for success. Descriptions of ejection as an event suggest intense emotional arousal could occur following ejection. This study provides first hand inputs into the psychological processes accompanying ejections. Such information could be very useful in understanding the critical factors that influence successful ejection.

  12. Pilot ejection, parachute, and helicopter crash injuries.

    McBratney, Colleen M; Rush, Stephen; Kharod, Chetan U

    2014-01-01

    USAF Pararescuemen (PJs) respond to downed aircrew as a fundamental mission for personnel recovery (PR), one of the Air Force's core functions. In addition to responding to these in Military settings, the PJs from the 212 Rescue Squadron routinely respond to small plane crashes in remote regions of Alaska. While there is a paucity of information on the latter, there have been articles detailing injuries sustained from helicopter crashes and while ejecting or parachuting from fixed wing aircraft. The following represents a new chapter added to the Pararescue Medical Operations Handbook, Sixth Edition (2014, editors Matt Wolf, MD, and Stephen Rush, MD, in press). It was designed to be a quick reference for PJs and their Special Operations flight surgeons to help with understanding of mechanism of injury with regard to pilot ejection, parachute, and helicopter accident injuries. It outlines the nature of the injuries sustained in such mishaps and provides an epidemiologic framework from which to approach the problem. 2014.

  13. Interplanetary Coronal Mass Ejections detected by HAWC

    Lara, Alejandro

    The High Altitude Water Cherenkov (HAWC) observatory is being constructed at the volcano Sierra Negra (4100 m a.s.l.) in Mexico. HAWC’s primary purpose is the study of both: galactic and extra-galactic sources of high energy gamma rays. HAWC will consist of 300 large water Cherenkov detectors (WCD), instrumented with 1200 photo-multipliers. The Data taking has already started while construction continues, with the completion projected for late 2014. The HAWC counting rate will be sensitive to cosmic rays with energies above the geomagnetic cutoff of the site (˜ 8 GV). In particular, HAWC will detect solar energetic particles known as Ground Level Enhancements (GLEs), and the effects of Coronal Mass Ejections on the galactic cosmic ray flux, known as Forbush Decreases. In this paper, we present a description of the instrument and its response to interplanetary coronal mass ejections, and other solar wind large scale structures, observed during the August-December 2013 period.

  14. Nonperiodic activity of the human anaphase-promoting complex-Cdh1 ubiquitin ligase results in continuous DNA synthesis uncoupled from mitosis

    Lukas, C; Kramer, E R; Peters, J M

    2000-01-01

    Ubiquitin-proteasome-mediated destruction of rate-limiting proteins is required for timely progression through the main cell cycle transitions. The anaphase-promoting complex (APC), periodically activated by the Cdh1 subunit, represents one of the major cellular ubiquitin ligases which, in Saccha......Ubiquitin-proteasome-mediated destruction of rate-limiting proteins is required for timely progression through the main cell cycle transitions. The anaphase-promoting complex (APC), periodically activated by the Cdh1 subunit, represents one of the major cellular ubiquitin ligases which......, in Saccharomyces cerevisiae and Drosophila spp., triggers exit from mitosis and during G(1) prevents unscheduled DNA replication. In this study we investigated the importance of periodic oscillation of the APC-Cdh1 activity for the cell cycle progression in human cells. We show that conditional interference...... transition and lowered the rate of DNA synthesis during S phase, some of the activities essential for DNA replication became markedly amplified, mainly due to a progressive increase of E2F-dependent cyclin E transcription and a rapid turnover of the p27(Kip1) cyclin-dependent kinase inhibitor. Consequently...

  15. Arsenic trioxide promotes mitochondrial DNA mutation and cell apoptosis in primary APL cells and NB4 cell line.

    Meng, Ran; Zhou, Jin; Sui, Meng; Li, ZhiYong; Feng, GuoSheng; Yang, BaoFeng

    2010-01-01

    This study aimed to investigate the effects of arsenic trioxide (As(2)O(3)) on the mitochondrial DNA (mtDNA) of acute promyelocytic leukemia (APL) cells. The NB4 cell line was treated with 2.0 micromol/L As(2)O(3) in vitro, and the primary APL cells were treated with 2.0 micromol/L As(2)O(3) in vitro and 0.16 mg kg(-1) d(-1) As(2)O(3) in vivo. The mitochondrial DNA of all the cells above was amplified by PCR, directly sequenced and analyzed by Sequence Navigatore and Factura software. The apoptosis rates were assayed by flow cytometry. Mitochondrial DNA mutation in the D-loop region was found in NB4 and APL cells before As(2)O(3) use, but the mutation spots were remarkably increased after As(2)O(3) treatment, which was positively correlated to the rates of cellular apoptosis, the correlation coefficient: r (NB4-As2O3)=0.973818, and r (APL-As2O3)=0.934703. The mutation types include transition, transversion, codon insertion or deletion, and the mutation spots in all samples were not constant and regular. It is revealed that As(2)O(3) aggravates mtDNA mutation in the D-loop region of acute promyelocytic leukemia cells both in vitro and in vivo. Mitochondrial DNA might be one of the targets of As(2)O(3) in APL treatment.

  16. Examining a DNA Replication Requirement for Bacteriophage λ Red- and Rac Prophage RecET-Promoted Recombination in Escherichia coli

    Lynn C. Thomason

    2016-09-01

    Full Text Available Recombineering, in vivo genetic engineering with bacteriophage homologous recombination systems, is a powerful technique for making genetic modifications in bacteria. Two systems widely used in Escherichia coli are the Red system from phage λ and RecET from the defective Rac prophage. We investigated the in vivo dependence of recombineering on DNA replication of the recombining substrate using plasmid targets. For λ Red recombination, when DNA replication of a circular target plasmid is prevented, recombination with single-stranded DNA oligonucleotides is greatly reduced compared to that under replicating conditions. For RecET recombination, when DNA replication of the targeted plasmid is prevented, the recombination frequency is also reduced, to a level identical to that seen for the Red system in the absence of replication. The very low level of oligonucleotide recombination observed in the absence of any phage recombination functions is the same in the presence or absence of DNA replication. In contrast, both the Red and RecET systems recombine a nonreplicating linear dimer plasmid with high efficiency to yield a circular monomer. Therefore, the DNA replication requirement is substrate dependent. Our data are consistent with recombination by both the Red and RecET systems occurring predominately by single-strand annealing rather than by strand invasion.

  17. Minimal traumatic brain injury causes persistent changes in DNA methylation at BDNF gene promoters in rat amygdala: A possible role in anxiety-like behaviors.

    Sagarkar, Sneha; Bhamburkar, Tanmayi; Shelkar, Gajanan; Choudhary, Amit; Kokare, Dadasaheb M; Sakharkar, Amul J

    2017-10-01

    Minimal traumatic brain injury (MTBI) often transforms into chronic neuropsychiatric conditions including anxiety, the underlying mechanisms of which are largely unknown. In the present study, we employed the closed-head injury paradigm to induce MTBI in rats and examined whether DNA methylation can explain long-term changes in the expression of the brain-derived neurotrophic factor (BDNF) in the amygdala as well as trauma-induced anxiety-like behaviors. The MTBI caused anxiety-like behaviors and altered the expression of DNA methyltransferase (DNMT) isoforms (DNMT1, DNMT3a, and DNMT3b) and factors involved in DNA demethylation such as the growth arrest and DNA damage 45 (GADD45a and GADD45b). After 30days of MTBI, the over-expression of DNMT3a and DNMT3b corresponded to heightened DNMT activity, whereas the mRNA levels of GADD45a and GADD45b were declined. The methylated cytosine levels at the BDNF promoters (Ip, IVp and IXp) were increased in the amygdala of the trauma-induced animals; these coincided negatively with the mRNA levels of exon IV and IXa, but not of exon I. Interestingly, treatment with 5-azacytidine, a pan DNMT inhibitor, normalized the MTBI-induced DNMT activity and DNA hypermethylation at exon IVp and IXp. Furthermore, 5-azacytidine also corrected the deficits in the expression of exons IV and IXa and reduced the anxiety-like behaviors. These results suggest that the DNMT-mediated DNA methylation at the BDNF IVp and IXp might be involved in the regulation of BDNF gene expression in the amygdala. Further, it could also be related to MTBI-induced anxiety-like behaviors via the regulation of synaptic plasticity. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. In silico analysis, mapping of regulatory elements and corresponding dna-protein interaction in polyphenol oxidase gene promoter from different rice varieties

    Mahmood, T.; Rehman, M.; Aziz, E.

    2015-01-01

    Polyphenol oxidase (PPO) is an important enzyme that has positive impact regarding plant resistance against different biotic and abiotic stresses. In the present study PPO promoter from six different rice varieties was amplified and then analyzed for cis- and trans-acting elements. The study revealed a total of 79 different cis-acting regulatory elements including 11 elements restricted to only one or other variety. Among six varieties Pakhal-Basmati had highest number (5) of these elements, whereas C-622 and Rachna-Basmati have no such sequences. Rachna-Basmati, IR-36-Basmati and Kashmir- Basmati had 1, 2 and 3 unique elements, respectively. Different elementsrelated to pathogen, salt and water stresses were found, which may be helpful in controlling PPO activity according to changing environment. Moreover, HADDOCK was used to understand molecular mechanism of PPO regulation and it was found that DNA-protein interactions are stabilized by many potential hydrogen bonds. Adenine and arginine were the most reactive residues in DNA and proteins respectively.Structural comparison of different protein-DNA complexes show that even a highly conserved transcriptional factor can adopt different conformations when they contact a different DNA binding sequence, however their stable interactions depend on the number of hydrogen bonds formed and distance. (author)

  19. HDAC4 and HDAC6 sustain DNA double strand break repair and stem-like phenotype by promoting radioresistance in glioblastoma cells.

    Marampon, Francesco; Megiorni, Francesca; Camero, Simona; Crescioli, Clara; McDowell, Heather P; Sferra, Roberta; Vetuschi, Antonella; Pompili, Simona; Ventura, Luca; De Felice, Francesca; Tombolini, Vincenzo; Dominici, Carlo; Maggio, Roberto; Festuccia, Claudio; Gravina, Giovanni Luca

    2017-07-01

    The role of histone deacetylase (HDAC) 4 and 6 in glioblastoma (GBM) radioresistance was investigated. We found that tumor samples from 31 GBM patients, who underwent temozolomide and radiotherapy combined treatment, showed HDAC4 and HDAC6 expression in 93.5% and 96.7% of cases, respectively. Retrospective clinical data analysis demonstrated that high-intensity HDAC4 and/or HDAC6 immunostaining was predictive of poor clinical outcome. In vitro experiments revealed that short hairpin RNA-mediated silencing of HDAC4 or HDAC6 radiosensitized U87MG and U251MG GBM cell lines by promoting DNA double-strand break (DSBs) accumulation and by affecting DSBs repair molecular machinery. We found that HDAC6 knock-down predisposes to radiation therapy-induced U251MG apoptosis- and U87MG autophagy-mediated cell death. HDAC4 silencing promoted radiation therapy-induced senescence, independently by the cellular context. Finally, we showed that p53 WT expression contributed to the radiotherapy lethal effects and that HDAC4 or HDAC6 sustained GBM stem-like radioresistant phenotype. Altogether, these observations suggest that HDAC4 and HDAC6 are guardians of irradiation-induced DNA damages and stemness, thus promoting radioresistance, and may represent potential prognostic markers and therapeutic targets in GBM. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Promoter hypermethylation of the DNA repair gene O(6)-methylguanine-DNA methyltransferase is associated with the presence of G:C to A:T transition mutations in p53 in human colorectal tumorigenesis.

    Esteller, M; Risques, R A; Toyota, M; Capella, G; Moreno, V; Peinado, M A; Baylin, S B; Herman, J G

    2001-06-15

    Defects in DNA repair may be responsible for the genesis of mutations in key genes in cancer cells. The tumor suppressor gene p53 is commonly mutated in human cancer by missense point mutations, most of them G:C to A:T transitions. A recognized cause for this type of change is spontaneous deamination of the methylcytosine. However, the persistence of a premutagenic O(6)-methylguanine can also be invoked. This last lesion is removed in the normal cell by the DNA repair enzyme O(6)-methylguanine-DNA methyltransferase (MGMT). In many tumor types, epigenetic silencing of MGMT by promoter hypermethylation has been demonstrated and linked to the appearance of G to A mutations in the K-ras oncogene in colorectal tumors. To study the relevance of defective MGMT function by aberrant methylation in relation to the presence of p53 mutations, we studied 314 colorectal tumors for MGMT promoter hypermethylation and p53 mutational spectrum. Inactivation of MGMT by aberrant methylation was associated with the appearance of G:C to A:T transition mutations at p53 (Fischer's exact test, two-tailed; P = 0.01). Overall, MGMT methylated tumors displayed p53 transition mutations in 43 of 126 (34%) cases, whereas MGMT unmethylated tumors only showed G:C to A:T changes in 37 of 188 (19%) tumors. A more striking association was found in G:C to A:T transitions in non-CpG dinucleotides; 71% (12 of 17) of the total non-CpG transition mutations in p53 were observed in MGMT aberrantly methylated tumors (Fischer's exact test, two-tailed; P = 0.008). Our data suggest that epigenetic silencing of MGMT by promoter hypermethylation may lead to G:C to A:T transition mutations in p53.

  1. A point mutation in the DNA-binding domain of HPV-2 E2 protein increases its DNA-binding capacity and reverses its transcriptional regulatory activity on the viral early promoter

    Gao Chen

    2012-02-01

    Full Text Available Abstract Background The human papillomavirus (HPV E2 protein is a multifunctional DNA-binding protein. The transcriptional activity of HPV E2 is mediated by binding to its specific binding sites in the upstream regulatory region of the HPV genomes. Previously we reported a HPV-2 variant from a verrucae vulgaris patient with huge extensive clustered cutaneous, which have five point mutations in its E2 ORF, L118S, S235P, Y287H, S293R and A338V. Under the control of HPV-2 LCR, co-expression of the mutated HPV E2 induced an increased activity on the viral early promoter. In the present study, a series of mammalian expression plasmids encoding E2 proteins with one to five amino acid (aa substitutions for these mutations were constructed and transfected into HeLa, C33A and SiHa cells. Results CAT expression assays indicated that the enhanced promoter activity was due to the co-expressions of the E2 constructs containing A338V mutation within the DNA-binding domain. Western blots analysis demonstrated that the transiently transfected E2 expressing plasmids, regardless of prototype or the A338V mutant, were continuously expressed in the cells. To study the effect of E2 mutations on its DNA-binding activity, a serial of recombinant E2 proteins with various lengths were expressed and purified. Electrophoresis mobility shift assays (EMSA showed that the binding affinity of E2 protein with A338V mutation to both an artificial probe with two E2 binding sites or HPV-2 and HPV-16 promoter-proximal LCR sequences were significantly stronger than that of the HPV-2 prototype E2. Furthermore, co-expression of the construct containing A338V mutant exhibited increased activities on heterologous HPV-16 early promoter P97 than that of prototype E2. Conclusions These results suggest that the mutation from Ala to Val at aa 338 is critical for E2 DNA-binding and its transcriptional regulation.

  2. Nuclear DNA damage-triggered NLRP3 inflammasome activation promotes UVB-induced inflammatory responses in human keratinocytes

    Hasegawa, Tatsuya; Nakashima, Masaya; Suzuki, Yoshiharu

    2016-01-01

    Ultraviolet (UV) radiation in sunlight can result in DNA damage and an inflammatory reaction of the skin commonly known as sunburn, which in turn can lead to cutaneous tissue disorders. However, little has been known about how UV-induced DNA damage mediates the release of inflammatory mediators from keratinocytes. Here, we show that UVB radiation intensity-dependently increases NLRP3 gene expression and IL-1β production in human keratinocytes. Knockdown of NLRP3 with siRNA suppresses UVB-induced production of not only IL-1β, but also other inflammatory mediators, including IL-1α, IL-6, TNF-α, and PGE_2. In addition, inhibition of DNA damage repair by knockdown of XPA, which is a major component of the nucleotide excision repair system, causes accumulation of cyclobutane pyrimidine dimer (CPD) and activation of NLRP3 inflammasome. In vivo immunofluorescence analysis confirmed that NLRP3 expression is also elevated in UV-irradiated human epidermis. Overall, our findings indicate that UVB-induced DNA damage initiates NLRP3 inflammasome activation, leading to release of various inflammatory mediators from human keratinocytes. - Highlights: • UVB radiation induces NLRP3 inflammasome activation in human keratinocytes. • NLRP3 knockdown suppresses production of UVB-induced inflammatory mediators. • UVB-induced DNA damage triggers NLRP3 inflammasome activation. • NLRP3 expression in human epidermis is elevated in response to UV radiation.

  3. Nuclear DNA damage-triggered NLRP3 inflammasome activation promotes UVB-induced inflammatory responses in human keratinocytes

    Hasegawa, Tatsuya, E-mail: tatsuya.hasegawa@to.shiseido.co.jp; Nakashima, Masaya; Suzuki, Yoshiharu

    2016-08-26

    Ultraviolet (UV) radiation in sunlight can result in DNA damage and an inflammatory reaction of the skin commonly known as sunburn, which in turn can lead to cutaneous tissue disorders. However, little has been known about how UV-induced DNA damage mediates the release of inflammatory mediators from keratinocytes. Here, we show that UVB radiation intensity-dependently increases NLRP3 gene expression and IL-1β production in human keratinocytes. Knockdown of NLRP3 with siRNA suppresses UVB-induced production of not only IL-1β, but also other inflammatory mediators, including IL-1α, IL-6, TNF-α, and PGE{sub 2}. In addition, inhibition of DNA damage repair by knockdown of XPA, which is a major component of the nucleotide excision repair system, causes accumulation of cyclobutane pyrimidine dimer (CPD) and activation of NLRP3 inflammasome. In vivo immunofluorescence analysis confirmed that NLRP3 expression is also elevated in UV-irradiated human epidermis. Overall, our findings indicate that UVB-induced DNA damage initiates NLRP3 inflammasome activation, leading to release of various inflammatory mediators from human keratinocytes. - Highlights: • UVB radiation induces NLRP3 inflammasome activation in human keratinocytes. • NLRP3 knockdown suppresses production of UVB-induced inflammatory mediators. • UVB-induced DNA damage triggers NLRP3 inflammasome activation. • NLRP3 expression in human epidermis is elevated in response to UV radiation.

  4. E2F1 interactions with hHR23A inhibit its degradation and promote DNA repair.

    Singh, Randeep K; Dagnino, Lina

    2016-05-03

    Nucleotide excision repair (NER) is a major mechanism for removal of DNA lesions induced by exposure to UV radiation in the epidermis. Recognition of damaged DNA sites is the initial step in their repair, and requires multiprotein complexes that contain XPC and hHR23 proteins, or their orthologues. A variety of transcription factors are also involved in NER, including E2F1. In epidermal keratinocytes, UV exposure induces E2F1 phosphorylation, which allows it to recruit various NER factors to sites of DNA damage. However, the relationship between E2F1 and hHR23 proteins vis-à-vis NER has remained unexplored. We now show that E2F1 and hHR23 proteins can interact, and this interaction stabilizes E2F1, inhibiting its proteasomal degradation. Reciprocally, E2F1 regulates hHR23A subcellular localization, recruiting it to sites of DNA photodamage. As a result, E2F1 and hHR23A enhance DNA repair following exposure to UV radiation, contributing to genomic stability in the epidermis.

  5. C/EBPβ represses p53 to promote cell survival downstream of DNA damage independent of oncogenic Ras and p19Arf

    Ewing, SJ; Zhu, S; Zhu, F; House, JS; Smart, RC

    2013-01-01

    CCAAT/enhancer-binding protein-β (C/EBPβ) is a mediator of cell survival and tumorigenesis. When C/EBPβ−/− mice are treated with carcinogens that produce oncogenic Ras mutations in keratinocytes, they respond with abnormally elevated keratinocyte apoptosis and a block in skin tumorigenesis. Although this aberrant carcinogen-induced apoptosis results from abnormal upregulation of p53, it is not known whether upregulated p53 results from oncogenic Ras and its ability to induce p19Arf and/or activate DNA-damage response pathways or from direct carcinogen-induced DNA damage. We report that p19Arf is dramatically elevated in C/EBPβ−/− epidermis and that C/EBPβ represses a p19Arf promoter reporter. To determine whether p19Arf is responsible for the proapoptotic phenotype in C/EBPβ−/− mice, C/EBPβ−/−;p19Arf−/− mice were generated. C/EBPβ−/−;p19Arf−/− mice responded to carcinogen treatment with increased p53 and apoptosis, indicating p19Arf is not essential. To ascertain whether oncogenic Ras activation induces aberrant p53 and apoptosis in C/EBPβ−/− epidermis, we generated K14-ER:Ras; C/EBPβ−/− mice. Oncogenic Ras activation induced by 4-hydroxytamoxifen did not produce increased p53 or apoptosis. Finally, when C/EBPβ−/− mice were treated with differing types of DNA-damaging agents, including alkylating chemotherapeutic agents, they displayed aberrant levels of p53 and apoptosis. These results indicate that C/EBPβ represses p53 to promote cell survival downstream of DNA damage and suggest that inhibition of C/EBPβ may be a target for cancer cotherapy to increase the efficacy of alkylating chemotherapeutic agents. PMID:18636078

  6. O6-methylguanine-DNA methyltransferase activity is associated with response to alkylating agent therapy and with MGMT promoter methylation in glioblastoma and anaplastic glioma

    Bobola, Michael S.; Alnoor, Mohammad; Chen, John Y.-S.; Kolstoe, Douglas D.; Silbergeld, Daniel L.; Rostomily, Robert C.; Blank, A.; Chamberlain, Marc C.; Silber, John R.

    2014-01-01

    Background CpG methylation in the O6-methylguanine-DNA methyltransferase (MGMT) promoter is associated with better outcome following alkylating agent chemotherapy in glioblastoma (GBM) and anaplastic glioma (AG). To what extent improved response reflects low or absent MGMT activity in glioma tissue has not been unequivocally assessed. This information is central to developing anti-resistance therapies. Methods We examined the relationship of MGMT activity in 91 GBMs and 84 AGs with progression-free survival (PFS) following alkylator therapy and with promoter methylation status determined by methylation-specific PCR (MSP). Results Cox regression analysis revealed that GBMs with high activity had a significantly greater risk for progression in dichotomous (P ≤ 0.001) and continuous (P ≤ 0.003) models, an association observed for different alkylator regimens, including concurrent chemo-radiation with temozolomide. Analysis of MGMT promoter methylation status in 47 of the GBMs revealed that methylated tumors had significantly lower activity (P ≤ 0.005) and longer PFS (P ≤ 0.036) compared to unmethylated tumors, despite overlapping activities. PFS was also significantly greater in methylated vs. unmethylated GBMs with comparable activity (P ≤ 0.005), and among unmethylated tumors with less than median activity (P ≤ 0.026), suggesting that mechanisms in addition to MGMT promote alkylator resistance. Similar associations of MGMT activity with PFS and promoter methylation status were observed for AGs. Conclusions Our results provide strong support for the hypotheses that MGMT activity promotes alkylator resistance and reflects promoter methylation status in malignant gliomas. General significance MGMT activity is an attractive target for anti-resistance therapy regardless of methylation status. PMID:25558448

  7. The discovery of X-rays diffraction: From crystals to DNA. A case study to promote understanding of the nature of science and of its interdisciplinary character

    Guerra, Francesco; Leone, Matteo; Robotti, Nadia

    2015-01-01

    The advantages of introducing history of science topics into the teaching of science has been advocated by a large number of scholars within the science education community. One of the main reasons given for using history of science in teaching is its power to promote understanding of the nature of science (NOS). In this respect, the historical case of X-rays diffraction, from the discovery of Max von Laue (1912) to the first X-rays diffraction photographs of DNA (1953), is a case in point for showing that a correct experimental strategy and a favourable theoretical context are not enough to make a scientific discovery.

  8. Inactivation of the DNA repair gene O6-methylguanine-DNA methyltransferase by promoter hypermethylation is associated with G to A mutations in K-ras in colorectal tumorigenesis.

    Esteller, M; Toyota, M; Sanchez-Cespedes, M; Capella, G; Peinado, M A; Watkins, D N; Issa, J P; Sidransky, D; Baylin, S B; Herman, J G

    2000-05-01

    O6-methylguanine DNA methyltransferase (MGMT) is a DNA repair protein that removes mutagenic and cytotoxic adducts from the O6 position of guanine. O6-methylguanine mispairs with thymine during replication, and if the adduct is not removed, this results in conversion from a guanine-cytosine pair to an adenine-thymine pair. In vitro assays show that MGMT expression avoids G to A mutations and MGMT transgenic mice are protected against G to A transitions at ras genes. We have recently demonstrated that the MGMT gene is silenced by promoter methylation in many human tumors, including colorectal carcinomas. To study the relevance of defective MGMT function by aberrant methylation in relation to the presence of K-ras mutations, we studied 244 colorectal tumor samples for MGMT promoter hypermethylation and K-ras mutational status. Our results show a clear association between the inactivation of MGMT by promoter hypermethylation and the appearance of G to A mutations at K-ras: 71% (36 of 51) of the tumors displaying this particular type of mutation had abnormal MGMT methylation, whereas only 32% (12 of 37) of those with other K-ras mutations not involving G to A transitions and 35% (55 of 156) of the tumors without K-ras mutations demonstrated MGMT methylation (P = 0.002). In addition, MGMT loss associated with hypermethylation was observed in the small adenomas, including those that do not yet contain K-ras mutations. Hypermethylation of other genes such as p16INK4a and p14ARF was not associated with either MGMT hypermethylation or K-ras mutation. Our data suggest that epigenetic silencing of MGMT by promoter hypermethylation may lead to a particular genetic change in human cancer, specifically G to A transitions in the K-ras oncogene.

  9. Overexpression of BLM promotes DNA damage and increased sensitivity to platinum salts in triple negative breast and serous ovarian cancers

    Birkbak, N. J.; Li, Y.; Pathania, S

    2018-01-01

    inhibitor treatment. We identified two genes, the Bloom helicase (BLM) and Fanconi anemia complementation group I (FANCI), that have both increased DNA copy number and gene expression in the platinum sensitive cases. Increased level of expression of these two genes was also associated with platinum...

  10. IFI16 is required for DNA sensing in human macrophages by promoting production and function of cGAMP

    Jønsson, K L; Laustsen, A; Krapp, C; Skipper, K A; Thavachelvam, K; Hotter, D; Egedal, J H; Kjolby, M; Mohammadi, P; Prabakaran, T; Sørensen, L K; Sun, C; Jensen, S B; Holm, C K; Lebbink, R J; Johannsen, M; Nyegaard, M; Mikkelsen, J G; Kirchhoff, F; Paludan, S R; Jakobsen, M R

    2017-01-01

    Innate immune activation by macrophages is an essential part of host defence against infection. Cytosolic recognition of microbial DNA in macrophages leads to induction of interferons and cytokines through activation of cyclic GMP-AMP synthase (cGAS) and stimulator of interferon genes (STING). Other

  11. Lithium chloride protects retinal neurocytes from nutrient deprivation by promoting DNA non-homologous end-joining

    Zhuang Jing; Li Fan; Liu Xuan; Liu Zhiping; Lin Jianxian; Ge Yihong; Kaminski, Joseph M.; Summers, James Bradley; Wang Zhichong; Ge Jian; Yu Keming

    2009-01-01

    Lithium chloride is a therapeutic agent for treatment of bipolar affective disorders. Increasing numbers of studies have indicated that lithium has neuroprotective effects. However, the molecular mechanisms underlying the actions of lithium have not been fully elucidated. This study aimed to investigate whether lithium chloride produces neuroprotective function by improving DNA repair pathway in retinal neurocyte. In vitro, the primary cultured retinal neurocytes (85.7% are MAP-2 positive cells) were treated with lithium chloride, then cultured with serum-free media to simulate the nutrient deprived state resulting from ischemic insult. The neurite outgrowth of the cultured cells increased significantly in a dose-dependent manner when exposed to different levels of lithium chloride. Genomic DNA electrophoresis demonstrated greater DNA integrity of retinal neurocytes when treated with lithium chloride as compared to the control. Moreover, mRNA and protein levels of Ligase IV (involved in DNA non-homologous end-joining (NHEJ) pathway) in retinal neurocytes increased with lithium chloride. The end joining activity assay was performed to determine the role of lithium on NHEJ in the presence of extract from retinal neurocytes. The rejoining levels in retinal neurocytes treated with lithium were significantly increased as compared to the control. Furthermore, XRCC4, the Ligase IV partner, and the transcriptional factor, CREB and CTCF, were up-regulated in retinal cells after treating with 1.0 mM lithium chloride. Therefore, our data suggest that lithium chloride protects the retinal neural cells from nutrient deprivation in vitro, which may be similar to the mechanism of cell death in glaucoma. The improvement in DNA repair pathway involving in Ligase IV might have an important role in lithium neuroprotection. This study provides new insights into the neural protective mechanisms of lithium chloride.

  12. Mutagenesis of the lac promoter region in M13 mp10 phage DNA by 4'-hydroxymethyl-4,5',8-trimethylpsoralen

    Piette, J.; Decuyper-Debergh, D.; Gamper, H.

    1985-01-01

    Double-stranded M13 phage DNA (M13 mp10 replicative form) was photoreacted with 4'-hydroxymethyl-4,5',8-trimethylpsoralen, using light of wavelength greater than 320 nm or greater than 390 nm to generate predominantly crosslinks or monoadducts, respectively. The damaged DNAs were scored for inactivation and mutagenesis after transfection into Escherichia coli. The appearance of light-blue or colorless plaques on indicator medium showed that mutation had occurred in the lac insert of the viral DNA. A comparison of the consequences of the two phototreatments with psoralen supports the idea that crosslinks are both more lethal and more mutagenic than monoadducts. Numerous mutant clones partially or totally deficient in beta-galactosidase were plaque-purified and amplified. The viral DNA of each clone was sequenced by the dideoxy chain-terminating procedure. All of the observed base-pair changes were mapped to the lac promoter region and consisted of 3 transition, 14 transversion, and 6 single base-pair frame-shift mutations. The predominant mutation was a T.A----G.C transversion

  13. Molecular population dynamics of DNA structures in a bcl-2 promoter sequence is regulated by small molecules and the transcription factor hnRNP LL.

    Cui, Yunxi; Koirala, Deepak; Kang, HyunJin; Dhakal, Soma; Yangyuoru, Philip; Hurley, Laurence H; Mao, Hanbin

    2014-05-01

    Minute difference in free energy change of unfolding among structures in an oligonucleotide sequence can lead to a complex population equilibrium, which is rather challenging for ensemble techniques to decipher. Herein, we introduce a new method, molecular population dynamics (MPD), to describe the intricate equilibrium among non-B deoxyribonucleic acid (DNA) structures. Using mechanical unfolding in laser tweezers, we identified six DNA species in a cytosine (C)-rich bcl-2 promoter sequence. Population patterns of these species with and without a small molecule (IMC-76 or IMC-48) or the transcription factor hnRNP LL are compared to reveal the MPD of different species. With a pattern recognition algorithm, we found that IMC-48 and hnRNP LL share 80% similarity in stabilizing i-motifs with 60 s incubation. In contrast, IMC-76 demonstrates an opposite behavior, preferring flexible DNA hairpins. With 120-180 s incubation, IMC-48 and hnRNP LL destabilize i-motifs, which has been previously proposed to activate bcl-2 transcriptions. These results provide strong support, from the population equilibrium perspective, that small molecules and hnRNP LL can modulate bcl-2 transcription through interaction with i-motifs. The excellent agreement with biochemical results firmly validates the MPD analyses, which, we expect, can be widely applicable to investigate complex equilibrium of biomacromolecules. © 2014 The Author(s). Published by Oxford University Press [on behalf of Nucleic Acids Research].

  14. miR-520 promotes DNA-damage-induced trophoblast cell apoptosis by targeting PARP1 in recurrent spontaneous abortion (RSA).

    Dong, Xiujuan; Yang, Long; Wang, Hui

    2017-04-01

    The establishment and maintenance of successful pregnancy mainly depends on trophoblast cells. Their dysfunction has been implicated in recurrent spontaneous abortion (RSA), a major complication of pregnancy. However, the underlying mechanisms of trophoblasts dysfunction remain unclear. DNA-damage-induced cell apoptosis has been reported to play a vital role in cell death. In this study, we identified a novel microRNA (miR-520) in RSA progression via regulating trophoblast cell apoptosis. Microarray analysis showed that miR-520 was highly expressed in villus of RSA patients. By using flow cytometry analysis, we observed miR-520 expression was correlated with human trophoblast cell apoptosis in vitro, along with decreased poly (ADP-ribose) polymerase-1 (PARP1) expression. With the analysis of clinic samples, we observed that miR-520 level was negatively correlated with PARP1 level in RSA villus. In addition, overexpression of PARP1 restored the miR-520-induced trophoblast cell apoptosis in vitro. The status of chromosome in trophoblast implied that miR-520-promoted DNA-damage-induced cell apoptosis to regulate RSA progression. These results indicated that the level of miR-520 might associate with RSA by prompting trophoblast cell apoptosis via PARP1 dependent DNA-damage pathway.

  15. Human T-cell leukemia virus type 1 Tax requires direct access to DNA for recruitment of CREB binding protein to the viral promoter.

    Lenzmeier, B A; Giebler, H A; Nyborg, J K

    1998-02-01

    Efficient human T-cell leukemia virus type 1 (HTLV-1) replication and viral gene expression are dependent upon the virally encoded oncoprotein Tax. To activate HTLV-1 transcription, Tax interacts with the cellular DNA binding protein cyclic AMP-responsive element binding protein (CREB) and recruits the coactivator CREB binding protein (CBP), forming a nucleoprotein complex on the three viral cyclic AMP-responsive elements (CREs) in the HTLV-1 promoter. Short stretches of dG-dC-rich (GC-rich) DNA, immediately flanking each of the viral CREs, are essential for Tax recruitment of CBP in vitro and Tax transactivation in vivo. Although the importance of the viral CRE-flanking sequences is well established, several studies have failed to identify an interaction between Tax and the DNA. The mechanistic role of the viral CRE-flanking sequences has therefore remained enigmatic. In this study, we used high resolution methidiumpropyl-EDTA iron(II) footprinting to show that Tax extended the CREB footprint into the GC-rich DNA flanking sequences of the viral CRE. The Tax-CREB footprint was enhanced but not extended by the KIX domain of CBP, suggesting that the coactivator increased the stability of the nucleoprotein complex. Conversely, the footprint pattern of CREB on a cellular CRE lacking GC-rich flanking sequences did not change in the presence of Tax or Tax plus KIX. The minor-groove DNA binding drug chromomycin A3 bound to the GC-rich flanking sequences and inhibited the association of Tax and the Tax-CBP complex without affecting CREB binding. Tax specifically cross-linked to the viral CRE in the 5'-flanking sequence, and this cross-link was blocked by chromomycin A3. Together, these data support a model where Tax interacts directly with both CREB and the minor-groove viral CRE-flanking sequences to form a high-affinity binding site for the recruitment of CBP to the HTLV-1 promoter.

  16. Temporal transcription of the lactococcal temperate phage TP901-1 and DNA sequence of the early promoter region

    Madsen, Hans Peter Lynge; Hammer, Karin

    1998-01-01

    to a phage repressor, a single-stranded DNA-binding protein, a topoisomerase, a Cro-like protein and two other phage proteins of unknown function were detected. The gene arrangement in the early transcribed region of TP901-1 thus consists of two transcriptional units: one from PR containing four genes......, of which at least two (the integrase gene and putative repressor) are needed for lysogeny, and the divergent and longer transcriptional unit from PL, presumably encoding functions required for the lytic life cycle. ORFs with homology to proteins involved in DNA replication were identified on the latter......Transcriptional analysis by Northern blotting identified clusters of early, middle and late transcribed regions of the temperate lactococcal bacteriophage TP901-1 during one-step growth experiments. The latent period was found to be 65 min and the burst size 40 +/- 10. The eight early transcripts...

  17. Cell-to-cell transformation in Escherichia coli: a novel type of natural transformation involving cell-derived DNA and a putative promoting pheromone.

    Rika Etchuuya

    Full Text Available Escherichia coli is not assumed to be naturally transformable. However, several recent reports have shown that E. coli can express modest genetic competence in certain conditions that may arise in its environment. We have shown previously that spontaneous lateral transfer of non-conjugative plasmids occurs in a colony biofilm of mixed E. coli strains (a set of a donor strain harbouring a plasmid and a plasmid-free recipient strain. In this study, with high-frequency combinations of strains and a plasmid, we constructed the same lateral plasmid transfer system in liquid culture. Using this system, we demonstrated that this lateral plasmid transfer was DNase-sensitive, indicating that it is a kind of transformation in which DNase-accessible extracellular naked DNA is essential. However, this transformation did not occur with purified plasmid DNA and required a direct supply of plasmid from co-existing donor cells. Based on this feature, we have termed this transformation type as 'cell-to-cell transformation'. Analyses using medium conditioned with the high-frequency strain revealed that this strain released a certain factor(s that promoted cell-to-cell transformation and arrested growth of the other strains. This factor is heat-labile and protease-sensitive, and its roughly estimated molecular mass was between ∼9 kDa and ∼30 kDa, indicating that it is a polypeptide factor. Interestingly, this factor was effective even when the conditioned medium was diluted 10(-5-10(-6, suggesting that it acts like a pheromone with high bioactivity. Based on these results, we propose that cell-to-cell transformation is a novel natural transformation mechanism in E. coli that requires cell-derived DNA and is promoted by a peptide pheromone. This is the first evidence that suggests the existence of a peptide pheromone-regulated transformation mechanism in E. coli and in Gram-negative bacteria.

  18. Methylation status of the APC and RASSF1A promoter in cell-free circulating DNA and its prognostic role in patients with colorectal cancer.

    Matthaios, Dimitrios; Balgkouranidou, Ioanna; Karayiannakis, Anastasios; Bolanaki, Helen; Xenidis, Nikolaos; Amarantidis, Kyriakos; Chelis, Leonidas; Romanidis, Konstantinos; Chatzaki, Aikaterini; Lianidou, Evi; Trypsianis, Grigorios; Kakolyris, Stylianos

    2016-07-01

    DNA methylation is the most frequent epigenetic alteration. Using methylation-specific polymerase chain reaction (MSP), the methylation status of the adenomatous polyposis coli ( APC ) and Ras association domain family 1 isoform A ( RASSF1A ) genes was examined in cell-free circulating DNA from 155 plasma samples obtained from patients with early and advanced colorectal cancer (CRC). APC and RASSF1A hypermethylation was frequently observed in both early and advanced disease, and was significantly associated with a poorer disease outcome. The methylation status of the APC and RASSF1A promoters was investigated in cell-free DNA of patients with CRC. Using MSP, the promoter methylation status of APC and RASSF1A was examined in 155 blood samples obtained from patients with CRC, 88 of whom had operable CRC (oCRC) and 67 had metastatic CRC (mCRC). The frequency of APC methylation in patients with oCRC was 33%. Methylated APC promoter was significantly associated with older age (P=0.012), higher stage (P=0.014) and methylated RASSF1A status (P=0.050). The frequency of APC methylation in patients with mCRC was 53.7%. In these patients, APC methylation was significantly associated with methylated RASSF1A status (P=0.016). The frequency of RASSF1A methylation in patients with oCRC was 25%. Methylated RASSF1A in oCRC was significantly associated with higher stage (P=0.021). The frequency of RASSF1A methylation in mCRC was 44.8%. Methylated RASSF1A in mCRC was associated with moderate differentiation (P=0.012), high levels of carcinoembryonic antigen (P=0.023) and methylated APC status (P=0.016). Patients with an unmethylated APC gene had better survival in both early (81±5 vs. 27±4 months, PAPC . Patients with an unmethylated RASSF1A gene had better survival in both early (71±6 vs. 46±8 months, PAPC and RASSF1A promoter methylation status and survival may be indicative of a prognostic role for these genes in CRC, which requires additional testing in larger studies.

  19. DNA Methylation Adjusts the Specificity of Memories Depending on the Learning Context and Promotes Relearning in Honeybees.

    Biergans, Stephanie D; Claudianos, Charles; Reinhard, Judith; Galizia, C G

    2016-01-01

    The activity of the epigenetic writers DNA methyltransferases (Dnmts) after olfactory reward conditioning is important for both stimulus-specific long-term memory (LTM) formation and extinction. It, however, remains unknown which components of memory formation Dnmts regulate (e.g., associative vs. non-associative) and in what context (e.g., varying training conditions). Here, we address these aspects in order to clarify the role of Dnmt-mediated DNA methylation in memory formation. We used a pharmacological Dnmt inhibitor and classical appetitive conditioning in the honeybee Apis mellifera, a well characterized model for classical conditioning. We quantified the effect of DNA methylation on naïve odor and sugar responses, and on responses following olfactory reward conditioning. We show that (1) Dnmts do not influence naïve odor or sugar responses, (2) Dnmts do not affect the learning of new stimuli, but (3) Dnmts influence odor-coding, i.e., 'correct' (stimulus-specific) LTM formation. Particularly, Dnmts reduce memory specificity when experience is low (one-trial training), and increase memory specificity when experience is high (multiple-trial training), generating an ecologically more useful response to learning. (4) In reversal learning conditions, Dnmts are involved in regulating both excitatory (re-acquisition) and inhibitory (forgetting) processes.

  20. A novel type of DNA-binding protein interacts with a conserved sequence in an early nodulin ENOD12 promoter.

    Christiansen, H.; Hansen, A.C.; Vijn, I.; Pallisgaard, N.; Larsen, K.; Yang, W.C.; Bisseling, T.; Marcker, K.A.; Jensen, E.O.

    1996-01-01

    The pea genes PsENOD12A and PsENOD12B are expressed in the root hairs shortly after infection with the nitrogen-fixing bacterium Rhizobium leguminosarum bv. viciae or after application of purified Nod factors. A 199 bp promoter fragment of the PsENOD12B gene contains sufficient information for Nod

  1. Mass ejections from the solar corona into interplanetary space

    Hildner, E.

    1977-01-01

    Mass ejections from the corona are common occurrances, as observations with the High Altitude Observatory's white light coronagraph aboard Skylab showed. During 227 days of operation in 1973 and 1974 at least 77 mass ejections were observed and as many more probably occurred unobserved. It is suggested that the frequency of ejections varies with the solar cycle and that ejections may contribute 10 percent or more of the total solar mass efflux to the interplanetary medium at solar maximum. Since ejections are confined to relatively low latitudes, their fractional mass flux contribution is greater near the ecliptic than far from it. From the behavior of ejecta, we can estimate the magnitude of the force driving them through the corona. It is also suggested that loop-shaped ejection - the largest fraction of ejections - are driven, primarily, by magnetic forces. By comparison, gas pressure forces are negligible, and forces due to wave pressure are completely inadequate. That magnetic forces are important is consistent with observation that ejections seem to come, primarily, from regions where the magnetic field is more intense and more complex than elsewhere. Indeed, ejections are associated with phenomena (flares and eruptive prominences) which occur over lines separating regions of opposite polarities. (Auth.)

  2. All-trans retinoic acid promotes TGF-β-induced Tregs via histone modification but not DNA demethylation on Foxp3 gene locus.

    Ling Lu

    Full Text Available It has been documented all-trans retinoic acid (atRA promotes the development of TGF-β-induced CD4(+Foxp3(+ regulatory T cells (iTreg that play a vital role in the prevention of autoimmune responses, however, molecular mechanisms involved remain elusive. Our objective, therefore, was to determine how atRA promotes the differentiation of iTregs.Addition of atRA to naïve CD4(+CD25(- cells stimulated with anti-CD3/CD28 antibodies in the presence of TGF-β not only increased Foxp3(+ iTreg differentiation, but maintained Foxp3 expression through apoptosis inhibition. atRA/TGF-β-treated CD4(+ cells developed complete anergy and displayed increased suppressive activity. Infusion of atRA/TGF-β-treated CD4(+ cells resulted in the greater effects on suppressing symptoms and protecting the survival of chronic GVHD mice with typical lupus-like syndromes than did CD4(+ cells treated with TGF-β alone. atRA did not significantly affect the phosphorylation levels of Smad2/3 and still promoted iTreg differentiation in CD4(+ cells isolated from Smad3 KO and Smad2 conditional KO mice. Conversely, atRA markedly increased ERK1/2 activation, and blockade of ERK1/2 signaling completely abolished the enhanced effects of atRA on Foxp3 expression. Moreover, atRA significantly increased histone methylation and acetylation within the promoter and conserved non-coding DNA sequence (CNS elements at the Foxp3 gene locus and the recruitment of phosphor-RNA polymerase II, while DNA methylation in the CNS3 was not significantly altered.We have identified the cellular and molecular mechanism(s by which atRA promotes the development and maintenance of iTregs. These results will help to enhance the quantity and quality of development of iTregs and may provide novel insights into clinical cell therapy for patients with autoimmune diseases and those needing organ transplantation.

  3. Delivery of a survivin promoter-driven antisense survivin-expressing plasmid DNA as a cancer therapeutic: a proof-of-concept study

    Lin KY

    2016-05-01

    Full Text Available Kun-Yuan Lin,1 Siao Muk Cheng,2 Shing-Ling Tsai,2 Ju-Ya Tsai,1 Chun-Hui Lin,1 Chun Hei Antonio Cheung1,2 1Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC; 2Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC Abstract: Survivin is a member of the inhibitor-of-apoptosis proteins family. It is overexpressed in many different cancer types but not in the differentiated normal tissue. In addition, overexpression of survivin promotes cancer cell survival and induces chemotherapeutic drug resistance, making it an attractive target for new anticancer interventions. Despite survivin being a promising molecular target for anticancer treatment, it is widely accepted that survivin is only a “semi-druggable” target. Therefore, it is important to develop a new strategy to target survivin for anticancer treatment. In this study, we constructed a novel survivin promoter-driven full-length antisense survivin (pSur/AS-Sur expression plasmid DNA. Promoter activity assay revealed that the activity of the survivin promoter of pSur/AS-Sur correlated with the endogenous expression of survivin at the transcriptional level in the transfected A549, MDA-MB-231, and PANC-1 cancer cells. Western blot analysis showed that liposomal delivery of pSur/AS-Sur successfully downregulated the expression of survivin in A549, MBA-MB-231, and PANC-1 cells in vitro. In addition, delivery of pSur/AS-Sur induced autophagy, caspase-dependent apoptosis, and caspase-independent apoptosis as indicated by the increased LC3B-II conversion, autophagosome formation, caspase-9/-3 and poly(ADP-ribose polymerase-1 cleavage, and apoptosis-inducing factor nuclear translocation in A549, MBA-MB-231, and PANC-1 cells. Importantly, liposomal delivery of pSur/AS-Sur was also capable of decreasing the proliferation of the survivin/MDR1 coexpressing multidrug-resistant KB-TAX50 cancer cells and

  4. Genetic basis of olfactory cognition: extremely high level of DNA sequence polymorphism in promoter regions of the human olfactory receptor genes revealed using the 1000 Genomes Project dataset.

    Ignatieva, Elena V; Levitsky, Victor G; Yudin, Nikolay S; Moshkin, Mikhail P; Kolchanov, Nikolay A

    2014-01-01

    The molecular mechanism of olfactory cognition is very complicated. Olfactory cognition is initiated by olfactory receptor proteins (odorant receptors), which are activated by olfactory stimuli (ligands). Olfactory receptors are the initial player in the signal transduction cascade producing a nerve impulse, which is transmitted to the brain. The sensitivity to a particular ligand depends on the expression level of multiple proteins involved in the process of olfactory cognition: olfactory receptor proteins, proteins that participate in signal transduction cascade, etc. The expression level of each gene is controlled by its regulatory regions, and especially, by the promoter [a region of DNA about 100-1000 base pairs long located upstream of the transcription start site (TSS)]. We analyzed single nucleotide polymorphisms using human whole-genome data from the 1000 Genomes Project and revealed an extremely high level of single nucleotide polymorphisms in promoter regions of olfactory receptor genes and HLA genes. We hypothesized that the high level of polymorphisms in olfactory receptor promoters was responsible for the diversity in regulatory mechanisms controlling the expression levels of olfactory receptor proteins. Such diversity of regulatory mechanisms may cause the great variability of olfactory cognition of numerous environmental olfactory stimuli perceived by human beings (air pollutants, human body odors, odors in culinary etc.). In turn, this variability may provide a wide range of emotional and behavioral reactions related to the vast variety of olfactory stimuli.

  5. Genetic basis of olfactory cognition: extremely high level of DNA sequence polymorphism in promoter regions of the human olfactory receptor genes revealed using the 1000 Genomes Project dataset

    Elena V. Ignatieva

    2014-03-01

    Full Text Available The molecular mechanism of olfactory cognition is very complicated. Olfactory cognition is initiated by olfactory receptor proteins (odorant receptors, which are activated by olfactory stimuli (ligands. Olfactory receptors are the initial player in the signal transduction cascade producing a nerve impulse, which is transmitted to the brain. The sensitivity to a particular ligand depends on the expression level of multiple proteins involved in the process of olfactory cognition: olfactory receptor proteins, proteins that participate in signal transduction cascade, etc. The expression level of each gene is controlled by its regulatory regions, and especially, by the promoter (a region of DNA about 100–1000 base pairs long located upstream of the transcription start site. We analyzed single nucleotide polymorphisms using human whole-genome data from the 1000 Genomes Project and revealed an extremely high level of single nucleotide polymorphisms in promoter regions of olfactory receptor genes and HLA genes. We hypothesized that the high level of polymorphisms in olfactory receptor promoters was responsible for the diversity in regulatory mechanisms controlling the expression levels of olfactory receptor proteins. Such diversity of regulatory mechanisms may cause the great variability of olfactory cognition of numerous environmental olfactory stimuli perceived by human beings (air pollutants, human body odors, odors in culinary etc.. In turn, this variability may provide a wide range of emotional and behavioral reactions related to the vast variety of olfactory stimuli.

  6. DNA replication origin function is promoted by H3K4 di-methylation in Saccharomyces cerevisiae.

    Rizzardi, Lindsay F; Dorn, Elizabeth S; Strahl, Brian D; Cook, Jeanette Gowen

    2012-10-01

    DNA replication is a highly regulated process that is initiated from replication origins, but the elements of chromatin structure that contribute to origin activity have not been fully elucidated. To identify histone post-translational modifications important for DNA replication, we initiated a genetic screen to identify interactions between genes encoding chromatin-modifying enzymes and those encoding proteins required for origin function in the budding yeast Saccharomyces cerevisiae. We found that enzymes required for histone H3K4 methylation, both the histone methyltransferase Set1 and the E3 ubiquitin ligase Bre1, are required for robust growth of several hypomorphic replication mutants, including cdc6-1. Consistent with a role for these enzymes in DNA replication, we found that both Set1 and Bre1 are required for efficient minichromosome maintenance. These phenotypes are recapitulated in yeast strains bearing mutations in the histone substrates (H3K4 and H2BK123). Set1 functions as part of the COMPASS complex to mono-, di-, and tri-methylate H3K4. By analyzing strains lacking specific COMPASS complex members or containing H2B mutations that differentially affect H3K4 methylation states, we determined that these replication defects were due to loss of H3K4 di-methylation. Furthermore, histone H3K4 di-methylation is enriched at chromosomal origins. These data suggest that H3K4 di-methylation is necessary and sufficient for normal origin function. We propose that histone H3K4 di-methylation functions in concert with other histone post-translational modifications to support robust genome duplication.

  7. Human RECQ5 helicase promotes repair of DNA double-strand breaks by synthesis-dependent strand annealing

    Paliwal, S.; Kanagaraj, R.; Sturzenegger, A.; Burdová, Kamila; Janščák, Pavel

    2014-01-01

    Roč. 42, č. 4 (2014), s. 2380-2390 ISSN 0305-1048 R&D Projects: GA ČR GA204/09/0565; GA ČR GAP305/10/0281 Grant - others:Swiss National Science Foundation(CH) 31003A-129747; Swiss National Science Foundation(CH) 31003A_146206 Institutional support: RVO:68378050 Keywords : Human RECQ5 helicase * DNA double-strand breaks * mitotic homologous recombination Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.112, year: 2014

  8. Coronal mass ejections and large geomagnetic storms

    Gosling, J.T.; Bame, S.J.; McComas, D.J.; Phillips, J.L.

    1990-01-01

    Previous work indicates that coronal mass ejection (CME) events in the solar wind at 1 AU can be identified by the presence of a flux of counterstreaming solar wind halo electrons (above about 80 eV). Using this technique to identify CMEs in 1 AU plasma data, the authors find that most large geomagnetic storms during the interval surrounding the last solar maximum (Aug. 1978-Oct. 1982) were associated with Earth-passage of interplanetary disturbances in which the Earth encountered both a shock and the CME driving the shock. However, only about one CME in six encountered by Earth was effective in causing a large geomagnetic storm. Slow CMEs which did not interact strongly with the ambient solar wind ahead were particularly ineffective in a geomagnetic sense

  9. STING-Dependent Cytosolic DNA Sensing Promotes Radiation-Induced Type I Interferon-Dependent Antitumor Immunity in Immunogenic Tumors.

    Deng, Liufu; Liang, Hua; Xu, Meng; Yang, Xuanming; Burnette, Byron; Arina, Ainhoa; Li, Xiao-Dong; Mauceri, Helena; Beckett, Michael; Darga, Thomas; Huang, Xiaona; Gajewski, Thomas F; Chen, Zhijian J; Fu, Yang-Xin; Weichselbaum, Ralph R

    2014-11-20

    Ionizing radiation-mediated tumor regression depends on type I interferon (IFN) and the adaptive immune response, but several pathways control I IFN induction. Here, we demonstrate that adaptor protein STING, but not MyD88, is required for type I IFN-dependent antitumor effects of radiation. In dendritic cells (DCs), STING was required for IFN-? induction in response to irradiated-tumor cells. The cytosolic DNA sensor cyclic GMP-AMP (cGAMP) synthase (cGAS) mediated sensing of irradiated-tumor cells in DCs. Moreover, STING was essential for radiation-induced adaptive immune responses, which relied on type I IFN signaling on DCs. Exogenous IFN-? treatment rescued the cross-priming by cGAS or STING-deficient DCs. Accordingly, activation of STING by a second messenger cGAMP administration enhanced antitumor immunity induced by radiation. Thus radiation-mediated antitumor immunity in immunogenic tumors requires a functional cytosolic DNA-sensing pathway and suggests that cGAMP treatment might provide a new strategy to improve radiotherapy. Copyright © 2014 Elsevier Inc. All rights reserved.

  10. Gene expression promoted by the SV40 DNA targeting sequence and the hypoxia-responsive element under normoxia and hypoxia

    C.B. Sacramento

    2010-08-01

    Full Text Available The main objective of the present study was to find suitable DNA-targeting sequences (DTS for the construction of plasmid vectors to be used to treat ischemic diseases. The well-known Simian virus 40 nuclear DTS (SV40-DTS and hypoxia-responsive element (HRE sequences were used to construct plasmid vectors to express the human vascular endothelial growth factor gene (hVEGF. The rate of plasmid nuclear transport and consequent gene expression under normoxia (20% O2 and hypoxia (less than 5% O2 were determined. Plasmids containing the SV40-DTS or HRE sequences were constructed and used to transfect the A293T cell line (a human embryonic kidney cell line in vitro and mouse skeletal muscle cells in vivo. Plasmid transport to the nucleus was monitored by real-time PCR, and the expression level of the hVEGF gene was measured by ELISA. The in vitro nuclear transport efficiency of the SV40-DTS plasmid was about 50% lower under hypoxia, while the HRE plasmid was about 50% higher under hypoxia. Quantitation of reporter gene expression in vitro and in vivo, under hypoxia and normoxia, confirmed that the SV40-DTS plasmid functioned better under normoxia, while the HRE plasmid was superior under hypoxia. These results indicate that the efficiency of gene expression by plasmids containing DNA binding sequences is affected by the concentration of oxygen in the medium.

  11. Control rod ejection analysis during a depressurization accident and the development of a rod-ejection-preventing device

    Mitake, S.; Itoh, K.; Fukushima, H.; Inoue, T.

    1982-01-01

    The control rods used for the experimental VHTR are suspended in the core by means of flexible steel cables and it is conceivable that an accidental rod ejection could occur due to a depressurization accident. The computer code AFLADE was developed in order to analyze the possibility of accidental rod ejection, and several studies were performed. The parametric study results showed that the adopted design condition for the VHTR core will not cause a rod ejection accident. In parallel with these accident analyses, a rod-ejection-preventing device was developed in preparation for a hypothetical accident, and its function was verified by the component tests

  12. Is the prognostic significance of O6-methylguanine- DNA methyltransferase promoter methylation equally important in glioblastomas of patients from different continents? A systematic review with meta-analysis.

    Meng, Wei; Jiang, Yangyang; Ma, Jie

    2017-01-01

    O6-methylguanine-DNA methyltransferase (MGMT) is an independent predictor of therapeutic response and potential prognosis in patients with glioblastoma multiforme (GBM). However, its significance of clinical prognosis in different continents still needs to be explored. To explore the effects of MGMT promoter methylation on both progression-free survival (PFS) and overall survival (OS) among GBM patients from different continents, a systematic review of published studies was conducted. A total of 5103 patients from 53 studies were involved in the systematic review and the total percentage of MGMT promoter methylation was 45.53%. Of these studies, 16 studies performed univariate analyses and 17 performed multivariate analyses of MGMT promoter methylation on PFS. The pooled hazard ratio (HR) estimated for PFS was 0.55 (95% CI 0.50, 0.60) by univariate analysis and 0.43 (95% CI 0.38, 0.48) by multivariate analysis. The effect of MGMT promoter methylation on OS was explored in 30 studies by univariate analysis and in 30 studies by multivariate analysis. The combined HR was 0.48 (95% CI 0.44, 0.52) and 0.42 (95% CI 0.38, 0.45), respectively. In each subgroup divided by areas, the prognostic significance still remained highly significant. The proportion of methylation in each group was in inverse proportion to the corresponding HR in the univariate and multivariate analyses of PFS. However, from the perspective of OS, compared with data from Europe and the US, higher methylation rates in Asia did not bring better returns.

  13. Hoxa5 Promotes Adipose Differentiation via Increasing DNA Methylation Level and Inhibiting PKA/HSL Signal Pathway in Mice

    Weina Cao

    2018-02-01

    Full Text Available Background/Aims: Impaired adipogenesis may be the underlying cause in the development of obesity and type II diabetes. Mechanistically, the family of Homeobox transcription factors is implicated in the regulation of adipocyte fate. Hoxa5 is highly expressed in adipocytes, and its mRNA expression is decreased during differentiation. However, the function of Hoxa5 in adipose tissue has been poorly understood. The aim of this study is to unveil the role of Hoxa5 on adipocyte differentiation and its underlying mechanisms. Methods: Quantitative real-time PCR (qPCR and western blot were performed to determine Hoxa5 expression in primary adipocytes and in adipose tissues from mice. Lipid accumulation was evaluated by bodipy staining. Dual luciferase assay was applied to explore the transcription factor of Hoxa5 and the transcriptional target gene modulated by Hoxa5. All measurements were performed at least for three times at least. Results: A significant reduction of Hoxa5 expression was observed in adipose tissue of High Fat Diet (HFD induced obesity mice. We determined Hoxa5 increased adipocytes differentiation and mitochondrial biogenesis in adipocytes in vitro. CEBPβ was determined a transcription factor of Hoxa5 and inhibited methylation level of Hoxa5 by combining on the promoter of Hoxa5. Importantly, we found Fabp4, a known positive regulator of adipocytes differentiation, was transcriptional activation by Hoxa5. In addition, Hoxa5 promotes adipocytes differentiation by inhibiting PKA/HSL pathway. Conclusion: Our study demonstrated the promoting role of Hoxa5 in adipocytes differentiation and therefore bringing a new therapeutic mean to the treatment of obesity and type II diabetes.

  14. Epigenetic Alteration by DNA Promoter Hypermethylation of Genes Related to Transforming Growth Factor-β (TGF-β) Signaling in Cancer

    Khin, Sann Sanda [Kobe University Graduate School of Medicine, Division of Diagnostic Molecular Pathology, Kobe 650-0017 (Japan); Pathology Research Unit, Department of Medical Research (Central Myanmar), Naypyitaw, Union of (Myanmar); Kitazawa, Riko [Kobe University Graduate School of Medicine, Division of Diagnostic Molecular Pathology, Kobe 650-0017 (Japan); Ehime University Graduate School of Medicine, Toon 791-0295, Ehime (Japan); Kondo, Takeshi; Idei, Yuka; Fujimoto, Masayo [Kobe University Graduate School of Medicine, Division of Diagnostic Molecular Pathology, Kobe 650-0017 (Japan); Haraguchi, Ryuma [Ehime University Graduate School of Medicine, Toon 791-0295, Ehime (Japan); Mori, Kiyoshi [Kobe University Graduate School of Medicine, Division of Diagnostic Molecular Pathology, Kobe 650-0017 (Japan); Kitazawa, Sohei, E-mail: kitazawa@m.ehime-u.ac.jp [Kobe University Graduate School of Medicine, Division of Diagnostic Molecular Pathology, Kobe 650-0017 (Japan); Ehime University Graduate School of Medicine, Toon 791-0295, Ehime (Japan)

    2011-03-03

    Epigenetic alterations in cancer, especially DNA methylation and histone modification, exert a significant effect on the deregulated expression of cancer-related genes and lay an epigenetic pathway to carcinogenesis and tumor progression. Global hypomethylation and local hypermethylation of CpG islands in the promoter region, which result in silencing tumor suppressor genes, constitute general and major epigenetic modification, the hallmark of the neoplastic epigenome. Additionally, methylation-induced gene silencing commonly affects a number of genes and increases with cancer progression. Indeed, cancers with a high degree of methylation (CpG island methylator phenotype/CIMP) do exist and represent a distinct subset of certain cancers including colorectal, bladder and kidney. On the other hand, signals from the microenvironment, especially those from transforming growth factor-β (TGF-β), induce targeted de novo epigenetic alterations of cancer-related genes. While TGF-β signaling has been implicated in two opposite roles in cancer, namely tumor suppression and tumor promotion, its deregulation is also partly induced by epigenetic alteration itself. Although the epigenetic pathway to carcinogenesis and cancer progression has such reciprocal complexity, the important issue is to identify genes or signaling pathways that are commonly silenced in various cancers in order to find early diagnostic and therapeutic targets. In this review, we focus on the epigenetic alteration by DNA methylation and its role in molecular modulations of the TGF-β signaling pathway that cause or underlie altered cancer-related gene expression in both phases of early carcinogenesis and late cancer progression.

  15. Epigenetic Alteration by DNA Promoter Hypermethylation of Genes Related to Transforming Growth Factor-β (TGF-β) Signaling in Cancer

    Khin, Sann Sanda; Kitazawa, Riko; Kondo, Takeshi; Idei, Yuka; Fujimoto, Masayo; Haraguchi, Ryuma; Mori, Kiyoshi; Kitazawa, Sohei

    2011-01-01

    Epigenetic alterations in cancer, especially DNA methylation and histone modification, exert a significant effect on the deregulated expression of cancer-related genes and lay an epigenetic pathway to carcinogenesis and tumor progression. Global hypomethylation and local hypermethylation of CpG islands in the promoter region, which result in silencing tumor suppressor genes, constitute general and major epigenetic modification, the hallmark of the neoplastic epigenome. Additionally, methylation-induced gene silencing commonly affects a number of genes and increases with cancer progression. Indeed, cancers with a high degree of methylation (CpG island methylator phenotype/CIMP) do exist and represent a distinct subset of certain cancers including colorectal, bladder and kidney. On the other hand, signals from the microenvironment, especially those from transforming growth factor-β (TGF-β), induce targeted de novo epigenetic alterations of cancer-related genes. While TGF-β signaling has been implicated in two opposite roles in cancer, namely tumor suppression and tumor promotion, its deregulation is also partly induced by epigenetic alteration itself. Although the epigenetic pathway to carcinogenesis and cancer progression has such reciprocal complexity, the important issue is to identify genes or signaling pathways that are commonly silenced in various cancers in order to find early diagnostic and therapeutic targets. In this review, we focus on the epigenetic alteration by DNA methylation and its role in molecular modulations of the TGF-β signaling pathway that cause or underlie altered cancer-related gene expression in both phases of early carcinogenesis and late cancer progression

  16. Epigenetic Alteration by DNA Promoter Hypermethylation of Genes Related to Transforming Growth Factor-β (TGF-β Signaling in Cancer

    Kiyoshi Mori

    2011-03-01

    Full Text Available Epigenetic alterations in cancer, especially DNA methylation and histone modification, exert a significant effect on the deregulated expression of cancer-related genes and lay an epigenetic pathway to carcinogenesis and tumor progression. Global hypomethylation and local hypermethylation of CpG islands in the promoter region, which result in silencing tumor suppressor genes, constitute general and major epigenetic modification, the hallmark of the neoplastic epigenome. Additionally, methylation-induced gene silencing commonly affects a number of genes and increases with cancer progression. Indeed, cancers with a high degree of methylation (CpG island methylator phenotype/CIMP do exist and represent a distinct subset of certain cancers including colorectal, bladder and kidney. On the other hand, signals from the microenvironment, especially those from transforming growth factor-β (TGF-β, induce targeted de novo epigenetic alterations of cancer-related genes. While TGF-β signaling has been implicated in two opposite roles in cancer, namely tumor suppression and tumor promotion, its deregulation is also partly induced by epigenetic alteration itself. Although the epigenetic pathway to carcinogenesis and cancer progression has such reciprocal complexity, the important issue is to identify genes or signaling pathways that are commonly silenced in various cancers in order to find early diagnostic and therapeutic targets. In this review, we focus on the epigenetic alteration by DNA methylation and its role in molecular modulations of the TGF-β signaling pathway that cause or underlie altered cancer-related gene expression in both phases of early carcinogenesis and late cancer progression.

  17. DNA hypomethylation of a transcription factor binding site within the promoter of a gout risk gene NRBP1 upregulates its expression by inhibition of TFAP2A binding.

    Zhu, Zaihua; Meng, Weida; Liu, Peiru; Zhu, Xiaoxia; Liu, Yun; Zou, Hejian

    2017-01-01

    Genome-wide association studies (GWASs) have identified dozens of loci associated with gout, but for most cases, the risk genes and the underlying molecular mechanisms contributing to these associations are unknown. This study sought to understand the molecular mechanism of a common genetic variant, rs780093, in the development of gout, both in vitro and in vivo. Nuclear receptor binding protein 1 ( NRBP1 ), as a gout risk gene, and its regulatory region, 72 bp upstream of the transcription start site, designated as B1, were identified through integrative analyses of genome-wide genotype and DNA methylation data. We observed elevated NRBP1 expression in human peripheral blood mononuclear cells (PBMCs) from gout patients. In vitro luciferase reporter and protein pulldown assay results showed that DNA methylation could increase the binding of the transcription factor TFAP2A to B1, leading to suppressed gene expression. There results were further confirmed by in vivo bisulfite pyrosequencing showing that hypomethylation on B1 is associated with increased NRBP1 expression in gout patients. Hypomethylation at the promoter region of NRBP1 reduces the binding of TFAP2A and thus leads to elevated NRBP1 expression, which might contribute to the development of gout.

  18. Air pollution and heart failure: Relationship with the ejection fraction

    Dominguez-Rodriguez, Alberto; Abreu-Afonso, Javier; Rodríguez, Sergio; Juarez-Prera, Ruben A; Arroyo-Ucar, Eduardo; Gonzalez, Yenny; Abreu-Gonzalez, Pedro; Avanzas, Pablo

    2013-01-01

    AIM: To study whether the concentrations of particulate matter in ambient air are associated with hospital admission due to heart failure in patients with heart failure with preserved ejection fraction and reduced ejection fraction. METHODS: We studied 353 consecutive patients admitted into a tertiary care hospital with a diagnosis of heart failure. Patients with ejection fraction of ≥ 45% were classified as having heart failure with preserved ejection fraction and those with an ejection fraction of < 45% were classified as having heart failure with reduced ejection fraction. We determined the average concentrations of different sizes of particulate matter (< 10, < 2.5, and < 1 μm) and the concentrations of gaseous pollutants (carbon monoxide, sulphur dioxide, nitrogen dioxide and ozone) from 1 d up to 7 d prior to admission. RESULTS: The heart failure with preserved ejection fraction population was exposed to higher nitrogen dioxide concentrations compared to the heart failure with reduced ejection fraction population (12.95 ± 8.22 μg/m3 vs 4.50 ± 2.34 μg/m3, P < 0.0001). Multivariate analysis showed that nitrogen dioxide was a significant predictor of heart failure with preserved ejection fraction (odds ratio ranging from (1.403, 95%CI: 1.003-2.007, P = 0.04) to (1.669, 95%CI: 1.043-2.671, P = 0.03). CONCLUSION: This study demonstrates that short-term nitrogen dioxide exposure is independently associated with admission in the heart failure with preserved ejection fraction population. PMID:23538391

  19. Ejection experience in Serbian air force, 1990-2010

    Pavlović Miroslav

    2014-01-01

    Full Text Available Background/Aim. Ejection injuries are the problem for air forces. The present risk for injuries is still too high, approximately 30-50%. This study was an effort to determine factors responsible for and contributing to injuries in the Serbian Air Force (SAF in the last two decades. Methods. All ejection cases in the SAF between 1990 and 2010 were analyzed. The collected data were: aircraft type, ejection seat generation, pilots ´ age and experience, causes of ejection, aeronautical parameters, the condition of aircraft control and types of injuries. For ease of comparison the U.S. Air Force Safety Regulation was used to define of major injuries: hospitalization for 5 days or more, loss of consciousness for over 5 min, bone fracture, joint dislocation, injury to any internal organ, any third-degree burn, or second-degree burn over 5% of the body surface area. Results. There were 52 ejections (51 pilots and 1 mechanic on 44 airplanes. The ejected persons were from 22 to 46 years, average 32 years. Major injuries were present in 25.49% cases. Of all the ejected pilots 9.61% had fractures of thoracic spine, 11.53% fractures of legs, 3.48% fractures of arms. Of all major injuries, fractures of thoracic spine were 38.46%. None of the pilots had experienced ejection previously. Conclusion. Our results suggest to obligatory take preventive measures: magnetic resonance imaging (MRI scan must be included in the standard pilot selection procedure and procedure after ejection. Physical conditioning of pilots has to be improved. Training on ejection trainer has to be accomplished, too.

  20. SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells.

    Toghill, Bradley J; Saratzis, Athanasios; Freeman, Peter J; Sylvius, Nicolas; Bown, Matthew J

    2018-01-01

    Abdominal aortic aneurysm (AAA) is a deadly cardiovascular disease characterised by the gradual, irreversible dilation of the abdominal aorta. AAA is a complex genetic disease but little is known about the role of epigenetics. Our objective was to determine if global DNA methylation and CpG-specific methylation at known AAA risk loci is associated with AAA, and the functional effects of methylation changes. We assessed global methylation in peripheral blood mononuclear cell DNA from 92 individuals with AAA and 93 controls using enzyme-linked immunosorbent assays, identifying hyper-methylation in those with large AAA and a positive linear association with AAA diameter ( P  AAA risk loci identified in genome-wide association studies, using bisulphite next-generation sequencing (NGS) in vascular smooth muscle cells (VSMCs) taken from aortic tissues of 44 individuals (24 AAAs and 20 controls). In IL6R , 2 CpGs were hyper-methylated ( P  = 0.0145); in ERG , 13 CpGs were hyper-methylated ( P  = 0.0005); in SERPINB9 , 6 CpGs were hypo-methylated ( P  = 0.0037) and 1 CpG was hyper-methylated ( P  = 0.0098); and in SMYD2 , 4 CpGs were hypo-methylated ( P  = 0.0012).RT-qPCR was performed for each differentially methylated gene on mRNA from the same VSMCs and compared with methylation. This analysis revealed downregulation of SMYD2 and SERPINB9 in AAA, and a direct linear relationship between SMYD2 promoter methylation and SMYD2 expression ( P  = 0.038). Furthermore, downregulation of SMYD2 at the site of aneurysm in the aortic wall was further corroborated in 6 of the same samples used for methylation and gene expression analysis with immunohistochemistry. This study is the first to assess DNA methylation in VSMCs from individuals with AAA using NGS, and provides further evidence there is an epigenetic basis to AAA. Our study shows that methylation status of the SMYD2 promoter may be linked with decreased SMYD2 expression in disease pathobiology. In

  1. RFWD3-Mediated Ubiquitination Promotes Timely Removal of Both RPA and RAD51 from DNA Damage Sites to Facilitate Homologous Recombination.

    Inano, Shojiro; Sato, Koichi; Katsuki, Yoko; Kobayashi, Wataru; Tanaka, Hiroki; Nakajima, Kazuhiro; Nakada, Shinichiro; Miyoshi, Hiroyuki; Knies, Kerstin; Takaori-Kondo, Akifumi; Schindler, Detlev; Ishiai, Masamichi; Kurumizaka, Hitoshi; Takata, Minoru

    2017-06-01

    RFWD3 is a recently identified Fanconi anemia protein FANCW whose E3 ligase activity toward RPA is essential in homologous recombination (HR) repair. However, how RPA ubiquitination promotes HR remained unknown. Here, we identified RAD51, the central HR protein, as another target of RFWD3. We show that RFWD3 polyubiquitinates both RPA and RAD51 in vitro and in vivo. Phosphorylation by ATR and ATM kinases is required for this activity in vivo. RFWD3 inhibits persistent mitomycin C (MMC)-induced RAD51 and RPA foci by promoting VCP/p97-mediated protein dynamics and subsequent degradation. Furthermore, MMC-induced chromatin loading of MCM8 and RAD54 is defective in cells with inactivated RFWD3 or expressing a ubiquitination-deficient mutant RAD51. Collectively, our data reveal a mechanism that facilitates timely removal of RPA and RAD51 from DNA damage sites, which is crucial for progression to the late-phase HR and suppression of the FA phenotype. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. A milk protein gene promoter directs the expression of human tissue plasminogen activator cDNA to the mammary gland in transgenic mice

    Pittius, C.W.; Hennighausen, L.; Lee, E.; Westphal, H.; Nicols, E.; Vitale, J.; Gordon, K.

    1988-01-01

    Whey acidic protein (WAP) is a major whey protein in mouse milk. Its gene is expressed in the lactating mammary gland and is inducible by steroid and peptide hormones. A series of transgenic mice containing a hybrid gene in which human tissue plasminogen activator (tPA) cDNA is under the control of the murine WAP gene promoter had previously been generated. In this study, 21 tissues from lactating and virgin transgenic female mice containing the WAP-tPA hybrid gene were screened for the distribution of murine WAP and human tPA transcripts. Like the endogenous WAP RNA, WAP-tPA RNA was expressed predominantly in mammary gland tissue and appeared to be inducible by lactation. Whereas WAP transcripts were not detected in 22 tissues of virgin mice, low levels of WAP-tPA RNA, which were not modulated during lactation, were found in tongue, kidney, and sublingual gland. These studies demonstrate that the WAP gene promoter can target the expression of a transgene to the mammary gland and that this expression is inducible during lactation

  3. Isolation and characterization of an atypical LEA protein coding cDNA and its promoter from drought-tolerant plant Prosopis juliflora.

    George, Suja; Usha, B; Parida, Ajay

    2009-05-01

    Plant growth and productivity are adversely affected by various abiotic and biotic stress factors. Despite the wealth of information on abiotic stress and stress tolerance in plants, many aspects still remain unclear. Prosopis juliflora is a hardy plant reported to be tolerant to drought, salinity, extremes of soil pH, and heavy metal stress. In this paper, we report the isolation and characterization of the complementary DNA clone for an atypical late embryogenesis abundant (LEA) protein (Pj LEA3) and its putative promoter sequence from P. juliflora. Unlike typical LEA proteins, rich in glycine, Pj LEA3 has alanine as the most abundant amino acid followed by serine and shows an average negative hydropathy. Pj LEA3 is significantly different from other LEA proteins in the NCBI database and shows high similarity to indole-3 acetic-acid-induced protein ARG2 from Vigna radiata. Northern analysis for Pj LEA3 in P. juliflora leaves under 90 mM H2O2 stress revealed up-regulation of transcript at 24 and 48 h. A 1.5-kb fragment upstream the 5' UTR of this gene (putative promoter) was isolated and analyzed in silico. The possible reasons for changes in gene expression during stress in relation to the host plant's stress tolerance mechanisms are discussed.

  4. Genome-wide screening identifies Plasmodium chabaudi-induced modifications of DNA methylation status of Tlr1 and Tlr6 gene promoters in liver, but not spleen, of female C57BL/6 mice.

    Al-Quraishy, Saleh; Dkhil, Mohamed A; Abdel-Baki, Abdel Azeem S; Delic, Denis; Santourlidis, Simeon; Wunderlich, Frank

    2013-11-01

    Epigenetic reprogramming of host genes via DNA methylation is increasingly recognized as critical for the outcome of diverse infectious diseases, but information for malaria is not yet available. Here, we investigate the effect of blood-stage malaria of Plasmodium chabaudi on the DNA methylation status of host gene promoters on a genome-wide scale using methylated DNA immunoprecipitation and Nimblegen microarrays containing 2,000 bp oligonucleotide features that were split into -1,500 to -500 bp Ups promoters and -500 to +500 bp Cor promoters, relative to the transcription site, for evaluation of differential DNA methylation. Gene expression was analyzed by Agilent and Affymetrix microarray technology. Challenging of female C57BL/6 mice with 10(6) P. chabaudi-infected erythrocytes resulted in a self-healing outcome of infections with peak parasitemia on day 8 p.i. These infections induced organ-specific modifications of DNA methylation of gene promoters. Among the 17,354 features on Nimblegen arrays, only seven gene promoters were identified to be hypermethylated in the spleen, whereas the liver exhibited 109 hyper- and 67 hypomethylated promoters at peak parasitemia in comparison with non-infected mice. Among the identified genes with differentially methylated Cor-promoters, only the 7 genes Pigr, Ncf1, Klkb1, Emr1, Ndufb11, and Tlr6 in the liver and Apol6 in the spleen were detected to have significantly changed their expression. Remarkably, the Cor promoter of the toll-like receptor Tlr6 became hypomethylated and Tlr6 expression increased by 3.4-fold during infection. Concomitantly, the Ups promoter of the Tlr1 was hypermethylated, but Tlr1 expression also increased by 11.3-fold. TLR6 and TLR1 are known as auxillary receptors to form heterodimers with TLR2 in plasma membranes of macrophages, which recognize different pathogen-associated molecular patterns (PAMPs), as, e.g., intact 3-acyl and sn-2-lyso-acyl glycosylphosphatidylinositols of P. falciparum

  5. Association between human papillomavirus and Epstein - Barr virus DNA and gene promoter methylation of RB1 and CDH1 in the cervical lesions: a transversal study.

    McCormick, Thaís M; Canedo, Nathalie H S; Furtado, Yara L; Silveira, Filomena A; de Lima, Roberto J; Rosman, Andréa D F; Almeida Filho, Gutemberg L; Carvalho, Maria da Glória da C

    2015-06-02

    Human papillomavirus (HPV) inactivates the retinoblastoma 1 (RB1) gene by promoter methylation and reduces cellular E-cadherin expression by overexpression of DNA methyltransferase 1 (DNMT1). The Epstein-Barr virus (EBV) is an oncogenic virus that may be related to cervical carcinogenesis. In gastric cancer, it has been demonstrated that E-cadherin gene (CDH1) hypermethylation is associated with DNMT1 overexpression by EBV infection. Our aim was to analyze the gene promoter methylation frequency of RB1 and CDH1 and verify the association between that methylation frequency and HPV and EBV infection in cervical lesions. Sixty-five samples were obtained from cervical specimens: 15 normal cervices, 17 low-grade squamous intraepithelial lesions (LSIL), 15 high-grade squamous intraepithelial lesions (HSIL), and 18 cervical cancers. HPV and EBV DNA testing was performed by PCR, and the methylation status was verified by MSP. HPV frequency was associated with cervical cancer cases (p = 0.005) but not EBV frequency (p = 0.732). Viral co-infection showed a statistically significant correlation with cancer (p = 0.027). No viral infection was detected in 33.3% (5/15) of controls. RB1 methylated status was associated with cancer (p = 0.009) and HPV infection (p = 0.042). CDH1 methylation was not associated with cancer (p = 0.181). Controls and LSIL samples did not show simultaneous methylation, while both genes were methylated in 27.8% (5/18) of cancer samples. In the presence of EBV, CDH1 methylation was present in 27.8% (5/18) of cancer samples. Only cancer cases presented RB1 promoter methylation in the presence of HPV and EBV (33.3%). The methylation status of both genes increased with disease progression. With EBV, RB1 methylation was a tumor-associated event because only the cancer group presented methylated RB1 with HPV infection. HPV infection was shown to be significantly correlated with cancer conditions. The global methylation frequency was

  6. Genome-wide Anaplasma phagocytophilum AnkA-DNA interactions are enriched in intergenic regions and gene promoters and correlate with infection-induced differential gene expression.

    J Stephen Dumler

    2016-09-01

    Full Text Available Anaplasma phagocytophilum, an obligate intracellular prokaryote, infects neutrophils and alters cardinal functions via reprogrammed transcription. Large contiguous regions of neutrophil chromosomes are differentially expressed during infection. Secreted A. phagocytophilum effector AnkA transits into the neutrophil or granulocyte nucleus to complex with DNA in heterochromatin across all chromosomes. AnkA binds to gene promoters to dampen cis-transcription and also has features of matrix attachment region (MAR-binding proteins that regulate three-dimensional chromatin architecture and coordinate transcriptional programs encoded in topologically-associated chromatin domains. We hypothesize that identification of additional AnkA binding sites will better delineate how A. phagocytophilum infection results in reprogramming of the neutrophil genome. Using AnkA-binding ChIP-seq, we showed that AnkA binds broadly throughout all chromosomes in a reproducible pattern, especially at: i intergenic regions predicted to be matrix attachment regions (MARs; ii within predicted lamina-associated domains; and iii at promoters ≤3,000 bp upstream of transcriptional start sites. These findings provide genome-wide support for AnkA as a regulator of cis-gene transcription. Moreover, the dominant mark of AnkA in distal intergenic regions known to be AT-enriched, coupled with frequent enrichment in the nuclear lamina, provides strong support for its role as a MAR-binding protein and genome re-organizer. AnkA must be considered a prime candidate to promote neutrophil reprogramming and subsequent functional changes that belie improved microbial fitness and pathogenicity.

  7. Expression profiling of O6 methylguanine-DNA-methyl transferase in prolactinomas: a correlative study of promoter methylation and pathological features in 136 cases

    Jiang, Xiao-Bing; Hu, Bin; He, Dong-Sheng; Mao, Zhi-Gang; Wang, Xin; Song, Bing-Bing; Zhu, Yong-Hong; Wang, Hai-Jun

    2015-01-01

    Low-level expression of O 6 methylguanine-DNA-methyl transferase (MGMT) prolactinomas has been noted previously in case reports, although what modulates MGMT expression remains unclear. This study therefore aimed to delineate the factors regulating MGMT expression in prolactinomas. We retrospectively reviewed 136 prolactinoma patients who were treated in our center between January 2000 and September 2013. Expression of MGMT, Ki-67, and p53 protein were examined by immunohistochemical staining, and MGMT promoter methylation evaluated with methylation-specific PCR. MGMT immunopositivity was <25 % in 106/136 tumor specimens (77.94 %). MGMT immunoexpression was positively correlated with age (r = 0.251, p = 0.003), but inversely correlated with p53 staining (r = −0.153, p = 0.021). Moreover, reduced MGMT expression was more frequent in atypical prolactinomas (p = 0.044). Methylated MGMT promoter was confirmed in 10/46 specimens (21.7 %), all of which had low level or absent MGMT staining. Both p53 protein (r = −0.33, p = 0.025) and promoter methylation (r = −0.331, p = 0.025) were negatively associated with MGMT expression. Multivariate logistic analysis indicated that age (odds ratio [OR] = 1.127. 95 % confidence interval [CI] 1.027–1.236, p = 0.012) and p53 (OR = 0.116. 95 % CI 0.018–0.761, p = 0.025) staining were independent determents of MGMT expression. The majority of prolactinomas, especially atypical prolactinomas, showed low-level or no MGMT immunoexpression, providing a rationale for the utility of temozolomide as an alternative to managing prolactinomas. In summary, epigenetic and transcriptional regulation are involved in silencing MGMT expression

  8. Active Longitude and Coronal Mass Ejection Occurrences

    Gyenge, N.; Kiss, T. S.; Erdélyi, R.; Singh, T.; Srivastava, A. K.

    2017-01-01

    The spatial inhomogeneity of the distribution of coronal mass ejection (CME) occurrences in the solar atmosphere could provide a tool to estimate the longitudinal position of the most probable CME-capable active regions in the Sun. The anomaly in the longitudinal distribution of active regions themselves is often referred to as active longitude (AL). In order to reveal the connection between the AL and CME spatial occurrences, here we investigate the morphological properties of active regions. The first morphological property studied is the separateness parameter, which is able to characterize the probability of the occurrence of an energetic event, such as a solar flare or CME. The second morphological property is the sunspot tilt angle. The tilt angle of sunspot groups allows us to estimate the helicity of active regions. The increased helicity leads to a more complex buildup of the magnetic structure and also can cause CME eruption. We found that the most complex active regions appear near the AL and that the AL itself is associated with the most tilted active regions. Therefore, the number of CME occurrences is higher within the AL. The origin of the fast CMEs is also found to be associated with this region. We concluded that the source of the most probably CME-capable active regions is at the AL. By applying this method, we can potentially forecast a flare and/or CME source several Carrington rotations in advance. This finding also provides new information for solar dynamo modeling.

  9. Active Longitude and Coronal Mass Ejection Occurrences

    Gyenge, N.; Kiss, T. S.; Erdélyi, R. [Solar Physics and Space Plasmas Research Centre (SP2RC), School of Mathematics and Statistics, University of Sheffield Hounsfield Road, Hicks Building, Sheffield S3 7RH (United Kingdom); Singh, T.; Srivastava, A. K., E-mail: n.g.gyenge@sheffield.ac.uk [Department of Physics, Indian Institute of Technology (Banaras Hindu University), Varanasi (India)

    2017-03-20

    The spatial inhomogeneity of the distribution of coronal mass ejection (CME) occurrences in the solar atmosphere could provide a tool to estimate the longitudinal position of the most probable CME-capable active regions in the Sun. The anomaly in the longitudinal distribution of active regions themselves is often referred to as active longitude (AL). In order to reveal the connection between the AL and CME spatial occurrences, here we investigate the morphological properties of active regions. The first morphological property studied is the separateness parameter, which is able to characterize the probability of the occurrence of an energetic event, such as a solar flare or CME. The second morphological property is the sunspot tilt angle. The tilt angle of sunspot groups allows us to estimate the helicity of active regions. The increased helicity leads to a more complex buildup of the magnetic structure and also can cause CME eruption. We found that the most complex active regions appear near the AL and that the AL itself is associated with the most tilted active regions. Therefore, the number of CME occurrences is higher within the AL. The origin of the fast CMEs is also found to be associated with this region. We concluded that the source of the most probably CME-capable active regions is at the AL. By applying this method, we can potentially forecast a flare and/or CME source several Carrington rotations in advance. This finding also provides new information for solar dynamo modeling.

  10. Active Longitude and Coronal Mass Ejection Occurrences

    Gyenge, N.; Singh, T.; Kiss, T. S.; Srivastava, A. K.; Erdélyi, R.

    2017-03-01

    The spatial inhomogeneity of the distribution of coronal mass ejection (CME) occurrences in the solar atmosphere could provide a tool to estimate the longitudinal position of the most probable CME-capable active regions in the Sun. The anomaly in the longitudinal distribution of active regions themselves is often referred to as active longitude (AL). In order to reveal the connection between the AL and CME spatial occurrences, here we investigate the morphological properties of active regions. The first morphological property studied is the separateness parameter, which is able to characterize the probability of the occurrence of an energetic event, such as a solar flare or CME. The second morphological property is the sunspot tilt angle. The tilt angle of sunspot groups allows us to estimate the helicity of active regions. The increased helicity leads to a more complex buildup of the magnetic structure and also can cause CME eruption. We found that the most complex active regions appear near the AL and that the AL itself is associated with the most tilted active regions. Therefore, the number of CME occurrences is higher within the AL. The origin of the fast CMEs is also found to be associated with this region. We concluded that the source of the most probably CME-capable active regions is at the AL. By applying this method, we can potentially forecast a flare and/or CME source several Carrington rotations in advance. This finding also provides new information for solar dynamo modeling.

  11. Solar origins of coronal mass ejections

    Kahler, Stephen

    1987-01-01

    The large scale properties of coronal mass ejections (CMEs), such as morphology, leading edge speed, and angular width and position, have been cataloged for many events observed with coronagraphs on the Skylab, P-78, and SMM spacecraft. While considerable study has been devoted to the characteristics of the SMEs, their solar origins are still only poorly understood. Recent observational work has involved statistical associations of CMEs with flares and filament eruptions, and some evidence exists that the flare and eruptive-filament associated CMEs define two classes of events, with the former being generally more energetic. Nevertheless, it is found that eruptive-filament CMEs can at times be very energetic, giving rise to interplanetary shocks and energetic particle events. The size of the impulsive phase in a flare-associated CME seems to play no significant role in the size or speed of the CME, but the angular sizes of CMEs may correlate with the scale sizes of the 1-8 angstrom x-ray flares. At the present time, He 10830 angstrom observations should be useful in studying the late development of double-ribbon flares and transient coronal holes to yield insights into the CME aftermath. The recently available white-light synoptic maps may also prove fruitful in defining the coronal conditions giving rise to CMEs.

  12. ANATOMY OF DEPLETED INTERPLANETARY CORONAL MASS EJECTIONS

    Kocher, M.; Lepri, S. T.; Landi, E.; Zhao, L.; Manchester, W. B. IV, E-mail: mkocher@umich.edu [Department of Climate and Space Sciences and Engineering, University of Michigan, 2455 Hayward Street, Ann Arbor, MI 48109-2143 (United States)

    2017-01-10

    We report a subset of interplanetary coronal mass ejections (ICMEs) containing distinct periods of anomalous heavy-ion charge state composition and peculiar ion thermal properties measured by ACE /SWICS from 1998 to 2011. We label them “depleted ICMEs,” identified by the presence of intervals where C{sup 6+}/C{sup 5+} and O{sup 7+}/O{sup 6+} depart from the direct correlation expected after their freeze-in heights. These anomalous intervals within the depleted ICMEs are referred to as “Depletion Regions.” We find that a depleted ICME would be indistinguishable from all other ICMEs in the absence of the Depletion Region, which has the defining property of significantly low abundances of fully charged species of helium, carbon, oxygen, and nitrogen. Similar anomalies in the slow solar wind were discussed by Zhao et al. We explore two possibilities for the source of the Depletion Region associated with magnetic reconnection in the tail of a CME, using CME simulations of the evolution of two Earth-bound CMEs described by Manchester et al.

  13. EIT Observations of Coronal Mass Ejections

    Gurman, J. B.; Fisher, Richard B. (Technical Monitor)

    2000-01-01

    Before the Solar and Heliospheric Observatory (SOHO), we had only the sketchiest of clues as to the nature and topology of coronal mass ejections (CMEs) below 1.1 - 1.2 solar radii. Occasionally, dimmings (or 'transient coronal holes') were observed in time series of soft X-ray images, but they were far less frequent than CME's. Simply by imaging the Sun frequently and continually at temperatures of 0.9 - 2.5 MK we have stumbled upon a zoo of CME phenomena in this previously obscured volume of the corona: (1) waves, (2) dimmings, and (3) a great variety of ejecta. In the three and a half years since our first observations of coronal waves associated with CME's, combined Large Angle Spectroscopic Coronagraph (LASCO) and extreme ultra-violet imaging telescope (EIT) synoptic observations have become a standard prediction tool for space weather forecasters, but our progress in actually understanding the CME phenomenon in the low corona has been somewhat slower. I will summarize the observations of waves, hot (> 0.9 MK) and cool ejecta, and some of the interpretations advanced to date. I will try to identify those phenomena, analysis of which could most benefit from the spectroscopic information available from ultraviolet coronograph spectrometer (UVCS) observations.

  14. Evidence linking coronal mass ejections with interplanetary magnetic clouds

    Wilson, R.M.; Hildner, E.

    1983-12-01

    Using proxy data for the occurrence of those mass ejections from the solar corona which are directed earthward, we investigate the association between the post-1970 interplanetary magnetic clouds of Klein and Burlaga and coronal mass ejections. The evidence linking magnetic clouds following shocks with coronal mass ejections is striking. Six of nine clouds observed at Earth were preceded an appropriate time earlier by meter-wave type II radio bursts indicative of coronal shock waves and coronal mass ejections occurring near central meridian. During the selected periods when no clouds were detected near Earth, the only type II bursts reported were associated with solar activity near the limbs. Where the proxy solar data to be sought are not so clearly suggested, that is, for clouds preceding interaction regions and clouds within cold magnetic enhancements, the evidence linking the clouds and coronal mass ejections is not as clear proxy data usually suggest many candidate mass-ejection events for each cloud. Overall, the data are consistent with and support the hypothesis suggested by Klein and Burlaga that magnetic clouds observed with spacecraft at 1 AU are manifestations of solar coronal mass ejection transients

  15. G4-DNA formation in the HRAS promoter and rational design of decoy oligonucleotides for cancer therapy.

    Alexandro Membrino

    Full Text Available HRAS is a proto-oncogene involved in the tumorigenesis of urinary bladder cancer. In the HRAS promoter we identified two G-rich elements, hras-1 and hras-2, that fold, respectively, into an antiparallel and a parallel quadruplex (qhras-1, qhras-2. When we introduced in sequence hras-1 or hras-2 two point mutations that block quadruplex formation, transcription increased 5-fold, but when we stabilized the G-quadruplexes by guanidinium phthalocyanines, transcription decreased to 20% of control. By ChIP we found that sequence hras-1 is bound only by MAZ, while hras-2 is bound by MAZ and Sp1: two transcription factors recognizing guanine boxes. We also discovered by EMSA that recombinant MAZ-GST binds to both HRAS quadruplexes, while Sp1-GST only binds to qhras-1. The over-expression of MAZ and Sp1 synergistically activates HRAS transcription, while silencing each gene by RNAi results in a strong down-regulation of transcription. All these data indicate that the HRAS G-quadruplexes behave as transcription repressors. Finally, we designed decoy oligonucleotides mimicking the HRAS quadruplexes, bearing (R-1-O-[4-(1-Pyrenylethynyl phenylmethyl] glycerol and LNA modifications to increase their stability and nuclease resistance (G4-decoys. The G4-decoys repressed HRAS transcription and caused a strong antiproliferative effect, mediated by apoptosis, in T24 bladder cancer cells where HRAS is mutated.

  16. Magnetohydrodynamic simulations of the ejection of a magnetic flux rope

    Pagano, P.; Mackay, D. H.; Poedts, S.

    2013-06-01

    Context. Coronal mass ejections (CME's) are one of the most violent phenomena found on the Sun. One model to explain their occurrence is the flux rope ejection model. In this model, magnetic flux ropes form slowly over time periods of days to weeks. They then lose equilibrium and are ejected from the solar corona over a few hours. The contrasting time scales of formation and ejection pose a serious problem for numerical simulations. Aims: We simulate the whole life span of a flux rope from slow formation to rapid ejection and investigate whether magnetic flux ropes formed from a continuous magnetic field distribution, during a quasi-static evolution, can erupt to produce a CME. Methods: To model the full life span of magnetic flux ropes we couple two models. The global non-linear force-free field (GNLFFF) evolution model is used to follow the quasi-static formation of a flux rope. The MHD code ARMVAC is used to simulate the production of a CME through the loss of equilibrium and ejection of this flux rope. Results: We show that the two distinct models may be successfully coupled and that the flux rope is ejected out of our simulation box, where the outer boundary is placed at 2.5 R⊙. The plasma expelled during the flux rope ejection travels outward at a speed of 100 km s-1, which is consistent with the observed speed of CMEs in the low corona. Conclusions: Our work shows that flux ropes formed in the GNLFFF can lead to the ejection of a mass loaded magnetic flux rope in full MHD simulations. Coupling the two distinct models opens up a new avenue of research to investigate phenomena where different phases of their evolution occur on drastically different time scales. Movies are available in electronic form at http://www.aanda.org

  17. Mycobacterium tuberculosis nucleoid-associated DNA-binding protein H-NS binds with high-affinity to the Holliday junction and inhibits strand exchange promoted by RecA protein.

    Sharadamma, N; Harshavardhana, Y; Singh, Pawan; Muniyappa, K

    2010-06-01

    A number of studies have shown that the structure and composition of bacterial nucleoid influences many a processes related to DNA metabolism. The nucleoid-associated proteins modulate not only the DNA conformation but also regulate the DNA metabolic processes such as replication, recombination, repair and transcription. Understanding of how these processes occur in the context of Mycobacterium tuberculosis nucleoid is of considerable medical importance because the nucleoid structure may be constantly remodeled in response to environmental signals and/or growth conditions. Many studies have concluded that Escherichia coli H-NS binds to DNA in a sequence-independent manner, with a preference for A-/T-rich tracts in curved DNA; however, recent studies have identified the existence of medium- and low-affinity binding sites in the vicinity of the curved DNA. Here, we show that the M. tuberculosis H-NS protein binds in a more structure-specific manner to DNA replication and repair intermediates, but displays lower affinity for double-stranded DNA with relatively higher GC content. Notably, M. tuberculosis H-NS was able to bind Holliday junction (HJ), the central recombination intermediate, with substantially higher affinity and inhibited the three-strand exchange promoted by its cognate RecA. Likewise, E. coli H-NS was able to bind the HJ and suppress DNA strand exchange promoted by E. coli RecA, although much less efficiently compared to M. tuberculosis H-NS. Our results provide new insights into a previously unrecognized function of H-NS protein, with implications for blocking the genome integration of horizontally transferred genes by homologous and/or homeologous recombination.

  18. Recurrent mass ejections observed in H-alpha and CIV

    Schmieder, B.; Simon, G.

    1984-01-01

    Time sequences of recurrent mass ejections have been observed during a coordinated SMY program (Sept. 1, 1980 - Sept. 23, 1980 - Oct. 2, 1980). Comparison of the temporal evolution of H-alpha and CIV brightnesses shows a weak phase lag between H-alpha and CIV maxima, in the case of homologous flares, with CIV brightness maxima preceding H-alpha maxima. The analysis of the variation of the ejection velocities is expected to lead to the determination of an energy balance. Such recurrent ejections could be due to periodic energy storage and periodic reorganization of magnetic field as envisaged to occur for flares, but at lower energy levels

  19. Magazine Influence on Cartridge Case Ejection Patterns with Glock Pistols.

    Kerkhoff, Wim; Alberink, Ivo; Mattijssen, Erwin J A T

    2018-01-01

    In this study, the cartridge case ejection patterns of six different Glock model pistols (one specimen per model) were compared under three conditions: firing with a loaded magazine, an empty magazine, and without magazine. The distances, covered by the ejected cartridge cases given these three conditions, were compared for each of the six models. A significant difference was found between the groups of data for each of the tested specimens. This indicates that it is important that, to reconstruct a shooting scene incident based on the ejection patterns of a pistol, test shots are fired with the same pistol type and under the correct magazine condition. © 2017 American Academy of Forensic Sciences.

  20. Synergy between the N-terminal and C-terminal domains of Mycobacterium tuberculosis HupB is essential for high-affinity binding, DNA supercoiling and inhibition of RecA-promoted strand exchange.

    Sharadamma, N; Khan, Krishnendu; Kumar, Sandeep; Patil, K Neelakanteshwar; Hasnain, Seyed E; Muniyappa, K

    2011-09-01

    The occurrence of DNA architectural proteins containing two functional domains derived from two different architectural proteins is an interesting emerging research theme in the field of nucleoid structure and function. Mycobacterium tuberculosis HupB, unlike Escherichia coli HU, is a two-domain protein that, in the N-terminal region, shows broad sequence homology with bacterial HU. The long C-terminal extension, on the other hand, contains seven PAKK/KAAK motifs, which are characteristic of the histone H1/H5 family of proteins. In this article, we describe several aspects of HupB function, in comparison with its truncated derivatives lacking either the C-terminus or N-terminus. We found that HupB binds a variety of DNA repair and replication intermediates with K(d) values in the nanomolar range. By contrast, the N-terminal fragment of M. tuberculosis HupB (HupB(MtbN)) showed diminished DNA-binding activity, with K(d) values in the micromolar range, and the C-terminal domain was completely devoid of DNA-binding activity. Unlike HupB(MtbN) , HupB was able to constrain DNA in negative supercoils and introduce negative superhelical turns into relaxed DNA. Similarly, HupB exerted a robust inhibitory effect on DNA strand exchange promoted by cognate and noncognate RecA proteins, whereas HupB(MtbN), even at a 50-fold molar excess, had no inhibitory effect. Considered together, these results suggest that synergy between the N-terminal and C-terminal domains of HupB is essential for its DNA-binding ability, and to modulate the topological features of DNA, which has implications for processes such as DNA compaction, gene regulation, homologous recombination, and DNA repair. © 2011 The Authors Journal compilation © 2011 FEBS.

  1. Environmental stress affects DNA methylation of a CpG rich promoter region of serotonin transporter gene in a nurse cohort.

    Jukka S Alasaari

    Full Text Available Shift-working nurses are exposed to a stressful work environment, which puts them at an increased risk for burnout and depression. We explored the effect of environmental stress on serotonin transporter gene (SLC6A4 promoter methylation among nurses from high and low work stress environments.Using bisulfite sequencing, we investigated the methylation status of five CpG residues of a CpG-rich region in the promoter of SLC6A4 by comparing female shift working nurses from a high work stress environment (n = 24 to low work stress environment (n = 25. We also analyzed the association of 5-HTTLPR polymorphism at 5' end of SLC6A4. Work stress was assessed by the Karasek's Model and possible signs of burnout or depression were measured by the Maslach Burnout Index General Survey and Beck Depression Index. Methylation levels were assessed by bisulfite sequencing of DNA extracted from peripheral blood leucocytes. Restriction enzyme treatment followed by standard PCR was used to identify 5-HTTLPR genotypes.We found that nurses in the high stress environment had significantly lower promoter methylation levels at all five CpG residues compared to nurses in the low stress environment (p<0.01. There was no significant interaction of 5-HTTLPR genotype and work stress with methylation (p = 0.58. In unadjusted (bivariate analysis, burnout was not significantly associated to methylation levels. However, when mutually adjusted for both, burnout and work stress were significant contributors (p = 0.038 and p<0.0001 respectively to methylation levels.Our findings show that environmental stress is concurrent with decreased methylation of the SLC6A4 promoter. This may lead to increased transcriptional activity of the gene, increased reuptake of serotonin from synaptic clefts, and termination of the activity of serotonin. This could present a possible coping mechanism for environmental stress in humans that could eventually increase risk for disturbed functional

  2. Coronal mass ejections and solar radio bursts

    Kundu, M.R.

    1990-01-01

    The properties of coronal mass ejection (CME) events and their radio signatures are discussed. These signatures are mostly in the form of type II and type IV burst emissions. Although type II bursts are temporally associated with CMEs, it is shown that there is no spatial relationship between them. Type II's associated with CMEs have in most cases a different origin, and they are not piston-driven by CMEs. Moving type IV and type II bursts can be associated with slow CMEs with speeds as low as 200 km/s, contrary to the earlier belief that only CMEs with speeds >400 km/s are associated with radio bursts. A specific event has been discussed in which the CME and type IV burst has nearly the same speed and direction, but the type II burst location was behind the CME and its motion was transverse. The speed and motion of the type II burst strongly suggest that the type II shock was decoupled from the CME and was probably due to a flare behind the limb. Therefore only the type IV source could be directly associated with the slow CME. The electrons responsble for the type IV emission could be produced in the flare or in the type II and then become trapped in a plasmoid associated with the CME. The reconnected loop could then move outwards as in the usual palsmoid model. Alternatively, the type IV emission could be interpreted as due to electrons produced by acceleration in wave turbulence driven by currents in the shock front driven by the CME. The lower-hybrid model Lampe and Papadopoulos (1982), which operates at both fast and slow mode shocks, could be applied to this situation. (author). 31 refs., 12 figs

  3. Violation of an evolutionarily conserved immunoglobulin diversity gene sequence preference promotes production of dsDNA-specific IgG antibodies.

    Aaron Silva-Sanchez

    Full Text Available Variability in the developing antibody repertoire is focused on the third complementarity determining region of the H chain (CDR-H3, which lies at the center of the antigen binding site where it often plays a decisive role in antigen binding. The power of VDJ recombination and N nucleotide addition has led to the common conception that the sequence of CDR-H3 is unrestricted in its variability and random in its composition. Under this view, the immune response is solely controlled by somatic positive and negative clonal selection mechanisms that act on individual B cells to promote production of protective antibodies and prevent the production of self-reactive antibodies. This concept of a repertoire of random antigen binding sites is inconsistent with the observation that diversity (DH gene segment sequence content by reading frame (RF is evolutionarily conserved, creating biases in the prevalence and distribution of individual amino acids in CDR-H3. For example, arginine, which is often found in the CDR-H3 of dsDNA binding autoantibodies, is under-represented in the commonly used DH RFs rearranged by deletion, but is a frequent component of rarely used inverted RF1 (iRF1, which is rearranged by inversion. To determine the effect of altering this germline bias in DH gene segment sequence on autoantibody production, we generated mice that by genetic manipulation are forced to utilize an iRF1 sequence encoding two arginines. Over a one year period we collected serial serum samples from these unimmunized, specific pathogen-free mice and found that more than one-fifth of them contained elevated levels of dsDNA-binding IgG, but not IgM; whereas mice with a wild type DH sequence did not. Thus, germline bias against the use of arginine enriched DH sequence helps to reduce the likelihood of producing self-reactive antibodies.

  4. Repair of exogenous DNA double-strand breaks promotes chromosome synapsis in SPO11-mutant mouse meiocytes, and is altered in the absence of HORMAD1.

    Carofiglio, Fabrizia; Sleddens-Linkels, Esther; Wassenaar, Evelyne; Inagaki, Akiko; van Cappellen, Wiggert A; Grootegoed, J Anton; Toth, Attila; Baarends, Willy M

    2018-03-01

    Repair of SPO11-dependent DNA double-strand breaks (DSBs) via homologous recombination (HR) is essential for stable homologous chromosome pairing and synapsis during meiotic prophase. Here, we induced radiation-induced DSBs to study meiotic recombination and homologous chromosome pairing in mouse meiocytes in the absence of SPO11 activity (Spo11 YF/YF model), and in the absence of both SPO11 and HORMAD1 (Spo11/Hormad1 dko). Within 30 min after 5 Gy irradiation of Spo11 YF/YF mice, 140-160 DSB repair foci were detected, which specifically localized to the synaptonemal complex axes. Repair of radiation-induced DSBs was incomplete in Spo11 YF/YF compared to Spo11 +/YF meiocytes. Still, repair of exogenous DSBs promoted partial recovery of chromosome pairing and synapsis in Spo11 YF/YF meiocytes. This indicates that at least part of the exogenous DSBs can be processed in an interhomolog recombination repair pathway. Interestingly, in a seperate experiment, using 3 Gy of irradiation, we observed that Spo11/Hormad1 dko spermatocytes contained fewer remaining DSB repair foci at 48 h after irradiation compared to irradiated Spo11 knockout spermatocytes. Together, these results show that recruitment of exogenous DSBs to the synaptonemal complex, in conjunction with repair of exogenous DSBs via the homologous chromosome, contributes to homology recognition. In addition, the data suggest a role for HORMAD1 in DNA repair pathway choice in mouse meiocytes. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

  5. DNA helicase HIM-6/BLM both promotes MutSγ-dependent crossovers and antagonizes MutSγ-independent interhomolog associations during caenorhabditis elegans meiosis.

    Schvarzstein, Mara; Pattabiraman, Divya; Libuda, Diana E; Ramadugu, Ajit; Tam, Angela; Martinez-Perez, Enrique; Roelens, Baptiste; Zawadzki, Karl A; Yokoo, Rayka; Rosu, Simona; Severson, Aaron F; Meyer, Barbara J; Nabeshima, Kentaro; Villeneuve, Anne M

    2014-09-01

    Meiotic recombination is initiated by the programmed induction of double-strand DNA breaks (DSBs), lesions that pose a potential threat to the genome. A subset of the DSBs induced during meiotic prophase become designated to be repaired by a pathway that specifically yields interhomolog crossovers (COs), which mature into chiasmata that temporarily connect the homologs to ensure their proper segregation at meiosis I. The remaining DSBs must be repaired by other mechanisms to restore genomic integrity prior to the meiotic divisions. Here we show that HIM-6, the Caenorhabditis elegans ortholog of the RecQ family DNA helicase BLM, functions in both of these processes. We show that him-6 mutants are competent to load the MutSγ complex at multiple potential CO sites, to generate intermediates that fulfill the requirements of monitoring mechanisms that enable meiotic progression, and to accomplish and robustly regulate CO designation. However, recombination events at a subset of CO-designated sites fail to mature into COs and chiasmata, indicating a pro-CO role for HIM-6/BLM that manifests itself late in the CO pathway. Moreover, we find that in addition to promoting COs, HIM-6 plays a role in eliminating and/or preventing the formation of persistent MutSγ-independent associations between homologous chromosomes. We propose that HIM-6/BLM enforces biased outcomes of recombination events to ensure that both (a) CO-designated recombination intermediates are reliably resolved as COs and (b) other recombination intermediates reliably mature into noncrossovers in a timely manner. Copyright © 2014 by the Genetics Society of America.

  6. Anti-ejection system for control rod drives

    Matthews, J.C.

    1977-01-01

    A linearly movable latch mechanism is provided to move into engagement with a deformable collet whenever an undesired ejection of a leadscrew is initiated from a nuclear reactor mounted control rod drive. Such an undesired ejection would occur in the event of a rupture in a housing of the control rod drive. The collet is deformed by the linear movement of the latch mechanism to wedge itself against the leadscrew and prevent the ejection of the leadscrew from the housing. The latch mechanism is made to be controllably engageable with the leadscrew and when thus engaged to allow the leadscrew to move in a control direction while moving with the leadscrew to engage and deform the collet when the leadscrew moves in an ejection direction. 13 claims, 2 figures

  7. Inhibition of mitogen-activated protein kinase kinase, DNA methyltransferase, and transforming growth factor-β promotes differentiation of human induced pluripotent stem cells into enterocytes.

    Kodama, Nao; Iwao, Takahiro; Kabeya, Tomoki; Horikawa, Takashi; Niwa, Takuro; Kondo, Yuki; Nakamura, Katsunori; Matsunaga, Tamihide

    2016-06-01

    We previously reported that small-molecule compounds were effective in generating pharmacokinetically functional enterocytes from human induced pluripotent stem (iPS) cells. In this study, to determine whether the compounds promote the differentiation of human iPS cells into enterocytes, we investigated the effects of a combination of mitogen-activated protein kinase kinase (MEK), DNA methyltransferase (DNMT), and transforming growth factor (TGF)-β inhibitors on intestinal differentiation. Human iPS cells cultured on feeder cells were differentiated into endodermal cells by activin A. These endodermal-like cells were then differentiated into intestinal stem cells by fibroblast growth factor 2. Finally, the cells were differentiated into enterocyte cells by epidermal growth factor and small-molecule compounds. After differentiation, mRNA expression levels and drug-metabolizing enzyme activities were measured. The mRNA expression levels of the enterocyte marker sucrase-isomaltase and the major drug-metabolizing enzyme cytochrome P450 (CYP) 3A4 were increased by a combination of MEK, DNMT, and TGF-β inhibitors. The mRNA expression of CYP3A4 was markedly induced by 1α,25-dihydroxyvitamin D3. Metabolic activities of CYP1A1/2, CYP2B6, CYP2C9, CYP2C19, CYP3A4/5, UDP-glucuronosyltransferase, and sulfotransferase were also observed in the differentiated cells. In conclusion, MEK, DNMT, and TGF-β inhibitors can be used to promote the differentiation of human iPS cells into pharmacokinetically functional enterocytes. Copyright © 2016 The Japanese Society for the Study of Xenobiotics. Published by Elsevier Ltd. All rights reserved.

  8. Reconstructing the Morphology of an Evolving Coronal Mass Ejection

    2009-01-01

    694, 707 Wood, B. E., Howard, R. A ., Thernisien, A ., Plunkett, S. P., & Socker, D. G. 2009b, Sol. Phys., 259, 163 Wood, B. E., Karovska , M., Chen, J...Reconstructing the Morphology of an Evolving Coronal Mass Ejection B. E. Wood, R. A . Howard, D. G. Socker Naval Research Laboratory, Space Science...mission, we empirically reconstruct the time-dependent three-dimensional morphology of a coronal mass ejection (CME) from 2008 June 1, which exhibits

  9. Jet behaviors and ejection mode recognition of electrohydrodynamic direct-write

    Zheng, Jianyi; Zhang, Kai; Jiang, Jiaxin; Wang, Xiang; Li, Wenwang; Liu, Yifang; Liu, Juan; Zheng, Gaofeng

    2018-01-01

    By introducing image recognition and micro-current testing, jet behavior research was conducted, in which the real-time recognition of ejection mode was realized. To study the factors influencing ejection modes and the current variation trends under different modes, an Electrohydrodynamic Direct-Write (EDW) system with functions of current detection and ejection mode recognition was firstly built. Then a program was developed to recognize the jet modes. As the voltage applied to the metal tip increased, four jet ejection modes in EDW occurred: droplet ejection mode, Taylor cone ejection mode, retractive ejection mode and forked ejection mode. In this work, the corresponding relationship between the ejection modes and the effect on fiber deposition as well as current was studied. The real-time identification of ejection mode and detection of electrospinning current was realized. The results in this paper are contributed to enhancing the ejection stability, providing a good technical basis to produce continuous uniform nanofibers controllably.

  10. Chromospheric Plasma Ejections in a Light Bridge of a Sunspot

    Song, Donguk; Chae, Jongchul; Yurchyshyn, Vasyl; Lim, Eun-Kyung; Cho, Kyung-Suk; Yang, Heesu; Cho, Kyuhyoun; Kwak, Hannah

    2017-02-01

    It is well-known that light bridges (LBs) inside a sunspot produce small-scale plasma ejections and transient brightenings in the chromosphere, but the nature and origin of such phenomena are still unclear. Utilizing the high-spatial and high-temporal resolution spectral data taken with the Fast Imaging Solar Spectrograph and the TiO 7057 Å broadband filter images installed at the 1.6 m New Solar Telescope of Big Bear Solar Observatory, we report arcsecond-scale chromospheric plasma ejections (1.″7) inside a LB. Interestingly, the ejections are found to be a manifestation of upwardly propagating shock waves as evidenced by the sawtooth patterns seen in the temporal-spectral plots of the Ca II 8542 Å and Hα intensities. We also found a fine-scale photospheric pattern (1″) diverging with a speed of about 2 km s-1 two minutes before the plasma ejections, which seems to be a manifestation of magnetic flux emergence. As a response to the plasma ejections, the corona displayed small-scale transient brightenings. Based on our findings, we suggest that the shock waves can be excited by the local disturbance caused by magnetic reconnection between the emerging flux inside the LB and the adjacent umbral magnetic field. The disturbance generates slow-mode waves, which soon develop into shock waves, and manifest themselves as the arcsecond-scale plasma ejections. It also appears that the dissipation of mechanical energy in the shock waves can heat the local corona.

  11. Mass ejection in failed supernovae: variation with stellar progenitor

    Fernández, Rodrigo; Quataert, Eliot; Kashiyama, Kazumi; Coughlin, Eric R.

    2018-05-01

    We study the ejection of mass during stellar core-collapse when the stalled shock does not revive and a black hole forms. Neutrino emission during the protoneutron star phase causes a decrease in the gravitational mass of the core, resulting in an outward going sound pulse that steepens into a shock as it travels out through the star. We explore the properties of this mass ejection mechanism over a range of stellar progenitors using spherically symmetric, time-dependent hydrodynamic simulations that treat neutrino mass-loss parametrically and follow the shock propagation over the entire star. We find that all types of stellar progenitor can eject mass through this mechanism. The ejected mass is a decreasing function of the surface gravity of the star, ranging from several M⊙ for red supergiants to ˜0.1 M⊙ for blue supergiants and ˜10-3 M⊙ for Wolf-Rayet stars. We find that the final shock energy at the surface is a decreasing function of the core-compactness, and is ≲ 1047-1048 erg in all cases. In progenitors with a sufficiently large envelope, high core-compactness, or a combination of both, the sound pulse fails to unbind mass. Successful mass ejection is accompanied by significant fallback accretion that can last from hours to years. We predict the properties of shock breakout and thermal plateau emission produced by the ejection of the outer envelope of blue supergiant and Wolf-Rayet progenitors in otherwise failed supernovae.

  12. The cAMP signaling system inhibits the repair of {gamma}-ray-induced DNA damage by promoting Epac1-mediated proteasomal degradation of XRCC1 protein in human lung cancer cells

    Cho, Eun-Ah [Department of Biochemistry and Molecular Biology, Cancer Research Center, Seoul National University College of Medicine, Seoul 110-799 (Korea, Republic of); Juhnn, Yong-Sung, E-mail: juhnn@snu.ac.kr [Department of Biochemistry and Molecular Biology, Cancer Research Center, Seoul National University College of Medicine, Seoul 110-799 (Korea, Republic of)

    2012-06-01

    Highlights: Black-Right-Pointing-Pointer cAMP signaling system inhibits repair of {gamma}-ray-induced DNA damage. Black-Right-Pointing-Pointer cAMP signaling system inhibits DNA damage repair by decreasing XRCC1 expression. Black-Right-Pointing-Pointer cAMP signaling system decreases XRCC1 expression by promoting its proteasomal degradation. Black-Right-Pointing-Pointer The promotion of XRCC1 degradation by cAMP signaling system is mediated by Epac1. -- Abstract: Cyclic AMP is involved in the regulation of metabolism, gene expression, cellular growth and proliferation. Recently, the cAMP signaling system was found to modulate DNA-damaging agent-induced apoptosis by regulating the expression of Bcl-2 family proteins and inhibitors of apoptosis. Thus, we hypothesized that the cAMP signaling may modulate DNA repair activity, and we investigated the effects of the cAMP signaling system on {gamma}-ray-induced DNA damage repair in lung cancer cells. Transient expression of a constitutively active mutant of stimulatory G protein (G{alpha}sQL) or treatment with forskolin, an adenylyl cyclase activator, augmented radiation-induced DNA damage and inhibited repair of the damage in H1299 lung cancer cells. Expression of G{alpha}sQL or treatment with forskolin or isoproterenol inhibited the radiation-induced expression of the XRCC1 protein, and exogenous expression of XRCC1 abolished the DNA repair-inhibiting effect of forskolin. Forskolin treatment promoted the ubiquitin and proteasome-dependent degradation of the XRCC1 protein, resulting in a significant decrease in the half-life of the protein after {gamma}-ray irradiation. The effect of forskolin on XRCC1 expression was not inhibited by PKA inhibitor, but 8-pCPT-2 Prime -O-Me-cAMP, an Epac-selective cAMP analog, increased ubiquitination of XRCC1 protein and decreased XRCC1 expression. Knockdown of Epac1 abolished the effect of 8-pCPT-2 Prime -O-Me-cAMP and restored XRCC1 protein level following {gamma}-ray irradiation. From

  13. Characterizing the original ejection velocity field of the Koronis family

    Carruba, V.; Nesvorný, D.; Aljbaae, S.

    2016-06-01

    An asteroid family forms as a result of a collision between an impactor and a parent body. The fragments with ejection speeds higher than the escape velocity from the parent body can escape its gravitational pull. The cloud of escaping debris can be identified by the proximity of orbits in proper element, or frequency, domains. Obtaining estimates of the original ejection speed can provide valuable constraints on the physical processes occurring during collision, and used to calibrate impact simulations. Unfortunately, proper elements of asteroids families are modified by gravitational and non-gravitational effects, such as resonant dynamics, encounters with massive bodies, and the Yarkovsky effect, such that information on the original ejection speeds is often lost, especially for older, more evolved families. It has been recently suggested that the distribution in proper inclination of the Koronis family may have not been significantly perturbed by local dynamics, and that information on the component of the ejection velocity that is perpendicular to the orbital plane (vW), may still be available, at least in part. In this work we estimate the magnitude of the original ejection velocity speeds of Koronis members using the observed distribution in proper eccentricity and inclination, and accounting for the spread caused by dynamical effects. Our results show that (i) the spread in the original ejection speeds is, to within a 15% error, inversely proportional to the fragment size, and (ii) the minimum ejection velocity is of the order of 50 m/s, with larger values possible depending on the orbital configuration at the break-up.

  14. DNA methyltransferase 3A promoter polymorphism is associated with the risk of human spontaneous abortion after assisted reproduction techniques and natural conception.

    Liu, Yudong; Zheng, Haiyan; Guo, Pingping; Feng, Shuxian; Zhou, Xingyu; Ye, Desheng; Chen, Xin; Chen, Shiling

    2017-02-01

    The aim of this study was to explore the association of the DNA-methyltransferase (DNMT)-3A and DNMT3B promoter polymorphisms with the risk of human spontaneous abortion after assisted reproduction techniques (ARTs) and natural conception. We collected tissues from women who underwent abortion procedures: (a) chorionic villus samples (CVS) and muscle samples (MS) from spontaneous abortions conceived by ART and natural cycle (study group), n = 152; and (b) CVS and MS from normal early pregnancy and second trimester (control group), n = 155. The single-nucleotide polymorphism (SNP) -448A > G in the DNMT3A promoter region and -149C/T polymorphism of DNMT3B were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and confirmed by sequencing. The allele frequency of -448A among pregnancy loss group and control group was 34.2 % vs. 16.5 %, respectively. Compared with GG carriers, the DNMT3A -448AA homozygotes had an about 16-fold increased risk of spontaneous abortion [odds ratio (OR) = 16.130, 95 % confidence interval (CI), 3.665-70.984], and AG heterozygotes had an OR of 2.027 (95 % CI, 1.247-3.293). However, the distribution of -448A > G in individuals derived from ART pregnancies was not statistically significantly compared with those derived from spontaneous pregnancies (P = 0.661). For DNMT3B, we observed genotype frequencies of 100 % (TT) in the study group and the control group. The DNMT3A -448A > G polymorphism may be a novel functional SNP and contribute to its genetic susceptibility to spontaneous abortion in Chinese women, and ART may not affect the distribution of -448A > G in pregnancy loss and normal pregnancy. The observed TT genotype of DMNT3B suggests that this is the predominant genotype of this population. The findings provide new insights into the etiology of human spontaneous abortion.

  15. POWER LEVEL EFFECT IN A PWR ROD EJECTION ACCIDENT

    Diamond, D.J.; Bromley, B.P.; Aronson, A.L.

    2002-01-01

    The purpose of this study is to determine the effect of the initial power level during a rod ejection accident (REA) on the ejected rod worth and the resulting energy deposition in the fuel. The model used is for the hot zero power (HZP) conditions at the end of a typical fuel cycle for the Three Mile Island Unit 1 pressurized water reactor. PARCS , a transient, three-dimensional, two-group neutron nodal diffusion code, coupled with its own thermal-hydraulics model, is used to perform both steady-state and transient simulations. The worth of an ejected control rod is affected by both power level, and the positions of control banks. As the power level is increased, the worth of a single central control rod tends to drop due to thermal-hydraulic feedback and control bank removal, both of which flatten the radial neutron flux and power distributions. Although the peak fuel pellet enthalpy rise during an REA will be greater for a given ejected rod worth at elevated initial power levels, it is more likely the HZP condition will cause a greater net energy deposition because an ejected rod will have the highest worth at HZP. Thus, the HZP condition can be considered the most conservative in a safety evaluation

  16. Tlys, a newly identified Sulfolobus spindle-shaped virus 1 transcript expressed in the lysogenic state, encodes a DNA-binding protein interacting at the promoters of the early genes

    Fusco, Salvatore; She, Qunxin; Bartolucci, Simonetta

    2013-01-01

    -binding motif. DNA-binding assays demonstrated that the recombinant F55, purified from Escherichia coli, is indeed a putative transcription factor able to recognize site specifically target sequences in the promoters of the early induced T5, T6, and Tind transcripts, as well as of its own promoter. Binding...... the growth of the lysogenic host. The correponding gene f55 lies between two transcriptional units (T6 and Tind) that are upregulated upon UV irradiation. The open reading frame f55 encodes a 6.3-kDa protein which shows sequence identity with negative regulators that fold into the ribbon-helix-helix DNA....... Taking together the transcriptional analysis data and the biochemical evidences, we surmise that the protein F55 is involved in the regulation of the lysogenic state of SSV1....

  17. 3-D rod ejection analysis using a conservative methodology

    Park, Min Ho; Park, Jin Woo; Park, Guen Tae; Um, Kil Sup; Ryu, Seok Hee; Lee, Jae Il; Choi, Tong Soo [KEPCO, Daejeon (Korea, Republic of)

    2016-05-15

    The point kinetics model which simplifies the core phenomena and physical specifications is used for the conventional rod ejection accident analysis. The point kinetics model is convenient to assume conservative core parameters but this simplification loses large amount of safety margin. The CHASER system couples the three-dimensional core neutron kinetics code ASTRA, the sub-channel analysis code THALES and the fuel performance analysis code FROST. The validation study for the CHASER system is addressed using the NEACRP three-dimensional PWR core transient benchmark problem. A series of conservative rod ejection analyses for the APR1400 type plant is performed for both hot full power (HFP) and hot zero power (HZP) conditions to determine the most limiting cases. The conservative rod ejection analysis methodology is designed to properly consider important phenomena and physical parameters.

  18. Round Robin computer simulation of ejection probability in sputtering

    Sigmund, P.; Hautala, M.; Yamamura, Y.; Hosaka, S.; Ishitani, T.; Shulga, V.I.; Harrison, D.E. Jr.; Chakarov, I.R.; Karpuzov, D.S.; Kawatoh, E.; Shimizu, R.; Valkealahti, S.; Nieminen, R.M.; Betz, G.; Husinsky, W.; Shapiro, M.H.; Vicanek, M.; Urbassek, H.M.

    1989-01-01

    We have studied the ejection of a copper atom through a planar copper surface as a function of recoil velocity and depth of origin. Results were obtained from six molecular dynamics codes, four binary collision lattice simulation codes, and eight Monte Carlo codes. Most results were found with a Born-Mayer interaction potential between the atoms with Gibson 2 parameters and a planar surface barrier, but variations on this standard were allowed for, as well as differences in the adopted cutoff radius for the interaction potential, electronic stopping, and target temperature. Large differences were found between the predictions of the various codes, but the cause of these differences could be determined in most cases. A fairly clear picture emerges from all three types of codes for the depth range and the angular range for ejection at energies relevant to sputter ejection, although a quantitative discussion would have to include an analysis of replacement collision events which has been left out here. (orig.)

  19. Ejection of a rear facing, golf cart passenger.

    Schau, Kyle; Masory, Oren

    2013-10-01

    The following report details the findings of a series of experiments and simulations performed on a commercially available, shuttle style golf cart during several maneuvers involving rapid accelerations of the vehicle. It is determined that the current set of passive restraints on these types of golf carts are not adequate in preventing ejection of a rear facing passenger during rapid accelerations in the forward and lateral directions. Experimental data and simulations show that a hip restraint must be a minimum of 13 in. above the seat in order to secure a rear facing passenger during sharp turns, compared to the current restraint height of 5 in. Furthermore, it is determined that a restraint directly in front of the rear facing passenger is necessary to prevent ejection. In addressing these issues, golf cart manufacturers could greatly reduce the likelihood of injury due to ejection of a rear facing, golf cart passenger. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. Hyperdynamic left ventricular ejection fraction in the intensive care unit.

    Paonessa, Joseph R; Brennan, Thomas; Pimentel, Marco; Steinhaus, Daniel; Feng, Mengling; Celi, Leo Anthony

    2015-08-07

    Limited information exists on the etiology, prevalence, and significance of hyperdynamic left ventricular ejection fraction (HDLVEF) in the intensive care unit (ICU). Our aim in the present study was to compare characteristics and outcomes of patients with HDLVEF with those of patients with normal left ventricular ejection fraction in the ICU using a large, public, deidentified critical care database. We conducted a longitudinal, single-center, retrospective cohort study of adult patients who underwent echocardiography during a medical or surgical ICU admission at the Beth Israel Deaconess Medical Center using the Multiparameter Intelligent Monitoring in Intensive Care II database. The final cohort had 2867 patients, of whom 324 had HDLVEF, defined as an ejection fraction >70%. Patients with an ejection fraction <55% were excluded. Compared with critically ill patients with normal left ventricular ejection fraction, the finding of HDLVEF in critically ill patients was associated with female sex, increased age, and the diagnoses of hypertension and cancer. Patients with HDLVEF had increased 28-day mortality compared with those with normal ejection fraction in multivariate logistic regression analysis adjusted for age, sex, Sequential Organ Failure Assessment score, Elixhauser score for comorbidities, vasopressor use, and mechanical ventilation use (odds ratio 1.38, 95% confidence interval 1.039-1.842, p =0.02). The presence of HDLVEF portended increased 28-day mortality, and may be helpful as a gravity marker for prognosis in patients admitted to the ICU. Further research is warranted to gain a better understanding of how these patients respond to common interventions in the ICU and to determine if pharmacologic modulation of HDLVEF improves outcomes.

  1. Chromospheric Plasma Ejections in a Light Bridge of a Sunspot

    Song, Donguk; Chae, Jongchul; Yang, Heesu; Cho, Kyuhyoun; Kwak, Hannah [Astronomy Program, Department of Physics and Astronomy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826 (Korea, Republic of); Yurchyshyn, Vasyl [Big Bear Solar Observatory, New Jersey Institute of Technology, 40386 North Shore Lane, Big Bear City, CA 92314-9672 (United States); Lim, Eun-Kyung; Cho, Kyung-Suk, E-mail: dusong@astro.snu.ac.kr [Korea Astronomy and Space Science Institute 776, Daedeokdae-ro, Yuseong-gu, Daejeon 34055 (Korea, Republic of)

    2017-02-01

    It is well-known that light bridges (LBs) inside a sunspot produce small-scale plasma ejections and transient brightenings in the chromosphere, but the nature and origin of such phenomena are still unclear. Utilizing the high-spatial and high-temporal resolution spectral data taken with the Fast Imaging Solar Spectrograph and the TiO 7057 Å broadband filter images installed at the 1.6 m New Solar Telescope of Big Bear Solar Observatory, we report arcsecond-scale chromospheric plasma ejections (1.″7) inside a LB. Interestingly, the ejections are found to be a manifestation of upwardly propagating shock waves as evidenced by the sawtooth patterns seen in the temporal-spectral plots of the Ca ii 8542 Å and H α intensities. We also found a fine-scale photospheric pattern (1″) diverging with a speed of about 2 km s{sup −1} two minutes before the plasma ejections, which seems to be a manifestation of magnetic flux emergence. As a response to the plasma ejections, the corona displayed small-scale transient brightenings. Based on our findings, we suggest that the shock waves can be excited by the local disturbance caused by magnetic reconnection between the emerging flux inside the LB and the adjacent umbral magnetic field. The disturbance generates slow-mode waves, which soon develop into shock waves, and manifest themselves as the arcsecond-scale plasma ejections. It also appears that the dissipation of mechanical energy in the shock waves can heat the local corona.

  2. Relative expression of rRNA transcripts and 45S rDNA promoter methylation status are dysregulated in tumors in comparison with matched-normal tissues in breast cancer.

    Karahan, Gurbet; Sayar, Nilufer; Gozum, Gokcen; Bozkurt, Betul; Konu, Ozlen; Yulug, Isik G

    2015-06-01

    Ribosomal RNA (rRNA) expression, one of the most important factors regulating ribosome production, is primarily controlled by a CG-rich 45 S rDNA promoter. However, the DNA methylation state of the 45 S rDNA promoter, as well as its effect on rRNA gene expression in types of human cancers is controversial. In the present study we analyzed the methylation status of the rDNA promoter (-380 to +53 bp) as well as associated rRNA expression levels in breast cancer cell lines and breast tumor-normal tissue pairs. We found that the aforementioned regulatory region was extensively methylated (74-96%) in all cell lines and in 68% (13/19 tumor-normal pairs) of the tumors. Expression levels of rRNA transcripts 18 S, 28 S, 5.8 S and 45 S external transcribed spacer (45 S ETS) greatly varied in the breast cancer cell lines regardless of their methylation status. Analyses of rRNA transcript expression levels in the breast tumor and normal matched tissues showed no significant difference when normalized with TBP. On the other hand, using the geometric mean of the rRNA expression values (GM-rRNA) as reference enabled us to identify significant changes in the relative expression of rRNAs in the tissue samples. We propose GM-rRNA normalization as a novel strategy to analyze expression differences between rRNA transcripts. Accordingly, the 18S rRNA/GM-rRNA ratio was significantly higher whereas the 5.8S rRNA/GM-rRNA ratio was significantly lower in breast tumor samples than this ratio in the matched normal samples. Moreover, the 18S rRNA/GM-rRNA ratio was negatively correlated with the 45 S rDNA promoter methylation level in the normal breast tissue samples, yet not in the breast tumors. Significant correlations observed between the expression levels of rRNA transcripts in the normal samples were lost in the tumor samples. We showed that the expression of rRNA transcripts may not be based solely on promoter methylation. Carcinogenesis may cause dysregulation of the correlation

  3. Hydration properties of natural and synthetic DNA sequences with methylated adenine or cytosine bases in the R.DpnI target and BDNF promoter studied by molecular dynamics simulations

    Shanak, Siba; Helms, Volkhard

    2014-12-01

    Adenine and cytosine methylation are two important epigenetic modifications of DNA sequences at the levels of the genome and transcriptome. To characterize the differential roles of methylating adenine or cytosine with respect to their hydration properties, we performed conventional MD simulations and free energy perturbation calculations for two particular DNA sequences, namely the brain-derived neurotrophic factor (BDNF) promoter and the R.DpnI-bound DNA that are known to undergo methylation of C5-methyl cytosine and N6-methyl adenine, respectively. We found that a single methylated cytosine has a clearly favorable hydration free energy over cytosine since the attached methyl group has a slightly polar character. In contrast, capping the strongly polar N6 of adenine with a methyl group gives a slightly unfavorable contribution to its free energy of solvation. Performing the same demethylation in the context of a DNA double-strand gave quite similar results for the more solvent-accessible cytosine but much more unfavorable results for the rather buried adenine. Interestingly, the same demethylation reactions are far more unfavorable when performed in the context of the opposite (BDNF or R.DpnI target) sequence. This suggests a natural preference for methylation in a specific sequence context. In addition, free energy calculations for demethylating adenine or cytosine in the context of B-DNA vs. Z-DNA suggest that the conformational B-Z transition of DNA transition is rather a property of cytosine methylated sequences but is not preferable for the adenine-methylated sequences investigated here.

  4. Ancient DNA

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  5. Radiation dose distributions due to sudden ejection of cobalt device

    Abdelhady, Amr

    2016-01-01

    The evaluation of the radiation dose during accident in a nuclear reactor is of great concern from the viewpoint of safety. One of important accident must be analyzed and may be occurred in open pool type reactor is the rejection of cobalt device. The study is evaluating the dose rate levels resulting from upset withdrawal of co device especially the radiation dose received by the operator in the control room. Study of indirect radiation exposure to the environment due to skyshine effect is also taken into consideration in order to evaluate the radiation dose levels around the reactor during the ejection trip. Microshield, SHLDUTIL, and MCSky codes were used in this study to calculate the radiation dose profiles during cobalt device ejection trip inside and outside the reactor building. - Highlights: • This study aims to calculate the dose rate profiles after cobalt device ejection from open-pool-type reactor core. • MicroShield code was used to evaluate the dose rates inside the reactor control room. • McSKY code was used to evaluate the dose rates outside the reactor building. • The calculated dose rates for workers are higher than the permissible limits after 18 s from device ejection.

  6. Initiation and Propagation of Coronal Mass Ejections P. F. Chen

    Introduction. Coronal mass ejections (CMEs) have been observed for over 30 years. They keep being an intriguing research topic, not only because they are now realized to be the major driver for space weather disturbances, which are intimately connected to human activities, but also because they themselves are full of ...

  7. Experimental Investigation of the Dispersion of Liquids by Ejection Atomizers

    Arkhipov, V. A.; Bondarchuk, S. S.; Evsevleev, M. Ya.; Zharova, I. K.; Zhukov, A. S.; Zmanovskii, S. V.; Kozlov, E. A.; Konovalenko, A. I.; Trofimov, V. F.

    2013-11-01

    This paper presents the results of an experimental investigation of the dispersivity of liquid droplets in the spray cone of ejection atomizers. The calculational droplet size distribution function was measured by the method of low angles of the probe laser radiation scattering indicatrix on a pneumohydraulic bench under cold blow conditions. The efficiency of the proposed circuit designs of atomizers has been analyzed.

  8. Invasive hemodynamic characterization of heart failure with preserved ejection fraction

    Andersen, Mads Jønsson; Borlaug, Barry A

    2014-01-01

    Recent hemodynamic studies have advanced our understanding of heart failure with preserved ejection fraction (HFpEF). Despite improved pathophysiologic insight, clinical trials have failed to identify an effective treatment for HFpEF. Invasive hemodynamic assessment can diagnose or exclude HFp...

  9. EJECTION AND CAPTURE DYNAMICS IN RESTRICTED THREE-BODY ENCOUNTERS

    Kobayashi, Shiho; Hainick, Yanir; Sari, Re'em; Rossi, Elena M.

    2012-01-01

    We study the tidal disruption of binaries by a massive point mass (e.g., the black hole at the Galactic center), and we discuss how the ejection and capture preference between unequal-mass binary members depends on which orbit they approach the massive object. We show that the restricted three-body approximation provides a simple and clear description of the dynamics. The orbit of a binary with mass m around a massive object M should be almost parabolic with an eccentricity of |1 – e| ∼ 1/3 1/3 times the binary rotation velocity, it would be abruptly disrupted, and the energy change at the encounter can be evaluated in a simple disruption model. We evaluate the probability distributions for the ejection and capture of circular binary members and for the final energies. In principle, for any hyperbolic (elliptic) orbit, the heavier member has more chance to be ejected (captured), because it carries a larger fraction of the orbital energy. However, if the orbital energy is close to zero, the difference between the two members becomes small, and there is practically no ejection and capture preferences. The preference becomes significant when the orbital energy is comparable to the typical energy change at the encounter. We discuss its implications to hypervelocity stars and irregular satellites around giant planets.

  10. Cobalt irradiation box ejection accident of ETRR-2

    El-Messiry, A.M.

    2000-01-01

    The new Egyptian test and research reactor number 2 ETRR-2, MTR type, is now under operational tests. It has a main central irradiation channel for the purpose of Co 60 isotope production with an intended rated capacity of 50000 Ci per year. The reactivity introduced in the reactor due to accidental ejection of the Co 60 irradiation box (CIB) should be discussed. This reactivity insertion accident (RIA) may be fast or slow with maximum reactivity worth 2.9428 $. The CIB may move with constant speed or variable acceleration according to its initial speed and the applied forces. This results in a linear, parabolic or sinusoidal motion, which in turn affects the reactivity insertion rate (RIR). The present work analyzes this type of perturbation during normal operating conditions: 22 MW full power and 1900 kg s -1 forced core cooling flow. The work serves as a part of the safety evaluation process applicable to similar MTR cores. The RIA code TRANSP20 is developed for this study. It simulates various types of RIR, fast or slow resulting from different CIB ejections. Scram signal due to power, period, inlet and outlet temperatures, or temperature difference is expected to activate the shutdown system. The work presents five case studies, two for fast ejection and three for slow. The transient behavior of the reactor during this is illustrated. The results show that the reactor can withstand slow ejection if the scram is available. However, for fast ejection the scram system does not prevent the clad temperature from exceeding safety limits. Recommendations to prevent or mitigate this accident are highlighted. (orig.)

  11. MsDpo4—a DinB Homolog from Mycobacterium smegmatis—Is an Error-Prone DNA Polymerase That Can Promote G:T and T:G Mismatches

    Amit Sharma

    2012-01-01

    Full Text Available Error-prone DNA synthesis in prokaryotes imparts plasticity to the genome to allow for evolution in unfavorable environmental conditions, and this phenomenon is termed adaptive mutagenesis. At a molecular level, adaptive mutagenesis is mediated by upregulating the expression of specialized error-prone DNA polymerases that generally belong to the Y-family, such as the polypeptide product of the dinB gene in case of E. coli. However, unlike E. coli, it has been seen that expression of the homologs of dinB in Mycobacterium tuberculosis are not upregulated under conditions of stress. These studies suggest that DinB homologs in Mycobacteria might not be able to promote mismatches and participate in adaptive mutagenesis. We show that a representative homolog from Mycobacterium smegmatis (MsDpo4 can carry out template-dependent nucleotide incorporation and therefore is a DNA polymerase. In addition, it is seen that MsDpo4 is also capable of misincorporation with a significant ability to promote G:T and T:G mismatches. The frequency of misincorporation for these two mismatches is similar to that exhibited by archaeal and prokaryotic homologs. Overall, our data show that MsDpo4 has the capacity to facilitate transition mutations and can potentially impart plasticity to the genome.

  12. Genomic sequencing and in vivo footprinting of an expression-specific DNase I-hypersensitive site of avian vitellogenin II promoter reveal a demethylation of a mCpG and a change in specific interactions of proteins with DNA.

    Saluz, H P; Feavers, I M; Jiricny, J; Jost, J P

    1988-01-01

    Genomic sequencing was used to study the in vivo methylation pattern of two CpG sites in the promoter region of the avian vitellogenin gene. The CpG at position +10 was fully methylated in DNA isolated from tissues that do not express the gene but was unmethylated in the liver of mature hens and estradiol-treated roosters. In the latter tissue, this site became demethylated and DNase I hypersensitive after estradiol treatment. A second CpG (position -52) was unmethylated in all tissues examined. In vivo genomic footprinting with dimethyl sulfate revealed different patterns of DNA protection in silent and expressed genes. In rooster liver cells, at least 10 base pairs of DNA, including the methylated CpG, were protected by protein(s). Gel-shift assays indicated that a protein factor, present in rooster liver nuclear extract, bound at this site only when it was methylated. In hen liver cells, the same unmethylated CpG lies within a protected region of approximately equal to 20 base pairs. In vitro DNase I protection and gel-shift assays indicate that this sequence is bound by a protein, which binds both double- and single-stranded DNA. For the latter substrate, this factor was shown to bind solely the noncoding (i.e., mRNA-like) strand. Images PMID:3413118

  13. Simulating AIA observations of a flux rope ejection

    Pagano, P.; Mackay, D. H.; Poedts, S.

    2014-08-01

    Context. Coronal mass ejections (CMEs) are the most violent phenomena observed on the Sun. Currently, extreme ultraviolet (EUV) images from the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamic Observatory (SDO) are providing new insights into the early phase of CME evolution. In particular, observations now show the ejection of magnetic flux ropes from the solar corona and how they evolve into CMEs. While this is the case, these observations are difficult to interpret in terms of basic physical mechanisms and quantities. To fully understand CMEs we need to compare equivalent quantities derived from both observations and theoretical models. This will aid in bridging the gap between observations and models. Aims: To this end, we aim to produce synthesised AIA observations from simulations of a flux rope ejection. To carry this out we include the role of thermal conduction and radiative losses, both of which are important for determining the temperature distribution of the solar corona during a CME. Methods: We perform a simulation where a flux rope is ejected from the solar corona. From the density and temperature of the plasma in the simulation we synthesise AIA observations. The emission is then integrated along the line of sight using the instrumental response function of AIA. Results: We sythesise observations of AIA in the channels at 304 Å, 171 Å, 335 Å, and 94 Å. The synthesised observations show a number of features similar to actual observations and in particular reproduce the general development of CMEs in the low corona as observed by AIA. In particular we reproduce an erupting and expanding arcade in the 304 Å and 171 Å channels with a high density core. Conclusions: The ejection of a flux rope reproduces many of the features found in the AIA observations. This work is therefore a step forward in bridging the gap between observations and models, and can lead to more direct interpretations of EUV observations in terms of flux rope

  14. DNA damage responsive miR-33b-3p promoted lung cancer cells survival and cisplatin resistance by targeting p21WAF1/CIP1.

    Xu, Shun; Huang, Haijiao; Chen, Yu-Ning; Deng, Yun-Ting; Zhang, Bing; Xiong, Xing-Dong; Yuan, Yuan; Zhu, Yanmei; Huang, Haiyong; Xie, Luoyijun; Liu, Xinguang

    2016-11-01

    Cisplatin is the most potent and widespread used chemotherapy drug for lung cancer treatment. However, the development of resistance to cisplatin is a major obstacle in clinical therapy. The principal mechanism of cisplatin is the induction of DNA damage, thus the capability of DNA damage response (DDR) is a key factor that influences the cisplatin sensitivity of cancer cells. Recent advances have demonstrated that miRNAs (microRNAs) exerted critical roles in DNA damage response; nonetheless, the association between DNA damage responsive miRNAs and cisplatin resistance and its underlying molecular mechanism still require further investigation. The present study has attempted to identify differentially expressed miRNAs in cisplatin induced DNA damage response in lung cancer cells, and probe into the effects of the misexpressed miRNAs on cisplatin sensitivity. Deep sequencing showed that miR-33b-3p was dramatically down-regulated in cisplatin-induced DNA damage response in A549 cells; and ectopic expression of miR-33b-3p endowed the lung cancer cells with enhanced survival and decreased γH2A.X expression level under cisplatin treatment. Consistently, silencing of miR-33b-3p in the cisplatin-resistant A549/DDP cells evidently sensitized the cells to cisplatin. Furthermore, we identified CDKN1A (p21) as a functional target of miR-33b-3p, a critical regulator of G1/S checkpoint, which potentially mediated the protection effects of miR-33b-3p against cisplatin. In aggregate, our results suggested that miR-33b-3p modulated the cisplatin sensitivity of cancer cells might probably through impairing the DNA damage response. And the knowledge of the drug resistance conferred by miR-33b-3p has great clinical implications for improving the efficacy of chemotherapies for treating lung cancers.

  15. DNA damage and autophagy

    Rodriguez-Rocha, Humberto; Garcia-Garcia, Aracely; Panayiotidis, Mihalis I.; Franco, Rodrigo

    2011-01-01

    Both exogenous and endogenous agents are a threat to DNA integrity. Exogenous environmental agents such as ultraviolet (UV) and ionizing radiation, genotoxic chemicals and endogenous byproducts of metabolism including reactive oxygen species can cause alterations in DNA structure (DNA damage). Unrepaired DNA damage has been linked to a variety of human disorders including cancer and neurodegenerative disease. Thus, efficient mechanisms to detect DNA lesions, signal their presence and promote their repair have been evolved in cells. If DNA is effectively repaired, DNA damage response is inactivated and normal cell functioning resumes. In contrast, when DNA lesions cannot be removed, chronic DNA damage triggers specific cell responses such as cell death and senescence. Recently, DNA damage has been shown to induce autophagy, a cellular catabolic process that maintains a balance between synthesis, degradation, and recycling of cellular components. But the exact mechanisms by which DNA damage triggers autophagy are unclear. More importantly, the role of autophagy in the DNA damage response and cellular fate is unknown. In this review we analyze evidence that supports a role for autophagy as an integral part of the DNA damage response.

  16. Histone H3.3 promotes IgV gene diversification by enhancing formation of AID-accessible single-stranded DNA.

    Romanello, Marina; Schiavone, Davide; Frey, Alexander; Sale, Julian E

    2016-07-01

    Immunoglobulin diversification is driven by activation-induced deaminase (AID), which converts cytidine to uracil within the Ig variable (IgV) regions. Central to the recruitment of AID to the IgV genes are factors that regulate the generation of single-stranded DNA (ssDNA), the enzymatic substrate of AID Here, we report that chicken DT40 cells lacking variant histone H3.3 exhibit reduced IgV sequence diversification. We show that this results from impairment of the ability of AID to access the IgV genes due to reduced formation of ssDNA during IgV transcription. Loss of H3.3 also diminishes IgV R-loop formation. However, reducing IgV R-loops by RNase HI overexpression in wild-type cells does not affect IgV diversification, showing that these structures are not necessary intermediates for AID access. Importantly, the reduction in the formation of AID-accessible ssDNA in cells lacking H3.3 is independent of any effect on the level of transcription or the kinetics of RNAPII elongation, suggesting the presence of H3.3 in the nucleosomes of the IgV genes increases the chances of the IgV DNA becoming single-stranded, thereby creating an effective AID substrate. © 2016 MRC Laboratory of Molecular Biology. Published under the terms of the CC BY 4.0 license.

  17. Measurement of effective left ventricular ejection fraction by radiocardiography associated with cardiac chamber scanning

    de Vernejoul, P; Fauchet, M; Rimbert, J -N; Gambini, D; Agnely, J [Hopital Necker-Enfants-Malades, 75 - Paris (France)

    1976-03-01

    Left ventricular ejection fraction is usually measured by cineangiocardiography. When radiocardiography and cardiac chamber scanning are associated, it allows an effective left ventricular ejection fraction assessment. Ejection fractions calculated by both methods are the same in normal subjects. They are different in the case of left valvular heart disease with insufficiency. The whole regurgitation fraction can be calculated from this difference.

  18. Measurement of effective left ventricular ejection fraction by radiocardiography associated with cardiac chamber scanning

    Vernejoul, Pierre de; Fauchet, Michel; Rimbert, J.-N.; Gambini, Denis; Agnely, Jacqueline

    1976-01-01

    Left ventricular ejection fraction is usually measured by cineangiocardiography. When radiocardiography and cardiac chamber scanning are associated, it allows an effective left ventricular ejection fraction assessment. Ejection fractions calculated by both methods are the same in normal subjects. They are different in the case of left valvular heart disease with insufficiency. The whole regurgitation fraction can be calculated from this difference [fr

  19. Quality of life is impaired similarly in heart failure patients with preserved and reduced ejection fraction

    Hoekstra, Tialda; Lesman-Leegte, Ivonne; van Veldhuisen, Dirk J.; Sanderman, Robbert; Jaarsma, Tiny

    Aims To compare quality of life (QoL) in heart failure (HF) patients with preserved ejection fraction (HF-PEF) and HF patients with reduced ejection fraction (HF-REF) in a well-defined HF population. Methods and results Patients with HF-PEF [left ventricular ejection fraction (LVEF) >= 40%] were

  20. The influence of occupant anthropometry and seat position on ejection risk in a rollover.

    Atkinson, Theresa; Fras, Andrew; Telehowski, Paul

    2010-08-01

    During rollover crashes, ejection increases an occupant's risk of severe to fatal injury as compared to risks for those retained in the vehicle. The current study examined whether occupant anthropometry might influence ejection risk. Factors such as restraint use/disuse, seating position, vehicle type, and roll direction were also considered in the analysis. The current study examined occupant ejections in 10 years of National Automotive Sampling System (NASS) single-event rollovers of passenger vehicles and light trucks. Statistical analysis of unweighted and weighted ejection data was carried out. No statistically significant differences in ejection rates were found based on occupant height, age, or body mass index. Drivers were ejected significantly more frequently than other occupants: 62 percent of unrestrained drivers were ejected vs. 51 percent unrestrained right front occupants. Second row unrestrained occupants were ejected at rates similar to right front-seated occupants. There were no significant differences in ejection rates for near- vs. far-side occupants. These data suggest that assessment of ejection prevention systems using either a 50th or 5th percentile adult anthropomorphic test dummy (ATD) might provide a reasonable measure of system function for a broad range of occupants. They also support the development of ejection mitigation technologies that extend beyond the first row to protect occupants in rear seat positions. Future studies should consider potential interaction effects (i.e., occupant size and vehicle dimensions) and the influence of occupant size on ejection risk in non-single-event rollovers.

  1. Analysis of aberrant methylation on promoter sequences of tumor suppressor genes and total DNA in sputum samples: a promising tool for early detection of COPD and lung cancer in smokers

    Guzmán Leda

    2012-07-01

    Full Text Available Abstract Background Chronic obstructive pulmonary disease (COPD is a disorder associated to cigarette smoke and lung cancer (LC. Since epigenetic changes in oncogenes and tumor suppressor genes (TSGs are clearly important in the development of LC. In this study, we hypothesize that tobacco smokers are susceptible for methylation in the promoter region of TSGs in airway epithelial cells when compared with non-smoker subjects. The purpose of this study was to investigate the usefulness of detection of genes promoter methylation in sputum specimens, as a complementary tool to identify LC biomarkers among smokers with early COPD. Methods We determined the amount of DNA in induced sputum from patients with COPD (n = 23, LC (n = 26, as well as in healthy subjects (CTR (n = 33, using a commercial kit for DNA purification, followed by absorbance measurement at 260 nm. The frequency of CDKN2A, CDH1 and MGMT promoter methylation in the same groups was determined by methylation-specific polymerase chain reaction (MSP. The Fisher’s exact test was employed to compare frequency of results between different groups. Results DNA concentration was 7.4 and 5.8 times higher in LC and COPD compared to the (CTR (p  Conclusions We provide evidence that aberrant methylation of TSGs in samples of induced sputum is a useful tool for early diagnostic of lung diseases (LC and COPD in smoker subjects. Virtual slides The abstract MUST finish with the following text: Virtual Slides The virtual slide(s for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1127865005664160

  2. Radiation dose distributions due to sudden ejection of cobalt device.

    Abdelhady, Amr

    2016-09-01

    The evaluation of the radiation dose during accident in a nuclear reactor is of great concern from the viewpoint of safety. One of important accident must be analyzed and may be occurred in open pool type reactor is the rejection of cobalt device. The study is evaluating the dose rate levels resulting from upset withdrawal of co device especially the radiation dose received by the operator in the control room. Study of indirect radiation exposure to the environment due to skyshine effect is also taken into consideration in order to evaluate the radiation dose levels around the reactor during the ejection trip. Microshield, SHLDUTIL, and MCSky codes were used in this study to calculate the radiation dose profiles during cobalt device ejection trip inside and outside the reactor building. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Neutrino diffusion and mass ejection in protoneutron stars

    Almeida, L. G.; Rodrigues, H.; Portes, D. Jr.; Duarte, S. B.

    2010-01-01

    We discuss the mass ejection mechanism induced by diffusion of neutrino during the early stage of the protoneutron star cooling. A dynamical calculation is employed in order to determine the amount of matter ejected and the remnant compact object mass. An equation of state considering hadronic and quark phases for the stellar dense matter was used to solve the whole time evolution of the system during the cooling phase. The initial neutrino population was obtained by considering beta equilibrium in the dense stellar matter with confined neutrinos, in the very early period of the deleptonic stage of the nascent pulsar. For specified initial configurations of the protoneutron star, we solve numerically the set of equations of motion together with neutrino diffusion through the dense stellar medium.

  4. Dynamics of post-flare ejections and magnetic loop geometry

    Mein, P.; Mein, N.

    1982-01-01

    Flare-associated mass ejections have been observed at the solar limb on June 29, 1980 in the Hα line, with the Multichannel Subtractive Double Pass spectrograph of the Meudon solar tower. Radial velocities were measured as a function of time in a two dimensional field, and kinematics investigated in one selected fine structure. A simple model of locally dipole-type magnetic field increasing with time can be fitted to the data. It can be checked from extrapolation that the model is consistent with an ejection starting roughly from the same point at the same time. Height of the loops (approx. equal to 135,000 km) is consistent with other determinations. Magnetic field is found to be increasing locally by a factor 1.14 within 10 min. (orig.)

  5. Multinucleon Ejection Model for Two Body Current Neutrino Interactions

    Sobczyk, Jan T.; /Fermilab

    2012-06-01

    A model is proposed to describe nucleons ejected from a nucleus as a result of two-body-current neutrino interactions. The model can be easily implemented in Monte Carlo neutrino event generators. Various possibilities to measure the two-body-current contribution are discussed. The model can help identify genuine charge current quasielastic events and allow for a better determination of the systematic error on neutrino energy reconstruction in neutrino oscillation experiments.

  6. Survivability rate among pilots in case of ejection

    Alexandru GHEORGHIU

    2015-06-01

    Full Text Available The current paper presents a statistical analysis of a recent research made by the author [1], showing the factors causing the accidents that happened in Romanian Air Force from 1952 to 2014. Also the decision of ejection is analyzed. The study contains 225 events: 110 catastrophes and 115 accidents. 280 fighter pilots and 235 aircraft were involved in this analysis. The below information is a personal one and does not reflect an official position of the Ministry of National Defence.

  7. Evidence for highly processed material ejected from Abell 30

    Hazard, C.; Terlvich, R.; Ferland, G.; Sargent, W.L.W.

    1980-01-01

    The discovery of compact knots of highly processed material apparently ejected from the central star of the emission nebula Abell 30 is reported here. Spectra obtained from the compact nebulosities surrounding the central star, which indicate a remarkable enhancement of helium relative to hydrogen, are discussed. Preliminary model calculations to investigate the properties of hydrogen deficient nebulae and to study the abundances of some heavy elements have been applied to the results. (UK)

  8. Analysis of Transportation Alternatives for Ejection Seat Training

    Gambel, Ray; Lundy, David; Murphy, William; Southmost Consulting

    2011-01-01

    EMBA Project Report EXECUTIVE SUMMARY Student Military Aviators who complete primary flight training at Training Wing FOUR and select jets for their advanced training track will require Naval Aviation Survival Training Program (NASTP) Class 1 training until the T-6B replaces the T-34C as the primary flight training aircraft. This Class 1 training instructs students in ejection seat equipment and procedures for emergency egress of their new aircraft. Of the eight available Aviation Survi...

  9. A new method of determining the ejected mass of novae

    Sparks, W.M.

    1994-12-31

    A new method of determining the ejected mass of novae based on simple, reasonable assumptions is presented. This method assumes that the remnant mass on the white dwarf is the same as that from the previous nova outburst. The hydrogen, helium, and metal abundances of the accreted material from the secondary must also be known or assumed. The white dwarf`s mass has a small effect because the amount of hydrogen consumed during the thermonuclear runaway only depends weakly upon this mass. If the composition of the ejecta and the time of the remnant shell burnout are determined from observations, then the ejected and remnant masses can be deduced. At present only a sharp decrease in the X-rays observed by ROSAT has been attributed to this remnant burnout and only for two novae: GQ Mus and V1974 Cyg. The ejected and remnant masses for these two novae are calculated. If other indicators of nova remnant burnout, such as a rapid decrease in high-ionization lines, can be identified, then this method could be applied to additional novae.

  10. Droplet ejection and sliding on a flapping film

    Xi Chen

    2017-03-01

    Full Text Available Water recovery and subsequent reuse are required for human consumption as well as industrial, and agriculture applications. Moist air streams, such as cooling tower plumes and fog, represent opportunities for water harvesting. In this work, we investigate a flapping mechanism to increase droplet shedding on thin, hydrophobic films for two vibrational cases (e.g., ± 9 mm and 11 Hz; ± 2 mm and 100 Hz. Two main mechanisms removed water droplets from the flapping film: vibrational-induced coalescence/sliding and droplet ejection from the surface. Vibrations mobilized droplets on the flapping film, increasing the probability of coalescence with neighboring droplets leading to faster droplet growth. Droplet departure sizes of 1–2 mm were observed for flapping films, compared to 3–4 mm on stationary films, which solely relied on gravity for droplet removal. Additionally, flapping films exhibited lower percentage area coverage by water after a few seconds. The second removal mechanism, droplet ejection was analyzed with respect to surface wave formation and inertia. Smaller droplets (e.g., 1-mm diameter were ejected at a higher frequency which is associated with a higher acceleration. Kinetic energy of the water was the largest contributor to energy required to flap the film, and low energy inputs (i.e., 3.3 W/m2 were possible. Additionally, self-flapping films could enable novel water collection and condensation with minimal energy input.

  11. Activity associated with the solar origin of coronal mass ejections

    Webb, D. F.; Hundhausen, A. J.

    1987-01-01

    Solar coronal mass ejections (CMEs) observed in 1980 with the HAO Coronagraph/Polarimeter on the Solar Maximum Mission (SMM) satellite are compared with other forms of solar activity that might be physically related to the ejections. The solar phenomena checked and the method of association used were intentionally patterned after those of Munro et al.'s (1979) analysis of mass ejections observed with the Skylab coronagraph to facilitate comparison of the two epochs. Comparison of the results reveals that the types and degree of CME associations are similar near solar activity minimum and at maximum. For both epochs, most CMEs with associations had associated eruptive prominences, and the proportions of association of all types of activity were similar. A high percentage of association between SMM CMEs and X-ray long duration events is also found, in agreement with Skylab results. It is concluded that most CMEs are the result of the destabilization and eruption of a prominence and its overlying coronal structure, or of a magnetic structure capable of supporting a prominence.

  12. Histone H3.3 promotes IgV gene diversification by?enhancing formation of AID?accessible single?stranded DNA

    Romanello, Marina; Schiavone, Davide; Frey, Alexander; Sale, Julian E

    2016-01-01

    Abstract Immunoglobulin diversification is driven by activation?induced deaminase (AID), which converts cytidine to uracil within the Ig variable (IgV) regions. Central to the recruitment of AID to the IgV genes are factors that regulate the generation of single?stranded DNA (ssDNA), the enzymatic substrate of AID. Here, we report that chicken DT40 cells lacking variant histone H3.3 exhibit reduced IgV sequence diversification. We show that this results from impairment of the ability of AID t...

  13. Nucleosome acidic patch promotes RNF168- and RING1B/BMI1-dependent H2AX and H2A ubiquitination and DNA damage signaling.

    Justin W Leung

    2014-03-01

    Full Text Available Histone ubiquitinations are critical for the activation of the DNA damage response (DDR. In particular, RNF168 and RING1B/BMI1 function in the DDR by ubiquitinating H2A/H2AX on Lys-13/15 and Lys-118/119, respectively. However, it remains to be defined how the ubiquitin pathway engages chromatin to provide regulation of ubiquitin targeting of specific histone residues. Here we identify the nucleosome acid patch as a critical chromatin mediator of H2A/H2AX ubiquitination (ub. The acidic patch is required for RNF168- and RING1B/BMI1-dependent H2A/H2AXub in vivo. The acidic patch functions within the nucleosome as nucleosomes containing a mutated acidic patch exhibit defective H2A/H2AXub by RNF168 and RING1B/BMI1 in vitro. Furthermore, direct perturbation of the nucleosome acidic patch in vivo by the expression of an engineered acidic patch interacting viral peptide, LANA, results in defective H2AXub and RNF168-dependent DNA damage responses including 53BP1 and BRCA1 recruitment to DNA damage. The acidic patch therefore is a critical nucleosome feature that may serve as a scaffold to integrate multiple ubiquitin signals on chromatin to compose selective ubiquitinations on histones for DNA damage signaling.

  14. Nonperiodic activity of the human anaphase-promoting complex-Cdh1 ubiquitin ligase results in continuous DNA synthesis uncoupled from mitosis

    Lukas, C; Kramer, E R; Peters, J M

    2000-01-01

    , in Saccharomyces cerevisiae and Drosophila spp., triggers exit from mitosis and during G(1) prevents unscheduled DNA replication. In this study we investigated the importance of periodic oscillation of the APC-Cdh1 activity for the cell cycle progression in human cells. We show that conditional interference...

  15. Ageing, chronic alcohol consumption and folate are determinants of genomic DNA methylation, p16 promoter methylation and the expression of p16 in the mouse colon

    Elder age and chronic alcohol consumption are important risk factors for the development of colon cancer. Each factor can alter genomic and gene-specific DNA methylation. This study examined the effects of aging and chronic alcohol consumption on genomic and p16-specific methylation, and p16 express...

  16. Aging and chronic alcohol consumption are determinants of p16 gene expression, genomic DNA methylation and p16 promoter methylation in the mouse colon

    Elder age and chronic alcohol consumption are important risk factors for the development of colon cancer. Each factor can alter genomic and gene-specific DNA methylation. This study examined the effects of aging and chronic alcohol consumption on genomic and p16-specific methylation, and p16 express...

  17. Decreased DNA Methylation in the Shati/Nat8l Promoter in Both Patients with Schizophrenia and a Methamphetamine-Induced Murine Model of Schizophrenia-Like Phenotype.

    Kyosuke Uno

    Full Text Available The number of patients with schizophrenia has increased over the past decade. Previously, many studies have been performed to establish its diagnostic criteria, prophylactic methods, and effective therapies. In this study, we analyzed whether the ratios of DNA methylation in CpG islands of the Shati/Nat8l is decreased in model mice of schizophrenia-like phenotype using genomic DNA collected from brain regions and peripheral blood, since the mouse model of schizophrenia-like phenotype, mice treated repeatedly with methamphetamine showed increase of Shati/Nat8l mRNA expression in our previous experiment. The ratios of Shati/Nat8l CpG island methylation were significantly decreased in both the nucleus accumbens and the peripheral blood of model mice compared with those of control mice. We also investigated Shati/Nat8l methylation in the blood of patients with schizophrenia. We found that Shati/Nat8l CpG island methylation ratios were lower in the patients with schizophrenia than in the healthy controls, which is consistent with our findings in the mice model. To our knowledge, this is the first study to show similar alterations in methylation status of a particular genomic DNA site in both the brain and peripheral blood of mice. Furthermore, the same phenomenon was observed in corresponding human genomic sequences of the DNA extracted from the peripheral blood of patients with schizophrenia. Based on our findings, DNA methylation profiles of the CpG island of Shati/Nat8l might be a diagnostic biomarker of schizophrenia.

  18. Cell cycle inhibitor, p19INK4d, promotes cell survival and decreases chromosomal aberrations after genotoxic insult due to enhanced DNA repair.

    Scassa, María E; Marazita, Mariela C; Ceruti, Julieta M; Carcagno, Abel L; Sirkin, Pablo F; González-Cid, Marcela; Pignataro, Omar P; Cánepa, Eduardo T

    2007-05-01

    Genome integrity and cell proliferation and survival are regulated by an intricate network of pathways that includes cell cycle checkpoints, DNA repair and recombination, and programmed cell death. It makes sense that there should be a coordinated regulation of these different processes, but the components of such mechanisms remain unknown. In this report, we demonstrate that p19INK4d expression enhances cell survival under genotoxic conditions. By using p19INK4d-overexpressing clones, we demonstrated that p19INK4d expression correlates with the cellular resistance to UV treatment with increased DNA repair activity against UV-induced lesions. On the contrary, cells transfected with p19INK4d antisense cDNA show reduced ability to repair DNA damage and increased sensitivity to genotoxic insult when compared with their p19INK4d-overexpressing counterparts. Consistent with these findings, our studies also show that p19INK4d-overexpressing cells present not only a minor accumulation of UV-induced chromosomal aberrations but a lower frequency of spontaneous chromosome abnormalities than p19INK4d-antisense cells. Lastly, we suggest that p19INK4d effects are dissociated from its role as CDK4/6 inhibitor. The results presented herein support a crucial role for p19INK4d in regulating genomic stability and overall cell viability under conditions of genotoxic stress. We propose that p19INK4d would belong to a protein network that would integrate DNA repair, apoptotic and checkpoint mechanisms in order to maintain the genomic integrity.

  19. Performance of a fully automated program for measurement of left ventricular ejection fraction

    Douglass, K.H.; Tibbits, P.; Kasecamp, W.; Han, S.T.; Koller, D.; Links, J.M.; Wagner, H.H. Jr.

    1982-01-01

    A fully automated program developed by us for measurement of left ventricular ejection fraction from equilibrium gated blood studies was evaluated in 130 additional patients. Both of 6-min (130 studies) and 2-min (142 studies in 31 patients) gated blood pool studies were acquired and processed. The program successfully generated ejection fractions in 86% of the studies. These automatically generated ejection fractions were compared with ejection fractions derived from manually drawn regions the interest. When studies were acquired for 6-min with the patient at rest, the correlation between automated and manual ejection fractions was 0.92. When studies were acquired for 2-min, both at rest and during bicycle exercise, the correlation was 0.81. In 25 studies from patients who also underwent contrast ventriculography, the program successfully generated regions of interest in 22 (88%). The correlation between the ejection fraction determined by contrast ventriculography and the automatically generated radionuclide ejection fraction was 0.79. (orig.)

  20. DNA replication and cancer

    Boyer, Anne-Sophie; Walter, David; Sørensen, Claus Storgaard

    2016-01-01

    A dividing cell has to duplicate its DNA precisely once during the cell cycle to preserve genome integrity avoiding the accumulation of genetic aberrations that promote diseases such as cancer. A large number of endogenous impacts can challenge DNA replication and cells harbor a battery of pathways...... causing DNA replication stress and genome instability. Further, we describe cellular and systemic responses to these insults with a focus on DNA replication restart pathways. Finally, we discuss the therapeutic potential of exploiting intrinsic replicative stress in cancer cells for targeted therapy....

  1. GSTP1 Loss results in accumulation of oxidative DNA base damage and promotes prostate cancer cell survival following exposure to protracted oxidative stress.

    Mian, Omar Y; Khattab, Mohamed H; Hedayati, Mohammad; Coulter, Jonathan; Abubaker-Sharif, Budri; Schwaninger, Julie M; Veeraswamy, Ravi K; Brooks, James D; Hopkins, Lisa; Shinohara, Debika Biswal; Cornblatt, Brian; Nelson, William G; Yegnasubramanian, Srinivasan; DeWeese, Theodore L

    2016-02-01

    Epigenetic silencing of glutathione S-transferase π (GSTP1) is a hallmark of transformation from normal prostatic epithelium to adenocarcinoma of the prostate. The functional significance of this loss is incompletely understood. The present study explores the effects of restored GSTP1 expression on glutathione levels, accumulation of oxidative DNA damage, and prostate cancer cell survival following oxidative stress induced by protracted, low dose rate ionizing radiation (LDR). GSTP1 protein expression was stably restored in LNCaP prostate cancer cells. The effect of GSTP1 restoration on protracted LDR-induced oxidative DNA damage was measured by GC-MS quantitation of modified bases. Reduced and oxidized glutathione levels were measured in control and GSTP1 expressing populations. Clonogenic survival studies of GSTP1- transfected LNCaP cells after exposure to protracted LDR were performed. Global gene expression profiling and pathway analysis were performed. GSTP1 expressing cells accumulated less oxidized DNA base damage and exhibited decreased survival compared to control LNCaP-Neo cells following oxidative injury induced by protracted LDR. Restoration of GSTP1 expression resulted in changes in modified glutathione levels that correlated with GSTP1 protein levels in response to protracted LDR-induced oxidative stress. Survival differences were not attributable to depletion of cellular glutathione stores. Gene expression profiling and pathway analysis following GSTP1 restoration suggests this protein plays a key role in regulating prostate cancer cell survival. The ubiquitous epigenetic silencing of GSTP1 in prostate cancer results in enhanced survival and accumulation of potentially promutagenic DNA adducts following exposure of cells to protracted oxidative injury suggesting a protective, anti-neoplastic function of GSTP1. The present work provides mechanistic backing to the tumor suppressor function of GSTP1 and its role in prostate carcinogenesis. © 2015

  2. Characteristics and long-term prognosis of patients with heart failure and mid-range ejection fraction compared with reduced and preserved ejection fraction

    Lauritsen, Josephine; Gustafsson, Finn; Abdulla, Jawdat

    2018-01-01

    AIMS: This study aimed to assess by a meta-analysis the clinical characteristics, all-cause and cardiovascular mortality, and hospitalization of patients with heart failure (HF) with mid-range ejection fraction (HFmrEF) compared with HF with reduced ejection fraction (HFrEF) and HF with preserved...

  3. Promotion of DNA strand breaks in cocultured mononuclear leukocytes by protein kinase C-dependent prooxidative interactions of benoxaprofen, human polymorphonuclear leukocytes, and ultraviolet radiation

    Schwalb, G.; Beyers, A.D.; Anderson, R.; Nel, A.E.

    1988-01-01

    At concentrations of 5 micrograms/ml and greater the nonsteroidal antiinflammatory drug benoxaprofen caused dose-related activation of lucigenin-enhanced chemiluminescence in human polymorphonuclear leukocytes (PMNL). Benoxaprofen-mediated activation of lucigenin-enhanced chemiluminescence by PMNL was increased by UV radiation and was particularly sensitive to inhibition by the selective protein kinase C inhibitor H-7. To identify the molecular mechanism of the prooxidative activity of benoxaprofen, the effects of the nonsteroidal antiinflammatory drug on the activity of purified protein kinase C in a cell-free system were investigated. Benoxaprofen caused a dose-related activation of protein kinase C by interaction with the binding site for the physiological activator phosphatidylserine, but could not replace diacylglycerol. When autologous mononuclear leukocytes (MNL) were cocultured with PMNL and benoxaprofen in combination, but not individually, the frequency of DNA strand breaks in MNL was markedly increased. UV radiation significantly potentiated damage to DNA mediated by benoxaprofen and PMNL. Inclusion of superoxide dismutase, H-7, and, to a much lesser extent, catalase during exposure of MNL to benoxaprofen-activated PMNL prevented oxidant damage to DNA. These results clearly demonstrate that potentially carcinogenic prooxidative interactions, which are unlikely to be detected by conventional assays of mutagenicity, may occur between phagocytes, UV radiation, and certain pharmacological agents

  4. Folate deficiency facilitates recruitment of upstream binding factor to hot spots of DNA double-strand breaks of rRNA genes and promotes its transcription.

    Xie, Qiu; Li, Caihua; Song, Xiaozhen; Wu, Lihua; Jiang, Qian; Qiu, Zhiyong; Cao, Haiyan; Yu, Kaihui; Wan, Chunlei; Li, Jianting; Yang, Feng; Huang, Zebing; Niu, Bo; Jiang, Zhengwen; Zhang, Ting

    2017-03-17

    The biogenesis of ribosomes in vivo is an essential process for cellular functions. Transcription of ribosomal RNA (rRNA) genes is the rate-limiting step in ribosome biogenesis controlled by environmental conditions. Here, we investigated the role of folate antagonist on changes of DNA double-strand breaks (DSBs) landscape in mouse embryonic stem cells. A significant DSB enhancement was detected in the genome of these cells and a large majority of these DSBs were found in rRNA genes. Furthermore, spontaneous DSBs in cells under folate deficiency conditions were located exclusively within the rRNA gene units, representing a H3K4me1 hallmark. Enrichment H3K4me1 at the hot spots of DSB regions enhanced the recruitment of upstream binding factor (UBF) to rRNA genes, resulting in the increment of rRNA genes transcription. Supplement of folate resulted in a restored UBF binding across DNA breakage sites of rRNA genes, and normal rRNA gene transcription. In samples from neural tube defects (NTDs) with low folate level, up-regulation of rRNA gene transcription was observed, along with aberrant UBF level. Our results present a new view by which alterations in folate levels affects DNA breakage through epigenetic control leading to the regulation of rRNA gene transcription during the early stage of development. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. Controlled tungsten melting and droplet ejection studies in ASDEX Upgrade

    Krieger, K; Lunt, T; Dux, R; Janzer, A; Müller, H W; Potzel, S; Pütterich, T; Yang, Z

    2011-01-01

    Tungsten rods of 1×1×3 mm 3 were exposed in single H-mode discharges at the outer divertor target plate of ASDEX Upgrade using the divertor manipulator system. Melting of the W rod at a pre-defined time was induced by moving the initially far away outer strike point close to the W-rod position. Visible light emissions of both the W pin and consecutively ejected W droplets were recorded by two fast cameras with crossed viewing cones. The time evolution of the local W source at the pin location was measured by spectroscopic observation of the WI line emission at 400.9 nm and compared to the subsequent increase of tungsten concentration in the confined plasma derived from tungsten vacuum UV line emission. Combining these measurements with the total amount of released tungsten due to the pin melt events and ejected droplets allowed us to derive an estimate of the screening factor for this type of tungsten source. The resulting values of the tungsten divertor retention in the range 10-20 agree with those found in previous studies using a W source of sublimated W(CO) 6 vapour at the same exposure location. Ejected droplets were found to be always accelerated in the general direction of the plasma flow, attributed to friction forces and to rocket forces. Furthermore, the vertically inclined target plates cause the droplets, which are repelled by the target plate surface potential due to their electric charge, to move upwards against gravity due to the centrifugal force component parallel to the target plate.

  6. The Prospect for Detecting Stellar Coronal Mass Ejections

    Osten, Rachel A.; Crosley, Michael Kevin

    2018-06-01

    The astrophysical study of mass loss, both steady-state and transient, on the cool half of the HR diagram has implications bothfor the star itself and the conditions created around the star that can be hospitable or inimical to supporting life. Recent results from exoplanet studies show that planets around M dwarfs are exceedingly common, which together with the commonality of M dwarfs in our galaxy make this the dominant mode of star and planet configurations. The closeness of the exoplanets to the parent M star motivate a comprehensive understanding of habitability for these systems. Radio observations provide the most clear signature of accelerated particles and shocks in stars arising as the result of MHD processes in the stellar outer atmosphere. Stellar coronal mass ejections have not been conclusively detected, despite the ubiquity with which their radiative counterparts in an eruptive event (stellar flares) have. I will review some of the different observational methods which have been used and possibly could be used in the future in the stellar case, emphasizing some of the difficulties inherent in such attempts. I will provide a framework for interpreting potential transient stellar mass loss in light of the properties of flares known to occur on magnetically active stars. This uses a physically motivated way to connect the properties of flares and coronal mass ejections and provides a testable hypothesis for observing or constraining transient stellar mass loss. I will describe recent results using radio observations to detect stellar coronal mass ejections, and what those results imply about transient stellar mass loss. I will provide some motivation for what could be learned in this topic from space-based low frequency radio experiments.

  7. An intact sequence-specific DNA-binding domain is required for human cytomegalovirus-mediated sequestration of p53 and may promote in vivo binding to the viral genome during infection

    Rosenke, Kyle; Samuel, Melanie A.; McDowell, Eric T.; Toerne, Melissa A.; Fortunato, Elizabeth A.

    2006-01-01

    The p53 protein is stabilized during infection of primary human fibroblasts with human cytomegalovirus (HCMV). However, the p53 in HCMV-infected cells is unable to activate its downstream targets. HCMV accomplishes this inactivation, at least in part, by sequestering p53 into viral replication centers within the cell's nucleus soon after they are established. In order to better understand the interplay between HCMV and p53 and the mechanism of sequestration, we constructed a panel of mutant p53-GFP fusion constructs for use in transfection/infection experiments. These mutants affected several post-translational modification sites and several sites within the central sequence-specific DNA-binding domain of the protein. Two categories of p53 sequestration were observed when the mutant constructs were transfected into primary fibroblasts and then infected at either high or low multiplicity. The first category, including all of the post-translational modification mutants, showed sequestration comparable to a wild-type (wt) control, while the second category, mutants affecting the DNA-binding core, were not specifically sequestered above control GFP levels. This suggested that the DNA-binding ability of the protein was required for sequestration. When the HCMV genome was analyzed for p53 consensus binding sites, 21 matches were found, which localized either to the promoters or the coding regions of viral proteins involved in DNA replication and processing as well as structural proteins. An analysis of in vivo binding to these identified sites via chromatin immunoprecipitation assays revealed differential binding to several of the sites over the course of infection

  8. Chemically triggered ejection of membrane tubules controlled by intermonolayer friction.

    Fournier, J-B; Khalifat, N; Puff, N; Angelova, M I

    2009-01-09

    We report a chemically driven membrane shape instability that triggers the ejection of a tubule growing exponentially toward a chemical source. The instability is initiated by a dilation of the exposed monolayer, which is coupled to the membrane spontaneous curvature and slowed down by intermonolayer friction. Our experiments are performed by local delivery of a basic pH solution to a giant vesicle. Quantitative fits of the data give an intermonolayer friction coefficient b approximately 2x10;{9} J s/m;{4}. The exponential growth of the tubule may be explained by a Marangoni stress yielding a pulling force proportional to its length.

  9. Epidemiology of heart failure with preserved ejection fraction

    Andersson, Charlotte; Vasan, Ramachandran S

    2014-01-01

    Heart failure with preserved ejection fraction (HFPEF) is a common condition, and the prevalence is projected to increase further. Studies differ in the reported incidence and mortality associated with this condition, although there is agreement that between a third and one-half of all patients...... with heart failure have HFPEF. Although several consensus statements and guidelines have been published, some recent randomized clinical trials have reported low mortality, raising doubts about whether all patients diagnosed with HFPEF have HFPEF or whether the condition is heterogeneous in its cause...

  10. PWR control rod ejection analysis with the numerical nuclear reactor

    Hursin, M.; Kochunas, B.; Downar, T. J.

    2008-01-01

    During the past several years, a comprehensive high fidelity reactor LWR core modeling capability has been developed and is referred to as the Numerical Nuclear Reactor (NNR). The NNR achieves high fidelity by integrating whole core neutron transport solution and ultra fine mesh computational fluid dynamics/heat transfer solution. The work described in this paper is a preliminary demonstration of the ability of NNR to provide a detailed intra pin power distribution during a control rod ejection accident. The motivation of the work is to quantify the impact on the fuel performance calculation of a more physically accurate representation of the power distribution within the fuel rod during the transient. The paper addresses first, the validation of the transient capability of the neutronic module of the NNR code system, DeCART. For this purpose, a 'mini core' problem consisting of a 3x3 array of typical PWR fuel assemblies is considered. The initial state of the 'mini core' is hot zero power with a control rod partially inserted into the central assembly which is fresh fuel and is adjacent to once and twice burned fuel representative of a realistic PWR arrangement. The thermal hydraulic feedbacks are provided by a simplified fluids and heat conduction solver consistent for both PARCS and DeCART. The control rod is ejected from the central assembly and the transient calculation is performed with DeCART and compared with the results of the U.S. NRC core simulation code PARCS. Because the pin power reconstruction in PARCS is based on steady state intra assembly pin power distributions which do not account for thermal feedback during the transient and which do not take into account neutron leakage from neighboring assemblies during the transient, there are some small differences in the PARCS and DeCART pin power prediction. Intra pin power density information obtained with DeCART represents new information not available with previous generation of methods. The paper then

  11. Exercise physiology in heart failure and preserved ejection fraction.

    Haykowsky, Mark J; Kitzman, Dalane W

    2014-07-01

    Recent advances in the pathophysiology of exercise intolerance in patients with heart failure with preserved ejection fraction (HFPEF) suggest that noncardiac peripheral factors contribute to the reduced peak V(o2) (peak exercise oxygen uptake) and to its improvement after endurance exercise training. A greater understanding of the peripheral skeletal muscle vascular adaptations that occur with physical conditioning may allow for tailored exercise rehabilitation programs. The identification of specific mechanisms that improve whole body and peripheral skeletal muscle oxygen uptake could establish potential therapeutic targets for medical therapies and a means to follow therapeutic response. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. The role of HERC2 and RNF8 ubiquitin E3 ligases in the promotion of translesion DNA synthesis in the chicken DT40 cell line

    Mohiuddin, Mohammed; Kobayashi, Shunsuke; Keka, Islam Shamima

    2016-01-01

    immediately after exposure to UV while retaining proficient post-replicative gap filling. These mutants are both proficient in mono-ubiquitination of PCNA. Taken together, these results suggest that HERC2 and RNF8 promote TLS past abasic sites and UV-lesions at or very close to stalled replication forks....

  13. A protein binding AT-rich sequence in the soybean leghemoglobin c3 promoter is a general cis element that requires proximal DNA elements to stimulate transcription

    Laursen, N B; Larsen, K; Knudsen, J Y

    1994-01-01

    in combination with other trans-acting factor(s) to increase expression. The finding of NAT2-like binding activities in different plant organs and the specific expression of the hybrid NAT2 BS1/-312 rbcS-8B promoter in leaves suggest that NAT2 is a general activator of transcription. Udgivelsesdato: 1994-May...

  14. Repulsive DNA-DNA interactions accelerate viral DNA packaging in phage Phi29.

    Keller, Nicholas; delToro, Damian; Grimes, Shelley; Jardine, Paul J; Smith, Douglas E

    2014-06-20

    We use optical tweezers to study the effect of attractive versus repulsive DNA-DNA interactions on motor-driven viral packaging. Screening of repulsive interactions accelerates packaging, but induction of attractive interactions by spermidine(3+) causes heterogeneous dynamics. Acceleration is observed in a fraction of complexes, but most exhibit slowing and stalling, suggesting that attractive interactions promote nonequilibrium DNA conformations that impede the motor. Thus, repulsive interactions facilitate packaging despite increasing the energy of the theoretical optimum spooled DNA conformation.

  15. Murine Models of Heart Failure With Preserved Ejection Fraction

    Maria Valero-Muñoz, PhD

    2017-12-01

    Full Text Available Heart failure with preserved ejection fraction (HFpEF is characterized by signs and symptoms of heart failure in the presence of a normal left ventricular ejection fraction. Despite accounting for up to 50% of all clinical presentations of heart failure, the mechanisms implicated in HFpEF are poorly understood, thus precluding effective therapy. The pathophysiological heterogeneity in the HFpEF phenotype also contributes to this disease and likely to the absence of evidence-based therapies. Limited access to human samples and imperfect animal models that completely recapitulate the human HFpEF phenotype have impeded our understanding of the mechanistic underpinnings that exist in this disease. Aging and comorbidities such as atrial fibrillation, hypertension, diabetes and obesity, pulmonary hypertension, and renal dysfunction are highly associated with HFpEF, yet the relationship and contribution between them remains ill-defined. This review discusses some of the distinctive clinical features of HFpEF in association with these comorbidities and highlights the advantages and disadvantage of commonly used murine models used to study the HFpEF phenotype.

  16. Promoter Engineering Reveals the Importance of Heptameric Direct Repeats for DNA Binding by Streptomyces Antibiotic Regulatory Protein-Large ATP-Binding Regulator of the LuxR Family (SARP-LAL) Regulators in Streptomyces natalensis.

    Barreales, Eva G; Vicente, Cláudia M; de Pedro, Antonio; Santos-Aberturas, Javier; Aparicio, Jesús F

    2018-05-15

    The biosynthesis of small-size polyene macrolides is ultimately controlled by a couple of transcriptional regulators that act in a hierarchical way. A Streptomyces antibiotic regulatory protein-large ATP-binding regulator of the LuxR family (SARP-LAL) regulator binds the promoter of a PAS-LuxR regulator-encoding gene and activates its transcription, and in turn, the gene product of the latter activates transcription from various promoters of the polyene gene cluster directly. The primary operator of PimR, the archetype of SARP-LAL regulators, contains three heptameric direct repeats separated by four-nucleotide spacers, but the regulator can also bind a secondary operator with only two direct repeats separated by a 3-nucleotide spacer, both located in the promoter region of its unique target gene, pimM A similar arrangement of operators has been identified for PimR counterparts encoded by gene clusters for different antifungal secondary metabolites, including not only polyene macrolides but peptidyl nucleosides, phoslactomycins, or cycloheximide. Here, we used promoter engineering and quantitative transcriptional analyses to determine the contributions of the different heptameric repeats to transcriptional activation and final polyene production. Optimized promoters have thus been developed. Deletion studies and electrophoretic mobility assays were used for the definition of DNA-binding boxes formed by 22-nucleotide sequences comprising two conserved heptameric direct repeats separated by four-nucleotide less conserved spacers. The cooperative binding of PimR SARP appears to be the mechanism involved in the binding of regulator monomers to operators, and at least two protein monomers are required for efficient binding. IMPORTANCE Here, we have shown that a modulation of the production of the antifungal pimaricin in Streptomyces natalensis can be accomplished via promoter engineering of the PAS-LuxR transcriptional activator pimM The expression of this gene is

  17. A Flexible Domain-Domain Hinge Promotes an Induced-fit Dominant Mechanism for the Loading of Guide-DNA into Argonaute Protein in Thermus thermophilus

    Zhu, Lizhe

    2016-02-24

    Argonaute proteins (Ago) are core components of the RNA Induced Silencing Complex (RISC) that load and utilize small guide nucleic acids to silence mRNAs or cleave foreign DNAs. Despite the essential role of Ago in gene regulation and defense against virus, the molecular mechanism of guide-strand loading into Ago remains unclear. We explore such a mechanism in the bacterium Thermus thermophilus Ago (TtAgo), via a computational approach combining molecular dynamics, bias-exchange metadynamics, and protein-DNA docking. We show that apo TtAgo adopts multiple closed states that are unable to accommodate guide-DNA. Conformations able to accommodate the guide are beyond the reach of thermal fluctuations from the closed states. These results suggest an induced-fit dominant mechanism for guide-strand loading in TtAgo, drastically different from the two-step mechanism for human Ago 2 (hAgo2) identified in our previous study. Such a difference between TtAgo and hAgo2 is found to mainly originate from the distinct rigidity of their L1-PAZ hinge. Further comparison among known Ago structures from various species indicates that the L1-PAZ hinge may be flexible in general for prokaryotic Agos but rigid for eukaryotic Agos. © 2016 American Chemical Society.

  18. A Flexible Domain-Domain Hinge Promotes an Induced-fit Dominant Mechanism for the Loading of Guide-DNA into Argonaute Protein in Thermus thermophilus.

    Zhu, Lizhe; Jiang, Hanlun; Sheong, Fu Kit; Cui, Xuefeng; Gao, Xin; Wang, Yanli; Huang, Xuhui

    2016-03-17

    Argonaute proteins (Ago) are core components of the RNA Induced Silencing Complex (RISC) that load and utilize small guide nucleic acids to silence mRNAs or cleave foreign DNAs. Despite the essential role of Ago in gene regulation and defense against virus, the molecular mechanism of guide-strand loading into Ago remains unclear. We explore such a mechanism in the bacterium Thermus thermophilus Ago (TtAgo), via a computational approach combining molecular dynamics, bias-exchange metadynamics, and protein-DNA docking. We show that apo TtAgo adopts multiple closed states that are unable to accommodate guide-DNA. Conformations able to accommodate the guide are beyond the reach of thermal fluctuations from the closed states. These results suggest an induced-fit dominant mechanism for guide-strand loading in TtAgo, drastically different from the two-step mechanism for human Ago 2 (hAgo2) identified in our previous study. Such a difference between TtAgo and hAgo2 is found to mainly originate from the distinct rigidity of their L1-PAZ hinge. Further comparison among known Ago structures from various species indicates that the L1-PAZ hinge may be flexible in general for prokaryotic Ago's but rigid for eukaryotic Ago's.

  19. Regulation of HFE expression by poly(ADP-ribose) polymerase-1 (PARP1) through an inverted repeat DNA sequence in the distal promoter.

    Pelham, Christopher; Jimenez, Tamara; Rodova, Marianna; Rudolph, Angela; Chipps, Elizabeth; Islam, M Rafiq

    2013-12-01

    Hereditary hemochromatosis (HH) is a common autosomal recessive disorder of iron overload among Caucasians of northern European descent. Over 85% of all cases with HH are due to mutations in the hemochromatosis protein (HFE) involved in iron metabolism. Although the importance in iron homeostasis is well recognized, the mechanism of sensing and regulating iron absorption by HFE, especially in the absence of iron response element in its gene, is not fully understood. In this report, we have identified an inverted repeat sequence (ATGGTcttACCTA) within 1700bp (-1675/+35) of the HFE promoter capable to form cruciform structure that binds PARP1 and strongly represses HFE promoter. Knockdown of PARP1 increases HFE mRNA and protein. Similarly, hemin or FeCl3 treatments resulted in increase in HFE expression by reducing nuclear PARP1 pool via its apoptosis induced cleavage, leading to upregulation of the iron regulatory hormone hepcidin mRNA. Thus, PARP1 binding to the inverted repeat sequence on the HFE promoter may serve as a novel iron sensing mechanism as increased iron level can trigger PARP1 cleavage and relief of HFE transcriptional repression. © 2013.

  20. An Evaluation of a New Format for Presenting Ejection Information in a NATOPS Manual.

    1979-11-01

    Assessment-the subject’s awareness of ejection system limits and knowledge of the specific principles and relationships involved in the ejection decision...percti & le pilot ejecting cannern tintiong onfigursesan at~ 71 knete arrtaeei.l From" th front cockpit. c. Normal aircraft pitc For conditions shown it...40) Arlington, VA 22209 700 Robbins Avenue * 1 CDR P.R. Chatelier Philadelphia, PA 19111 Office of the Undersecretary of Defense for Research

  1. Ejection fraction improvement and reverse remodeling achieved with Sacubitril/Valsartan in heart failure with reduced ejection fraction patients.

    Almufleh, Aws; Marbach, Jeffrey; Chih, Sharon; Stadnick, Ellamae; Davies, Ross; Liu, Peter; Mielniczuk, Lisa

    2017-01-01

    Sacubitril/Valsartan has been shown to improve mortality and reduce hospitalizations in patients with heart failure with reduced ejection fraction (HFrEF). The effect of Sacubitril/Valsartan on ejection fraction (EF) and reverse remodeling parameters have not been previously described. We performed a single-center, retrospective, cohort study of HFrEF patients (n=48) who were treated with Sacubitril/Valsartan for a median duration of 3 months (Interquartile range 2-6 months). Clinical and echocardiographic parameters were reviewed at three time points (pre-baseline which was median of 18 months before starting Sacubitril/Valsartan, baseline before treatment started, and post-Sacubitril/Valsartan). Paired sample t-test and one-way repeated measures ANOVA were used for normally distributed data, while Wilcoxon Signed Rank test for non-normally distributed data. Sacubitril/Valsartan use was associated with an average 5% (±1.2) increase in EF, from a mean baseline of 25.33% to 30.14% (pSacubitril/Valsartan was found to improve EF and multiple measures of reverse remodeling beyond the effects of concomitant optimal medical therapy. Though these results are encouraging, our small sample, observational study requires confirmation in larger cohorts with longer follow-up periods.

  2. Abrus agglutinin promotes irreparable DNA damage by triggering ROS generation followed by ATM-p73 mediated apoptosis in oral squamous cell carcinoma.

    Sinha, Niharika; Panda, Prashanta K; Naik, Prajna P; Das, Durgesh N; Mukhopadhyay, Subhadip; Maiti, Tapas K; Shanmugam, Muthu K; Chinnathambi, Arunachalam; Zayed, M E; Alharbi, Sulaiman A; Sethi, Gautam; Agarwal, Rajesh; Bhutia, Sujit K

    2017-11-01

    Oral cancer, a type of head and neck cancer, is ranked as one of the top most malignancies in India. Herein, we evaluated the anticancer efficacy of Abrus agglutinin (AGG), a plant lectin, in oral squamous cell carcinoma. AGG selectively inhibited cell growth, and caused cell cycle arrest and mitochondrial apoptosis through a reactive oxygen species (ROS)-mediated ATM-p73 dependent pathway in FaDu cells. AGG-induced ROS accumulation was identified as the major mechanism regulating apoptosis, DNA damage and DNA-damage response, which were significantly reversed by ROS scavenger N-acetylcysteine (NAC). Moreover, AGG was found to interact with mitochondrial manganese-dependent superoxide dismutase that might inhibit its activity and increase ROS in FaDu cells. In oral cancer p53 is mutated, thus we focused on p73; AGG resulted in p73 upregulation and knock down of p73 caused a decrease in AGG-induced apoptosis. Interestingly, AGG-dependent p73 expression was found to be regulated by ROS, which was reversed by NAC treatment. A reduction in the level of p73 in AGG-treated shATM cells was found to be associated with a decreased apoptosis. Moreover, administration of AGG (50 μg/kg body weight) significantly inhibited the growth of FaDu xenografts in athymic nude mice. In immunohistochemical analysis, the xenografts from AGG-treated mice displayed a decrease in PCNA expression and an increase in caspase-3 activation as compared to the controls. In conclusion, we established a connection among ROS, ATM and p73 in AGG-induced apoptosis, which might be useful in enhancing the therapeutic targeting of p53 deficient oral squamous cell carcinoma. © 2017 Wiley Periodicals, Inc.

  3. Ejection fraction response to exercise in patients with chest pain and normal coronary arteriograms

    Gibbons, R.L.; Lee, K.L.; Cobb, F.; Jones, R.H.

    1981-01-01

    In this study we describe the ejection fraction response to upright exercise using first-pass radionuclide angiocardiography in a group of 60 patients with chest pain, normal coronary ateriograms and normal resting ventricular function. A wide range of resting function (heart rate and ejection fraction) and exercise function (heart rate, ejection fraction, peak work load and estimated peak oxygen uptake) were measured. The ejection fraction response to exercise demonstrated wide variation, ranging from a decrease of 23% to an increase of 24%. Six of 22 clinical and radionuclide angiocardiographic variables (resting ejection fraction, peak work load, age, sex, body surface area and the change in end-diastolic volume index with exercise) were significant univariate predictors of the ejection fraction response to exercise. Multivariable analysis identified resting ejection fraction, the change in end-diastolic volume index with exercise and either sex or peak work load as variables that provided significant independent predictive information. These observations indicate that the ejection fraction response to exercise is a complex response that is influenced by multiple physiologic variables. The wide variation in this population suggests that the ejection fraction response to exercise is not a reliable test for the diagnosis of coronary artery disease because of its low specificity

  4. Binding of the cyclic AMP receptor protein of Escherichia coli and DNA bending at the P4 promoter of pBR322.

    Brierley, I; Hoggett, J G

    1992-07-01

    The binding of the Escherichia coli cyclic AMP receptor protein (CRP) to its specific site on the P4 promoter of pBR322 has been studied by gel electrophoresis. Binding to the P4 site was about 40-50-fold weaker than to the principal CRP site on the lactose promoter at both low (0.01 M) and high (0.1 M) ionic strengths. CRP-induced bending at the P4 site was investigated from the mobilities of CRP bound to circularly permuted P4 fragments. The estimated bending angle, based on comparison with Zinkel & Crothers [(1990) Biopolymers 29, 29-38] A-tract bending standards, was found to be approximately 96 degrees, similar to that found for binding to the lac site. These observations suggest that there is not a simple relationship between strength of CRP binding and the extent of induced bending for different CRP sites. The apparent centre of bending in P4 is displaced about 6-8 bp away from the conserved TGTGA sequence and the P4 transcription start site.

  5. Measurement of right and left ventricular ejection fraction in dogs

    Brynjolf, I.; Qvist, J.; Mygind, T.; Jordening, H.; Dorph, S.; Munck, O.

    1983-08-01

    Three techniques for measurement of right (RVEF) and two techniques for left (LVEF) ventricular ejection fraction were evaluated in five dogs. RVEF was measured with a first-pass radionuclide technique using erythrocytes labelled in vitro with Technetium-99m methylene disphosphonate (MDP) and compared with RVEF measured with a thermodilution technique. Thermodilution-determined RVEF was compared with RVEF values measured with cine angiocardiography. LVEF was measured with a radionuclide ECG-gated equilibrium technique and compared with cine angiocardiography. Measurements were performed before and during a continuous infusion of dopamine. There was an excellent correlation between RVEF measured with the first-pass and the thermodilution technique. LVEF measured with the ECG-gated equilibrium technique correlated well with cine angiocardiography.

  6. The effects of stress on left ventricular ejection fraction

    Kiess, M.C.; Dimsdale, J.E.; Moore, R.H.; Liu, P.; Newell, J.; Barlai-Kovach, M.; Boucher, C.A.; Strauss, H.W.; Massachusetts General Hospital, Boston; Massachusetts General Hospital, Boston

    1988-01-01

    The left ventricular ejection fraction (EF) was studied in 17 healthy volunteers with a new ambulatory left ventricular function monitor. Heart rate, EF, and blood pressure measurements were made during rest, a psychiatric stress interview, cold exposure, exercise, and eating. An increase in EF was seen during emotional stress (from 0.45±0.09 to 0.51±0.13, P<0.001). This increase was comparable to that observed during exercise (0.52±0.14) and eating (0.52±0.10, P<0.001). In contrast, cold exposure caused a decrease in EF (0.43±0.13, P<0.05). These observations demonstrate the powerful hemodynamic consequences of common behaviors as well as the utility and feasability of studying such behavioral factors in ambulatory subjects. (orig.)

  7. Fast, controlled stepping drive for D2 filament ejection

    Amenda, W.; Lang, R.S.

    1985-01-01

    Centrifugal pellet injectors are required to refuel plasma machines. The pellet feed into the centrifuge should, if possible, be direct to keep the exit angle divergence small. The D 2 filaments used are first stored in a cryostat and then rapidly transported to the intake region of the centrifuge. An intermittent drive for fast, controlled ejection of D 2 filaments is described here. Mean filament speed of up to 0.6 m/s per step (1.2 mm) are achieved for the centrifugal pellet injector which refuels the ASDEX tokamak at Garching. The timing of the (81) step shifts can be synchronized with the rotor motion. The drive allows rates of up to 50 pellets per second. The drive method also seems to be suitable for direct feeding of other known centrifugal pellet injectors

  8. On interplanetary coronal mass ejection identification at 1 AU

    Mulligan, T.; Russell, C.T.; Gosling, J.T.

    1999-01-01

    Coronal mass ejections are believed to be produced in the corona from closed magnetic regions not previously participating in the solar wind expansion. At 1 AU their interplanetary counterparts (ICMEs) generally have a number of distinct plasma and field signatures that distinguish them from the ambient solar wind. These include heat flux dropouts, bi-directional streaming, enhanced alpha particle events, times of depressed proton temperatures, intervals of distorted or enhanced magnetic field, and times of large magnetic field rotations characteristic of magnetic clouds. The first three of these signatures are phenomena that occur at some point within the ICME, but do not necessarily persist throughout the entire ICME. The large scale magnetic field rotations, distortions and enhancements, and the proton temperature depressions tend to mark more accurately the beginning and end of the ICME proper. We examine herein the reliability with which each of these markers identifies ICMEs utilizing ISEE-3 data from 1978 - 1980. copyright 1999 American Institute of Physics

  9. An ice-cream cone model for coronal mass ejections

    Xue, X. H.; Wang, C. B.; Dou, X. K.

    2005-08-01

    In this study, we use an ice-cream cone model to analyze the geometrical and kinematical properties of the coronal mass ejections (CMEs). Assuming that in the early phase CMEs propagate with near-constant speed and angular width, some useful properties of CMEs, namely the radial speed (v), the angular width (α), and the location at the heliosphere, can be obtained considering the geometrical shapes of a CME as an ice-cream cone. This model is improved by (1) using an ice-cream cone to show the near real configuration of a CME, (2) determining the radial speed via fitting the projected speeds calculated from the height-time relation in different azimuthal angles, (3) not only applying to halo CMEs but also applying to nonhalo CMEs.

  10. CORONAL MASS EJECTION INDUCED OUTFLOWS OBSERVED WITH HINODE/EIS

    Jin, M.; Ding, M. D.; Chen, P. F.; Fang, C.; Imada, S.

    2009-01-01

    We investigate the outflows associated with two halo coronal mass ejections (CMEs) that occurred on 2006 December 13 and 14 in NOAA 10930, using the Hinode/EIS observations. Each CME was accompanied by an EIT wave and coronal dimmings. Dopplergrams in the dimming regions are obtained from the spectra of seven EIS lines. The results show that strong outflows are visible in the dimming regions during the CME eruption at different heights from the lower transition region to the corona. It is found that the velocity is positively correlated with the photospheric magnetic field, as well as the magnitude of the dimming. We estimate the mass loss based on height-dependent EUV dimmings and find it to be smaller than the CME mass derived from white-light observations. The mass difference is attributed partly to the uncertain atmospheric model, and partly to the transition region outflows, which refill the coronal dimmings.

  11. Demethylation by 5-aza-2'-deoxycytidine in colorectal cancer cells targets genomic DNA whilst promoter CpG island methylation persists

    Mossman, David; Kim, Kyu-Tae; Scott, Rodney J

    2010-01-01

    DNA methylation and histone acetylation are epigenetic modifications that act as regulators of gene expression. Aberrant epigenetic gene silencing in tumours is a frequent event, yet the factors which dictate which genes are targeted for inactivation are unknown. DNA methylation and histone acetylation can be modified with the chemical agents 5-aza-2'-deoxycytidine (5-aza-dC) and Trichostatin A (TSA) respectively. The aim of this study was to analyse de-methylation and re-methylation and its affect on gene expression in colorectal cancer cell lines treated with 5-aza-dC alone and in combination with TSA. We also sought to identify methylation patterns associated with long term reactivation of previously silenced genes. Colorectal cancer cell lines were treated with 5-aza-dC, with and without TSA, to analyse global methylation decreases by High Performance Liquid Chromatography (HPLC). Re-methylation was observed with removal of drug treatments. Expression arrays identified silenced genes with differing patterns of expression after treatment, such as short term reactivation or long term reactivation. Sodium bisulfite sequencing was performed on the CpG island associated with these genes and expression was verified with real time PCR. Treatment with 5-aza-dC was found to affect genomic methylation and to a lesser extent gene specific methylation. Reactivated genes which remained expressed 10 days post 5-aza-dC treatment featured hypomethylated CpG sites adjacent to the transcription start site (TSS). In contrast, genes with uniformly hypermethylated CpG islands were only temporarily reactivated. These results imply that 5-aza-dC induces strong de-methylation of the genome and initiates reactivation of transcriptionally inactive genes, but this does not require gene associated CpG island de-methylation to occur. In addition, for three of our selected genes, hypomethylation at the TSS of an epigenetically silenced gene is associated with the long term reversion of

  12. Coronal mass ejection kinematics deduced from white light (Solar Mass Ejection Imager) and radio (Wind/WAVES) observations

    Reiner, M. J.; Jackson, B. V.; Webb, D. F.; Mizuno, D. R.; Kaiser, M. L.; Bougeret, J.-L.

    2005-09-01

    White-light and radio observations are combined to deduce the coronal and interplanetary kinematics of a fast coronal mass ejection (CME) that was ejected from the Sun at about 1700 UT on 2 November 2003. The CME, which was associated with an X8.3 solar flare from W56°, was observed by the Mauna Loa and Solar and Heliospheric Observatory (SOHO) Large-Angle Spectrometric Coronograph (LASCO) coronagraphs to 14 R⊙. The measured plane-of-sky speed of the LASCO CME was 2600 km s-1. To deduce the kinematics of this CME, we use the plane-of-sky white light observations from both the Solar Mass Ejection Imager (SMEI) all-sky camera on board the Coriolis spacecraft and the SOHO/LASCO coronagraph, as well as the frequency drift rate of the low-frequency radio data and the results of the radio direction-finding analysis from the WAVES experiment on the Wind spacecraft. In agreement with the in situ observations for this event, we find that both the white light and radio observations indicate that the CME must have decelerated significantly beginning near the Sun and continuing well into the interplanetary medium. More specifically, by requiring self-consistency of all the available remote and in situ data, together with a simple, but not unreasonable, assumption about the general characteristic of the CME deceleration, we were able to deduce the radial speed and distance time profiles for this CME as it propagated from the Sun to 1 AU. The technique presented here, which is applicable to mutual SMEI/WAVES CME events, is expected to provide a more complete description and better quantitative understanding of how CMEs propagate through interplanetary space, as well as how the radio emissions, generated by propagating CME/shocks, relate to the shock and CME. This understanding can potentially lead to more accurate predictions for the onset times of space weather events, such as those that were observed during this unique period of intense solar activity.

  13. Differences in the ovine HSP90AA1 gene expression rates caused by two linked polymorphisms at its promoter affect rams sperm DNA fragmentation under environmental heat stress conditions.

    Salces-Ortiz, Judit; Ramón, Manuel; González, Carmen; Pérez-Guzmán, M Dolores; Garde, J Julián; García-Álvarez, Olga; Maroto-Morales, Alejandro; Calvo, Jorge H; Serrano, M Magdalena

    2015-01-01

    Heat shock (HS) is one of the best-studied exogenous cellular stresses. Almost all tissues, cell types, metabolic pathways and biochemical reactions are affected in greater or lesser extent by HS. However, there are some especially thermo sensible cellular types such as the mammalian male germ cells. The present study examined the role of three INDELs in conjunction with the -660G/C polymorphism located at the HSP90AA1 promoter region over the gene expression rate under HS. Specially, the -668insC INDEL, which is very close to the -660G/C transversion, is a good candidate to be implied in the transcriptional regulation of the gene by itself or in a cooperative way with this SNP. Animals carrying the genotype II-668 showed higher transcription rates than those with ID-668 (FC = 3.07) and DD-668 (FC = 3.40) genotypes for samples collected under HS. A linkage between gene expression and sperm DNA fragmentation was also found. When HS conditions were present along or in some stages of the spermatogenesis, alternative genotypes of the -668insC and -660G/C mutations are involved in the effect of HS over sperm DNA fragmentation. Thus, unfavorable genotypes in terms of gene expression induction (ID-668GC-660 and DD-668GG-660) do not produce enough mRNA (stored as messenger ribonucleoprotein particles) and Hsp90α protein to cope with future thermal stress which might occur in posterior stages when transcriptional activity is reduced and cell types and molecular processes are more sensible to heat (spermatocytes in pachytene and spermatids protamination). This would result in the impairment of DNA packaging and the consequent commitment of the events occurring shortly after fertilization and during embryonic development. In the short-term, the assessment of the relationship between sperm DNA fragmentation sensitivity and ram's fertility will be of interest to a better understanding of the mechanisms of response to HS and its consequences on animal production and

  14. Inter-observer variation in estimates by nuclear angiography of left ventricular ejection fraction and ejection rate

    Young, K.C.; Railton, R.

    1980-01-01

    The recent decline in the cost of computing has led to the introduction of data processing of gamma-camera images in many medical centres, allowing the development and widespread use of radionuclide techniques for assessing left ventricular performance. Methods such as ECG-gated blood-pool imaging have the advantage of being less invasive than contrast ventriculography and do not rely on geometrical assumptions about the shape of the ventricle. A study has been made of the inter-observer variation in estimates of ejection fraction and average and maximum systolic contraction rates using a micro-computer (VIP-450 Video Image Processor, Ohio-Nuclear Limited, Rugby) to analyse gated blood-pool images of the left ventricle. (author)

  15. HPV DNA methylation at the early promoter and E1/E2 integrity: A comparison between HPV16, HPV18 and HPV45 in cervical cancer.

    Amaro-Filho, Sérgio Menezes; Pereira Chaves, Cláudia Bessa; Felix, Shayany Pinto; Basto, Diogo Lisbôa; de Almeida, Liz Maria; Moreira, Miguel Angelo Martins

    2018-04-09

    To compare and describe type-specific characteristics of HPV16, HPV18 and HPV45 in cervical cancer with respect to 3'LCR methylation and disruption of E1/E2. The methylation level of 137 cervical cancer samples (70 with HPV16, 37 with HPV18, and 30 with HPV45) of Brazilian patients was analyzed by pyrosequencing. PCR amplifications were performed to characterize E1 and E2 disruption as an episomal surrogate. The 3'LCR of HPV16 showed a higher methylation at all CpG sites (7%, 9%, 11%, 10% and 10%) than homologous HPV18 regions (4%, 5%. 6%, 9% and 5%) and HPV45 regions (7%, 7% and 5%). Presence of intact E1/E2 was associated with higher HPV16 and HPV18 methylation levels at all CpG sites (p < 0.05). Disruption of E1/E2 was more frequently found in HPV45 (97%) and HPV18 (84%) than in HPV16 DNA (30%). HPV16 disruption was more frequently found in E1 (48%) unlike HPV18, where it was found in E2 (61%). Concomitant disruption of E1/E2 was most frequent in HPV45 (72%). The findings showed a higher methylation associated with intact E1/E2 for HPV16 and HPV18. The closely phylogenetic related HPV18 and HPV45 share a similar methylation level and the frequency of viral genome disruption. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

  16. Speeds of coronal mass ejections: SMM observations from 1980 and 1984-1989

    Hundhausen, A. J.; Burkepile, J. T.; St. Cyr, O. C.

    1994-01-01

    The speeds of 936 features in 673 coronal mass ejections have been determined from trajectories observed with the Solar Maximum Mission (SMM) coronagraph in 1980 and 1984 to 1989. The distribution of observed speeds has a range (from 5th to 95th percentile) of 35 to 911 km/s; the average and median speeds are 349 and 285 km/s. The speed distributions of some selected classes of mass ejections are significantly different. For example, the speeds of 331 'outer loops' range from 80 to 1042 km/s; the average and median speeds for this class of ejections are 445 and 372 km/s. The speed distributions from each year of SMM observations show significant changes, with the annual average speeds varying from 157 (1984) to 458 km/s (1985). These variations are not simply related to the solar activity cycle; the annual averages from years near the sunspot maxima and minimum are not significantly different. The widths, latitudes, and speeds of mass ejections determined from the SMM observations are only weakly correlated. In particular, mass ejection speeds vary only slightly with the heliographic latitudes of the ejection. High-latitude ejections, which occur well poleward of the active latitudes, have speeds similar to active latitude ejections.

  17. Heart failure with preserved ejection fraction in women : The dutch queen of hearts program

    den Ruijter, H.; Pasterkamp, G.; Rutten, F. H.; Lam, C. S P; Chi, C.; Tan, K. H.; van Zonneveld, A. J.; Spaanderman, M.; de Kleijn, D. P V

    2015-01-01

    Heart failure (HF) poses a heavy burden on patients, their families and society. The syndrome of HF comes in two types: with reduced ejection fraction (HFrEF) and preserved ejection fraction (HFpEF). The latter is on the increase and predominantly present in women, especially the older ones. There

  18. Septum magnet for ejection from the PS to the E-Hall

    CERN PhotoLab

    1977-01-01

    Pulsed septum magnet for ejection from PS straight sections 61/62 to the East-Hall. This septum magnet, for ss 61, had only 1 turn, for minimum thickness. It was followed by another septum in ss 62, with 2 turns, as there the ejected beam was already farther away from the circulating beam. Both septa were water-cooled.

  19. Ejection Regimes in Picosecond Laser-Induced Forward Transfer of Metals

    Pohl, Ralph; Visser, C.W.; Römer, Gerardus Richardus, Bernardus, Engelina; Lohse, Detlef; Sun, Chao; Huis in 't Veld, Bert

    2015-01-01

    Laser-induced forward transfer (LIFT) is a 3D direct-write method suitable for precision printing of various materials, including pure metals. To understand the ejection mechanism and thereby improve deposition, here we present visualizations of ejection events at high-spatial (submicrometer) and

  20. DNA repair synthesis in human fibroblasts requires DNA polymerase delta

    Nishida, C.; Reinhard, P.; Linn, S.

    1988-01-01

    When UV-irradiated cultured diploid human fibroblasts were permeabilized with Brij-58 then separated from soluble material by centrifugation, conservative DNA repair synthesis could be restored by a soluble factor obtained from the supernatant of similarly treated HeLa cells. Extensive purification of this factor yielded a 10.2 S, 220,000-dalton polypeptide with the DNA polymerase and 3'- to 5'-exonuclease activities reported for DNA polymerase delta II. Monoclonal antibody to KB cell DNA polymerase alpha, while binding to HeLa DNA polymerase alpha, did not bind to the HeLa DNA polymerase delta. Moreover, at micromolar concentrations N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate (BuPdGTP) and 2-(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate (BuAdATP) were potent inhibitors of DNA polymerase alpha, but did not inhibit the DNA polymerase delta. Neither purified DNA polymerase alpha nor beta could promote repair DNA synthesis in the permeabilized cells. Furthermore, under conditions which inhibited purified DNA polymerase alpha by greater than 90%, neither monoclonal antibodies to DNA polymerase alpha, BuPdGTP, nor BuAdATP was able to inhibit significantly the DNA repair synthesis mediated by the DNA polymerase delta. Thus, it appears that a major portion of DNA repair synthesis induced by UV irradiation might be catalyzed by DNA polymerase delta. When xeroderma pigmentosum human diploid fibroblasts were utilized, DNA repair synthesis dependent upon ultraviolet light could be restored by addition of both T4 endonuclease V and DNA polymerase delta, but not by addition of either one alone

  1. Sizes and locations of coronal mass ejections - SMM observations from 1980 and 1984-1989

    Hundhausen, A. J.

    1993-01-01

    A statistical description of the sizes and locations of 1209 mass ejections observed with the SMM coronagraph/polarimeter in 1980 and 1984-1989 is presented. The average width of the coronal mass ejections detected with this instrument was close to 40 deg in angle for the entire period of SMM observations. No evidence was found for a significant change in mass ejection widths as reported by Howard et al. (1986). There is clear evidence for changes in the latitude distribution of mass ejections over this epoch. Mass ejections occurred over a much wider range of latitudes at the times of high solar activity (1980 and 1989) than at times of low activity (1985-1986).

  2. Femtosecond pulse-width dependent trapping and directional ejection dynamics of dielectric nanoparticles

    Chiang, Weiyi

    2013-09-19

    We demonstrate that laser pulse duration, which determines its impulsive peak power, is an effective parameter to control the number of optically trapped dielectric nanoparticles, their ejections along the directions perpendicular to polarization vector, and their migration distances from the trapping site. This ability to controllably confine and eject the nanoparticle is explained by pulse width-dependent optical forces exerted on nanoparticles in the trapping site and ratio between the repulsive and attractive forces. We also show that the directional ejections occur only when the number of nanoparticles confined in the trapping site exceeds a definite threshold. We interpret our data by considering the formation of transient assembly of the optically confined nanoparticles, partial ejection of the assembly, and subsequent filling of the trapping site. The understanding of optical trapping and directional ejections by ultrashort laser pulses paves the way to optically controlled manipulation and sorting of nanoparticles. © 2013 American Chemical Society.

  3. Experimental and Computational Analysis of Water-Droplet Formation and Ejection Process Using Hollow Microneedle

    Kato, Norihisa; Oka, Ryotaro; Sakai, Takahiro; Shibata, Takayuki; Kawashima, Takahiro; Nagai, Moeto; Mineta, Takashi; Makino, Eiji

    2011-06-01

    In this paper, we present the possibility of liquid delivery using fabricated hollow silicon dioxide microneedles of approximately 2 µm in diameter. As a fundamental study, the water-droplet formation and ejection process was examined via dynamic observations during water ejection tests and computational fluid dynamics (CFD) analysis. The experimental results indicated that fluid flow in a microneedle follows the Hagen-Poiseuille law, i.e., the flow rate is approximately directly proportional to the fourth power of the inner diameter. Moreover, the ejection pressure and maximum droplet curvature obtained using the proposed microfluid ejection model were in good agreement with the experimental results. The resulting ejection pressure is equal to the theoretical pressure difference of a spherical droplet, which is determined using the Young-Laplace equation. The maximum curvature of a droplet formed at the tip of a microneedle can be estimated on the basis of the contact angle theory expressed by the Young equation.

  4. Accretion and ejection in resistive GR-MHD

    Qian, Qian

    2017-05-10

    In this thesis, the accretion and ejection processes from a black hole accretion system is investigated by means of resistive general relativistic magnetohydrodynamic simulations. As a supplement to the results from prior research with non-relativistic simulations, my results confirm that the winds and outflows originated from thin accretion disks can also be observed in general relativistic simulations. In the first part, the execution of the implementation of resistivity, namely magnetic diffusivity, into the existing non-resistive general relativistic magnetohydrodynamic code HARM is illustrated. The test simulations of the new code rHARM include the comparison with analytical solution of the diffusion equation and a classic shock tube test. rHARM shows reliable performances in these tests. In the second part, rHARM is applied to investigate the evolution of magnetized tori. The results show that the existence of resistivity leads to inefficient accretions of matter from tori onto black holes by weakening the magnetorotational instability inside the tori. An indication for a critical magnetic diffusivity in this simulation setup is found beyond which no magnetorotational instability develops in the linear regime. In the third part, as the main purpose of this PhD project, rHARM is used to perform simulations of magnetically diffusive thin accretion disks that are threaded by a large-scale poloidal magnetic field around non-rotating and rotating black holes. These long-term simulations last 3000 code time units, which are about 195 rotation periods at the disk inner boundary, correspondingly. Their computational domains extend from black hole horizon to 80 Schwarzschild radii. Outflows driven from the accretion disk are clearly seen. These outflows have the typical radial velocity of 0.1 speed of light. In my analyses, I argue that these outflows are driven by the magnetic pressure gradient from the toroidal magnetic field generated by the rotation of the disk

  5. Fitting and Reconstruction of Thirteen Simple Coronal Mass Ejections

    Al-Haddad, Nada; Nieves-Chinchilla, Teresa; Savani, Neel P.; Lugaz, Noé; Roussev, Ilia I.

    2018-05-01

    Coronal mass ejections (CMEs) are the main drivers of geomagnetic disturbances, but the effects of their interaction with Earth's magnetic field depend on their magnetic configuration and orientation. Fitting and reconstruction techniques have been developed to determine important geometrical and physical CME properties, such as the orientation of the CME axis, the CME size, and its magnetic flux. In many instances, there is disagreement between different methods but also between fitting from in situ measurements and reconstruction based on remote imaging. This could be due to the geometrical or physical assumptions of the models, but also to the fact that the magnetic field inside CMEs is only measured at one point in space as the CME passes over a spacecraft. In this article we compare three methods that are based on different assumptions for measurements by the Wind spacecraft for 13 CMEs from 1997 to 2015. These CMEs are selected from the interplanetary coronal mass ejections catalog on https://wind.nasa.gov/ICMEindex.php https://wind.nasa.gov/ICMEindex.php" TargetType="URL"/> because of their simplicity in terms of: 1) slow expansion speed throughout the CME and 2) weak asymmetry in the magnetic field profile. This makes these 13 events ideal candidates for comparing codes that do not include expansion or distortion. We find that for these simple events, the codes are in relatively good agreement in terms of the CME axis orientation for six of the 13 events. Using the Grad-Shafranov technique, we can determine the shape of the cross-section, which is assumed to be circular for the other two models, a force-free fitting and a circular-cylindrical non force-free fitting. Five of the events are found to have a clear circular cross-section, even when this is not a precondition of the reconstruction. We make an initial attempt at evaluating the adequacy of the different assumptions for these simple CMEs. The conclusion of this work strongly suggests that attempts

  6. Insulin-like growth factor-1 (IGF-1) promotes primordial follicle growth and reduces DNA fragmentation through the phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) signalling pathway.

    Bezerra, Maria É S; Barberino, Ricássio S; Menezes, Vanúzia G; Gouveia, Bruna B; Macedo, Taís J S; Santos, Jamile M S; Monte, Alane P O; Barros, Vanessa R P; Matos, Maria H T

    2018-05-30

    We investigated the effects of insulin-like growth factor 1 (IGF-1) on the morphology and follicular activation of ovine preantral follicles cultured in situ and whether the phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) pathway is involved in IGF-1 action in the sheep ovary. Ovine ovarian fragments were fixed for histological and terminal deoxynucleotidyl transferase dUTP nick-end labelling (TUNEL) analyses (fresh control) or cultured in supplemented alpha-minimum essential medium (α-MEM+; control) or α-MEM+ with IGF-1 (1, 10, 50, 100 or 200ngmL-1) for 7 days. Follicles were classified as normal or atretic, primordial or growing and the oocyte and follicle diameters were measured. DNA fragmentation was evaluated by TUNEL assay. Proliferating cell nuclear antigen (PCNA) immunohistochemistry was performed on the fresh control, α-MEM+ and 100ngmL-1 IGF-1 samples. Inhibition of PI3K activity was performed through pretreatment with the PI3K inhibitor LY294002 and phosphorylated AKT (pAKT) expression was analysed after culture in the absence or presence of LY294002. IGF-1 at 100ngmL-1 increased (PIGF-1. LY294002 significantly inhibited follicular activation stimulated by α-MEM+ and 100ngmL-1 IGF-1 and reduced pAKT expression in follicles. Overall, IGF-1 at 100ngmL-1 promoted primordial follicle activation, cell proliferation and reduced DNA fragmentation after in situ culture through the PI3K/AKT pathway.

  7. Repulsive DNA-DNA interactions accelerate viral DNA packaging in phage phi29

    Keller, Nicholas; delToro, Damian; Grimes, Shelley; Jardine, Paul J.; Smith, Douglas E.

    2014-01-01

    We use optical tweezers to study the effect of attractive versus repulsive DNA-DNA interactions on motor-driven viral packaging. Screening of repulsive interactions accelerates packaging, but induction of attractive interactions by spermidine3+ causes heterogeneous dynamics. Acceleration is observed in a fraction of complexes, but most exhibit slowing and stalling, suggesting that attractive interactions promote nonequilibrium DNA conformations that impede the motor. Thus, repulsive interacti...

  8. DNA Methylation at the DAT Promoter and Risk for Psychopathology: Intergenerational Transmission between School-Age Youths and Their Parents in a Community Sample

    Silvia Cimino

    2018-01-01

    Full Text Available BackgroundThe effect of gene polymorphisms and promoter methylation, associated with maladaptive developmental outcomes, vary depending on environmental factors (e.g., parental psychopathology. Most studies have focused on 0- to 5-year-old children, adolescents, or adults, whereas there is dearth of research on school-age youths and pre-adolescents.MethodsIn a sample of 21 families recruited at schools, we addressed parents’ psychopathological symptoms (through SCL-90-R; offspring emotional–behavioral functioning (through CBCL-6–18; dopamine transporter gene (DAT1 for epigenetic status of the 5′-untranslated region (UTR and for genotype, i.e., variable number of tandem repeats polymorphism at the 3′-UTR. Possible associations were explored between bio-genetic and psychological characteristics within the same individual and between triplets of children, mothers, and fathers.ResultsDAT methylation of CpG at positions M1, M6, and M7 in mothers was correlated with maternal (phobic anxiety, whereas in fathers’ position M6 was related to paternal depression, anxiety, hostility, psychoticism, and higher Global Severity Index (GSI. No significant correlations were found between maternal and offspring DAT methylation. Significant correlations were found between fathers’ methylation at CpG M1 and children’s methylation at CpG M6. Linear regressions showed that mothers and fathers’ GSI predicted children’s methylation at CpG sites M2, M3, and M6, whereas fathers’ GSI predicted children’s methylation at CpG sites, particularly M1, M2, and M6. Moreover, offspring methylation of DAT at CpG M2 predicted somatic complaint, internalizing and attention problems; methylation of DAT at CpG M6 predicted withdraw.ConclusionThis study may have important clinical implication for the prevention and treatment of emotional–behavioral difficulties in children, as it adds to previous knowledge about the role of genetic and environmental factors in

  9. MAGNETIC FIELD STRUCTURES TRIGGERING SOLAR FLARES AND CORONAL MASS EJECTIONS

    Kusano, K.; Bamba, Y.; Yamamoto, T. T.; Iida, Y.; Toriumi, S.; Asai, A.

    2012-01-01

    Solar flares and coronal mass ejections, the most catastrophic eruptions in our solar system, have been known to affect terrestrial environments and infrastructure. However, because their triggering mechanism is still not sufficiently understood, our capacity to predict the occurrence of solar eruptions and to forecast space weather is substantially hindered. Even though various models have been proposed to determine the onset of solar eruptions, the types of magnetic structures capable of triggering these eruptions are still unclear. In this study, we solved this problem by systematically surveying the nonlinear dynamics caused by a wide variety of magnetic structures in terms of three-dimensional magnetohydrodynamic simulations. As a result, we determined that two different types of small magnetic structures favor the onset of solar eruptions. These structures, which should appear near the magnetic polarity inversion line (PIL), include magnetic fluxes reversed to the potential component or the nonpotential component of major field on the PIL. In addition, we analyzed two large flares, the X-class flare on 2006 December 13 and the M-class flare on 2011 February 13, using imaging data provided by the Hinode satellite, and we demonstrated that they conform to the simulation predictions. These results suggest that forecasting of solar eruptions is possible with sophisticated observation of a solar magnetic field, although the lead time must be limited by the timescale of changes in the small magnetic structures.

  10. Coronal mass ejections and their sheath regions in interplanetary space

    Kilpua, Emilia; Koskinen, Hannu E. J.; Pulkkinen, Tuija I.

    2017-11-01

    Interplanetary coronal mass ejections (ICMEs) are large-scale heliospheric transients that originate from the Sun. When an ICME is sufficiently faster than the preceding solar wind, a shock wave develops ahead of the ICME. The turbulent region between the shock and the ICME is called the sheath region. ICMEs and their sheaths and shocks are all interesting structures from the fundamental plasma physics viewpoint. They are also key drivers of space weather disturbances in the heliosphere and planetary environments. ICME-driven shock waves can accelerate charged particles to high energies. Sheaths and ICMEs drive practically all intense geospace storms at the Earth, and they can also affect dramatically the planetary radiation environments and atmospheres. This review focuses on the current understanding of observational signatures and properties of ICMEs and the associated sheath regions based on five decades of studies. In addition, we discuss modelling of ICMEs and many fundamental outstanding questions on their origin, evolution and effects, largely due to the limitations of single spacecraft observations of these macro-scale structures. We also present current understanding of space weather consequences of these large-scale solar wind structures, including effects at the other Solar System planets and exoplanets. We specially emphasize the different origin, properties and consequences of the sheaths and ICMEs.

  11. Spironolactone in patients with heart failure and preserved ejection fraction.

    Sánchez-Sánchez, C; Mendoza-Ruiz de Zuazu, H F; Formiga, F; Manzano, L; Ceresuela, L M; Carrera-Izquierdo, M; González Franco, Á; Epelde-Gonzalo, F; Cerqueiro-González, J M; Montero-Pérez-Barquero, M

    2015-01-01

    Aldosterone inhibitors have been shown to be beneficial for patients with systolic heart failure. However, the evidence from patients with heart failure and preserved ejection fraction (HFPEF) is limited. We evaluated the role of spironolactone in the prognosis of a cohort of patients with HFPEF. We analyzed the outcomes of patients hospitalized for HFPEF in 52 departments of internal medicine of the Spanish RICA registry according to those who did and did not take spironolactone. We recorded the posthospital mortality rate and readmissions at 1 year and performed a multivariate survival analysis. We included 1212 patients with HFPEF, with a mean age of 79 years (standard deviation, 7.9), (64.1% women), the majority of whom had hypertensive heart disease (50.7%). The patients treated with spironolactone, compared with those who were not treated with this diuretic, had a more advanced functional class, a higher number of readmissions (44.3 vs. 29.1%; p<0.001) and a higher rate in the combined variable of readmissions/mortality (39.0 vs. 29.0%; p=0.001). In the multivariate analysis, the administration of spironolactone was associated with an increase in readmissions (RR, 1.4; 95% CI, 1.16-1.78; p=0.001). For patients with HFPEF, the administration of spironolactone was associated with an increase in all-cause readmission, perhaps due to the higher rate of hyperpotassemia. Copyright © 2015. Published by Elsevier España, S.L.U.

  12. INTERCOMPARISON OF RESULTS FOR A PWR ROD EJECTION ACCIDENT

    DIAMOND,D.J.; ARONSON,A.; JO,J.; AVVAKUMOV,A.; MALOFEEV,V.; SIDOROV,V.; FERRARESI,P.; GOUIN,C.; ANIEL,S.; ROYER,M.E.

    1999-10-01

    This study is part of an overall program to understand the uncertainty in best-estimate calculations of the local fuel enthalpy during the rod ejection accident. Local fuel enthalpy is used as the acceptance criterion for this design-basis event and can also be used to estimate fuel damage for the purpose of determining radiological consequences. The study used results from neutron kinetics models in PARCS, BARS, and CRONOS2, codes developed in the US, the Russian Federation, and France, respectively. Since BARS uses a heterogeneous representation of the fuel assembly as opposed to the homogeneous representations in PARCS and CRONOS, the effect of the intercomparison was primarily to compare different intra-assembly models. Quantitative comparisons for core power, reactivity, assembly fuel enthalpy and pin power were carried out. In general the agreement between methods was very good providing additional confidence in the codes and providing a starting point for a quantitative assessment of the uncertainty in calculated fuel enthalpy using best-estimate methods.

  13. Determination of left ventricular ejection fraction by radionuclide angiocardiography

    Hoeilund-Carlsen, P.F.; Rasmussen, S.; Hesse, B.; Dige-Petersen, H.; Folke, K.; Godtfredsen, J.; Jensen, G.; Fabricius, J.

    1982-01-01

    Radionuclide angiocardiography is a non-invasive gamma camera investigation for evaluation and quantification of heart performance. We investigated the reliability of the method in measuring left ventricular ejection fraction (EF). The accuracy was determined by measuring EF in 29 patients by both radionuclide angiocardiography and conventional single-plane cineventriculography. The two methods correlated well: r=0.92; y=0.86x+0.07. The precision of the method was evaluated as follows: The coefficient of variance was 6% for duplicate determinations performed on the same day (n=27) and 5% for determinations with 1-3 days interval (n=21). The interobserver variation expressed by the coefficient of variance was maximally 6% with the radionuclide method (n=29, three observers). The intraobserver variation was 4% compared to 9% with cineventriculography (P<0.01). Radionuclide angiocardiography is a reliable way of measuring EF. As the method is non-invasive, it is well suited for sequential determinations of EF in the same patient. (authors)

  14. Sheath-accumulating Propagation of Interplanetary Coronal Mass Ejection

    Takahashi, Takuya; Shibata, Kazunari, E-mail: takahasi@kusastro.kyoto-u.ac.jp [Kwasan and Hida Observatories, Kyoto University, Yamashina, Kyoto 607–8471 (Japan)

    2017-03-10

    Fast interplanetary coronal mass ejections (ICMEs) are the drivers of strong space weather storms such as solar energetic particle events and geomagnetic storms. The connection between the space-weather-impacting solar wind disturbances associated with fast ICMEs at Earth and the characteristics of causative energetic CMEs observed near the Sun is a key question in the study of space weather storms, as well as in the development of practical space weather prediction. Such shock-driving fast ICMEs usually expand at supersonic speeds during the propagation, resulting in the continuous accumulation of shocked sheath plasma ahead. In this paper, we propose a “sheath-accumulating propagation” (SAP) model that describes the coevolution of the interplanetary sheath and decelerating ICME ejecta by taking into account the process of upstream solar wind plasma accumulation within the sheath region. Based on the SAP model, we discuss (1) ICME deceleration characteristics; (2) the fundamental condition for fast ICMEs at Earth; (3) the thickness of interplanetary sheaths; (4) arrival time prediction; and (5) the super-intense geomagnetic storms associated with huge solar flares. We quantitatively show that not only the speed but also the mass of the CME are crucial for discussing the above five points. The similarities and differences between the SAP model, the drag-based model, and the“snow-plow” model proposed by Tappin are also discussed.

  15. Control assembly ejection accident analysis for WWER-440 (Armenian NPP)

    Bznuni, S.; Malakyan, Ts.; Amirjanyan, A.; Ghasabyan, L.

    2007-01-01

    Control Assembly ejection in WWER-440 initiated by the loss of integrity of the Control Assemblies drive housing has been analyzed. This event causes a very rapid reactivity insertion to the core and small break LOCA which potentially could lead to rapid power increase and redistribution of heat release in the core resulting in a fuel, cladding and coolant temperature rise; primary pressure increase, radiological consequences due to loss of primary coolant and potential loss of cladding integrity and fuel disintegration (if applicable). Methodology of the analysis is based on conservative assumptions as well as on deterministic approach for selection of functioning logic of systems and equipment's to maximize reactor core power and minimize power decreasing reactivity feedback. Computational analyses were performed by 3D kinetics PARCS-RELAP coupled code. WWER-440 fuel cross-section libraries, diffusion coefficients and kinetics parameters were calculated by HELOS code. In this paper analysis of accident for Hot Full Power was presented. Results of analysis show that ANPP WWER-440 reactor design meets acceptance criteria prescribed for RIA type design based accidents (Authors)

  16. FORECASTING A CORONAL MASS EJECTION'S ALTERED TRAJECTORY: ForeCAT

    Kay, C.; Opher, M.; Evans, R. M.

    2013-01-01

    To predict whether a coronal mass ejection (CME) will impact Earth, the effects of the background on the CME's trajectory must be taken into account. We develop a model, ForeCAT (Forecasting a CME's Altered Trajectory), of CME deflection due to magnetic forces. ForeCAT includes CME expansion, a three-part propagation model, and the effects of drag on the CME's deflection. Given the background solar wind conditions, the launch site of the CME, and the properties of the CME (mass, final propagation speed, initial radius, and initial magnetic strength), ForeCAT predicts the deflection of the CME. Two different magnetic backgrounds are considered: a scaled background based on type II radio burst profiles and a potential field source surface (PFSS) background. For a scaled background where the CME is launched from an active region located between a coronal hole and streamer region, the strong magnetic gradients cause a deflection of 8.°1 in latitude and 26.°4 in longitude for a 10 15 g CME propagating out to 1 AU. Using the PFSS background, which captures the variation of the streamer belt (SB) position with height, leads to a deflection of 1.°6 in latitude and 4.°1 in longitude for the control case. Varying the CME's input parameters within observed ranges leads to the majority of CMEs reaching the SB within the first few solar radii. For these specific backgrounds, the SB acts like a potential well that forces the CME into an equilibrium angular position

  17. Coronal mass ejections and their sheath regions in interplanetary space

    Emilia Kilpua

    2017-11-01

    Full Text Available Abstract Interplanetary coronal mass ejections (ICMEs are large-scale heliospheric transients that originate from the Sun. When an ICME is sufficiently faster than the preceding solar wind, a shock wave develops ahead of the ICME. The turbulent region between the shock and the ICME is called the sheath region. ICMEs and their sheaths and shocks are all interesting structures from the fundamental plasma physics viewpoint. They are also key drivers of space weather disturbances in the heliosphere and planetary environments. ICME-driven shock waves can accelerate charged particles to high energies. Sheaths and ICMEs drive practically all intense geospace storms at the Earth, and they can also affect dramatically the planetary radiation environments and atmospheres. This review focuses on the current understanding of observational signatures and properties of ICMEs and the associated sheath regions based on five decades of studies. In addition, we discuss modelling of ICMEs and many fundamental outstanding questions on their origin, evolution and effects, largely due to the limitations of single spacecraft observations of these macro-scale structures. We also present current understanding of space weather consequences of these large-scale solar wind structures, including effects at the other Solar System planets and exoplanets. We specially emphasize the different origin, properties and consequences of the sheaths and ICMEs.

  18. Coronal ``Wave'': Magnetic Footprint of a Coronal Mass Ejection?

    Attrill, Gemma D. R.; Harra, Louise K.; van Driel-Gesztelyi, Lidia; Démoulin, Pascal

    2007-02-01

    We investigate the properties of two ``classical'' EUV Imaging Telescope (EIT) coronal waves. The two source regions of the associated coronal mass ejections (CMEs) possess opposite helicities, and the coronal waves display rotations in opposite senses. We observe deep core dimmings near the flare site and also widespread diffuse dimming, accompanying the expansion of the EIT wave. We also report a new property of these EIT waves, namely, that they display dual brightenings: persistent ones at the outermost edge of the core dimming regions and simultaneously diffuse brightenings constituting the leading edge of the coronal wave, surrounding the expanding diffuse dimmings. We show that such behavior is consistent with a diffuse EIT wave being the magnetic footprint of a CME. We propose a new mechanism where driven magnetic reconnections between the skirt of the expanding CME magnetic field and quiet-Sun magnetic loops generate the observed bright diffuse front. The dual brightenings and the widespread diffuse dimming are identified as innate characteristics of this process.

  19. A numerical study of two interacting coronal mass ejections

    J. M. Schmidt

    2004-06-01

    Full Text Available The interaction in the solar wind between two coronal mass ejections (CMEs is investigated using numerical simulations. We show that the nature of the interaction depends on whether the CME magnetic structures interact, but in all cases the result is an equilisation of the speed of the two CMEs. In the absence of magnetic interaction, the forward shock of the faster trailing CME interacts with the slow leading CME, and accelerates it. When the two CMEs have magnetic fields with the same sense of rotation, magnetic reconnection occurs between the two CMEs, leading to the formation of a single magnetic structure: in the most extreme cases, one CME "eats" the other. When the senses of rotation are opposite, reconnection does not occur, but the CMEs collide in a highly non-elastic manner, again forming a single structure. The possibility of enhanced particle acceleration in such processes is assessed. The presence of strong magnetic reconnection provides excellent opportunities for the acceleration of thermal particles, which then form a seed population for further acceleration at the CME shocks. The presence of a large population of seed particles will thus lead to an overall increase in energetic particle fluxes, as suggested by some observations.

  20. Sheath-accumulating Propagation of Interplanetary Coronal Mass Ejection

    Takahashi, Takuya; Shibata, Kazunari

    2017-01-01

    Fast interplanetary coronal mass ejections (ICMEs) are the drivers of strong space weather storms such as solar energetic particle events and geomagnetic storms. The connection between the space-weather-impacting solar wind disturbances associated with fast ICMEs at Earth and the characteristics of causative energetic CMEs observed near the Sun is a key question in the study of space weather storms, as well as in the development of practical space weather prediction. Such shock-driving fast ICMEs usually expand at supersonic speeds during the propagation, resulting in the continuous accumulation of shocked sheath plasma ahead. In this paper, we propose a “sheath-accumulating propagation” (SAP) model that describes the coevolution of the interplanetary sheath and decelerating ICME ejecta by taking into account the process of upstream solar wind plasma accumulation within the sheath region. Based on the SAP model, we discuss (1) ICME deceleration characteristics; (2) the fundamental condition for fast ICMEs at Earth; (3) the thickness of interplanetary sheaths; (4) arrival time prediction; and (5) the super-intense geomagnetic storms associated with huge solar flares. We quantitatively show that not only the speed but also the mass of the CME are crucial for discussing the above five points. The similarities and differences between the SAP model, the drag-based model, and the“snow-plow” model proposed by Tappin are also discussed.

  1. Regarding the detectability and measurement of coronal mass ejections

    Howard Timothy A.

    2015-01-01

    Full Text Available In this review I discuss the problems associated with the detection and measurement of coronal mass ejections (CMEs. CMEs are important phenomena both scientifically, as they play a crucial role in the evolution of the solar corona, and technologically, as their impact with the Earth leads to severe space weather activity in the form of magnetic storms. I focus on the observation of CMEs using visible white light imagers (coronagraphs and heliospheric imagers, as they may be regarded as the binding agents between different datasets and different models that are used to reconstruct them. Our ability to accurately measure CMEs observed by these imagers is hampered by many factors, from instrumental to geometrical to physical. Following a brief review of the history of CME observation and measurement, I explore the impediments to our ability to measure them and describe possible means for which we may be able to mitigate those impediments. I conclude with a discussion of the claim that we have reached the limit of the information that we can extract from the current generation of white light imagers, and discuss possible ways forward regarding future instrument capabilities.

  2. Incremental first pass technique to measure left ventricular ejection fraction

    Kocak, R.; Gulliford, P.; Hoggard, C.; Critchley, M.

    1980-01-01

    An incremental first pass technique was devised to assess the acute effects of any drug on left ventricular ejection fraction (LVEF) with or without a physiological stress. In particular, the effects of the vasodilater isosorbide dinitrate on LVEF before and after exercise were studied in 11 patients who had suffered cardiac failure. This was achieved by recording the passage of sup(99m)Tc pertechnetate through the heart at each stage of the study using a gamma camera computer system. Consistent values for four consecutive first pass values without exercise or drug in normal subjects illustrated the reproducibility of the technique. There was no significant difference between LVEF values obtained at rest and exercise before or after oral isosorbide dinitrate with the exception of one patient with gross mitral regurgitation. The advantages of the incremental first pass technique are that the patient need not be in sinus rhythm, the effects of physiological intervention may be studied and tests may also be repeated at various intervals during long term follow-up of patients. A disadvantage of the method is the limitation in the number of sequential measurements which can be carried out due to the amount of radioactivity injected. (U.K.)

  3. GLOBAL ENERGETICS OF SOLAR FLARES. IV. CORONAL MASS EJECTION ENERGETICS

    Aschwanden, Markus J.

    2016-01-01

    This study entails the fourth part of a global flare energetics project, in which the mass m cme , kinetic energy E kin , and the gravitational potential energy E grav of coronal mass ejections (CMEs) is measured in 399 M and X-class flare events observed during the first 3.5 years of the Solar Dynamics Observatory (SDO) mission, using a new method based on the EUV dimming effect. EUV dimming is modeled in terms of a radial adiabatic expansion process, which is fitted to the observed evolution of the total emission measure of the CME source region. The model derives the evolution of the mean electron density, the emission measure, the bulk plasma expansion velocity, the mass, and the energy in the CME source region. The EUV dimming method is truly complementary to the Thomson scattering method in white light, which probes the CME evolution in the heliosphere at r ≳ 2 R ⊙ , while the EUV dimming method tracks the CME launch in the corona. We compare the CME parameters obtained in white light with the LASCO/C2 coronagraph with those obtained from EUV dimming with the Atmospheric Imaging Assembly onboard the SDO for all identical events in both data sets. We investigate correlations between CME parameters, the relative timing with flare parameters, frequency occurrence distributions, and the energy partition between magnetic, thermal, nonthermal, and CME energies. CME energies are found to be systematically lower than the dissipated magnetic energies, which is consistent with a magnetic origin of CMEs.

  4. Global Energetics in Solar Flares and Coronal Mass Ejections

    Aschwanden, Markus J.

    2017-08-01

    We present a statistical study of the energetics of coronal mass ejections (CME) and compare it with the magnetic, thermal, and nonthermal energy dissipated in flares. The physical parameters of CME speeds, mass, and kinetic energies are determined with two different independent methods, i.e., the traditional white-light scattering method using LASCO/SOHO data, and the EUV dimming method using AIA/SDO data. We analyze all 860 GOES M- and X-class flare events observed during the first 7 years (2010-2016) of the SDO mission. The new ingredients of our CME modeling includes: (1) CME geometry in terms of a self-similar adiabatic expansion, (2) DEM analysis of CME mass over entire coronal temperature range, (3) deceleration of CME due to gravity force which controls the kinetic and potentail CME energy as a function of time, (4) the critical speed that controls eruptive and confined CMEs, (5) the relationship between the center-of-mass motion during EUV dimming and the leading edge motion observed in white-light coronagraphs. Novel results are: (1) Physical parameters obtained from both the EUV dimming and white-light method can be reconciled; (2) the equi-partition of CME kinetic and thermal flare energy; (3) the Rosner-Tucker-Vaiana scaling law. We find that the two methods in EUV and white-light wavelengths are highly complementary and yield more complete models than each method alone.

  5. Coronal Mass Ejections: Models and Their Observational Basis

    P. F. Chen

    2011-04-01

    Full Text Available Coronal mass ejections (CMEs are the largest-scale eruptive phenomenon in the solar system, expanding from active region-sized nonpotential magnetic structure to a much larger size. The bulk of plasma with a mass of ∼10^11 – 10^13 kg is hauled up all the way out to the interplanetary space with a typical velocity of several hundred or even more than 1000 km s^-1, with a chance to impact our Earth, resulting in hazardous space weather conditions. They involve many other much smaller-sized solar eruptive phenomena, such as X-ray sigmoids, filament/prominence eruptions, solar flares, plasma heating and radiation, particle acceleration, EIT waves, EUV dimmings, Moreton waves, solar radio bursts, and so on. It is believed that, by shedding the accumulating magnetic energy and helicity, they complete the last link in the chain of the cycling of the solar magnetic field. In this review, I try to explicate our understanding on each stage of the fantastic phenomenon, including their pre-eruption structure, their triggering mechanisms and the precursors indicating the initiation process, their acceleration and propagation. Particular attention is paid to clarify some hot debates, e.g., whether magnetic reconnection is necessary for the eruption, whether there are two types of CMEs, how the CME frontal loop is formed, and whether halo CMEs are special.

  6. THE RELATION BETWEEN EIT WAVES AND CORONAL MASS EJECTIONS

    Chen, P. F.

    2009-01-01

    More and more evidence indicates that 'EIT waves' are strongly related to coronal mass ejections (CMEs). However, it is still not clear how the two phenomena are related to each other. We investigate a CME event on 1997 September 9, which was well observed by both the EUV Imaging Telescope (EIT) and the high-cadence Mark-III K-Coronameter at Mauna Loa Solar Observatory, and compare the spatial relation between the 'EIT wave' fronts and the CME leading loops. It is found that 'EIT wave' fronts are cospatial with the CME leading loops, and the expanding EUV dimmings are cospatial with the CME cavity. It is also found that the CME stopped near the boundary of a coronal hole, a feature common to observations of 'EIT waves'. It is suggested that 'EIT waves'/dimmings are the EUV counterparts of the CME leading loop/cavity, based on which we propose that, as in the case of 'EIT waves', CME leading loops are apparently moving density enhancements that are generated by successive stretching (or opening-up) of magnetic loops.

  7. NEAR-SIMULTANEOUS OBSERVATIONS OF X-RAY PLASMA EJECTION, CORONAL MASS EJECTION, AND TYPE II RADIO BURST

    Kim, Yeon-Han; Bong, Su-Chan; Park, Y.-D.; Cho, K.-S.; Moon, Y.-J.

    2009-01-01

    We report the first simultaneous observation of X-ray plasma ejection (XPE), coronal mass ejection (CME), and type II solar radio burst on 1999 October 26. First, an XPE was observed from 21:12 UT to 21:24 UT in the Yohkoh SXT field of view (1.1 to 1.4 R sun ). The XPE was accelerated with a speed range from 190 to 410 km s -1 and its average speed is about 290 km s -1 . Second, the associated CME was observed by the Mauna Loa Mk4 coronameter (1.1-2.8 R sun ) from 21:16 UT. The CME front was clearly identified at 21:26 UT and propagated with a deceleration of about -110 m s -2 . Its average speed is about 360 km s -1 . At the type II burst start time (21:25 UT), the height of the CME front is around 1.7 R sun and its speed is about 470 km s -1 . Third, a type II solar radio burst was observed from 21:25 UT to 21:43 UT by the Culgoora solar radio spectrograph. The burst shows three emission patches during this observing period and the emission heights of the burst are estimated to be about 1.3 R sun (21:25 UT), 1.4 R sun (21:30 UT), and 1.8 R sun (21:40 UT). By comparing these three phenomena, we find that: (1) kinematically, while the XPE shows acceleration, the associated CME front shows deceleration; (2) there is an obvious height difference (0.3 R sun ) between the CME front and the XPE front around 21:24 UT and the formation height of the type II burst is close to the trajectory extrapolated from the XPE front; (3) both speeds of the XPE and the CME are comparable with each other around the starting time of the type II burst. Considering the formation height and the speed of the type II burst, we suggest that its first emission is due to the coronal shock generated by the XPE and the other two emissions are driven by the CME flank interacting with the high-density streamer.

  8. Ejection of Uranium Atoms from UO{sub 2} by Fission Fragments

    Nilsson, Goesta

    1964-02-15

    The numbers of uranium atoms ejected from the surface of sintered plates of UO{sub 2} by fission fragments have been measured over the fission density range 5x10{sup 15} to 7x10{sup 16} fissions/cm{sup 3}. The number of uranium atoms ejected per escaping fragment was about 9. The measurements were performed by irradiating the plates in vacuum and collecting a fraction of the uranium atoms ejected on catcher foils. The amount collected was determined by fission counting. Saturation of the amount collected, as reported by Rogers and Adam, was not observed. The numbers of uranium atoms ejected as knock-ons under the same experimental conditions have been calculated. The reasonably close agreement between the experimental and theoretical values indicates that, under the prevailing experimental conditions, mainly knock-ons are ejected. Other ejection mechanisms, e. g. evaporation of material in thermal spikes, are probably insignificant; this is in contrast to the usual interpretation of the ejection process. The mean range in UO{sub 2}, of fission products of mass number 140 was found to be 7.37 {+-} 0. 05 mg/cm{sup 2} by direct gamma spectrometric, determination of the fraction of {sup 140}La escaping from the surface of the plates.

  9. Left atrial ejection force predicts the outcome after catheter ablation for paroxysmal atrial fibrillation.

    Kishima, Hideyuki; Mine, Takanao; Takahashi, Satoshi; Ashida, Kenki; Ishihara, Masaharu; Masuyama, Tohru

    2018-02-01

    Left atrium (LA) systolic dysfunction is observed in the early stages of atrial fibrillation (AF) prior to LA anatomical change. We investigated whether LA systolic dysfunction predicts recurrent AF after catheter ablation (CA) in patients with paroxysmal AF. We studied 106 patients who underwent CA for paroxysmal AF. LA systolic function was assessed with the LA emptying volume = Maximum LA volume (LAV max ) - Minimum LA volume (LAV min ), LA emptying fraction = [(LAV max - LAV min )/LAV max ] × 100, and LA ejection force calculated with Manning's method [LA ejection force = (0.5 × ρ × mitral valve area × A 2 )], where ρ is the blood density and A is the late-diastolic mitral inflow velocity. Recurrent AF was detected in 35/106 (33%) during 14.6 ± 9.1 months. Univariate analysis revealed reduced LA ejection force, decreased LA emptying fraction, larger LA diameter, and elevated brain natriuretic peptide as significant variables. On multivariate analysis, reduced LA ejection force and larger LA diameter were independently associated with recurrent AF. Moreover, patients with reduced LA ejection force and larger LA diameter had a higher risk of recurrent AF than preserved LA ejection force (log-rank P = 0.0004). Reduced LA ejection force and larger LA diameter were associated with poor outcome after CA for paroxysmal AF, and could be a new index to predict recurrent AF. © 2017 Wiley Periodicals, Inc.

  10. New Classification for Heart Failure with Mildly Reduced Ejection Fraction; Greater clarity or more confusion?

    Sunil Nadar

    2017-03-01

    Full Text Available The latest European Society of Cardiology (ESC guidelines for the diagnosis and management of heart failure include a new patient group for those with heart failure with mildly reduced ejection fraction (HFmrEF. By defining this group of patients as a separate entity, the ESC hope to encourage more research focusing on patients with HFmrEF. Previously, patients with this condition were caught between two classifications—heart failure with reduced ejection fraction and heart failure with preserved ejection fraction. Hopefully, the inclusion of new terminology will not increase confusion, but rather aid our understanding of heart failure, a complex clinical syndrome.

  11. Two codes used in analysis of rod ejection accident for Qinshan Nuclear Power Plant

    Zhu Xinguan

    1987-12-01

    Two codes were developed to analyse rod ejection accident for Qinshan Nuclear Power Plant. One was based on point model with temperature reactivity feedback. In this code, the worth of ejected rod was obtained under'adiabatic' approximation. In the other code, the Nodal Green's Function Method was used to solve space-time dependent neutron diffusion equation. Using these codes, the transient core-power have been calculated for two rod ejection cases at beginning of core-life in Qinshan Nuclear Power Plant

  12. DNA damage and polyploidization.

    Chow, Jeremy; Poon, Randy Y C

    2010-01-01

    A growing body of evidence indicates that polyploidization triggers chromosomal instability and contributes to tumorigenesis. DNA damage is increasingly being recognized for its roles in promoting polyploidization. Although elegant mechanisms known as the DNA damage checkpoints are responsible for halting the cell cycle after DNA damage, agents that uncouple the checkpoints can induce unscheduled entry into mitosis. Likewise, defects of the checkpoints in several disorders permit mitotic entry even in the presence of DNA damage. Forcing cells with damaged DNA into mitosis causes severe chromosome segregation defects, including lagging chromosomes, chromosomal fragments and chromosomal bridges. The presence of these lesions in the cleavage plane is believed to abort cytokinesis. It is postulated that if cytokinesis failure is coupled with defects of the p53-dependent postmitotic checkpoint pathway, cells can enter S phase and become polyploids. Progress in the past several years has unraveled some of the underlying principles of these pathways and underscored the important role of DNA damage in polyploidization. Furthermore, polyploidization per se may also be an important determinant of sensitivity to DNA damage, thereby may offer an opportunity for novel therapies.

  13. Predicting Coronal Mass Ejections Using Machine Learning Methods

    Bobra, M. G.; Ilonidis, S.

    2016-04-01

    Of all the activity observed on the Sun, two of the most energetic events are flares and coronal mass ejections (CMEs). Usually, solar active regions that produce large flares will also produce a CME, but this is not always true. Despite advances in numerical modeling, it is still unclear which circumstances will produce a CME. Therefore, it is worthwhile to empirically determine which features distinguish flares associated with CMEs from flares that are not. At this time, no extensive study has used physically meaningful features of active regions to distinguish between these two populations. As such, we attempt to do so by using features derived from (1) photospheric vector magnetic field data taken by the Solar Dynamics Observatory’s Helioseismic and Magnetic Imager instrument and (2) X-ray flux data from the Geostationary Operational Environmental Satellite’s X-ray Flux instrument. We build a catalog of active regions that either produced both a flare and a CME (the positive class) or simply a flare (the negative class). We then use machine-learning algorithms to (1) determine which features distinguish these two populations, and (2) forecast whether an active region that produces an M- or X-class flare will also produce a CME. We compute the True Skill Statistic, a forecast verification metric, and find that it is a relatively high value of ∼0.8 ± 0.2. We conclude that a combination of six parameters, which are all intensive in nature, will capture most of the relevant information contained in the photospheric magnetic field.

  14. Evolution of coronal mass ejections and their heliospheric imprints

    Rollett, T.

    2014-01-01

    Coronal mass ejections (CMEs) are the most powerful eruptions on the Sun and can reach speeds up to more than 3000 km/s. CMEs are the most important drivers of space weather and can cause geomagnetic storms when interacting with the Earth magnetosphere.The evolution and propagation of CMEs in interplanetary space is still not well understood. Interactions with the solar wind as well as other CMEs make accurate forecasting of arrival times difficult. The Constrained Harmonic Mean (CHM) method combines remote sensing white light data of STEREO/HI with in situ data and offers the possibility to derive kinematical profiles for any segment along the CME front to study its evolution in interplanetary space. We studied the influence of the ambient solar wind flow on the propagation behavior for three CME events. The kinematics revealed by the CHM method were compared to the simulated background solar wind. We found that CMEs are highly dependent on speed variations of the ambient medium. The CHM method was tested by analyzing a simulated CME as observed by STEREO/HI. After applying the CHM method, the resulting CME kinematics were compared to the real kinematics of the simulated CME. We found that the CHM method works best for small separation angles between the spacecraft. A case study of a fast CME that has been remotely observed by both STEREO/HI and in situ measured by four spacecraft at different heliocentric distances is also presented. Using this high number of in situ detections and the two side views we derived different speed profiles for the two different segments of the same CME causing a deformation of the overall structure of the CME. The studies presented show the effects of different influences of the ambient solar wind on the CME evolution. Interaction of CMEs with the solar wind or other CMEs lead to disturbances of the speed as well as the shape of CMEs, affecting their arrival time and their geoeffectivity. (author) [de

  15. Reproducibility of gallbladder ejection fraction measured by fatty meal cholescintigraphy

    Al-Muqbel, Kusai M.; Hani, M. N. Hani; Elheis, M. A.; Al-Omari, M. H.

    2010-01-01

    There are conflicting data in the literature regarding the reproducibility of the gallbladder ejection fraction (GBEF) measured by fatty meal cholescintigraphy (CS). We aimed to test the reproducibility of GBEF measured by fatty meal CS. Thirty-five subjects (25 healthy volunteers and 10 patients with chronic abdominal pain) underwent fatty meal CS twice in order to measure GBEF1 and GBEF2. The healthy volunteers underwent a repeat scan within 1-13 months from the first scan. The patients underwent a repeat scan within 1-4 years from the first scan and were not found to have chronic acalculous cholecystitis (CAC). Our standard fatty meal was composed of a 60-g Snickers chocolate bar and 200 ml full-fat yogurt. The mean ± SD values for GBEF1 and GBEF2 were 52±17% and 52±16%, respectively. There was a direct linear correlation between the values of GBEF1 and GBEF2 for the subjects, with a correlation coefficient of 0.509 (p=0.002). Subgroup data analysis of the volunteer group showed that there was significant linear correlation between volunteer values of GBEF1 and GBEF2, with a correlation coefficient of 0.473 (p=0.017). Subgroup data analysis of the non-CAC patient group showed no significant correlation between patient values of GBEF1 and GBEF2, likely due to limited sample size. This study showed that fatty meal CS is a reliable test in gallbladder motility evaluation and that GBEF measured by fatty meal CS is reproducible

  16. Reproducibility of gallbladder ejection fraction measured by fatty meal cholescintigraphy

    Al-Muqbel, Kusai M.; Hani, M. N. Hani; Elheis, M. A.; Al-Omari, M. H. [School of Medicine, Jordan University of Science and Technology, Irbid (Jordan)

    2010-12-15

    There are conflicting data in the literature regarding the reproducibility of the gallbladder ejection fraction (GBEF) measured by fatty meal cholescintigraphy (CS). We aimed to test the reproducibility of GBEF measured by fatty meal CS. Thirty-five subjects (25 healthy volunteers and 10 patients with chronic abdominal pain) underwent fatty meal CS twice in order to measure GBEF1 and GBEF2. The healthy volunteers underwent a repeat scan within 1-13 months from the first scan. The patients underwent a repeat scan within 1-4 years from the first scan and were not found to have chronic acalculous cholecystitis (CAC). Our standard fatty meal was composed of a 60-g Snickers chocolate bar and 200 ml full-fat yogurt. The mean {+-} SD values for GBEF1 and GBEF2 were 52{+-}17% and 52{+-}16%, respectively. There was a direct linear correlation between the values of GBEF1 and GBEF2 for the subjects, with a correlation coefficient of 0.509 (p=0.002). Subgroup data analysis of the volunteer group showed that there was significant linear correlation between volunteer values of GBEF1 and GBEF2, with a correlation coefficient of 0.473 (p=0.017). Subgroup data analysis of the non-CAC patient group showed no significant correlation between patient values of GBEF1 and GBEF2, likely due to limited sample size. This study showed that fatty meal CS is a reliable test in gallbladder motility evaluation and that GBEF measured by fatty meal CS is reproducible

  17. Coronal Mass Ejection Data Clustering and Visualization of Decision Trees

    Ma, Ruizhe; Angryk, Rafal A.; Riley, Pete; Filali Boubrahimi, Soukaina

    2018-05-01

    Coronal mass ejections (CMEs) can be categorized as either “magnetic clouds” (MCs) or non-MCs. Features such as a large magnetic field, low plasma-beta, and low proton temperature suggest that a CME event is also an MC event; however, so far there is neither a definitive method nor an automatic process to distinguish the two. Human labeling is time-consuming, and results can fluctuate owing to the imprecise definition of such events. In this study, we approach the problem of MC and non-MC distinction from a time series data analysis perspective and show how clustering can shed some light on this problem. Although many algorithms exist for traditional data clustering in the Euclidean space, they are not well suited for time series data. Problems such as inadequate distance measure, inaccurate cluster center description, and lack of intuitive cluster representations need to be addressed for effective time series clustering. Our data analysis in this work is twofold: clustering and visualization. For clustering we compared the results from the popular hierarchical agglomerative clustering technique to a distance density clustering heuristic we developed previously for time series data clustering. In both cases, dynamic time warping will be used for similarity measure. For classification as well as visualization, we use decision trees to aggregate single-dimensional clustering results to form a multidimensional time series decision tree, with averaged time series to present each decision. In this study, we achieved modest accuracy and, more importantly, an intuitive interpretation of how different parameters contribute to an MC event.

  18. PREDICTING CORONAL MASS EJECTIONS USING MACHINE LEARNING METHODS

    Bobra, M. G.; Ilonidis, S. [W.W. Hansen Experimental Physics Laboratory, Stanford University, Stanford, CA 94305 (United States)

    2016-04-20

    Of all the activity observed on the Sun, two of the most energetic events are flares and coronal mass ejections (CMEs). Usually, solar active regions that produce large flares will also produce a CME, but this is not always true. Despite advances in numerical modeling, it is still unclear which circumstances will produce a CME. Therefore, it is worthwhile to empirically determine which features distinguish flares associated with CMEs from flares that are not. At this time, no extensive study has used physically meaningful features of active regions to distinguish between these two populations. As such, we attempt to do so by using features derived from (1) photospheric vector magnetic field data taken by the Solar Dynamics Observatory ’s Helioseismic and Magnetic Imager instrument and (2) X-ray flux data from the Geostationary Operational Environmental Satellite’s X-ray Flux instrument. We build a catalog of active regions that either produced both a flare and a CME (the positive class) or simply a flare (the negative class). We then use machine-learning algorithms to (1) determine which features distinguish these two populations, and (2) forecast whether an active region that produces an M- or X-class flare will also produce a CME. We compute the True Skill Statistic, a forecast verification metric, and find that it is a relatively high value of ∼0.8 ± 0.2. We conclude that a combination of six parameters, which are all intensive in nature, will capture most of the relevant information contained in the photospheric magnetic field.

  19. Modeling DNA

    Robertson, Carol

    2016-01-01

    Deoxyribonucleic acid (DNA) is life's most amazing molecule. It carries the genetic instructions that almost every organism needs to develop and reproduce. In the human genome alone, there are some three billion DNA base pairs. The most difficult part of teaching DNA structure, however, may be getting students to visualize something as small as a…

  20. Femtosecond pulse-width dependent trapping and directional ejection dynamics of dielectric nanoparticles

    Chiang, Weiyi; Usman, Anwar; Masuhara, Hiroshi

    2013-01-01

    the repulsive and attractive forces. We also show that the directional ejections occur only when the number of nanoparticles confined in the trapping site exceeds a definite threshold. We interpret our data by considering the formation of transient assembly

  1. Improved Rock Core Sample Break-off, Retention and Ejection System, Phase I

    National Aeronautics and Space Administration — The proposed effort advances the design of an innovative core sampling and acquisition system with improved core break-off, retention and ejection features. The...

  2. Improved Rock Core Sample Break-off, Retention and Ejection System, Phase II

    National Aeronautics and Space Administration — The proposed effort advances the design of an innovative core sampling and acquisition system with improved core break-off, retention and ejection features. Phase 1...

  3. Relationships between egg-recognition and egg-ejection in a grasp-ejector species.

    Manuel Soler

    Full Text Available Brood parasitism frequently leads to a total loss of host fitness, which selects for the evolution of defensive traits in host species. Experimental studies have demonstrated that recognition and rejection of the parasite egg is the most common and efficient defence used by host species. Egg-recognition experiments have advanced our knowledge of the evolutionary and coevolutionary implications of egg recognition and rejection. However, our understanding of the proximate mechanisms underlying both processes remains poor. Egg rejection is a complex behavioural process consisting of three stages: egg recognition, the decision whether or not to reject the putative parasitic egg and the act of ejection itself. We have used the blackbird (Turdus merula as a model species to explore the relationship between egg recognition and the act of egg ejection. We have manipulated the two main characteristics of parasitic eggs affecting egg ejection in this grasp-ejector species: the degree of colour mimicry (mimetic and non-mimetic, which mainly affects the egg-recognition stage of the egg-rejection process and egg size (small, medium and large, which affects the decision to eject, while maintaining a control group of non-parasitized nests. The behaviour of the female when confronted with an experimental egg was filmed using a video camera. Our results show that egg touching is an indication of egg recognition and demonstrate that blackbirds recognized (i.e., touched non-mimetic experimental eggs significantly more than mimetic eggs. However, twenty per cent of the experimental eggs were touched but not subsequently ejected, which confirms that egg recognition does not necessarily mean egg ejection and that accepting parasitic eggs, at least sometimes, is the consequence of acceptance decisions. Regarding proximate mechanisms, our results show that the delay in egg ejection is not only due to recognition problems as usually suggested, given that experimental

  4. DNA cytosine methylation in the bovine leukemia virus promoter is associated with latency in a lymphoma-derived B-cell line: potential involvement of direct inhibition of cAMP-responsive element (CRE)-binding protein/CRE modulator/activation transcription factor binding.

    Pierard, Valérie; Guiguen, Allan; Colin, Laurence; Wijmeersch, Gaëlle; Vanhulle, Caroline; Van Driessche, Benoît; Dekoninck, Ann; Blazkova, Jana; Cardona, Christelle; Merimi, Makram; Vierendeel, Valérie; Calomme, Claire; Nguyên, Thi Liên-Anh; Nuttinck, Michèle; Twizere, Jean-Claude; Kettmann, Richard; Portetelle, Daniel; Burny, Arsène; Hirsch, Ivan; Rohr, Olivier; Van Lint, Carine

    2010-06-18

    Bovine leukemia virus (BLV) proviral latency represents a viral strategy to escape the host immune system and allow tumor development. Besides the previously demonstrated role of histone deacetylation in the epigenetic repression of BLV expression, we showed here that BLV promoter activity was induced by several DNA methylation inhibitors (such as 5-aza-2'-deoxycytidine) and that overexpressed DNMT1 and DNMT3A, but not DNMT3B, down-regulated BLV promoter activity. Importantly, cytosine hypermethylation in the 5'-long terminal repeat (LTR) U3 and R regions was associated with true latency in the lymphoma-derived B-cell line L267 but not with defective latency in YR2 cells. Moreover, the virus-encoded transactivator Tax(BLV) decreased DNA methyltransferase expression levels, which could explain the lower level of cytosine methylation observed in the L267(LTaxSN) 5'-LTR compared with the L267 5'-LTR. Interestingly, DNA methylation inhibitors and Tax(BLV) synergistically activated BLV promoter transcriptional activity in a cAMP-responsive element (CRE)-dependent manner. Mechanistically, methylation at the -154 or -129 CpG position (relative to the transcription start site) impaired in vitro binding of CRE-binding protein (CREB) transcription factors to their respective CRE sites. Methylation at -129 CpG alone was sufficient to decrease BLV promoter-driven reporter gene expression by 2-fold. We demonstrated in vivo the recruitment of CREB/CRE modulator (CREM) and to a lesser extent activating transcription factor-1 (ATF-1) to the hypomethylated CRE region of the YR2 5'-LTR, whereas we detected no CREB/CREM/ATF recruitment to the hypermethylated corresponding region in the L267 cells. Altogether, these findings suggest that site-specific DNA methylation of the BLV promoter represses viral transcription by directly inhibiting transcription factor binding, thereby contributing to true proviral latency.

  5. Right Ventricular Ejection Fraction using ECG-Gated First Pass Cardioangiography

    Moon, Young Hee; Lee, Hae Giu; Lee, Sung Yong; Park, Suk Min; Chung, Soo Kyo; Yim, Jeong Ik; Bahk, Yong Whee; Shinn, Kyung Sub; Kim, Young Gyun; Kwon, Soon Seog [Catholic University College of Medicine, Seoul (Korea, Republic of)

    1993-03-15

    Radionuclide cardioangiography has been widely applied and has played major roles in moninvasive assessment of cardiac function. Three techniques, first-pass gated first and gated equilibrium methods have commonly been used to evaluate right ventricular ejection fraction which usually abnormal in the patients with cardiopulmonary disease. It has been known that the gated first pass method is most accurate method among the three techniques in assessment of fight ventricular ejection fraction. The radionuclide right ventricular ejection fraction values were determined in 13 normal subjects and in 15 patients with chronic obstructive pulmonary disease by the gated first pass method and compared with those of the first pass method because there has been no published data of fight ejection fraction by the gated first pass method were compared with the defects from the pulmonary function test performed in the patients with chronic obstructive pulmomary disease. The results were as follows; 1) The values of fight ventricular ejection fraction by the gated first pass method were 50.1 +- 6.1% in normal subjects and 38.5 +- 8.5 in the patients with chronic obstructive pulmonary disease. There was statistically significant difference between the right ventricular ejection fraction of each of the two groups (p<0.05) 2) The right ventricular ejection fraction by the gated first pass method was not linearly correlated ith FEV{sub 1}, VC. DLCO. and FVC as well as P{sub a}O2 and P{sub a}CO2 of the patients with chronic obstructive pulmonary disease. We concluded that right ventricular ejection fraction by the gated first pass method using radionuclide cardioangiography may be useful in clinical assessment of the right ventricular function.

  6. The control system for the CERN proton synchrotron continuous transfer ejection

    Bloess, D.; Boucheron, J.; Flander, D.; Grier, D.; Krusche, A.; Ollenhauer, F.; Pearce, P.; Riege, H.; Schneider, G.C.

    1978-01-01

    This report describes the hardware and the software structure of a stand-alone control system for the continuous transfer ejection from the CERN Proton Synchrotron to the Super Proton Synchrotron. The process control system is built around a PDP 11/40 mini-computer interfaced to the ejection elements via CAMAC. It features automatic failure recovery and real-time process optimization. Performance, flexibility, and reliability of the system is evaluated. (Auth.)

  7. Overall performance assessment for scramjet with boundary-layer ejection control based on thermodynamics

    He, Yubao; Cao, Ruifeng; Huang, Hongyan; Qin, Jiang; Yu, Daren

    2017-01-01

    To avoid the inlet unstart at high equivalence ratio and increase the performance of scramjet with ram-mode, a flow control method of boundary-layer ejection is implemented based on the potential thermodynamic process in a turbo-pump supply system of fuel vapor within a cooling channel. The effect of ejection on overall scramjet performance is studied by taking the integration of measures including numerical simulation and stream thrust analysis. Results indicate that the critical backpressure is significantly increased as the ejection total pressure increased, thereby increasing the compression capacity and efficiency, and decreasing the irreversible losses of shock wave and viscous dissipation. For the ejection total pressure of P_t_,_e_j_e = 2.40–4.00 × 10"6 Pa, the critical backpressure ratio is quantitatively increased by 1.18–11.8% along with the utilization of ejection mass flow rate of about 88.0–100% overall mass flow rate of methane fuel gas, and simultaneously the total pressure ratio, kinetic efficiency is also increased by 7.32–13.1%, and 1.63–2.96%, respectively, while the dimensionless entropy increase is decreased by 14.5–26.8%. On this basis, the specific thrust, specific impulse, and total efficiency is increased by 2.84–4.69%, 2.80–4.68%, and 2.87–4.70%, respectively, which re-emphasizes that the boundary-layer ejection is an available fluid control method. - Highlights: • Pressure ratio affects cycle efficiency based on Brayton cycle analysis. • Ejection control concept is defined based on potential thermodynamic process. • Ejection increases compression capacity, efficiency and engine overall performance.

  8. Comparison of rod-ejection transient calculations in hexagonal-Z geometry

    Knight, M.P.; Brohan, P.; Finnemann, H.; Huesken, J.

    1995-01-01

    This paper proposes a set of 3-dimensional benchmark rod ejection problems for a VVER reactor, based on the well-known NEACRP PWR rod-ejection problems defined by Siemens/KWU. Predictions for these benchmarks derived using three hexagonal-z nodal transient codes, the PANTHER code of Nuclear Electric, the HEXTIME code of Siemens/KWU, and the DYN3D code of FZ-Rossendorf are presented and compared

  9. Assessment of poststress left ventricular ejection fraction by gated SPECT: comparison with equilibrium radionuclide angiocardiography

    Acampa, Wanda; Liuzzi, Raffaele; De Luca, Serena; Capasso, Enza; Luongo, Luca; Cuocolo, Alberto; Caprio, Maria Grazia; Nicolai, Emanuele; Petretta, Mario

    2010-01-01

    We compared left ventricular (LV) ejection fraction obtained by gated SPECT with that obtained by equilibrium radionuclide angiocardiography in a large cohort of patients. Within 1 week, 514 subjects with suspected or known coronary artery disease underwent same-day stress-rest 99m Tc-sestamibi gated SPECT and radionuclide angiocardiography. For both studies, data were acquired 30 min after completion of exercise and after 3 h rest. In the overall study population, a good correlation between ejection fraction measured by gated SPECT and by radionuclide angiocardiography was observed at rest (r=0.82, p<0.0001) and after stress (r=0.83, p<0.0001). In Bland-Altman analysis, the mean differences in ejection fraction (radionuclide angiocardiography minus gated SPECT) were -0.6% at rest and 1.7% after stress. In subjects with normal perfusion (n=362), a good correlation between ejection fraction measured by gated SPECT and by radionuclide angiocardiography was observed at rest (r=0.72, p<0.0001) and after stress (r=0.70, p<0.0001) and the mean differences in ejection fraction were -0.9% at rest and 1.4% after stress. Also in patients with abnormal perfusion (n=152), a good correlation between the two techniques was observed both at rest (r=0.89, p<0.0001) and after stress (r=0.90, p<0.0001) and the mean differences in ejection fraction were 0.1% at rest and 2.5% after stress. In a large study population, a good agreement was observed in the evaluation of LV ejection fraction between gated SPECT and radionuclide angiocardiography. However, in patients with perfusion abnormalities, a slight underestimation in poststress LV ejection fraction was observed using gated SPECT as compared to equilibrium radionuclide angiocardiography. (orig.)

  10. The survival of patients with heart failure with preserved or reduced left ventricular ejection fraction

    Boesgaard, Søren

    2012-01-01

    A substantial proportion of patients with heart failure have preserved left ventricular ejection fraction (HF-PEF). Previous studies have reported mixed results whether survival is similar to those patients with heart failure and reduced EF (HF-REF).......A substantial proportion of patients with heart failure have preserved left ventricular ejection fraction (HF-PEF). Previous studies have reported mixed results whether survival is similar to those patients with heart failure and reduced EF (HF-REF)....

  11. UV and ionizing radiations induced DNA damage, differences and similarities

    Ravanat, Jean-Luc; Douki, Thierry

    2016-11-01

    Both UV and ionizing radiations damage DNA. Two main mechanisms, so-called direct and indirect pathways, are involved in the degradation of DNA induced by ionizing radiations. The direct effect of radiation corresponds to direct ionization of DNA (one electron ejection) whereas indirect effects are produced by reactive oxygen species generated through water radiolysis, including the highly reactive hydroxyl radicals, which damage DNA. UV (and visible) light damages DNA by again two distinct mechanisms. UVC and to a lesser extend UVB photons are directly absorbed by DNA bases, generating their excited states that are at the origin of the formation of pyrimidine dimers. UVA (and visible) light by interaction with endogenous or exogenous photosensitizers induce the formation of DNA damage through photosensitization reactions. The excited photosensitizer is able to induce either a one-electron oxidation of DNA (type I) or to produce singlet oxygen (type II) that reacts with DNA. In addition, through an energy transfer from the excited photosensitizer to DNA bases (sometime called type III mechanism) formation of pyrimidine dimers could be produced. Interestingly it has been shown recently that pyrimidine dimers are also produced by direct absorption of UVA light by DNA, even if absorption of DNA bases at these wavelengths is very low. It should be stressed that some excited photosensitizers (such as psoralens) could add directly to DNA bases to generate adducts. The review will described the differences and similarities in terms of damage formation (structure and mechanisms) between these two physical genotoxic agents.

  12. Rollover Car Crashes with Ejection: A Deadly Combination—An Analysis of 719 Patients

    Rifat Latifi

    2014-01-01

    Full Text Available Rollover car crashes (ROCs are serious public safety concerns worldwide. Objective. To determine the incidence and outcomes of ROCs with or without ejection of occupants in the State of Qatar. Methods. A retrospective study of all patients involved in ROCs admitted to Level I trauma center in Qatar (2011-2012. Patients were divided into Group I (ROC with ejection and Group II (ROC without ejection. Results. A total of 719 patients were evaluated (237 in Group I and 482 in Group II. The mean age in Group I was lower than in Group II (24.3±10.3 versus 29±12.2; P=0.001. Group I had higher injury severity score and sustained significantly more head, chest, and abdominal injuries in comparison to Group II. The mortality rate was higher in Group I (25% versus 7%; P=0.001. Group I patients required higher ICU admission rate (P=0.001. Patients in Group I had a 5-fold increased risk for age-adjusted mortality (OR 5.43; 95% CI 3.11–9.49, P=0.001. Conclusion. ROCs with ejection are associated with higher rate of morbidity and mortality compared to ROCs without ejection. As an increased number of young Qatari males sustain ROCs with ejection, these findings highlight the need for research-based injury prevention initiatives in the country.

  13. Classification of the ejection mechanisms of charged macromolecules from liquid droplets.

    Consta, Styliani; Malevanets, Anatoly

    2013-01-28

    The relation between the charge state of a macromolecule and its ejection mechanism from droplets is one of the important questions in electrospray ionization methods. In this article, effects of solvent-solute interaction on the manifestation of the charge induced instability in a droplet are examined. We studied the instabilities in a prototype system of a droplet comprised of charged poly(ethylene glycol) and methanol, acetonitrile, and water solvents. We observed instances of three, previously only conjectured, [S. Consta, J. Phys. Chem. B 114, 5263 (2010)] mechanisms of macroion ejection. The mechanism of ejection of charged macroion in methanol is reminiscent of "pearl" model in polymer physics. In acetonitrile droplets, the instability manifests through formation of solvent spines around the solvated macroion. In water, we find that the macroion is ejected from the droplet through contiguous extrusion of a part of the chain. The difference in the morphology of the instabilities is attributed to the interplay between forces arising from the macroion solvation energy and the surface energy of the droplet interface. For the contiguous extrusion of a charged macromolecule from a droplet, we demonstrate that the proposed mechanism leads to ejection of the macromolecule from droplets with sizes well below the Rayleigh limit. The ejected macromolecule may hold charge significantly higher than that suggested by prevailing theories. The simulations reveal new mechanisms of macroion evaporation that differ from conventional charge residue model and ion evaporation mechanisms.

  14. Linear theory on temporal instability of megahertz faraday waves for monodisperse microdroplet ejection.

    Tsai, Shirley C; Tsai, Chen S

    2013-08-01

    A linear theory on temporal instability of megahertz Faraday waves for monodisperse microdroplet ejection based on mass conservation and linearized Navier-Stokes equations is presented using the most recently observed micrometer- sized droplet ejection from a millimeter-sized spherical water ball as a specific example. The theory is verified in the experiments utilizing silicon-based multiple-Fourier horn ultrasonic nozzles at megahertz frequency to facilitate temporal instability of the Faraday waves. Specifically, the linear theory not only correctly predicted the Faraday wave frequency and onset threshold of Faraday instability, the effect of viscosity, the dynamics of droplet ejection, but also established the first theoretical formula for the size of the ejected droplets, namely, the droplet diameter equals four-tenths of the Faraday wavelength involved. The high rate of increase in Faraday wave amplitude at megahertz drive frequency subsequent to onset threshold, together with enhanced excitation displacement on the nozzle end face, facilitated by the megahertz multiple Fourier horns in resonance, led to high-rate ejection of micrometer- sized monodisperse droplets (>10(7) droplets/s) at low electrical drive power (<;1 W) with short initiation time (<;0.05 s). This is in stark contrast to the Rayleigh-Plateau instability of a liquid jet, which ejects one droplet at a time. The measured diameters of the droplets ranging from 2.2 to 4.6 μm at 2 to 1 MHz drive frequency fall within the optimum particle size range for pulmonary drug delivery.

  15. ON SUN-TO-EARTH PROPAGATION OF CORONAL MASS EJECTIONS

    Liu, Ying D.; Luhmann, Janet G.; Möstl, Christian; Bale, Stuart D.; Lin, Robert P.; Lugaz, Noé; Davies, Jackie A.

    2013-01-01

    We investigate how coronal mass ejections (CMEs) propagate through, and interact with, the inner heliosphere between the Sun and Earth, a key question in CME research and space weather forecasting. CME Sun-to-Earth kinematics are constrained by combining wide-angle heliospheric imaging observations, interplanetary radio type II bursts, and in situ measurements from multiple vantage points. We select three events for this study, the 2012 January 19, 23, and March 7 CMEs. Different from previous event studies, this work attempts to create a general picture for CME Sun-to-Earth propagation and compare different techniques for determining CME interplanetary kinematics. Key results are obtained concerning CME Sun-to-Earth propagation: (1) the Sun-to-Earth propagation of fast CMEs can be approximately formulated into three phases: an impulsive acceleration, then a rapid deceleration, and finally a nearly constant speed propagation (or gradual deceleration); (2) the CMEs studied here are still accelerating even after the flare maximum, so energy must be continuously fed into the CME even after the time of the maximum heating and radiation has elapsed in the corona; (3) the rapid deceleration, presumably due to interactions with the ambient medium, mainly occurs over a relatively short timescale following the acceleration phase; and (4) CME-CME interactions seem a common phenomenon close to solar maximum. Our comparison between different techniques (and data sets) has important implications for CME observations and their interpretations: (1) for the current cases, triangulation assuming a compact CME geometry is more reliable than triangulation assuming a spherical front attached to the Sun for distances below 50-70 solar radii from the Sun, but beyond about 100 solar radii we would trust the latter more; (2) a proper treatment of CME geometry must be performed in determining CME Sun-to-Earth kinematics, especially when the CME propagation direction is far away from the

  16. DNA methylation and memory formation.

    Day, Jeremy J; Sweatt, J David

    2010-11-01

    Memory formation and storage require long-lasting changes in memory-related neuronal circuits. Recent evidence indicates that DNA methylation may serve as a contributing mechanism in memory formation and storage. These emerging findings suggest a role for an epigenetic mechanism in learning and long-term memory maintenance and raise apparent conundrums and questions. For example, it is unclear how DNA methylation might be reversed during the formation of a memory, how changes in DNA methylation alter neuronal function to promote memory formation, and how DNA methylation patterns differ between neuronal structures to enable both consolidation and storage of memories. Here we evaluate the existing evidence supporting a role for DNA methylation in memory, discuss how DNA methylation may affect genetic and neuronal function to contribute to behavior, propose several future directions for the emerging subfield of neuroepigenetics, and begin to address some of the broader implications of this work.

  17. Re-wiring of energy metabolism promotes viability during hyperreplication stress in E. coli

    Charbon, Godefroid; Campion, Christopher; Chan, Siu Hung Joshua

    2017-01-01

    Chromosome replication in Escherichia coli is initiated by DnaA. DnaA binds ATP which is essential for formation of a DnaA-oriC nucleoprotein complex that promotes strand opening, helicase loading and replisome assembly. Following initiation, DnaAATP is converted to DnaAADP primarily by the Regul......Chromosome replication in Escherichia coli is initiated by DnaA. DnaA binds ATP which is essential for formation of a DnaA-oriC nucleoprotein complex that promotes strand opening, helicase loading and replisome assembly. Following initiation, DnaAATP is converted to DnaAADP primarily...

  18. Coronal Mass Ejections: a Summary of Recent Results

    Gopalswamy, Nat; Davila, J. M.

    2010-01-01

    Coronal mass ejections (CMEs) have been recognized as the most energetic phenomenon in the heliosphere, deriving their energy from the stressed magnetic fields on the Sun. This paper highlights some of the recent results on CMEs obtained from the Solar and Heliospheric Observatory (SOHO) and the Solar Terrestrial Relations Observatory (STEREO) missions. The summary of the talk follows. SOHO observations revealed that the CME rate is almost a factor of two larger than previously thought and varied with the solar activity cycle in a complex way (e.g., high-latitude CMEs occurred in great abundance during the solar maximum years). CMEs were found to interact with other CMEs as well as with other large-scale structures (coronal holes), resulting in deflections and additional particle acceleration. STEREO observations have confirmed the three-dimensional nature of CMEs and the shocks surrounding them. The EUV signatures (flare arcades, corona) dimming, filament eruption, and EUV waves) associated with CMEs have become vital in the identification of solar sources from which CMEs erupt. CMEs with speeds exceeding the characteristic speeds of the corona and the interplanetary medium drive shocks, which produce type II radio bursts. The wavelength range of type II bursts depends on the CME kinetic energy: type II bursts with emission components at all wavelengths (metric to kilometric) are due to CMEs of the highest kinetic energy. Some CMEs, as fast as 1600 km/s do not produce type II bursts, while slow CMEs (400 km/s) occasionally produce type II bursts. These observations can be explained as the variation in the ambient flow speed (solar wind) and the Alfven speed. Not all CME-driven shocks produce type II bursts because either they are subcritical or do not have the appropriate geometry. The same shocks that produce type II bursts also produce solar energetic particles (SEPs), whose release near the Sun seems to be delayed with respect to the onset of type II bursts

  19. Coronal mass ejections, interplanetary shocks in relation with forbush decreases associated with intense geomagnetic storms

    Verma, P L; Patel, Nand Kumar; Prajapati, Mateswari

    2014-01-01

    Coronal mass ejections (CMEs} are the most energetic solar events in which large amount of solar plasma materials are ejected from the sun into heliosphere, causing major disturbances in solar wind plasma, Interplanetary shocks, Forbush decrease(Fds) in cosmic ray intensity and geomagnetic storms. We have studied Forbush decreases associated with intense geomagnetic storms observed at Oulu super neutron monitor, during the period of May 1998-Dec 2006 with coronal mass ejections (CMEs), X-ray solar flares and interplanetary shocks. We have found that all the (100%) Forbush decreases associated with intense geomagnetic storms are associated with halo and partial halo coronal mass ejections (CMEs). The association rate between halo and partial halo coronal mass ejections are found 96.00%and 04.00% respectively. Most of the Forbush decreases associated with intense geomagnetic storms (96.29%) are associated with X-ray solar flares of different categories . The association rates for X-Class, M-Class, and C- Class X -ray solar flares are found 34.62%, 50.00% and 15.38% respectively .Further we have concluded that majority of the Forbush decrease associated with intense geomagnetic storms are related to interplanetary shocks (92.30 %) and the related shocks are forward shocks. We have found positive co-relation with co-relation co-efficient .7025 between magnitudes of Forbush decreases associated with intense geomagnetic storms and speed of associated coronal mass ejections. Positive co-relation with co-relation co-efficient 0.48 has also been found between magnitudes of intense geomagnetic storms and speed of associated coronal mass ejections.

  20. Insights into the quality of DnaA boxes and their cooperativity

    Hansen, Flemming G.; Christensen, Bjarke Bak; Nielsen, Christina Bang

    2006-01-01

    Plasmids carrying the mioC promoter region with its two DnaA boxes are as efficient in titration of DnaA protein as plasmids carrying a replicationinactivated oriC region with its five DnaA boxes. The two DnaA boxes upstream of the mioC promoter were mutated in various ways to study the cooperati......Plasmids carrying the mioC promoter region with its two DnaA boxes are as efficient in titration of DnaA protein as plasmids carrying a replicationinactivated oriC region with its five DnaA boxes. The two DnaA boxes upstream of the mioC promoter were mutated in various ways to study...... the cooperativity between the DnaA boxes, and to study in vivo the in vitrodefined 9mer DnaA box consensus sequence TTA/TTNCACA). The quality and cooperativity of the DnaA oxes were determined in two complementary ways: as titration of DnaA protein leading to derepression of the dnaA promoter, and as repression...... of the mioC promoter caused by the DnaA protein binding to the DnaA boxes. Titration of DnaA protein correlated with repression of the mioC promoter. The level of titration and repression with the normal promoter-proximal box (TTTTCCACA) depends strongly on the presence and the quality of a DnaA box...

  1. DNA Camouflage

    2016-01-08

    1 DNA Camouflage Supplementary Information Bijan Zakeri1,2*, Timothy K. Lu1,2*, Peter A. Carr2,3* 1Department of Electrical Engineering and...ll.mit.edu). Distribution A: Public Release   2 Supplementary Figure 1 DNA camouflage with the 2-state device. (a) In the presence of Cre, DSD-2[α...10 1 + Cre 1 500 1,000 length (bp) chromatogram alignment template − Cre   4 Supplementary Figure 3 DNA camouflage with a switchable

  2. Promoter scanning of the human COX-2 gene with 8-ring polyamides: unexpected weakening of polyamide-DNA binding and selectivity by replacing an internal N-Me-pyrrole with β-alanine.

    Bashkin, James K; Aston, Karl; Ramos, Joseph P; Koeller, Kevin J; Nanjunda, Rupesh; He, Gaofei; Dupureur, Cynthia M; David Wilson, W

    2013-02-01

    Rules for polyamide-DNA recognition have proved invaluable for the design of sequence-selective DNA binding agents in cell-free systems. However, these rules are not fully transferrable to predicting activity in cells, tissues or animals, and additional refinements to our understanding of DNA recognition would help biomedical studies. Similar complexities are encountered when using internal β-alanines as polyamide building blocks in place of N-methylpyrrole; β-alanines were introduced in polyamide designs to maintain good hydrogen bonding registry with the target DNA, especially for long polyamides or those with several GC bp (P.B. Dervan, A.R. Urbach, Essays Contemp. Chem. (2001) 327-339). Thus, to clarify important subtleties of molecular recognition, we studied the effects of replacing a single pyrrole with β-alanine in 8-ring polyamides designed against the Ets-1 transcription factor. Replacement of a single internal N-methylpyrrole with β-alanine to generate a β/Im pairing in two 8-ring polyamides causes a decrease in DNA binding affinity by two orders of magnitude and decreases DNA binding selectivity, contrary to expectations based on the literature. Measurements were made by fluorescence spectroscopy, quantitative DNA footprinting and surface plasmon resonance, with these vastly different techniques showing excellent agreement. Furthermore, results were validated for a range of DNA substrates from small hairpins to long dsDNA sequences. Docking studies helped show that β-alanine does not make efficient hydrophobic contacts with the rest of the polyamide or nearby DNA, in contrast to pyrrole. These results help refine design principles and expectations for polyamide-DNA recognition. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  3. Activity associated with coronal mass ejections at solar minimum - SMM observations from 1984-1986

    St. Cyr, O. C.; Webb, D. F.

    1991-01-01

    Seventy-three coronal mass ejections (CMEs) observed by the coronagraph aboard SMM between 1984 and 1986 were examined in order to determine the distribution of various forms of solar activity that were spatially and temporally associated with mass ejections during solar minimum phase. For each coronal mass ejection a speed was measured, and the departure time of the transient from the lower corona estimated. Other forms of solar activity that appeared within 45 deg longitude and 30 deg latitude of the mass ejection and within +/-90 min of its extrapolated departure time were explored. The statistical results of the analysis of these 73 CMEs are presented, and it is found that slightly less than half of them were infrequently associated with other forms of solar activity. It is suggested that the distribution of the various forms of activity related to CMEs does not change at different phases of the solar cycle. For those CMEs with associations, it is found that eruptive prominences and soft X-rays were the most likely forms of activity to accompany the appearance of mass ejections.

  4. Beat-to-beat assessment of left ventricular ejection in atrial fibrillation

    Benjelloun, H; Brochier, M; Itti, R; Philippe, L; Lorgeron, J M

    1983-05-01

    Beat-to-beat left ventricular ejection was evaluated in a group of 20 patients with chronic atrial fibrillation using a computerized single probe detector. The reference group consisted of 10 patients with sinus rhythm. For each patient 30 successive cardiac cycles were analyzed and the relative variations of four parameters were assessed: R-R interval, diastolic and systolic time intervals, and ejection amplitude, corresponding to the left ventricular stroke volume. The mean variations were respectively 3.4%, 10.4%, 8.4%, and 11.8% in patients with sinus rhythm, and 21.9%, 37.9%, 10.6% and 30.5% in patients with artrial fibrillation. This demonstrates that changes in ejection are mainly related to the duration of the filling phase, with nearly constant systolic times. Correlations between R-R intervals and systolic ejection amplitudes were highly significant (P<0.001) in patients with atrial fibrillation in 85% of cases. This information complements the average ejection fraction obtained from multiple cycle superimposition.

  5. Regional ejection fraction: a quantitative radionuclide index of regional left ventricular performance

    Maddox, D.E.; Wynne, J.; Uren, R.; Parker, J.A.; Idoine, J.; Siegel, L.C.; Neill, J.M.; Cohn, P.F.; Holman, B.L.

    1979-01-01

    Left ventricular regional ejection fractions were derived from background-corrected, time-activity curves in 43 patients assessed by both gated equilibrium radionuclide angiocardiography and left ventricular contrast angiography. From a single, modified left anterior oblique projection, the regional change in background corrected counts was determined in each of three anatomic regions. The normal range for regional radionuclide ejection fraction was determined in 10 patients with normal contrast ventriculograms and without obstructive coronary artery disease at coronary arteriography. Regional ejection fraction was compared with percent segmental axis shortening and extent of akinetic segments in corresponding regions of the contrast ventriculogram. Radionuclide and roentgenographic methods were in agreement as to the presence or absence of abnormal wall motion in 83 of 99 left ventricular regions (84%) in 33 patients evaluated prospectively. Comparison of regional ejection fraction demonstrated significant differences between regions with roentgenographically determined normokinesis hypokinesis, and akinesis. We conclude that the left ventricular regional ejection fraction provides a reliable quantitative assessment of regional left ventricular performance

  6. Beat-to-beat assessment of left ventricular ejection in atrial fibrillation

    Benjelloun, H.; Brochier, M.; Itti, R.; Philippe, L.; Lorgeron, J.M.

    1983-01-01

    Beat-to-beat left ventricular ejection was evaluated in a group of 20 patients with chronic atrial fibrillation using a computerized single probe detector. The reference group consisted of 10 patients with sinus rhythm. For each patient 30 successive cardiac cycles were analyzed and the relative variations of four parameters were assessed: R-R interval, diastolic and systolic time intervals, and ejection amplitude, corresponding to the left ventricular stroke volume. The mean variations were respectively 3.4%, 10.4%, 8.4%, and 11.8% in patients with sinus rhythm, and 21.9%, 37.9%, 10.6% and 30.5% in patients with artrial fibrillation. This demonstrates that changes in ejection are mainly related to the duration of the filling phase, with nearly constant systolic times. Correlations between R-R intervals and systolic ejection amplitudes were highly significant (P<0.001) in patients with atrial fibrillation in 85% of cases. This information complements the average ejection fraction obtained from multiple cycle superimposition. (orig.)

  7. A three-dimensional pin-wise analysis for CEA ejection accident

    Park, Guen-Tae; Park, Min-Ho; Park, Jin-Woo; Um, Kil-Sup; Choi, Tong-Soo [KEPCO NF, Daejeon (Korea, Republic of)

    2016-10-15

    The ejection of a control element assembly (CEA) with high reactivity worth causes the sudden insertion of reactivity into the core. Immediately after the CEA ejection, the nuclear power of the reactor dramatically increases in an exponential behavior until the doppler effect becomes important and turns the reactivity balance and power down to lower levels. The 3-D CEA ejection analysis methodology has been developed using the multi-dimensional code coupling system, CHASER, which couples three dimensional core neutron kinetics code ASTRA, subchannel analysis code THALES, and fuel performance analysis code FROST using message passing interface (MPI). This paper presents the pin-by-pin level analysis result with the 3-D CEA ejection analysis methodology using the CHASER. The pin-by-pin level analysis consists of DNBR, enthalpy and Pellet/Clad Mechanical Interaction (PCMI) analysis. All the evaluations are simulated for APR1400 plant loaded with PLUS7 fuel. In this paper, the pin-by-pin analysis using the multidimensional core transient code, CHASER, is presented with respect to enthalpy, DNBR and PCMI for APR1400 plant loaded with PLUS7 fuel. For the pin-by-pin enthalpy and DNBR analysis, the quarter core for HFP case or 15 - 20 assemblies around the most severe assembly for part powers or HZP cases are selected. And PCMI calculation is performed for all the rods in the whole core during a conservative time period. The pin-by-pin analysis results show that the regulatory guidelines of CEA ejection accident are satisfied.

  8. Ejection dynamics of hydrogen molecular ions from methanol in intense laser fields

    Okino, T; Furukawa, Y; Liu, P; Ichikawa, T; Itakura, R; Hoshina, K; Yamanouchi, K; Nakano, H

    2006-01-01

    The ejection of hydrogen molecular ions from two-body Coulomb explosion processes of methanol (CH 3 OH, CD 3 OH and CH 3 OD) in an intense laser field (800 nm, 60 fs, 0.2 PW cm -2 ) is investigated by a coincidence momentum imaging method. From the coincidence momentum maps, the ejection processes of hydrogen molecular ions, CH 3 OH 2+ → H m + + CH (3-m) OH + (m = 2, 3), CD 3 OH 2+ → D m + + CH (3-m) OH + (m = 2, 3) and CH 3 OD 2+ → H m + + CH (3-m) OD + (m = 2, 3), are identified. Based on the results obtained with isotopically substituted methanol, the isotope effect on the ejection process of hydrogen molecular ions is discussed. Furthermore, the ejection of H/D exchanged hydrogen molecular ions (HD + , HD 2 + and H 2 D + ) is identified, and the timescales for the H/D exchanging processes are estimated from the extent of anisotropy in the ejection directions

  9. THE NATURE OF HYPERVELOCITY STARS AND THE TIME BETWEEN THEIR FORMATION AND EJECTION

    Brown, Warren R.; Geller, Margaret J.; Kenyon, Scott J. [Smithsonian Astrophysical Observatory, 60 Garden Street, Cambridge, MA 02138 (United States); Cohen, Judith G., E-mail: wbrown@cfa.harvard.edu, E-mail: mgeller@cfa.harvard.edu, E-mail: skenyon@cfa.harvard.edu, E-mail: jlc@astro.caltech.edu [Palomar Observatory, Mail Stop 249-17, California Institute of Technology, Pasadena, CA 91125 (United States)

    2012-07-20

    We obtain Keck HIRES spectroscopy of HVS5, one of the fastest unbound stars in the Milky Way halo. We show that HVS5 is a 3.62 {+-} 0.11 M{sub Sun} main-sequence B star at a distance of 50 {+-} 5 kpc. The difference between its age and its flight time from the Galactic center is 105 {+-} 18 (stat) {+-}30 (sys) Myr; flight times from locations elsewhere in the Galactic disk are similar. This 10{sup 8} yr 'arrival time' between formation and ejection is difficult to reconcile with any ejection scenario involving massive stars that live for only 10{sup 7} yr. For comparison, we derive arrival times of 10{sup 7} yr for two unbound runaway B stars, consistent with their disk origin where ejection results from a supernova in a binary system or dynamical interactions between massive stars in a dense star cluster. For HVS5, ejection during the first 10{sup 7} yr of its lifetime is ruled out at the 3{sigma} level. Together with the 10{sup 8} yr arrival times inferred for three other well-studied hypervelocity stars (HVSs), these results are consistent with a Galactic center origin for the HVSs. If the HVSs were indeed ejected by the central black hole, then the Galactic center was forming stars {approx_equal}200 Myr ago, and the progenitors of the HVSs took {approx_equal}100 Myr to enter the black hole's loss cone.

  10. THE NATURE OF HYPERVELOCITY STARS AND THE TIME BETWEEN THEIR FORMATION AND EJECTION

    Brown, Warren R.; Geller, Margaret J.; Kenyon, Scott J.; Cohen, Judith G.

    2012-01-01

    We obtain Keck HIRES spectroscopy of HVS5, one of the fastest unbound stars in the Milky Way halo. We show that HVS5 is a 3.62 ± 0.11 M ☉ main-sequence B star at a distance of 50 ± 5 kpc. The difference between its age and its flight time from the Galactic center is 105 ± 18 (stat) ±30 (sys) Myr; flight times from locations elsewhere in the Galactic disk are similar. This 10 8 yr 'arrival time' between formation and ejection is difficult to reconcile with any ejection scenario involving massive stars that live for only 10 7 yr. For comparison, we derive arrival times of 10 7 yr for two unbound runaway B stars, consistent with their disk origin where ejection results from a supernova in a binary system or dynamical interactions between massive stars in a dense star cluster. For HVS5, ejection during the first 10 7 yr of its lifetime is ruled out at the 3σ level. Together with the 10 8 yr arrival times inferred for three other well-studied hypervelocity stars (HVSs), these results are consistent with a Galactic center origin for the HVSs. If the HVSs were indeed ejected by the central black hole, then the Galactic center was forming stars ≅200 Myr ago, and the progenitors of the HVSs took ≅100 Myr to enter the black hole's loss cone.

  11. Extracting and analyzing ejection fraction values from electronic echocardiography reports in a large health maintenance organization.

    Xie, Fagen; Zheng, Chengyi; Yuh-Jer Shen, Albert; Chen, Wansu

    2017-12-01

    The left ventricular ejection fraction value is an important prognostic indicator of cardiovascular outcomes including morbidity and mortality and is often used clinically to indicate severity of heart disease. However, it is usually reported in free-text echocardiography reports. We developed and validated a computerized algorithm to extract ejection fraction values from echocardiography reports and applied the algorithm to a large volume of unstructured echocardiography reports between 1995 and 2011 in a large health maintenance organization. A total of 621,856 echocardiography reports with a description of ejection fraction values or systolic functions were identified, of which 70 percent contained numeric ejection fraction values and the rest (30%) were text descriptions explicitly indicating the systolic left ventricular function. The 12.1 percent (16.0% for male and 8.4% for female) of these extracted ejection fraction values are <45 percent. Validation conducted based on a random sample of 200 reports yielded 95.0 percent sensitivity and 96.9 percent positive predictive value.

  12. DNA glue

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.

    2008-01-01

    Significant alterations in thermal stability of parallel DNA triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in the structure of phenylmethylglycerol inserted as a bulge into DNA (TINA). Insertions of two ortho-TINAs as a pseudo...

  13. Hyperstretching DNA

    Schakenraad, Koen; Biebricher, Andreas S.; Sebregts, Maarten; Ten Bensel, Brian; Peterman, Erwin J.G.; Wuite, Gijs J L; Heller, Iddo; Storm, Cornelis; Van Der Schoot, Paul

    2017-01-01

    The three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro. In particular, large increases in base pair spacing compared to regular B-DNA are effected by mechanical (over)stretching and by intercalation of compounds that are widely

  14. Nest Sanitation as the Evolutionary Background for Egg Ejection Behaviour and the Role of Motivation for Object Removal

    Pol??ek, Miroslav; Griggio, Matteo; Bart?kov?, Michaela; Hoi, Herbert

    2013-01-01

    Higher interclutch colour variation can evolve under the pressure of brood parasitism to increase the detection of parasitic eggs. Nest sanitation could be a prerequisite for the evolution of anti-parasite defence in terms of egg ejection. In this respect, we used nest sanitation behaviour as a tool to identify: i) motivation and its underlying function and, ii) which features provoke ejection behaviour. Therefore, we experimentally tested whether size, colour or shape may influence ejection ...

  15. Anti-ejection device, which can be released, for control rods of nuclear reactor

    Belz, G.

    1983-01-01

    The present invention proposes an anti-ejection device which allows to withdraw the control rod out of a PWR reactor core if the locking systems of the rod translation are streck. This device prohibits the control rod ejection as long as an effort lower than a predetermined value is not applied on the control rod. This limit value is determined with regard of the efforts which may be applied on the control rod in case of an external accidental source. Nevertheless, if the anti-ejection mechanism remains stuck, it is however possible to withdraw the control rod out of the core applying on its control rod drives an effort higher than the limit value [fr

  16. Geomagnetic response of interplanetary coronal mass ejections in the Earth's magnetosphere

    Badruddin; Mustajab, F.; Derouich, M.

    2018-05-01

    A coronal mass ejections (CME) is the huge mass of plasma with embedded magnetic field ejected abruptly from the Sun. These CMEs propagate into interplanetary space with different speed. Some of them hit the Earth's magnetosphere and create many types of disturbances; one of them is the disturbance in the geomagnetic field. Individual geomagnetic disturbances differ not only in their magnitudes, but the nature of disturbance is also different. It is, therefore, desirable to understand these differences not only to understand the physics of geomagnetic disturbances but also to understand the properties of solar/interplanetary structures producing these disturbances of different magnitude and nature. In this work, we use the spacecraft measurements of CMEs with distinct magnetic properties propagating in the interplanetary space and generating disturbances of different levels and nature. We utilize their distinct plasma and field properties to search for the interplanetary parameter(s) playing important role in influencing the geomagnetic response of different coronal mass ejections.

  17. A study of stresses in powder compacted components during and after ejection

    Redanz, Pia

    2001-01-01

    A finite strain finite element method is used to examine the residual stresses in a cup-shaped powder compact. Two rate-independent strain hardening porous material models are used: the combined material model (Fleck, N.A., Kuhn, L.T., McMeeking, R.M., 1992a. J. Mech. Phys. Solids 40 (5), 1139......-1162) and a material model which includes the dependency of inter-particle cohesive strength (Fleck, N.A., 1995. J. Mech. Phys. Solids 43, 1409-1431). The residual stress state in the unloaded cup is highly dependent on the compaction process and less dependent on the ejection route. The maximum principal stress...... plotted during ejection shows that higher stresses are found during the ejection process than those found in the completely unloaded specimen. The degree of inter-particle cohesive strength has hardly any effect on the porosity distributions in the compacts but it has a strong influence on the stress...

  18. Influence of edge conditions on material ejection from periodic grooves in laser shock-loaded tin

    Rességuier, T. de; Roland, C. [Institut PPRIME, UPR 3346, CNRS, ENSMA, Université de Poitiers, 1 ave. Clément Ader, 86961 Futuroscope Cedex (France); Prudhomme, G.; Lescoute, E.; Mercier, P. [CEA, DAM, DIF, 91297 Arpajon (France); Loison, D. [Institut de Physique de Rennes, CNRS, Université de Rennes 1, 35042 Rennes (France)

    2016-05-14

    In a material subjected to high dynamic compression, the breakout of a shock wave at a rough free surface can lead to the ejection of high velocity debris. Anticipating the ballistic properties of such debris is a key safety issue in many applications involving shock loading, including pyrotechnics and inertial confinement fusion experiments. In this paper, we use laser driven shocks to investigate particle ejection from calibrated grooves of micrometric dimensions and approximately sinusoidal profile in tin samples, with various boundary conditions at the groove edges, including single groove and periodic patterns. Fast transverse shadowgraphy provides ejection velocities after shock breakout. They are found to depend not only on the groove depth and wavelength, as predicted theoretically and already observed in the past, but also, unexpectedly, on the edge conditions, with a jet tip velocity significantly lower in the case of a single groove than behind a periodic pattern.

  19. Some elements of understanding about the cluster ejection accident in the EPR

    Vignon, Dominique

    2010-01-01

    The author answers to a publication made by an association (Sortir du Nucleaire) which is provided in appendix (some parts of this text are highlighted) and denounced risks associated with a cluster ejection accident in an EPR in relationship with steering modes which, according to this association, would be essentially related to an objective of economic profitability. The author first recalls some elements regarding the control and neutron stopping of pressurized water reactors. Then, after having outlined some specific aspects of the EPR design, he addresses the cluster ejection accident: safety approach and its application to this type of accident. He recalls the conclusions of studies of cluster ejection performed by EDF and AREVA, comments the consequences for the EPR power

  20. Gravitational wave generated by mass ejection in protoneutron star neutrino burst

    Almeida, L. G.; Rodrigues, H.; Portes, D. JR.; Duarte, S. B.

    2010-01-01

    In this work we discuss the mechanism of mass ejection in protoneutron stars induced by diffusion of neutrinos. A dynamical calculation is employed in order to determine the amount of matter ejected and the properties of the remnant compact object [1]. The equations of state of this supra-nuclear regime [2] is properly linked with others describing the different sub-nuclear regimes of density [3, 4, 5]. For specified initial configurations of the protoneutron star, we solve numerically the set of equations of motion together with a schematic treatment of the neutrino transport through the dense stellar medium. We investigate the gravitational waves production accompanying the mass ejection induced by the neutrino burst. It is estimated the gravitational wave intensity and the detection of such wave by the existing detector or near future project for this purpose is discussed.

  1. Synergistic effects in radiation-induced particle ejection from solid surfaces

    Itoh, Noriaki

    1990-01-01

    A description is given on radiation-induced particle ejection from solid surfaces, emphasizing synergistic effects arising from multi-species particle irradiation and from irradiation under complex environments. First, it is pointed out that synergisms can be treated by introducing the effects of material modification on radiation-induced particle ejection. As examples of the effects of surface modification on the sputtering induced by elastic encounters, sputtering of alloys and chemical sputtering of graphite are briefly discussed. Then the particle ejection induced by electronic encounters is explained emphasizing the difference in the behaviors from materials to materials. The possible synergistic effects of electronic and elastic encounters are also described. Lastly, we point out the importance of understanding the elementary processes of material-particle interaction and of developing computer codes describing material behaviors under irradiation. (author)

  2. ISAAC: A REXUS Student Experiment to Demonstrate an Ejection System with Predefined Direction

    Balmer, G.; Berquand, A.; Company-Vallet, E.; Granberg, V.; Grigore, V.; Ivchenko, N.; Kevorkov, R.; Lundkvist, E.; Olentsenko, G.; Pacheco-Labrador, J.; Tibert, G.; Yuan, Y.

    2015-09-01

    ISAAC Infrared Spectroscopy to Analyse the middle Atmosphere Composition — was a student experiment launched from SSC's Esrange Space Centre, Sweden, on 29th May 2014, on board the sounding rocket REXUS 15 in the frame of the REXUS/BEXUS programme. The main focus of the experiment was to implement an ejection system for two large Free Falling Units (FFUs) (240 mm x 80 mm) to be ejected from a spinning rocket into a predefined direction. The system design relied on a spring-based ejection system. Sun and angular rate sensors were used to control and time the ejection. The flight data includes telemetry from the Rocket Mounted Unit (RMU), received and saved during flight, as well as video footage from the GoPro camera mounted inside the RMU and recovered after the flight. The FFUs' direction, speed and spin frequency as well as the rocket spin frequency were determined by analyzing the video footage. The FFU-Rocket-Sun angles were 64.3° and 104.3°, within the required margins of 90°+45°. The FFU speeds were 3.98 mIs and 3.74 mIs, lower than the expected 5± 1 mIs. The FFUs' spin frequencies were 1 .38 Hz and 1 .60 Hz, approximately half the rocket's spin frequency. The rocket spin rate slightly changed from 3. 163 Hz before the ejection to 3.1 17 Hz after the ejection of the two FFUs. The angular rate, sun sensor data and temperature on the inside of the rocket module skin were also recorded. The experiment design and results of the data analysis are presented in this paper.

  3. Coronal mass ejections and disturbances in solar wind plasma parameters in relation with geomagnetic storms

    Verma, P L; Singh, Puspraj; Singh, Preetam

    2014-01-01

    Coronal Mass Ejections (CMEs) are the drastic solar events in which huge amount of solar plasma materials are ejected into the heliosphere from the sun and are mainly responsible to generate large disturbances in solar wind plasma parameters and geomagnetic storms in geomagnetic field. We have studied geomagnetic storms, (Dst ≤-75 nT) observed during the period of 1997-2007 with Coronal Mass Ejections and disturbances in solar wind plasma parameters (solar wind temperature, velocity, density and interplanetary magnetic field) .We have inferred that most of the geomagnetic storms are associated with halo and partial halo Coronal Mass Ejections (CMEs).The association rate of halo and partial halo coronal mass ejections are found 72.37 % and 27.63 % respectively. Further we have concluded that geomagnetic storms are closely associated with the disturbances in solar wind plasma parameters. We have determined positive co-relation between magnitudes of geomagnetic storms and magnitude of jump in solar wind plasma temperature, jump in solar wind plasma density, jump in solar wind plasma velocity and jump in average interplanetary magnetic field with co-relation co-efficient 0 .35 between magnitude of geomagnetic storms and magnitude of jump in solar wind plasma temperature, 0.19 between magnitude of geomagnetic storms and magnitude of jump in solar wind density, 0.34 between magnitude of geomagnetic storms and magnitude of jump in solar wind plasma velocity, 0.66 between magnitude of geomagnetic storms and magnitude of jump in average interplanetary magnetic field respectively. We have concluded that geomagnetic storms are mainly caused by Coronal Mass Ejections and disturbances in solar wind plasma parameters that they generate.

  4. DNA probes

    Castelino, J.

    1992-01-01

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with 32 P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism's genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens

  5. DNA probes

    Castelino, J

    1993-12-31

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with {sup 32}P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism`s genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens 10 figs, 2 tabs

  6. 3-Dimensional Methodology for the Control Rod Ejection Accident Analysis Using UNICORN{sup TM}

    Jang, Chan-su; Um, Kil-sup; Ahn, Dawk-hwan [Korea Nuclear Fuel Company, Taejon (Korea, Republic of); Kim, Yo-han; Sung, Chang-kyung [KEPRI, Taejon (Korea, Republic of); Song, Jae-seung [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    2006-07-01

    The control rod ejection accident has been analyzed with STRIKIN-II code using the point kinetics model coupled with conservative factors to address the three dimensional aspects. This may result in a severe transient with very high fuel enthalpy deposition. KNFC, under the support of KEPRI and KAERI, is developing 3-dimensional methodology for the rod ejection accident analysis using UNICORNTM (Unified Code of RETRAN, TORC and MASTER). For this purpose, 3-dimensional MASTER-TORC codes, which have been combined with the dynamic-link library by KAERI, are used in the transient analysis of the core and RETRAN code is used to estimate the enthalpy deposition in the hot rod.

  7. Gated cardiac imaging: manual calculations and observations of left ventricular ejection fraction

    Hawkins, T.; Keavey, P.M.

    1984-01-01

    Using gamma camera imaging, the fixed region and moving region methods of calculating left ventricular ejection fraction were studied. Data were obtained from gated blood pool studies on 125 cardiac patients with myocardial infarcts of varying extent and location. Ejection fractions ranged from 10 to 76%. The left anterior oblique angulation for optimal visualisation of the ventricles showed considerable patient variation. The authors conclude that a fixed angulation cannot be recommended and that there is little to justify it. Where the septum is not seen distinctly during setting up, a larger rather than smaller angle is generally advised. (U.K.)

  8. 3-Dimensional Methodology for the Control Rod Ejection Accident Analysis Using UNICORNTM

    Jang, Chan-su; Um, Kil-sup; Ahn, Dawk-hwan; Kim, Yo-han; Sung, Chang-kyung; Song, Jae-seung

    2006-01-01

    The control rod ejection accident has been analyzed with STRIKIN-II code using the point kinetics model coupled with conservative factors to address the three dimensional aspects. This may result in a severe transient with very high fuel enthalpy deposition. KNFC, under the support of KEPRI and KAERI, is developing 3-dimensional methodology for the rod ejection accident analysis using UNICORNTM (Unified Code of RETRAN, TORC and MASTER). For this purpose, 3-dimensional MASTER-TORC codes, which have been combined with the dynamic-link library by KAERI, are used in the transient analysis of the core and RETRAN code is used to estimate the enthalpy deposition in the hot rod

  9. Finite-element solutions of the AER-2 rod ejection benchmark by CRONOS

    Kolev, N.P.; Lenain, R.; Fedon-Magnaud, C.

    2001-01-01

    The finite-element option in CRONOS was used to analyse the AER-2 rod-ejection benchmark for WWER-440. The objective is to obtain spatially converged solutions by means of node subdivision and approximation refinement. This paper presents the first phase of analysis dealing with the initial and just-ejected states used for calculation of the initial reactivity. Fine-mesh and extrapolated to zero mesh size solutions were obtained and verified by comparison to MAG code solutions. These differences provide potential for large deviations in the transient results and deserve further attention in reactor safety analysis (Authors)

  10. Ejection fraction and outcomes in patients with atrial fibrillation and heart failure

    Banerjee, Amitava; Taillandier, Sophie; Olesen, Jonas Bjerring

    2012-01-01

    Heart failure (HF) increases the risk of stroke and thrombo-embolism (TE) in non-valvular atrial fibrillation (NVAF), and is incorporated in stroke risk stratification scores. We aimed to establish the role of ejection fraction (EF) in risk prediction in patients with NVAF and HF.......Heart failure (HF) increases the risk of stroke and thrombo-embolism (TE) in non-valvular atrial fibrillation (NVAF), and is incorporated in stroke risk stratification scores. We aimed to establish the role of ejection fraction (EF) in risk prediction in patients with NVAF and HF....

  11. Analysis of a control rod ejection transient in a mox-fuelled PWR

    Lenain, R.; Mathonniere, G.; Perrutel, J.P.; Schaeffer, H.; Stelletta, S.; Lam Hime, M.

    1988-09-01

    The decision to use mixed-oxide (MOX) fuel in PWR's involved re-investigation of a certain number of accidents and notably control rod ejection transients. It has thus been shown that this accident would be no more severe than in the case of all-uranium cores, since the positive effects on the ejected rod worth would counterbalance the negative effects on the delayed neutron fraction. A new approach to the kinetics aspect of the calculation method for this accident is also presented, involving a 3-D kinetic calculation with only a few axial meshes

  12. Promoter2.0: for the recognition of PolII promoter sequences

    Knudsen, Steen; Knudsen, Steen

    1999-01-01

    transcription start sites. On standardized test setsconsisting of human genomic DNA, the performance of Promoter2.0 compares well with other softwaredeveloped for the same purpose. Availability : Promoter2.0 is available as a Web server at http://www.cbs.dtu.dk/services/promoter/ Contact : steen@cbs.dtu.dk...

  13. DNA methylation

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  14. DNA data

    National Oceanic and Atmospheric Administration, Department of Commerce — Raw DNA chromatogram data produced by the ABI 373, 377, 3130 and 3730 automated sequencing machines in ABI format. These are from fish (primarily Sebastes spp.,...

  15. DNA nanotechnology

    Seeman, Nadrian C.; Sleiman, Hanadi F.

    2018-01-01

    DNA is the molecule that stores and transmits genetic information in biological systems. The field of DNA nanotechnology takes this molecule out of its biological context and uses its information to assemble structural motifs and then to connect them together. This field has had a remarkable impact on nanoscience and nanotechnology, and has been revolutionary in our ability to control molecular self-assembly. In this Review, we summarize the approaches used to assemble DNA nanostructures and examine their emerging applications in areas such as biophysics, diagnostics, nanoparticle and protein assembly, biomolecule structure determination, drug delivery and synthetic biology. The introduction of orthogonal interactions into DNA nanostructures is discussed, and finally, a perspective on the future directions of this field is presented.

  16. DNA expressions - A formal notation for DNA

    Vliet, Rudy van

    2015-01-01

    We describe a formal notation for DNA molecules that may contain nicks and gaps. The resulting DNA expressions denote formal DNA molecules. Different DNA expressions may denote the same molecule. Such DNA expressions are called equivalent. We examine which DNA expressions are minimal, which

  17. Rapid estimation of left ventricular ejection fraction in acute myocardial infarction by echocardiographic wall motion analysis

    Berning, J; Rokkedal Nielsen, J; Launbjerg, J

    1992-01-01

    Echocardiographic estimates of left ventricular ejection fraction (ECHO-LVEF) in acute myocardial infarction (AMI) were obtained by a new approach, using visual analysis of left ventricular wall motion in a nine-segment model. The method was validated in 41 patients using radionuclide...

  18. CORONAL MASS EJECTIONS AS A MECHANISM FOR PRODUCING IR VARIABILITY IN DEBRIS DISKS

    Osten, Rachel; Livio, Mario; Lubow, Steve; Pringle, J. E.; Soderblom, David; Valenti, Jeff

    2013-01-01

    Motivated by recent observations of short-timescale variations in the infrared emission of circumstellar disks, we propose that coronal mass ejections can remove dust grains on timescales as short as a few days. Continuous monitoring of stellar activity, coupled with infrared observations, can place meaningful constraints on the proposed mechanism.

  19. Angular distribution of electrons ejected by charged particles. IV. Combined classical and quantum-mechanical treatment

    Boesten, L.G.J.; Bonsen, T.F.M.

    1975-01-01

    Angular distributions of electrons ejected from helium by 100 and 300 keV protons have been calculated by a method which is a comination of the classical three-body collision theory and the quantum-mechanical Born approximation. The results of this theory have been compared with the corresponding

  20. The classification of ambiguity in polarimetric reconstruction of coronal mass ejection

    Dai, Xinghua; Wang, Huaning; Huang, Xin; Du, Zhanle; He, Han

    2014-01-01

    The Thomson scattering theory indicates that there exist explicit and implicit ambiguities in polarimetric analyses of coronal mass ejection (CME) observations. We suggest a classification for these ambiguities in CME reconstruction. Three samples, including double explicit, mixed, and double implicit ambiguity, are shown with the polarimetric analyses of STEREO CME observations. These samples demonstrate that this classification is helpful for improving polarimetric reconstruction.

  1. Factors related to outcome in heart failure with a preserved (or normal) left ventricular ejection fraction.

    Sanderson, John E

    2016-07-01

    Heart failure with a preserved ejection faction (HFpEF) is a growing and expensive cause of heart failure (HF) affecting particularly the elderly. It differs in substantial ways in addition to the normal left ventricular ejection fraction, from the more easily recognized form of heart failure with a reduced ejection fraction (HFrEF or 'systolic heart failure') and unlike HFrEF there have been little advances in treatment. In part, this relates to the complexity of the pathophysiology and identifying the correct targets. In HFpEF, there appears to be widespread stiffening of the vasculature and the myocardium affecting ventricular function (both systolic and diastolic), impeding ventricular suction, and thus early diastolic filling leading to breathlessness on exertion and later atrial failure and fibrillation. Left ventricular ejection fraction tends to gradually decline and some evolve into HFrEF. Most patients also have a mixture of several co-morbidities including hypertension, diabetes, obesity, poor renal function, lack of fitness, and often poor social conditions. Therefore, many factors may influence outcome in an individual patient. In this review, the epidemiology, possible causation, pathophysiology, the influence of co-morbidities and some of the many potential predictors of outcome will be considered.

  2. Global ejection fraction and phase analysis assessed by radionuclide angiography during exercise and after isoproterenol infusion

    Righetti, A.; Ratib, O.; Merier, G.; Widmann, T.; Donath, A.

    1983-01-01

    Radionuclide angiography obtained during and following Isoproterenol infusion is a new approach for detecting latent myocardial ischemia. It is very sensitive and could be considered as an alternative to conventional exercice radionuclide angiography. The data presented show that phase analysis assessment of regional systolic wall motion is a better indicator than global ejection fraction for quantifying left ventricular dysfunction

  3. The size distributions of fragments ejected at a given velocity from impact craters

    O'Keefe, John D.; Ahrens, Thomas J.

    1987-01-01

    The mass distribution of fragments that are ejected at a given velocity for impact craters is modeled to allow extrapolation of laboratory, field, and numerical results to large scale planetary events. The model is semi-empirical in nature and is derived from: (1) numerical calculations of cratering and the resultant mass versus ejection velocity, (2) observed ejecta blanket particle size distributions, (3) an empirical relationship between maximum ejecta fragment size and crater diameter, (4) measurements and theory of maximum ejecta size versus ejecta velocity, and (5) an assumption on the functional form for the distribution of fragments ejected at a given velocity. This model implies that for planetary impacts into competent rock, the distribution of fragments ejected at a given velocity is broad, e.g., 68 percent of the mass of the ejecta at a given velocity contains fragments having a mass less than 0.1 times a mass of the largest fragment moving at that velocity. The broad distribution suggests that in impact processes, additional comminution of ejecta occurs after the upward initial shock has passed in the process of the ejecta velocity vector rotating from an initially downward orientation. This additional comminution produces the broader size distribution in impact ejecta as compared to that obtained in simple brittle failure experiments.

  4. Awake craniotomy in a patient with ejection fraction of 10%: considerations of cerebrovascular and cardiovascular physiology.

    Meng, Lingzhong; Weston, Stephen D; Chang, Edward F; Gelb, Adrian W

    2015-05-01

    A 37-year-old man with nonischemic 4-chamber dilated cardiomyopathy and low-output cardiac failure (estimated ejection fraction of 10%) underwent awake craniotomy for a low-grade oligodendroglioma resection under monitored anesthesia care. The cerebrovascular and cardiovascular physiologic challenges and our management of this patient are discussed. Published by Elsevier Inc.

  5. A transcatheter intracardiac shunt device for heart failure with preserved ejection fraction (REDUCE LAP-HF)

    Hasenfuß, Gerd; Hayward, Chris; Burkhoff, Dan

    2016-01-01

    BACKGROUND: Heart failure with preserved ejection fraction (HFPEF) is a common, globally recognised, form of heart failure for which no treatment has yet been shown to improve symptoms or prognosis. The pathophysiology of HFPEF is complex but characterised by increased left atrial pressure, espec...

  6. Association between Hypotension, Low Ejection Fraction and Cognitive Performance in Cardiac Patients

    Rebecca F. Gottesman

    2010-01-01

    Full Text Available Background and Purpose: Impaired cardiac function can adversely affect the brain via decreased perfusion. The purpose of this study was to determine if cardiac ejection fraction (EF is associated with cognitive performance, and whether this is modified by low blood pressure.

  7. PINEX-2: pinhole-TV imaging of fuel ejection from an internally vented capsule

    Berzins, G.J.; Lumpkin, A.H.

    1979-01-01

    The LASL pinhole-intensified TV system was used at the TREAT reactor to image an internally vented, fuel-ejection capsule designed and built by HEDL. Several improvements in the imaging system over PINEX-1 were incorporated. A sequence of 16-ms TV frames shows axial expansion, expulsion of fuel from the pin, and retention of clad integrity during the time of coverage

  8. Comparative Influences of Fluid and Shell on Modeled Ejection Performance of a Piezoelectric Micro-Jet

    Kai Li

    2017-01-01

    Full Text Available The piezoelectric micro-jet, which can achieve the drop-on-demand requirement, is based on ink-jet technology and small droplets can be ejected out by precise control. The droplets are driven out of the nozzle by the acoustic pressure waves which are generated by the piezoelectric vibrator. The propagation processes of the acoustic pressure waves are affected by the acoustic properties of the fluid and the shell material of the micro-jet, as well as the excitations and the structure sizes. The influences of the fluid density and acoustic velocity in the fluid on the nozzle pressure and support reaction force of the vibrator are analyzed in this paper. The effects of the shell material on the ejection performance are studied as well. In order to improve the ejection performance of the micro-jet, for ejecting a given fluid, the recommended methods of selecting the shell material and adjusting excitations are provided based on the results, and the influences of the factors on working frequencies are obtained as well.

  9. Internal Energy Loss of the Electrons Ejected in Neutrinoless Double Beta Decay

    Drukarev, E. G.; Amusia, M. Ya.; Chernysheva, L. V.

    2017-01-01

    The excitations of the electron shell in neutrinoless double beta decay shifts the limiting energy available for ejected electrons. We present the general equations for this shift and make computations for the decays of two nuclei—germanium and xenon. (author)

  10. Ejection of solvated ions from electrosprayed methanol/water nanodroplets studied by molecular dynamics simulations.

    Ahadi, Elias; Konermann, Lars

    2011-06-22

    The ejection of solvated small ions from nanometer-sized droplets plays a central role during electrospray ionization (ESI). Molecular dynamics (MD) simulations can provide insights into the nanodroplet behavior. Earlier MD studies have largely focused on aqueous systems, whereas most practical ESI applications involve the use of organic cosolvents. We conduct simulations on mixed water/methanol droplets that carry excess NH(4)(+) ions. Methanol is found to compromise the H-bonding network, resulting in greatly increased rates of ion ejection and solvent evaporation. Considerable differences in the water and methanol escape rates cause time-dependent changes in droplet composition. Segregation occurs at low methanol concentration, such that layered droplets with a methanol-enriched periphery are formed. This phenomenon will enhance the partitioning of analyte molecules, with possible implications for their ESI efficiencies. Solvated ions are ejected from the tip of surface protrusions. Solvent bridging prior to ion secession is more extensive for methanol/water droplets than for purely aqueous systems. The ejection of solvated NH(4)(+) is visualized as diffusion-mediated escape from a metastable basin. The process involves thermally activated crossing of a ~30 kJ mol(-1) free energy barrier, in close agreement with the predictions of the classical ion evaporation model.

  11. Identification of ultrasound-contrast-agent dilution systems for ejection fraction measurements

    Mischi, M.; Jansen, A.H.M.; Kalker, A.A.C.M.; Korsten, H.H.M.

    2005-01-01

    Left ventricular ejection fraction is an important cardiac-efficiency measure. Standard estimations are based on geometric analysis and modeling; they require time and experienced cardiologists. Alternative methods make use of indicator dilutions, but they are invasive due to the need for

  12. Impact-driven ejection of micro metal droplets on-demand

    Luo, Jun; Qi, Lehua; Tao, Yuan; Ma, Qian; Visser, C.W.

    2016-01-01

    On-demand metal droplet deposition will be a cornerstone technology in 3D metal printing. However, suitable small nozzles are hardly available, limiting the resolution and surface finish of final products. Here, the ejection of record-small metal droplets with a diameter of only 0.55±0.07 times the

  13. Simultaneous Observations of p-mode Light Walls and Magnetic Reconnection Ejections above Sunspot Light Bridges

    Hou, Yijun; Zhang, Jun; Li, Ting; Yang, Shuhong; Li, Xiaohong, E-mail: yijunhou@nao.cas.cn, E-mail: zjun@nao.cas.cn [Key Laboratory of Solar Activity, National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China)

    2017-10-10

    Recent high-resolution observations from the Interface Region Imaging Spectrograph reveal bright wall-shaped structures in active regions (ARs), especially above sunspot light bridges. Their most prominent feature is the bright oscillating front in the 1400/1330 Å channel. These structures are named light walls and are often interpreted to be driven by p-mode waves. Above the light bridge of AR 12222 on 2014 December 06, we observed intermittent ejections superimposed on an oscillating light wall in the 1400 Å passband. At the base location of each ejection, the emission enhancement was detected in the Solar Dynamics Observatory 1600 Å channel. Thus, we suggest that in wall bases (light bridges), in addition to the leaked p-mode waves consistently driving the oscillating light wall, magnetic reconnection could happen intermittently at some locations and eject the heated plasma upward. Similarly, in the second event occurring in AR 12371 on 2015 June 16, a jet was simultaneously detected in addition to the light wall with a wave-shaped bright front above the light bridge. At the footpoint of this jet, lasting brightening was observed, implying magnetic reconnection at the base. We propose that in these events, two mechanisms, p-mode waves and magnetic reconnection, simultaneously play roles in the light bridge, and lead to the distinct kinetic features of the light walls and the ejection-like activities, respectively. To illustrate the two mechanisms and their resulting activities above light bridges, in this study we present a cartoon model.

  14. Evaluation of the rod ejection accident in Westinghouse Pressurized Water Reactors using spatial kinetics methods

    Risher, D.H. Jr.

    1975-01-01

    The consequences of a rod ejection accident are investigated in relation to the latest, high power density Westinghouse reactors. Limiting criteria are presented, based on experimental evidence, and if not exceeded these criteria will ensure that there will be no interference with core cooling capability, and radiation releases, if any, will be within the guidelines of 10CFR100. A basis is presented for the conservative selection of plant parameters to be used in the analysis, such that the analysis is applicable to a wide range of past, present, and future reactors. The calculational method employs a one-dimensional spatial kinetics computer code and a transient fuel heat transfer computer code to determine the hot spot fuel temperature versus time following a rod ejection. Using these computer codes, the most limiting hot channel factor (which does not cause the fuel damage limit criteria to be exceeded) has been determined as a function of the ejected rod worth. By this means, the limit criteria have been translated into ejected rod worths and hot channel factors which can be used effectively by the nuclear designer and safety analyst. The calculational method is shown to be conservative, compared to the results of a three-dimensional spatial kinetics analysis

  15. Impact of Ejection Fraction on the Clinical Response to Cardiac Resynchronization Therapy in Mild Heart Failure

    Linde, Cecilia; Daubert, Claude; Abraham, William T

    2013-01-01

    Current guidelines recommend cardiac resynchronization therapy (CRT) in mild heart failure (HF) patients with QRS prolongation and ejection fraction (EF) ≤30%. To assess the effect of CRT in less severe systolic dysfunction, outcomes in the REsynchronization reVErses Remodeling in Systolic left v...

  16. "Trampoline" ejection of organic molecules from graphene and graphite via keV cluster ions impacts

    Verkhoturov, Stanislav V.; Gołuński, Mikołaj; Verkhoturov, Dmitriy S.; Geng, Sheng; Postawa, Zbigniew; Schweikert, Emile A.

    2018-04-01

    We present the data on ejection of molecules and emission of molecular ions caused by single impacts of 50 keV C602+ on a molecular layer of deuterated phenylalanine (D8Phe) deposited on free standing, 2-layer graphene. The projectile impacts on the graphene side stimulate the abundant ejection of intact molecules and the emission of molecular ions in the transmission direction. To gain insight into the mechanism of ejection, Molecular Dynamic simulations were performed. It was found that the projectile penetrates the thin layer of graphene, partially depositing the projectile's kinetic energy, and molecules are ejected from the hot area around the hole that is made by the projectile. The yield, Y, of negative ions of deprotonated phenylalanine, (D8Phe-H)-, emitted in the transmission direction is 0.1 ions per projectile impact. To characterize the ejection and ionization of molecules, we have performed the experiments on emission of (D8Phe-H)- from the surface of bulk D8Phe (Y = 0.13) and from the single molecular layer of D8Phe deposited on bulk pyrolytic graphite (Y = 0.15). We show that, despite the similar yields of molecular ions, the scenario of the energy deposition and ejection of molecules is different for the case of graphene due to the confined volume of projectile-analyte interaction. The projectile impact on the graphene-D8Phe sample stimulates the collective radial movement of analyte atoms, which compresses the D8Phe layer radially from the hole. At the same time, this compression bends and stretches the graphene membrane around the hole thus accumulating potential energy. The accumulated potential energy is transformed into the kinetic energy of correlated movement upward for membrane atoms, thus the membrane acts as a trampoline for the molecules. The ejected molecules are effectively ionized; the ionization probability is ˜30× higher compared to that obtained for the bulk D8Phe target. The proposed mechanism of ionization involves tunneling of

  17. "Trampoline" ejection of organic molecules from graphene and graphite via keV cluster ions impacts.

    Verkhoturov, Stanislav V; Gołuński, Mikołaj; Verkhoturov, Dmitriy S; Geng, Sheng; Postawa, Zbigniew; Schweikert, Emile A

    2018-04-14

    We present the data on ejection of molecules and emission of molecular ions caused by single impacts of 50 keV C 60 2+ on a molecular layer of deuterated phenylalanine (D8Phe) deposited on free standing, 2-layer graphene. The projectile impacts on the graphene side stimulate the abundant ejection of intact molecules and the emission of molecular ions in the transmission direction. To gain insight into the mechanism of ejection, Molecular Dynamic simulations were performed. It was found that the projectile penetrates the thin layer of graphene, partially depositing the projectile's kinetic energy, and molecules are ejected from the hot area around the hole that is made by the projectile. The yield, Y, of negative ions of deprotonated phenylalanine, (D8Phe-H) - , emitted in the transmission direction is 0.1 ions per projectile impact. To characterize the ejection and ionization of molecules, we have performed the experiments on emission of (D8Phe-H) - from the surface of bulk D8Phe (Y = 0.13) and from the single molecular layer of D8Phe deposited on bulk pyrolytic graphite (Y = 0.15). We show that, despite the similar yields of molecular ions, the scenario of the energy deposition and ejection of molecules is different for the case of graphene due to the confined volume of projectile-analyte interaction. The projectile impact on the graphene-D8Phe sample stimulates the collective radial movement of analyte atoms, which compresses the D8Phe layer radially from the hole. At the same time, this compression bends and stretches the graphene membrane around the hole thus a