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Sample records for transcription bubbles replication

  1. Chromosome biology: conflict management for replication and transcription.

    Science.gov (United States)

    Dewar, James M; Walter, Johannes C

    2013-03-04

    A recent study has uncovered a new mechanism that attenuates DNA replication during periods of heightened gene expression to avoid collisions between replication and transcription. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. The Role of the Transcriptional Response to DNA Replication Stress.

    Science.gov (United States)

    Herlihy, Anna E; de Bruin, Robertus A M

    2017-03-02

    During DNA replication many factors can result in DNA replication stress. The DNA replication stress checkpoint prevents the accumulation of replication stress-induced DNA damage and the potential ensuing genome instability. A critical role for post-translational modifications, such as phosphorylation, in the replication stress checkpoint response has been well established. However, recent work has revealed an important role for transcription in the cellular response to DNA replication stress. In this review, we will provide an overview of current knowledge of the cellular response to DNA replication stress with a specific focus on the DNA replication stress checkpoint transcriptional response and its role in the prevention of replication stress-induced DNA damage.

  3. The Role of the Transcriptional Response to DNA Replication Stress

    Science.gov (United States)

    Herlihy, Anna E.; de Bruin, Robertus A.M.

    2017-01-01

    During DNA replication many factors can result in DNA replication stress. The DNA replication stress checkpoint prevents the accumulation of replication stress-induced DNA damage and the potential ensuing genome instability. A critical role for post-translational modifications, such as phosphorylation, in the replication stress checkpoint response has been well established. However, recent work has revealed an important role for transcription in the cellular response to DNA replication stress. In this review, we will provide an overview of current knowledge of the cellular response to DNA replication stress with a specific focus on the DNA replication stress checkpoint transcriptional response and its role in the prevention of replication stress-induced DNA damage. PMID:28257104

  4. Intracellular Detection of Viral Transcription and Replication Using RNA FISH

    Science.gov (United States)

    2016-05-26

    Chapter 14. Intracellular detection of viral transcription and replication using RNA FISH i. Summary/Abstract Many hemorrhagic fever viruses...only allow entirely new investigations into the replication of these viruses, but also how this method can be applied to any virus with a known...localization, TurboFISH, hemorrhagic fever virus replication 1. Introduction RNA FISH was developed as a method to visualize cellular RNA by binding a

  5. Separation of replication and transcription domains in nucleoli.

    Science.gov (United States)

    Smirnov, E; Borkovec, J; Kováčik, L; Svidenská, S; Schröfel, A; Skalníková, M; Švindrych, Z; Křížek, P; Ovesný, M; Hagen, G M; Juda, P; Michalová, K; Cardoso, M C; Cmarko, D; Raška, I

    2014-12-01

    In mammalian cells, active ribosomal genes produce the 18S, 5.8S and 28S RNAs of ribosomal particles. Transcription levels of these genes are very high throughout interphase, and the cell needs a special strategy to avoid collision of the DNA polymerase and RNA polymerase machineries. To investigate this problem, we measured the correlation of various replication and transcription signals in the nucleoli of HeLa, HT-1080 and NIH 3T3 cells using a specially devised software for analysis of confocal images. Additionally, to follow the relationship between nucleolar replication and transcription in living cells, we produced a stable cell line expressing GFP-RPA43 (subunit of RNA polymerase I, pol I) and RFP-PCNA (the sliding clamp protein) based on human fibrosarcoma HT-1080 cells. We found that replication and transcription signals are more efficiently separated in nucleoli than in the nucleoplasm. In the course of S phase, separation of PCNA and pol I signals gradually increased. During the same period, separation of pol I and incorporated Cy5-dUTP signals decreased. Analysis of single molecule localization microscopy (SMLM) images indicated that transcriptionally active FC/DFC units (i.e. fibrillar centers with adjacent dense fibrillar components) did not incorporate DNA nucleotides. Taken together, our data show that replication of the ribosomal genes is spatially separated from their transcription, and FC/DFC units may provide a structural basis for that separation. Copyright © 2014 Elsevier Inc. All rights reserved.

  6. Coordinating repair of oxidative DNA damage with transcription and replication

    International Nuclear Information System (INIS)

    Cooper, P.K.

    2003-01-01

    Transcription-coupled repair (TCR) preferentially removes DNA lesions from template strands of active genes. Defects in TCR, which acts both on lesions removed by nucleotide excision repair (NER) and on oxidative lesions removed by base excision repair (BER), underlie the fatal developmental disorder Cockayne syndrome. Although its detailed mechanism remains unknown, TCR involves recognition of a stalled RNA polymerase (RNAP), removal or remodeling of RNAP to allow access to the lesion, and recruitment of repair enzymes. At a minimum, these early steps require a non-enzymatic function of the multifunctional repair protein XPG, the CSB protein with ATP-dependent chromatin remodeling activity, and the TFIIH complex (including the XPB and XPD helicases) that is also required for basal transcription initiation and NER. XPG exists in the cell in a complex with TFIIH, and in vitro evidence has suggested that it interacts with CSB. To address the mechanism of TCR, we are characterizing protein-DNA and protein-protein interactions of XPG. We show that XPG preferentially binds to double-stranded DNA containing bubbles resembling in size the unpaired regions associated with transcription. Two distinct domains of XPG are required for the observed strong binding specificity and stability. XPG both interacts directly with CSB and synergistically binds with it to bubble DNA, and it strongly stimulates the bubble DNA-dependent ATPase activity of CSB. Significantly for TCR, XPG also interacts directly with RNAP II, binds both the protein and nucleic acid components (the R-loop) of a stalled RNA polymerase, and forms a ternary complex with CSB and the stalled RNAP. These results are consistent with the model that XPG and CSB jointly interact with the DNA/chromatin structure in the vicinity of the stalled transcriptional apparatus and with the transcriptional machinery itself to remodel the chromatin and either move or remodel the blocked RNA polymerase to expose the lesion

  7. DNA intercalator stimulates influenza transcription and virus replication

    Directory of Open Access Journals (Sweden)

    Poon Leo LM

    2011-03-01

    Full Text Available Abstract Influenza A virus uses its host transcription machinery to facilitate viral RNA synthesis, an event that is associated with cellular RNA polymerase II (RNAPII. In this study, various RNAPII transcription inhibitors were used to investigate the effect of RNAPII phosphorylation status on viral RNA transcription. A low concentration of DNA intercalators, such as actinomycin D (ActD, was found to stimulate viral polymerase activity and virus replication. This effect was not observed in cells treated with RNAPII kinase inhibitors. In addition, the loss of RNAPIIa in infected cells was due to the shift of nonphosphorylated RNAPII (RNAPIIa to hyperphosphorylated RNAPII (RNAPIIo.

  8. Modeling Ebola Virus Genome Replication and Transcription with Minigenome Systems.

    Science.gov (United States)

    Cressey, Tessa; Brauburger, Kristina; Mühlberger, Elke

    2017-01-01

    In this chapter, we describe the minigenome system for Ebola virus (EBOV), which reconstitutes EBOV polymerase activity in cells and can be used to model viral genome replication and transcription. This protocol comprises all steps including cell culture, plasmid preparation, transfection, and luciferase reporter assay readout.

  9. Porcine circovirus: transcription and rolling-circle DNA replication

    Science.gov (United States)

    This review summarizes the molecular studies pertaining to porcine circovirus (PCV) transcription and DNA replication. The genome of PCV is circular, single-stranded DNA and contains 1759-1768 nucleotides. Both the genome-strand (packaged in the virus particle) and the complementary-strand (synthesi...

  10. Bubbles

    DEFF Research Database (Denmark)

    Dholakia, Nikhilesh; Turcan, Romeo V.

    2013-01-01

    A goal of our ongoing research stream is to develop a multidisciplinary metatheory of bubbles. In this viewpoint paper we put forward a typology of bubbles by comparing four types of assets – entertainment, commodities, financial securities (stocks), and housing properties – where bubbles could...... and do form occasionally. Cutting across and comparing such varied asset types provides some rich insights into the nature of bubbles – and offers an inductive way to arrive at the typology of bubbles....

  11. Transcription-replication conflicts at chromosomal fragile sites—consequences in M phase and beyond

    DEFF Research Database (Denmark)

    Østergaard, Vibe Hallundbæk; Lisby, Michael

    2017-01-01

    transcription and replication patterns. At the same time, these chromosomal fragile sites engage in aberrant DNA structures in mitosis. Here, we discuss the mechanistic details of transcription–replication conflicts including putative scenarios for R-loop-induced replication inhibition to understand how...... transcription–replication conflicts transition from S phase into various aberrant DNA structures in mitosis....

  12. Transcription and replication result in distinct epigenetic marks following repression of early gene expression

    OpenAIRE

    Kallestad, Les; Woods, Emily; Christensen, Kendra; Gefroh, Amanda; Balakrishnan, Lata; Milavetz, Barry

    2013-01-01

    Simian Virus 40 (SV40) early transcription is repressed when the product of early transcription, T-antigen, binds to its cognate regulatory sequence, Site I, in the promoter of the SV40 minichromosome. Because SV40 minichromosomes undergo replication and transcription potentially repression could occur during active transcription or during DNA replication. Since repression is frequently epigenetically marked by the introduction of specific forms of methylated histone H3, we characterized th...

  13. Shaping the landscape of the Escherichia coli chromosome: replication-transcription encounters in cells with an ectopic replication origin

    DEFF Research Database (Denmark)

    Ivanova, Darja; Taylor, Toni; Smith, Sarah L

    2015-01-01

    Each cell division requires the unwinding of millions of DNA base pairs to allow chromosome duplication and gene transcription. As DNA replication and transcription share the same template, conflicts between both processes are unavoidable and head-on collisions are thought to be particularly...

  14. The DNA replication checkpoint directly regulates MBF-dependent G1/S transcription.

    Science.gov (United States)

    Dutta, Chaitali; Patel, Prasanta K; Rosebrock, Adam; Oliva, Anna; Leatherwood, Janet; Rhind, Nicholas

    2008-10-01

    The DNA replication checkpoint transcriptionally upregulates genes that allow cells to adapt to and survive replication stress. Our results show that, in the fission yeast Schizosaccharomyces pombe, the replication checkpoint regulates the entire G(1)/S transcriptional program by directly regulating MBF, the G(1)/S transcription factor. Instead of initiating a checkpoint-specific transcriptional program, the replication checkpoint targets MBF to maintain the normal G(1)/S transcriptional program during replication stress. We propose a mechanism for this regulation, based on in vitro phosphorylation of the Cdc10 subunit of MBF by the Cds1 replication-checkpoint kinase. Replacement of two potential phosphorylation sites with phosphomimetic amino acids suffices to promote the checkpoint transcriptional program, suggesting that Cds1 phosphorylation directly regulates MBF-dependent transcription. The conservation of MBF between fission and budding yeast, and recent results implicating MBF as a target of the budding yeast replication checkpoint, suggests that checkpoint regulation of the MBF transcription factor is a conserved strategy for coping with replication stress. Furthermore, the structural and regulatory similarity between MBF and E2F, the metazoan G(1)/S transcription factor, suggests that this checkpoint mechanism may be broadly conserved among eukaryotes.

  15. The transcription elongation factor Bur1-Bur2 interacts with replication protein A and maintains genome stability during replication stress

    DEFF Research Database (Denmark)

    Clausing, Emanuel; Mayer, Andreas; Chanarat, Sittinan

    2010-01-01

    Multiple DNA-associated processes such as DNA repair, replication, and recombination are crucial for the maintenance of genome integrity. Here, we show a novel interaction between the transcription elongation factor Bur1-Bur2 and replication protein A (RPA), the eukaryotic single-stranded DNA......-binding protein with functions in DNA repair, recombination, and replication. Bur1 interacted via its C-terminal domain with RPA, and bur1-¿C mutants showed a deregulated DNA damage response accompanied by increased sensitivity to DNA damage and replication stress as well as increased levels of persisting Rad52...... foci. Interestingly, the DNA damage sensitivity of an rfa1 mutant was suppressed by bur1 mutation, further underscoring a functional link between these two protein complexes. The transcription elongation factor Bur1-Bur2 interacts with RPA and maintains genome integrity during DNA replication stress....

  16. The Transcription Bubble of the RNA Polymerase-Promoter Open Complex Exhibits Conformational Heterogeneity and Millisecond-Scale Dynamics : Implications for Transcription Start-Site Selection

    NARCIS (Netherlands)

    Robb, Nicole C.; Cordes, Thorben; Hwang, Ling Chin; Gryte, Kristofer; Duchi, Diego; Craggs, Timothy D.; Santoso, Yusdi; Weiss, Shimon; Ebright, Richard H.; Kapanidis, Achillefs N.

    2013-01-01

    Bacterial transcription is initiated after RNA polymerase (RNAP) binds to promoter DNA, melts similar to 14 bp around the transcription start site and forms a single-stranded "transcription bubble" within a catalytically active RNAP-DNA open complex (RPo). There is significant flexibility in the

  17. Replicative Stress Induces Intragenic Transcription of the ASE1 Gene that Negatively Regulates Ase1 Activity

    OpenAIRE

    McKnight, Kelly; Liu, Hong; Wang, Yanchang

    2014-01-01

    Intragenic transcripts initiate within the coding region of a gene, thereby producing shorter mRNAs and proteins. Although intragenic transcripts are widely expressed [1], their role in the functional regulation of genes remains largely unknown. In budding yeast, DNA replication stress activates the S-phase checkpoint that stabilizes replication forks and arrests cells in S-phase with a short spindle [2-4]. When yeast cells were treated with hydroxyurea (HU) to block DNA synthesis and induce ...

  18. Effects of integration and replication on transcription of the HIV-1 long terminal repeat

    NARCIS (Netherlands)

    Jeang, K. T.; Berkhout, B.; Dropulic, B.

    1993-01-01

    The activity of a promoter is influenced by chromosomal and cell cycle/replication context. We analyzed the influences of integration and replication on transcription of the human immunodeficiency virus (HIV)-1 long terminal repeat (LTR). We found that one requirement for Tat trans-activated

  19. Conflict Resolution in the Genome: How Transcription and Replication Make It Work.

    Science.gov (United States)

    Hamperl, Stephan; Cimprich, Karlene A

    2016-12-01

    The complex machineries involved in replication and transcription translocate along the same DNA template, often in opposing directions and at different rates. These processes routinely interfere with each other in prokaryotes, and mounting evidence now suggests that RNA polymerase complexes also encounter replication forks in higher eukaryotes. Indeed, cells rely on numerous mechanisms to avoid, tolerate, and resolve such transcription-replication conflicts, and the absence of these mechanisms can lead to catastrophic effects on genome stability and cell viability. In this article, we review the cellular responses to transcription-replication conflicts and highlight how these inevitable encounters shape the genome and impact diverse cellular processes. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Replication and Transcription of Eukaryotic DNA in Esherichia coli

    Science.gov (United States)

    Morrow, John F.; Cohen, Stanley N.; Chang, Annie C. Y.; Boyer, Herbert W.; Goodman, Howard M.; Helling, Robert B.

    1974-01-01

    Fragments of amplified Xenopus laevis DNA, coding for 18S and 28S ribosomal RNA and generated by EcoRI restriction endonuclease, have been linked in vitro to the bacterial plasmid pSC101; and the recombinant molecular species have been introduced into E. coli by transformation. These recombinant plasmids, containing both eukaryotic and prokaryotic DNA, replicate stably in E. coli. RNA isolated from E. coli minicells harboring the plasmids hybridizes to amplified X. laevis rDNA. Images PMID:4600264

  1. Transcriptionally Driven DNA Replication Program of the Human Parasite Leishmania major

    Directory of Open Access Journals (Sweden)

    Rodrigo Lombraña

    2016-08-01

    Full Text Available Faithful inheritance of eukaryotic genomes requires the orchestrated activation of multiple DNA replication origins (ORIs. Although origin firing is mechanistically conserved, how origins are specified and selected for activation varies across different model systems. Here, we provide a complete analysis of the nucleosomal landscape and replication program of the human parasite Leishmania major, building on a better evolutionary understanding of replication organization in Eukarya. We found that active transcription is a driving force for the nucleosomal organization of the L. major genome and that both the spatial and the temporal program of DNA replication can be explained as associated to RNA polymerase kinetics. This simple scenario likely provides flexibility and robustness to deal with the environmental changes that impose alterations in the genetic programs during parasitic life cycle stages. Our findings also suggest that coupling replication initiation to transcription elongation could be an ancient solution used by eukaryotic cells for origin maintenance.

  2. Susceptibility to bystander DNA damage is influenced by replication and transcriptional activity

    Science.gov (United States)

    Dickey, Jennifer S.; Baird, Brandon J.; Redon, Christophe E.; Avdoshina, Valeriya; Palchik, Guillermo; Wu, Junfang; Kondratyev, Alexei; Bonner, William M.; Martin, Olga A.

    2012-01-01

    Direct cellular DNA damage may lead to genome destabilization in unexposed, bystander, cells sharing the same milieu with directly damaged cells by means of the bystander effect. One proposed mechanism involves double strand break (DSB) formation in S phase cells at sites of single strand lesions in the DNA of replication complexes, which has a more open structure compared with neighboring DNA. The DNA in transcription complexes also has a more open structure, and hence may be susceptible to bystander DSB formation from single strand lesions. To examine whether transcription predisposes non-replicating cells to bystander effect-induced DNA DSBs, we examined two types of primary cells that exhibit high levels of transcription in the absence of replication, rat neurons and human lymphocytes. We found that non-replicating bystander cells with high transcription rates exhibited substantial levels of DNA DSBs, as monitored by γ-H2AX foci formation. Additionally, as reported in proliferating cells, TGF-β and NO were found to mimic bystander effects in cell populations lacking DNA synthesis. These results indicate that cell vulnerability to bystander DSB damage may result from transcription as well as replication. The findings offer insights into which tissues may be vulnerable to bystander genomic destabilization in vivo. PMID:22941641

  3. Effects of Replication and Transcription on DNA Structure-Related Genetic Instability.

    Science.gov (United States)

    Wang, Guliang; Vasquez, Karen M

    2017-01-05

    Many repetitive sequences in the human genome can adopt conformations that differ from the canonical B-DNA double helix (i.e., non-B DNA), and can impact important biological processes such as DNA replication, transcription, recombination, telomere maintenance, viral integration, transposome activation, DNA damage and repair. Thus, non-B DNA-forming sequences have been implicated in genetic instability and disease development. In this article, we discuss the interactions of non-B DNA with the replication and/or transcription machinery, particularly in disease states (e.g., tumors) that can lead to an abnormal cellular environment, and how such interactions may alter DNA replication and transcription, leading to potential conflicts at non-B DNA regions, and eventually result in genetic stability and human disease.

  4. DNA replication initiator Cdc6 also regulates ribosomal DNA transcription initiation.

    Science.gov (United States)

    Huang, Shijiao; Xu, Xiaowei; Wang, Guopeng; Lu, Guoliang; Xie, Wenbing; Tao, Wei; Zhang, Hongyin; Jiang, Qing; Zhang, Chuanmao

    2016-04-01

    RNA-polymerase-I-dependent ribosomal DNA (rDNA) transcription is fundamental to rRNA processing, ribosome assembly and protein synthesis. However, how this process is initiated during the cell cycle is not fully understood. By performing a proteomic analysis of transcription factors that bind RNA polymerase I during rDNA transcription initiation, we identified that the DNA replication initiator Cdc6 interacts with RNA polymerase I and its co-factors, and promotes rDNA transcription in G1 phase in an ATPase-activity-dependent manner. We further showed that Cdc6 is targeted to the nucleolus during late mitosis and G1 phase in a manner that is dependent on B23 (also known as nucleophosmin, NPM1), and preferentially binds to the rDNA promoter through its ATP-binding domain. Overexpression of Cdc6 increases rDNA transcription, whereas knockdown of Cdc6 results in a decreased association of both RNA polymerase I and the RNA polymerase I transcription factor RRN3 with rDNA, and a reduction of rDNA transcription. Furthermore, depletion of Cdc6 impairs the interaction between RRN3 and RNA polymerase I. Taken together, our data demonstrate that Cdc6 also serves as a regulator of rDNA transcription initiation, and indicate a mechanism by which initiation of rDNA transcription and DNA replication can be coordinated in cells. © 2016. Published by The Company of Biologists Ltd.

  5. Transcriptional repression is epigenetically marked by H3K9 methylation during SV40 replication

    OpenAIRE

    Kallestad, Les; Christensen, Kendra; Woods, Emily; Milavetz, Barry

    2014-01-01

    Background We have recently shown that T-antigen binding to Site I results in the replication-dependent introduction of H3K9me1 into SV40 chromatin late in infection. Since H3K9me2 and H3K9me3 are also present late in infection, we determined whether their presence was also related to the status of ongoing transcription and replication. Transcription was either inhibited with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidizole (DRB) or stimulated with sodium butyrate and the effects on histone m...

  6. Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses.

    Science.gov (United States)

    Hamperl, Stephan; Bocek, Michael J; Saldivar, Joshua C; Swigut, Tomek; Cimprich, Karlene A

    2017-08-10

    Conflicts between transcription and replication are a potent source of DNA damage. Co-transcriptional R-loops could aggravate such conflicts by creating an additional barrier to replication fork progression. Here, we use a defined episomal system to investigate how conflict orientation and R-loop formation influence genome stability in human cells. R-loops, but not normal transcription complexes, induce DNA breaks and orientation-specific DNA damage responses during conflicts with replication forks. Unexpectedly, the replisome acts as an orientation-dependent regulator of R-loop levels, reducing R-loops in the co-directional (CD) orientation but promoting their formation in the head-on (HO) orientation. Replication stress and deregulated origin firing increase the number of HO collisions leading to genome-destabilizing R-loops. Our findings connect DNA replication to R-loop homeostasis and suggest a mechanistic basis for genome instability resulting from deregulated DNA replication, observed in cancer and other disease states. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Direct non transcriptional role of NF-Y in DNA replication.

    Science.gov (United States)

    Benatti, Paolo; Belluti, Silvia; Miotto, Benoit; Neusiedler, Julia; Dolfini, Diletta; Drac, Marjorie; Basile, Valentina; Schwob, Etienne; Mantovani, Roberto; Blow, J Julian; Imbriano, Carol

    2016-04-01

    NF-Y is a heterotrimeric transcription factor, which plays a pioneer role in the transcriptional control of promoters containing the CCAAT-box, among which genes involved in cell cycle regulation, apoptosis and DNA damage response. The knock-down of the sequence-specific subunit NF-YA triggers defects in S-phase progression, which lead to apoptotic cell death. Here, we report that NF-Y has a critical function in DNA replication progression, independent from its transcriptional activity. NF-YA colocalizes with early DNA replication factories, its depletion affects the loading of replisome proteins to DNA, among which Cdc45, and delays the passage from early to middle-late S phase. Molecular combing experiments are consistent with a role for NF-Y in the control of fork progression. Finally, we unambiguously demonstrate a direct non-transcriptional role of NF-Y in the overall efficiency of DNA replication, specifically in the DNA elongation process, using a Xenopus cell-free system. Our findings broaden the activity of NF-Y on a DNA metabolism other than transcription, supporting the existence of specific TFs required for proper and efficient DNA replication. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

  8. p53 Maintains Genomic Stability by Preventing Interference between Transcription and Replication

    Directory of Open Access Journals (Sweden)

    Constance Qiao Xin Yeo

    2016-04-01

    Full Text Available p53 tumor suppressor maintains genomic stability, typically acting through cell-cycle arrest, senescence, and apoptosis. We discovered a function of p53 in preventing conflicts between transcription and replication, independent of its canonical roles. p53 deficiency sensitizes cells to Topoisomerase (Topo II inhibitors, resulting in DNA damage arising spontaneously during replication. Topoisomerase IIα (TOP2A-DNA complexes preferentially accumulate in isogenic p53 mutant or knockout cells, reflecting an increased recruitment of TOP2A to regulate DNA topology. We propose that p53 acts to prevent DNA topological stress originating from transcription during the S phase and, therefore, promotes normal replication fork progression. Consequently, replication fork progression is impaired in the absence of p53, which is reversed by transcription inhibition. Pharmacologic inhibition of transcription also attenuates DNA damage and decreases Topo-II-DNA complexes, restoring cell viability in p53-deficient cells. Together, our results demonstrate a function of p53 that may underlie its role in tumor suppression.

  9. Human Metapneumovirus Induces Formation of Inclusion Bodies for Efficient Genome Replication and Transcription.

    Science.gov (United States)

    Cifuentes-Muñoz, Nicolás; Branttie, Jean; Slaughter, Kerri Beth; Dutch, Rebecca Ellis

    2017-12-15

    Human metapneumovirus (HMPV) causes significant upper and lower respiratory disease in all age groups worldwide. The virus possesses a negative-sense single-stranded RNA genome of approximately 13.3 kb encapsidated by multiple copies of the nucleoprotein (N), giving rise to helical nucleocapsids. In addition, copies of the phosphoprotein (P) and the large RNA polymerase (L) decorate the viral nucleocapsids. After viral attachment, endocytosis, and fusion mediated by the viral glycoproteins, HMPV nucleocapsids are released into the cell cytoplasm. To visualize the subsequent steps of genome transcription and replication, a fluorescence in situ hybridization (FISH) protocol was established to detect different viral RNA subpopulations in infected cells. The FISH probes were specific for detection of HMPV positive-sense RNA (+RNA) and viral genomic RNA (vRNA). Time course analysis of human bronchial epithelial BEAS-2B cells infected with HMPV revealed the formation of inclusion bodies (IBs) from early times postinfection. HMPV IBs were shown to be cytoplasmic sites of active transcription and replication, with the translation of viral proteins being closely associated. Inclusion body formation was consistent with an actin-dependent coalescence of multiple early replicative sites. Time course quantitative reverse transcription-PCR analysis suggested that the coalescence of inclusion bodies is a strategy to efficiently replicate and transcribe the viral genome. These results provide a better understanding of the steps following HMPV entry and have important clinical implications. IMPORTANCE Human metapneumovirus (HMPV) is a recently discovered pathogen that affects human populations of all ages worldwide. Reinfections are common throughout life, but no vaccines or antiviral treatments are currently available. In this work, a spatiotemporal analysis of HMPV replication and transcription in bronchial epithelial cell-derived immortal cells was performed. HMPV was shown to

  10. Distinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomes

    KAUST Repository

    Cui, Peng; Ding, Feng; Lin, Qiang; Zhang, Lingfang; Li, Ang; Zhang, Zhang; Hu, Songnian; Yu, Jun

    2012-01-01

    Here, we evaluate the contribution of two major biological processes—DNA replication and transcription—to mutation rate variation in human genomes. Based on analysis of the public human tissue transcriptomics data, high-resolution replicating map of Hela cells and dbSNP data, we present significant correlations between expression breadth, replication time in local regions and SNP density. SNP density of tissue-specific (TS) genes is significantly higher than that of housekeeping (HK) genes. TS genes tend to locate in late-replicating genomic regions and genes in such regions have a higher SNP density compared to those in early-replication regions. In addition, SNP density is found to be positively correlated with expression level among HK genes. We conclude that the process of DNA replication generates stronger mutational pressure than transcription-associated biological processes do, resulting in an increase of mutation rate in TS genes while having weaker effects on HK genes. In contrast, transcription-associated processes are mainly responsible for the accumulation of mutations in highly-expressed HK genes.

  11. Distinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomes

    KAUST Repository

    Cui, Peng

    2012-03-23

    Here, we evaluate the contribution of two major biological processes—DNA replication and transcription—to mutation rate variation in human genomes. Based on analysis of the public human tissue transcriptomics data, high-resolution replicating map of Hela cells and dbSNP data, we present significant correlations between expression breadth, replication time in local regions and SNP density. SNP density of tissue-specific (TS) genes is significantly higher than that of housekeeping (HK) genes. TS genes tend to locate in late-replicating genomic regions and genes in such regions have a higher SNP density compared to those in early-replication regions. In addition, SNP density is found to be positively correlated with expression level among HK genes. We conclude that the process of DNA replication generates stronger mutational pressure than transcription-associated biological processes do, resulting in an increase of mutation rate in TS genes while having weaker effects on HK genes. In contrast, transcription-associated processes are mainly responsible for the accumulation of mutations in highly-expressed HK genes.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  15. Varicella-zoster virus (VZV) origin of DNA replication oriS influences origin-dependent DNA replication and flanking gene transcription.

    Science.gov (United States)

    Khalil, Mohamed I; Sommer, Marvin H; Hay, John; Ruyechan, William T; Arvin, Ann M

    2015-07-01

    The VZV genome has two origins of DNA replication (oriS), each of which consists of an AT-rich sequence and three origin binding protein (OBP) sites called Box A, C and B. In these experiments, the mutation in the core sequence CGC of the Box A and C not only inhibited DNA replication but also inhibited both ORF62 and ORF63 expression in reporter gene assays. In contrast the Box B mutation did not influence DNA replication or flanking gene transcription. These results suggest that efficient DNA replication enhances ORF62 and ORF63 transcription. Recombinant viruses carrying these mutations in both sites and one with a deletion of the whole oriS were constructed. Surprisingly, the recombinant virus lacking both copies of oriS retained the capacity to replicate in melanoma and HELF cells suggesting that VZV has another origin of DNA replication. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. In vitro-reconstituted nucleoids can block mitochondrial DNA replication and transcription.

    Science.gov (United States)

    Farge, Géraldine; Mehmedovic, Majda; Baclayon, Marian; van den Wildenberg, Siet M J L; Roos, Wouter H; Gustafsson, Claes M; Wuite, Gijs J L; Falkenberg, Maria

    2014-07-10

    The mechanisms regulating the number of active copies of mtDNA are still unclear. A mammalian cell typically contains 1,000-10,000 copies of mtDNA, which are packaged into nucleoprotein complexes termed nucleoids. The main protein component of these structures is mitochondrial transcription factor A (TFAM). Here, we reconstitute nucleoid-like particles in vitro and demonstrate that small changes in TFAM levels dramatically impact the fraction of DNA molecules available for transcription and DNA replication. Compaction by TFAM is highly cooperative, and at physiological ratios of TFAM to DNA, there are large variations in compaction, from fully compacted nucleoids to naked DNA. In compacted nucleoids, TFAM forms stable protein filaments on DNA that block melting and prevent progression of the replication and transcription machineries. Based on our observations, we suggest that small variations in the TFAM-to-mtDNA ratio may be used to regulate mitochondrial gene transcription and DNA replication. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  17. Transcriptionally Driven DNA Replication Program of the Human Parasite Leishmania major.

    Science.gov (United States)

    Lombraña, Rodrigo; Álvarez, Alba; Fernández-Justel, José Miguel; Almeida, Ricardo; Poza-Carrión, César; Gomes, Fábia; Calzada, Arturo; Requena, José María; Gómez, María

    2016-08-09

    Faithful inheritance of eukaryotic genomes requires the orchestrated activation of multiple DNA replication origins (ORIs). Although origin firing is mechanistically conserved, how origins are specified and selected for activation varies across different model systems. Here, we provide a complete analysis of the nucleosomal landscape and replication program of the human parasite Leishmania major, building on a better evolutionary understanding of replication organization in Eukarya. We found that active transcription is a driving force for the nucleosomal organization of the L. major genome and that both the spatial and the temporal program of DNA replication can be explained as associated to RNA polymerase kinetics. This simple scenario likely provides flexibility and robustness to deal with the environmental changes that impose alterations in the genetic programs during parasitic life cycle stages. Our findings also suggest that coupling replication initiation to transcription elongation could be an ancient solution used by eukaryotic cells for origin maintenance. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  18. Involvement of DNA gyrase in replication and transcription of bacteriophage T7 DNA

    International Nuclear Information System (INIS)

    De Wyngaert, M.A.; Hinkle, D.C.

    1979-01-01

    Growth of bacteriophage T7 is inhibited by the antibiotic coumermycin A 1 , an inhibitor of the Escherichia coli DNA gyrase. Since growth of the phage is insensitive to the antibiotic in strains containing a coumermycin-resistent DNA gyrase, this enzyme appears to be required for phage growth. We have investigated the effect of coumermycin on the kinetics of DNA, RNA, and protein synthesis during T7 infection. DNA synthesis is completely inhibited by the antibiotic. In addition, coumermycin significantly inhibits transcription of late but not early genes. Thus, E. coli DNA gyrase may play an important role in transcription as well as in replication of T7 DNA

  19. In Situ Tagged nsp15 Reveals Interactions with Coronavirus Replication/Transcription Complex-Associated Proteins

    Directory of Open Access Journals (Sweden)

    Jeremiah Athmer

    2017-01-01

    Full Text Available Coronavirus (CoV replication and transcription are carried out in close proximity to restructured endoplasmic reticulum (ER membranes in replication/transcription complexes (RTC. Many of the CoV nonstructural proteins (nsps are required for RTC function; however, not all of their functions are known. nsp15 contains an endoribonuclease domain that is conserved in the CoV family. While the enzymatic activity and crystal structure of nsp15 are well defined, its role in replication remains elusive. nsp15 localizes to sites of RNA replication, but whether it acts independently or requires additional interactions for its function remains unknown. To begin to address these questions, we created an in situ tagged form of nsp15 using the prototypic CoV, mouse hepatitis virus (MHV. In MHV, nsp15 contains the genomic RNA packaging signal (P/S, a 95-bp RNA stem-loop structure that is not required for viral replication or nsp15 function. Utilizing this knowledge, we constructed an internal hemagglutinin (HA tag that replaced the P/S. We found that nsp15-HA was localized to discrete perinuclear puncta and strongly colocalized with nsp8 and nsp12, both well-defined members of the RTC, but not the membrane (M protein, involved in virus assembly. Finally, we found that nsp15 interacted with RTC-associated proteins nsp8 and nsp12 during infection, and this interaction was RNA independent. From this, we conclude that nsp15 localizes and interacts with CoV proteins in the RTC, suggesting it plays a direct or indirect role in virus replication. Furthermore, the use of in situ epitope tags could be used to determine novel nsp-nsp interactions in coronaviruses.

  20. A DNA Binding Protein Is Required for Viral Replication and Transcription in Bombyx mori Nucleopolyhedrovirus.

    Directory of Open Access Journals (Sweden)

    Cui Zhao

    Full Text Available A DNA-binding protein (DBP [GenBank accession number: M63416] of Bombyx mori nuclear polyhedrosis virus (BmNPV has been reported to be a regulatory factor in BmNPV, but its detailed functions remain unknown. In order to study the regulatory mechanism of DBP on viral proliferation, genome replication, and gene transcription, a BmNPV dbp gene knockout virus dbp-ko-Bacmid was generated by the means of Red recombination system. In addition, dbp-repaired virus dbp-re-Bacmid was constructed by the means of the Bac to Bac system. Then, the Bacmids were transfected into BmN cells. The results of this viral titer experiment revealed that the TCID50 of the dbp-ko-Bacmid was 0; however, the dbp-re-Bacmid was similar to the wtBacmid (p>0.05, indicating that the dbp-deficient would lead to failure in the assembly of virus particles. In the next step, Real-Time PCR was used to analyze the transcriptional phases of dbp gene in BmN cells, which had been infected with BmNPV. The results of the latter experiment revealed that the transcript of dbp gene was first detected at 3 h post-infection. Furthermore, the replication level of virus genome and the transcriptional level of virus early, late, and very late genes in BmN cells, which had been transfected with 3 kinds of Bacmids, were analyzed by Real-Time PCR. The demonstrating that the replication level of genome was lower than that of wtBacmid and dbp-re-Bacmid (p<0.01. The transcriptional level of dbp-ko-Bacmid early gene lef-3, ie-1, dnapol, late gene vp39 and very late gene p10 were statistically significantly lower than dbp-re-Bacmid and wtBacmid (p<0.01. The results presented are based on Western blot analysis, which indicated that the lack of dbp gene would lead to low expressions of lef3, vp39, and p10. In conclusion, dbp was not only essential for early viral replication, but also a viral gene that has a significant impact on transcription and expression during all periods of baculovirus life cycle.

  1. Transcriptional and physiological changes during Mycobacterium tuberculosis reactivation from non-replicating persistence

    Directory of Open Access Journals (Sweden)

    Peicheng Du

    2016-08-01

    Full Text Available Mycobacterium tuberculosis can persist for years in the hostile environment of the host in a non-replicating or slowly replicating state. While active disease predominantly results from reactivation of a latent infection, the molecular mechanisms of M. tuberculosis reactivation are still poorly understood. We characterized the physiology and global transcriptomic profiles of M. tuberculosis during reactivation from hypoxia-induced non-replicating persistence. We found that M. tuberculosis reactivation upon reaeration was associated with a lag phase, in which the recovery of cellular physiological and metabolic functions preceded the resumption of cell replication. Enrichment analysis of the transcriptomic dynamics revealed changes to many metabolic pathways and transcription regulons/subnetworks that orchestrated the metabolic and physiological transformation in preparation for cell division. In particular, we found that M. tuberculosis reaeration lag phase is associated with down-regulation of persistence-associated regulons/subnetworks, including DosR, MprA, SigH, SigE and ClgR, as well as metabolic pathways including those involved in the uptake of lipids and their catabolism. More importantly, we identified a number of up-regulated transcription regulons and metabolic pathways, including those involved in metal transport and remobilization, second messenger-mediated responses, DNA repair and recombination, and synthesis of major cell wall components. We also found that inactivation of the major alternative sigma factors SigE or SigH disrupted exit from persistence, underscoring the importance of the global transcriptional reprogramming during M. tuberculosis reactivation. Our observations suggest that M. tuberculosis lag phase is associated with a global gene expression reprogramming that defines the initiation of a reactivation process.

  2. A DNA Binding Protein Is Required for Viral Replication and Transcription in Bombyx mori Nucleopolyhedrovirus.

    Science.gov (United States)

    Zhao, Cui; Zhang, Chen; Chen, Bin; Shi, Yanghui; Quan, Yanping; Nie, Zuoming; Zhang, Yaozhou; Yu, Wei

    2016-01-01

    A DNA-binding protein (DBP) [GenBank accession number: M63416] of Bombyx mori nuclear polyhedrosis virus (BmNPV) has been reported to be a regulatory factor in BmNPV, but its detailed functions remain unknown. In order to study the regulatory mechanism of DBP on viral proliferation, genome replication, and gene transcription, a BmNPV dbp gene knockout virus dbp-ko-Bacmid was generated by the means of Red recombination system. In addition, dbp-repaired virus dbp-re-Bacmid was constructed by the means of the Bac to Bac system. Then, the Bacmids were transfected into BmN cells. The results of this viral titer experiment revealed that the TCID50 of the dbp-ko-Bacmid was 0; however, the dbp-re-Bacmid was similar to the wtBacmid (p>0.05), indicating that the dbp-deficient would lead to failure in the assembly of virus particles. In the next step, Real-Time PCR was used to analyze the transcriptional phases of dbp gene in BmN cells, which had been infected with BmNPV. The results of the latter experiment revealed that the transcript of dbp gene was first detected at 3 h post-infection. Furthermore, the replication level of virus genome and the transcriptional level of virus early, late, and very late genes in BmN cells, which had been transfected with 3 kinds of Bacmids, were analyzed by Real-Time PCR. The demonstrating that the replication level of genome was lower than that of wtBacmid and dbp-re-Bacmid (plife cycle.

  3. Human-Phosphate-Binding-Protein inhibits HIV-1 gene transcription and replication

    Directory of Open Access Journals (Sweden)

    Candolfi Ermanno

    2011-07-01

    Full Text Available Abstract The Human Phosphate-Binding protein (HPBP is a serendipitously discovered lipoprotein that binds phosphate with high affinity. HPBP belongs to the DING protein family, involved in various biological processes like cell cycle regulation. We report that HPBP inhibits HIV-1 gene transcription and replication in T cell line, primary peripherical blood lymphocytes and primary macrophages. We show that HPBP is efficient in naïve and HIV-1 AZT-resistant strains. Our results revealed HPBP as a new and potent anti HIV molecule that inhibits transcription of the virus, which has not yet been targeted by HAART and therefore opens new strategies in the treatment of HIV infection.

  4. Ancient mtDNA genetic variants modulate mtDNA transcription and replication.

    Directory of Open Access Journals (Sweden)

    Sarit Suissa

    2009-05-01

    Full Text Available Although the functional consequences of mitochondrial DNA (mtDNA genetic backgrounds (haplotypes, haplogroups have been demonstrated by both disease association studies and cell culture experiments, it is not clear which of the mutations within the haplogroup carry functional implications and which are "evolutionary silent hitchhikers". We set forth to study the functionality of haplogroup-defining mutations within the mtDNA transcription/replication regulatory region by in vitro transcription, hypothesizing that haplogroup-defining mutations occurring within regulatory motifs of mtDNA could affect these processes. We thus screened >2500 complete human mtDNAs representing all major populations worldwide for natural variation in experimentally established protein binding sites and regulatory regions comprising a total of 241 bp in each mtDNA. Our screen revealed 77/241 sites showing point mutations that could be divided into non-fixed (57/77, 74% and haplogroup/sub-haplogroup-defining changes (i.e., population fixed changes, 20/77, 26%. The variant defining Caucasian haplogroup J (C295T increased the binding of TFAM (Electro Mobility Shift Assay and the capacity of in vitro L-strand transcription, especially of a shorter transcript that maps immediately upstream of conserved sequence block 1 (CSB1, a region associated with RNA priming of mtDNA replication. Consistent with this finding, cybrids (i.e., cells sharing the same nuclear genetic background but differing in their mtDNA backgrounds harboring haplogroup J mtDNA had a >2 fold increase in mtDNA copy number, as compared to cybrids containing haplogroup H, with no apparent differences in steady state levels of mtDNA-encoded transcripts. Hence, a haplogroup J regulatory region mutation affects mtDNA replication or stability, which may partially account for the phenotypic impact of this haplogroup. Our analysis thus demonstrates, for the first time, the functional impact of particular mt

  5. Transcription factor genes essential for cell proliferation and replicative lifespan in budding yeast

    Energy Technology Data Exchange (ETDEWEB)

    Kamei, Yuka; Tai, Akiko; Dakeyama, Shota; Yamamoto, Kaori; Inoue, Yamato; Kishimoto, Yoshifumi; Ohara, Hiroya; Mukai, Yukio, E-mail: y_mukai@nagahama-i-bio.ac.jp

    2015-07-31

    Many of the lifespan-related genes have been identified in eukaryotes ranging from the yeast to human. However, there is limited information available on the longevity genes that are essential for cell proliferation. Here, we investigated whether the essential genes encoding DNA-binding transcription factors modulated the replicative lifespan of Saccharomyces cerevisiae. Heterozygous diploid knockout strains for FHL1, RAP1, REB1, and MCM1 genes showed significantly short lifespan. {sup 1}H-nuclear magnetic resonance analysis indicated a characteristic metabolic profile in the Δfhl1/FHL1 mutant. These results strongly suggest that FHL1 regulates the transcription of lifespan related metabolic genes. Thus, heterozygous knockout strains could be the potential materials for discovering further novel lifespan genes. - Highlights: • Involvement of yeast TF genes essential for cell growth in lifespan was evaluated. • The essential TF genes, FHL1, RAP1, REB1, and MCM1, regulate replicative lifespan. • Heterozygous deletion of FHL1 changes cellular metabolism related to lifespan.

  6. Curaxin CBL0100 Blocks HIV-1 Replication and Reactivation through Inhibition of Viral Transcriptional Elongation

    Directory of Open Access Journals (Sweden)

    Maxime J. Jean

    2017-10-01

    Full Text Available Despite combination antiretroviral therapy (cART, acquired immunodeficiency syndrome (AIDS, predominantly caused by the human immunodeficiency virus type 1 (HIV-1, remains incurable. The barrier to a cure lies in the virus' ability to establish a latent infection in HIV/AIDS patients. Unsurprisingly, efforts for a sterilizing cure have focused on the “shock and kill” strategy using latency-reversing agents (LRAs to complement cART in order to eliminate these latent reservoirs. However, this method faces numerous challenges. Recently, the “block and lock” strategy has been proposed. It aims to reinforce a deep state of latency and prevent sporadic reactivation (“blip” of HIV-1 using latency-promoting agents (LPAs for a functional cure. Our studies of curaxin 100 (CBL0100, a small-molecule targeting the facilitates chromatin transcription (FACT complex, show that it blocks both HIV-1 replication and reactivation in in vitro and ex vivo models of HIV-1. Mechanistic investigation elucidated that CBL0100 preferentially targets HIV-1 transcriptional elongation and decreases the occupancy of RNA Polymerase II (Pol II and FACT at the HIV-1 promoter region. In conclusion, CBL0100 is a newly identified inhibitor of HIV-1 transcription that can be used as an LPA in the “block and lock” cure strategy.

  7. DNA replication factor C1 mediates genomic stability and transcriptional gene silencing in Arabidopsis

    KAUST Repository

    Liu, Qian; Wang, Junguo; Miki, Daisuke; Xia, Ran; Yu, Wenxiang; He, Junna; Zheng, Zhimin; Zhu, Jian-Kang; Gonga, Zhizhong

    2010-01-01

    Genetic screening identified a suppressor of ros1-1, a mutant of REPRESSOR OF SILENCING1 (ROS1; encoding a DNA demethylation protein). The suppressor is a mutation in the gene encoding the largest subunit of replication factor C (RFC1). This mutation of RFC1 reactivates the unlinked 35S-NPTII transgene, which is silenced in ros1 and also increases expression of the pericentromeric Athila retrotransposons named transcriptional silent information in a DNA methylationindependent manner. rfc1 is more sensitive than the wild type to the DNA-damaging agent methylmethane sulphonate and to the DNA inter- and intra- cross-linking agent cisplatin. The rfc1 mutant constitutively expresses the G2/M-specific cyclin CycB1;1 and other DNA repair-related genes. Treatment with DNA-damaging agents mimics the rfc1 mutation in releasing the silenced 35S-NPTII, suggesting that spontaneously induced genomic instability caused by the rfc1 mutation might partially contribute to the released transcriptional gene silencing (TGS). The frequency of somatic homologous recombination is significantly increased in the rfc1 mutant. Interestingly, ros1 mutants show increased telomere length, but rfc1 mutants show decreased telomere length and reduced expression of telomerase. Our results suggest that RFC1 helps mediate genomic stability and TGS in Arabidopsis thaliana. © 2010 American Society of Plant Biologists.

  8. DNA replication factor C1 mediates genomic stability and transcriptional gene silencing in Arabidopsis

    KAUST Repository

    Liu, Qian

    2010-07-01

    Genetic screening identified a suppressor of ros1-1, a mutant of REPRESSOR OF SILENCING1 (ROS1; encoding a DNA demethylation protein). The suppressor is a mutation in the gene encoding the largest subunit of replication factor C (RFC1). This mutation of RFC1 reactivates the unlinked 35S-NPTII transgene, which is silenced in ros1 and also increases expression of the pericentromeric Athila retrotransposons named transcriptional silent information in a DNA methylationindependent manner. rfc1 is more sensitive than the wild type to the DNA-damaging agent methylmethane sulphonate and to the DNA inter- and intra- cross-linking agent cisplatin. The rfc1 mutant constitutively expresses the G2/M-specific cyclin CycB1;1 and other DNA repair-related genes. Treatment with DNA-damaging agents mimics the rfc1 mutation in releasing the silenced 35S-NPTII, suggesting that spontaneously induced genomic instability caused by the rfc1 mutation might partially contribute to the released transcriptional gene silencing (TGS). The frequency of somatic homologous recombination is significantly increased in the rfc1 mutant. Interestingly, ros1 mutants show increased telomere length, but rfc1 mutants show decreased telomere length and reduced expression of telomerase. Our results suggest that RFC1 helps mediate genomic stability and TGS in Arabidopsis thaliana. © 2010 American Society of Plant Biologists.

  9. Characterizing highly dynamic conformational states: The transcription bubble in RNAP-promoter open complex as an example

    Science.gov (United States)

    Lerner, Eitan; Ingargiola, Antonino; Weiss, Shimon

    2018-03-01

    Bio-macromolecules carry out complicated functions through structural changes. To understand their mechanism of action, the structure of each step has to be characterized. While classical structural biology techniques allow the characterization of a few "structural snapshots" along the enzymatic cycle (usually of stable conformations), they do not cover all (and often fast interconverting) structures in the ensemble, where each may play an important functional role. Recently, several groups have demonstrated that structures of different conformations in solution could be solved by measuring multiple distances between different pairs of residues using single-molecule Förster resonance energy transfer (smFRET) and using them as constrains for hybrid/integrative structural modeling. However, this approach is limited in cases where the conformational dynamics is faster than the technique's temporal resolution. In this study, we combine existing tools that elucidate sub-millisecond conformational dynamics together with hybrid/integrative structural modeling to study the conformational states of the transcription bubble in the bacterial RNA polymerase-promoter open complex (RPo). We measured microsecond alternating laser excitation-smFRET of differently labeled lacCONS promoter dsDNA constructs. We used a combination of burst variance analysis, photon-by-photon hidden Markov modeling, and the FRET-restrained positioning and screening approach to identify two conformational states for RPo. The experimentally derived distances of one conformational state match the known crystal structure of bacterial RPo. The experimentally derived distances of the other conformational state have characteristics of a scrunched RPo. These findings support the hypothesis that sub-millisecond dynamics in the transcription bubble are responsible for transcription start site selection.

  10. Engineered zinc-finger transcription factors inhibit the replication and transcription of HBV in vitro and in vivo.

    Science.gov (United States)

    Luo, Wei; Wang, Junxia; Xu, Dengfeng; Bai, Huili; Zhang, Yangli; Zhang, Yuhong; Li, Xiaosong

    2018-04-01

    In the present study, an artificial zinc-finger transcription factor eukaryotic expression vector specifically recognizing and binding to the hepatitis B virus (HBV) enhancer (Enh) was constructed, which inhibited the replication and expression of HBV DNA. The HBV EnhI‑specific pcDNA3.1‑artificial transcription factor (ATF) vector was successfully constructed, and then transformed or injected into HepG2.2.15 cells and HBV transgenic mice, respectively. The results demonstrated that the HBV EnhI (1,070‑1,234 bp)‑specific ATF significantly inhibited the replication and transcription of HBV DNA in vivo and in vitro. The HBV EnhI‑specific ATF may be a meritorious component of progressive combination therapies for eliminating HBV DNA in infected patients. A radical cure for chronic HBV infection may become feasible by using this bioengineering technology.

  11. Bacteriophage T5 encodes a homolog of the eukaryotic transcription coactivator PC4 implicated in recombination-dependent DNA replication.

    Science.gov (United States)

    Steigemann, Birthe; Schulz, Annina; Werten, Sebastiaan

    2013-11-15

    The RNA polymerase II cofactor PC4 globally regulates transcription of protein-encoding genes through interactions with unwinding DNA, the basal transcription machinery and transcription activators. Here, we report the surprising identification of PC4 homologs in all sequenced representatives of the T5 family of bacteriophages, as well as in an archaeon and seven phyla of eubacteria. We have solved the crystal structure of the full-length T5 protein at 1.9Å, revealing a striking resemblance to the characteristic single-stranded DNA (ssDNA)-binding core domain of PC4. Intriguing novel structural features include a potential regulatory region at the N-terminus and a C-terminal extension of the homodimerisation interface. The genome organisation of T5-related bacteriophages points at involvement of the PC4 homolog in recombination-dependent DNA replication, strongly suggesting that the protein corresponds to the hitherto elusive replicative ssDNA-binding protein of the T5 family. Our findings imply that PC4-like factors intervene in multiple unwinding-related processes by acting as versatile modifiers of nucleic acid conformation and raise the possibility that the eukaryotic transcription coactivator derives from ancestral DNA replication, recombination and repair factors. © 2013.

  12. Rift valley fever virus nonstructural protein NSs promotes viral RNA replication and transcription in a minigenome system.

    Science.gov (United States)

    Ikegami, Tetsuro; Peters, C J; Makino, Shinji

    2005-05-01

    Rift Valley fever virus (RVFV), which belongs to the genus Phlebovirus, family Bunyaviridae, has a tripartite negative-strand genome (S, M, and L segments) and is an important mosquito-borne pathogen for domestic animals and humans. We established an RVFV T7 RNA polymerase-driven minigenome system in which T7 RNA polymerase from an expression plasmid drove expression of RNA transcripts for viral proteins and minigenome RNA transcripts carrying a reporter gene between both termini of the M RNA segment in 293T cells. Like other viruses of the Bunyaviridae family, replication and transcription of the RVFV minigenome required expression of viral N and L proteins. Unexpectedly, the coexpression of an RVFV nonstructural protein, NSs, with N and L proteins resulted in a significant enhancement of minigenome RNA replication. Coexpression of NSs protein with N and L proteins also enhanced minigenome mRNA transcription in the cells expressing viral-sense minigenome RNA transcripts. NSs protein expression increased the RNA replication of minigenomes that originated from S and L RNA segments. Enhancement of minigenome RNA synthesis by NSs protein occurred in cells lacking alpha/beta interferon (IFN-alpha/beta) genes, indicating that the effect of NSs protein on minigenome RNA replication was unrelated to a putative NSs protein-induced inhibition of IFN-alpha/beta production. Our finding that RVFV NSs protein augmented minigenome RNA synthesis was in sharp contrast to reports that Bunyamwera virus (genus Bunyavirus) NSs protein inhibits viral minigenome RNA synthesis, suggesting that RVFV NSs protein and Bunyamwera virus NSs protein have distinctly different biological roles in viral RNA synthesis.

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

    Science.gov (United States)

    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

  14. Wolbachia Blocks Viral Genome Replication Early in Infection without a Transcriptional Response by the Endosymbiont or Host Small RNA Pathways.

    Directory of Open Access Journals (Sweden)

    Stephanie M Rainey

    2016-04-01

    Full Text Available The intracellular endosymbiotic bacterium Wolbachia can protect insects against viral infection, and is being introduced into mosquito populations in the wild to block the transmission of arboviruses that infect humans and are a major public health concern. To investigate the mechanisms underlying this antiviral protection, we have developed a new model system combining Wolbachia-infected Drosophila melanogaster cell culture with the model mosquito-borne Semliki Forest virus (SFV; Togaviridae, Alphavirus. Wolbachia provides strong antiviral protection rapidly after infection, suggesting that an early stage post-infection is being blocked. Wolbachia does appear to have major effects on events distinct from entry, assembly or exit as it inhibits the replication of an SFV replicon transfected into the cells. Furthermore, it causes a far greater reduction in the expression of proteins from the 3' open reading frame than the 5' non-structural protein open reading frame, indicating that it is blocking the replication of viral RNA. Further to this separation of the replicase proteins and viral RNA in transreplication assays shows that uncoupling of viral RNA and replicase proteins does not overcome Wolbachia's antiviral activity. This further suggests that replicative processes are disrupted, such as translation or replication, by Wolbachia infection. This may occur by Wolbachia mounting an active antiviral response, but the virus did not cause any transcriptional response by the bacterium, suggesting that this is not the case. Host microRNAs (miRNAs have been implicated in protection, but again we found that host cell miRNA expression was unaffected by the bacterium and neither do our findings suggest any involvement of the antiviral siRNA pathway. We conclude that Wolbachia may directly interfere with early events in virus replication such as translation of incoming viral RNA or RNA transcription, and this likely involves an intrinsic (as opposed to

  15. Interaction between FMDV Lpro and transcription factor ADNP is required for viral replication

    Science.gov (United States)

    The foot-and-mouth disease virus (FMDV) leader protease (Lpro) inhibits host translation and transcription affecting the expression of several factors involved in innate immunity. In this study, we have identified the host transcription factor ADNP (activity dependent neuroprotective protein) as an ...

  16. A transgenic mouse marking live replicating cells reveals in vivo transcriptional program of proliferation

    DEFF Research Database (Denmark)

    Klochendler, Agnes; Weinberg-Corem, Noa; Moran, Maya

    2012-01-01

    Most adult mammalian tissues are quiescent, with rare cell divisions serving to maintain homeostasis. At present, the isolation and study of replicating cells from their in vivo niche typically involves immunostaining for intracellular markers of proliferation, causing the loss of sensitive biolo...

  17. Genomics and structure/function studies of Rhabdoviridae proteins involved in replication and transcription.

    Science.gov (United States)

    Assenberg, R; Delmas, O; Morin, B; Graham, S C; De Lamballerie, X; Laubert, C; Coutard, B; Grimes, J M; Neyts, J; Owens, R J; Brandt, B W; Gorbalenya, A; Tucker, P; Stuart, D I; Canard, B; Bourhy, H

    2010-08-01

    Some mammalian rhabdoviruses may infect humans, and also infect invertebrates, dogs, and bats, which may act as vectors transmitting viruses among different host species. The VIZIER programme, an EU-funded FP6 program, has characterized viruses that belong to the Vesiculovirus, Ephemerovirus and Lyssavirus genera of the Rhabdoviridae family to perform ground-breaking research on the identification of potential new drug targets against these RNA viruses through comprehensive structural characterization of the replicative machinery. The contribution of VIZIER programme was of several orders. First, it contributed substantially to research aimed at understanding the origin, evolution and diversity of rhabdoviruses. This diversity was then used to obtain further structural information on the proteins involved in replication. Two strategies were used to produce recombinant proteins by expression of both full length or domain constructs in either E. coli or insect cells, using the baculovirus system. In both cases, parallel cloning and expression screening at small-scale of multiple constructs based on different viruses including the addition of fusion tags, was key to the rapid generation of expression data. As a result, some progress has been made in the VIZIER programme towards dissecting the multi-functional L protein into components suitable for structural and functional studies. However, the phosphoprotein polymerase co-factor and the structural matrix protein, which play a number of roles during viral replication and drives viral assembly, have both proved much more amenable to structural biology. Applying the multi-construct/multi-virus approach central to protein production processes in VIZIER has yielded new structural information which may ultimately be exploitable in the derivation of novel ways of intervening in viral replication. Copyright 2010 Elsevier B.V. All rights reserved.

  18. RECQ5 helicase promotes resolution of conflicts between replication and transcription in human cells

    Czech Academy of Sciences Publication Activity Database

    Urban, Václav; Dobrovolná, Jana; Hühn, D.; Fryzelkova, Jana; Bartek, Jiří; Janščák, Pavel

    2016-01-01

    Roč. 214, č. 4 (2016), s. 401-415 ISSN 0021-9525 R&D Projects: GA ČR(CZ) GA14-05743S; GA MŠk LH14037 Institutional support: RVO:68378050 Keywords : rna-polymerase-ii * fragile sites * homologous recombination * genome instability * dna-replication * genes * fork * protein * stress * brca1 Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 7.955, year: 2016

  19. In vitro-reconstituted nucleoids can block mitochondrial DNA replication and transcription

    NARCIS (Netherlands)

    Farge, Géraldine; Mehmedovic, Majda; Baclayon, Marian; van den Wildenberg, Siet M J L; Roos, Wouter H; Gustafsson, Claes M; Wuite, Gijs J L; Falkenberg, Maria

    2014-01-01

    The mechanisms regulating the number of active copies of mtDNA are still unclear. A mammalian cell typically contains 1,000-10,000 copies of mtDNA, which are packaged into nucleoprotein complexes termed nucleoids. The main protein component of these structures is mitochondrial transcription factor A

  20. Genome-Wide Search for Competing Endogenous RNAs Responsible for the Effects Induced by Ebola Virus Replication and Transcription Using a trVLP System

    Directory of Open Access Journals (Sweden)

    Zhong-Yi Wang

    2017-11-01

    Full Text Available Understanding how infected cells respond to Ebola virus (EBOV and how this response changes during the process of viral replication and transcription are very important for establishing effective antiviral strategies. In this study, we conducted a genome-wide screen to identify long non-coding RNAs (lncRNAs, circular RNAs (circRNAs, micro RNAs (miRNAs, and mRNAs differentially expressed during replication and transcription using a tetracistronic transcription and replication-competent virus-like particle (trVLP system that models the life cycle of EBOV in 293T cells. To characterize the expression patterns of these differentially expressed RNAs, we performed a series cluster analysis, and up- or down-regulated genes were selected to establish a gene co-expression network. Competing endogenous RNA (ceRNA networks based on the RNAs responsible for the effects induced by EBOV replication and transcription in human cells, including circRNAs, lncRNAs, miRNAs, and mRNAs, were constructed for the first time. Based on these networks, the interaction details of circRNA-chr19 were explored. Our results demonstrated that circRNA-chr19 targeting miR-30b-3p regulated CLDN18 expression by functioning as a ceRNA. These findings may have important implications for further studies of the mechanisms of EBOV replication and transcription. These RNAs potentially have important functions and may be promising targets for EBOV therapy.

  1. Transcriptional Changes during Naturally Acquired Zika Virus Infection Render Dendritic Cells Highly Conducive to Viral Replication.

    Science.gov (United States)

    Sun, Xiaoming; Hua, Stephane; Chen, Hsiao-Rong; Ouyang, Zhengyu; Einkauf, Kevin; Tse, Samantha; Ard, Kevin; Ciaranello, Andrea; Yawetz, Sigal; Sax, Paul; Rosenberg, Eric S; Lichterfeld, Mathias; Yu, Xu G

    2017-12-19

    Although dendritic cells are among the human cell population best equipped for cell-intrinsic antiviral immune defense, they seem highly susceptible to infection with the Zika virus (ZIKV). Using highly purified myeloid dendritic cells isolated from individuals with naturally acquired acute infection, we here show that ZIKV induces profound perturbations of transcriptional signatures relative to healthy donors. Interestingly, we noted a remarkable downregulation of antiviral interferon-stimulated genes and innate immune sensors, suggesting that ZIKV can actively suppress interferon-dependent immune responses. In contrast, several host factors known to support ZIKV infection were strongly upregulated during natural ZIKV infection; these transcripts included AXL, the main entry receptor for ZIKV; SOCS3, a negative regulator of ISG expression; and IDO-1, a recognized inducer of regulatory T cell responses. Thus, during in vivo infection, ZIKV can transform the transcriptome of dendritic cells in favor of the virus to render these cells highly conducive to ZIKV infection. Published by Elsevier Inc.

  2. Morphological correlates of genital HPV infection: Viral replication, transcription and gene expression

    International Nuclear Information System (INIS)

    Crum, C.P.; Friedman, D.; Nuovo, G.; Silverstein, S.J.

    1987-01-01

    Current studies indicate a strong correlation between specific morphological changes and the presence of certain HPV strains in precancerous squamous epithelium of the cervix, vulva and vagina. HPV type 16 is the most commonly detected HPV type in cervical lesions in our experience, and 85% of these lesions exhibit some morphological features associated with aneuploid epithelium (CIN). However, over 50% of these lesions containing HPV 16 DNA exhibit, in addition, foci of epithelium indistinguishable from condyloma, although in our experience, only one HPV type(16) is detected in the majority of these lesions. DNA-DNA in situ hybridization analysis of these lesions containing HPV 16 DNA has demonstrated nucleic acids in areas resembling both condyloma and CIN, with the greatest concentration in mature cells containing cytoplasmic maturation. Ten percent of lesions containing HPV 16 produce detectable capsid antigens, and we have confirmed the presence of these antigens in the same areas which hybridize in-situ for HPV DNA. Recent studies using biotin and S-35 labeled RNa probes constructed in GEM-1 vectors indicate that early HPV genes are expressed primarily in the upper (more mature) regions of the neoplastic epithelium. Thus maturation appears to exert a positive influence on a variety of HPV functions in neoplastic epithelium, including DNA replication, early and late gene expression. It is possible that patterns of gene expression may vary between lesions associated with different HPV types or different morphologies. This possibility is being explored

  3. BRD4 Phosphorylation Regulates HPV E2-Mediated Viral Transcription, Origin Replication, and Cellular MMP-9 Expression

    Directory of Open Access Journals (Sweden)

    Shwu-Yuan Wu

    2016-08-01

    Full Text Available Post-translational modification can modulate protein conformation and alter binding partner recruitment within gene regulatory regions. Here, we report that bromodomain-containing protein 4 (BRD4, a transcription co-factor and chromatin regulator, uses a phosphorylation-induced switch mechanism to recruit E2 protein encoded by cancer-associated human papillomavirus (HPV to viral early gene and cellular matrix metalloproteinase-9 (MMP-9 promoters. Enhanced MMP-9 expression, induced upon keratinocyte differentiation, occurs via BRD4-dependent recruitment of active AP-1 and NF-κB to their target sequences. This is triggered by replacement of AP-1 family members JunB and JunD by c-Jun and by re-localization of NF-κB from the cytoplasm to the nucleus. In addition, BRD4 phosphorylation is critical for E2- and origin-dependent HPV DNA replication. A class of phospho-BRD4-targeting compounds, distinct from the BET bromodomain inhibitors, effectively blocks BRD4 phosphorylation-specific functions in transcription and factor recruitment.

  4. In Vitro Whole Genome DNA Binding Analysis of the Bacterial Replication Initiator and Transcription Factor DnaA.

    Directory of Open Access Journals (Sweden)

    Janet L Smith

    2015-05-01

    Full Text Available DnaA, the replication initiation protein in bacteria, is an AAA+ ATPase that binds and hydrolyzes ATP and exists in a heterogeneous population of ATP-DnaA and ADP-DnaA. DnaA binds cooperatively to the origin of replication and several other chromosomal regions, and functions as a transcription factor at some of these regions. We determined the binding properties of Bacillus subtilis DnaA to genomic DNA in vitro at single nucleotide resolution using in vitro DNA affinity purification and deep sequencing (IDAP-Seq. We used these data to identify 269 binding regions, refine the consensus sequence of the DnaA binding site, and compare the relative affinity of binding regions for ATP-DnaA and ADP-DnaA. Most sites had a slightly higher affinity for ATP-DnaA than ADP-DnaA, but a few had a strong preference for binding ATP-DnaA. Of the 269 sites, only the eight strongest binding ones have been observed to bind DnaA in vivo, suggesting that other cellular factors or the amount of available DnaA in vivo restricts DnaA binding to these additional sites. Conversely, we found several chromosomal regions that were bound by DnaA in vivo but not in vitro, and that the nucleoid-associated protein Rok was required for binding in vivo. Our in vitro characterization of the inherent ability of DnaA to bind the genome at single nucleotide resolution provides a backdrop for interpreting data on in vivo binding and regulation of DnaA, and is an approach that should be adaptable to many other DNA binding proteins.

  5. msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.

    Directory of Open Access Journals (Sweden)

    Anil Raj

    Full Text Available Understanding global gene regulation depends critically on accurate annotation of regulatory elements that are functional in a given cell type. CENTIPEDE, a powerful, probabilistic framework for identifying transcription factor binding sites from tissue-specific DNase I cleavage patterns and genomic sequence content, leverages the hypersensitivity of factor-bound chromatin and the information in the DNase I spatial cleavage profile characteristic of each DNA binding protein to accurately infer functional factor binding sites. However, the model for the spatial profile in this framework fails to account for the substantial variation in the DNase I cleavage profiles across different binding sites. Neither does it account for variation in the profiles at the same binding site across multiple replicate DNase I experiments, which are increasingly available. In this work, we introduce new methods, based on multi-scale models for inhomogeneous Poisson processes, to account for such variation in DNase I cleavage patterns both within and across binding sites. These models account for the spatial structure in the heterogeneity in DNase I cleavage patterns for each factor. Using DNase-seq measurements assayed in a lymphoblastoid cell line, we demonstrate the improved performance of this model for several transcription factors by comparing against the Chip-seq peaks for those factors. Finally, we explore the effects of DNase I sequence bias on inference of factor binding using a simple extension to our framework that allows for a more flexible background model. The proposed model can also be easily applied to paired-end ATAC-seq and DNase-seq data. msCentipede, a Python implementation of our algorithm, is available at http://rajanil.github.io/msCentipede.

  6. msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.

    Science.gov (United States)

    Raj, Anil; Shim, Heejung; Gilad, Yoav; Pritchard, Jonathan K; Stephens, Matthew

    2015-01-01

    Understanding global gene regulation depends critically on accurate annotation of regulatory elements that are functional in a given cell type. CENTIPEDE, a powerful, probabilistic framework for identifying transcription factor binding sites from tissue-specific DNase I cleavage patterns and genomic sequence content, leverages the hypersensitivity of factor-bound chromatin and the information in the DNase I spatial cleavage profile characteristic of each DNA binding protein to accurately infer functional factor binding sites. However, the model for the spatial profile in this framework fails to account for the substantial variation in the DNase I cleavage profiles across different binding sites. Neither does it account for variation in the profiles at the same binding site across multiple replicate DNase I experiments, which are increasingly available. In this work, we introduce new methods, based on multi-scale models for inhomogeneous Poisson processes, to account for such variation in DNase I cleavage patterns both within and across binding sites. These models account for the spatial structure in the heterogeneity in DNase I cleavage patterns for each factor. Using DNase-seq measurements assayed in a lymphoblastoid cell line, we demonstrate the improved performance of this model for several transcription factors by comparing against the Chip-seq peaks for those factors. Finally, we explore the effects of DNase I sequence bias on inference of factor binding using a simple extension to our framework that allows for a more flexible background model. The proposed model can also be easily applied to paired-end ATAC-seq and DNase-seq data. msCentipede, a Python implementation of our algorithm, is available at http://rajanil.github.io/msCentipede.

  7. Spermine attenuates the action of the DNA intercalator, actinomycin D, on DNA binding and the inhibition of transcription and DNA replication.

    Science.gov (United States)

    Wang, Sheng-Yu; Lee, Alan Yueh-Luen; Lee, Yueh-Luen; Lai, Yi-Hua; Chen, Jeremy J W; Wu, Wen-Lin; Yuann, Jeu-Ming P; Su, Wang-Lin; Chuang, Show-Mei; Hou, Ming-Hon

    2012-01-01

    The anticancer activity of DNA intercalators is related to their ability to intercalate into the DNA duplex with high affinity, thereby interfering with DNA replication and transcription. Polyamines (spermine in particular) are almost exclusively bound to nucleic acids and are involved in many cellular processes that require nucleic acids. Until now, the effects of polyamines on DNA intercalator activities have remained unclear because intercalation is the most important mechanism employed by DNA-binding drugs. Herein, using actinomycin D (ACTD) as a model, we have attempted to elucidate the effects of spermine on the action of ACTD, including its DNA-binding ability, RNA and DNA polymerase interference, and its role in the transcription and replication inhibition of ACTD within cells. We found that spermine interfered with the binding and stabilization of ACTD to DNA. The presence of increasing concentrations of spermine enhanced the transcriptional and replication activities of RNA and DNA polymerases, respectively, in vitro treated with ActD. Moreover, a decrease in intracellular polyamine concentrations stimulated by methylglyoxal-bis(guanylhydrazone) (MGBG) enhanced the ACTD-induced inhibition of c-myc transcription and DNA replication in several cancer cell lines. The results indicated that spermine attenuates ACTD binding to DNA and its inhibition of transcription and DNA replication both in vitro and within cells. Finally, a synergistic antiproliferative effect of MGBG and ACTD was observed in a cell viability assay. Our findings will be of significant relevance to future developments in combination with cancer therapy by enhancing the anticancer activity of DNA interactors through polyamine depletion.

  8. Spermine attenuates the action of the DNA intercalator, actinomycin D, on DNA binding and the inhibition of transcription and DNA replication.

    Directory of Open Access Journals (Sweden)

    Sheng-Yu Wang

    Full Text Available The anticancer activity of DNA intercalators is related to their ability to intercalate into the DNA duplex with high affinity, thereby interfering with DNA replication and transcription. Polyamines (spermine in particular are almost exclusively bound to nucleic acids and are involved in many cellular processes that require nucleic acids. Until now, the effects of polyamines on DNA intercalator activities have remained unclear because intercalation is the most important mechanism employed by DNA-binding drugs. Herein, using actinomycin D (ACTD as a model, we have attempted to elucidate the effects of spermine on the action of ACTD, including its DNA-binding ability, RNA and DNA polymerase interference, and its role in the transcription and replication inhibition of ACTD within cells. We found that spermine interfered with the binding and stabilization of ACTD to DNA. The presence of increasing concentrations of spermine enhanced the transcriptional and replication activities of RNA and DNA polymerases, respectively, in vitro treated with ActD. Moreover, a decrease in intracellular polyamine concentrations stimulated by methylglyoxal-bis(guanylhydrazone (MGBG enhanced the ACTD-induced inhibition of c-myc transcription and DNA replication in several cancer cell lines. The results indicated that spermine attenuates ACTD binding to DNA and its inhibition of transcription and DNA replication both in vitro and within cells. Finally, a synergistic antiproliferative effect of MGBG and ACTD was observed in a cell viability assay. Our findings will be of significant relevance to future developments in combination with cancer therapy by enhancing the anticancer activity of DNA interactors through polyamine depletion.

  9. Olean-18-ene triterpenoids from Celastraceae species inhibit HIV replication targeting NF-kB and Sp1 dependent transcription.

    Science.gov (United States)

    Osorio, Alex A; Muñóz, Alejandro; Torres-Romero, David; Bedoya, Luis M; Perestelo, Nayra R; Jiménez, Ignacio A; Alcamí, José; Bazzocchi, Isabel L

    2012-06-01

    In the present study we report the isolation of nine new olean-18-ene triterpenes (1-9), along with three known ones (10-12), from Cassine xylocarpa and Maytenus jelskii. Their stereostructures have been elucidated on the basis of spectroscopic analysis, including 1D and 2D NMR techniques (COSY, ROESY, HSQC and HMBC), and spectrometric methods. The natural compounds and derivatives 13-15 have been tested for their potential as inhibitors of human immunodeficiency virus type 1 replication. Five compounds from this series displayed potent antiviral activity with IC(50)s in the micromolar range (1, 3, 4, 7 and 8) being 1 and 8 the most active compounds. The target of these compounds was different from antiretroviral drugs currently licensed as they act as inhibitors of enhancer-dependent transcription. The structure-activity relationships were established based on the regiosubstitution and oxidation degree of the triterpene scaffold, revealing that these aspects were able to modulate the selectivity and intensity of HIV inhibition. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  10. Science Bubbles

    DEFF Research Database (Denmark)

    Hendricks, Vincent Fella; Pedersen, David Budtz

    2013-01-01

    Much like the trade and trait sof bubbles in financial markets,similar bubbles appear on the science market. When economic bubbles burst, the drop in prices causes the crash of unsustainable investments leading to an investor confidence crisis possibly followed by a financial panic. But when...... bubbles appear in science, truth and reliability are the first victims. This paper explores how fashions in research funding and research management may turn science into something like a bubble economy....

  11. A Rapid Screen for Host-Encoded miRNAs with Inhibitory Effects against Ebola Virus Using a Transcription- and Replication-Competent Virus-Like Particle System

    Directory of Open Access Journals (Sweden)

    Zhongyi Wang

    2018-05-01

    Full Text Available MicroRNAs (miRNAs may become efficient antiviral agents against the Ebola virus (EBOV targeting viral genomic RNAs or transcripts. We previously conducted a genome-wide search for differentially expressed miRNAs during viral replication and transcription. In this study, we established a rapid screen for miRNAs with inhibitory effects against EBOV using a tetracistronic transcription- and replication-competent virus-like particle (trVLP system. This system uses a minigenome comprising an EBOV leader region, luciferase reporter, VP40, GP, VP24, EBOV trailer region, and three noncoding regions from the EBOV genome and can be used to model the life cycle of EBOV under biosafety level (BSL 2 conditions. Informatic analysis was performed to select up-regulated miRNAs targeting the coding regions of the minigenome with the highest binding energy to perform inhibitory effect screening. Among these miRNAs, miR-150-3p had the most significant inhibitory effect. Reverse transcription polymerase chain reaction (RT-PCR, Western blot, and double fluorescence reporter experiments demonstrated that miR-150-3p inhibited the reproduction of trVLPs via the regulation of GP and VP40 expression by directly targeting the coding regions of GP and VP40. This novel, rapid, and convenient screening method will efficiently facilitate the exploration of miRNAs against EBOV under BSL-2 conditions.

  12. Efficient replication of the in vitro transcripts from cloned cDNA of tomato black ring virus satellite RNA requires the 48K satellite RNA-encoded protein.

    Science.gov (United States)

    Hemmer, O; Oncino, C; Fritsch, C

    1993-06-01

    Tomato black ring virus isolate L supports the multiplication of a large satellite RNA of 1376 nt which has no common features with the two genomic RNAs except for the terminal motif 5' VPg UUGAAAA and a 3' poly(A) tail. The TBRV sat-RNA contains an ORF for a protein of 48K which is translated both in vitro and in vivo. To determine the function of the 48K protein we have studied the effect of different mutations introduced in the ORF of the cDNA clone on the capacity of transcripts to multiply in Chenopodium quinoa plants or protoplasts when inoculated along with the genomic RNAs. Transcripts in which nucleotides have been substituted within the 5' proximal region of the ORF multiplied poorly even when the modification conserved the 48K protein sequence, suggesting that this portion of the ORF contains cis-acting RNA sequences. Transcripts with alterations in the internal region of the ORF retained their multiplication capacity provided the mutation did not destroy the ORF or modify the length of the protein expressed. The absence of multiplication in plants of transcripts unable to express the 48K protein and their inability to replicate in protoplasts suggest strongly that the sat-RNA translation product itself is implicated in the replication of sat-RNA.

  13. SIRT3 restricts HBV transcription and replication via epigenetic regulation of cccDNA involving SUV39H1 and SETD1A histone methyltransferases.

    Science.gov (United States)

    Ren, Ji-Hua; Hu, Jie-Li; Cheng, Sheng-Tao; Yu, Hai-Bo; Wong, Vincent Kam Wai; Law, Betty Yuen Kwan; Yang, Yong-Feng; Huang, Ying; Liu, Yi; Chen, Wei-Xian; Cai, Xue-Fei; Tang, Hua; Hu, Yuan; Zhang, Wen-Lu; Liu, Xiang; Long, Quan-Xin; Zhou, Li; Tao, Na-Na; Zhou, Hong-Zhong; Yang, Qiu-Xia; Ren, Fang; He, Lin; Gong, Rui; Huang, Ai-Long; Chen, Juan

    2018-04-06

    Hepatitis B virus (HBV) infection remains a major health problem worldwide. Maintenance of the covalently closed circular DNA (cccDNA) which serves as a template for HBV RNA transcription is responsible for the failure of eradicating chronic HBV during current antiviral therapy. cccDNA is assembled with cellular histone proteins into chromatin, but little is known about the regulation of HBV chromatin by histone posttranslational modifications. In this study, we identified SIRT3 as a host factor restricting HBV transcription and replication by screening seven members of Sirtuin family which is the class III histone deacetylase. Ectopic SIRT3 expression significantly reduced total HBV RNAs, 3.5-kb RNA as well as replicative intermediate DNA in HBV-infected HepG2-NTCP cells and PHH. In contrast, gene silencing of SIRT3 promoted HBV transcription and replication. Mechanistic study found nuclear SIRT3 was recruited to the HBV cccDNA, where it deacetylated histone 3 lysine 9 (H3K9). Importantly, occupancy of SIRT3 onto cccDNA could increase the recruitment of histone methyltransferase SUV39H1 to cccDNA and decrease recruitment of SETD1A, leading to a marked increase of H3K9me3 and a decrease of H3K4me3 on cccDNA. Moreover, SIRT3-mediated HBV cccDNA transcriptional repression involved decreased binding of host RNA polymerase II and transcription factor YY1 to cccDNA. Finally, viral protein HBx could relieve SIRT3-mediated cccDNA transcriptional repression by inhibiting both SIRT3 expression and its recruitment to cccDNA. SIRT3 is a novel host factor epigenetically restricting HBV cccDNA transcription by acting cooperatively with histone methyltransferase. These data provided a rational for the use of SIRT3 activators in the prevention or treatment of HBV infection. This article is protected by copyright. All rights reserved. © 2018 by the American Association for the Study of Liver Diseases.

  14. Ddx19 links mRNA nuclear export with progression of transcription and replication and suppresses genomic instability upon DNA damage in proliferating cells.

    Science.gov (United States)

    Hodroj, Dana; Serhal, Kamar; Maiorano, Domenico

    2017-09-03

    The DEAD-box Helicase 19 (Ddx19) gene codes for an RNA helicase involved in both mRNA (mRNA) export from the nucleus into the cytoplasm and in mRNA translation. In unperturbed cells, Ddx19 localizes in the cytoplasm and at the cytoplasmic face of the nuclear pore. Here we review recent findings related to an additional Ddx19 function in the nucleus in resolving RNA:DNA hybrids (R-loops) generated during collision between transcription and replication, and upon DNA damage. Activation of a DNA damage response pathway dependent upon the ATR kinase, a major regulator of replication fork progression, stimulates translocation of the Ddx19 protein from the cytoplasm into the nucleus. Only nuclear Ddx19 is competent to resolve R-loops, and down regulation of Ddx19 expression induces DNA double strand breaks only in proliferating cells. Overall these observations put forward Ddx19 as an important novel mediator of the crosstalk between transcription and replication.

  15. Regulation of human histone gene expression: transcriptional and posttranscriptional control in the coupling of histone messenger RNA stability with DNA replication

    International Nuclear Information System (INIS)

    Baumbach, L.L.; Stein, G.S.; Stein, J.L.

    1987-01-01

    The extent to which transcriptional and posttranscriptional regulation contributes to the coupling of histone gene expression and DNA replication was examined during the cell cycle in synchronized HeLa S3 cells. Rates of transcription were determined in vitro in isolated nuclei. A 3-5-fold increase in cell cycle dependent histone gene transcription was observed in early S phase, prior to the peak of DNA synthesis. This result is consistent with a previous determination of histone mRNA synthesis in intact cells. The transcription of these genes did not change appreciably after inhibition of DNA replication by hydroxyurea treatment, although Northern blot analysis indicated that cellular levels of histone mRNA decreased rapidly in the presence of the drug. Total cellular levels of histone mRNA closely parallel the rate of DNA synthesis as a function of cell cycle progression, reaching a maximal 20-fold increase as compared with non S phase levels. This DNA synthesis dependent accumulation of histone mRNA occurs predominantly in the cytoplasm and appears to be mediated primarily by control of histone mRNA stability. Changes in nuclear histone mRNA levels were less pronounced. These combined observations suggest that both transcriptional regulation and posttranscriptional regulation contribute toward control of the cell cycle dependent accumulation of histone mRNA during S phase, while the stability of histone mRNA throughout S phase and the selective turnover of histone mRNAs, either at the natural termination of S phase or following inhibition of DNA synthesis, are posttranscriptionally regulated

  16. Sticky bubbles

    NARCIS (Netherlands)

    Antoniuk, O.; Bos, van der A.; Driessen, T.W.; Es, van B.; Jeurissen, R.J.M.; Michler, D.; Reinten, H.; Schenker, M.; Snoeijer, J.H.; Srivastava, S.; Toschi, F.; Wijshoff, H.M.A.

    2011-01-01

    We discuss the physical forces that are required to remove an air bubble immersed in a liquid from a corner. This is relevant for inkjet printing technology, as the presence of air bubbles in the channels of a printhead perturbs the jetting of droplets. A simple strategy to remove the bubble is to

  17. PRMT5 restricts hepatitis B virus replication through epigenetic repression of covalently closed circular DNA transcription and interference with pregenomic RNA encapsidation.

    Science.gov (United States)

    Zhang, Wen; Chen, Jieliang; Wu, Min; Zhang, Xiaonan; Zhang, Min; Yue, Lei; Li, Yaming; Liu, Jiangxia; Li, Baocun; Shen, Fang; Wang, Yang; Bai, Lu; Protzer, Ulrike; Levrero, Massimo; Yuan, Zhenghong

    2017-08-01

    Chronic hepatitis B virus (HBV) infection remains a major health problem worldwide. The covalently closed circular DNA (cccDNA) minichromosome, which serves as the template for the transcription of viral RNAs, plays a key role in viral persistence. While accumulating evidence suggests that cccDNA transcription is regulated by epigenetic machinery, particularly the acetylation of cccDNA-bound histone 3 (H3) and H4, the potential contributions of histone methylation and related host factors remain obscure. Here, by screening a series of methyltransferases and demethylases, we identified protein arginine methyltransferase 5 (PRMT5) as an effective restrictor of HBV transcription and replication. In cell culture-based models for HBV infection and in liver tissues of patients with chronic HBV infection, we found that symmetric dimethylation of arginine 3 on H4 on cccDNA was a repressive marker of cccDNA transcription and was regulated by PRMT5 depending on its methyltransferase domain. Moreover, PRMT5-triggered symmetric dimethylation of arginine 3 on H4 on the cccDNA minichromosome involved an interaction with the HBV core protein and the Brg1-based human SWI/SNF chromatin remodeler, which resulted in down-regulation of the binding of RNA polymerase II to cccDNA. In addition to the inhibitory effect on cccDNA transcription, PRMT5 inhibited HBV core particle DNA production independently of its methyltransferase activity. Further study revealed that PRMT5 interfered with pregenomic RNA encapsidation by preventing its interaction with viral polymerase protein through binding to the reverse transcriptase-ribonuclease H region of polymerase, which is crucial for the polymerase-pregenomic RNA interaction. PRMT5 restricts HBV replication through a two-part mechanism including epigenetic suppression of cccDNA transcription and interference with pregenomic RNA encapsidation; these findings improve the understanding of epigenetic regulation of HBV transcription and host

  18. Freezing Bubbles

    Science.gov (United States)

    Kingett, Christian; Ahmadi, Farzad; Nath, Saurabh; Boreyko, Jonathan

    2017-11-01

    The two-stage freezing process of a liquid droplet on a substrate is well known; however, how bubbles freeze has not yet been studied. We first deposited bubbles on a silicon substrate that was chilled at temperatures ranging from -10 °C to -40 °C, while the air was at room temperature. We observed that the freeze front moved very slowly up the bubble, and in some cases, even came to a complete halt at a critical height. This slow freezing front propagation can be explained by the low thermal conductivity of the thin soap film, and can be observed more clearly when the bubble size or the surface temperature is increased. This delayed freezing allows the frozen portion of the bubble to cool the air within the bubble while the top part is still liquid, which induces a vapor pressure mismatch that either collapses the top or causes the top to pop. In cases where the freeze front reaches the top of the bubble, a portion of the top may melt and slowly refreeze; this can happen more than just once for a single bubble. We also investigated freezing bubbles inside of a freezer where the air was held at -20 °C. In this case, the bubbles freeze quickly and the ice grows radially from nucleation sites instead of perpendicular to the surface, which provides a clear contrast with the conduction limited room temperature bubbles.

  19. Codon and amino acid usage in two major human pathogens of genus Bartonella--optimization between replicational-transcriptional selection, translational control and cost minimization.

    Science.gov (United States)

    Das, Sabyasachi; Paul, Sandip; Chatterjee, Sanjib; Dutta, Chitra

    2005-01-01

    Intra-genomic variation in synonymous codon and amino acid usage in two human pathogens Bartonella henselae and B. quintana has been carried out through multivariate analysis. Asymmetric mutational bias, coupled with replicational-transcriptional selection, has been identified as the prime selection force behind synonymous codon selection--a characteristic of the genus Bartonella, not exhibited by any other alpha-proteobacterial genome. Distinct codon usage patterns and low synonymous divergence values between orthologous sequences of highly expressed genes from the two Bartonella species indicate that there exists a residual intra-strand synonymous codon bias in the highly expressed genes, possibly operating at the level of translation. In the case of amino acid usage, the mean hydropathy level and aromaticity are the major sources of variation, both having nearly equal impact, while strand-specific mutational pressure and gene expressivity strongly influence the inter-strand variations. In both species under study, the highly expressed gene products tend not to contain heavy and/or aromatic residues, following the cost-minimization hypothesis in spite of their intracellular lifestyle. The codon and amino acid usage in these two human pathogens are, therefore, consequences of a complex balance between replicational-transcriptional selection, translational control, protein hydropathy and cost minimization.

  20. DNA-Binding Properties of African Swine Fever Virus pA104R, a Histone-Like Protein Involved in Viral Replication and Transcription.

    Science.gov (United States)

    Frouco, Gonçalo; Freitas, Ferdinando B; Coelho, João; Leitão, Alexandre; Martins, Carlos; Ferreira, Fernando

    2017-06-15

    African swine fever virus (ASFV) codes for a putative histone-like protein (pA104R) with extensive sequence homology to bacterial proteins that are implicated in genome replication and packaging. Functional characterization of purified recombinant pA104R revealed that it binds to single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) over a wide range of temperatures, pH values, and salt concentrations and in an ATP-independent manner, with an estimated binding site size of about 14 to 16 nucleotides. Using site-directed mutagenesis, the arginine located in pA104R's DNA-binding domain, at position 69, was found to be relevant for efficient DNA-binding activity. Together, pA104R and ASFV topoisomerase II (pP1192R) display DNA-supercoiling activity, although none of the proteins by themselves do, indicating that the two cooperate in this process. In ASFV-infected cells, A104R transcripts were detected from 2 h postinfection (hpi) onward, reaching a maximum concentration around 16 hpi. pA104R was detected from 12 hpi onward, localizing with viral DNA replication sites and being found exclusively in the Triton-insoluble fraction. Small interfering RNA (siRNA) knockdown experiments revealed that pA104R plays a critical role in viral DNA replication and gene expression, with transfected cells showing lower viral progeny numbers (up to a reduction of 82.0%), lower copy numbers of viral genomes (-78.3%), and reduced transcription of a late viral gene (-47.6%). Taken together, our results strongly suggest that pA104R participates in the modulation of viral DNA topology, probably being involved in viral DNA replication, transcription, and packaging, emphasizing that ASFV mutants lacking the A104R gene could be used as a strategy to develop a vaccine against ASFV. IMPORTANCE Recently reintroduced in Europe, African swine fever virus (ASFV) causes a fatal disease in domestic pigs, causing high economic losses in affected countries, as no vaccine or treatment is currently

  1. Bubble systems

    CERN Document Server

    Avdeev, Alexander A

    2016-01-01

    This monograph presents a systematic analysis of bubble system mathematics, using the mechanics of two-phase systems in non-equilibrium as the scope of analysis. The author introduces the thermodynamic foundations of bubble systems, ranging from the fundamental starting points to current research challenges. This book addresses a range of topics, including description methods of multi-phase systems, boundary and initial conditions as well as coupling requirements at the phase boundary. Moreover, it presents a detailed study of the basic problems of bubble dynamics in a liquid mass: growth (dynamically and thermally controlled), collapse, bubble pulsations, bubble rise and breakup. Special emphasis is placed on bubble dynamics in turbulent flows. The analysis results are used to write integral equations governing the rate of vapor generation (condensation) in non-equilibrium flows, thus creating a basis for solving a number of practical problems. This book is the first to present a comprehensive theory of boil...

  2. Cellular corepressor TLE2 inhibits replication-and-transcription- activator-mediated transactivation and lytic reactivation of Kaposi's sarcoma-associated herpesvirus.

    Science.gov (United States)

    He, Zhiheng; Liu, Yunhua; Liang, Deguang; Wang, Zhuo; Robertson, Erle S; Lan, Ke

    2010-02-01

    Replication and transcription activator (RTA) encoded by open reading frame 50 (ORF50) of Kaposi's sarcoma-associated herpesvirus (KSHV) is essential and sufficient to initiate lytic reactivation. RTA activates its target genes through direct binding with high affinity to its responsive elements or by interaction with cellular factors, such as RBP-Jkappa, Ap-1, C/EBP-alpha, and Oct-1. In this study, we identified transducin-like enhancer of split 2 (TLE2) as a novel RTA binding protein by using yeast two-hybrid screening of a human spleen cDNA library. The interaction between TLE2 and RTA was confirmed by glutathione S-transferase (GST) binding and coimmunoprecipitation assays. Immunofluorescence analysis showed that TLE2 and RTA were colocalized in the same nuclear compartment in KSHV-infected cells. This interaction recruited TLE2 to RTA bound to its recognition sites on DNA and repressed RTA auto-activation and transactivation activity. Moreover, TLE2 also inhibited the induction of lytic replication and virion production driven by RTA. We further showed that the Q (Gln-rich), SP (Ser-Pro-rich), and WDR (Trp-Asp repeat) domains of TLE2 and the Pro-rich domain of RTA were essential for this interaction. RBP-Jkappa has been shown previously to bind to the same Pro-rich domain of RTA, and this binding can be subject to competition by TLE2. In addition, TLE2 can form a complex with RTA to access the cognate DNA sequence of the RTA-responsive element at different promoters. Intriguingly, the transcription level of TLE2 could be upregulated by RTA during the lytic reactivation process. In conclusion, we identified a new RTA binding protein, TLE2, and demonstrated that TLE2 inhibited replication and transactivation mediated by RTA. This provides another potentially important mechanism for maintenance of KSHV viral latency through interaction with a host protein.

  3. Bubbles & Squat

    DEFF Research Database (Denmark)

    Højbjerre Larsen, Signe

    , a new concept called ‘Bubbles & Squat’, where fitness training is combined with Champagne and a live DJ. One of the invitations for this event describes how “we spice up your friday training with live DJ and lots of refreshing bubbles, to make sure that you are ready for the weekend (...).” Before New...

  4. Dynamic regulation of genes involved in mitochondrial DNA replication and transcription during mouse brown fat cell differentiation and recruitment

    DEFF Research Database (Denmark)

    Murholm, Maria; Dixen, Karen; Qvortrup, Klaus

    2009-01-01

    BACKGROUND: Brown adipocytes are specialised in dissipating energy through adaptive thermogenesis, whereas white adipocytes are specialised in energy storage. These essentially opposite functions are possible for two reasons relating to mitochondria, namely expression of uncoupling protein 1 (UCP1...... and brown fat, brown adipose tissue fractions and in selected adipose tissues during cold exposure. We find a massive induction of the majority of such genes during brown adipocyte differentiation and recruitment, e.g. of the mitochondrial transcription factors A (Tfam) and B2 (Tfb2m), whereas only a subset...

  5. Drosophila S2 cells are non-permissive for vaccinia virus DNA replication following entry via low pH-dependent endocytosis and early transcription.

    Directory of Open Access Journals (Sweden)

    Zain Bengali

    Full Text Available Vaccinia virus (VACV, a member of the chordopox subfamily of the Poxviridae, abortively infects insect cells. We have investigated VACV infection of Drosophila S2 cells, which are useful for protein expression and genome-wide RNAi screening. Biochemical and electron microscopic analyses indicated that VACV entry into Drosophila S2 cells depended on the VACV multiprotein entry-fusion complex but appeared to occur exclusively by a low pH-dependent endocytic mechanism, in contrast to both neutral and low pH entry pathways used in mammalian cells. Deep RNA sequencing revealed that the entire VACV early transcriptome, comprising 118 open reading frames, was robustly expressed but neither intermediate nor late mRNAs were made. Nor was viral late protein synthesis or inhibition of host protein synthesis detected by pulse-labeling with radioactive amino acids. Some reduction in viral early proteins was noted by Western blotting. Nevertheless, synthesis of the multitude of early proteins needed for intermediate gene expression was demonstrated by transfection of a plasmid containing a reporter gene regulated by an intermediate promoter. In addition, expression of a reporter gene with a late promoter was achieved by cotransfection of intermediate genes encoding the late transcription factors. The requirement for transfection of DNA templates for intermediate and late gene expression indicated a defect in viral genome replication in VACV-infected S2 cells, which was confirmed by direct analysis. Furthermore, VACV-infected S2 cells did not support the replication of a transfected plasmid, which occurs in mammalian cells and is dependent on all known viral replication proteins, indicating a primary restriction of DNA synthesis.

  6. The lytic origin of herpesvirus papio is highly homologous to Epstein-Barr virus ori-Lyt: evolutionary conservation of transcriptional activation and replication signals.

    Science.gov (United States)

    Ryon, J J; Fixman, E D; Houchens, C; Zong, J; Lieberman, P M; Chang, Y N; Hayward, G S; Hayward, S D

    1993-01-01

    Herpesvirus papio (HVP) is a B-lymphotropic baboon virus with an estimated 40% homology to Epstein-Barr virus (EBV). We have cloned and sequenced ori-Lyt of herpesvirus papio and found a striking degree of nucleotide homology (89%) with ori-Lyt of EBV. Transcriptional elements form an integral part of EBV ori-Lyt. The promoter and enhancer domains of EBV ori-Lyt are conserved in herpesvirus papio. The EBV ori-Lyt promoter contains four binding sites for the EBV lytic cycle transactivator Zta, and the enhancer includes one Zta and two Rta response elements. All five of the Zta response elements and one of the Rta motifs are conserved in HVP ori-Lyt, and the HVP DS-L leftward promoter and the enhancer were activated in transient transfection assays by the EBV Zta and Rta transactivators. The EBV ori-Lyt enhancer contains a palindromic sequence, GGTCAGCTGACC, centered on a PvuII restriction site. This sequence, with a single base change, is also present in the HVP ori-Lyt enhancer. DNase I footprinting demonstrated that the PvuII sequence was bound by a protein present in a Raji nuclear extract. Mobility shift and competition assays using oligonucleotide probes identified this sequence as a binding site for the cellular transcription factor MLTF. Mutagenesis of the binding site indicated that MLTF contributes significantly to the constitutive activity of the ori-Lyt enhancer. The high degree of conservation of cis-acting signal sequences in HVP ori-Lyt was further emphasized by the finding that an HVP ori-Lyt-containing plasmid was replicated in Vero cells by a set of cotransfected EBV replication genes. The central domain of EBV ori-Lyt contains two related AT-rich palindromes, one of which is partially duplicated in the HVP sequence. The AT-rich palindromes are functionally important cis-acting motifs. Deletion of these palindromes severely diminished replication of an ori-Lyt target plasmid. Images PMID:8389916

  7. Stimulation of pancreatic beta-cell replication by incretins involves transcriptional induction of cyclin D1 via multiple signalling pathways

    DEFF Research Database (Denmark)

    Friedrichsen, Birgitte N; Neubauer, Nicole; Lee, Ying C

    2006-01-01

    pathways leading to mitosis by incretins and cytokines, respectively. The response to both GLP-1 and GIP was completely blocked by the protein kinase A (PKA) inhibitor, H89. In addition, the phosphoinositol 3-kinase (PI3K) inhibitor wortmannin and the mitogen-activated protein kinase kinase (MEK) inhibitor...... and we have previously demonstrated hGH-induced cyclin D2 expression in the insulinoma cell line, INS-1. GLP-1 time-dependently induced the cyclin D1 mRNA and protein levels in INS-1E, whereas the cyclin D2 levels were unaffected. However, minor effect of GLP-1 stimulation was observed on the cyclin D3 m......RNA levels. Transient transfection of a cyclin D1 promoter-luciferase reporter construct into islet monolayer cells or INS-1 cells revealed approximately a 2-3 fold increase of transcriptional activity in response to GLP-1 and GIP, and a 4-7 fold increase in response to forskolin. However, treatment...

  8. Bubbling away

    Energy Technology Data Exchange (ETDEWEB)

    Anon.

    1993-10-15

    Bubble chambers may have almost vanished from the front line of physics research, but the vivid memory of their intricate and sometimes beautiful patterns of particle tracks lives on, and has greatly influenced the computer graphics of track reconstruction in today's big experiments. 'Seeing' an interaction makes it more understandable. Bubble chambers, with their big collaborations of physicists from many widely scattered research institutes, started another ball rolling. The groups formed are even now only surpassed in size by the big collaborations working on today's major detectors at colliding beam machines. From 14-16 July, about 130 physicists gathered at CERN to commemorate the 40th anniversary of the invention of the bubble chamber by Donald Glaser. The meeting, organized by Derek C. Colley from Birmingham, gave a comprehensive overview of bubble chamber contributions to physics, their challenging technology, and the usefulness of bubble chamber photographs in education, both for physics and the public at large. After opening remarks by CERN Director Carlo Rubbia, Donald Glaser began with a brief review of the work which led to his invention - there was much more to it than idly watching beer bubbles rise up the wall of the glass - before turning to his present line of research, biophysics, also very visually oriented.

  9. Bubbling away

    International Nuclear Information System (INIS)

    Anon.

    1993-01-01

    Bubble chambers may have almost vanished from the front line of physics research, but the vivid memory of their intricate and sometimes beautiful patterns of particle tracks lives on, and has greatly influenced the computer graphics of track reconstruction in today's big experiments. 'Seeing' an interaction makes it more understandable. Bubble chambers, with their big collaborations of physicists from many widely scattered research institutes, started another ball rolling. The groups formed are even now only surpassed in size by the big collaborations working on today's major detectors at colliding beam machines. From 14-16 July, about 130 physicists gathered at CERN to commemorate the 40th anniversary of the invention of the bubble chamber by Donald Glaser. The meeting, organized by Derek C. Colley from Birmingham, gave a comprehensive overview of bubble chamber contributions to physics, their challenging technology, and the usefulness of bubble chamber photographs in education, both for physics and the public at large. After opening remarks by CERN Director Carlo Rubbia, Donald Glaser began with a brief review of the work which led to his invention - there was much more to it than idly watching beer bubbles rise up the wall of the glass - before turning to his present line of research, biophysics, also very visually oriented

  10. Nuttier bubbles

    International Nuclear Information System (INIS)

    Astefanesei, Dumitru; Mann, Robert B.; Stelea, Cristian

    2006-01-01

    We construct new explicit solutions of general relativity from double analytic continuations of Taub-NUT spacetimes. This generalizes previous studies of 4-dimensional nutty bubbles. One 5-dimensional locally asymptotically AdS solution in particular has a special conformal boundary structure of AdS 3 x S 1 . We compute its boundary stress tensor and relate it to the properties of the dual field theory. Interestingly enough, we also find consistent 6-dimensional bubble solutions that have only one timelike direction. The existence of such spacetimes with non-trivial topology is closely related to the existence of the Taub-NUT(-AdS) solutions with more than one NUT charge. Finally, we begin an investigation of generating new solutions from Taub-NUT spacetimes and nuttier bubbles. Using the so-called Hopf duality, we provide new explicit time-dependent backgrounds in six dimensions

  11. Leverage bubble

    Science.gov (United States)

    Yan, Wanfeng; Woodard, Ryan; Sornette, Didier

    2012-01-01

    Leverage is strongly related to liquidity in a market and lack of liquidity is considered a cause and/or consequence of the recent financial crisis. A repurchase agreement is a financial instrument where a security is sold simultaneously with an agreement to buy it back at a later date. Repurchase agreement (repo) market size is a very important element in calculating the overall leverage in a financial market. Therefore, studying the behavior of repo market size can help to understand a process that can contribute to the birth of a financial crisis. We hypothesize that herding behavior among large investors led to massive over-leveraging through the use of repos, resulting in a bubble (built up over the previous years) and subsequent crash in this market in early 2008. We use the Johansen-Ledoit-Sornette (JLS) model of rational expectation bubbles and behavioral finance to study the dynamics of the repo market that led to the crash. The JLS model qualifies a bubble by the presence of characteristic patterns in the price dynamics, called log-periodic power law (LPPL) behavior. We show that there was significant LPPL behavior in the market before that crash and that the predicted range of times predicted by the model for the end of the bubble is consistent with the observations.

  12. Functional characterization of Bombyx mori nucleopolyhedrovirus late gene transcription and genome replication factors in the non-permissive insect cell line SF-21

    International Nuclear Information System (INIS)

    Berretta, Marcelo F.; Deshpande, Mandar; Crouch, Erin A.; Passarelli, A. Lorena

    2006-01-01

    We compared the abilities of late gene transcription and DNA replication machineries of the baculoviruses Autographa californica nucleopolyhedrovirus (AcMNPV) and Bombyx mori NPV (BmNPV) in SF-21 cells, an insect-derived cell line permissive for AcMNPV infection. It has been well established that 19 AcMNPV late expression factors (lefs) stimulate substantial levels of late gene promoter activity in SF-21 cells. Thus, we constructed a set of clones containing the BmNPV homologs of the AcMNPV lefs under control of the constitutive Drosophila heat shock 70 protein promoter and tested their ability to activate an AcMNPV late promoter-reporter gene cassette in SF-21 cells. We tested the potential of individual or predicted functional groups of BmNPV lefs to successfully replace the corresponding AcMNPV gene(s) in transient late gene expression assays. We found that most, but not all, BmNPV lefs were able to either fully or partially substitute for the corresponding AcMNPV homolog in the context of the remaining AcMNPV lefs with the exception of BmNPV p143, ie-2, and p35. BmNPV p143 was unable to support late gene expression or be imported into the nucleus of cells in the presence of the AcMNPV or the BmNPV LEF-3, a P143 nuclear shuttling factor. Our results suggest that host-specific factors may affect the function of homologous proteins

  13. Transcriptional profiling reveals molecular signatures associated with HIV permissiveness in Th1Th17 cells and identifies Peroxisome Proliferator-Activated Receptor Gamma as an intrinsic negative regulator of viral replication

    Science.gov (United States)

    2013-01-01

    Background We previously demonstrated that primary Th1Th17 cells are highly permissive to HIV-1, whereas Th1 cells are relatively resistant. Molecular mechanisms underlying these differences remain unknown. Results Exposure to replication competent and single-round VSV-G pseudotyped HIV strains provide evidence that superior HIV replication in Th1Th17 vs. Th1 cells was regulated by mechanisms located at entry and post-entry levels. Genome-wide transcriptional profiling identified transcripts upregulated (n = 264) and downregulated (n = 235) in Th1Th17 vs. Th1 cells (p-value Th17 (nuclear receptors, trafficking, p38/MAPK, NF-κB, p53/Ras, IL-23) vs. Th1 cells (proteasome, interferon α/β). Differentially expressed genes were classified into biological categories using Gene Ontology. Th1Th17 cells expressed typical Th17 markers (IL-17A/F, IL-22, CCL20, RORC, IL-26, IL-23R, CCR6) and transcripts functionally linked to regulating cell trafficking (CEACAM1, MCAM), activation (CD28, CD40LG, TNFSF13B, TNFSF25, PTPN13, MAP3K4, LTB, CTSH), transcription (PPARγ, RUNX1, ATF5, ARNTL), apoptosis (FASLG), and HIV infection (CXCR6, FURIN). Differential expression of CXCR6, PPARγ, ARNTL, PTPN13, MAP3K4, CTSH, SERPINB6, PTK2, and ISG20 was validated by RT-PCR, flow cytometry and/or confocal microscopy. The nuclear receptor PPARγ was preferentially expressed by Th1Th17 cells. PPARγ RNA interference significantly increased HIV replication at levels post-entry and prior HIV-DNA integration. Finally, the activation of PPARγ pathway via the agonist Rosiglitazone induced the nuclear translocation of PPARγ and a robust inhibition of viral replication. Conclusions Thus, transcriptional profiling in Th1Th17 vs. Th1 cells demonstrated that HIV permissiveness is associated with a superior state of cellular activation and limited antiviral properties and identified PPARγ as an intrinsic negative regulator of viral replication. Therefore, triggering PPARγ pathway via non

  14. The Canonical Immediate Early 3 Gene Product pIE611 of Mouse Cytomegalovirus Is Dispensable for Viral Replication but Mediates Transcriptional and Posttranscriptional Regulation of Viral Gene Products.

    Science.gov (United States)

    Rattay, Stephanie; Trilling, Mirko; Megger, Dominik A; Sitek, Barbara; Meyer, Helmut E; Hengel, Hartmut; Le-Trilling, Vu Thuy Khanh

    2015-08-01

    Transcription of mouse cytomegalovirus (MCMV) immediate early ie1 and ie3 is controlled by the major immediate early promoter/enhancer (MIEP) and requires differential splicing. Based on complete loss of genome replication of an MCMV mutant carrying a deletion of the ie3-specific exon 5, the multifunctional IE3 protein (611 amino acids; pIE611) is considered essential for viral replication. Our analysis of ie3 transcription resulted in the identification of novel ie3 isoforms derived from alternatively spliced ie3 transcripts. Construction of an IE3-hemagglutinin (IE3-HA) virus by insertion of an in-frame HA epitope sequence allowed detection of the IE3 isoforms in infected cells, verifying that the newly identified transcripts code for proteins. This prompted the construction of an MCMV mutant lacking ie611 but retaining the coding capacity for the newly identified isoforms ie453 and ie310. Using Δie611 MCMV, we demonstrated the dispensability of the canonical ie3 gene product pIE611 for viral replication. To determine the role of pIE611 for viral gene expression during MCMV infection in an unbiased global approach, we used label-free quantitative mass spectrometry to delineate pIE611-dependent changes of the MCMV proteome. Interestingly, further analysis revealed transcriptional as well as posttranscriptional regulation of MCMV gene products by pIE611. Cytomegaloviruses are pathogenic betaherpesviruses persisting in a lifelong latency from which reactivation can occur under conditions of immunosuppression, immunoimmaturity, or inflammation. The switch from latency to reactivation requires expression of immediate early genes. Therefore, understanding of immediate early gene regulation might add insights into viral pathogenesis. The mouse cytomegalovirus (MCMV) immediate early 3 protein (611 amino acids; pIE611) is considered essential for viral replication. The identification of novel protein isoforms derived from alternatively spliced ie3 transcripts prompted

  15. Genome-wide identification and characterisation of human DNA replication origins by initiation site sequencing (ini-seq).

    Science.gov (United States)

    Langley, Alexander R; Gräf, Stefan; Smith, James C; Krude, Torsten

    2016-12-01

    Next-generation sequencing has enabled the genome-wide identification of human DNA replication origins. However, different approaches to mapping replication origins, namely (i) sequencing isolated small nascent DNA strands (SNS-seq); (ii) sequencing replication bubbles (bubble-seq) and (iii) sequencing Okazaki fragments (OK-seq), show only limited concordance. To address this controversy, we describe here an independent high-resolution origin mapping technique that we call initiation site sequencing (ini-seq). In this approach, newly replicated DNA is directly labelled with digoxigenin-dUTP near the sites of its initiation in a cell-free system. The labelled DNA is then immunoprecipitated and genomic locations are determined by DNA sequencing. Using this technique we identify >25,000 discrete origin sites at sub-kilobase resolution on the human genome, with high concordance between biological replicates. Most activated origins identified by ini-seq are found at transcriptional start sites and contain G-quadruplex (G4) motifs. They tend to cluster in early-replicating domains, providing a correlation between early replication timing and local density of activated origins. Origins identified by ini-seq show highest concordance with sites identified by SNS-seq, followed by OK-seq and bubble-seq. Furthermore, germline origins identified by positive nucleotide distribution skew jumps overlap with origins identified by ini-seq and OK-seq more frequently and more specifically than do sites identified by either SNS-seq or bubble-seq. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Bubble bath soap poisoning

    Science.gov (United States)

    ... medlineplus.gov/ency/article/002762.htm Bubble bath soap poisoning To use the sharing features on this page, please enable JavaScript. Bubble bath soap poisoning occurs when someone swallows bubble bath soap. ...

  17. Rational equity bubbles

    OpenAIRE

    Zhou, Ge

    2012-01-01

    This paper discusses the existence of a bubble in the pricing of an asset that pays positive dividends. I show that rational bubbles can exist in a growing economy. The existence of bubbles depends on the relative magnitudes of risk aversion to consumption and to wealth. Furthermore, I examine how an exogenous shock in technology might trigger bubbles.

  18. How are soap bubbles blown? Fluid dynamics of soap bubble blowing

    Science.gov (United States)

    Davidson, John; Lambert, Lori; Sherman, Erica; Wei, Timothy; Ryu, Sangjin

    2013-11-01

    Soap bubbles are a common interfacial fluid dynamics phenomenon having a long history of delighting not only children and artists but also scientists. In contrast to the dynamics of liquid droplets in gas and gas bubbles in liquid, the dynamics of soap bubbles has not been well documented. This is possibly because studying soap bubbles is more challenging due to there existing two gas-liquid interfaces. Having the thin-film interface seems to alter the characteristics of the bubble/drop creation process since the interface has limiting factors such as thickness. Thus, the main objective of this study is to determine how the thin-film interface differentiates soap bubbles from gas bubbles and liquid drops. To investigate the creation process of soap bubbles, we constructed an experimental model consisting of air jet flow and a soap film, which consistently replicates the conditions that a human produces when blowing soap bubbles, and examined the interaction between the jet and the soap film using the high-speed videography and the particle image velocimetry.

  19. Fama on Bubbles

    DEFF Research Database (Denmark)

    Engsted, Tom

    2016-01-01

    While Eugene Fama has repeatedly expressed his discontent with the notion of an “irrational bubble,” he has never publicly expressed his opinion on “rational bubbles.” On empirical grounds Fama rejects bubbles by referring to the lack of reliable evidence that price declines are predictable....... However, this argument cannot be used to rule out rational bubbles because such bubbles do not necessarily imply return predictability, and return predictability of the kind documented by Fama does not rule out rational bubbles. On data samples that include the 1990s, there is evidence of an explosive...... component in stock market valuation ratios, consistent with a rational bubble....

  20. Anti-Bubbles

    Science.gov (United States)

    Tufaile, Alberto; Sartorelli, José Carlos

    2003-08-01

    An anti-bubble is a striking kind of bubble in liquid that seemingly does not comply the buoyancy, and after few minutes it disappears suddenly inside the liquid. Different from a simple air bubble that rises directly to the liquid surface, an anti-bubble wanders around in the fluid due to its slightly lesser density than the surrounding liquid. In spite of this odd behavior, an anti-bubble can be understood as the opposite of a conventional soap bubble in air, which is a shell of liquid surrounding air, and an anti-bubble is a shell of air surrounding a drop of the liquid inside the liquid. Two-phase flow has been a subject of interest due to its relevance to process equipment for contacting gases and liquids applied in industry. A chain of bubbles rising in a liquid formed from a nozzle is a two-phase flow, and there are certain conditions in which spherical air shells, called anti-bubbles, are produced. The purpose of this work is mainly to note the existence of anti-bubbling regime as a sequel of a bubbling system. We initially have presented the experimental apparatus. After this we have described the evolution of the bubbling regimes, and emulated the effect of bubbling coalescence with simple maps. Then is shown the inverted dripping as a consequence of the bubble coalescence, and finally the conditions for anti-bubble formation.

  1. Systems-wide RNAi analysis of CASP8AP2/FLASH shows transcriptional deregulation of the replication-dependent histone genes and extensive effects on the transcriptome of colorectal cancer cells.

    Science.gov (United States)

    Hummon, Amanda B; Pitt, Jason J; Camps, Jordi; Emons, Georg; Skube, Susan B; Huppi, Konrad; Jones, Tamara L; Beissbarth, Tim; Kramer, Frank; Grade, Marian; Difilippantonio, Michael J; Ried, Thomas; Caplen, Natasha J

    2012-01-04

    Colorectal carcinomas (CRC) carry massive genetic and transcriptional alterations that influence multiple cellular pathways. The study of proteins whose loss-of-function (LOF) alters the growth of CRC cells can be used to further understand the cellular processes cancer cells depend upon for survival. A small-scale RNAi screen of ~400 genes conducted in SW480 CRC cells identified several candidate genes as required for the viability of CRC cells, most prominently CASP8AP2/FLASH. To understand the function of this gene in maintaining the viability of CRC cells in an unbiased manner, we generated gene specific expression profiles following RNAi. Silencing of CASP8AP2/FLASH resulted in altered expression of over 2500 genes enriched for genes associated with cellular growth and proliferation. Loss of CASP8AP2/FLASH function was significantly associated with altered transcription of the genes encoding the replication-dependent histone proteins as a result of the expression of the non-canonical polyA variants of these transcripts. Silencing of CASP8AP2/FLASH also mediated enrichment of changes in the expression of targets of the NFκB and MYC transcription factors. These findings were confirmed by whole transcriptome analysis of CASP8AP2/FLASH silenced cells at multiple time points. Finally, we identified and validated that CASP8AP2/FLASH LOF increases the expression of neurofilament heavy polypeptide (NEFH), a protein recently linked to regulation of the AKT1/ß-catenin pathway. We have used unbiased RNAi based approaches to identify and characterize the function of CASP8AP2/FLASH, a protein not previously reported as required for cell survival. This study further defines the role CASP8AP2/FLASH plays in the regulating expression of the replication-dependent histones and shows that its LOF results in broad and reproducible effects on the transcriptome of colorectal cancer cells including the induction of expression of the recently described tumor suppressor gene NEFH.

  2. Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation | Center for Cancer Research

    Science.gov (United States)

    Dubbed "Tom's T" by Dhruba Chattoraj, the unusually conserved thymine at position +7 in bacteriophage P1 plasmid RepA DNA binding sites rises above repressor and acceptor sequence logos. The T appears to represent base flipping prior to helix opening in this DNA replication initation protein.

  3. Distributional Replication

    OpenAIRE

    Beare, Brendan K.

    2009-01-01

    Suppose that X and Y are random variables. We define a replicating function to be a function f such that f(X) and Y have the same distribution. In general, the set of replicating functions for a given pair of random variables may be infinite. Suppose we have some objective function, or cost function, defined over the set of replicating functions, and we seek to estimate the replicating function with the lowest cost. We develop an approach to estimating the cheapest replicating function that i...

  4. Fama on bubbles

    DEFF Research Database (Denmark)

    Engsted, Tom

    Eugene Fama has repeatedly expressed his discontent with the notion of an irrational bubble. However, he has never publicly expressed his opinion on rational bubbles. This is peculiar since such bubbles build naturally from the rational efficient markets paradigm that Fama strongly adheres to...

  5. Replication Catastrophe

    DEFF Research Database (Denmark)

    Toledo, Luis; Neelsen, Kai John; Lukas, Jiri

    2017-01-01

    Proliferating cells rely on the so-called DNA replication checkpoint to ensure orderly completion of genome duplication, and its malfunction may lead to catastrophic genome disruption, including unscheduled firing of replication origins, stalling and collapse of replication forks, massive DNA...... breakage, and, ultimately, cell death. Despite many years of intensive research into the molecular underpinnings of the eukaryotic replication checkpoint, the mechanisms underlying the dismal consequences of its failure remain enigmatic. A recent development offers a unifying model in which the replication...... checkpoint guards against global exhaustion of rate-limiting replication regulators. Here we discuss how such a mechanism can prevent catastrophic genome disruption and suggest how to harness this knowledge to advance therapeutic strategies to eliminate cancer cells that inherently proliferate under...

  6. Systems-wide RNAi analysis of CASP8AP2/FLASH shows transcriptional deregulation of the replication-dependent histone genes and extensive effects on the transcriptome of colorectal cancer cells

    Directory of Open Access Journals (Sweden)

    Hummon Amanda B

    2012-01-01

    Full Text Available Abstract Background Colorectal carcinomas (CRC carry massive genetic and transcriptional alterations that influence multiple cellular pathways. The study of proteins whose loss-of-function (LOF alters the growth of CRC cells can be used to further understand the cellular processes cancer cells depend upon for survival. Results A small-scale RNAi screen of ~400 genes conducted in SW480 CRC cells identified several candidate genes as required for the viability of CRC cells, most prominently CASP8AP2/FLASH. To understand the function of this gene in maintaining the viability of CRC cells in an unbiased manner, we generated gene specific expression profiles following RNAi. Silencing of CASP8AP2/FLASH resulted in altered expression of over 2500 genes enriched for genes associated with cellular growth and proliferation. Loss of CASP8AP2/FLASH function was significantly associated with altered transcription of the genes encoding the replication-dependent histone proteins as a result of the expression of the non-canonical polyA variants of these transcripts. Silencing of CASP8AP2/FLASH also mediated enrichment of changes in the expression of targets of the NFκB and MYC transcription factors. These findings were confirmed by whole transcriptome analysis of CASP8AP2/FLASH silenced cells at multiple time points. Finally, we identified and validated that CASP8AP2/FLASH LOF increases the expression of neurofilament heavy polypeptide (NEFH, a protein recently linked to regulation of the AKT1/ß-catenin pathway. Conclusions We have used unbiased RNAi based approaches to identify and characterize the function of CASP8AP2/FLASH, a protein not previously reported as required for cell survival. This study further defines the role CASP8AP2/FLASH plays in the regulating expression of the replication-dependent histones and shows that its LOF results in broad and reproducible effects on the transcriptome of colorectal cancer cells including the induction of

  7. Evolution of Replication Machines

    Science.gov (United States)

    Yao, Nina Y.; O'Donnell, Mike E.

    2016-01-01

    The machines that decode and regulate genetic information require the translation, transcription and replication pathways essential to all living cells. Thus, it might be expected that all cells share the same basic machinery for these pathways that were inherited from the primordial ancestor cell from which they evolved. A clear example of this is found in the translation machinery that converts RNA sequence to protein. The translation process requires numerous structural and catalytic RNAs and proteins, the central factors of which are homologous in all three domains of life, bacteria, archaea and eukarya. Likewise, the central actor in transcription, RNA polymerase, shows homology among the catalytic subunits in bacteria, archaea and eukarya. In contrast, while some “gears” of the genome replication machinery are homologous in all domains of life, most components of the replication machine appear to be unrelated between bacteria and those of archaea and eukarya. This review will compare and contrast the central proteins of the “replisome” machines that duplicate DNA in bacteria, archaea and eukarya, with an eye to understanding the issues surrounding the evolution of the DNA replication apparatus. PMID:27160337

  8. Chaotic bubbling and nonstagnant foams.

    Science.gov (United States)

    Tufaile, Alberto; Sartorelli, José Carlos; Jeandet, Philippe; Liger-Belair, Gerard

    2007-06-01

    We present an experimental investigation of the agglomeration of bubbles obtained from a nozzle working in different bubbling regimes. This experiment consists of a continuous production of bubbles from a nozzle at the bottom of a liquid column, and these bubbles create a two-dimensional (2D) foam (or a bubble raft) at the top of this column. The bubbles can assemble in various dynamically stable arrangement, forming different kinds of foams in a liquid mixture of water and glycerol, with the effect that the bubble formation regimes influence the foam obtained from this agglomeration of bubbles. The average number of bubbles in the foam is related to the bubble formation frequency and the bubble mean lifetime. The periodic bubbling can generate regular or irregular foam, while a chaotic bubbling only generates irregular foam.

  9. Database Replication

    CERN Document Server

    Kemme, Bettina

    2010-01-01

    Database replication is widely used for fault-tolerance, scalability and performance. The failure of one database replica does not stop the system from working as available replicas can take over the tasks of the failed replica. Scalability can be achieved by distributing the load across all replicas, and adding new replicas should the load increase. Finally, database replication can provide fast local access, even if clients are geographically distributed clients, if data copies are located close to clients. Despite its advantages, replication is not a straightforward technique to apply, and

  10. Sonoluminescence and bubble fusion

    OpenAIRE

    Arakeri, Vijay H

    2003-01-01

    Sonoluminescence (SL), the phenomenon of light emission from nonlinear motion of a gas bubble, involves an extreme degree of energy focusing. The conditions within the bubble during the last stages of the nearly catastrophic implosion are thought to parallel the efforts aimed at developing inertial confinement fusion. A limited review on the topic of SL and its possible connection to bubble nuclear fusion is presented here. The emphasis is on looking for a link between the various forms o...

  11. Prospects for bubble fusion

    Energy Technology Data Exchange (ETDEWEB)

    Nigmatulin, R.I. [Tyumen Institute of Mechanics of Multiphase Systems (TIMMS), Marx (Russian Federation); Lahey, R.T. Jr. [Rensselaer Polytechnic Institute, Troy, NY (United States)

    1995-09-01

    In this paper a new method for the realization of fusion energy is presented. This method is based on the superhigh compression of a gas bubble (deuterium or deuterium/thritium) in heavy water or another liquid. The superhigh compression of a gas bubble in a liquid is achieved through forced non-linear, non-periodic resonance oscillations using moderate amplitudes of forcing pressure. The key feature of this new method is a coordination of the forced liquid pressure change with the change of bubble volume. The corresponding regime of the bubble oscillation has been called {open_quotes}basketball dribbling (BD) regime{close_quotes}. The analytical solution describing this process for spherically symmetric bubble oscillations, neglecting dissipation and compressibility of the liquid, has been obtained. This solution shown no limitation on the supercompression of the bubble and the corresponding maximum temperature. The various dissipation mechanisms, including viscous, conductive and radiation heat losses have been considered. It is shown that in spite of these losses it is possible to achieve very high gas bubble temperatures. This because the time duration of the gas bubble supercompression becomes very short when increasing the intensity of compression, thus limiting the energy losses. Significantly, the calculated maximum gas temperatures have shown that nuclear fusion may be possible. First estimations of the affect of liquid compressibility have been made to determine possible limitations on gas bubble compression. The next step will be to investigate the role of interfacial instability and breaking down of the bubble, shock wave phenomena around and in the bubble and mutual diffusion of the gas and the liquid.

  12. The DNA Replication Checkpoint Directly Regulates MBF-Dependent G1/S Transcription▿

    OpenAIRE

    Dutta, Chaitali; Patel, Prasanta K.; Rosebrock, Adam; Oliva, Anna; Leatherwood, Janet; Rhind, Nicholas

    2008-01-01

    The DNA replication checkpoint transcriptionally upregulates genes that allow cells to adapt to and survive replication stress. Our results show that, in the fission yeast Schizosaccharomyces pombe, the replication checkpoint regulates the entire G1/S transcriptional program by directly regulating MBF, the G1/S transcription factor. Instead of initiating a checkpoint-specific transcriptional program, the replication checkpoint targets MBF to maintain the normal G1/S transcriptional program du...

  13. Soap Bubbles and Crystals

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 6. Soap Bubbles and Crystals. Jean E Taylor. General Article Volume 11 Issue 6 June 2006 pp 26-30. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/011/06/0026-0030. Keywords. Soap bubble ...

  14. Turbulence, bubbles and drops

    NARCIS (Netherlands)

    van der Veen, Roeland

    2016-01-01

    In this thesis, several questions related to drop impact and Taylor-Couette turbulence are answered. The deformation of a drop just before impact can cause a bubble to be entrapped. For many applications, such as inkjet printing, it is crucial to control the size of this entrapped bubble. To study

  15. Single bubble sonoluminescence

    NARCIS (Netherlands)

    Brenner, Michael P.; Hilgenfeldt, Sascha; Lohse, Detlef

    2002-01-01

    Single-bubble sonoluminescence occurs when an acoustically trapped and periodically driven gas bubble collapses so strongly that the energy focusing at collapse leads to light emission. Detailed experiments have demonstrated the unique properties of this system: the spectrum of the emitted light

  16. Flow visualization using bubbles

    International Nuclear Information System (INIS)

    Henry, J.P.

    1974-01-01

    Soap bubbles were used for visualizing flows. The tests effected allowed some characteristics of flows around models in blow tunnels to be precised at mean velocities V 0 5 . The velocity of a bubble is measured by chronophotography, the bulk envelope of the trajectories is also registered [fr

  17. HCDA bubble experiment, (2)

    International Nuclear Information System (INIS)

    Sakata, Kaoru; Mashiko, Hiroyuki; Oka, Yoshiaki; An, Shigehiro; Isozaki, Tadashi.

    1981-06-01

    An experiment simulating the behavior of the very large steam bubbles generated at the time of an accident of core collapse was carried out with a warm water tank, and the applicability of the theory of very small bubble disappearance known at present was examined. The bubbles generated in HCDA (hypothetical core disruptive accident) are expected to be very large, containing sodium, fuel, FP gas and so on, and play important role in the mechanism of emitting radioactive substances in the safety analysis of LMFBRs. In this experiment, the degree of subcool of the warm water pool, the initial radii of steam bubbles and the blowoff pressure of steam were taken as the parameters. The radius of the steam bubbles generated in the experiment was about 6.5 cm, and the state of disappearance was different above and below the degree of unsaturation of 10 deg C. Comparing the disappearance curve obtained by the experiment with the theory of disappearance of small bubbles, the experimental values were between inertia-controlled disappearance and heat transfer-controlled disappearance, and this result was able to be explained generally with the model taking the pressure change within steam bubbles into account. The rise of bubbles was also observed. (Kako, I.)

  18. Bubbles in graphene

    DEFF Research Database (Denmark)

    Settnes, Mikkel; Power, Stephen; Lin, Jun

    2015-01-01

    Strain-induced deformations in graphene are predicted to give rise to large pseudomagnetic fields. We examine theoretically the case of gas-inflated bubbles to determine whether signatures of such fields are present in the local density of states. Sharp-edged bubbles are found to induce Friedel...

  19. Evaporation, Boiling and Bubbles

    Science.gov (United States)

    Goodwin, Alan

    2012-01-01

    Evaporation and boiling are both terms applied to the change of a liquid to the vapour/gaseous state. This article argues that it is the formation of bubbles of vapour within the liquid that most clearly differentiates boiling from evaporation although only a minority of chemistry textbooks seems to mention bubble formation in this context. The…

  20. Interfacial Bubble Deformations

    Science.gov (United States)

    Seymour, Brian; Shabane, Parvis; Cypull, Olivia; Cheng, Shengfeng; Feitosa, Klebert

    Soap bubbles floating at an air-water experience deformations as a result of surface tension and hydrostatic forces. In this experiment, we investigate the nature of such deformations by taking cross-sectional images of bubbles of different volumes. The results show that as their volume increases, bubbles transition from spherical to hemispherical shape. The deformation of the interface also changes with bubble volume with the capillary rise converging to the capillary length as volume increases. The profile of the top and bottom of the bubble and the capillary rise are completely determined by the volume and pressure differences. James Madison University Department of Physics and Astronomy, 4VA Consortium, Research Corporation for Advancement of Science.

  1. Pinch-off Scaling Law of Soap Bubbles

    Science.gov (United States)

    Davidson, John; Ryu, Sangjin

    2014-11-01

    Three common interfacial phenomena that occur daily are liquid drops in gas, gas bubbles in liquid and thin-film bubbles. One aspect that has been studied for these phenomena is the formation or pinch-off of the drop/bubble from the liquid/gas threads. In contrast to the formation of liquid drops in gas and gas bubbles in liquid, thin-film bubble pinch-off has not been well documented. Having thin-film interfaces may alter the pinch-off process due to the limiting factor of the film thickness. We observed the pinch-off of one common thin-film bubble, soap bubbles, in order to characterize its pinch-off behavior. We achieved this by constructing an experimental model replicating the process of a human producing soap bubbles. Using high-speed videography and image processing, we determined that the minimal neck radius scaled with the time left till pinch-off, and that the scaling law exponent was 2/3, similar to that of liquid drops in gas.

  2. Identifying Functional Neighborhoods within the Cell Nucleus: Proximity Analysis of Early S-Phase Replicating Chromatin Domains to Sites of Transcription, RNA Polymerase II, HP1γ, Matrin 3 and SAF-A

    Science.gov (United States)

    Malyavantham, Kishore S; Bhattacharya, Sambit; Barbeitos, Marcos; Mukherjee, Lopamudra; Xu, Jinhui; Fackelmayer, Frank O; Berezney, Ronald

    2009-01-01

    Higher order chromatin organization in concert with epigenetic regulation is a key process that determines gene expression at the global level. The organization of dynamic chromatin domains and their associated protein factors is intertwined with nuclear function to create higher levels of functional zones within the cell nucleus. As a step towards elucidating the organization and dynamics of these functional zones, we have investigated the spatial proximities among a constellation of functionally related sites that are found within euchromatic regions of the cell nucleus including: HP1γ, nascent transcript sites (TS), active DNA replicating sites in early S phase (PCNA) and RNA polymerase II sites. We report close associations among these different sites with proximity values specific for each combination. Analysis of matrin 3 and SAF-A sites demonstrates that these nuclear matrix proteins are highly proximal with the functionally related sites as well as to each other and display closely aligned and overlapping regions following application of the minimal spanning tree (MST) algorithm to visualize higher order network-like patterns. Our findings suggest that multiple factors within the nuclear microenvironment collectively form higher order combinatorial arrays of function. We propose a model for the organization of these functional neighborhoods which takes into account the proximity values of the individual sites and their spatial organization within the nuclear architecture. PMID:18618731

  3. Theory calculation of combination of 'embryo' bubble growing-up visible bubble in bubble chamber

    International Nuclear Information System (INIS)

    Ye Zipiao; Sheng Xiangdong; Dai Changjiang

    2004-01-01

    By aid of island combination theory of 'embryo' bubble, it is resolved well the question which 'embryo' bubble grows up a visible bubble in the bubble chamber. Through theory calculation it is shown that radius of the big' embryo' bubble combinated not only relates with work matter such as surface tension coefficient, saturation vapour pressure and boiling point of liquid, but also does absorbing quantity of heat and the numbers of 'embryo' bubbles combination. It is explained reasonably that the radius of bubbles in bubble chamber is different for the same energies of neutrons and proton. The track of neutron in bubble chamber is long and thin, and the track of proton in bubble chamber is wide and short. It is also explained reasonably that the bubble radius of the incident particles with more charges which there are the same energies will be wider than that of the incident particles with less charges in the track. (author)

  4. Bubbles and breaking waves

    Science.gov (United States)

    Thorpe, S. A.

    1980-01-01

    The physical processes which control the transfer of gases between the atmosphere and oceans or lakes are poorly understood. Clouds of micro-bubbles have been detected below the surface of Loch Ness when the wind is strong enough to cause the waves to break. The rate of transfer of gas into solution from these bubbles is estimated to be significant if repeated on a global scale. We present here further evidence that the bubbles are caused by breaking waves, and discuss the relationship between the mean frequency of wave breaking at a fixed point and the average distance between breaking waves, as might be estimated from an aerial photograph.

  5. Rotating bubble membrane radiator

    Science.gov (United States)

    Webb, Brent J.; Coomes, Edmund P.

    1988-12-06

    A heat radiator useful for expelling waste heat from a power generating system aboard a space vehicle is disclosed. Liquid to be cooled is passed to the interior of a rotating bubble membrane radiator, where it is sprayed into the interior of the bubble. Liquid impacting upon the interior surface of the bubble is cooled and the heat radiated from the outer surface of the membrane. Cooled liquid is collected by the action of centrifical force about the equator of the rotating membrane and returned to the power system. Details regarding a complete space power system employing the radiator are given.

  6. Bubble Collision in Curved Spacetime

    International Nuclear Information System (INIS)

    Hwang, Dong-il; Lee, Bum-Hoon; Lee, Wonwoo; Yeom, Dong-han

    2014-01-01

    We study vacuum bubble collisions in curved spacetime, in which vacuum bubbles were nucleated in the initial metastable vacuum state by quantum tunneling. The bubbles materialize randomly at different times and then start to grow. It is known that the percolation by true vacuum bubbles is not possible due to the exponential expansion of the space among the bubbles. In this paper, we consider two bubbles of the same size with a preferred axis and assume that two bubbles form very near each other to collide. The two bubbles have the same field value. When the bubbles collide, the collided region oscillates back-and-forth and then the collided region eventually decays and disappears. We discuss radiation and gravitational wave resulting from the collision of two bubbles

  7. Chemistry in Soap Bubbles.

    Science.gov (United States)

    Lee, Albert W. M.; Wong, A.; Lee, H. W.; Lee, H. Y.; Zhou, Ning-Huai

    2002-01-01

    Describes a laboratory experiment in which common chemical gases are trapped inside soap bubbles. Examines the physical and chemical properties of the gases such as relative density and combustion. (Author/MM)

  8. Nucleation in bubble chambers

    International Nuclear Information System (INIS)

    Harigel, G.G.

    1988-01-01

    Various sources and mechanisms for bubble formation in superheated liquids are discussed. Bubble chambers can be filled with a great variety of liquids, such as e.g. the cryogenic liquids hydrogen, deuterium, neon, neon/hydrogen mixtures, argon, nitrogen, argon/nitrogen mixtures, or the warm liquids propane and various Freon like Freon-13B1. The superheated state is normally achieved by a rapid movement of an expansion piston or membrane, but can also be produced by standing ultrasonic waves, shock waves, or putting liquids under tension. Bubble formation can be initiated by ionizing particles, by intense (laser) light, or on rough surfaces. The creation of embryonic bubbles is not completely understood, but the macroscopic growth and condensation can be calculated, allowing to estimate the dynamic heat load [fr

  9. Bubble chamber: antiproton annihilation

    CERN Multimedia

    1971-01-01

    These images show real particle tracks from the annihilation of an antiproton in the 80 cm Saclay liquid hydrogen bubble chamber. A negative kaon and a neutral kaon are produced in this process, as well as a positive pion. The invention of bubble chambers in 1952 revolutionized the field of particle physics, allowing real tracks left by particles to be seen and photographed by expanding liquid that had been heated to boiling point.

  10. Magnetic-bubble devices

    International Nuclear Information System (INIS)

    Fairholme, R.J.

    1978-01-01

    Magnetic bubbles were first described only ten years ago when research workers were discussing orthoferrites containing μm diameter bubbles. However, problems of material fabrication limit crystals to a few mm across which severely curtailed device development. Since then materials have changed and rare-earth-iron garnet films can be grown up 3 inches in diameter with bubble diameters down to sizes below 1 μm. The first commercial products have device capacities in the range 64 000 to 100 000 bits with bubble diameters between 4 and 6 μm. Chip capacities of 1 Mbit are presently under development in the laboratory, as are new techniques to use submicrometre bubbles. The operation and fabrication of a bubble device is described using the serial loop devices currently being manufactured at Plessey as models. Chip organization is one important variable which directly affects the access time. A range of access times and capacities is available which offers a wide range of market opportunities, ranging from consumer products to fixed head disc replacements. some of the application areas are described. (author)

  11. Bubble transport in bifurcations

    Science.gov (United States)

    Bull, Joseph; Qamar, Adnan

    2017-11-01

    Motivated by a developmental gas embolotherapy technique for cancer treatment, we examine the transport of bubbles entrained in liquid. In gas embolotherapy, infarction of tumors is induced by selectively formed vascular gas bubbles that originate from acoustic vaporization of vascular droplets. In the case of non-functionalized droplets with the objective of vessel occlusion, the bubbles are transported by flow through vessel bifurcations, where they may split prior to eventually reach vessels small enough that they become lodged. This splitting behavior affects the distribution of bubbles and the efficacy of flow occlusion and the treatment. In these studies, we investigated bubble transport in bifurcations using computational and theoretical modeling. The model reproduces the variety of experimentally observed splitting behaviors. Splitting homogeneity and maximum shear stress along the vessel walls is predicted over a variety of physical parameters. Maximum shear stresses were found to decrease with increasing Reynolds number. The initial bubble length was found to affect the splitting behavior in the presence of gravitational asymmetry. This work was supported by NIH Grant R01EB006476.

  12. Colliding with a crunching bubble

    Energy Technology Data Exchange (ETDEWEB)

    Freivogel, Ben; Freivogel, Ben; Horowitz, Gary T.; Shenker, Stephen

    2007-03-26

    In the context of eternal inflation we discuss the fate of Lambda = 0 bubbles when they collide with Lambda< 0 crunching bubbles. When the Lambda = 0 bubble is supersymmetric, it is not completely destroyed by collisions. If the domain wall separating the bubbles has higher tension than the BPS bound, it is expelled from the Lambda = 0 bubble and does not alter its long time behavior. If the domain wall saturates the BPS bound, then it stays inside the Lambda = 0 bubble and removes a finite fraction of future infinity. In this case, the crunch singularity is hidden behind the horizon of a stable hyperbolic black hole.

  13. Bubble fusion: Preliminary estimates

    International Nuclear Information System (INIS)

    Krakowski, R.A.

    1995-01-01

    The collapse of a gas-filled bubble in disequilibrium (i.e., internal pressure much-lt external pressure) can occur with a significant focusing of energy onto the entrapped gas in the form of pressure-volume work and/or acoustical shocks; the resulting heating can be sufficient to cause ionization and the emission of atomic radiations. The suggestion that extreme conditions necessary for thermonuclear fusion to occur may be possible has been examined parametrically in terms of the ratio of initial bubble pressure relative to that required for equilibrium. In this sense, the disequilibrium bubble is viewed as a three-dimensional ''sling shot'' that is ''loaded'' to an extent allowed by the maximum level of disequilibrium that can stably be achieved. Values of this disequilibrium ratio in the range 10 -5 --10 -6 are predicted by an idealized bubble-dynamics model as necessary to achieve conditions where nuclear fusion of deuterium-tritium might be observed. Harmonic and aharmonic pressurizations/decompressions are examined as means to achieve the required levels of disequilibrium required to create fusion conditions. A number of phenomena not included in the analysis reported herein could enhance or reduce the small levels of nuclear fusions predicted

  14. Critical scattering by bubbles

    International Nuclear Information System (INIS)

    Fiedler-Ferrari, N.; Nussenzveig, H.M.

    1986-11-01

    We apply the complex angular momentum theory to the problem of the critical scattering of light by spherical cavities in the high frequency limit (permittivity greater than the external media) (e.g, air bubble in water) (M.W.O.) [pt

  15. Heavy liquid bubble chamber

    CERN Multimedia

    CERN PhotoLab

    1965-01-01

    The CERN Heavy liquid bubble chamber being installed in the north experimental hall at the PS. On the left, the 1180 litre body; in the centre the magnet, which can produce a field of 26 800 gauss; on the right the expansion mechanism.

  16. MISSING: BUBBLE CHAMBER LENS

    CERN Multimedia

    2001-01-01

    Would the person who borrowed the large bubble chamber lens from the Microcosm workshops on the ISR please return it. This is a much used piece from our object archives. If anybody has any information about the whereabouts of this object, please contact Emma.Sanders@cern.ch Thank you

  17. BEBC bubble chamber

    CERN Multimedia

    CERN PhotoLab

    1972-01-01

    Looking up into the interior of BEBC bubble chamber from the expansion cylinder. At the top of the chamber two fish-eye lenses are installed and three other fish-eye ports are blanked off. In the centre is a heat exchanger.

  18. Bubble dynamics and bubble-induced turbulence of a single-bubble chain

    Science.gov (United States)

    Lee, Joohyoung; Park, Hyungmin

    2016-11-01

    In the present study, the bubble dynamics and liquid-phase turbulence induced by a chain of bubbles injected from a single nozzle have been experimentally investigated. Using a high-speed two-phase particle image velociemtry, measurements on the bubbles and liquid-phase velocity field are conducted in a transparent tank filled with water, while varying the bubble release frequency from 0.1 to 35 Hz. The tested bubble size ranges between 2.0-3.2 mm, and the corresponding bubble Reynolds number is 590-1100, indicating that it belongs to the regime of path instability. As the release frequency increases, it is found that the global shape of bubble dispersion can be classified into two regimes: from asymmetric (regular) to axisymmetric (irregular). In particular, at higher frequency, the wake vortices of leading bubbles cause an irregular behaviour of the following bubble. For the liquid phase, it is found that a specific trend on the bubble-induced turbulence appears in a strong relation to the above bubble dynamics. Considering this, we try to provide a theoretical model to estimate the liquid-phase turbulence induced by a chain of bubbles. Supported by a Grant funded by Samsung Electronics, Korea.

  19. Bubble properties of heterogeneous bubbly flow in a square bubble column

    NARCIS (Netherlands)

    Bai, Wei; Deen, Niels G.; Kuipers, J.A.M.

    2010-01-01

    The present work focuses on the measurements of bubble properties in heterogeneous bubbly flows in a square bubble column. A four-point optical fibre probe was used for this purpose. The accuracy and intrusive effect of the optical probe was investigated first. The results show that the optical

  20. Characteristics of bubble plumes, bubble-plume bubbles and waves from wind-steepened wave breaking

    NARCIS (Netherlands)

    Leifer, I.; Caulliez, G.; Leeuw, G. de

    2007-01-01

    Observations of breaking waves, associated bubble plumes and bubble-plume size distributions were used to explore the coupled evolution of wave-breaking, wave properties and bubble-plume characteristics. Experiments were made in a large, freshwater, wind-wave channel with mechanical wind-steepened

  1. Bubbles generated from wind-steepened breaking waves: 1. Bubble plume bubbles

    NARCIS (Netherlands)

    Leifer, I.; Leeuw, G. de

    2006-01-01

    Measurements of bubble plumes from paddle-amplified, wind stress breaking waves were made in a large wind-wave channel during the LUMINY experiment in fresh (but not clean) water. Bubble plumes exhibited considerable variability with respect to dynamics, bubble size distribution, and physical

  2. Autonomous replication of plasmids bearing monkey DNA origin-enriched sequences

    International Nuclear Information System (INIS)

    Frappier, L.; Zannis-Hadjopoulos, M.

    1987-01-01

    Twelve clones of origin-enriched sequences (ORS) isolated from early replicating monkey (CV-1) DNA were examined for transient episomal replication in transfected CV-1, COS-7, and HeLa cells. Plasmid DNA was isolated at time intervals after transfection and screened by the Dpn I resistance assay or by the bromodeoxyuridine substitution assay to differentiate between input and replicated DNA. The authors have identified four monkey ORS (ORS3, -8, -9, and -12) that can support plasmid replication in mammalian cells. This replication is carried out in a controlled and semiconservative manner characteristic of mammalian replicons. ORS replication was most efficient in HeLa cells. Electron microscopy showed ORS8 and ORS12 plasmids of the correct size with replication bubbles. Using a unique restriction site in ORS12, we have mapped the replication bubble within the monkey DNA sequence

  3. Bubble Dynamics and Shock Waves

    CERN Document Server

    2013-01-01

    This volume of the Shock Wave Science and Technology Reference Library is concerned with the interplay between bubble dynamics and shock waves. It is divided into four parts containing twelve chapters written by eminent scientists. Topics discussed include shock wave emission by laser generated bubbles (W Lauterborn, A Vogel), pulsating bubbles near boundaries (DM Leppinen, QX Wang, JR Blake), interaction of shock waves with bubble clouds (CD Ohl, SW Ohl), shock propagation in polydispersed bubbly liquids by model equations (K Ando, T Colonius, CE Brennen. T Yano, T Kanagawa,  M Watanabe, S Fujikawa) and by DNS (G Tryggvason, S Dabiri), shocks in cavitating flows (NA Adams, SJ Schmidt, CF Delale, GH Schnerr, S Pasinlioglu) together with applications involving encapsulated bubble dynamics in imaging (AA Doinikov, A Novell, JM Escoffre, A Bouakaz),  shock wave lithotripsy (P Zhong), sterilization of ships’ ballast water (A Abe, H Mimura) and bubbly flow model of volcano eruptions ((VK Kedrinskii, K Takayama...

  4. SUMO and KSHV Replication

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Pei-Ching [Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 112, Taiwan (China); Kung, Hsing-Jien, E-mail: hkung@nhri.org.tw [Institute for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan (China); Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616 (United States); UC Davis Cancer Center, University of California, Davis, CA 95616 (United States); Division of Molecular and Genomic Medicine, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 35053, Taiwan (China)

    2014-09-29

    Small Ubiquitin-related MOdifier (SUMO) modification was initially identified as a reversible post-translational modification that affects the regulation of diverse cellular processes, including signal transduction, protein trafficking, chromosome segregation, and DNA repair. Increasing evidence suggests that the SUMO system also plays an important role in regulating chromatin organization and transcription. It is thus not surprising that double-stranded DNA viruses, such as Kaposi’s sarcoma-associated herpesvirus (KSHV), have exploited SUMO modification as a means of modulating viral chromatin remodeling during the latent-lytic switch. In addition, SUMO regulation allows the disassembly and assembly of promyelocytic leukemia protein-nuclear bodies (PML-NBs), an intrinsic antiviral host defense, during the viral replication cycle. Overcoming PML-NB-mediated cellular intrinsic immunity is essential to allow the initial transcription and replication of the herpesvirus genome after de novo infection. As a consequence, KSHV has evolved a way as to produce multiple SUMO regulatory viral proteins to modulate the cellular SUMO environment in a dynamic way during its life cycle. Remarkably, KSHV encodes one gene product (K-bZIP) with SUMO-ligase activities and one gene product (K-Rta) that exhibits SUMO-targeting ubiquitin ligase (STUbL) activity. In addition, at least two viral products are sumoylated that have functional importance. Furthermore, sumoylation can be modulated by other viral gene products, such as the viral protein kinase Orf36. Interference with the sumoylation of specific viral targets represents a potential therapeutic strategy when treating KSHV, as well as other oncogenic herpesviruses. Here, we summarize the different ways KSHV exploits and manipulates the cellular SUMO system and explore the multi-faceted functions of SUMO during KSHV’s life cycle and pathogenesis.

  5. Hyperthermia stimulates HIV-1 replication.

    Directory of Open Access Journals (Sweden)

    Ferdinand Roesch

    Full Text Available HIV-infected individuals may experience fever episodes. Fever is an elevation of the body temperature accompanied by inflammation. It is usually beneficial for the host through enhancement of immunological defenses. In cultures, transient non-physiological heat shock (42-45°C and Heat Shock Proteins (HSPs modulate HIV-1 replication, through poorly defined mechanisms. The effect of physiological hyperthermia (38-40°C on HIV-1 infection has not been extensively investigated. Here, we show that culturing primary CD4+ T lymphocytes and cell lines at a fever-like temperature (39.5°C increased the efficiency of HIV-1 replication by 2 to 7 fold. Hyperthermia did not facilitate viral entry nor reverse transcription, but increased Tat transactivation of the LTR viral promoter. Hyperthermia also boosted HIV-1 reactivation in a model of latently-infected cells. By imaging HIV-1 transcription, we further show that Hsp90 co-localized with actively transcribing provirus, and this phenomenon was enhanced at 39.5°C. The Hsp90 inhibitor 17-AAG abrogated the increase of HIV-1 replication in hyperthermic cells. Altogether, our results indicate that fever may directly stimulate HIV-1 replication, in a process involving Hsp90 and facilitation of Tat-mediated LTR activity.

  6. Constrained Vapor Bubble Experiment

    Science.gov (United States)

    Gokhale, Shripad; Plawsky, Joel; Wayner, Peter C., Jr.; Zheng, Ling; Wang, Ying-Xi

    2002-11-01

    Microgravity experiments on the Constrained Vapor Bubble Heat Exchanger, CVB, are being developed for the International Space Station. In particular, we present results of a precursory experimental and theoretical study of the vertical Constrained Vapor Bubble in the Earth's environment. A novel non-isothermal experimental setup was designed and built to study the transport processes in an ethanol/quartz vertical CVB system. Temperature profiles were measured using an in situ PC (personal computer)-based LabView data acquisition system via thermocouples. Film thickness profiles were measured using interferometry. A theoretical model was developed to predict the curvature profile of the stable film in the evaporator. The concept of the total amount of evaporation, which can be obtained directly by integrating the experimental temperature profile, was introduced. Experimentally measured curvature profiles are in good agreement with modeling results. For microgravity conditions, an analytical expression, which reveals an inherent relation between temperature and curvature profiles, was derived.

  7. Bubble dynamics in drinks

    Directory of Open Access Journals (Sweden)

    Broučková Zuzana

    2014-03-01

    Full Text Available This study introduces two physical effects known from beverages: the effect of sinking bubbles and the hot chocolate sound effect. The paper presents two simple „kitchen” experiments. The first and second effects are indicated by means of a flow visualization and microphone measurement, respectively. To quantify the second (acoustic effect, sound records are analyzed using time-frequency signal processing, and the obtained power spectra and spectrograms are discussed.

  8. Bubble dynamics in drinks

    Science.gov (United States)

    Broučková, Zuzana; Trávníček, Zdeněk; Šafařík, Pavel

    2014-03-01

    This study introduces two physical effects known from beverages: the effect of sinking bubbles and the hot chocolate sound effect. The paper presents two simple "kitchen" experiments. The first and second effects are indicated by means of a flow visualization and microphone measurement, respectively. To quantify the second (acoustic) effect, sound records are analyzed using time-frequency signal processing, and the obtained power spectra and spectrograms are discussed.

  9. Influence of Bubble-Bubble interactions on the macroscale circulation patterns in a bubbling gas-solid fluidized bed

    NARCIS (Netherlands)

    Laverman, J.A.; van Sint Annaland, M.; Kuipers, J.A.M.

    2007-01-01

    The macro-scale circulation patterns in the emulsion phase of a gas-solid fluidized bed in the bubbling regime have been studied with a 3D Discrete Bubble Model. It has been shown that bubble-bubble interactions strongly influence the extent of the solids circulation and the bubble size

  10. Characterization of Bubble Size Distributions within a Bubble Column

    OpenAIRE

    Shahrouz Mohagheghian; Brian R. Elbing

    2018-01-01

    The current study experimentally examines bubble size distribution (BSD) within a bubble column and the associated characteristic length scales. Air was injected into a column of water via a single injection tube. The column diameter (63–102 mm), injection tube diameter (0.8–1.6 mm) and superficial gas velocity (1.4–55 mm/s) were varied. Large samples (up to 54,000 bubbles) of bubble sizes measured via 2D imaging were used to produce probability density functions (PDFs). The PDFs were used to...

  11. Database Replication Prototype

    OpenAIRE

    Vandewall, R.

    2000-01-01

    This report describes the design of a Replication Framework that facilitates the implementation and com-parison of database replication techniques. Furthermore, it discusses the implementation of a Database Replication Prototype and compares the performance measurements of two replication techniques based on the Atomic Broadcast communication primitive: pessimistic active replication and optimistic active replication. The main contributions of this report can be split into four parts....

  12. Rational Asset Pricing Bubbles Revisited

    OpenAIRE

    Jan Werner

    2012-01-01

    Price bubble arises when the price of an asset exceeds the asset's fundamental value, that is, the present value of future dividend payments. The important result of Santos and Woodford (1997) says that price bubbles cannot exist in equilibrium in the standard dynamic asset pricing model with rational agents as long as assets are in strictly positive supply and the present value of total future resources is finite. This paper explores the possibility of asset price bubbles when either one of ...

  13. Droplets, Bubbles and Ultrasound Interactions.

    Science.gov (United States)

    Shpak, Oleksandr; Verweij, Martin; de Jong, Nico; Versluis, Michel

    2016-01-01

    The interaction of droplets and bubbles with ultrasound has been studied extensively in the last 25 years. Microbubbles are broadly used in diagnostic and therapeutic medical applications, for instance, as ultrasound contrast agents. They have a similar size as red blood cells, and thus are able to circulate within blood vessels. Perfluorocarbon liquid droplets can be a potential new generation of microbubble agents as ultrasound can trigger their conversion into gas bubbles. Prior to activation, they are at least five times smaller in diameter than the resulting bubbles. Together with the violent nature of the phase-transition, the droplets can be used for local drug delivery, embolotherapy, HIFU enhancement and tumor imaging. Here we explain the basics of bubble dynamics, described by the Rayleigh-Plesset equation, bubble resonance frequency, damping and quality factor. We show the elegant calculation of the above characteristics for the case of small amplitude oscillations by linearizing the equations. The effect and importance of a bubble coating and effective surface tension are also discussed. We give the main characteristics of the power spectrum of bubble oscillations. Preceding bubble dynamics, ultrasound propagation is introduced. We explain the speed of sound, nonlinearity and attenuation terms. We examine bubble ultrasound scattering and how it depends on the wave-shape of the incident wave. Finally, we introduce droplet interaction with ultrasound. We elucidate the ultrasound-focusing concept within a droplets sphere, droplet shaking due to media compressibility and droplet phase-conversion dynamics.

  14. Helium bubble bursting in tungsten

    International Nuclear Information System (INIS)

    Sefta, Faiza; Juslin, Niklas; Wirth, Brian D.

    2013-01-01

    Molecular dynamics simulations have been used to systematically study the pressure evolution and bursting behavior of sub-surface helium bubbles and the resulting tungsten surface morphology. This study specifically investigates how bubble shape and size, temperature, tungsten surface orientation, and ligament thickness above the bubble influence bubble stability and surface evolution. The tungsten surface is roughened by a combination of adatom “islands,” craters, and pinholes. The present study provides insight into the mechanisms and conditions leading to various tungsten topology changes, which we believe are the initial stages of surface evolution leading to the formation of nanoscale fuzz

  15. Bubble Coalescence: Effect of Bubble Approach Velocity and Liquid Viscosity

    Czech Academy of Sciences Publication Activity Database

    Orvalho, Sandra; Růžička, Marek; Olivieri, G.; Marzocchella, A.

    2015-01-01

    Roč. 134, SEP 29 (2015), s. 205-216 ISSN 0009-2509 R&D Projects: GA MŠk(CZ) LD13018 Institutional support: RVO:67985858 Keywords : bubble coalescence * bubble approach velocity * liquid viscosity Subject RIV: CI - Industrial Chemistry, Chemical Engineering Impact factor: 2.750, year: 2015

  16. Bubble Size Distribution in a Vibrating Bubble Column

    Science.gov (United States)

    Mohagheghian, Shahrouz; Wilson, Trevor; Valenzuela, Bret; Hinds, Tyler; Moseni, Kevin; Elbing, Brian

    2016-11-01

    While vibrating bubble columns have increased the mass transfer between phases, a universal scaling law remains elusive. Attempts to predict mass transfer rates in large industrial scale applications by extrapolating laboratory scale models have failed. In a stationary bubble column, mass transfer is a function of phase interfacial area (PIA), while PIA is determined based on the bubble size distribution (BSD). On the other hand, BSD is influenced by the injection characteristics and liquid phase dynamics and properties. Vibration modifies the BSD by impacting the gas and gas-liquid dynamics. This work uses a vibrating cylindrical bubble column to investigate the effect of gas injection and vibration characteristics on the BSD. The bubble column has a 10 cm diameter and was filled with water to a depth of 90 cm above the tip of the orifice tube injector. BSD was measured using high-speed imaging to determine the projected area of individual bubbles, which the nominal bubble diameter was then calculated assuming spherical bubbles. The BSD dependence on the distance from the injector, injector design (1.6 and 0.8 mm ID), air flow rates (0.5 to 5 lit/min), and vibration conditions (stationary and vibration conditions varying amplitude and frequency) will be presented. In addition to mean data, higher order statistics will also be provided.

  17. Understanding the bubbles

    DEFF Research Database (Denmark)

    Turcan, Romeo V.

    that are identified to exist between the Internet and housing market bubbles: uncertainty and sentiments. The iteration between uncertainty and sentiments leads to the emergence of the third commonality: residue. The residue is the difference between the actors’ overall sentiment about exaggerated future prospects...... all boils down to the role pricing plays vis-à-vis the emergence of a new venture and its perceived value. Being in the midst of the global economic crisis provides us with a unique opportunity to refine the proposed model, especially by understanding its temporal and contextual boundaries....

  18. Visualization of airflow growing soap bubbles

    Science.gov (United States)

    Al Rahbi, Hamood; Bock, Matthew; Ryu, Sangjin

    2016-11-01

    Visualizing airflow inside growing soap bubbles can answer questions regarding the fluid dynamics of soap bubble blowing, which is a model system for flows with a gas-liquid-gas interface. Also, understanding the soap bubble blowing process is practical because it can contribute to controlling industrial processes similar to soap bubble blowing. In this study, we visualized airflow which grows soap bubbles using the smoke wire technique to understand how airflow blows soap bubbles. The soap bubble blower setup was built to mimic the human blowing process of soap bubbles, which consists of a blower, a nozzle and a bubble ring. The smoke wire was placed between the nozzle and the bubble ring, and smoke-visualized airflow was captured using a high speed camera. Our visualization shows how air jet flows into the growing soap bubble on the ring and how the airflow interacts with the soap film of growing bubble.

  19. Bubble levitation and translation under single-bubble sonoluminescence conditions.

    Science.gov (United States)

    Matula, Thomas J

    2003-08-01

    Bubble levitation in an acoustic standing wave is re-examined for conditions relevant to single-bubble sonoluminescence. Unlike a previous examination [Matula et al., J. Acoust. Soc. Am. 102, 1522-1527 (1997)], the stable parameter space [Pa,R0] is accounted for in this realization. Forces such as the added mass force and drag are included, and the results are compared with a simple force balance that equates the Bjerknes force to the buoyancy force. Under normal sonoluminescence conditions, the comparison is quite favorable. A more complete accounting of the forces shows that a stably levitated bubble does undergo periodic translational motion. The asymmetries associated with translational motion are hypothesized to generate instabilities in the spherical shape of the bubble. A reduction in gravity results in reduced translational motion. It is hypothesized that such conditions may lead to increased light output from sonoluminescing bubbles.

  20. New mechanism for bubble nucleation: Classical transitions

    International Nuclear Information System (INIS)

    Easther, Richard; Giblin, John T. Jr; Hui Lam; Lim, Eugene A.

    2009-01-01

    Given a scalar field with metastable minima, bubbles nucleate quantum mechanically. When bubbles collide, energy stored in the bubble walls is converted into kinetic energy of the field. This kinetic energy can facilitate the classical nucleation of new bubbles in minima that lie below those of the 'parent' bubbles. This process is efficient and classical, and changes the dynamics and statistics of bubble formation in models with multiple vacua, relative to that derived from quantum tunneling.

  1. Blistering and bubble formation

    International Nuclear Information System (INIS)

    Roth, J.

    1976-01-01

    Blister formation in metals has been observed during bombardment with inert-gas ions in the energy range between 1 and 2000 keV at doses of about 10 17 to 10 19 cm -2 . The changes in surface topography and the erosion yields were mainly studied in the scanning electron microscope (SEM). Additionally the release of the implanted gas during blister formation was observed. Recently measurements on single crystals were performed determining simultaneously the implantation profile, the total amount of trapped ions, the depth distribution of the induced lattice damage and the thickness of the covers of the blisters. In several stages of the formation process of blisters the implanted layer was observed in the transmission electron microscope (TEM) showing the formation of gas bubbles. Using the results of all these measurements in this review an attempt is made to develop a model of blister formation combining the effects of hydrostatic pressure in the gas bubbles and lateral stress due to volume swelling. (author)

  2. Sonoluminescing Air Bubbles Rectify Argon

    NARCIS (Netherlands)

    Lohse, Detlef; Brenner, Michael P.; Dupont, Todd F.; Hilgenfeldt, Sascha; Johnston, Blaine

    1997-01-01

    The dynamics of single bubble sonoluminescence (SBSL) strongly depends on the percentage of inert gas within the bubble. We propose a theory for this dependence, based on a combination of principles from sonochemistry and hydrodynamic stability. The nitrogen and oxygen dissociation and subsequent

  3. Bubble coalescence in breathing DNA

    DEFF Research Database (Denmark)

    Novotný, Tomas; Pedersen, Jonas Nyvold; Ambjörnsson, Tobias

    2007-01-01

    We investigate the coalescence of two DNA bubbles initially located at weak segments and separated by a more stable barrier region in a designed construct of double-stranded DNA. The characteristic time for bubble coalescence and the corresponding distribution are derived, as well as the distribu...... vicious walkers in opposite potentials....

  4. A prediction for bubbling geometries

    OpenAIRE

    Okuda, Takuya

    2007-01-01

    We study the supersymmetric circular Wilson loops in N=4 Yang-Mills theory. Their vacuum expectation values are computed in the parameter region that admits smooth bubbling geometry duals. The results are a prediction for the supergravity action evaluated on the bubbling geometries for Wilson loops.

  5. Preparation of bubble damage detectors

    International Nuclear Information System (INIS)

    Tu Caiqing; Guo Shilun; Wang Yulan; Hao Xiuhong; Chen Changmao; Su Jingling

    1997-01-01

    Bubble damage detectors have been prepared by using polyacrylamide as detector solid and freon as detector liquid. Tests show that the prepared detectors are sensitive to fast neutrons and have proportionality between bubble number and neutron fluence within a certain range of neutron fluence. Therefore, it can be used as a fast neutron detector and a dosimeter

  6. The little holographic bubble chambers

    International Nuclear Information System (INIS)

    Herve, A.

    1983-01-01

    The lifetime study of the charmed particles has readvanced the idea to use holography for the little fast-cycle bubble chambers. A pilot experiment has been realised in 1982 with a little bubble chamber filled up with freon-115. 40000 holograms have been recorded [fr

  7. Bubble chamber: colour enhanced tracks

    CERN Multimedia

    1998-01-01

    This artistically-enhanced image of real particle tracks was produced in the Big European Bubble Chamber (BEBC). Liquid hydrogen is used to create bubbles along the paths of the particles as a piston expands the medium. A magnetic field is produced in the detector causing the particles to travel in spirals, allowing charge and momentum to be measured.

  8. Prelife catalysts and replicators

    OpenAIRE

    Ohtsuki, Hisashi; Nowak, Martin A.

    2009-01-01

    Life is based on replication and evolution. But replication cannot be taken for granted. We must ask what there was prior to replication and evolution. How does evolution begin? We have proposed prelife as a generative system that produces information and diversity in the absence of replication. We model prelife as a binary soup of active monomers that form random polymers. ‘Prevolutionary’ dynamics can have mutation and selection prior to replication. Some sequences might have catalytic acti...

  9. Sinking bubbles in stout beers

    Science.gov (United States)

    Lee, W. T.; Kaar, S.; O'Brien, S. B. G.

    2018-04-01

    A surprising phenomenon witnessed by many is the sinking bubbles seen in a settling pint of stout beer. Bubbles are less dense than the surrounding fluid so how does this happen? Previous work has shown that the explanation lies in a circulation of fluid promoted by the tilted sides of the glass. However, this work has relied heavily on computational fluid dynamics (CFD) simulations. Here, we show that the phenomenon of sinking bubbles can be predicted using a simple analytic model. To make the model analytically tractable, we work in the limit of small bubbles and consider a simplified geometry. The model confirms both the existence of sinking bubbles and the previously proposed mechanism.

  10. Transcription and recombination: when RNA meets DNA.

    Science.gov (United States)

    Aguilera, Andrés; Gaillard, Hélène

    2014-08-01

    A particularly relevant phenomenon in cell physiology and proliferation is the fact that spontaneous mitotic recombination is strongly enhanced by transcription. The most accepted view is that transcription increases the occurrence of double-strand breaks and/or single-stranded DNA gaps that are repaired by recombination. Most breaks would arise as a consequence of the impact that transcription has on replication fork progression, provoking its stalling and/or breakage. Here, we discuss the mechanisms responsible for the cross talk between transcription and recombination, with emphasis on (1) the transcription-replication conflicts as the main source of recombinogenic DNA breaks, and (2) the formation of cotranscriptional R-loops as a major cause of such breaks. The new emerging questions and perspectives are discussed on the basis of the interference between transcription and replication, as well as the way RNA influences genome dynamics. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

  11. Chromatin Structure and Replication Origins: Determinants Of Chromosome Replication And Nuclear Organization

    Science.gov (United States)

    Smith, Owen K.; Aladjem, Mirit I.

    2014-01-01

    The DNA replication program is, in part, determined by the epigenetic landscape that governs local chromosome architecture and directs chromosome duplication. Replication must coordinate with other biochemical processes occurring concomitantly on chromatin, such as transcription and remodeling, to insure accurate duplication of both genetic and epigenetic features and to preserve genomic stability. The importance of genome architecture and chromatin looping in coordinating cellular processes on chromatin is illustrated by two recent sets of discoveries. First, chromatin-associated proteins that are not part of the core replication machinery were shown to affect the timing of DNA replication. These chromatin-associated proteins could be working in concert, or perhaps in competition, with the transcriptional machinery and with chromatin modifiers to determine the spatial and temporal organization of replication initiation events. Second, epigenetic interactions are mediated by DNA sequences that determine chromosomal replication. In this review we summarize recent findings and current models linking spatial and temporal regulation of the replication program with epigenetic signaling. We discuss these issues in the context of the genome’s three-dimensional structure with an emphasis on events occurring during the initiation of DNA replication. PMID:24905010

  12. Sonochemistry and the acoustic bubble

    CERN Document Server

    Grieser, Franz; Enomoto, Naoya; Harada, Hisashi; Okitsu, Kenji; Yasui, Kyuichi

    2015-01-01

    Sonochemistry and the Acoustic Bubble provides an introduction to the way ultrasound acts on bubbles in a liquid to cause bubbles to collapse violently, leading to localized 'hot spots' in the liquid with temperatures of 5000° celcius and under pressures of several hundred atmospheres. These extreme conditions produce events such as the emission of light, sonoluminescence, with a lifetime of less than a nanosecond, and free radicals that can initiate a host of varied chemical reactions (sonochemistry) in the liquid, all at room temperature. The physics and chemistry behind the p

  13. Initiation of DNA replication requires actin dynamics and formin activity.

    Science.gov (United States)

    Parisis, Nikolaos; Krasinska, Liliana; Harker, Bethany; Urbach, Serge; Rossignol, Michel; Camasses, Alain; Dewar, James; Morin, Nathalie; Fisher, Daniel

    2017-11-02

    Nuclear actin regulates transcriptional programmes in a manner dependent on its levels and polymerisation state. This dynamics is determined by the balance of nucleocytoplasmic shuttling, formin- and redox-dependent filament polymerisation. Here, using Xenopus egg extracts and human somatic cells, we show that actin dynamics and formins are essential for DNA replication. In proliferating cells, formin inhibition abolishes nuclear transport and initiation of DNA replication, as well as general transcription. In replicating nuclei from transcriptionally silent Xenopus egg extracts, we identified numerous actin regulators, and disruption of actin dynamics abrogates nuclear transport, preventing NLS (nuclear localisation signal)-cargo release from RanGTP-importin complexes. Nuclear formin activity is further required to promote loading of cyclin-dependent kinase (CDK) and proliferating cell nuclear antigen (PCNA) onto chromatin, as well as initiation and elongation of DNA replication. Therefore, actin dynamics and formins control DNA replication by multiple direct and indirect mechanisms. © 2017 The Authors.

  14. Systems-wide RNAi analysis of CASP8AP2/FLASH shows transcriptional deregulation of the replication-dependent histone genes and extensive effects on the transcriptome of colorectal cancer cells

    OpenAIRE

    Hummon Amanda B; Pitt Jason J; Camps Jordi; Emons Georg; Skube Susan B; Huppi Konrad; Jones Tamara L; Beissbarth Tim; Kramer Frank; Grade Marian; Difilippantonio Michael J; Ried Thomas; Caplen Natasha J

    2012-01-01

    Abstract Background Colorectal carcinomas (CRC) carry massive genetic and transcriptional alterations that influence multiple cellular pathways. The study of proteins whose loss-of-function (LOF) alters the growth of CRC cells can be used to further understand the cellular processes cancer cells depend upon for survival. Results A small-scale RNAi screen of ~400 genes conducted in SW480 CRC cells identified several candidate genes as required for the viability of CRC cells, most prominently C...

  15. Effect of bubble interface parameters on predicted of bubble departure diameter in a narrow channel

    International Nuclear Information System (INIS)

    Xu Jianjun; Xie Tianzhou; Zhou Wenbin; Chen Bingde; Huang Yanping

    2014-01-01

    The predicted model on the bubble departure diameter in a narrow channel is built by analysis of forces acting on the bubble, and effects of bubble interface parameters such as the bubble inclination angle, upstream contact angle, downstream contact angle and bubble contact diameter on predicted bubble departure diameters in a narrow channel are analysed by comparing with the visual experimental data. Based on the above results, the bubble interface parameters as the input parameters used to obtain the bubble departure diameter in a narrow channel are assured, and the bubble departure diameters in a narrow channel are predicted by solving the force equation. The predicted bubble departure diameters are verified by the 58 bubble departure diameters obtained from the vertical and inclined visual experiment, and the predicted results agree with the experimental results. The different forces acting on the bubble are obtained and the effect of thermal parameters in this experiment on bubble departure diameters is analysed. (authors)

  16. New evidence on the first financial bubble

    NARCIS (Netherlands)

    Frehen, R.G.P.; Goetzmann, W.; Rouwenhorst, K.G.

    2013-01-01

    The Mississippi Bubble, South Sea Bubble and the Dutch Windhandel of 1720 together represent the world's first global financial bubble. We hand-collect cross-sectional price data and investor account data from 1720 to test theories about market bubbles. Our tests suggest that innovation was a key

  17. Chromosomal Replication Complexity: A Novel DNA Metrics and Genome Instability Factor.

    Directory of Open Access Journals (Sweden)

    Andrei Kuzminov

    2016-10-01

    Full Text Available As the ratio of the copy number of the most replicated to the unreplicated regions in the same chromosome, the definition of chromosomal replication complexity (CRC appears to leave little room for variation, being either two during S-phase or one otherwise. However, bacteria dividing faster than they replicate their chromosome spike CRC to four and even eight. A recent experimental inquiry about the limits of CRC in Escherichia coli revealed two major reasons to avoid elevating it further: (i increased chromosomal fragmentation and (ii complications with subsequent double-strand break repair. Remarkably, examples of stable elevated CRC in eukaryotic chromosomes are well known under various terms like "differential replication," "underreplication," "DNA puffs," "onion-skin replication," or "re-replication" and highlight the phenomenon of static replication fork (sRF. To accurately describe the resulting "amplification by overinitiation," I propose a new term: "replification" (subchromosomal overreplication. In both prokaryotes and eukaryotes, replification, via sRF processing, causes double-strand DNA breaks and, with their repair elevating chromosomal rearrangements, represents a novel genome instability factor. I suggest how static replication bubbles could be stabilized and speculate that some tandem duplications represent such persistent static bubbles. Moreover, I propose how static replication bubbles could be transformed into tandem duplications, double minutes, or inverted triplications. Possible experimental tests of these models are discussed.

  18. Characterization of Bubble Size Distributions within a Bubble Column

    Directory of Open Access Journals (Sweden)

    Shahrouz Mohagheghian

    2018-02-01

    Full Text Available The current study experimentally examines bubble size distribution (BSD within a bubble column and the associated characteristic length scales. Air was injected into a column of water via a single injection tube. The column diameter (63–102 mm, injection tube diameter (0.8–1.6 mm and superficial gas velocity (1.4–55 mm/s were varied. Large samples (up to 54,000 bubbles of bubble sizes measured via 2D imaging were used to produce probability density functions (PDFs. The PDFs were used to identify an alternative length scale termed the most frequent bubble size (dmf and defined as the peak in the PDF. This length scale as well as the traditional Sauter mean diameter were used to assess the sensitivity of the BSD to gas injection rate, injector tube diameter, injection tube angle and column diameter. The dmf was relatively insensitive to most variation, which indicates these bubbles are produced by the turbulent wakes. In addition, the current work examines higher order statistics (standard deviation, skewness and kurtosis and notes that there is evidence in support of using these statistics to quantify the influence of specific parameters on the flow-field as well as a potential indicator of regime transitions.

  19. Bubble Formation in Basalt-like Melts

    DEFF Research Database (Denmark)

    Jensen, Martin; Keding, Ralf; Yue, Yuanzheng

    2011-01-01

    and their diameter. The variation in melting temperature has little influence on the overall bubble volume. However, the size distribution of the bubbles varies with the melting temperature. When the melt is slowly cooled, the bubble volume increases, implying decreased solubility of the gaseous species. Mass...... spectroscopy analysis of gases liberated during heating of the glass reveals that small bubbles contain predominantly CH4, CO and CO2, whereas large bubbles bear N2, SO2 and H2S. The methodology utilised in this work can, besides mapping the bubbles in a glass, be applied to shed light on the sources of bubble...

  20. Activation of human herpesvirus replication by apoptosis.

    Science.gov (United States)

    Prasad, Alka; Remick, Jill; Zeichner, Steven L

    2013-10-01

    A central feature of herpesvirus biology is the ability of herpesviruses to remain latent within host cells. Classically, exposure to inducing agents, like activating cytokines or phorbol esters that stimulate host cell signal transduction events, and epigenetic agents (e.g., butyrate) was thought to end latency. We recently showed that Kaposi's sarcoma-associated herpesvirus (KSHV, or human herpesvirus-8 [HHV-8]) has another, alternative emergency escape replication pathway that is triggered when KSHV's host cell undergoes apoptosis, characterized by the lack of a requirement for the replication and transcription activator (RTA) protein, accelerated late gene kinetics, and production of virus with decreased infectivity. Caspase-3 is necessary and sufficient to initiate the alternative replication program. HSV-1 was also recently shown to initiate replication in response to host cell apoptosis. These observations suggested that an alternative apoptosis-triggered replication program might be a general feature of herpesvirus biology and that apoptosis-initiated herpesvirus replication may have clinical implications, particularly for herpesviruses that almost universally infect humans. To explore whether an alternative apoptosis-initiated replication program is a common feature of herpesvirus biology, we studied cell lines latently infected with Epstein-Barr virus/HHV-4, HHV-6A, HHV-6B, HHV-7, and KSHV. We found that apoptosis triggers replication for each HHV studied, with caspase-3 being necessary and sufficient for HHV replication. An alternative apoptosis-initiated replication program appears to be a common feature of HHV biology. We also found that commonly used cytotoxic chemotherapeutic agents activate HHV replication, which suggests that treatments that promote apoptosis may lead to activation of latent herpesviruses, with potential clinical significance.

  1. Microstreaming from Sessile Semicylindrical Bubbles

    Science.gov (United States)

    Hilgenfeldt, Sascha; Rallabandi, Bhargav; Guo, Lin; Wang, Cheng

    2014-03-01

    Powerful steady streaming flows result from the ultrasonic driving of microbubbles, in particular when these bubbles have semicylindrical cross section and are positioned in contact with a microfluidic channel wall. We have used this streaming in experiment to develop novel methods for trapping and sorting of microparticles by size, as well as for micromixing. Theoretically, we arrive at an analytical description of the streaming flow field through an asymptotic computation that, for the first time, reconciles the boundary layers around the bubble and along the substrate wall, and also takes into account the oscillation modes of the bubble. This approach gives insight into changes in the streaming pattern with bubble size and driving frequency, including a reversal of the flow direction at high frequencies with potentially useful applications. Present address: Mechanical and Aerospace Engineering, Missouri S &T.

  2. Electroweak bubble wall speed limit

    Energy Technology Data Exchange (ETDEWEB)

    Bödeker, Dietrich [Fakultät für Physik, Universität Bielefeld, 33501 Bielefeld (Germany); Moore, Guy D., E-mail: bodeker@physik.uni-bielefeld.de, E-mail: guymoore@ikp.physik.tu-darmstadt.de [Institut für Kernphysik, Technische Universität Darmstadt, Schlossgartenstraße 2, 64289 Darmstadt (Germany)

    2017-05-01

    In extensions of the Standard Model with extra scalars, the electroweak phase transition can be very strong, and the bubble walls can be highly relativistic. We revisit our previous argument that electroweak bubble walls can 'run away,' that is, achieve extreme ultrarelativistic velocities γ ∼ 10{sup 14}. We show that, when particles cross the bubble wall, they can emit transition radiation. Wall-frame soft processes, though suppressed by a power of the coupling α, have a significance enhanced by the γ-factor of the wall, limiting wall velocities to γ ∼ 1/α. Though the bubble walls can move at almost the speed of light, they carry an infinitesimal share of the plasma's energy.

  3. Holography in small bubble chambers

    International Nuclear Information System (INIS)

    Lecoq, P.

    1984-01-01

    This chapter reports on an experiment to determine the total charm cross section at different incident momenta using the small, heavy liquid bubble chamber HOBC. Holography in liquid hydrogen is also tested using the holographic lexan bubble chamber HOLEBC with the aim of preparing a future holographic experiment in hydrogen. The high intensity tests show that more than 100 incident tracks per hologram do not cause a dramatic effect on the picture quality. Hydrogen is more favorable than freon as the bubble growth is much slower in hydrogen. An advantage of holography is to have the maximum resolution in the full volume of the bubble chamber, which allows a gain in sensitivity by a factor of 10 compared to classical optics as 100 tracks per hologram look reasonable. Holograms are not more difficult to analyze than classical optics high-resolution pictures. The results show that holography is a very powerful technique which can be used in very high resolution particle physics experiments

  4. Bubbles in a freshwater lake.

    Science.gov (United States)

    Thorpe, S A; Stubbs, A R

    1979-05-31

    WHEN the wind is strong enough to produce whitecaps on Loch Ness, patchy 'clouds' of acoustic reflectors are detected well below the surface, the depth to which they penetrate increasing with wind speed (Fig. 1). No seasonal variation in the occurrence of the reflectors has been detected. A biological explanation is therefore discounted and we suggest here that they are bubbles caused by waves breaking and forming whitecaps in deep water. Similar bubble clouds may occur in other lakes and in the sea.

  5. Slowing down bubbles with sound

    Science.gov (United States)

    Poulain, Cedric; Dangla, Remie; Guinard, Marion

    2009-11-01

    We present experimental evidence that a bubble moving in a fluid in which a well-chosen acoustic noise is superimposed can be significantly slowed down even for moderate acoustic pressure. Through mean velocity measurements, we show that a condition for this effect to occur is for the acoustic noise spectrum to match or overlap the bubble's fundamental resonant mode. We render the bubble's oscillations and translational movements using high speed video. We show that radial oscillations (Rayleigh-Plesset type) have no effect on the mean velocity, while above a critical pressure, a parametric type instability (Faraday waves) is triggered and gives rise to nonlinear surface oscillations. We evidence that these surface waves are subharmonic and responsible for the bubble's drag increase. When the acoustic intensity is increased, Faraday modes interact and the strongly nonlinear oscillations behave randomly, leading to a random behavior of the bubble's trajectory and consequently to a higher slow down. Our observations may suggest new strategies for bubbly flow control, or two-phase microfluidic devices. It might also be applicable to other elastic objects, such as globules, cells or vesicles, for medical applications such as elasticity-based sorting.

  6. Bubble bursting at an interface

    Science.gov (United States)

    Kulkarni, Varun; Sajjad, Kumayl; Anand, Sushant; Fezzaa, Kamel

    2017-11-01

    Bubble bursting is crucial to understanding the life span of bubbles at an interface and more importantly the nature of interaction between the bulk liquid and the outside environment from the point of view of chemical and biological material transport. The dynamics of the bubble as it rises from inside the liquid bulk to its disappearance on the interface after bursting is an intriguing process, many aspects of which are still being explored. In our study, we make detailed high speed imaging measurements to examine carefully the hole initiation and growth in bursting bubbles that unearth some interesting features of the process. Previous analyses available in literature are revisited based on our novel experimental visualizations. Using a combination of experiments and theory we investigate the role of various forces during the rupturing process. This work aims to further our current knowledge of bubble dynamics at an interface with an aim of predicting better the bubble evolution from its growth to its eventual integration with the liquid bulk.

  7. Measuring online social bubbles

    Directory of Open Access Journals (Sweden)

    Dimitar Nikolov

    2015-12-01

    Full Text Available Social media have become a prevalent channel to access information, spread ideas, and influence opinions. However, it has been suggested that social and algorithmic filtering may cause exposure to less diverse points of view. Here we quantitatively measure this kind of social bias at the collective level by mining a massive datasets of web clicks. Our analysis shows that collectively, people access information from a significantly narrower spectrum of sources through social media and email, compared to a search baseline. The significance of this finding for individual exposure is revealed by investigating the relationship between the diversity of information sources experienced by users at both the collective and individual levels in two datasets where individual users can be analyzed—Twitter posts and search logs. There is a strong correlation between collective and individual diversity, supporting the notion that when we use social media we find ourselves inside “social bubbles.” Our results could lead to a deeper understanding of how technology biases our exposure to new information.

  8. Beyond the gas bubble

    International Nuclear Information System (INIS)

    Hilt, R.H.

    1990-01-01

    The deliverability issue currently being discussed within the natural gas industry involves both near-term and long-term questions. In the near-term, over the next two or three years, it is probable that the natural gas industry will need to mobilize for much greater levels of investment than have been the experience over the past few years. In the longer-term, it is expected that new opportunities for gas will arise as the nation seeks to meet increasing energy requirements within new environmental constraints. Methane for emissions control, CNG vehicles, expanded gas-fired electricity generation, and increased efficiency of traditional energy services are just a few examples. The issues in the longer-term center on the ability of the gas industry to meet increasing supply requirements reliably and at cost-competitive prices for these markets. This paper begins by reviewing the historical situation of gas deliverability that is the capability of the gas producing and transportation portions of the industry. The delivery system's ability to handle shifts in the centers of consumption and production is discussed, with an emphasis on regional problems of gas deliverability and potential bottlenecks. On the production side, the paper reviews the capability and the required investment necessary to handle an orderly transition to a stable supply and demand balance once the elusive bubble had finally disappeared

  9. PA from an H5N1 highly pathogenic avian influenza virus activates viral transcription and replication and induces apoptosis and interferon expression at an early stage of infection

    Directory of Open Access Journals (Sweden)

    Wang Qiang

    2012-06-01

    Full Text Available Abstract Background Although gene exchange is not likely to occur freely, reassortment between the H5N1 highly pathogenic avian influenza virus (HPAIV and currently circulating human viruses is a serious concern. The PA polymerase subunit of H5N1 HPAIV was recently reported to activate the influenza replicon activity. Methods The replicon activities of PR8 and WSN strains (H1N1 of influenza containing PA from HPAIV A/Cambodia/P0322095/2005 (H5N1 and the activity of the chimeric RNA polymerase were analyzed. A reassortant WSN virus containing the H5N1 Cambodia PA (C-PA was then reconstituted and its growth in cells and pathogenicity in mice examined. The interferon promoter, TUNEL, and caspase 3, 8, and 9 activities of C-PA-infected cells were compared with those of WSN-infected cells. Results The activity of the chimeric RNA polymerase was slightly higher than that of WSN, and C-PA replicated better than WSN in cells. However, the multi-step growth of C-PA and its pathogenicity in mice were lower than those of WSN. The interferon promoter, TUNEL, and caspase 3, 8, and 9 activities were strongly induced in early infection in C-PA-infected cells but not in WSN-infected cells. Conclusions Apoptosis and interferon were strongly induced early in C-PA infection, which protected the uninfected cells from expansion of viral infection. In this case, these classical host-virus interactions contributed to the attenuation of this strongly replicating virus.

  10. FEASTING BLACK HOLE BLOWS BUBBLES

    Science.gov (United States)

    2002-01-01

    A monstrous black hole's rude table manners include blowing huge bubbles of hot gas into space. At least, that's the gustatory practice followed by the supermassive black hole residing in the hub of the nearby galaxy NGC 4438. Known as a peculiar galaxy because of its unusual shape, NGC 4438 is in the Virgo Cluster, 50 million light-years from Earth. These NASA Hubble Space Telescope images of the galaxy's central region clearly show one of the bubbles rising from a dark band of dust. The other bubble, emanating from below the dust band, is barely visible, appearing as dim red blobs in the close-up picture of the galaxy's hub (the colorful picture at right). The background image represents a wider view of the galaxy, with the central region defined by the white box. These extremely hot bubbles are caused by the black hole's voracious eating habits. The eating machine is engorging itself with a banquet of material swirling around it in an accretion disk (the white region below the bright bubble). Some of this material is spewed from the disk in opposite directions. Acting like high-powered garden hoses, these twin jets of matter sweep out material in their paths. The jets eventually slam into a wall of dense, slow-moving gas, which is traveling at less than 223,000 mph (360,000 kph). The collision produces the glowing material. The bubbles will continue to expand and will eventually dissipate. Compared with the life of the galaxy, this bubble-blowing phase is a short-lived event. The bubble is much brighter on one side of the galaxy's center because the jet smashed into a denser amount of gas. The brighter bubble is 800 light-years tall and 800 light-years across. The observations are being presented June 5 at the American Astronomical Society meeting in Rochester, N.Y. Both pictures were taken March 24, 1999 with the Wide Field and Planetary Camera 2. False colors were used to enhance the details of the bubbles. The red regions in the picture denote the hot gas

  11. MOF Suppresses Replication Stress and Contributes to Resolution of Stalled Replication Forks.

    Science.gov (United States)

    Singh, Dharmendra Kumar; Pandita, Raj K; Singh, Mayank; Chakraborty, Sharmistha; Hambarde, Shashank; Ramnarain, Deepti; Charaka, Vijaya; Ahmed, Kazi Mokim; Hunt, Clayton R; Pandita, Tej K

    2018-03-15

    The human MOF (hMOF) protein belongs to the MYST family of histone acetyltransferases and plays a critical role in transcription and the DNA damage response. MOF is essential for cell proliferation; however, its role during replication and replicative stress is unknown. Here we demonstrate that cells depleted of MOF and under replicative stress induced by cisplatin, hydroxyurea, or camptothecin have reduced survival, a higher frequency of S-phase-specific chromosome damage, and increased R-loop formation. MOF depletion decreased replication fork speed and, when combined with replicative stress, also increased stalled replication forks as well as new origin firing. MOF interacted with PCNA, a key coordinator of replication and repair machinery at replication forks, and affected its ubiquitination and recruitment to the DNA damage site. Depletion of MOF, therefore, compromised the DNA damage repair response as evidenced by decreased Mre11, RPA70, Rad51, and PCNA focus formation, reduced DNA end resection, and decreased CHK1 phosphorylation in cells after exposure to hydroxyurea or cisplatin. These results support the argument that MOF plays an important role in suppressing replication stress induced by genotoxic agents at several stages during the DNA damage response. Copyright © 2018 American Society for Microbiology.

  12. The DNA Replication Checkpoint Directly Regulates MBF-Dependent G1/S Transcription▿

    Science.gov (United States)

    Dutta, Chaitali; Patel, Prasanta K.; Rosebrock, Adam; Oliva, Anna; Leatherwood, Janet; Rhind, Nicholas

    2008-01-01

    The DNA replication checkpoint transcriptionally upregulates genes that allow cells to adapt to and survive replication stress. Our results show that, in the fission yeast Schizosaccharomyces pombe, the replication checkpoint regulates the entire G1/S transcriptional program by directly regulating MBF, the G1/S transcription factor. Instead of initiating a checkpoint-specific transcriptional program, the replication checkpoint targets MBF to maintain the normal G1/S transcriptional program during replication stress. We propose a mechanism for this regulation, based on in vitro phosphorylation of the Cdc10 subunit of MBF by the Cds1 replication-checkpoint kinase. Replacement of two potential phosphorylation sites with phosphomimetic amino acids suffices to promote the checkpoint transcriptional program, suggesting that Cds1 phosphorylation directly regulates MBF-dependent transcription. The conservation of MBF between fission and budding yeast, and recent results implicating MBF as a target of the budding yeast replication checkpoint, suggests that checkpoint regulation of the MBF transcription factor is a conserved strategy for coping with replication stress. Furthermore, the structural and regulatory similarity between MBF and E2F, the metazoan G1/S transcription factor, suggests that this checkpoint mechanism may be broadly conserved among eukaryotes. PMID:18662996

  13. Bubble nucleation in an explosive micro-bubble actuator

    International Nuclear Information System (INIS)

    Van den Broek, D M; Elwenspoek, M

    2008-01-01

    Explosive evaporation occurs when a thin layer of liquid reaches a temperature close to the critical temperature in a very short time. At these temperatures spontaneous nucleation takes place. The nucleated bubbles instantly coalesce forming a vapour film followed by rapid growth due to the pressure impulse. In this paper we take a closer look at the bubble nucleation. The moment of bubble nucleation was determined by both stroboscopic imaging and resistance thermometry. Two nucleation regimes could be distinguished. Several different heater designs were investigated under heat fluxes of hundreds of W mm −2 . A close correspondence between current density in the heater and point of nucleation was found. This results in design rules for effective heaters

  14. Spherical Solutions of an Underwater Explosion Bubble

    Directory of Open Access Journals (Sweden)

    Andrew B. Wardlaw

    1998-01-01

    Full Text Available The evolution of the 1D explosion bubble flow field out to the first bubble minimum is examined in detail using four different models. The most detailed is based on the Euler equations and accounts for the internal bubble fluid motion, while the simplest links a potential water solution to a stationary, Isentropic bubble model. Comparison of the different models with experimental data provides insight into the influence of compressibility and internal bubble dynamics on the behavior of the explosion bubble.

  15. Bifurcation scenarios for bubbling transition.

    Science.gov (United States)

    Zimin, Aleksey V; Hunt, Brian R; Ott, Edward

    2003-01-01

    Dynamical systems with chaos on an invariant submanifold can exhibit a type of behavior called bubbling, whereby a small random or fixed perturbation to the system induces intermittent bursting. The bifurcation to bubbling occurs when a periodic orbit embedded in the chaotic attractor in the invariant manifold becomes unstable to perturbations transverse to the invariant manifold. Generically the periodic orbit can become transversely unstable through a pitchfork, transcritical, period-doubling, or Hopf bifurcation. In this paper a unified treatment of the four types of bubbling bifurcation is presented. Conditions are obtained determining whether the transition to bubbling is soft or hard; that is, whether the maximum burst amplitude varies continuously or discontinuously with variation of the parameter through its critical value. For soft bubbling transitions, the scaling of the maximum burst amplitude with the parameter is derived. For both hard and soft transitions the scaling of the average interburst time with the bifurcation parameter is deduced. Both random (noise) and fixed (mismatch) perturbations are considered. Results of numerical experiments testing our theoretical predictions are presented.

  16. Shock formation within sonoluminescence bubbles

    International Nuclear Information System (INIS)

    Vuong, V.Q.; Szeri, A.J.; Young, D.A.

    1999-01-01

    A strong case has been made by several authors that sharp, spherically symmetric shocks converging on the center of a spherical bubble driven by a strong acoustic field give rise to rapid compression and heating that produces the brief flash of light known as sonoluminescence. The formation of such shocks is considered. It is found that, although at the main collapse the bubble wall does indeed launch an inwardly-traveling compression wave, and although the subsequent reflection of the wave at the bubble center produces a very rapid temperature peak, the wave is prevented from steepening into a sharp shock by an adverse gradient in the sound speed caused by heat transfer. It is shown that the mathematical characteristics of the flow can be prevented from accumulating into a shock front by this adverse sound speed gradient. A range of results is presented for a variety of bubble ambient radii and sound field amplitudes suggested by experiments. The time scale of the peak temperature in the bubble is set by the dynamics of the compression wave: this is typically in the range 100 - 300 ps (FWHM) in concert with recent measurements of the sonoluminescence pulse width. copyright 1999 American Institute of Physics

  17. DNA replication and cancer

    DEFF Research Database (Denmark)

    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....

  18. Gene organization inside replication domains in mammalian genomes

    Science.gov (United States)

    Zaghloul, Lamia; Baker, Antoine; Audit, Benjamin; Arneodo, Alain

    2012-11-01

    We investigate the large-scale organization of human genes with respect to "master" replication origins that were previously identified as bordering nucleotide compositional skew domains. We separate genes in two categories depending on their CpG enrichment at the promoter which can be considered as a marker of germline DNA methylation. Using expression data in mouse, we confirm that CpG-rich genes are highly expressed in germline whereas CpG-poor genes are in a silent state. We further show that, whether tissue-specific or broadly expressed (housekeeping genes), the CpG-rich genes are over-represented close to the replication skew domain borders suggesting some coordination of replication and transcription. We also reveal that the transcription of the longest CpG-rich genes is co-oriented with replication fork progression so that the promoter of these transcriptionally active genes be located into the accessible open chromatin environment surrounding the master replication origins that border the replication skew domains. The observation of a similar gene organization in the mouse genome confirms the interplay of replication, transcription and chromatin structure as the cornerstone of mammalian genome architecture.

  19. Growth process of helium bubbles in aluminium

    International Nuclear Information System (INIS)

    Shiraishi, Haruki; Sakairi, Hideo; Yagi, Eiichi; Karasawa, Takashi; Hashiguti, R.R.

    1975-01-01

    The growth process of helium bubbles in α-particle bombarded pure aluminum during isothermal anneal ranging 200 to 645 0 C and 1 to 100 hr was observed by a transmission electron microscope and the possible growth mechanisms are discussed. The effects of helium concentration and cold work were investigated. The helium bubbles are detectable only at the anneal above 550 0 C in both annealed and cold worked samples. The cold work does not cause any extra coarsening trend of bubbles. The observed types of bubble distribution in the grain interior are divided into two categories, irrespective of helium concentration and cold work; (1) the fine and uniform bubble distribution, in which case the average size is limited to about 200 A or less in diameter even at the anneal just below the melting point, and (2) the coarsened and non-uniform bubble distribution ranging 500 to 4000 A in diameter. The intermediate size bubbles are scarcely found in any cases. In the above fine bubble distribution, the increase of helium concentration by a factor of two increases the density by the same factor of two, but does not change the mean size of bubbles. Corresponding to the above two characteristic bubble distributions, it is concluded that two different mechanisms are operative in this experiment; (1) the growth of bubbles by the Brownian motion, in which the growth rate of bubbles is decreased to almost zero by bubble faceting and this results in the bubble size constancy during the prolonged annealing, and (2) the growth of bubbles by the grain boundary sweep-out mechanism, by which the abrupt coarsening of bubbles is caused. The lack of existence of the intermediate size bubbles is explained in this way. (auth.)

  20. Aspherical bubble dynamics and oscillation times

    Energy Technology Data Exchange (ETDEWEB)

    Godwin, R.P.; Chapyak, E.J. [Los Alamos National Lab., NM (United States); Noack, J.; Vogel, A. [Medizinisches Laserzentrum Luebeck (Germany)

    1999-03-01

    The cavitation bubbles common in laser medicine are rarely perfectly spherical and are often located near tissue boundaries, in vessels, etc., which introduce aspherical dynamics. Here, novel features of aspherical bubble dynamics are explored. Time-resolved experimental photographs and simulations of large aspect ratio (length:diameter {approximately}20) cylindrical bubble dynamics are presented. The experiments and calculations exhibit similar dynamics. A small high-pressure cylindrical bubble initially expands radially with hardly any axial motion. Then, after reaching its maximum volume, a cylindrical bubble collapses along its long axis with relatively little radial motion. The growth-collapse period of these very aspherical bubbles differs only sightly from twice the Rayleigh collapse time for a spherical bubble with an equivalent maximum volume. This fact justifies using the temporal interval between the acoustic signals emitted upon bubble creation and collapse to estimate the maximum bubble volume. As a result, hydrophone measurements can provide an estimate of the bubble energy even for aspherical bubbles. The prolongation of the oscillation period of bubbles near solid boundaries relative to that of isolated spherical bubbles is also discussed.

  1. Bursting Bubbles and Bilayers

    Directory of Open Access Journals (Sweden)

    Steven P. Wrenn, Stephen M. Dicker, Eleanor F. Small, Nily R. Dan, Michał Mleczko, Georg Schmitz, Peter A. Lewin

    2012-01-01

    Full Text Available This paper discusses various interactions between ultrasound, phospholipid monolayer-coated gas bubbles, phospholipid bilayer vesicles, and cells. The paper begins with a review of microbubble physics models, developed to describe microbubble dynamic behavior in the presence of ultrasound, and follows this with a discussion of how such models can be used to predict inertial cavitation profiles. Predicted sensitivities of inertial cavitation to changes in the values of membrane properties, including surface tension, surface dilatational viscosity, and area expansion modulus, indicate that area expansion modulus exerts the greatest relative influence on inertial cavitation. Accordingly, the theoretical dependence of area expansion modulus on chemical composition - in particular, poly (ethylene glyclol (PEG - is reviewed, and predictions of inertial cavitation for different PEG molecular weights and compositions are compared with experiment. Noteworthy is the predicted dependence, or lack thereof, of inertial cavitation on PEG molecular weight and mole fraction. Specifically, inertial cavitation is predicted to be independent of PEG molecular weight and mole fraction in the so-called mushroom regime. In the “brush” regime, however, inertial cavitation is predicted to increase with PEG mole fraction but to decrease (to the inverse 3/5 power with PEG molecular weight. While excellent agreement between experiment and theory can be achieved, it is shown that the calculated inertial cavitation profiles depend strongly on the criterion used to predict inertial cavitation. This is followed by a discussion of nesting microbubbles inside the aqueous core of microcapsules and how this significantly increases the inertial cavitation threshold. Nesting thus offers a means for avoiding unwanted inertial cavitation and cell death during imaging and other applications such as sonoporation. A review of putative sonoporation mechanisms is then presented

  2. Bubble Dynamics in Laser Lithotripsy

    International Nuclear Information System (INIS)

    Mohammadzadeh, Milad; Mercado, Julian Martinez; Ohl, Claus-Dieter

    2015-01-01

    Laser lithotripsy is a medical procedure for fragmentation of urinary stones with a fiber guided laser pulse of several hundred microseconds long. Using high-speed photography, we present an in-vitro study of bubble dynamics and stone motion induced by Ho:YAG laser lithotripsy. The experiments reveal that detectable stone motion starts only after the bubble collapse, which we relate with the collapse-induced liquid flow. Additionally, we model the bubble formation and dynamics using a set of 2D Rayleigh-Plesset equations with the measured laser pulse profile as an input. The aim is to reduce stone motion through modification of the temporal laser pulse profile, which affects the collapse scenario and consequently the remnant liquid motion. (paper)

  3. Hamiltonian description of bubble dynamics

    International Nuclear Information System (INIS)

    Maksimov, A. O.

    2008-01-01

    The dynamics of a nonspherical bubble in a liquid is described within the Hamiltonian formalism. Primary attention is focused on the introduction of the canonical variables into the computational algorithm. The expansion of the Dirichlet-Neumann operator in powers of the displacement of a bubble wall from an equilibrium position is obtained in the explicit form. The first three terms (more specifically, the second-, third-, and fourth-order terms) in the expansion of the Hamiltonian in powers of the canonical variables are determined. These terms describe the spectrum and interaction of three essentially different modes, i.e., monopole oscillations (pulsations), dipole oscillations (translational motions), and surface oscillations. The cubic nonlinearity is analyzed for the problem associated with the generation of Faraday ripples on the wall of a bubble in an acoustic field. The possibility of decay processes occurring in the course of interaction of surface oscillations for the first fifteen (experimentally observed) modes is investigated.

  4. How Stressful Is "Deep Bubbling"?

    Science.gov (United States)

    Tyrmi, Jaana; Laukkanen, Anne-Maria

    2017-03-01

    Water resistance therapy by phonating through a tube into the water is used to treat dysphonia. Deep submersion (≥10 cm in water, "deep bubbling") is used for hypofunctional voice disorders. Using it with caution is recommended to avoid vocal overloading. This experimental study aimed to investigate how strenuous "deep bubbling" is. Fourteen subjects, half of them with voice training, repeated the syllable [pa:] in comfortable speaking pitch and loudness, loudly, and in strained voice. Thereafter, they phonated a vowel-like sound both in comfortable loudness and loudly into a glass resonance tube immersed 10 cm into the water. Oral pressure, contact quotient (CQ, calculated from electroglottographic signal), and sound pressure level were studied. The peak oral pressure P(oral) during [p] and shuttering of the outer end of the tube was measured to estimate the subglottic pressure P(sub) and the mean P(oral) during vowel portions to enable calculation of transglottic pressure P(trans). Sensations during phonation were reported with an open-ended interview. P(sub) and P(oral) were higher in "deep bubbling" and P(trans) lower than in loud syllable phonation, but the CQ did not differ significantly. Similar results were obtained for the comparison between loud "deep bubbling" and strained phonation, although P(sub) did not differ significantly. Most of the subjects reported "deep bubbling" to be stressful only for respiratory and lip muscles. No big differences were found between trained and untrained subjects. The CQ values suggest that "deep bubbling" may increase vocal fold loading. Further studies should address impact stress during water resistance exercises. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  5. Cavitation inception from bubble nuclei

    DEFF Research Database (Denmark)

    Mørch, Knud Aage

    2015-01-01

    , and experimental investigations of bubbles and cavitation inception have been presented. These results suggest that cavitation nuclei in equilibrium are gaseous voids in the water, stabilized by a skin which allows diffusion balance between gas inside the void and gas in solution in the surrounding liquid....... The cavitation nuclei may be free gas bubbles in the bulk of water, or interfacial gaseous voids located on the surface of particles in the water, or on bounding walls. The tensile strength of these nuclei depends not only on the water quality but also on the pressure-time history of the water. A recent model...

  6. Bubble dynamics equations in Newton fluid

    International Nuclear Information System (INIS)

    Xiao, J

    2008-01-01

    For the high-speed flow of Newton fluid, bubble is produced and expanded when it moves toward the surface of fluid. Bubble dynamics is a very important research field to understand the intrinsic feature of bubble production and motion. This research formulates the bubble expansion by expansion-local rotation transformation, which can be calculated by the measured velocity field. Then, the related dynamic equations are established to describe the interaction between the fluid and the bubble. The research shows that the bubble production condition can be expressed by critical vortex value and fluid pressure; and the bubble expansion rate can be obtained by solving the non-linear dynamic equation of bubble motion. The results may help the related research as it shows a special kind of fluid motion in theoretic sense. As an application example, the nanofiber radium-voltage relation and threshold voltage-surface tension relation in electrospinning process are discussed

  7. Replicating animal mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Emily A. McKinney

    2013-01-01

    Full Text Available The field of mitochondrial DNA (mtDNA replication has been experiencing incredible progress in recent years, and yet little is certain about the mechanism(s used by animal cells to replicate this plasmid-like genome. The long-standing strand-displacement model of mammalian mtDNA replication (for which single-stranded DNA intermediates are a hallmark has been intensively challenged by a new set of data, which suggests that replication proceeds via coupled leading-and lagging-strand synthesis (resembling bacterial genome replication and/or via long stretches of RNA intermediates laid on the mtDNA lagging-strand (the so called RITOLS. The set of proteins required for mtDNA replication is small and includes the catalytic and accessory subunits of DNA polymerase y, the mtDNA helicase Twinkle, the mitochondrial single-stranded DNA-binding protein, and the mitochondrial RNA polymerase (which most likely functions as the mtDNA primase. Mutations in the genes coding for the first three proteins are associated with human diseases and premature aging, justifying the research interest in the genetic, biochemical and structural properties of the mtDNA replication machinery. Here we summarize these properties and discuss the current models of mtDNA replication in animal cells.

  8. Who Needs Replication?

    Science.gov (United States)

    Porte, Graeme

    2013-01-01

    In this paper, the editor of a recent Cambridge University Press book on research methods discusses replicating previous key studies to throw more light on their reliability and generalizability. Replication research is presented as an accepted method of validating previous research by providing comparability between the original and replicated…

  9. Bubble nucleation in an explosive micro-bubble actuator

    NARCIS (Netherlands)

    van den Broek, D.M.; Elwenspoek, Michael Curt

    2008-01-01

    Explosive evaporation occurs when a thin layer of liquid reaches a temperature close to the critical temperature in a very short time. At these temperatures spontaneous nucleation takes place. The nucleated bubbles instantly coalesce forming a vapour film followed by rapid growth due to the pressure

  10. Discrete bubble modeling for a micro-structured bubble column

    NARCIS (Netherlands)

    Jain, D.; Lau, Y.M.; Kuipers, J.A.M.; Deen, N.G.

    2013-01-01

    Gas–liquid flows with solid catalyst particles are encountered in many applications in the chemical, petrochemical, pharmaceutical industries, etc. Most commonly, two reactor types are applied for large scale in the industry. They are slurry bubble column and trickle bed reactors. Both of these

  11. Flock House virus subgenomic RNA3 is replicated and its replication correlates with transactivation of RNA2

    International Nuclear Information System (INIS)

    Eckerle, Lance D.; Albarino, Cesar G.; Ball, L. Andrew.

    2003-01-01

    The nodavirus Flock House virus has a bipartite genome composed of RNAs 1 and 2, which encode the catalytic component of the RNA-dependent RNA polymerase (RdRp) and the capsid protein precursor, respectively. In addition to catalyzing replication of the viral genome, the RdRp also transcribes from RNA1 a subgenomic RNA3, which is both required for and suppressed by RNA2 replication. Here, we show that in the absence of RNA1 replication, FHV RdRp replicated positive-sense RNA3 transcripts fully and copied negative-sense RNA3 transcripts into positive strands. The two nonstructural proteins encoded by RNA3 were dispensable for replication, but sequences in the 3'-terminal 58 nucleotides were required. RNA3 variants that failed to replicate also failed to transactivate RNA2. These results imply that RNA3 is naturally produced both by transcription from RNA1 and by subsequent RNA1-independent replication and that RNA3 replication may be necessary for transactivation of RNA2

  12. Formation of soap bubbles by gas jet

    OpenAIRE

    Zhou, M. L.; Li, M.; Chen, Z. Y.; Han, J. F.; Liu, D.

    2017-01-01

    Soap bubbles can be easily generated by varies methods, while their formation process is complicated and still worth study. A model about the bubble formation process was proposed in Phys. Rev. Lett. 116, 077801 recently, and it was reported that the bubbles were formed when the gas blowing velocity was above one threshold. However, after repeating these experiments, we found the bubbles could be generated in two velocities ranges which corresponded to laminar and turbulent gas jet respective...

  13. Fluid dynamics of bubbly flows

    International Nuclear Information System (INIS)

    Ziegenhein, Thomas

    2016-01-01

    Bubbly flows can be found in many applications in chemical, biological and power engineering. Reliable simulation tools of such flows that allow the design of new processes and optimization of existing one are therefore highly desirable. CFD-simulations applying the multi-fluid approach are very promising to provide such a design tool for complete facilities. In the multi-fluid approach, however, closure models have to be formulated to model the interaction between the continuous and dispersed phase. Due to the complex nature of bubbly flows, different phenomena have to be taken into account and for every phenomenon different closure models exist. Therefore, reliable predictions of unknown bubbly flows are not yet possible with the multi-fluid approach. A strategy to overcome this problem is to define a baseline model in which the closure models including the model constants are fixed so that the limitations of the modeling can be evaluated by validating it on different experiments. Afterwards, the shortcomings are identified so that the baseline model can be stepwise improved without losing the validity for the already validated cases. This development of a baseline model is done in the present work by validating the baseline model developed at the Helmholtz-Zentrum Dresden-Rossendorf mainly basing on experimental data for bubbly pipe flows to bubble columns, bubble plumes and air-lift reactors that are relevant in chemical and biological engineering applications. In the present work, a large variety of such setups is used for validation. The buoyancy driven bubbly flows showed thereby a transient behavior on the scale of the facility. Since such large scales are characterized by the geometry of the facility, turbulence models cannot describe them. Therefore, the transient simulation of bubbly flows with two equation models based on the unsteady Reynolds-averaged Navier-Stokes equations is investigated. In combination with the before mentioned baseline model these

  14. Fluid dynamics of bubbly flows

    Energy Technology Data Exchange (ETDEWEB)

    Ziegenhein, Thomas

    2016-07-08

    Bubbly flows can be found in many applications in chemical, biological and power engineering. Reliable simulation tools of such flows that allow the design of new processes and optimization of existing one are therefore highly desirable. CFD-simulations applying the multi-fluid approach are very promising to provide such a design tool for complete facilities. In the multi-fluid approach, however, closure models have to be formulated to model the interaction between the continuous and dispersed phase. Due to the complex nature of bubbly flows, different phenomena have to be taken into account and for every phenomenon different closure models exist. Therefore, reliable predictions of unknown bubbly flows are not yet possible with the multi-fluid approach. A strategy to overcome this problem is to define a baseline model in which the closure models including the model constants are fixed so that the limitations of the modeling can be evaluated by validating it on different experiments. Afterwards, the shortcomings are identified so that the baseline model can be stepwise improved without losing the validity for the already validated cases. This development of a baseline model is done in the present work by validating the baseline model developed at the Helmholtz-Zentrum Dresden-Rossendorf mainly basing on experimental data for bubbly pipe flows to bubble columns, bubble plumes and air-lift reactors that are relevant in chemical and biological engineering applications. In the present work, a large variety of such setups is used for validation. The buoyancy driven bubbly flows showed thereby a transient behavior on the scale of the facility. Since such large scales are characterized by the geometry of the facility, turbulence models cannot describe them. Therefore, the transient simulation of bubbly flows with two equation models based on the unsteady Reynolds-averaged Navier-Stokes equations is investigated. In combination with the before mentioned baseline model these

  15. Mechanics of gas-vapor bubbles

    NARCIS (Netherlands)

    Hao, Yue; Zhang, Yuhang; Prosperetti, Andrea

    2017-01-01

    Most bubbles contain a mixture of vapor and incondensible gases. While the limit cases of pure vapor and pure gas bubbles are well studied, much less is known about the more realistic case of a mixture. The bubble contents continuously change due to the combined effects of evaporation and

  16. Vapor Bubbles in Flow and Acoustic Fields

    NARCIS (Netherlands)

    Prosperetti, Andrea; Hao, Yue; Sadhal, S.S

    2002-01-01

    A review of several aspects of the interaction of bubbles with acoustic and flow fields is presented. The focus of the paper is on bubbles in hot liquids, in which the bubble contains mostly vapor, with little or no permanent gas. The topics covered include the effect of translation on condensation

  17. Computing bubble-points of CO

    NARCIS (Netherlands)

    Ramdin, M.; Balaji, S.P.; Vicent Luna, J.M.; Torres-Knoop, A; Chen, Q.; Dubbeldam, D.; Calero, S; de Loos, T.W.; Vlugt, T.J.H.

    2016-01-01

    Computing bubble-points of multicomponent mixtures using Monte Carlo simulations is a non-trivial task. A new method is used to compute gas compositions from a known temperature, bubble-point pressure, and liquid composition. Monte Carlo simulations are used to calculate the bubble-points of

  18. Cutting bubbles with a single wire

    NARCIS (Netherlands)

    Baltussen, M.W.; Segers, Q.I.E.; Kuipers, J.A.M.; Deen, N.G.

    2017-01-01

    Many gas-liquid-solid contactors, such as trickle bed and bubble slurry columns, suffer from heat and mass transfer limitations. To overcome these limitations, new micro-structured bubble column reactor is proposed. In this reactor, a catalyst coated wire mesh is introduced in a bubble column to cut

  19. Experimental study of vapor bubble dynamics

    International Nuclear Information System (INIS)

    Pasquini, Maria-Elena

    2015-01-01

    The object of this thesis is an experimental study of vapor bubble dynamics in sub-cooled nucleate boiling. The test section is locally heated by focusing a laser beam: heat fluxes from 1 e4 to 1.5 e6 W/m 2 and water temperature between 100 and 88 C have been considered. Three boiling regimes have been observed. Under saturated conditions and with low heat fluxes a developed nucleate boiling regime has been observed. Under higher sub-cooling and still with low heat fluxes an equilibrium regime has been observed in which the liquid flowrate evaporating at the bubble base is compensated by the vapor condensing flowrate at bubble top. A third regime have been observed at high heat fluxes for all water conditions: it is characterized by the formation of a large dry spot on the heated surface that keeps the nucleation site dry after bubble detachment. The condensation phase starts after bubble detachment. Bubble equivalent radius at detachment varies between 1 and 2.5 mm. Bubble properties have been measured and non-dimensional groups have been used to characterize bubble dynamics. Capillary waves have been observed on the bubble surface thanks to high-speed images acquisition. Two main phenomena have been proposed to explain capillary waves effects on bubble condensation: increasing of the phases interface area and decreasing of vapor bubble translation velocity, because of the increased drag force on the deformed bubble. (author) [fr

  20. Identifying sites of replication initiation in yeast chromosomes: looking for origins in all the right places.

    Science.gov (United States)

    van Brabant, A J; Hunt, S Y; Fangman, W L; Brewer, B J

    1998-06-01

    DNA fragments that contain an active origin of replication generate bubble-shaped replication intermediates with diverging forks. We describe two methods that use two-dimensional (2-D) agarose gel electrophoresis along with DNA sequence information to identify replication origins in natural and artificial Saccharomyces cerevisiae chromosomes. The first method uses 2-D gels of overlapping DNA fragments to locate an active chromosomal replication origin within a region known to confer autonomous replication on a plasmid. A variant form of 2-D gels can be used to determine the direction of fork movement, and the second method uses this technique to find restriction fragments that are replicated by diverging forks, indicating that a bidirectional replication origin is located between the two fragments. Either of these two methods can be applied to the analysis of any genomic region for which there is DNA sequence information or an adequate restriction map.

  1. Droplets, Bubbles and Ultrasound Interactions

    NARCIS (Netherlands)

    Shpak, O.; Verweij, M.; de Jong, N.; Versluis, Michel; Escoffre, J.M.; Bouakaz, A.

    2016-01-01

    The interaction of droplets and bubbles with ultrasound has been studied extensively in the last 25 years. Microbubbles are broadly used in diagnostic and therapeutic medical applications, for instance, as ultrasound contrast agents. They have a similar size as red blood cells, and thus are able to

  2. "Financial Bubbles" and Monetary Policy

    Science.gov (United States)

    Tikhonov, Yuriy A.; Pudovkina, Olga E.; Permjakova, Juliana V.

    2016-01-01

    The relevance of this research is caused by the need of strengthening a role of monetary regulators to prevent financial bubbles in the financial markets. The aim of the article is the analysis of a problem of crisis phenomena in the markets of financial assets owing to an inadequate growth of their cost, owing to subjective reasons. The leading…

  3. Soliton bubbles and phase transformations

    International Nuclear Information System (INIS)

    Masperi, L.

    1989-01-01

    It is shown that no topological classical solutions in form of bubbles of a real scalar field theory with Lagrangian of quartet and sextet self interactions in 1+1 dimensions are responsible to discontinue transitions in the quantum problem between phases with degenerated and disordered excited level. (M.C.K.)

  4. Impurity bubbles in a BEC

    Science.gov (United States)

    Timmermans, Eddy; Blinova, Alina; Boshier, Malcolm

    2013-05-01

    Polarons (particles that interact with the self-consistent deformation of the host medium that contains them) self-localize when strongly coupled. Dilute Bose-Einstein condensates (BECs) doped with neutral distinguishable atoms (impurities) and armed with a Feshbach-tuned impurity-boson interaction provide a unique laboratory to study self-localized polarons. In nature, self-localized polarons come in two flavors that exhibit qualitatively different behavior: In lattice systems, the deformation is slight and the particle is accompanied by a cloud of collective excitations as in the case of the Landau-Pekar polarons of electrons in a dielectric lattice. In natural fluids and gases, the strongly coupled particle radically alters the medium, e.g. by expelling the host medium as in the case of the electron bubbles in superfluid helium. We show that BEC-impurities can self-localize in a bubble, as well as in a Landau-Pekar polaron state. The BEC-impurity system is fully characterized by only two dimensionless coupling constants. In the corresponding phase diagram the bubble and Landau-Pekar polaron limits correspond to large islands separated by a cross-over region. The same BEC-impurity species can be adiabatically Feshbach steered from the Landau-Pekar to the bubble regime. This work was funded by the Los Alamos LDRD program.

  5. Explosive micro-bubble actuator

    NARCIS (Netherlands)

    van den Broek, D.M.; Elwenspoek, Michael Curt

    2007-01-01

    Explosive evaporation occurs when a thin layer of liquid reaches a very high temperature in a very short time. At these temperatures homogeneous nucleation takes place. The nucleated bubbles almost instantly coalesce forming a vapour film followed by rapid growth due to the pressure impulse and

  6. Studies on the effects of persistent RNA priming on DNA replication and genomic stability

    OpenAIRE

    Stuckey, Ruth

    2014-01-01

    [EN]: DNA replication and transcription take place on the same DNA template, and the correct interplay between these processes ensures faithful genome duplication. DNA replication must be highly coordinated with other cell cycle events, such as segregation of fully replicated DNA in order to maintain genomic integrity. Transcription generates RNA:DNA hybrids, transient intermediate structures that are degraded by the ribonuclease H (RNaseH) class of enzymes. RNA:DNA hybrids can form R-loops, ...

  7. Registered Replication Report

    DEFF Research Database (Denmark)

    Bouwmeester, S.; Verkoeijen, P. P.J.L.; Aczel, B.

    2017-01-01

    and colleagues. The results of studies using time pressure have been mixed, with some replication attempts observing similar patterns (e.g., Rand et al., 2014) and others observing null effects (e.g., Tinghög et al., 2013; Verkoeijen & Bouwmeester, 2014). This Registered Replication Report (RRR) assessed...... the size and variability of the effect of time pressure on cooperative decisions by combining 21 separate, preregistered replications of the critical conditions from Study 7 of the original article (Rand et al., 2012). The primary planned analysis used data from all participants who were randomly assigned...

  8. Hydrodynamics in a swarm of rising bubbles

    International Nuclear Information System (INIS)

    Riboux, G.

    2007-04-01

    In many applications, bubbles are used to agitate a liquid in order to enhance mixing and transfer. This work is devoted to the study of the hydrodynamics in a stable bubble column. Experimentally, we have determined the properties of the velocity fluctuations inside and behind a homogeneous swarm of rising bubbles for different bubble sizes and gas volume fractions α: self-similarity in α 0,4 , spectrum in k -3 and integral length scale controlled by buoyancy. Numerically, we have reproduced these properties by means of large-scale simulations, the bubbles being modeled by volume-forces. This confirms that the dynamics is controlled by wake interactions. (author)

  9. The replication recipe : What makes for a convincing replication?

    NARCIS (Netherlands)

    Brandt, M.J.; IJzerman, H.; Dijksterhuis, Ap; Farach, Frank J.; Geller, Jason; Giner-Sorolla, Roger; Grange, James A.; Perugini, Marco; Spies, Jeffrey R.; van 't Veer, Anna

    Psychological scientists have recently started to reconsider the importance of close replications in building a cumulative knowledge base; however, there is no consensus about what constitutes a convincing close replication study. To facilitate convincing close replication attempts we have developed

  10. The Replication Recipe: What makes for a convincing replication?

    NARCIS (Netherlands)

    Brandt, M.J.; IJzerman, H.; Dijksterhuis, A.J.; Farach, F.J.; Geller, J.; Giner-Sorolla, R.; Grange, J.A.; Perugini, M.; Spies, J.R.; Veer, A. van 't

    2014-01-01

    Psychological scientists have recently started to reconsider the importance of close replications in building a cumulative knowledge base; however, there is no consensus about what constitutes a convincing close replication study. To facilitate convincing close replication attempts we have developed

  11. Bubbles generated from wind-steepened breaking waves: 2. Bubble plumes, bubbles, and wave characteristics

    NARCIS (Netherlands)

    Leifer, I.; Caulliez, G.; Leeuw, G.de

    2006-01-01

    Measurements of breaking-wave-generated bubble plumes were made in fresh (but not clean) water in a large wind-wave tunnel. To preserve diversity, a classification scheme was developed on the basis of plume dimensions and "optical density," or the plume's ability to obscure the background. Optically

  12. Chromatin Controls DNA Replication Origin Selection, Lagging-Strand Synthesis, and Replication Fork Rates.

    Science.gov (United States)

    Kurat, Christoph F; Yeeles, Joseph T P; Patel, Harshil; Early, Anne; Diffley, John F X

    2017-01-05

    The integrity of eukaryotic genomes requires rapid and regulated chromatin replication. How this is accomplished is still poorly understood. Using purified yeast replication proteins and fully chromatinized templates, we have reconstituted this process in vitro. We show that chromatin enforces DNA replication origin specificity by preventing non-specific MCM helicase loading. Helicase activation occurs efficiently in the context of chromatin, but subsequent replisome progression requires the histone chaperone FACT (facilitates chromatin transcription). The FACT-associated Nhp6 protein, the nucleosome remodelers INO80 or ISW1A, and the lysine acetyltransferases Gcn5 and Esa1 each contribute separately to maximum DNA synthesis rates. Chromatin promotes the regular priming of lagging-strand DNA synthesis by facilitating DNA polymerase α function at replication forks. Finally, nucleosomes disrupted during replication are efficiently re-assembled into regular arrays on nascent DNA. Our work defines the minimum requirements for chromatin replication in vitro and shows how multiple chromatin factors might modulate replication fork rates in vivo. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  13. An equation of motion for bubble growth

    Energy Technology Data Exchange (ETDEWEB)

    Lesage, F.J. [College d' Enseignement General et Professionnel de L' Outaouais, Gatineau, Quebec (Canada). Dept. of Mathematics; Cotton, J.S. [McMaster University, Hamilton, ON (Canada). Dept. of Mechanical Engineering; Robinson, A.J. [Trinity College Dublin (Ireland). Dept. of Mechanical and Manufacturing Engineering

    2009-07-01

    A mathematical model is developed which describes asymmetric bubble growth, either during boiling or bubble injection from submerged orifices. The model is developed using the integral form of the continuity and momentum equations, resulting in a general expression for the acceleration of the bubble's centre of gravity. The proposed model highlights the need to include acceleration due to an asymmetric gain or loss of mass in order to accurately predict bubble motion. Some scenarios are posed by which the growth of bubbles, particularly idealized bubbles that remain a section of a sphere, must include the fact that bubble growth can be asymmetric. In particular, for approximately hemispherical bubble growth the sum of the forces acting on the bubble is negligible compared with the asymmetric term. Further, for bubble injection from a submerged needle this component in the equation of motion is very significant during the initial rapid growth phase as the bubble issues from the nozzle changing from a near hemisphere to truncated sphere geometry. (author)

  14. An equation of motion for bubble growth

    International Nuclear Information System (INIS)

    Lesage, F.J.; Cotton, J.S.; Robinson, A.J.

    2009-01-01

    A mathematical model is developed which describes asymmetric bubble growth, either during boiling or bubble injection from submerged orifices. The model is developed using the integral form of the continuity and momentum equations, resulting in a general expression for the acceleration of the bubble's centre of gravity. The proposed model highlights the need to include acceleration due to an asymmetric gain or loss of mass in order to accurately predict bubble motion. Some scenarios are posed by which the growth of bubbles, particularly idealized bubbles that remain a section of a sphere, must include the fact that bubble growth can be asymmetric. In particular, for approximately hemispherical bubble growth the sum of the forces acting on the bubble is negligible compared with the asymmetric term. Further, for bubble injection from a submerged needle this component in the equation of motion is very significant during the initial rapid growth phase as the bubble issues from the nozzle changing from a near hemisphere to truncated sphere geometry. (author)

  15. Eukaryotic DNA Replication Fork.

    Science.gov (United States)

    Burgers, Peter M J; Kunkel, Thomas A

    2017-06-20

    This review focuses on the biogenesis and composition of the eukaryotic DNA replication fork, with an emphasis on the enzymes that synthesize DNA and repair discontinuities on the lagging strand of the replication fork. Physical and genetic methodologies aimed at understanding these processes are discussed. The preponderance of evidence supports a model in which DNA polymerase ε (Pol ε) carries out the bulk of leading strand DNA synthesis at an undisturbed replication fork. DNA polymerases α and δ carry out the initiation of Okazaki fragment synthesis and its elongation and maturation, respectively. This review also discusses alternative proposals, including cellular processes during which alternative forks may be utilized, and new biochemical studies with purified proteins that are aimed at reconstituting leading and lagging strand DNA synthesis separately and as an integrated replication fork.

  16. Modeling DNA Replication.

    Science.gov (United States)

    Bennett, Joan

    1998-01-01

    Recommends the use of a model of DNA made out of Velcro to help students visualize the steps of DNA replication. Includes a materials list, construction directions, and details of the demonstration using the model parts. (DDR)

  17. Chromatin Immunoprecipitation of Replication Factors Moving with the Replication Fork

    OpenAIRE

    Rapp, Jordan B.; Ansbach, Alison B.; Noguchi, Chiaki; Noguchi, Eishi

    2009-01-01

    Replication of chromosomes involves a variety of replication proteins including DNA polymerases, DNA helicases, and other accessory factors. Many of these proteins are known to localize at replication forks and travel with them as components of the replisome complex. Other proteins do not move with replication forks but still play an essential role in DNA replication. Therefore, in order to understand the mechanisms of DNA replication and its controls, it is important to examine localization ...

  18. Bidirectional cinematography of steam-bubble growth

    International Nuclear Information System (INIS)

    Deason, V.A.; Reynolds, L.D.

    1982-01-01

    Single steam bubbles were generated in superheated water in an optical cell. The growth process of the bubbles was recorded with a high-speed motion picture camera at 5000 and 10,000 frames per second. A technique was developed to simultaneously image two orthogonal views of the bubbles on each frame of film. The vertical and horizontal diameters of the bubbles were measured on a frame-by-frame basis, and the data analyzed to determine oscillatory frequencies. The analysis also attempted to determine whether the bubbles were undergoing volumetric oscillations during early growth or whether simple surface wave/rotational behavior caused the observed periodic variations in bubble dimensions. For the bubbles studied, typical oscillation frequencies for the diameters were in the range of 100 to 500 Hz

  19. Bidirectional cinematography of steam-bubble growth

    Energy Technology Data Exchange (ETDEWEB)

    Deason, V.A.; Reynolds, L.D.

    1982-01-01

    Single steam bubbles were generated in superheated water in an optical cell. The growth process of the bubbles was recorded with a high-speed motion picture camera at 5000 and 10,000 frames per second. A technique was developed to simultaneously image two orthogonal views of the bubbles on each frame of film. The vertical and horizontal diameters of the bubbles were measured on a frame-by-frame basis, and the data analyzed to determine oscillatory frequencies. The analysis also attempted to determine whether the bubbles were undergoing volumetric oscillations during early growth or whether simple surface wave/rotational behavior caused the observed periodic variations in bubble dimensions. For the bubbles studied, typical oscillation frequencies for the diameters were in the range of 100 to 500 Hz.

  20. Bubble entrapment through topological change

    KAUST Repository

    Thoroddsen, Sigurdur T.

    2010-05-03

    When a viscousdrop impacts onto a solid surface, it entraps a myriad of microbubbles at the interface between liquid and solid. We present direct high-speed video observations of this entrapment. For viscousdrops, the tip of the spreading lamella is separated from the surface and levitated on a cushion of air. We show that the primary mechanism for the bubble entrapment is contact between this precursor sheet of liquid with the solid and not air pulled directly through cusps in the contact line. The sheet makes contact with the solid surface,forming a wetted patch, which grows in size, but only entraps a bubble when it meets the advancing contact line. The leading front of this wet patch can also lead to the localized thinning and puncturing of the liquid film producing strong splashing of droplets.

  1. Bubbling in vibrated granular films.

    Science.gov (United States)

    Zamankhan, Piroz

    2011-02-01

    With the help of experiments, computer simulations, and a theoretical investigation, a general model is developed of the flow dynamics of dense granular media immersed in air in an intermediate regime where both collisional and frictional interactions may affect the flow behavior. The model is tested using the example of a system in which bubbles and solid structures are produced in granular films shaken vertically. Both experiments and large-scale, three-dimensional simulations of this system are performed. The experimental results are compared with the results of the simulation to verify the validity of the model. The data indicate evidence of formation of bubbles when peak acceleration relative to gravity exceeds a critical value Γ(b). The air-grain interfaces of bubblelike structures are found to exhibit fractal structure with dimension D=1.7±0.05.

  2. Bubble entrapment through topological change

    KAUST Repository

    Thoroddsen, Sigurdur T; Takehara, K.; Etoh, T. G.

    2010-01-01

    When a viscousdrop impacts onto a solid surface, it entraps a myriad of microbubbles at the interface between liquid and solid. We present direct high-speed video observations of this entrapment. For viscousdrops, the tip of the spreading lamella is separated from the surface and levitated on a cushion of air. We show that the primary mechanism for the bubble entrapment is contact between this precursor sheet of liquid with the solid and not air pulled directly through cusps in the contact line. The sheet makes contact with the solid surface,forming a wetted patch, which grows in size, but only entraps a bubble when it meets the advancing contact line. The leading front of this wet patch can also lead to the localized thinning and puncturing of the liquid film producing strong splashing of droplets.

  3. Bubble collisions in general relativity

    International Nuclear Information System (INIS)

    Siklos, S.T.C.; Wu, Z.C.; University of Science and Technology of China, Hofei, Anhwei)

    1983-01-01

    The collision of two bubbles of true vacuum in a background of false vacuum is considered in the context of General Relativity. It is found that in the thin wall approximation, the problem, can be solved exactly. The region to the future of the collision is described by the pseudo-Schwarzschild de Sitter metric. The parameters in this metric are found by solving the junction conditions at each collision. (author)

  4. BEBC Big European Bubble Chamber

    CERN Multimedia

    CERN PhotoLab

    1974-01-01

    A view of the dismantling of the magnet of BEBC, the 3.7 m European Bubble Chamber : iron magnetic shielding ; lower and upper parts of the vacuum enclosure of the magnet; turbo-molecular vacuum pumps for the "fish-eye" windows; the two superconducting coils; a handling platform; the two cryostats suspended from the bar of the travelling crane which has a 170 ton carrying capacity. The chamber proper, not dismantled, is inside the shielding.

  5. Bubbling Controlled by Needle Movement

    Czech Academy of Sciences Publication Activity Database

    Vejražka, Jiří; Zedníková, Mária; Stanovský, Petr; Růžička, Marek; Drahoš, Jiří

    2008-01-01

    Roč. 40, 7-8 (2008), s. 521-533 ISSN 0169-5983 R&D Projects: GA ČR GP101/05/P229; GA ČR(CZ) GA104/05/2566 Institutional research plan: CEZ:AV0Z40720504 Keywords : bubble * detechment * control Subject RIV: CI - Industrial Chemistry, Chemical Engineering Impact factor: 1.012, year: 2008

  6. Informational pathologies and interest bubbles

    DEFF Research Database (Denmark)

    Hendricks, Vincent Fella; Wiewiura, Joachim Schmidt

    2017-01-01

    This article contends that certain configurations of information networks facilitate specific cognitive states that are instrumental for decision and action on social media. Group-related knowledge and belief states—in particular common knowledge and pluralistic ignorance—may enable strong public...... signals. Indeed, some network configurations and attitude states foster informational pathologies that may fuel interest bubbles affecting agenda-setting and the generation of narratives in public spheres....

  7. Direct Visualization of DNA Replication Dynamics in Zebrafish Cells.

    Science.gov (United States)

    Kuriya, Kenji; Higashiyama, Eriko; Avşar-Ban, Eriko; Tamaru, Yutaka; Ogata, Shin; Takebayashi, Shin-ichiro; Ogata, Masato; Okumura, Katsuzumi

    2015-12-01

    Spatiotemporal regulation of DNA replication in the S-phase nucleus has been extensively studied in mammalian cells because it is tightly coupled with the regulation of other nuclear processes such as transcription. However, little is known about the replication dynamics in nonmammalian cells. Here, we analyzed the DNA replication processes of zebrafish (Danio rerio) cells through the direct visualization of replicating DNA in the nucleus and on DNA fiber molecules isolated from the nucleus. We found that zebrafish chromosomal DNA at the nuclear interior was replicated first, followed by replication of DNA at the nuclear periphery, which is reminiscent of the spatiotemporal regulation of mammalian DNA replication. However, the relative duration of interior DNA replication in zebrafish cells was longer compared to mammalian cells, possibly reflecting zebrafish-specific genomic organization. The rate of replication fork progression and ori-to-ori distance measured by the DNA combing technique were ∼ 1.4 kb/min and 100 kb, respectively, which are comparable to those in mammalian cells. To our knowledge, this is a first report that measures replication dynamics in zebrafish cells.

  8. When Will Occur the Crude Oil Bubbles?

    International Nuclear Information System (INIS)

    Su, Chi-Wei; Li, Zheng-Zheng; Chang, Hsu-Ling; Lobonţ, Oana-Ramona

    2017-01-01

    In this paper, we apply a recursive unit root test to investigate whether there exist multiple bubbles in crude oil price. The method is best suited for a practical implementation of a time series and delivers a consistent date-stamping strategy for the origination and termination of multiple bubbles. The empirical result indicates that there exist six bubbles during 1986–2016 when the oil price deviate from its intrinsic value based on market fundamentals. Specifically, oil price contains the fundamentals and bubble components. The dates of the bubbles correspond to specific events in the politics and financial markets. The authorities should actively fight speculative bubbles or just observe their evolutions and speculation activities may decrease, which is favour of the stabilisation of the staple commodities including crude oil price. These findings have important economic and policy implications to recognise the cause of bubbles and take corresponding measures to reduce the impact on the real economy cause of the fluctuation of crude oil price. - Highlights: • Investigate multiple bubbles in crude oil price. • Indicate six bubbles deviate from its intrinsic value based on market fundamentals. • The bubbles correspond to specific events in the politics and financial markets. • Reduce the impact on the real economy cause of the fluctuation of crude oil price.

  9. Armoring confined bubbles in concentrated colloidal suspensions

    Science.gov (United States)

    Yu, Yingxian; Khodaparast, Sepideh; Stone, Howard

    2016-11-01

    Encapsulation of a bubble with microparticles is known to significantly improve the stability of the bubble. This phenomenon has recently gained increasing attention due to its application in a variety of technologies such as foam stabilization, drug encapsulation and colloidosomes. Nevertheless, the production of such colloidal armored bubble with controlled size and particle coverage ratio is still a great challenge industrially. We study the coating process of a long air bubble by microparticles in a circular tube filled with a concentrated microparticles colloidal suspension. As the bubble proceeds in the suspension of particles, a monolayer of micro-particles forms on the interface of the bubble, which eventually results in a fully armored bubble. We investigate the phenomenon that triggers and controls the evolution of the particle accumulation on the bubble interface. Moreover, we examine the effects of the mean flow velocity, the size of the colloids and concentration of the suspension on the dynamics of the armored bubble. The results of this study can potentially be applied to production of particle-encapsulated bubbles, surface-cleaning techniques, and gas-assisted injection molding.

  10. Numerical simulation of bubbles motion in lifting pipe of bubble pump for lithium bromide absorption chillers

    International Nuclear Information System (INIS)

    Gao, Hongtao; Liu, Bingbing; Yan, Yuying

    2017-01-01

    A bubble pump is proposed to replace the traditional mechanical solution pump in lithium bromide absorption chillers, for its advantageous feature that can be driven by industrial waste heat or solar energy or other low-grade energy. In two-stage bubble pump driven lithium bromide absorption refrigeration system, flow patterns in lifting pipe have significant effects on the performance of bubble pump. In this paper, the single bubble motion and the double bubbles coalescence in vertical ascending pipe are simulated by an improved free energy model of lattice Boltzmann method, in which the two-phase liquid to gas density ratio is 2778. The details of bubbles coalescence process are studied. Density and velocity of bubbles have been obtained. The computational results show that the initial radius of each bubble has a great influence on the coalescence time. The larger the initial bubble radius, the shorter the coalescence time. The pipe diameter has a little effect on the two bubbles coalescence time while it has a significant effect on the bubble velocity. As the pipe diameter increases, the bubble velocity increases. The obtained results are helpful for studying the transition mechanisms of two-phase flow patterns and useful for improving the bubble pump performance by controlling the flow patterns in lifting pipe.

  11. Single DNA denaturation and bubble dynamics

    International Nuclear Information System (INIS)

    Metzler, Ralf; Ambjoernsson, Tobias; Hanke, Andreas; Fogedby, Hans C

    2009-01-01

    While the Watson-Crick double-strand is the thermodynamically stable state of DNA in a wide range of temperature and salt conditions, even at physiological conditions local denaturation bubbles may open up spontaneously due to thermal activation. By raising the ambient temperature, titration, or by external forces in single molecule setups bubbles proliferate until full denaturation of the DNA occurs. Based on the Poland-Scheraga model we investigate both the equilibrium transition of DNA denaturation and the dynamics of the denaturation bubbles with respect to recent single DNA chain experiments for situations below, at, and above the denaturation transition. We also propose a new single molecule setup based on DNA constructs with two bubble zones to measure the bubble coalescence and extract the physical parameters relevant to DNA breathing. Finally we consider the interplay between denaturation bubbles and selectively single-stranded DNA binding proteins.

  12. Bernoulli Suction Effect on Soap Bubble Blowing?

    Science.gov (United States)

    Davidson, John; Ryu, Sangjin

    2015-11-01

    As a model system for thin-film bubble with two gas-liquid interfaces, we experimentally investigated the pinch-off of soap bubble blowing. Using the lab-built bubble blower and high-speed videography, we have found that the scaling law exponent of soap bubble pinch-off is 2/3, which is similar to that of soap film bridge. Because air flowed through the decreasing neck of soap film tube, we studied possible Bernoulli suction effect on soap bubble pinch-off by evaluating the Reynolds number of airflow. Image processing was utilized to calculate approximate volume of growing soap film tube and the volume flow rate of the airflow, and the Reynolds number was estimated to be 800-3200. This result suggests that soap bubbling may involve the Bernoulli suction effect.

  13. Formation of soap bubbles by gas jet

    Science.gov (United States)

    Zhou, Maolei; Li, Min; Chen, Zhiyuan; Han, Jifeng; Liu, Dong

    2017-12-01

    Soap bubbles can be easily generated by various methods, while their formation process is complicated and still worth studying. A model about the bubble formation process was proposed in the study by Salkin et al. [Phys. Rev. Lett. 116, 077801 (2016)] recently, and it was reported that the bubbles were formed when the gas blowing velocity was above one threshold. However, after a detailed study of these experiments, we found that the bubbles could be generated in two velocity ranges which corresponded to the laminar and turbulent gas jet, respectively, and the predicted threshold was only effective for turbulent gas flow. The study revealed that the bubble formation was greatly influenced by the aerodynamics of the gas jet blowing to the film, and these results will help to further understand the formation mechanism of the soap bubble as well as the interaction between the gas jet and the thin liquid film.

  14. Manipulating bubbles with secondary Bjerknes forces

    Energy Technology Data Exchange (ETDEWEB)

    Lanoy, Maxime [Institut Langevin, ESPCI ParisTech, CNRS (UMR 7587), PSL Research University, 1 rue Jussieu, 75005 Paris (France); Laboratoire Matière et Systèmes Complexes, Université Paris-Diderot, CNRS (UMR 7057), 10 rue Alice Domon et Léonie Duquet, 75013 Paris (France); Derec, Caroline; Leroy, Valentin [Laboratoire Matière et Systèmes Complexes, Université Paris-Diderot, CNRS (UMR 7057), 10 rue Alice Domon et Léonie Duquet, 75013 Paris (France); Tourin, Arnaud [Institut Langevin, ESPCI ParisTech, CNRS (UMR 7587), PSL Research University, 1 rue Jussieu, 75005 Paris (France)

    2015-11-23

    Gas bubbles in a sound field are submitted to a radiative force, known as the secondary Bjerknes force. We propose an original experimental setup that allows us to investigate in detail this force between two bubbles, as a function of the sonication frequency, as well as the bubbles radii and distance. We report the observation of both attractive and, more interestingly, repulsive Bjerknes force, when the two bubbles are driven in antiphase. Our experiments show the importance of taking multiple scatterings into account, which leads to a strong acoustic coupling of the bubbles when their radii are similar. Our setup demonstrates the accuracy of secondary Bjerknes forces for attracting or repealing a bubble, and could lead to new acoustic tools for noncontact manipulation in microfluidic devices.

  15. Mechanism of bubble detachment from vibrating walls

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Dongjun; Park, Jun Kwon, E-mail: junkeun@postech.ac.kr; Kang, Kwan Hyoung [Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), San 31, Hyoja-dong, Pohang 790-784 (Korea, Republic of); Kang, In Seok [Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), San 31, Hyoja-dong, Pohang 790-784 (Korea, Republic of)

    2013-11-15

    We discovered a previously unobserved mechanism by which air bubbles detach from vibrating walls in glasses containing water. Chaotic oscillation and subsequent water jets appeared when a wall vibrated at greater than a critical level. Wave forms were developed at water-air interface of the bubble by the wall vibration, and water jets were formed when sufficiently grown wave-curvatures were collapsing. Droplets were pinched off from the tip of jets and fell to the surface of the glass. When the solid-air interface at the bubble-wall attachment point was completely covered with water, the bubble detached from the wall. The water jets were mainly generated by subharmonic waves and were generated most vigorously when the wall vibrated at the volume resonant frequency of the bubble. Bubbles of specific size can be removed by adjusting the frequency of the wall's vibration.

  16. The KEK 1 m hydrogen bubble chamber

    International Nuclear Information System (INIS)

    Doi, Yoshikuni; Araoka, Osamu; Hayashi, Kohei; Hayashi, Yoshio; Hirabayashi, Hiromi.

    1978-03-01

    A medium size hydrogen bubble chamber has been constructed at the National Laboratory for High Energy Physics, KEK. The bubble chamber has been designed to be operated with a maximum rate of three times per half a second in every two second repetition time of the accelerator, by utilizing a hydraulic expansion system. The bubble chamber has a one meter diameter and a visible volume of about 280 l. A three-view stereo camera system is used for taking photographic pictures of the chamber. A 2 MW bubble chamber magnet is constructed. The main part of the bubble chamber vessel is supported by the magnet yoke. The magnet gives a maximum field of 18.4 kG at the centre of the fiducial volume of the chamber. The overall system of the KEK 1 m hydrogen bubble chamber facility is described in some detail. Some operational characteristics of the facility are also reported. (auth.)

  17. Manipulating bubbles with secondary Bjerknes forces

    International Nuclear Information System (INIS)

    Lanoy, Maxime; Derec, Caroline; Leroy, Valentin; Tourin, Arnaud

    2015-01-01

    Gas bubbles in a sound field are submitted to a radiative force, known as the secondary Bjerknes force. We propose an original experimental setup that allows us to investigate in detail this force between two bubbles, as a function of the sonication frequency, as well as the bubbles radii and distance. We report the observation of both attractive and, more interestingly, repulsive Bjerknes force, when the two bubbles are driven in antiphase. Our experiments show the importance of taking multiple scatterings into account, which leads to a strong acoustic coupling of the bubbles when their radii are similar. Our setup demonstrates the accuracy of secondary Bjerknes forces for attracting or repealing a bubble, and could lead to new acoustic tools for noncontact manipulation in microfluidic devices

  18. Transcription-associated mutational pressure in the Parvovirus B19 genome: Reactivated genomes contribute to the variability of viral populations.

    Science.gov (United States)

    Khrustalev, Vladislav Victorovich; Ermalovich, Marina Anatolyevna; Hübschen, Judith M; Khrustaleva, Tatyana Aleksandrovna

    2017-12-21

    In this study we used non-overlapping parts of the two long open reading frames coding for nonstructural (NS) and capsid (VP) proteins of all available sequences of the Parvovirus B19 subgenotype 1a genome and found out that the rates of A to G, C to T and A to T mutations are higher in the first long reading frame (NS) of the virus than in the second one (VP). This difference in mutational pressure directions for two parts of the same viral genome can be explained by the fact of transcription of just the first long reading frame during the lifelong latency in nonerythroid cells. Adenine deamination (producing A to G and A to T mutations) and cytosine deamination (producing C to T mutations) occur more frequently in transcriptional bubbles formed by DNA "plus" strand of the first open reading frame. These mutations can be inherited only in case of reactivation of the infectious virus due to the help of Adenovirus that allows latent Parvovirus B19 to start transcription of the second reading frame and then to replicate its genome by the rolling circle mechanism using the specific origin. Results of this study provide evidence that the genomes reactivated from latency make significant contributions to the variability of Parvovirus B19. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Study of stream flow effects on bubble motion

    International Nuclear Information System (INIS)

    Sami, S.S.

    1983-01-01

    The formation of air bubbles at constant-pressure by submerged orifices was investigated in both quiescent and moving streams inside a vertical tube. Parameters affecting the bubble rise velocity, such as bubble generating frequency and diameter, were studied and analyzed for bubbles rising in a chain and homogeneous mixture. A special technique for measuring bubble motion parameters has been developed, tested, and employed throughout the experimental investigation. The method is based on a water-air impedance variation. Results obtained in stagnant liquid show that increasing the bubble diameter serves to increase bubble rise velocity, while an opposite trend has been observed for stream liquid where the bubble diameter increase reduces the bubble rise velocity. The increase of bubble generation frequency generally increases the bubble rise velocity. Experimental data covered with bubble radial distribution showed symmetrical profiles of bubble velocity and frequency, and the radial distribution of the velocity profiles sometimes has two maxima and one minimum depending on the liquid velocity. Finally, in stagnant liquid, a normalized correlation has been developed to predict the terminal rise velocity in terms of bubble generating frequency, bubble diameter, single bubble rise velocity, and conduit dimensions. Another correlation is presented for forced bubbly flow, where the bubble rise velocity is expressed as a function of bubble generating frequency, bubble diameter, and water superficial velocity

  20. Local measurements in turbulent bubbly flows

    International Nuclear Information System (INIS)

    Suzanne, C.; Ellingsen, K.; Risso, F.; Roig, V.

    1998-01-01

    Local measurements methods in bubbly flows are discussed. Concerning liquid velocity measurement, problems linked to HFA and LDA are first analysed. Then simultaneously recorded velocity signals obtained by both anemometers are compared. New signal processing are developed for the two techniques. Bubble sizes and velocities measurements methods using intrusive double optical sensor probe are presented. Plane bubbly mixing layer has been investigated. Local measurements using the described methods are presented as examples. (author)

  1. Bursting the bubble of melt inclusions

    Science.gov (United States)

    Lowenstern, Jacob B.

    2015-01-01

    Most silicate melt inclusions (MI) contain bubbles, whose significance has been alternately calculated, pondered, and ignored, but rarely if ever directly explored. Moore et al. (2015) analyze the bubbles, as well as their host glasses, and conclude that they often hold the preponderance of CO2 in the MI. Their findings entreat future researchers to account for the presence of bubbles in MI when calculating volatile budgets, saturation pressures, and eruptive flux.

  2. On Bubble Rising in Countercurrent Flow

    Czech Academy of Sciences Publication Activity Database

    Večeř, M.; Leštinský, P.; Wichterle, K.; Růžička, Marek

    2012-01-01

    Roč. 10, č. 2012 (2012), A30 ISSN 1542-6580 R&D Projects: GA ČR GA104/09/0972; GA ČR GA104/07/1110 Grant - others:GA MŠMT(CZ) CZ.1.05/2.1.00/03.0069 Institutional support: RVO:67985858 Keywords : ellipsoidal bubble * bubble shape * bubble velocity Subject RIV: CI - Industrial Chemistry, Chemical Engineering Impact factor: 0.790, year: 2011

  3. Fast Initialization of Bubble-Memory Systems

    Science.gov (United States)

    Looney, K. T.; Nichols, C. D.; Hayes, P. J.

    1986-01-01

    Improved scheme several orders of magnitude faster than normal initialization scheme. State-of-the-art commercial bubble-memory device used. Hardware interface designed connects controlling microprocessor to bubblememory circuitry. System software written to exercise various functions of bubble-memory system in comparison made between normal and fast techniques. Future implementations of approach utilize E2PROM (electrically-erasable programable read-only memory) to provide greater system flexibility. Fastinitialization technique applicable to all bubble-memory devices.

  4. DNA Replication and Transcription: An Innovative Teaching Strategy

    Science.gov (United States)

    Fossey, Annabel; Hancock, Carolyn

    2005-01-01

    First-year students in genetics at the University of KwaZulu-Natal, South Africa, attend two general biology modules, one in each semester. Teaching involves four formal lectures per week of 45 min each, one 3-h practical, and one lecture period tutorial. These students, graduating from secondary education, are well schooled in rote learning but…

  5. Bubble nuclei in relativistic mean field theory

    International Nuclear Information System (INIS)

    Shukla, A.; Aberg, S.; Patra, S.K.

    2011-01-01

    Bubble nuclei are characterized by a depletion of their central density, i.e. the formation of the proton or neutron void and subsequently forming proton or neutron bubble nuclei. Possibility of the formation of bubble nuclei has been explored through different nuclear models and in different mass regions. Advancements in experimental nuclear physics has led our experimental access to many new shapes and structures, which were inaccessible hitherto. In the present paper, the possibility of observing nuclear bubble in oxygen isotopes, particularly for 22 O has been studied

  6. Improvised bubble continuous positive airway pressure (BCPAP ...

    African Journals Online (AJOL)

    Improvised bubble continuous positive airway pressure (BCPAP) device at the National Hospital Abuja gives immediate improvement in respiratory rate and oxygenation in neonates with respiratory distress.

  7. Replication studies in longevity

    DEFF Research Database (Denmark)

    Varcasia, O; Garasto, S; Rizza, T

    2001-01-01

    In Danes we replicated the 3'APOB-VNTR gene/longevity association study previously carried out in Italians, by which the Small alleles (less than 35 repeats) had been identified as frailty alleles for longevity. In Danes, neither genotype nor allele frequencies differed between centenarians and 20...

  8. The Behavior of Micro Bubbles and Bubble Cluster in Ultrasound Field

    Science.gov (United States)

    Yoshizawa, Shin; Matsumoto, Yoichiro

    2001-11-01

    Ultrasound is widely applied in the clinical field today, such as ultrasound imaging, Extracorporeal Shock Wave Lithotripsy (ESWL) and so on. It is essential to take a real understanding of the dynamics of micro bubbles and bubble cluster in these applications. Thus we numerically simulate them in ultrasound field in this paper. In the numerical simulation, we consider the thermal behavior inside the bubble and the pressure wave phenomena in the bubble cluster in detail, namely, the evaporation and condensation of liquid at the bubble wall, heat transfer through the bubble wall, diffusion of non-condensable gas inside the bubble and the compressibility of liquid. Initial cluster radius is to 0.5[mm], bubble radius is 1.7[mm], void fraction is 0.1[ambient pressure is 101.3[kPa], temperature is 293[K] and the amplitude of ultrasound is 50[kPa]. We simulate bubble cluster in ultrasound field at various frequencies and we obtain the following conclusions. 1) The maximum pressure inside bubble cluster reaches 5[MPa] and this is much higher than that of a bubble. 2) Bubble cluster behaves like a rigid body acoustically when the frequency of ultrasound is much higher than its natural frequency.

  9. Interaction of a bubble and a bubble cluster in an ultrasonic field

    International Nuclear Information System (INIS)

    Wang Cheng-Hui; Cheng Jian-Chun

    2013-01-01

    Using an appropriate approximation, we have formulated the interacting equation of multi-bubble motion for a system of a single bubble and a spherical bubble cluster. The behavior of the bubbles is observed in coupled and uncoupled states. The oscillation of bubbles inside the cluster is in a coupled state. The numerical simulation demonstrates that the secondary Bjerknes force can be influenced by the number density, initial radius, distance, driving frequency, and amplitude of ultrasound. However, if a bubble approaches a bubble cluster of the same initial radii, coupled oscillation would be induced and a repulsive force is evoked, which may be the reason why the bubble cluster can exist steadily. With the increment of the number density of the bubble cluster, a secondary Bjerknes force acting on the bubbles inside the cluster decreases due to the strong suppression of the coupled bubbles. It is shown that there may be an optimal number density for a bubble cluster which can generate an optimal cavitation effect in liquid for a stable driving ultrasound. (electromagnetism, optics, acoustics, heat transfer, classical mechanics, and fluid dynamics)

  10. Bubbling in unbounded coflowing liquids.

    Science.gov (United States)

    Gañán-Calvo, Alfonso M; Herrada, Miguel A; Garstecki, Piotr

    2006-03-31

    An investigation of the stability of low density and viscosity fluid jets and spouts in unbounded coflowing liquids is presented. A full parametrical analysis from low to high Weber and Reynolds numbers shows that the presence of any fluid of finite density and viscosity inside the hollow jet elicits a transition from an absolute to a convective instability at a finite value of the Weber number, for any value of the Reynolds number. Below that critical value of the Weber number, the absolute character of the instability leads to local breakup, and consequently to local bubbling. Experimental data support our model.

  11. Scales and structures in bubbly flows. Experimental analysis of the flow in bubble columns and in bubbling fluidized beds

    NARCIS (Netherlands)

    Groen, J.S.

    2004-01-01

    In this project a detailed experimental analysis was performed of the dynamic flow field in bubbly flows, with the purpose of determining local hydrodynamics and scale effects. Measurements were done in gas-liquid systems (air-water bubble columns) and in gas-solid systems (air-sand bubbing

  12. Suppression of Coronavirus Replication by Cyclophilin Inhibitors

    Directory of Open Access Journals (Sweden)

    Takashi Sasaki

    2013-05-01

    Full Text Available Coronaviruses infect a variety of mammalian and avian species and cause serious diseases in humans, cats, mice, and birds in the form of severe acute respiratory syndrome (SARS, feline infectious peritonitis (FIP, mouse hepatitis, and avian infectious bronchitis, respectively. No effective vaccine or treatment has been developed for SARS-coronavirus or FIP virus, both of which cause lethal diseases. It has been reported that a cyclophilin inhibitor, cyclosporin A (CsA, could inhibit the replication of coronaviruses. CsA is a well-known immunosuppressive drug that binds to cellular cyclophilins to inhibit calcineurin, a calcium-calmodulin-activated serine/threonine-specific phosphatase. The inhibition of calcineurin blocks the translocation of nuclear factor of activated T cells from the cytosol into the nucleus, thus preventing the transcription of genes encoding cytokines such as interleukin-2. Cyclophilins are peptidyl-prolyl isomerases with physiological functions that have been described for many years to include chaperone and foldase activities. Also, many viruses require cyclophilins for replication; these include human immunodeficiency virus, vesicular stomatitis virus, and hepatitis C virus. However, the molecular mechanisms leading to the suppression of viral replication differ for different viruses. This review describes the suppressive effects of CsA on coronavirus replication.

  13. Simple improvements to classical bubble nucleation models.

    Science.gov (United States)

    Tanaka, Kyoko K; Tanaka, Hidekazu; Angélil, Raymond; Diemand, Jürg

    2015-08-01

    We revisit classical nucleation theory (CNT) for the homogeneous bubble nucleation rate and improve the classical formula using a correct prefactor in the nucleation rate. Most of the previous theoretical studies have used the constant prefactor determined by the bubble growth due to the evaporation process from the bubble surface. However, the growth of bubbles is also regulated by the thermal conduction, the viscosity, and the inertia of liquid motion. These effects can decrease the prefactor significantly, especially when the liquid pressure is much smaller than the equilibrium one. The deviation in the nucleation rate between the improved formula and the CNT can be as large as several orders of magnitude. Our improved, accurate prefactor and recent advances in molecular dynamics simulations and laboratory experiments for argon bubble nucleation enable us to precisely constrain the free energy barrier for bubble nucleation. Assuming the correction to the CNT free energy is of the functional form suggested by Tolman, the precise evaluations of the free energy barriers suggest the Tolman length is ≃0.3σ independently of the temperature for argon bubble nucleation, where σ is the unit length of the Lennard-Jones potential. With this Tolman correction and our prefactor one gets accurate bubble nucleation rate predictions in the parameter range probed by current experiments and molecular dynamics simulations.

  14. Bubble Swarm Rise Velocity in Fluidized Beds.

    Czech Academy of Sciences Publication Activity Database

    Punčochář, Miroslav; Růžička, Marek; Šimčík, Miroslav

    2016-01-01

    Roč. 152, OCT 2 (2016), s. 84-94 ISSN 0009-2509 R&D Projects: GA ČR(CZ) GA15-05534S Institutional support: RVO:67985858 Keywords : bubbling fluidized bed * gas-solid * bubble swarm velocity Subject RIV: CI - Industrial Chemistry, Chemical Engineering Impact factor: 2.895, year: 2016

  15. The use of microholography in bubble chambers

    CERN Document Server

    Royer, H

    1981-01-01

    In-line holography has been used for the first time in a bubble chamber for the account of the CERN (Geneva, CH). The holograms were recorded with the help of a single-mode pulse laser. Bubble tracks of 25 microns in diameter have been reconstructed with a resolution of 2 microns. (12 refs).

  16. Cavitation bubble nucleation induced by shock-bubble interaction in a gelatin gel

    Science.gov (United States)

    Oguri, Ryota; Ando, Keita

    2018-05-01

    An optical visualization technique is developed to study cavitation bubble nucleation that results from interaction between a laser-induced shock and a preexisting gas bubble in a 10 wt. % gelatin gel; images of the nucleated cavitation bubbles are captured and the cavitation inception pressure is determined based on Euler flow simulation. A spherical gas cavity is generated by focusing an infrared laser pulse into a gas-supersaturated gel and the size of the laser-generated bubble in mechanical equilibrium is tuned via mass transfer of the dissolved gas into the bubble. A spherical shock is then generated, through rapid expansion of plasma induced by the laser focusing, in the vicinity of the gas bubble. The shock-bubble interaction is recorded by a CCD camera with flash illumination of a nanosecond green laser pulse. The observation captures cavitation inception in the gel under tension that results from acoustic impedance mismatching at the bubble interface interacting with the shock. We measure the probability of cavitation inception from a series of the repeated experiments, by varying the bubble radius and the standoff distance. The threshold pressure is defined at the cavitation inception probability equal to one half and is calculated, through comparisons to Euler flow simulation, at -24.4 MPa. This threshold value is similar to that from shock-bubble interaction experiments using water, meaning that viscoelasticity of the 10 wt. % gelatin gel has a limited impact on bubble nucleation dynamics.

  17. Nonlinear Bubble Dynamics And The Effects On Propagation Through Near-Surface Bubble Layers

    Science.gov (United States)

    Leighton, Timothy G.

    2004-11-01

    Nonlinear bubble dynamics are often viewed as the unfortunate consequence of having to use high acoustic pressure amplitudes when the void fraction in the near-surface oceanic bubble layer is great enough to cause severe attenuation (e.g. >50 dB/m). This is seen as unfortunate since existing models for acoustic propagation in bubbly liquids are based on linear bubble dynamics. However, the development of nonlinear models does more than just allow quantification of the errors associated with the use of linear models. It also offers the possibility of propagation modeling and acoustic inversions which appropriately incorporate the bubble nonlinearity. Furthermore, it allows exploration and quantification of possible nonlinear effects which may be exploited. As a result, high acoustic pressure amplitudes may be desirable even in low void fractions, because they offer opportunities to gain information about the bubble cloud from the nonlinearities, and options to exploit the nonlinearities to enhance communication and sonar in bubbly waters. This paper presents a method for calculating the nonlinear acoustic cross-sections, scatter, attenuations and sound speeds from bubble clouds which may be inhomogeneous. The method allows prediction of the time dependency of these quantities, both because the cloud may vary and because the incident acoustic pulse may have finite and arbitrary time history. The method can be readily adapted for bubbles in other environments (e.g. clouds of interacting bubbles, sediments, structures, in vivo, reverberant conditions etc.). The possible exploitation of bubble acoustics by marine mammals, and for sonar enhancement, is explored.

  18. Galactic Teamwork Makes Distant Bubbles

    Science.gov (United States)

    Kohler, Susanna

    2016-03-01

    During the period of reionization that followed the dark ages of our universe, hydrogen was transformed from a neutral state, which is opaque to radiation, to an ionized one, which is transparent to radiation. But what generated the initial ionizing radiation? The recent discovery of multiple distant galaxies offers evidence for how this process occurred.Two Distant GalaxiesWe believe reionization occurred somewhere between a redshift of z = 6 and 7, because Ly-emitting galaxies drop out at roughly this redshift. Beyond this distance, were generally unable to see the light from these galaxies, because the universe is no longer transparent to their emission. This is not always the case, however: if a bubble of ionized gas exists around a distant galaxy, the radiation can escape, allowing us to see the galaxy.This is true of two recently-discovered Ly-emitting galaxies, confirmed to be at a redshift of z~7 and located near one another in a region known as the Bremer Deep Field. The fact that were able to see the radiation from these galaxies means that they are in an ionized HII region presumably one of the earlier regions to have become reionized in the universe.But on their own, neither of these galaxies is capable of generating an ionized bubble large enough for their light to escape. So what ionized the region around them, and what does this mean for our understanding of how reionization occurred in the universe?A Little Help From FriendsLocation in different filters of the objects in the Hubble Bremer Deep Field catalog. The z~7 selection region is outlined by the grey box. BDF-521 and BDF-3299 were the two originally discovered galaxies; the remaining red markers indicate the additional six galaxies discovered in the same region. [Castellano et al. 2016]A team of scientists led by Marco Castellano (Rome Observatory, INAF) investigated the possibility that there are other, faint galaxies near these two that have helped to ionize the region. Performing a survey

  19. Impact of bubble wakes on a developing bubble flow in a vertical pipe

    International Nuclear Information System (INIS)

    Tomiyama, A.; Makino, Y.; Miyoshi, K.; Tamai, H.; Serizawa, A.; Zun, I.

    1998-01-01

    Three-dimensional two-way bubble tracking simulation of single large air bubbles rising through a stagnant water filled in a vertical pipe was conducted to investigate the structures of bubble wakes. Spatial distributions of time-averaged liquid velocity field, turbulent intensity and Reynolds stress caused by bubble wakes were deduced from the calculated local instantaneous liquid velocities. It was confirmed that wake structures are completely different from the ones estimated by a conventional wake model. Then, we developed a simple wake model based on the predicted time-averaged wake velocity fields, and implemented it into a 3D one-way bubble tracking method to examine the impact of bubble wake structures on time-spatial evolution of a developing air-water bubble flow in a vertical pipe. As a results, we confirmed that the developed wake model can give better prediction for flow pattern evolution than a conventional wake model

  20. Optical tweezers reveal how proteins alter replication

    Science.gov (United States)

    Chaurasiya, Kathy

    Single molecule force spectroscopy is a powerful method that explores the DNA interaction properties of proteins involved in a wide range of fundamental biological processes such as DNA replication, transcription, and repair. We use optical tweezers to capture and stretch a single DNA molecule in the presence of proteins that bind DNA and alter its mechanical properties. We quantitatively characterize the DNA binding mechanisms of proteins in order to provide a detailed understanding of their function. In this work, we focus on proteins involved in replication of Escherichia coli (E. coli ), endogenous eukaryotic retrotransposons Ty3 and LINE-1, and human immunodeficiency virus (HIV). DNA polymerases replicate the entire genome of the cell, and bind both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) during DNA replication. The replicative DNA polymerase in the widely-studied model system E. coli is the DNA polymerase III subunit alpha (DNA pol III alpha). We use optical tweezers to determine that UmuD, a protein that regulates bacterial mutagenesis through its interactions with DNA polymerases, specifically disrupts alpha binding to ssDNA. This suggests that UmuD removes alpha from its ssDNA template to allow DNA repair proteins access to the damaged DNA, and to facilitate exchange of the replicative polymerase for an error-prone translesion synthesis (TLS) polymerase that inserts nucleotides opposite the lesions, so that bacterial DNA replication may proceed. This work demonstrates a biophysical mechanism by which E. coli cells tolerate DNA damage. Retroviruses and retrotransposons reproduce by copying their RNA genome into the nuclear DNA of their eukaryotic hosts. Retroelements encode proteins called nucleic acid chaperones, which rearrange nucleic acid secondary structure and are therefore required for successful replication. The chaperone activity of these proteins requires strong binding affinity for both single- and double-stranded nucleic

  1. Single DNA denaturation and bubble dynamics

    DEFF Research Database (Denmark)

    Metzler, Ralf; Ambjörnsson, Tobias; Hanke, Andreas

    2009-01-01

    While the Watson-Crick double-strand is the thermodynamically stable state of DNA in a wide range of temperature and salt conditions, even at physiological conditions local denaturation bubbles may open up spontaneously due to thermal activation. By raising the ambient temperature, titration......, or by external forces in single molecule setups bubbles proliferate until full denaturation of the DNA occurs. Based on the Poland-Scheraga model we investigate both the equilibrium transition of DNA denaturation and the dynamics of the denaturation bubbles with respect to recent single DNA chain experiments...... for situations below, at, and above the denaturation transition. We also propose a new single molecule setup based on DNA constructs with two bubble zones to measure the bubble coalescence and extract the physical parameters relevant to DNA breathing. Finally we consider the interplay between denaturation...

  2. Oscillation of large air bubble cloud

    Energy Technology Data Exchange (ETDEWEB)

    Bae, Y.Y.; Kim, H.Y.; Park, J.K. [Korea Atomic Energy Research Inst., Daejeon (Korea, Republic of)

    2001-07-01

    The behavior of a large air bubble cloud, which is generated by the air discharged from a perforated sparger, is analyzed by solving Rayleigh-Plesset equation, energy equations and energy balance equation. The equations are solved by Runge-Kutta integration and MacCormack finite difference method. Initial conditions such as driving pressure, air volume, and void fraction strongly affect the bubble pressure amplitude and oscillation frequency. The pool temperature has a strong effect on the oscillation frequency and a negligible effect on the pressure amplitude. The polytropic constant during the compression and expansion processes of individual bubbles ranges from 1.0 to 1.4, which may be attributed to the fact that small bubbles oscillated in frequencies different from their resonance. The temperature of the bubble cloud rapidly approaches the ambient temperature, as is expected from the polytropic constants being between 1.0 and 1.4. (authors)

  3. Oscillation of large air bubble cloud

    International Nuclear Information System (INIS)

    Bae, Y.Y.; Kim, H.Y.; Park, J.K.

    2001-01-01

    The behavior of a large air bubble cloud, which is generated by the air discharged from a perforated sparger, is analyzed by solving Rayleigh-Plesset equation, energy equations and energy balance equation. The equations are solved by Runge-Kutta integration and MacCormack finite difference method. Initial conditions such as driving pressure, air volume, and void fraction strongly affect the bubble pressure amplitude and oscillation frequency. The pool temperature has a strong effect on the oscillation frequency and a negligible effect on the pressure amplitude. The polytropic constant during the compression and expansion processes of individual bubbles ranges from 1.0 to 1.4, which may be attributed to the fact that small bubbles oscillated in frequencies different from their resonance. The temperature of the bubble cloud rapidly approaches the ambient temperature, as is expected from the polytropic constants being between 1.0 and 1.4. (authors)

  4. Mesoporous hollow spheres from soap bubbling.

    Science.gov (United States)

    Yu, Xianglin; Liang, Fuxin; Liu, Jiguang; Lu, Yunfeng; Yang, Zhenzhong

    2012-02-01

    The smaller and more stable bubbles can be generated from the large parent bubbles by rupture. In the presence of a bubble blowing agent, hollow spheres can be prepared by bubbling a silica sol. Herein, the trapped gas inside the bubble acts as a template. When the porogen, i.e., other surfactant, is introduced, a mesostructured shell forms by the co-assembly with the silica sol during sol-gel process. Morphological evolution emphasizes the prerequisite of an intermediate interior gas flow rate and high exterior gas flow rate for hollow spheres. The method is valid for many compositions from inorganic, polymer to their composites. Copyright © 2011 Elsevier Inc. All rights reserved.

  5. Structure and kinematics of bubble flow

    International Nuclear Information System (INIS)

    Lackme, C.

    1967-01-01

    This report deals with the components and use of resistivity probes in bubble flow. With a single probe, we have studied the longitudinal and radial structure of the flow. The very complicated evolution of the radial structure is shown by the measurement of the mean bubble flux at several points in the tube. A double probe associated with a device the principle of which is given in this report, permits the measure of the local velocity of bubbles. Unlike the mean bubble flux profile, the change in the velocity profile along the tube is not significant. We have achieved the synthesis of these two pieces of information, mean local bubble flux and local velocity, by computing the mean weighed velocity in the tube. This weighed velocity compares remarkably with the velocity computed from the volumetric gas flow rate and the mean void fraction. (author) [fr

  6. Interaction mechanism of double bubbles in hydrodynamic cavitation

    Science.gov (United States)

    Li, Fengchao; Cai, Jun; Huai, Xiulan; Liu, Bin

    2013-06-01

    Bubble-bubble interaction is an important factor in cavitation bubble dynamics. In this paper, the dynamic behaviors of double cavitation bubbles driven by varying pressure field downstream of an orifice plate in hydrodynamic cavitation reactor are examined. The bubble-bubble interaction between two bubbles with different radii is considered. We have shown the different dynamic behaviors between double cavitation bubbles and a single bubble by solving two coupling nonlinear equations using the Runge-Kutta fourth order method with adaptive step size control. The simulation results indicate that, when considering the role of the neighbor smaller bubble, the oscillation of the bigger bubble gradually exhibits a lag in comparison with the single-bubble case, and the extent of the lag becomes much more obvious as time goes by. This phenomenon is more easily observed with the increase of the initial radius of the smaller bubble. In comparison with the single-bubble case, the oscillation of the bigger bubble is enhanced by the neighbor smaller bubble. Especially, the pressure pulse of the bigger bubble rises intensely when the sizes of two bubbles approach, and a series of peak values for different initial radii are acquired when the initial radius ratio of two bubbles is in the range of 0.9˜1.0. Although the increase of the center distance between two bubbles can weaken the mutual interaction, it has no significant influence on the enhancement trend. On the one hand, the interaction between two bubbles with different radii can suppress the growth of the smaller bubble; on the other hand, it also can enhance the growth of the bigger one at the same time. The significant enhancement effect due to the interaction of multi-bubbles should be paid more attention because it can be used to reinforce the cavitation intensity for various potential applications in future.

  7. Mechanisms of DNA replication termination.

    Science.gov (United States)

    Dewar, James M; Walter, Johannes C

    2017-08-01

    Genome duplication is carried out by pairs of replication forks that assemble at origins of replication and then move in opposite directions. DNA replication ends when converging replication forks meet. During this process, which is known as replication termination, DNA synthesis is completed, the replication machinery is disassembled and daughter molecules are resolved. In this Review, we outline the steps that are likely to be common to replication termination in most organisms, namely, fork convergence, synthesis completion, replisome disassembly and decatenation. We briefly review the mechanism of termination in the bacterium Escherichia coli and in simian virus 40 (SV40) and also focus on recent advances in eukaryotic replication termination. In particular, we discuss the recently discovered E3 ubiquitin ligases that control replisome disassembly in yeast and higher eukaryotes, and how their activity is regulated to avoid genome instability.

  8. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

    Stability and function of eukaryotic genomes are closely linked to chromatin structure and organization. During cell division the entire genome must be accurately replicated and the chromatin landscape reproduced on new DNA. Chromatin and nuclear structure influence where and when DNA replication...... initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. If DNA...

  9. Legacies of the bubble chamber

    International Nuclear Information System (INIS)

    Mulvey, J.H.

    1994-01-01

    Legacies are what we pass on to those who follow us, the foundations on which the next advances in our science are being made; the things by which we shall be remembered, recorded in learned journals, written in the text books -food for the historians of science. This is not a summary, and it will draw no conclusions. It is a personal view which will look a little wider than the main physics results to include a mention of one or two of the technologies and methods handed on to both particle physics and other branches of sciences, a brief reference to bubble chamber pictures as aids in teaching, and a comment on the challenge now increasingly applied in the UK - and perhaps elsewhere -as a criterion for funding research: will it contribute to ''wealth creation''? (orig.)

  10. An experimental propane bubble chamber

    International Nuclear Information System (INIS)

    Rogozinski, A.

    1957-01-01

    Describes a propane bubble chamber 10 cm in diameter and 5 cm deep. The body of the chamber is in stainless steel, and it has two windows of polished hardened glass. The compression and decompression of the propane are performed either through a piston in direct contact with the liquid, or by the action on the liquid, through a triple-mylar-Perbunan membrane, of a compressed gas. The general and also optimum working conditions of the chamber are described, and a few results are given concerning, in particular, the tests of the breakage-resistance of the windows and the measurements of the thermal expansion of the compressibility isotherm for the propane employed. (author) [fr

  11. Replication Research and Special Education

    Science.gov (United States)

    Travers, Jason C.; Cook, Bryan G.; Therrien, William J.; Coyne, Michael D.

    2016-01-01

    Replicating previously reported empirical research is a necessary aspect of an evidence-based field of special education, but little formal investigation into the prevalence of replication research in the special education research literature has been conducted. Various factors may explain the lack of attention to replication of special education…

  12. Numerical modeling of bubble dynamics in magmas

    Science.gov (United States)

    Huber, Christian; Su, Yanqing; Parmigiani, Andrea

    2014-05-01

    Understanding the complex non-linear physics that governs volcanic eruptions is contingent on our ability to characterize the dynamics of bubbles and its effect on the ascending magma. The exsolution and migration of bubbles has also a great impact on the heat and mass transport in and out of magma bodies stored at shallow depths in the crust. Multiphase systems like magmas are by definition heterogeneous at small scales. Although mixture theory or homogenization methods are convenient to represent multiphase systems as a homogeneous equivalent media, these approaches do not inform us on possible feedbacks at the pore-scale and can be significantly misleading. In this presentation, we discuss the development and application of bubble-scale multiphase flow modeling to address the following questions : How do bubbles impact heat and mass transport in magma chambers ? How efficient are chemical exchanges between the melt and bubbles during magma decompression? What is the role of hydrodynamic interactions on the deformation of bubbles while the magma is sheared? Addressing these questions requires powerful numerical methods that accurately model the balance between viscous, capillary and pressure stresses. We discuss how these bubble-scale models can provide important constraints on the dynamics of magmas stored at shallow depth or ascending to the surface during an eruption.

  13. Performance Tests for Bubble Blockage Device

    International Nuclear Information System (INIS)

    Ha, Kwang Soon; Wi, Kyung Jin; Park, Rae Joon; Wan, Han Seong

    2014-01-01

    Postulated severe core damage accidents have a high threat risk for the safety of human health and jeopardize the environment. Versatile measures have been suggested and applied to mitigate severe accidents in nuclear power plants. To improve the thermal margin for the severe accident measures in high-power reactors, engineered corium cooling systems involving boiling-induced two-phase natural circulation have been proposed for decay heat removal. A boiling-induced natural circulation flow is generated in a coolant path between a hot vessel wall and cold coolant reservoir. In general, it is possible for some bubbles to be entrained in the natural circulation loop. If some bubbles entrain in the liquid phase flow passage, flow instability may occur, that is, the natural circulation mass flow rate may be oscillated. A new device to block the entraining bubbles is proposed and verified using air-water test loop. To avoid bubbles entrained in the natural circulation flow loop, a new device was proposed and verified using an air-water test loop. The air injection and liquid circulation loop was prepared, and the tests for the bubble blockage devices were performed by varying the geometry and shape of the devices. The performance of the bubble blockage device was more effective as the area ratio of the inlet to the down-comer increased, and the device height decreased. If the device has a rim to generate a vortex zone, the bubbles will be most effectively blocked

  14. Bubbles in the self-accelerating universe

    International Nuclear Information System (INIS)

    Izumi, Keisuke; Tanaka, Takahiro; Koyama, Kazuya; Pujolas, Oriol

    2007-01-01

    We revisit the issue of the stability in the Dvali-Gabadadze-Porrati model by considering the nucleation of bubbles of the conventional branch within the self-accelerating branch. We construct an instanton describing this process in the thin wall approximation. On one side of the bubble wall, the bulk consists of the exterior of the brane, while on the other side it is the interior. The solution requires the presence of a 2-brane (the bubble wall) which induces the transition. However, we show that this instanton cannot be realized as the thin wall limit of any smooth solution. Once the bubble thickness is resolved, the equations of motion do not allow O(4) symmetric solutions joining the two branches. We conclude that the thin wall instanton is unphysical, and that one cannot have processes connecting the two branches, unless negative tension bubble walls are introduced. This also suggests that the self-accelerating branch does not decay into the conventional branch nucleating bubbles. We comment on other kinds of bubbles that could interpolate between the two branches

  15. Average properties of bidisperse bubbly flows

    Science.gov (United States)

    Serrano-García, J. C.; Mendez-Díaz, S.; Zenit, R.

    2018-03-01

    Experiments were performed in a vertical channel to study the properties of a bubbly flow composed of two distinct bubble size species. Bubbles were produced using a capillary bank with tubes with two distinct inner diameters; the flow through each capillary size was controlled such that the amount of large or small bubbles could be controlled. Using water and water-glycerin mixtures, a wide range of Reynolds and Weber number ranges were investigated. The gas volume fraction ranged between 0.5% and 6%. The measurements of the mean bubble velocity of each species and the liquid velocity variance were obtained and contrasted with the monodisperse flows with equivalent gas volume fractions. We found that the bidispersity can induce a reduction of the mean bubble velocity of the large species; for the small size species, the bubble velocity can be increased, decreased, or remain unaffected depending of the flow conditions. The liquid velocity variance of the bidisperse flows is, in general, bound by the values of the small and large monodisperse values; interestingly, in some cases, the liquid velocity fluctuations can be larger than either monodisperse case. A simple model for the liquid agitation for bidisperse flows is proposed, with good agreement with the experimental measurements.

  16. The Minnaert bubble: an acoustic approach

    Energy Technology Data Exchange (ETDEWEB)

    Devaud, Martin; Hocquet, Thierry; Bacri, Jean-Claude [Laboratoire Matiere et Systemes Complexes, Universite Paris Diderot and CNRS UMR 7057, 10 rue Alice Domont et Leonie Duquet, 75013 Paris (France); Leroy, Valentin [Laboratoire Ondes et Acoustique, Universite Paris 7 and CNRS UMR 7587, ESPCI, 10 rue Vauquelin, 75005 Paris (France)], E-mail: martin.devaud@univ-paris-diderot.fr

    2008-11-15

    We propose an ab initio introduction to the well-known Minnaert pulsating bubble at graduate level. After a brief recall of the standard stuff, we begin with a detailed discussion of the radial movements of an air bubble in water. This discussion is managed from an acoustic point of view, and using the Lagrangian rather than the Eulerian variables. In unbounded water, the air-water system has a continuum of eigenmodes, some of them correspond to regular Fabry-Perot resonances. A singular resonance, the lowest one, is shown to coincide with that of Minnaert. In bounded water, the eigenmodes spectrum is discrete, with a finite fundamental frequency. A spectacular quasi-locking of the latter occurs if it happens to exceed the Minnaert frequency, which provides an unforeseen one-bubble alternative version of the famous 'hot chocolate effect'. In the (low) frequency domain in which sound propagation inside the bubble reduces to a simple 'breathing' (i.e. inflation/deflation), the light air bubble can be 'dressed' by the outer water pressure forces, and is turned into the heavy Minnaert bubble. Thanks to this unexpected renormalization process, we demonstrate that the Minnaert bubble definitely behaves like a true harmonic oscillator of the spring-bob type, but with a damping term and a forcing term in apparent disagreement with those commonly admitted in the literature. Finally, we underline the double role played by the water. In order to tell the water motion associated with water compressibility (i.e. the sound) from the simple incompressible accompaniment of the bubble breathing, we introduce a new picture analogous to the electromagnetic radiative picture in Coulomb gauge, which naturally leads us to split the water displacement in an instantaneous and a retarded part. The Minnaert renormalized mass of the dressed bubble is then automatically recovered.

  17. Pressure waves in a supersaturated bubbly magma

    Science.gov (United States)

    Kurzon, I.; Lyakhovsky, V.; Navon, O.; Chouet, B.

    2011-01-01

    We study the interaction of acoustic pressure waves with an expanding bubbly magma. The expansion of magma is the result of bubble growth during or following magma decompression and leads to two competing processes that affect pressure waves. On the one hand, growth in vesicularity leads to increased damping and decreased wave amplitudes, and on the other hand, a decrease in the effective bulk modulus of the bubbly mixture reduces wave velocity, which in turn, reduces damping and may lead to wave amplification. The additional acoustic energy originates from the chemical energy released during bubble growth. We examine this phenomenon analytically to identify conditions under which amplification of pressure waves is possible. These conditions are further examined numerically to shed light on the frequency and phase dependencies in relation to the interaction of waves and growing bubbles. Amplification is possible at low frequencies and when the growth rate of bubbles reaches an optimum value for which the wave velocity decreases sufficiently to overcome the increased damping of the vesicular material. We examine two amplification phase-dependent effects: (1) a tensile-phase effect in which the inserted wave adds to the process of bubble growth, utilizing the energy associated with the gas overpressure in the bubble and therefore converting a large proportion of this energy into additional acoustic energy, and (2) a compressive-phase effect in which the pressure wave works against the growing bubbles and a large amount of its acoustic energy is dissipated during the first cycle, but later enough energy is gained to amplify the second cycle. These two effects provide additional new possible mechanisms for the amplification phase seen in Long-Period (LP) and Very-Long-Period (VLP) seismic signals originating in magma-filled cracks.

  18. In Vivo Regulation of Hepatitis B Virus Replication by Peroxisome Proliferators†

    Science.gov (United States)

    Guidotti, Luca G.; Eggers, Carrie M.; Raney, Anneke K.; Chi, Susan Y.; Peters, Jeffrey M.; Gonzalez, Frank J.; McLachlan, Alan

    1999-01-01

    The role of the peroxisome proliferator-activated receptor α (PPARα) in regulating hepatitis B virus (HBV) transcription and replication in vivo was investigated in an HBV transgenic mouse model. Treatment of HBV transgenic mice with the peroxisome proliferators Wy-14,643 and clofibric acid resulted in a less than twofold increase in HBV transcription rates and steady-state levels of HBV RNAs in the livers of these mice. In male mice, this increase in transcription was associated with a 2- to 3-fold increase in replication intermediates, whereas in female mice it was associated with a 7- to 14-fold increase in replication intermediates. The observed increases in transcription and replication were dependent on PPARα. HBV transgenic mice lacking this nuclear hormone receptor showed similar levels of HBV transcripts and replication intermediates as untreated HBV transgenic mice expressing PPARα but failed to demonstrate alterations in either RNA or DNA synthesis in response to peroxisome proliferators. Therefore, it appears that very modest alterations in transcription can, under certain circumstances, result in relatively large increases in HBV replication in HBV transgenic mice. PMID:10559356

  19. Inhibition of histone deacetylases stimulates HBV replication independent of protein X

    NARCIS (Netherlands)

    van de Klundert, Maarten A. A.; Swart, Marjolein; Zaaijer, Hans L.; Kootstra, Neeltje A.

    2015-01-01

    Aim: HBV expresses an accessory protein called X (HBx), which supports HBV replication by increasing transcription from episomal templates. Here, we investigate whether HBx augments HBV replication by interfering with the deacetylation of HBV DNA associated histones by histone deacetylases (HDACs).

  20. Lifetime of Bubble Rafts: Cooperativity and Avalanches

    Science.gov (United States)

    Ritacco, Hernán; Kiefer, Flavien; Langevin, Dominique

    2007-06-01

    We have studied the collapse of pseudo-bi-dimensional foams. These foams are made of uniformly sized soap bubbles packed in an hexagonal lattice sitting at the top of a liquid surface. The collapse process follows the sequence: (1) rupture of a first bubble, driven by thermal fluctuations and (2) a cascade of bursting bubbles. We present a simple numerical model which captures the main characteristics of the dynamics of foam collapse. We show that in a certain range of viscosities of the foaming solutions, the size distribution of the avalanches follows power laws as in self-organized criticality processes.

  1. Decay of bubble of disoriented chiral condensate

    International Nuclear Information System (INIS)

    Gani, V.A.; Kudryavtsev, A.E.; Belova, T.I.

    1999-01-01

    The space-time structure for the process of decay of a bubble of hypothetical phase -disoriented chiral condensate (DCC) i discussed. The evolution of the initial classical field configuration corresponding to the bubble of DCC is studied, both numerically and analytically. The decay of this initial configuration depends crucially on self-interaction of the pionic fields. It is shown that in some cases this self-interaction leads to the formation of sort of breather solution, formed from pionic fields situated in the center of the initial bubble of DCC. This breather looks like a long-lived source of pionic fields [ru

  2. Experimental investigation of shock wave - bubble interaction

    Energy Technology Data Exchange (ETDEWEB)

    Alizadeh, Mohsen

    2010-04-09

    In this work, the dynamics of laser-generated single cavitation bubbles exposed to lithotripter shock waves has been investigated experimentally. The energy of the impinging shock wave is varied in several steps. High-speed photography and pressure field measurements simultaneously with image acquisition provide the possibility of capturing the fast bubble dynamics under the effect of the shock wave impact. The pressure measurement is performed using a fiber optic probe hydrophone (FOPH) which operates based on optical diagnostics of the shock wave propagating medium. After a short introduction in chapter 1 an overview of the previous studies in chapter 2 is presented. The reported literatures include theoretical and experimental investigations of several configurations of physical problems in the field of bubble dynamics. In chapter 3 a theoretical description of propagation of a shock wave in a liquid like water has been discussed. Different kinds of reflection of a shock wave at an interface are taken into account. Undisturbed bubble dynamics as well as interaction between a planar shock wave and an initially spherical bubble are explored theoretically. Some physical parameters which are important in this issue such as the velocity of the shock-induced liquid jet, Kelvin impulse and kinetic energy are explained. The shock waves are generated in a water filled container by a focusing piezoelectric generator. The shock wave profile has a positive part with pulse duration of ∼1 μs followed by a longer tension tail (i.e. ∼3 μs). In chapter 4 high-speed images depict the propagation of a shock wave in the water filled tank. The maximum pressure is also derived for different intensity levels of the shock wave generator. The measurement is performed in the free field (i.e. in the absence of laser-generated single bubbles). In chapter 5 the interaction between lithotripter shock waves and laserinduced single cavitation bubbles is investigated experimentally. An

  3. Dechanneling of particles by gas bubbles

    International Nuclear Information System (INIS)

    Ronikier-Polonsky, Danuta.

    1976-01-01

    The dechanneling probability P of a particle hitting a gas bubble in a solid is evaluated theoretically. This probability is found to depend neither on the energy of the particle, nor on the radius of the bubble. A simple expression of P is given in the case of a harmonic channeling potential. Then an experiment is described concerning α particles channeled along (111) planes in aluminium containing helium bubbles. In this particular case, the measured probabilitity (P=0.27+-0.09) is in good agreement with the corresponding theoretical values (0.34 for a harmonic potential and 0.24 for a more realistic potential) [fr

  4. Experimental observation of exploding electron bubbles

    International Nuclear Information System (INIS)

    Classen, J.; Su, C.K.; Hall, S.C.; Pettersen, M.S.; Maris, H.J.

    1996-01-01

    Since free electrons form small voids in liquid helium they are expected to be preferred sites for nucleating macroscopic bubbles when the liquid is exposed to sufficiently large negative pressures. We have performed a series of cavitation experiments using focussed ultrasound where free electrons were introduced into the liquid by a radioactive source. The electron bubbles are found to explode at negative pressures significantly lower than those required for homogeneous nucleation. We present measurements of the thresholds for cavitation at electrons in the temperature range 1 - 4.5 K. Reasonable agreement with a simple model for the stability limit of the electron bubble is obtained. (author)

  5. A view inside the Gargamelle bubble chamber

    CERN Multimedia

    1970-01-01

    Gargamelle was the name given to a big bubble chamber built at the Saclay Laboratory in France during the late 1960s. It was designed principally for the detection at CERN of the elusive particles called neutrinos. A bubble chamber contains a liquid under pressure, which reveals the tracks of electrically charged particles as trails of tiny bubbles when the pressure is reduced. Neutrinos have no charge, and so leave no tracks, but the aim with Gargamelle was "see neutrinos" by making visible any charged particles set in motion by the interaction of neutrinos in the liquid

  6. A model established of a 'Embryo' bubble growing-up some visible bubble in bubble chamber and its primary theory calculation

    International Nuclear Information System (INIS)

    Ye Zipiao; Sheng Xiangdong

    2006-01-01

    A model of a 'embryo' bubble growing up a visible bubble in the bubble chamber is established. Through primary theory calculation it is shown that the 'embryo' bubble is not only absorbing quantity of heat, but also some molecules get into the 'embryo' bubble from its environment. It is explained reasonably that the radius of bubbles in bubble camber is different for the same energies of neutrons and proton. The track of neutron in bubble camber is long and thin, and the track of proton in bubble camber is wide and short. It is explained reasonably that the bubble radius of the incident particles with more charges which there are the same energies will be wider than that of the incident particles with less charges in the track. It is also explained reasonably that there are a little different radius of the bubbles of a track at the some region. It can be predicted theoretically that there should be big bubbles to burst when incident particles enter the bubble chamber at first. The sensitivity and the detective efficiency of bubble camber can be enhanced by choosing appropriate work matter. (authors)

  7. Bubbles, Bubbles, Tremors & Trouble: The Bayou Corne Sinkhole

    Science.gov (United States)

    Nunn, J. A.

    2013-12-01

    In May 2012, thermogenic methane bubbles were first observed in Bayou Corne in Assumption Parish, Louisiana. As of July 2013, ninety one bubbling sites have been identified. Gas was also found in the top of the Mississippi River Alluvial Aquifer (MRAA) about 125 ft below the surface. Vent wells drilled into the MRAA have flared more 16 million SCF of gas. Trace amounts of hydrogen sulfide also have been detected. Bayou Corne flows above the Napoleonville salt dome which has been an active area for oil and gas exploration since the 1920s. The dome is also a site of dissolution salt mining which has produced large caverns with diameters of up to 300 ft and heights of 2000 ft. Some caverns are used for storage of natural gas. Microseismic activity was confirmed by an Earthscope seismic station in White Castle, LA in July 2012. An array of microseismic stations set up in the area recorded more than 60 microseismic events in late July and early August, 2012. These microseismic events were located on the western side of the dome. Estimated focal depths are just above the top of salt. In August 2012, a sinkhole developed overnight just to the northwest of a plugged and abandoned brine filled cavern (see figure below). The sinkhole continues to grow in area to more than 20 acres and has consumed a pipeline right of way. The sinkhole is more than 750 ft deep at its center. Microseismic activity was reduced for several months following the formation of the sinkhole. Microseismic events have reoccurred episodically since then with periods of frequent events preceding slumping of material into the sinkhole or a 'burp' where fluid levels in the sinkhole drop and then rebound followed by a decrease in microseismic activity. Some gas and/or oil may appear at the surface of the sinkhole following a 'burp'. Very long period events also have been observed which are believed to be related to subsurface fluid movement. A relief well drilled into the abandoned brine cavern found that

  8. Stability of a Bubble Expanding and Translating Through an Inviscid ...

    Indian Academy of Sciences (India)

    A bubble expands adiabatically and translates in an incompressible and inviscid liquid. We investigate the number of equilibrium points of the bubble and the nature of stability of the bubble at these points. We find that there is only one equilibrium point and the bubble is stable there.

  9. Fluctuation effects on bubble growth in hot nuclear matter

    International Nuclear Information System (INIS)

    Santiago, A.J.; Chung, K.C.

    1991-01-01

    The evolution of bubbles with arbitrary density in an infinite nuclear system is studied in a simplified treatment. Kinetic pressure fluctuations on the bubble surface are considered. The critical radius, evolution time and probability for bubble expansion are shown to depend significantly on the initial bubble density. (author)

  10. International Expansion through Flexible Replication

    DEFF Research Database (Denmark)

    Jonsson, Anna; Foss, Nicolai Juul

    2011-01-01

    Business organizations may expand internationally by replicating a part of their value chain, such as a sales and marketing format, in other countries. However, little is known regarding how such “international replicators” build a format for replication, or how they can adjust it in order to ada......, etc.) are replicated in a uniform manner across stores, and change only very slowly (if at all) in response to learning (“flexible replication”). We conclude by discussing the factors that influence the approach to replication adopted by an international replicator.......Business organizations may expand internationally by replicating a part of their value chain, such as a sales and marketing format, in other countries. However, little is known regarding how such “international replicators” build a format for replication, or how they can adjust it in order to adapt...

  11. Modeling inhomogeneous DNA replication kinetics.

    Directory of Open Access Journals (Sweden)

    Michel G Gauthier

    Full Text Available In eukaryotic organisms, DNA replication is initiated at a series of chromosomal locations called origins, where replication forks are assembled proceeding bidirectionally to replicate the genome. The distribution and firing rate of these origins, in conjunction with the velocity at which forks progress, dictate the program of the replication process. Previous attempts at modeling DNA replication in eukaryotes have focused on cases where the firing rate and the velocity of replication forks are homogeneous, or uniform, across the genome. However, it is now known that there are large variations in origin activity along the genome and variations in fork velocities can also take place. Here, we generalize previous approaches to modeling replication, to allow for arbitrary spatial variation of initiation rates and fork velocities. We derive rate equations for left- and right-moving forks and for replication probability over time that can be solved numerically to obtain the mean-field replication program. This method accurately reproduces the results of DNA replication simulation. We also successfully adapted our approach to the inverse problem of fitting measurements of DNA replication performed on single DNA molecules. Since such measurements are performed on specified portion of the genome, the examined DNA molecules may be replicated by forks that originate either within the studied molecule or outside of it. This problem was solved by using an effective flux of incoming replication forks at the model boundaries to represent the origin activity outside the studied region. Using this approach, we show that reliable inferences can be made about the replication of specific portions of the genome even if the amount of data that can be obtained from single-molecule experiments is generally limited.

  12. IMPLEMENTATION OF SERIAL AND PARALLEL BUBBLE SORT ON FPGA

    Directory of Open Access Journals (Sweden)

    Dwi Marhaendro Jati Purnomo

    2016-06-01

    Full Text Available Sorting is common process in computational world. Its utilization are on many fields from research to industry. There are many sorting algorithm in nowadays. One of the simplest yet powerful is bubble sort. In this study, bubble sort is implemented on FPGA. The implementation was taken on serial and parallel approach. Serial and parallel bubble sort then compared by means of its memory, execution time, and utility which comprises slices and LUTs. The experiments show that serial bubble sort required smaller memory as well as utility compared to parallel bubble sort. Meanwhile, parallel bubble sort performed faster than serial bubble sort

  13. Generation of a bubble universe using a negative energy bath

    International Nuclear Information System (INIS)

    Hwang, Dong-il; Yeom, Dong-han

    2011-01-01

    This paper suggests a model for a bubble universe using buildable false vacuum bubbles. We study the causal structures of collapsing false vacuum bubbles using double-null simulations. False vacuum bubbles violate the null energy condition and emit negative energy along the outgoing direction through semi-classical effects. If there are a few collapsing false vacuum bubbles and they emit negative energy to a certain region, then the region can be approximated by a negative energy bath, which means that the region is homogeneously filled by negative energy. If a false vacuum bubble is generated in the negative energy bath and the tension of the bubble effectively becomes negative in the bath, then the bubble can expand and form an inflating bubble universe. This scenario uses a set of assumptions different from those in previous studies because it does not require tunneling to unbuildable bubbles.

  14. Effect of supercritical water shell on cavitation bubble dynamics

    International Nuclear Information System (INIS)

    Shao Wei-Hang; Chen Wei-Zhong

    2015-01-01

    Based on reported experimental data, a new model for single cavitation bubble dynamics is proposed considering a supercritical water (SCW) shell surrounding the bubble. Theoretical investigations show that the SCW shell apparently slows down the oscillation of the bubble and cools the gas temperature inside the collapsing bubble. Furthermore, the model is simplified to a Rayleigh–Plesset-like equation for a thin SCW shell. The dependence of the bubble dynamics on the thickness and density of the SCW shell is studied. The results show the bubble dynamics depends on the thickness but is insensitive to the density of the SCW shell. The thicker the SCW shell is, the smaller are the wall velocity and the gas temperature in the bubble. In the authors’ opinion, the SCW shell works as a buffering agent. In collapsing, it is compressed to absorb a good deal of the work transformed into the bubble internal energy during bubble collapse so that it weakens the bubble oscillations. (paper)

  15. Lattice Boltzmann Simulation of Multiple Bubbles Motion under Gravity

    Directory of Open Access Journals (Sweden)

    Deming Nie

    2015-01-01

    Full Text Available The motion of multiple bubbles under gravity in two dimensions is numerically studied through the lattice Boltzmann method for the Eotvos number ranging from 1 to 12. Two kinds of initial arrangement are taken into account: vertical and horizontal arrangement. In both cases the effects of Eotvos number on the bubble coalescence and rising velocity are investigated. For the vertical arrangement, it has been found that the coalescence pattern is similar. The first coalescence always takes place between the two uppermost bubbles. And the last coalescence always takes place between the coalesced bubble and the bottommost bubble. For four bubbles in a horizontal arrangement, the outermost bubbles travel into the wake of the middle bubbles in all cases, which allows the bubbles to coalesce. The coalescence pattern is more complex for the case of eight bubbles, which strongly depends on the Eotvos number.

  16. BARE retrotransposons are translated and replicated via distinct RNA pools.

    Directory of Open Access Journals (Sweden)

    Wei Chang

    Full Text Available The replication of Long Terminal Repeat (LTR retrotransposons, which can constitute over 80% of higher plant genomes, resembles that of retroviruses. A major question for retrotransposons and retroviruses is how the two conflicting roles of their transcripts, in translation and reverse transcription, are balanced. Here, we show that the BARE retrotransposon, despite its organization into just one open reading frame, produces three distinct classes of transcripts. One is capped, polyadenylated, and translated, but cannot be copied into cDNA. The second is not capped or polyadenylated, but is destined for packaging and ultimate reverse transcription. The third class is capped, polyadenylated, and spliced to favor production of a subgenomic RNA encoding only Gag, the protein forming virus-like particles. Moreover, the BARE2 subfamily, which cannot synthesize Gag and is parasitic on BARE1, does not produce the spliced sub-genomic RNA for translation but does make the replication competent transcripts, which are packaged into BARE1 particles. To our knowledge, this is first demonstration of distinct RNA pools for translation and transcription for any retrotransposon.

  17. Letter: Entrapment and interaction of an air bubble with an oscillating cavitation bubble

    Science.gov (United States)

    Kannan, Y. S.; Karri, Badarinath; Sahu, Kirti Chandra

    2018-04-01

    The mechanism of the formation of an air bubble due to an oscillating cavitation bubble in its vicinity is reported from an experimental study using high-speed imaging. The cavitation bubble is created close to the free surface of water using a low-voltage spark circuit comprising two copper electrodes in contact with each other. Before the bubble is created, a third copper wire is positioned in contact with the free surface of water close to the two crossing electrodes. Due to the surface tension at the triple point (wire-water-air) interface, a small dip is observed in the free surface at the point where the wire is immersed. When the cavitation bubble is created, the bubble pushes at the dip while expanding and pulls at it while collapsing. The collapse phase leads to the entrapment of an air bubble at the wire immersion point. During this phase, the air bubble undergoes a "catapult" effect, i.e., it expands to a maximum size and then collapses with a microjet at the free surface. To the best of our knowledge, this mechanism has not been reported so far. A parametric study is also conducted to understand the effects of wire orientation and bubble distance from the free surface.

  18. Optimization of the bubble radius in a moving single bubble sonoluminescence

    International Nuclear Information System (INIS)

    Mirheydari, Mona; Sadighi-Bonabi, Rasoul; Rezaee, Nastaran; Ebrahimi, Homa

    2011-01-01

    A complete study of the hydrodynamic force on a moving single bubble sonoluminescence in N-methylformamide is presented in this work. All forces exerted, trajectory, interior temperature and gas pressure are discussed. The maximum values of the calculated components of the hydrodynamic force for three different radii at the same driving pressure were compared, while the optimum bubble radius was determined. The maximum value of the buoyancy force appears at the start of bubble collapse, earlier than the other forces whose maximum values appear at the moment of bubble collapse. We verified that for radii larger than the optimum radius, the temperature peak value decreases.

  19. Bubble collisions and measures of the multiverse

    International Nuclear Information System (INIS)

    Salem, Michael P.

    2012-01-01

    To compute the spectrum of bubble collisions seen by an observer in an eternally-inflating multiverse, one must choose a measure over the diverging spacetime volume, including choosing an ''initial'' hypersurface below which there are no bubble nucleations. Previous calculations focused on the case where the initial hypersurface is pushed arbitrarily deep into the past. Interestingly, the observed spectrum depends on the orientation of the initial hypersurface, however one's ability observe the effect rapidly decreases with the ratio of inflationary Hubble rates inside and outside one's bubble. We investigate whether this conclusion might be avoided under more general circumstances, including placing the observer's bubble near the initial hypersurface. We find that it is not. As a point of reference, a substantial appendix reviews relevant aspects of the measure problem of eternal inflation

  20. Bubble collisions and measures of the multiverse

    Energy Technology Data Exchange (ETDEWEB)

    Salem, Michael P., E-mail: salem@cosmos.phy.tufts.edu [Department of Physics, Stanford University, Stanford, CA 94305 (United States)

    2012-01-01

    To compute the spectrum of bubble collisions seen by an observer in an eternally-inflating multiverse, one must choose a measure over the diverging spacetime volume, including choosing an ''initial'' hypersurface below which there are no bubble nucleations. Previous calculations focused on the case where the initial hypersurface is pushed arbitrarily deep into the past. Interestingly, the observed spectrum depends on the orientation of the initial hypersurface, however one's ability observe the effect rapidly decreases with the ratio of inflationary Hubble rates inside and outside one's bubble. We investigate whether this conclusion might be avoided under more general circumstances, including placing the observer's bubble near the initial hypersurface. We find that it is not. As a point of reference, a substantial appendix reviews relevant aspects of the measure problem of eternal inflation.

  1. The charged bubble oscillator: Dynamics and thresholds

    Indian Academy of Sciences (India)

    The nonlinear, forced oscillations of a bubble in a fluid due to an external pressure field are studied theoretically. ... for the system, delineating different dynamics. Keywords. ..... (c) Power spectral density of the charged and uncharged bub-.

  2. The 2008 oil bubble. Causes and consequences

    International Nuclear Information System (INIS)

    Tokic, Damir

    2010-01-01

    We argue that 'the 2008 Oil Bubble' was directly and indirectly created by the Federal Reserve in response to deflationary risks that resurfaced after the housing bubble burst and the resulting credit crisis of 2008. Deflationary risks first appeared after the dot.com bubble burst in 2000 and after the terrorist attacks on September 11, 2001. Manipulation of the US dollar value has been one of the key emergency tools in the Fed's arsenal. During the entire period from 2000 to 2008, the US dollar has been falling, while the price of crude oil has been rising, with the culmination in July 2008. If other global central banks embrace the Fed's anti-deflationary strategies, the consequences could be dire for the global economy, potentially resulting in an ultimate gold bubble. (author)

  3. Universe out of a breathing bubble

    International Nuclear Information System (INIS)

    Guendelman, Eduardo I.; Sakai, Nobuyuki

    2008-01-01

    We consider the model of a false-vacuum bubble with a thin wall where the surface energy density is composed of two different components, 'domain-wall' type and 'dust' type, with opposite signs. We find stably oscillating solutions, which we call 'breathing bubbles'. By decay to a lower mass state, such a breathing bubble could become either (i) a child universe or ii) a bubble that 'eats up' the original universe, depending on the sign of the surface energy of the domain-wall component. We also discuss the effect of the finite-thickness corrections to the thin-wall approximation and possible origins of the energy contents of our model

  4. Electron acceleration in the bubble regime

    Energy Technology Data Exchange (ETDEWEB)

    Jansen, Oliver

    2014-02-03

    The bubble regime of laser-wakefield acceleration has been studied over the recent years as an important alternative to classical accelerators. Several models and theories have been published, in particular a theory which provides scaling laws for acceleration parameters such as energy gain and acceleration length. This thesis deals with numerical simulations within the bubble regime, their comparison to these scaling laws and data obtained from experiments, as well as some specific phenomenona. With a comparison of the scaling laws with numerical results a parameter scan was able to show a large parameter space in which simulation and theory agree. An investigation of the limits of this parameter space revealed boundaries to other regimes, especially at very high (a{sub 0} > 100) and very low laser amplitudes (a{sub 0} < 4). Comparing simulation data with data from experiments concerning laser pulse development and electron energies, it was found that experimental results can be adequately reproduced using the Virtual-Laser-Plasma-Laboratory code. In collaboration with the Institut fuer Optik und Quantenelektronik at the Friedrich-Schiller University Jena synchrotron radiation emitted from the inside of the bubble was investigated. A simulation of the movement of the electrons inside the bubble together with time dependent histograms of the emitted radiation helped to prove that the majority of radiation created during a bubble acceleration originates from the inside of the bubble. This radiation can be used to diagnose the amplitude of oscillation of the trapped electrons. During a further study it was proven that the polarisation of synchrotron radiation from a bubble contains information about the exact oscillation direction. This oscillation was successfully controlled by using either a laser pulse with a tilted pulse front or an asymmetric laser pulse. First results of ongoing studies concerning injecting electrons into an existing bubble and a scheme called

  5. Sono-chemiluminescence from a single cavitation bubble in water

    International Nuclear Information System (INIS)

    Brotchie, Adam; Shchukin, Dmitry; Moehwald, Helmuth; Schneider, Julia; Pflieger, Rachel

    2012-01-01

    In summary, this study has revealed the conditions required for a single bubble to be sono-chemically active. Evidence of radical-induced processes surrounding the bubble was only observed below the SL threshold, where the bubble was not spatially stable, and did not correlate with emission from excited molecular states inside the bubble. Moreover, this work substantiates recent progress that has been made in bridging the gap between single and multi-bubble cavitation. (authors)

  6. Effects of Gas Dynamics on Rapidly Collapsing Bubbles

    OpenAIRE

    Bauman, Spenser; Fomitchev-Zamilov, Max

    2013-01-01

    The dynamics of rapidly collapsing bubbles are of great interest due to the high degree of energy focusing that occurs withing the bubble. Molecular dynamics provides a way to model the interior of the bubble and couple the gas dynamics with the equations governing the bubble wall. While much theoretical work has been done to understand how a bubble will respond to an external force, the internal dynamics of the gas system are usually simplified greatly in such treatments. This paper shows ho...

  7. Astronaut Pedro Duque Watches A Water Bubble

    Science.gov (United States)

    2003-01-01

    Aboard the International Space Station (ISS), European Space Agency astronaut Pedro Duque of Spain watches a water bubble float between a camera and himself. The bubble shows his reflection (reversed). Duque was launched aboard a Russian Soyuz TMA-3 spacecraft from the Baikonur Cosmodrome, Kazakhstan on October 18th, along with expedition-8 crew members Michael C. Foale, Mission Commander and NASA ISS Science Officer, and Cosmonaut Alexander Y. Kaleri, Soyuz Commander and flight engineer.

  8. Acoustic waves in polydispersed bubbly liquids

    International Nuclear Information System (INIS)

    Gubaidullin, D A; Gubaidullina, D D; Fedorov, Yu V

    2014-01-01

    The propagation of acoustic waves in polydispersed mixtures of liquid with two sorts of gas bubbles each of which has its own bubble size distribution function is studied. The system of the differential equations of the perturbed motion of a mixture is presented, the dispersion relation is obtained. Equilibrium speed of sound, low-frequency and high-frequency asymptotes of the attenuation coefficient are found. Comparison of the developed theory with known experimental data is presented

  9. Acoustic waves in polydispersed bubbly liquids

    Science.gov (United States)

    Gubaidullin, D. A.; Gubaidullina, D. D.; Fedorov, Yu V.

    2014-11-01

    The propagation of acoustic waves in polydispersed mixtures of liquid with two sorts of gas bubbles each of which has its own bubble size distribution function is studied. The system of the differential equations of the perturbed motion of a mixture is presented, the dispersion relation is obtained. Equilibrium speed of sound, low-frequency and high-frequency asymptotes of the attenuation coefficient are found. Comparison of the developed theory with known experimental data is presented.

  10. Bubbles on the river of time

    International Nuclear Information System (INIS)

    Gribbin, J.

    1988-01-01

    The paper is concerned with modern cosmology, and the possibility that our Universe is just one bubble among many in some greater suprauniverse. These ideas are connected with the concept of inflation; inflation occurred shortly after the moment of creation of the Universe and just before the fireball stage that represents the big bang proper. A description is given of inflation and its use to explain the creation of the Universe from bubbles of mass-energy. (U.K.)

  11. Test ventilation with smoke, bubbles, and balloons

    International Nuclear Information System (INIS)

    Pickering, P.L.; Cucchiara, A.L.; McAtee, J.L.; Gonzales, M.

    1987-01-01

    The behavior of smoke, bubbles, and helium-filled balloons was videotaped to demonstrate the mixing of air in the plutonium chemistry laboratories, a plutonium facility. The air-distribution patterns, as indicated by each method, were compared. Helium-filled balloons proved more useful than bubbles or smoke in the visualization of airflow patterns. The replay of various segments of the videotape proved useful in evaluating the different techniques and in identifying airflow trends responsible for air mixing. 6 refs

  12. Beer tapping: dynamics of bubbles after impact

    OpenAIRE

    Mantic-Lugo, V.; Cayron, A.; Brun, P-T; Gallaire, F.

    2015-01-01

    Beer tapping is a well known prank where a bottle of beer is impacted from the top by a solid object, usually another bottle, leading to a sudden foam overflow. A description of the shock-driven bubble dynamics leading to foaming is presented based on an experimental and numerical study evoking the following physical picture. First, the solid impact produces a sudden downwards acceleration of the bottle creating a strong depression in the liquid bulk. The existing bubbles undergo a strong exp...

  13. Beer tapping: dynamics of bubbles after impact

    Science.gov (United States)

    Mantič-Lugo, V.; Cayron, A.; Brun, P.-T.; Gallaire, F.

    2015-12-01

    Beer tapping is a well known prank where a bottle of beer is impacted from the top by a solid object, usually another bottle, leading to a sudden foam overflow. A description of the shock-driven bubble dynamics leading to foaming is presented based on an experimental and numerical study evoking the following physical picture. First, the solid impact produces a sudden downwards acceleration of the bottle creating a strong depression in the liquid bulk. The existing bubbles undergo a strong expansion and a sudden contraction ending in their collapse and fragmentation into a large amount of small bubbles. Second, the bubble clouds present a large surface area to volume ratio, enhancing the CO2 diffusion from the supersaturated liquid, hence growing rapidly and depleting the CO2. The clouds of bubbles migrate upwards in the form of plumes pulling the surrounding liquid with them and eventually resulting in the foam overflow. The sudden pressure drop that triggers the bubble dynamics with a collapse and oscillations is modelled by the Rayleigh-Plesset equation. The bubble dynamics from impact to collapse occurs over a time (tb ≃ 800 μs) much larger than the acoustic time scale of the liquid bulk (tac = 2H/c ≃ 80 μs), for the experimental container of height H = 6 cm and a speed of sound around c ≃ 1500 m/s. This scale separation, together with the comparison of numerical and experimental results, suggests that the pressure drop is controlled by two parameters: the acceleration of the container and the distance from the bubble to the free surface.

  14. Numerical simulation of single bubble boiling behavior

    Directory of Open Access Journals (Sweden)

    Junjie Liu

    2017-06-01

    Full Text Available The phenomena of a single bubble boiling process are studied with numerical modeling. The mass, momentum, energy and level set equations are solved using COMSOL multi-physics software. The bubble boiling dynamics, the transient pressure field, velocity field and temperature field in time are analyzed, and reasonable results are obtained. The numeral model is validated by the empirical equation of Fritz and could be used for various applications.

  15. Bubble nonlinear dynamics and stimulated scattering process

    Science.gov (United States)

    Jie, Shi; De-Sen, Yang; Sheng-Guo, Shi; Bo, Hu; Hao-Yang, Zhang; Shi-Yong, Hu

    2016-02-01

    A complete understanding of the bubble dynamics is deemed necessary in order to achieve their full potential applications in industry and medicine. For this purpose it is first needed to expand our knowledge of a single bubble behavior under different possible conditions including the frequency and pressure variations of the sound field. In addition, stimulated scattering of sound on a bubble is a special effect in sound field, and its characteristics are associated with bubble oscillation mode. A bubble in liquid can be considered as a representative example of nonlinear dynamical system theory with its resonance, and its dynamics characteristics can be described by the Keller-Miksis equation. The nonlinear dynamics of an acoustically excited gas bubble in water is investigated by using theoretical and numerical analysis methods. Our results show its strongly nonlinear behavior with respect to the pressure amplitude and excitation frequency as the control parameters, and give an intuitive insight into stimulated sound scattering on a bubble. It is seen that the stimulated sound scattering is different from common dynamical behaviors, such as bifurcation and chaos, which is the result of the nonlinear resonance of a bubble under the excitation of a high amplitude acoustic sound wave essentially. The numerical analysis results show that the threshold of stimulated sound scattering is smaller than those of bifurcation and chaos in the common condition. Project supported by the Program for Changjiang Scholars and Innovative Research Team in University, China (Grant No. IRT1228) and the Young Scientists Fund of the National Natural Science Foundation of China (Grant Nos. 11204050 and 11204049).

  16. A simple circuit to deliver bubbling CPAP.

    Science.gov (United States)

    Kaur, Charanjit; Sema, Akatoli; Beri, Rajbir S; Puliyel, Jacob M

    2008-04-01

    Nasal continuous positive airway pressure (CPAP), especially bubbling CPAP, is known to reduce the need for more invasive ventilation. We here describe a circuit that can deliver bubbling CPAP in resource poor settings. We describe how the oxygen concentration can be altered from 98% to 21% oxygen using this system. Addition of a humidifier in the circuit has the effect of reducing the oxygen concentration by 1 to 5%. The cost of putting together the system is approximately Rs 5000.

  17. Bubble chamber: Omega production and decay

    CERN Document Server

    1973-01-01

    This image is taken from one of CERN's bubble chambers and shows the decay of a positive kaon in flight. The decay products of this kaon can be seen spiraling in the magnetic field of the chamber. The invention of bubble chambers in 1952 revolutionized the field of particle physics, allowing real tracks left by particles to be seen and photographed by expanding liquid that has been heated to boiling point.

  18. The role of ion beam etching in magnetic bubble device manufacture

    International Nuclear Information System (INIS)

    Brambley, D.R.; Vanner, K.C.

    1979-01-01

    The most critical stage of fabrication of magnetic bubble memories is the etching of a pattern in a permalloy (80/20 Ni/Fe) film approximately 0.4 microns thick. The permalloy elements so made are used to produce perturbations in an externally applied magnetic bias field, and these perturbations cause the translation of magnetic bubbles within an underlying film. Devices now being produced have memory-cell sizes of less than 16 microns and require the etched features to have minimum dimensions of less than 2 microns. The only practicable way of achieving this with the requisite precision is by the use of sputter or ion beam etching. In addition, ion beam etching is used for defining gold conductor elements which perform the functions of bubble nucleation, replication and transfer. This paper briefly outlines the bubble device fabrication process, with special emphasis on the role of ion beam etching. The wafer temperature, element profile and uniformity obtained during ion beam etching are of considerable significance, and some of the factors affecting these will be discussed. Finally some of the limitations of ion beam etching will be described. (author)

  19. PRC1 Prevents Replication Stress during Chondrogenic Transit Amplification

    Directory of Open Access Journals (Sweden)

    Frank Spaapen

    2017-12-01

    Full Text Available Transit amplification (TA, a state of combined, rapid proliferative expansion and differentiation of stem cell-descendants, remains poorly defined at the molecular level. The Polycomb Repressive Complex 1 (PRC1 protein BMI1 has been localized to TA compartments, yet its exact role in TA is unclear. PRC1 proteins control gene expression, cell proliferation and DNA-damage repair. Coordination of such DNA-templated activities during TA is predicted to be crucial to support DNA replication and differentiation-associated transcriptional programming. We here examined whether chondrogenesis provides a relevant biological context for synchronized coordination of these chromatin-based tasks by BMI1. Taking advantage of a prominently featuring TA-phase during chondrogenesis in vitro and in vivo, we here report that TA is completely dependent on intact PRC1 function. BMI1-depleted chondrogenic progenitors rapidly accumulate double strand DNA breaks during DNA replication, present massive non-H3K27me3-directed transcriptional deregulation and fail to undergo chondrogenic TA. Genome-wide accumulation of Topoisomerase 2α and Geminin suggests a model in which PRC1 synchronizes replication and transcription during rapid chondrogenic progenitor expansion. Our combined data reveals for the first time a vital cell-autonomous role for PRC1 during chondrogenesis. We provide evidence that chondrocyte hyper-replication and hypertrophy represent a unique example of programmed senescence in vivo. These findings provide new perspectives on PRC1 function in development and disease.

  20. Bubble parameters analysis of gas-liquid two-phase sparse bubbly flow based on image method

    International Nuclear Information System (INIS)

    Zhou Yunlong; Zhou Hongjuan; Song Lianzhuang; Liu Qian

    2012-01-01

    The sparse rising bubbles of gas-liquid two-phase flow in vertical pipe were measured and studied based on image method. The bubble images were acquired by high-speed video camera systems, the characteristic parameters of bubbles were extracted by using image processing techniques. Then velocity variation of rising bubbles were drawn. Area and centroid variation of single bubble were also drawn. And then parameters and movement law of bubbles were analyzed and studied. The test results showed that parameters of bubbles had been analyzed well by using image method. (authors)

  1. A CI-Independent Form of Replicative Inhibition: Turn Off of Early Replication of Bacteriophage Lambda

    Science.gov (United States)

    Hayes, Sidney; Horbay, Monique A.; Hayes, Connie

    2012-01-01

    Several earlier studies have described an unusual exclusion phenotype exhibited by cells with plasmids carrying a portion of the replication region of phage lambda. Cells exhibiting this inhibition phenotype (IP) prevent the plating of homo-immune and hybrid hetero-immune lambdoid phages. We have attempted to define aspects of IP, and show that it is directed to repλ phages. IP was observed in cells with plasmids containing a λ DNA fragment including oop, encoding a short OOP micro RNA, and part of the lambda origin of replication, oriλ, defined by iteron sequences ITN1-4 and an adjacent high AT-rich sequence. Transcription of the intact oop sequence from its promoter, pO is required for IP, as are iterons ITN3–4, but not the high AT-rich portion of oriλ. The results suggest that IP silencing is directed to theta mode replication initiation from an infecting repλ genome, or an induced repλ prophage. Phage mutations suppressing IP, i.e., Sip, map within, or adjacent to cro or in O, or both. Our results for plasmid based IP suggest the hypothesis that there is a natural mechanism for silencing early theta-mode replication initiation, i.e. the buildup of λ genomes with oop + oriλ+ sequence. PMID:22590552

  2. Intensely oscillating cavitation bubble in microfluidics

    International Nuclear Information System (INIS)

    Siew-Wan, Ohl; Tandiono; Klaseboer, Evert; Dave, Ow; Choo, Andre; Claus-Dieter, Ohl

    2015-01-01

    This study reports the technical breakthrough in generating intense ultrasonic cavitation in the confinement of a microfluidics channel [1], and applications that has been developed on this platform for the past few years [2,3,4,5]. Our system consists of circular disc transducers (10-20 mm in diameter), the microfluidics channels on PDMS (polydimethylsiloxane), and a driving circuitry. The cavitation bubbles are created at the gas- water interface due to strong capillary waves which are generated when the system is driven at its natural frequency (around 100 kHz) [1]. These bubbles oscillate and collapse within the channel. The bubbles are useful for sonochemistry and the generation of sonoluminescence [2]. When we add bacteria (Escherichia coli), and yeast cells (Pichia pastoris) into the microfluidics channels, the oscillating and collapsing bubbles stretch and lyse these cells [3]. Furthermore, the system is effective (DNA of the harvested intracellular content remains largely intact), and efficient (yield reaches saturation in less than 1 second). In another application, human red blood cells are added to a microchamber. Cell stretching and rapture are observed when a laser generated cavitation bubble expands and collapses next to the cell [4]. A numerical model of a liquid pocket surrounded by a membrane with surface tension which was placed next to an oscillating bubble was developed using the Boundary Element Method. The simulation results showed that the stretching of the liquid pocket occurs only when the surface tension is within a certain range. (paper)

  3. Gas transfer in a bubbly wake flow

    Science.gov (United States)

    Karn, A.; Gulliver, J. S.; Monson, G. M.; Ellis, C.; Arndt, R. E. A.; Hong, J.

    2016-05-01

    The present work reports simultaneous bubble size and gas transfer measurements in a bubbly wake flow of a hydrofoil, designed to be similar to a hydroturbine blade. Bubble size was measured by a shadow imaging technique and found to have a Sauter mean diameter of 0.9 mm for a reference case. A lower gas flow rate, greater liquid velocities, and a larger angle of attack all resulted in an increased number of small size bubbles and a reduced weighted mean bubble size. Bubble-water gas transfer is measured by the disturbed equilibrium technique. The gas transfer model of Azbel (1981) is utilized to characterize the liquid film coefficient for gas transfer, with one scaling coefficient to reflect the fact that characteristic turbulent velocity is replaced by cross-sectional mean velocity. The coefficient was found to stay constant at a particular hydrofoil configuration while it varied within a narrow range of 0.52-0.60 for different gas/water flow conditions.

  4. Gas Bubble Dynamics under Mechanical Vibrations

    Science.gov (United States)

    Mohagheghian, Shahrouz; Elbing, Brian

    2017-11-01

    The scientific community has a limited understanding of the bubble dynamics under mechanical oscillations due to over simplification of Navier-Stockes equation by neglecting the shear stress tensor and not accounting for body forces when calculating the acoustic radiation force. The current work experimental investigates bubble dynamics under mechanical vibration and resulting acoustic field by measuring the bubble size and velocity using high-speed imaging. The experimental setup consists of a custom-designed shaker table, cast acrylic bubble column, compressed air injection manifold and an optical imaging system. The mechanical vibrations resulted in accelerations between 0.25 to 10 times gravitational acceleration corresponding to frequency and amplitude range of 8 - 22Hz and 1 - 10mm respectively. Throughout testing the void fraction was limited to <5%. The bubble size is larger than resonance size and smaller than acoustic wavelength. The amplitude of acoustic pressure wave was estimated using the definition of Bjerknes force in combination with Rayleigh-Plesset equation. Physical behavior of the system was capture and classified. Bubble size, velocity as well as size and spatial distribution will be presented.

  5. Bubbling AdS3

    International Nuclear Information System (INIS)

    Martelli, Dario; Morales, Jose Francisco

    2005-01-01

    In the light of the recent Lin, Lunin, Maldacena (LLM) results, we investigate 1/2-BPS geometries in minimal (and next to minimal) supergravity in D = 6 dimensions. In the case of minimal supergravity, solutions are given by fibrations of a two-torus T 2 specified by two harmonic functions. For a rectangular torus the two functions are related by a non-linear equation with rare solutions: AdS 3 x S 3 , the pp-wave and the multi-center string. 'Bubbling', i.e. superpositions of droplets, is accommodated by allowing the complex structure of the T 2 to vary over the base. The analysis is repeated in the presence of a tensor multiplet and similar conclusions are reached, with generic solutions describing D1D5 (or their dual fundamental string-momentum) systems. In this framework, the profile of the dual fundamental string-momentum system is identified with the boundaries of the droplets in a two-dimensional plane. (author)

  6. DNA Replication Profiling Using Deep Sequencing.

    Science.gov (United States)

    Saayman, Xanita; Ramos-Pérez, Cristina; Brown, Grant W

    2018-01-01

    Profiling of DNA replication during progression through S phase allows a quantitative snap-shot of replication origin usage and DNA replication fork progression. We present a method for using deep sequencing data to profile DNA replication in S. cerevisiae.

  7. Hydroxyurea-Induced Replication Stress

    Directory of Open Access Journals (Sweden)

    Kenza Lahkim Bennani-Belhaj

    2010-01-01

    Full Text Available Bloom's syndrome (BS displays one of the strongest known correlations between chromosomal instability and a high risk of cancer at an early age. BS cells combine a reduced average fork velocity with constitutive endogenous replication stress. However, the response of BS cells to replication stress induced by hydroxyurea (HU, which strongly slows the progression of replication forks, remains unclear due to publication of conflicting results. Using two different cellular models of BS, we showed that BLM deficiency is not associated with sensitivity to HU, in terms of clonogenic survival, DSB generation, and SCE induction. We suggest that surviving BLM-deficient cells are selected on the basis of their ability to deal with an endogenous replication stress induced by replication fork slowing, resulting in insensitivity to HU-induced replication stress.

  8. DATABASE REPLICATION IN HETEROGENOUS PLATFORM

    OpenAIRE

    Hendro Nindito; Evaristus Didik Madyatmadja; Albert Verasius Dian Sano

    2014-01-01

    The application of diverse database technologies in enterprises today is increasingly a common practice. To provide high availability and survavibality of real-time information, a database replication technology that has capability to replicate databases under heterogenous platforms is required. The purpose of this research is to find the technology with such capability. In this research, the data source is stored in MSSQL database server running on Windows. The data will be replicated to MyS...

  9. Nucleoside Triphosphate Phosphohydrolase I (NPH I) Functions as a 5′ to 3′ Translocase in Transcription Termination of Vaccinia Early Genes*

    Science.gov (United States)

    Hindman, Ryan; Gollnick, Paul

    2016-01-01

    Vaccinia virus early genes are transcribed immediately upon infection. Nucleoside triphosphate phosphohydrolase I (NPH I) is an essential component of the early gene transcription complex. NPH I hydrolyzes ATP to release transcripts during transcription termination. The ATPase activity of NPH I requires single-stranded (ss) DNA as a cofactor; however, the source of this cofactor within the transcription complex is not known. Based on available structures of transcription complexes it has been hypothesized that the ssDNA cofactor is obtained from the unpaired non-template strand within the transcription bubble. In vitro transcription on templates that lack portions of the non-template strand within the transcription bubble showed that the upstream portion of the transcription bubble is required for efficient NPH I-mediated transcript release. Complementarity between the template and non-template strands in this region is also required for NPH I-mediated transcript release. This observation complicates locating the source of the ssDNA cofactor within the transcription complex because removal of the non-template strand also disrupts transcription bubble reannealing. Prior studies have shown that ssRNA binds to NPH I, but it does not activate ATPase activity. Chimeric transcription templates with RNA in the non-template strand confirm that the source of the ssDNA cofactor for NPH I is the upstream portion of the non-template strand in the transcription bubble. Consistent with this conclusion we also show that isolated NPH I acts as a 5′ to 3′ translocase on single-stranded DNA. PMID:27189950

  10. Application of coalescence and breakup models in a discrete bubble model for bubble columns

    NARCIS (Netherlands)

    van den Hengel, E.I.V.; Deen, N.G.; Kuipers, J.A.M.

    2005-01-01

    In this work, a discrete bubble model (DBM) is used to investigate the hydrodynamics, coalescence, and breakup occurring in a bubble column. The DBM, originally developed by Delnoij et al. (Chem. Eng. Sci. 1997, 52, 1429-1458; Chem. Eng. Sci. 1999, 54, 2217-2226),1,2 was extended to incorporate

  11. Development of three-dimensional individual bubble-velocity measurement method by bubble tracking

    International Nuclear Information System (INIS)

    Kanai, Taizo; Furuya, Masahiro; Arai, Takahiro; Shirakawa, Kenetsu; Nishi, Yoshihisa

    2012-01-01

    A gas-liquid two-phase flow in a large diameter pipe exhibits a three-dimensional flow structure. Wire-Mesh Sensor (WMS) consists of a pair of parallel wire layers located at the cross section of a pipe. Both the parallel wires cross at 90o with a small gap and each intersection acts as an electrode. The WMS allows the measurement of the instantaneous two-dimensional void-fraction distribution over the cross-section of a pipe, based on the difference between the local instantaneous conductivity of the two-phase flow. Furthermore, the WMS can acquire a phasic-velocity on the basis of the time lag of void signals between two sets of WMS. Previously, the acquired phasic velocity was one-dimensional with time-averaged distributions. The authors propose a method to estimate the three-dimensional bubble-velocity individually WMS data. The bubble velocity is determined by the tracing method. In this tracing method, each bubble is separated from WMS signal, volume and center coordinates of the bubble is acquired. Two bubbles with near volume at two WMS are considered as the same bubble and bubble velocity is estimated from the displacement of the center coordinates of the two bubbles. The validity of this method is verified by a swirl flow. The proposed method can successfully visualize a swirl flow structure and the results of this method agree with the results of cross-correlation analysis. (author)

  12. Formation and evolution of bubbly screens in confined oscillating bubbly liquids

    Science.gov (United States)

    Shklyaev, Sergey; Straube, Arthur V.

    2010-01-01

    We consider the dynamics of dilute monodisperse bubbly liquid confined by two plane solid walls and subject to small-amplitude high-frequency oscillations normal to the walls. The initial state corresponds to the uniform distribution of bubbles and motionless liquid. The period of external driving is assumed much smaller than typical relaxation times for a single bubble but larger than the period of volume eigenoscillations. The time-averaged description accounting for the two-way coupling between the liquid and the bubbles is applied. We show that the model predicts accumulation of bubbles in thin sheets parallel to the walls. These singular structures, which are formally characterized by infinitely thin width and infinitely high concentration, are referred to as bubbly screens. The formation of a bubbly screen is described analytically in terms of a self-similar solution, which is in agreement with numerical simulations. We study the evolution of bubbly screens and detect a one-dimensional stationary state, which is shown to be unconditionally unstable.

  13. Financial Bubbles, Real Estate Bubbles, Derivative Bubbles, and the Financial and Economic Crisis

    Science.gov (United States)

    Sornette, Didier; Woodard, Ryan

    The financial crisis of 2008, which started with an initially well-defined epicenter focused on mortgage backed securities (MBS), has been cascading into a global economic recession, whose increasing severity and uncertain duration has led and is continuing to lead to massive losses and damage for billions of people. Heavy central bank interventions and government spending programs have been launched worldwide and especially in the USA and Europe, with the hope to unfreeze credit and bolster consumption. Here, we present evidence and articulate a general framework that allows one to diagnose the fundamental cause of the unfolding financial and economic crisis: the accumulation of several bubbles and their interplay and mutual reinforcement have led to an illusion of a "perpetual money machine" allowing financial institutions to extract wealth from an unsustainable artificial process. Taking stock of this diagnostic, we conclude that many of the interventions to address the so-called liquidity crisis and to encourage more consumption are ill-advised and even dangerous, given that precautionary reserves were not accumulated in the "good times" but that huge liabilities were. The most "interesting" present times constitute unique opportunities but also great challenges, for which we offer a few recommendations.

  14. Effects of additional inertia force on bubble breakup

    International Nuclear Information System (INIS)

    Pan Liangming; Zhang Wenzhi; Chen Deqi; Xu Jianhui; Xu Jianjun; Huang Yanping

    2011-01-01

    Through VOF two-phase flow model, the single bubble deformation and breakup in a vertical narrow channel is numerically investigated in the study based on the force balance at the process of bubble breakup. The effect of surface tension force, the additional inertia force and bubble initial shape on bubble breakup are analyzed according to the velocity variation at the break-up point and the minimum necking size when the bubble is breaking up. It is found that the surface tension force, the additional inertia force and the bubble initial shape have significant effects on the bubble breakup through the fluid injection toward to the bubble, which finally induces the onset of bubble breakup. (authors)

  15. Non-intuitive bubble effects in reactor and containment technology

    International Nuclear Information System (INIS)

    Moody, F.J.

    1991-01-01

    Most people know a lot about bubbles, including how they rise in liquids and the way they appear when the cap is removed from a bottle of carbonated beverage. A lot of bubble knowledge is obtained from bubbling air through water in aquariums to keep the fish alive and happy, or watching scuba divers feed the sharks in large glass tanks at the local zoo. But innocent bubbles can be sources of structural loadings and sometimes destructive fluid behavior. In fact, there are many non-intuitive effects associated with bubbles which have been discovered by experiments and analyses. It has been necessary to design various reactor and containment components in the nuclear energy industry to accommodate the fact that bubbles can expand like compressed springs, or oscillate, or collapse abruptly, and create structural loads. This paper describes several important phenomena associated with bubble action in nuclear reactor and containment systems and the associated loads exerted. An awareness of these effects can help to avoid unwelcome surprises in general thermal-hydraulic applications when a system is disturbed by bubble behavior. Major topics discussed include expanding and collapsing submerged bubbles, steam chugging and ringout, bubble shattering, surprising hot bubble action in a saturated pool, bubble effects on fluid-structure-interaction, waterhammer from collapsing bubble in pipes, and vapor bubble effects on sound speed in saturated mixtures

  16. Effect of microstructure on helium bubble growth in irradiated nickel

    International Nuclear Information System (INIS)

    Sattler, M.L.

    1986-01-01

    Thin nickel films were irradiated with 80 keV helium ions at varying doses and varying temperatures in order to obtain a variety of final microstructures. The growth of bubbles was examined during in-situ irradiations at 950 0 C where migration and coalescence events were observed for bubbles as large as 60 nm. Further direct observations of bubble growth were made during annealing of the irradiated specimens. For sample with no visible bubbles before annealing, the heating to 0.51 T/sub M/ produced bubbles that increased in diameter with annealing time to the power n. For bubbles in the grain interior, n ∼ 1, and on the grain boundaries, n ∼ 0.6. Since no migration and coalescence or ripening theories predict this behavior, a theory described by transient diffusion to spherical sinks was developed to discuss the behavior. This theory predicts that n = 1 for bubbles growing in the grain interior and n = 0.5 for bubbles on the grain boundary. In other annealing of irradiated samples containing large bubble populations, the growth of large bubbles and shrinking of small bubbles was observed at a temperature equal to 0.54 T/sub M/. The theory of Ostwald ripening properly described this type of bubble growth. Mass spectrometer measurements of He content in the irradiated specimens showed a greater He retention in the Ni films that contained a significant bubble population than those with no visible bubbles

  17. Convective mass transfer around a dissolving bubble

    Science.gov (United States)

    Duplat, Jerome; Grandemange, Mathieu; Poulain, Cedric

    2017-11-01

    Heat or mass transfer around an evaporating drop or condensing vapor bubble is a complex issue due to the interplay between the substrate properties, diffusion- and convection-driven mass transfer, and Marangoni effects, to mention but a few. In order to disentangle these mechanisms, we focus here mainly on the convective mass transfer contribution in an isothermal mass transfer problem. For this, we study the case of a millimetric carbon dioxide bubble which is suspended under a substrate and dissolved into pure liquid water. The high solubility of CO2 in water makes the liquid denser and promotes a buoyant-driven flow at a high (solutal) Rayleigh number (Ra˜104 ). The alteration of p H allows the concentration field in the liquid to be imaged by laser fluorescence enabling us to measure both the global mass flux (bubble volume, contact angle) and local mass flux around the bubble along time. After a short period of mass diffusion, where the boundary layer thickens like the square root of time, convection starts and the CO2 is carried by a plume falling at constant velocity. The boundary layer thickness then reaches a plateau which depends on the bubble cross section. Meanwhile the plume velocity scales like (dV /d t )1 /2 with V being the volume of the bubble. As for the rate of volume loss, we recover a constant mass flux in the diffusion-driven regime followed by a decrease in the volume V like V2 /3 after convection has started. We present a model which agrees well with the bubble dynamics and discuss our results in the context of droplet evaporation, as well as high Rayleigh convection.

  18. A grid-independent EMMS/bubbling drag model for bubbling and turbulent fluidization

    DEFF Research Database (Denmark)

    Luo, Hao; Lu, Bona; Zhang, Jingyuan

    2017-01-01

    The EMMS/bubbling drag model takes the effects of meso-scale structures (i.e. bubbles) into modeling of drag coefficient and thus improves coarse-grid simulation of bubbling and turbulent fluidized beds. However, its dependence on grid size has not been fully investigated. In this article, we adopt...... a two-step scheme to extend the EMMS/bubbling model to the sub-grid level. Thus the heterogeneity index, HD, which accounts for the hydrodynamic disparity between homogeneous and heterogeneous fluidization, can be correlated as a function of both local voidage and slip velocity. Simulations over...... a periodic domain show the new drag model is less sensitive to grid size because of the additional dependence on local slip velocity. When applying the new drag model to simulations of realistic bubbling and turbulent fluidized beds, we find grid-independent results are easier to obtain for high...

  19. GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris.

    Science.gov (United States)

    Liachko, Ivan; Youngblood, Rachel A; Tsui, Kyle; Bubb, Kerry L; Queitsch, Christine; Raghuraman, M K; Nislow, Corey; Brewer, Bonita J; Dunham, Maitreya J

    2014-03-01

    The well-studied DNA replication origins of the model budding and fission yeasts are A/T-rich elements. However, unlike their yeast counterparts, both plant and metazoan origins are G/C-rich and are associated with transcription start sites. Here we show that an industrially important methylotrophic budding yeast, Pichia pastoris, simultaneously employs at least two types of replication origins--a G/C-rich type associated with transcription start sites and an A/T-rich type more reminiscent of typical budding and fission yeast origins. We used a suite of massively parallel sequencing tools to map and dissect P. pastoris origins comprehensively, to measure their replication dynamics, and to assay the global positioning of nucleosomes across the genome. Our results suggest that some functional overlap exists between promoter sequences and G/C-rich replication origins in P. pastoris and imply an evolutionary bifurcation of the modes of replication initiation.

  20. GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris.

    Directory of Open Access Journals (Sweden)

    Ivan Liachko

    2014-03-01

    Full Text Available The well-studied DNA replication origins of the model budding and fission yeasts are A/T-rich elements. However, unlike their yeast counterparts, both plant and metazoan origins are G/C-rich and are associated with transcription start sites. Here we show that an industrially important methylotrophic budding yeast, Pichia pastoris, simultaneously employs at least two types of replication origins--a G/C-rich type associated with transcription start sites and an A/T-rich type more reminiscent of typical budding and fission yeast origins. We used a suite of massively parallel sequencing tools to map and dissect P. pastoris origins comprehensively, to measure their replication dynamics, and to assay the global positioning of nucleosomes across the genome. Our results suggest that some functional overlap exists between promoter sequences and G/C-rich replication origins in P. pastoris and imply an evolutionary bifurcation of the modes of replication initiation.

  1. Particle-bubble aggregate stability on static bubble generated by single nozzle on flotation process

    Science.gov (United States)

    Warjito, Harinaldi, Setyantono, Manus; Siregar, Sahala D.

    2016-06-01

    There are three sub-processes on flotation. These processes are intervening liquid film into critical thickness, rupture of liquid film forming three phase contact line, and expansion three phase contact line forming aggregate stability. Aggregate stability factor contribute to determine flotation efficiency. Aggregate stability has some important factors such as reagent and particle geometry. This research focussed on to understand effect of particle geometry to aggregate stability. Experimental setup consists of 9 x 9 x26 cm flotation column made of glass, bubble generator, particle feeding system, and high speed video camera. Bubble generator made from single nozzle with 0.3 mm diameter attached to programmable syringe pump. Particle feeding system made of pipette. Particle used in this research is taken from open pit Grasberg in Timika, Papua. Particle has sub-angular geometry and its size varies from 38 to 300 µm. Bubble-particle interaction are recorded using high speed video camera. Recordings from high speed video camera analyzed using image processing software. Experiment result shows that aggregate particle-bubble and induction time depends on particle size. Small particle (38-106 µm) has long induction time and able to rupture liquid film and also forming three phase contact line. Big particle (150-300 µm) has short induction time, so it unable to attach with bubble easily. This phenomenon is caused by apparent gravity work on particle-bubble interaction. Apparent gravity worked during particle sliding on bubble surface experience increase and reached its maximum magnitude at bubble equator. After particle passed bubble equator, apparent gravity force experience decrease. In conclusion particle size from 38-300 µm can form stable aggregate if particle attached with bubble in certain condition.

  2. Replication of bacteriophage lambda DNA

    International Nuclear Information System (INIS)

    Tsurimoto, T.; Matsubara, K.

    1983-01-01

    In this paper results of studies on the mechanism of bacteriophage lambda replication using molecular biological and biochemical approaches are reported. The purification of the initiator proteins, O and P, and the role of the O and P proteins in the initiation of lambda DNA replication through interactions with specific DNA sequences are described. 47 references, 15 figures

  3. Pattern replication by confined dewetting

    NARCIS (Netherlands)

    Harkema, S.; Schäffer, E.; Morariu, M.D.; Steiner, U

    2003-01-01

    The dewetting of a polymer film in a confined geometry was employed in a pattern-replication process. The instability of dewetting films is pinned by a structured confining surface, thereby replicating its topographic pattern. Depending on the surface energy of the confining surface, two different

  4. Charter School Replication. Policy Guide

    Science.gov (United States)

    Rhim, Lauren Morando

    2009-01-01

    "Replication" is the practice of a single charter school board or management organization opening several more schools that are each based on the same school model. The most rapid strategy to increase the number of new high-quality charter schools available to children is to encourage the replication of existing quality schools. This policy guide…

  5. Herds of methane chambers grazing bubbles

    Science.gov (United States)

    Grinham, Alistair; Dunbabin, Matthew

    2014-05-01

    Water to air methane emissions from freshwater reservoirs can be dominated by sediment bubbling (ebullitive) events. Previous work to quantify methane bubbling from a number of Australian sub-tropical reservoirs has shown that this can contribute as much as 95% of total emissions. These bubbling events are controlled by a variety of different factors including water depth, surface and internal waves, wind seiching, atmospheric pressure changes and water levels changes. Key to quantifying the magnitude of this emission pathway is estimating both the bubbling rate as well as the areal extent of bubbling. Both bubbling rate and areal extent are seldom constant and require persistent monitoring over extended time periods before true estimates can be generated. In this paper we present a novel system for persistent monitoring of both bubbling rate and areal extent using multiple robotic surface chambers and adaptive sampling (grazing) algorithms to automate the quantification process. Individual chambers are self-propelled and guided and communicate between each other without the need for supervised control. They can maintain station at a sampling site for a desired incubation period and continuously monitor, record and report fluxes during the incubation. To exploit the methane sensor detection capabilities, the chamber can be automatically lowered to decrease the head-space and increase concentration. The grazing algorithms assign a hierarchical order to chambers within a preselected zone. Chambers then converge on the individual recording the highest 15 minute bubbling rate. Individuals maintain a specified distance apart from each other during each sampling period before all individuals are then required to move to different locations based on a sampling algorithm (systematic or adaptive) exploiting prior measurements. This system has been field tested on a large-scale subtropical reservoir, Little Nerang Dam, and over monthly timescales. Using this technique

  6. Creeping motion of long bubbles and drops in capillary tubes

    DEFF Research Database (Denmark)

    Westborg, Henrik; Hassager, Ole

    1989-01-01

    The flow of inviscid bubbles and viscous drops in capillary tubes has been simulated by a Galerkin finite element method with surface tension included at the bubble/liquid interface. The results show good agreement with published experimental results. At low capillary numbers the front and the rear...... of the bubble are nearly spherical. As the capillary number increases the thickness of the wetting film between the tube wall and the bubble increases, and the bubble assumes a more slender shape with a characteristic bump at the rear. Recirculations are found in front and behind the bubble, which disappear...

  7. Interferometric measurement of film thickness during bubble blowing

    Science.gov (United States)

    Wang, Z.; Mandracchia, B.; Ferraro, V.; Tammaro, D.; Di Maio, E.; Maffettone, P. L.; Ferraro, P.

    2017-06-01

    In this paper, we propose digital holography in transmission configuration as an effective method to measure the time-dependent thickness of polymeric films during bubble blowing. We designed a complete set of experiments to measure bubble thickness, including the evaluation of the refractive index of the polymer solution. We report the measurement of thickness distribution along the film during the bubble formation process until the bubble`s rupture. Based on those data, the variation range and variation trend of bubble film thickness are clearly measured during the process of expansion to fracture is indicated.

  8. Tombusviruses upregulate phospholipid biosynthesis via interaction between p33 replication protein and yeast lipid sensor proteins during virus replication in yeast

    International Nuclear Information System (INIS)

    Barajas, Daniel; Xu, Kai; Sharma, Monika; Wu, Cheng-Yu; Nagy, Peter D.

    2014-01-01

    Positive-stranded RNA viruses induce new membranous structures and promote membrane proliferation in infected cells to facilitate viral replication. In this paper, the authors show that a plant-infecting tombusvirus upregulates transcription of phospholipid biosynthesis genes, such as INO1, OPI3 and CHO1, and increases phospholipid levels in yeast model host. This is accomplished by the viral p33 replication protein, which interacts with Opi1p FFAT domain protein and Scs2p VAP protein. Opi1p and Scs2p are phospholipid sensor proteins and they repress the expression of phospholipid genes. Accordingly, deletion of OPI1 transcription repressor in yeast has a stimulatory effect on TBSV RNA accumulation and enhanced tombusvirus replicase activity in an in vitro assay. Altogether, the presented data convincingly demonstrate that de novo lipid biosynthesis is required for optimal TBSV replication. Overall, this work reveals that a (+)RNA virus reprograms the phospholipid biosynthesis pathway in a unique way to facilitate its replication in yeast cells. - Highlights: • Tombusvirus p33 replication protein interacts with FFAT-domain host protein. • Tombusvirus replication leads to upregulation of phospholipids. • Tombusvirus replication depends on de novo lipid synthesis. • Deletion of FFAT-domain host protein enhances TBSV replication. • TBSV rewires host phospholipid synthesis

  9. Bubble coalescence in a Newtonian fluid

    Science.gov (United States)

    Garg, Vishrut; Basaran, Osman

    2017-11-01

    Bubble coalescence plays a central role in the hydrodynamics of gas-liquid systems such as bubble column reactors, spargers, and foams. Two bubbles approaching each other at velocity V coalesce when the thin film between them ruptures, which is often the rate-limiting step. Experimental studies of this system are difficult, and recent works provide conflicting results on the effect of V on coalescence times. We simulate the head-on approach of two bubbles of equal radii R in an incompressible Newtonian fluid (density ρ, viscosity μ, and surface tension σ) by solving numerically the free boundary problem comprised of the Navier Stokes and continuity equations. Simulations are made challenging by the existence of highly disparate lengthscales, i.e. film thickness and drop radii, which are resolved by using the method of elliptic mesh generation. For a given liquid, the bubbles are shown to coalesce for all velocities below a critical value. The effects of Ohnesorge number Oh = μ /√{ ρσR } on coalescence time and critical velocity are also investigated.

  10. Argonne Bubble Experiment Thermal Model Development III

    Energy Technology Data Exchange (ETDEWEB)

    Buechler, Cynthia Eileen [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2018-01-11

    This report describes the continuation of the work reported in “Argonne Bubble Experiment Thermal Model Development” and “Argonne Bubble Experiment Thermal Model Development II”. The experiment was performed at Argonne National Laboratory (ANL) in 2014. A rastered 35 MeV electron beam deposited power in a solution of uranyl sulfate, generating heat and radiolytic gas bubbles. Irradiations were performed at beam power levels between 6 and 15 kW. Solution temperatures were measured by thermocouples, and gas bubble behavior was recorded. The previous report2 described the Monte-Carlo N-Particle (MCNP) calculations and Computational Fluid Dynamics (CFD) analysis performed on the as-built solution vessel geometry. The CFD simulations in the current analysis were performed using Ansys Fluent, Ver. 17.2. The same power profiles determined from MCNP calculations in earlier work were used for the 12 and 15 kW simulations. The primary goal of the current work is to calculate the temperature profiles for the 12 and 15 kW cases using reasonable estimates for the gas generation rate, based on images of the bubbles recorded during the irradiations. Temperature profiles resulting from the CFD calculations are compared to experimental measurements.

  11. Drop impact entrapment of bubble rings

    KAUST Repository

    Thoraval, M.-J.

    2013-04-29

    We use ultra-high-speed video imaging to look at the initial contact of a drop impacting on a liquid layer. We observe experimentally the vortex street and the bubble-ring entrapments predicted numerically, for high impact velocities, by Thoraval et al. (Phys. Rev. Lett., vol. 108, 2012, article 264506). These dynamics mainly occur within 50 -s after the first contact, requiring imaging at 1 million f.p.s. For a water drop impacting on a thin layer of water, the entrapment of isolated bubbles starts through azimuthal instability, which forms at low impact velocities, in the neck connecting the drop and pool. For Reynolds number Re above -12 000, up to 10 partial bubble rings have been observed at the base of the ejecta, starting when the contact is -20% of the drop size. More regular bubble rings are observed for a pool of ethanol or methanol. The video imaging shows rotation around some of these air cylinders, which can temporarily delay their breakup into micro-bubbles. The different refractive index in the pool liquid reveals the destabilization of the vortices and the formation of streamwise vortices and intricate vortex tangles. Fine-scale axisymmetry is thereby destroyed. We show also that the shape of the drop has a strong influence on these dynamics. 2013 Cambridge University Press.

  12. Bubble growth in a narrow horizontal space

    Energy Technology Data Exchange (ETDEWEB)

    Stutz, Benoit; Goulet, Remi [CETHIL, UMR5008, CNRS, INSA-Lyon, Universite Lyon1 (France); Passos, Julio Cesar [Universidade Federal de Santa Catarina (UFSC), Florianopolis, SC (Brazil). Dept. de Engenharia Mecanica. LABSOLAR

    2009-07-01

    The purpose of this work is to develop an axis-symmetric two-phase flow model describing the growth of a single bubble squeezed between a horizontal heated upward-facing disc and an insulating surface placed parallel to the heated surface. Heat transfers at the liquid-vapour interfaces are predicted by the kinetic limit of vaporisation. The depths of the liquid films deposed on the surfaces (heated surface and confinement space) are determined using the Moriyama and Inoue correlation (1996). Transient heat transfers within the heated wall are taken into account. The model is applied to pentane bubble growth. The influence of the gap size, the initial temperature of the system, the thermal effusivity of the heated wall and the kinetic limit of vaporisation are studied. The results show that the expansion of the bubbles strongly depends on the gap size and can be affected by the effusivity of the material. Mechanical inertia effects are mainly dominant at the beginning of the bubble expansion. Pressure drop induced by viscous effects have to be taken into account for high capillary numbers. Heat transfers at the meniscus are negligible except at the early stages of the bubble growth. (author)

  13. Bubble growth in a narrow horizontal space

    International Nuclear Information System (INIS)

    Stutz, Benoit; Goulet, Remi; Passos, Julio Cesar

    2009-01-01

    The purpose of this work is to develop an axis-symmetric two-phase flow model describing the growth of a single bubble squeezed between a horizontal heated upward-facing disc and an insulating surface placed parallel to the heated surface. Heat transfers at the liquid-vapour interfaces are predicted by the kinetic limit of vaporisation. The depths of the liquid films deposed on the surfaces (heated surface and confinement space) are determined using the Moriyama and Inoue correlation (1996). Transient heat transfers within the heated wall are taken into account. The model is applied to pentane bubble growth. The influence of the gap size, the initial temperature of the system, the thermal effusivity of the heated wall and the kinetic limit of vaporisation are studied. The results show that the expansion of the bubbles strongly depends on the gap size and can be affected by the effusivity of the material. Mechanical inertia effects are mainly dominant at the beginning of the bubble expansion. Pressure drop induced by viscous effects have to be taken into account for high capillary numbers. Heat transfers at the meniscus are negligible except at the early stages of the bubble growth. (author)

  14. Turbulent shear control with oscillatory bubble injection

    International Nuclear Information System (INIS)

    Park, Hyun Jin; Oishi, Yoshihiko; Tasaka, Yuji; Murai, Yuichi; Takeda, Yasushi

    2009-01-01

    It is known that injecting bubbles into shear flow can reduce the frictional drag. This method has advantages in comparison to others in simplicity of installation and also in environment. The amount of drag reduction by bubbles depends on the void fraction provided in the boundary layer. It means, however, that certain power must be consumed to generate bubbles in water, worsening the total power-saving performance. We propose oscillatory bubble injection technique to improve the performance in this study. In order to prove this idea of new type of drag reduction, velocity vector field and shear stress profile in a horizontal channel flow are measured by ultrasonic velocity profiler (UVP) and shear stress transducer, respectively. We measure the gas-liquid interface from the UVP signal, as well. This compound measurement with different principles leads to deeper understanding of bubble-originated drag reduction phenomena, in particular for unsteady process of boundary layer alternation. At these experiments, the results have demonstrated that the intermittency promotes the drag reduction more than normal continuous injection for the same void fraction supplied.

  15. LHCb experience with LFC replication

    International Nuclear Information System (INIS)

    Bonifazi, F; Carbone, A; D'Apice, A; Dell'Agnello, L; Re, G L; Martelli, B; Ricci, P P; Sapunenko, V; Vitlacil, D; Perez, E D; Duellmann, D; Girone, M; Peco, G; Vagnoni, V

    2008-01-01

    Database replication is a key topic in the framework of the LHC Computing Grid to allow processing of data in a distributed environment. In particular, the LHCb computing model relies on the LHC File Catalog, i.e. a database which stores information about files spread across the GRID, their logical names and the physical locations of all the replicas. The LHCb computing model requires the LFC to be replicated at Tier-1s. The LCG 3D project deals with the database replication issue and provides a replication service based on Oracle Streams technology. This paper describes the deployment of the LHC File Catalog replication to the INFN National Center for Telematics and Informatics (CNAF) and to other LHCb Tier-1 sites. We performed stress tests designed to evaluate any delay in the propagation of the streams and the scalability of the system. The tests show the robustness of the replica implementation with performance going much beyond the LHCb requirements

  16. LHCb experience with LFC replication

    CERN Document Server

    Bonifazi, F; Perez, E D; D'Apice, A; dell'Agnello, L; Düllmann, D; Girone, M; Re, G L; Martelli, B; Peco, G; Ricci, P P; Sapunenko, V; Vagnoni, V; Vitlacil, D

    2008-01-01

    Database replication is a key topic in the framework of the LHC Computing Grid to allow processing of data in a distributed environment. In particular, the LHCb computing model relies on the LHC File Catalog, i.e. a database which stores information about files spread across the GRID, their logical names and the physical locations of all the replicas. The LHCb computing model requires the LFC to be replicated at Tier-1s. The LCG 3D project deals with the database replication issue and provides a replication service based on Oracle Streams technology. This paper describes the deployment of the LHC File Catalog replication to the INFN National Center for Telematics and Informatics (CNAF) and to other LHCb Tier-1 sites. We performed stress tests designed to evaluate any delay in the propagation of the streams and the scalability of the system. The tests show the robustness of the replica implementation with performance going much beyond the LHCb requirements.

  17. The cytoprotective enzyme heme oxygenase-1 suppresses Ebola virus replication.

    Science.gov (United States)

    Hill-Batorski, Lindsay; Halfmann, Peter; Neumann, Gabriele; Kawaoka, Yoshihiro

    2013-12-01

    Ebola virus (EBOV) is the causative agent of a severe hemorrhagic fever in humans with reported case fatality rates as high as 90%. There are currently no licensed vaccines or antiviral therapeutics to combat EBOV infections. Heme oxygenase-1 (HO-1), an enzyme that catalyzes the rate-limiting step in heme degradation, has antioxidative properties and protects cells from various stresses. Activated HO-1 was recently shown to have antiviral activity, potently inhibiting the replication of viruses such as hepatitis C virus and human immunodeficiency virus. However, the effect of HO-1 activation on EBOV replication remains unknown. To determine whether the upregulation of HO-1 attenuates EBOV replication, we treated cells with cobalt protoporphyrin (CoPP), a selective HO-1 inducer, and assessed its effects on EBOV replication. We found that CoPP treatment, pre- and postinfection, significantly suppressed EBOV replication in a manner dependent upon HO-1 upregulation and activity. In addition, stable overexpression of HO-1 significantly attenuated EBOV growth. Although the exact mechanism behind the antiviral properties of HO-1 remains to be elucidated, our data show that HO-1 upregulation does not attenuate EBOV entry or budding but specifically targets EBOV transcription/replication. Therefore, modulation of the cellular enzyme HO-1 may represent a novel therapeutic strategy against EBOV infection.

  18. Structural disorder in proteins of the rhabdoviridae replication complex.

    Science.gov (United States)

    Leyrat, Cédric; Gérard, Francine C A; de Almeida Ribeiro, Euripedes; Ivanov, Ivan; Ruigrok, Rob W H; Jamin, Marc

    2010-08-01

    Rhabdoviridae are single stranded negative sense RNA viruses. The viral RNA condensed by the nucleoprotein (N), the phosphoprotein (P) and the large subunit (L) of the RNA-dependent RNA polymerase are the viral components of the transcription/replication machineries. Both P and N contain intrinsically disordered regions (IDRs) that play different roles in the virus life cycle. Here, we describe the modular organization of P based on recent structural, biophysical and bioinformatics data. We show how flexible loops in N participate in the attachment of P to the N-RNA template by an induced-fit mechanism. Finally, we discuss the roles of IDRs in the mechanism of replication/transcription, and propose a new model for the interaction of the L subunit with its N-RNA template.

  19. Modelling of boiling bubbly flows using a polydisperse approach

    International Nuclear Information System (INIS)

    Zaepffel, D.

    2011-01-01

    The objective of this work was to improve the modelling of boiling bubbly flows.We focused on the modelling of the polydisperse aspect of a bubble population, i.e. the fact that bubbles have different sizes and different velocities. The multi-size aspect of a bubble population can originate from various mechanisms. For the bubbly flows we are interested in, bubble coalescence, bubble break-up, phase change kinematics and/or gas compressibility inside the bubbles can be mentioned. Since, bubble velocity depends on bubble size, the bubble size spectrum also leads to a bubble velocity spectrum. An averaged model especially dedicated to dispersed flows is introduced in this thesis. Closure of averaged interphase transfer terms are written in a polydisperse framework, i.e. using a distribution function of the bubble sizes and velocities. A quadratic law and a cubic law are here proposed for the modelling of the size distribution function, whose evolution in space and time is then obtained with the use of the moment method. Our averaged model has been implemented in the NEPTUNE-CFD computation code in order to simulate the DEBORA experiment. The ability of our model to deal with sub-cooled boiling flows has therefore been evaluated. (author) [fr

  20. The bubble method of water purification

    Science.gov (United States)

    Smirnov, B. M.; Babaeva, N. Yu.; Naidis, G. V.; Panov, V. A.; Saveliev, A. S.; Son, E. E.; Tereshonok, D. V.

    2018-02-01

    The processes of water purification from admixture molecules are analyzed. The purification rate is limited due to a low diffusion coefficient of the admixture molecules in water. At non-small concentrations of the admixture molecules, the water purication can proceed through association of molecules in condensed nanoparticles which fall on the bottom of the water volume. The rate of association may be increased in an external electric field, but in reality this cannot change significantly the rate of the purification process. The bubble method of water purification is considered, where air bubbles formed at the bottom of the water volume, transfer admixture molecules to the interface. This method allows one to clean small water volumes fast. This mechanism of water purification is realized experimentally and exhibits the promises of the bubble purification method.

  1. Bubbles, sparks, and the postwar laboratory

    International Nuclear Information System (INIS)

    Galison, P.

    1989-01-01

    The development and use of bubble chambers and spark chambers in the 1950s form the main thrust of this article, the bubble chamber as an example of ''image-producing'' instruments and the spark chamber as a ''logic'' device. Work on a cloud chamber by Glaser led to the development of the bubble chamber detector using liquid hydrogen, which was later linked to a computer for accurate automatic track analysis. It made possible demonstrations of the existence of a particle or interaction. Spark chambers were easier to build and so soon became common, various types being developed across the world. The development of spark chambers originated in the need for timing devices for the Manhattan Project, but work on their design occurred in a number of units worldwide. (UK)

  2. Bubble and Drop Nonlinear Dynamics experiment

    Science.gov (United States)

    2003-01-01

    The Bubble and Drop Nonlinear Dynamics (BDND) experiment was designed to improve understanding of how the shape and behavior of bubbles respond to ultrasound pressure. By understanding this behavior, it may be possible to counteract complications bubbles cause during materials processing on the ground. This 12-second sequence came from video downlinked from STS-94, July 5 1997, MET:3/19:15 (approximate). The BDND guest investigator was Gary Leal of the University of California, Santa Barbara. The experiment was part of the space research investigations conducted during the Microgravity Science Laboratory-1R mission (STS-94, July 1-17 1997). Advanced fluid dynamics experiments will be a part of investigations plarned for the International Space Station. (189KB JPEG, 1293 x 1460 pixels; downlinked video, higher quality not available) The MPG from which this composite was made is available at http://mix.msfc.nasa.gov/ABSTRACTS/MSFC-0300163.html.

  3. ON THE ANALYSIS OF BUBBLE CHAMBER TRACKS

    International Nuclear Information System (INIS)

    Bradner, H.; Solmitz, F.

    1958-01-01

    Since its invention by Glaser in 1953, the bubble chamber has become a most valuable tool in high-energy physics. It combines a number of advantages of various older methods of particle detection: it offers high spatial resolution, rapid accumulation of data, some time resolution, and some choice of the nucleus whose interaction one wants to study (bubble chambers have been made to operate with a large number of different liquids, including H 2 , D 2 , He, Xe, and several hydrocarbons). In order to exploit the advantages of spatial resolution and rapid data accumulation, high-speed high-precision analysis procedures must be developed. In this article they discuss some of the problems posed by such analysis. The discussion is based largely on experience gained in performing hydrogen bubble chamber experiments with the University of California's Bevatron (6-Bev proton synchrotron)

  4. Bubbles, shocks and elementary technical trading strategies

    Science.gov (United States)

    Fry, John

    2014-01-01

    In this paper we provide a unifying framework for a set of seemingly disparate models for bubbles, shocks and elementary technical trading strategies in financial markets. Markets operate by balancing intrinsic levels of risk and return. This seemingly simple observation is commonly over-looked by academics and practitioners alike. Our model shares its origins in statistical physics with others. However, under our approach, changes in market regime can be explicitly shown to represent a phase transition from random to deterministic behaviour in prices. This structure leads to an improved physical and econometric model. We develop models for bubbles, shocks and elementary technical trading strategies. The list of empirical applications is both interesting and topical and includes real-estate bubbles and the on-going Eurozone crisis. We close by comparing the results of our model with purely qualitative findings from the finance literature.

  5. Experimental investigation of bubble plume structure instability

    Energy Technology Data Exchange (ETDEWEB)

    Marco Simiano; Robert Zboray; Francois de Cachard [Thermal-Hydraulics Laboratory, Paul Scherrer Institut, 5232 Villigen PSI (Switzerland); Djamel Lakehal; George Yadigaroglu [Institute of Energy Technology, Swiss Federal Institute of Technology, ETH-Zentrum/CLT, 8092 Zurich (Switzerland)

    2005-07-01

    Full text of publication follows: The hydrodynamic properties of a 3D bubble plume in a large water pool are investigated experimentally. Bubble plumes are present in various industrial processes, including chemical plants, stirred reactors, and nuclear power plants, e.g. in BWR suppression pools. In these applications, the main issue is to predict the currents induced by the bubbles in the liquid phase, and to determine the consequent mixing. Bubble plumes, especially large and unconfined ones, present strong 3D effects and a superposition of different characteristic length scales. Thus, they represent relevant test cases for assessment and verification of 3D models in thermal-hydraulic codes. Bubble plumes are often unsteady, with fluctuations in size and shape of the bubble swarm, and global movements of the plume. In this case, local time-averaged data are not sufficient to characterize the flow. Additional information regarding changes in plume shape and position is required. The effect of scale on the 3D flow structure and stability being complex, there was a need to conduct studies in a fairly large facility, closer to industrial applications. Air bubble plumes, up to 30 cm in base diameter and 2 m in height were extensively studied in a 2 m diameter water pool. Homogeneously sized bubbles were obtained using a particular injector. The main hydrodynamic parameters. i.e., gas and liquid velocities, void fraction, bubble shape and size, plume shape and position, were determined experimentally. Photographic and image processing techniques were used to characterize the bubble shape, and double-tip optical probes to measure bubble size and void fraction. Electromagnetic probes measured the recirculation velocity in the pool. Simultaneous two-phase flow particle image velocimetry (STPFPIV) in a vertical plane containing the vessel axis provided instantaneous velocity fields for both phases and therefore the relative velocity field. Video recording using two CCD

  6. Rational speculative bubbles: A critical view

    Directory of Open Access Journals (Sweden)

    Radonjić Ognjen

    2007-01-01

    Full Text Available According to the theory of rational bubbles, the bubble is present whenever asset prices progressively diverge from their fundamental value, which occurs because agents expect that asset prices will continue to grow exponentially (self-fulfilling prophecies far in the future and consistently, which promises the realization of ever larger capital gains. In our opinion, the basic shortcoming of this theory refers to the assumption that all market agents are perfectly informed and rational and, accordingly, form homogeneous expectations. The model does not explain decision-making processes or expectation formation, nor does it detect potential psychological and institutional factors that might significantly influence decision making processes and market participants’ reactions to news. Since assumptions of the model critically determine its validity, we conclude that comprehensiveness of the rational bubble model is, to put it mildly, limited.

  7. Toward a Metatheory of Economic Bubbles

    DEFF Research Database (Denmark)

    Dholakia, Nikhilesh; Turcan, Romeo V.

    Dholakia and Turcan present their interdisciplinary metatheory of bubbles with short case studies of minor and major bubbles. They comprehensively identify and exemplify constructs of the theory, set its temporal and contextual boundaries, and examine the underlying economic, psychological......, and social dynamics assumptions, explaining how these elements are related. By doing so, they provide a partial window into the precarious nature of contemporary finance-driven capitalism and suggest some possible ways of overcoming the wrenching ups and downs of the prevalent system. The case studies...... and original research in Toward a Metatheory of Economic Bubbles have far-reaching implications for the study and practice of entrepreneurship and marketing, public and corporate finance, and public policies towards innovation, economy, and finance. It contributes to the defining issues for economic sociology...

  8. Gas and vapor bubble growth and collapse

    International Nuclear Information System (INIS)

    Bonnin, J.; Reali, M.; Sardella, L.

    1976-01-01

    The rate of growth or collapse of a spherical bubble of gas or vapor under the effect of a nonequilibrium with the ambient liquid can be expressed in terms of generalized parameters taking into account either mass or heat diffusion. Diffusion equations have been solved either by numerical computation or under the form of a asymptotical solution, for a growing bubble only and with a constant nonequilibrium. Solutions are compared between them and with already published ones. Experimental results obtained match with a unique nonequilibrium parameter, analogous to a Jacob number. Discrepancies with asymptotical solutions can require in some cases complete numerical computation. But taking into account convection due to bubble lift will require a more sophisticated numerical computation [fr

  9. NACSA Charter School Replication Guide: The Spectrum of Replication Options. Authorizing Matters. Replication Brief 1

    Science.gov (United States)

    O'Neill, Paul

    2010-01-01

    One of the most important and high-profile issues in public education reform today is the replication of successful public charter school programs. With more than 5,000 failing public schools in the United States, there is a tremendous need for strong alternatives for parents and students. Replicating successful charter school models is an…

  10. pUL34 binding near the human cytomegalovirus origin of lytic replication enhances DNA replication and viral growth.

    Science.gov (United States)

    Slayton, Mark; Hossain, Tanvir; Biegalke, Bonita J

    2018-05-01

    The human cytomegalovirus (HCMV) UL34 gene encodes sequence-specific DNA-binding proteins (pUL34) which are required for viral replication. Interactions of pUL34 with DNA binding sites represses transcription of two viral immune evasion genes, US3 and US9. 12 additional predicted pUL34-binding sites are present in the HCMV genome (strain AD169) with three binding sites concentrated near the HCMV origin of lytic replication (oriLyt). We used ChIP-seq analysis of pUL34-DNA interactions to confirm that pUL34 binds to the oriLyt region during infection. Mutagenesis of the UL34-binding sites in an oriLyt-containing plasmid significantly reduced viral-mediated oriLyt-dependent DNA replication. Mutagenesis of these sites in the HCMV genome reduced the replication efficiencies of the resulting viruses. Protein-protein interaction analyses demonstrated that pUL34 interacts with the viral proteins IE2, UL44, and UL84, that are essential for viral DNA replication, suggesting that pUL34-DNA interactions in the oriLyt region are involved in the DNA replication cascade. Copyright © 2018 Elsevier Inc. All rights reserved.

  11. Megabase replication domains along the human genome: relation to chromatin structure and genome organisation.

    Science.gov (United States)

    Audit, Benjamin; Zaghloul, Lamia; Baker, Antoine; Arneodo, Alain; Chen, Chun-Long; d'Aubenton-Carafa, Yves; Thermes, Claude

    2013-01-01

    In higher eukaryotes, the absence of specific sequence motifs, marking the origins of replication has been a serious hindrance to the understanding of (i) the mechanisms that regulate the spatio-temporal replication program, and (ii) the links between origins activation, chromatin structure and transcription. In this chapter, we review the partitioning of the human genome into megabased-size replication domains delineated as N-shaped motifs in the strand compositional asymmetry profiles. They collectively span 28.3% of the genome and are bordered by more than 1,000 putative replication origins. We recapitulate the comparison of this partition of the human genome with high-resolution experimental data that confirms that replication domain borders are likely to be preferential replication initiation zones in the germline. In addition, we highlight the specific distribution of experimental and numerical chromatin marks along replication domains. Domain borders correspond to particular open chromatin regions, possibly encoded in the DNA sequence, and around which replication and transcription are highly coordinated. These regions also present a high evolutionary breakpoint density, suggesting that susceptibility to breakage might be linked to local open chromatin fiber state. Altogether, this chapter presents a compartmentalization of the human genome into replication domains that are landmarks of the human genome organization and are likely to play a key role in genome dynamics during evolution and in pathological situations.

  12. A large bubble around the Crab Nebula

    Science.gov (United States)

    Romani, Roger W.; Reach, William T.; Koo, Bon Chul; Heiles, Carl

    1990-01-01

    IRAS and 21 cm observations of the interstellar medium around the Crab nebula show evidence of a large bubble surrounded by a partial shell. If located at the canonical 2 kpc distance of the Crab pulsar, the shell is estimated to have a radius of about 90 pc and to contain about 50,000 solar masses of swept-up gas. The way in which interior conditions of this bubble can have important implications for observations of the Crab are described, and the fashion in which presupernova evolution of the pulsar progenitor has affected its local environment is described.

  13. On the maximum drawdown during speculative bubbles

    Science.gov (United States)

    Rotundo, Giulia; Navarra, Mauro

    2007-08-01

    A taxonomy of large financial crashes proposed in the literature locates the burst of speculative bubbles due to endogenous causes in the framework of extreme stock market crashes, defined as falls of market prices that are outlier with respect to the bulk of drawdown price movement distribution. This paper goes on deeper in the analysis providing a further characterization of the rising part of such selected bubbles through the examination of drawdown and maximum drawdown movement of indices prices. The analysis of drawdown duration is also performed and it is the core of the risk measure estimated here.

  14. Bubble chamber: Omega production and decay

    CERN Multimedia

    1973-01-01

    This image is of real particle tracks taken from the CERN 2 m liquid hydrogen bubble chamber and shows the production and decay of a negative omega particle. A negative kaon enters the chamber which decays into many particles, including a negative omega that travels a short distance before decaying into more particles. The invention of bubble chambers in 1952 revolutionized the field of particle physics, allowing real tracks left by particles to be seen and photographed by expanding liquid that had been heated to boiling point.

  15. Bubbling in delay-coupled lasers.

    Science.gov (United States)

    Flunkert, V; D'Huys, O; Danckaert, J; Fischer, I; Schöll, E

    2009-06-01

    We theoretically study chaos synchronization of two lasers which are delay coupled via an active or a passive relay. While the lasers are synchronized, their dynamics is identical to a single laser with delayed feedback for a passive relay and identical to two delay-coupled lasers for an active relay. Depending on the coupling parameters the system exhibits bubbling, i.e., noise-induced desynchronization, or on-off intermittency. We associate the desynchronization dynamics in the coherence collapse and low-frequency fluctuation regimes with the transverse instability of some of the compound cavity's antimodes. Finally, we demonstrate how, by using an active relay, bubbling can be suppressed.

  16. Bubble dynamics in a superheated liquid

    International Nuclear Information System (INIS)

    Sha, W.T.; Shah, V.L.

    1977-09-01

    The report presents an extensive literature survey on bubble dynamics. Growth of a single spherical bubble moving in a uniformly superheated liquid is considered. Equations of motion and energy are presented in the forms that take into consideration the interaction between the motion and the growth. The fourth-order Runge-Kutta method is used to obtain a simultaneous solution of equations of motion and growth rate, and the solution is compared with available experimental results. Results for liquid sodium are presented for a range of pressures and Jakob numbers

  17. Resolving single bubble sonoluminescence flask width

    OpenAIRE

    Arakeri, Vijay H

    1998-01-01

    Single bubble sonoluminescence (SBSL), first studied and observed by Gaitan et al., is the of light emission from a single gas bubble trapped at the pressure maximum of a resonant sound field in a liquid medium, generally water. One of the most striking aspects of SBSL was the estimated optical flash width being less than 50 picoseconds (ps)3; this upper estimate was based on the relative response of a SBSL flash in comparison to a 34 ps laser pulse using a microchannel platephotomultiplier ...

  18. Vapor bubble growth in highly superheated liquid

    International Nuclear Information System (INIS)

    Pavlov, P.A.

    1981-01-01

    Dynamics of the bubble growth in the volume of the uniformally superheated liquid is considered. It is supposed that its growth is hampered by heat transfer. An asymptotic expression for the bubble growth rate at high superheatings when heat hold by liquid is comparable with heat of steam formation, is found by the automodel solution of the heat transfer equation. Writing the radius square in the form of a functional applicable for the calculation of steam formation at the pressure change in superheated liquid is suggested for eveluation calculations [ru

  19. Partial coalescence from bubbles to drops

    KAUST Repository

    Zhang, F. H.

    2015-10-07

    The coalescence of drops is a fundamental process in the coarsening of emulsions. However, counter-intuitively, this coalescence process can produce a satellite, approximately half the size of the original drop, which is detrimental to the overall coarsening. This also occurs during the coalescence of bubbles, while the resulting satellite is much smaller, approximately 10 %. To understand this difference, we have conducted a set of coalescence experiments using xenon bubbles inside a pressure chamber, where we can continuously raise the pressure from 1 up to 85 atm and thereby vary the density ratio between the inner and outer fluid, from 0.005 up to unity. Using high-speed video imaging, we observe a continuous increase in satellite size as the inner density is varied from the bubble to emulsion-droplet conditions, with the most rapid changes occurring as the bubble density grows up to 15 % of that of the surrounding liquid. We propose a model that successfully relates the satellite size to the capillary wave mode responsible for its pinch-off and the overall deformations from the drainage. The wavelength of the primary wave changes during its travel to the apex, with the instantaneous speed adjusting to the local wavelength. By estimating the travel time of this wave mode on the bubble surface, we also show that the model is consistent with the experiments. This wavenumber is determined by both the global drainage as well as the interface shapes during the rapid coalescence in the neck connecting the two drops or bubbles. The rate of drainage is shown to scale with the density of the inner fluid. Empirically, we find that the pinch-off occurs when 60 % of the bubble fluid has drained from it. Numerical simulations using the volume-of-fluid method with dynamic adaptive grid refinement can reproduce these dynamics, as well as show the associated vortical structure and stirring of the coalescing fluid masses. Enhanced stirring is observed for cases with second

  20. Structural Basis of Mitochondrial Transcription Initiation.

    Science.gov (United States)

    Hillen, Hauke S; Morozov, Yaroslav I; Sarfallah, Azadeh; Temiakov, Dmitry; Cramer, Patrick

    2017-11-16

    Transcription in human mitochondria is driven by a single-subunit, factor-dependent RNA polymerase (mtRNAP). Despite its critical role in both expression and replication of the mitochondrial genome, transcription initiation by mtRNAP remains poorly understood. Here, we report crystal structures of human mitochondrial transcription initiation complexes assembled on both light and heavy strand promoters. The structures reveal how transcription factors TFAM and TFB2M assist mtRNAP to achieve promoter-dependent initiation. TFAM tethers the N-terminal region of mtRNAP to recruit the polymerase to the promoter whereas TFB2M induces structural changes in mtRNAP to enable promoter opening and trapping of the DNA non-template strand. Structural comparisons demonstrate that the initiation mechanism in mitochondria is distinct from that in the well-studied nuclear, bacterial, or bacteriophage transcription systems but that similarities are found on the topological and conceptual level. These results provide a framework for studying the regulation of gene expression and DNA replication in mitochondria. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Cyclophilin B facilitates the replication of Orf virus.

    Science.gov (United States)

    Zhao, Kui; Li, Jida; He, Wenqi; Song, Deguang; Zhang, Ximu; Zhang, Di; Zhou, Yanlong; Gao, Feng

    2017-06-15

    Viruses interact with host cellular factors to construct a more favourable environment for their efficient replication. Expression of cyclophilin B (CypB), a cellular peptidyl-prolyl cis-trans isomerase (PPIase), was found to be significantly up-regulated. Recently, a number of studies have shown that CypB is important in the replication of several viruses, including Japanese encephalitis virus (JEV), hepatitis C virus (HCV) and human papillomavirus type 16 (HPV 16). However, the function of cellular CypB in ORFV replication has not yet been explored. Suppression subtractive hybridization (SSH) technique was applied to identify genes differentially expressed in the ORFV-infected MDBK cells at an early phase of infection. Cellular CypB was confirmed to be significantly up-regulated by quantitative reverse transcription-PCR (qRT-PCR) analysis and Western blotting. The role of CypB in ORFV infection was further determined using Cyclosporin A (CsA) and RNA interference (RNAi). Effect of CypB gene silencing on ORFV replication by 50% tissue culture infectious dose (TCID 50 ) assay and qRT-PCR detection. In the present study, CypB was found to be significantly up-regulated in the ORFV-infected MDBK cells at an early phase of infection. Cyclosporin A (CsA) exhibited suppressive effects on ORFV replication through the inhibition of CypB. Silencing of CypB gene inhibited the replication of ORFV in MDBK cells. In conclusion, these data suggest that CypB is critical for the efficient replication of the ORFV genome. Cellular CypB was confirmed to be significantly up-regulated in the ORFV-infected MDBK cells at an early phase of infection, which could effectively facilitate the replication of ORFV.

  2. Direct numerical simulation of turbulent channel flow with deformed bubbles

    International Nuclear Information System (INIS)

    Yamamoto, Yoshinobu; Kunugi, Tomoaki

    2010-01-01

    In this study, the direct numerical simulation of a fully-developed turbulent channel flow with deformed bubbles were conducted by means of the refined MARS method, turbulent Reynolds number 150, and Bubble Reynolds number 120. As the results, large-scale wake motions were observed round the bubbles. At the bubble located region, mean velocity was degreased and turbulent intensities and Reynolds shear stress were increased by the effects of the large-scale wake motions round bubbles. On the other hands, near wall region, bubbles might effect on the flow laminarlize and drag reduction. Two types of drag coefficient of bubble were estimated from the accelerated velocity of bubble and correlation equation as a function of Particle Reynolds number. Empirical correlation equation might be overestimated the drag effects in this Particle Reynolds number range. (author)

  3. A note on effects of rational bubble on portfolios

    Science.gov (United States)

    Wang, Chan; Nie, Pu-yan

    2018-02-01

    In general, demand increases in wealth and decreases in price in microeconomics. We thereby propose a completely different perspective. By establishing expected utility function of investors, this article introduces one rational bubble asset and one bubble free asset in portfolios and focuses on the effects of bubble on investment portfolios from wealth and price perspectives. All conclusions are obtained by theoretical analysis with microeconomics theory. We argue that inferior goods and Giffen behavior can occur for the bubble free asset in microeconomic fields. The results can help investors to recognize bubble assets and bubble free assets more scientifically. Both bubble and bubble free assets can be inferior goods under some conditions, so we cannot to say which asset better than the other one absolutely.

  4. Motion of air bubbles in stagnant water condition

    International Nuclear Information System (INIS)

    Bezdegumeli, U.; Ozdemir, S.; Yesin, O.

    2004-01-01

    Full text: In this study, air bubble motion in stagnant water condition in a vertical pipe is investigated experimentally. For this purpose, a test set-up was designed and constructed. Motions of single bubbles, having different diameters in the range of 3.0-4.8 mm, were recorded by using a monochrome camera, an image capture card and a PC. Recorded video images were processed to analyse bubble motion and to obtain the necessary data. The purpose of the study is to determine the variation of bubble axial velocity and bubble drag coefficient as a function of equivalent bubble diameter and bubble Reynolds number, Re b . Therefore, detailed information for this range of bubble diameters was obtained. The results have shown good consistency with the previous studies found in the literature

  5. Motion of air bubbles in stagnant water condition

    International Nuclear Information System (INIS)

    Bezdegumeli, U.; Ozdemir, S.; Yesin, O.

    2004-01-01

    In this study, air bubble motion in stagnant water condition in a vertical pipe of 4.6 cm diameter is investigated experimentally. For this purpose, a test set-up was designed and constructed. Motions of single bubbles, having different diameters in the range of 3.0-4.8 mm, were recorded by using a monochrome camera, an image capture card and a PC. Recorded video images were processed to analyse bubble motion and to obtain the necessary data. The purpose of the study is to determine the variation of bubble axial velocity and bubble drag coefficient as a function of equivalent bubble diameter and bubble Reynolds number, Re b . Therefore, detailed information for this range of bubble diameters was obtained. The results have shown good consistency with the previous studies found in the literature. (author)

  6. High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins

    Directory of Open Access Journals (Sweden)

    Federico Comoglio

    2015-05-01

    Full Text Available At every cell cycle, faithful inheritance of metazoan genomes requires the concerted activation of thousands of DNA replication origins. However, the genetic and chromatin features defining metazoan replication start sites remain largely unknown. Here, we delineate the origin repertoire of the Drosophila genome at high resolution. We address the role of origin-proximal G-quadruplexes and suggest that they transiently stall replication forks in vivo. We dissect the chromatin configuration of replication origins and identify a rich spatial organization of chromatin features at initiation sites. DNA shape and chromatin configurations, not strict sequence motifs, mark and predict origins in higher eukaryotes. We further examine the link between transcription and origin firing and reveal that modulation of origin activity across cell types is intimately linked to cell-type-specific transcriptional programs. Our study unravels conserved origin features and provides unique insights into the relationship among DNA topology, chromatin, transcription, and replication initiation across metazoa.

  7. HSV-1 Remodels Host Telomeres to Facilitate Viral Replication

    Directory of Open Access Journals (Sweden)

    Zhong Deng

    2014-12-01

    Full Text Available Telomeres protect the ends of cellular chromosomes. We show here that infection with herpes simplex virus 1 (HSV-1 results in chromosomal structural aberrations at telomeres and the accumulation of telomere dysfunction-induced DNA damage foci (TIFs. At the molecular level, HSV-1 induces transcription of telomere repeat-containing RNA (TERRA, followed by the proteolytic degradation of the telomere protein TPP1 and loss of the telomere repeat DNA signal. The HSV-1-encoded E3 ubiquitin ligase ICP0 is required for TERRA transcription and facilitates TPP1 degradation. Small hairpin RNA (shRNA depletion of TPP1 increases viral replication, indicating that TPP1 inhibits viral replication. Viral replication protein ICP8 forms foci that coincide with telomeric proteins, and ICP8-null virus failed to degrade telomere DNA signal. These findings suggest that HSV-1 reorganizes telomeres to form ICP8-associated prereplication foci and to promote viral genomic replication.

  8. Real-time observation of the initiation of RNA polymerase II transcription.

    Science.gov (United States)

    Fazal, Furqan M; Meng, Cong A; Murakami, Kenji; Kornberg, Roger D; Block, Steven M

    2015-09-10

    Biochemical and structural studies have shown that the initiation of RNA polymerase II transcription proceeds in the following stages: assembly of the polymerase with general transcription factors and promoter DNA in a 'closed' preinitiation complex (PIC); unwinding of about 15 base pairs of the promoter DNA to form an 'open' complex; scanning downstream to a transcription start site; synthesis of a short transcript, thought to be about 10 nucleotides long; and promoter escape. Here we have assembled a 32-protein, 1.5-megadalton PIC derived from Saccharomyces cerevisiae, and observe subsequent initiation processes in real time with optical tweezers. Contrary to expectation, scanning driven by the transcription factor IIH involved the rapid opening of an extended transcription bubble, averaging 85 base pairs, accompanied by the synthesis of a transcript up to the entire length of the extended bubble, followed by promoter escape. PICs that failed to achieve promoter escape nevertheless formed open complexes and extended bubbles, which collapsed back to closed or open complexes, resulting in repeated futile scanning.

  9. A three field two fluid CFD model for the bubbly-cap bubble regime

    International Nuclear Information System (INIS)

    Martin Lopez de Bertodano; Xiaodong Sun; Mamoru Ishii; Asim Ulke

    2005-01-01

    Full text of publication follows: The lateral phase distribution of a two phase duct flow in the cap bubble regime is analyzed with a three dimensional three field two-fluid CFD model based on the turbulent k-ε model for bubbly flows developed by Lopez de Bertodano et. al. [2]. The turbulent diffusion of the bubbles is the dominant phase distribution mechanism. A new analytic result is presented to support the development of the model for the bubble induced turbulent diffusion force. New experimental data obtained with a state-of-the-art four sensor miniature conductivity probe are used to validate the two-fluid model. The focus of this work is modeling the transport of the dispersed phase. Previous work (e.g., Lopez de Bertodano et. al.) was focused on the interfacial forces of drag, lift and virtual mass. However, the dispersion of the bubbles by the turbulent eddies of the continuous phase must be considered too. The rigorous formulation of a model for the turbulent dispersion of the bubbles results in a turbulent diffusion force which is obtained from a probability distribution function average (i.e., Boltzmann averaging) of the dispersed phase momentum equation. This force was recently applied to a turbulent bubbly jet with small bubbles (i.e., 1 mm diameter) without adjusting any coefficient. However, the application of this force to industrial conditions (i.e., larger bubbles) requires specific two-phase flow experimental data to calibrate the model due to the uncertainties of the flow around large bubbles. In particular the void distribution and the interfacial area concentration are measured in a mixture of big and small bubbles. The state-of-the-art miniaturized four-sensor conductivity probe developed by Kim et al. [3] is used to obtain the interfacial area concentration in complex two-phase flow situations. This probe can discriminate between small and large bubbles so it offers an opportunity to perform further developments of the multidimensional two

  10. Implementation of Serial and Parallel Bubble Sort on Fpga

    OpenAIRE

    Purnomo, Dwi Marhaendro Jati; Arinaldi, Ahmad; Priyantini, Dwi Teguh; Wibisono, Ari; Febrian, Andreas

    2016-01-01

    Sorting is common process in computational world. Its utilization are on many fields from research to industry. There are many sorting algorithm in nowadays. One of the simplest yet powerful is bubble sort. In this study, bubble sort is implemented on FPGA. The implementation was taken on serial and parallel approach. Serial and parallel bubble sort then compared by means of its memory, execution time, and utility which comprises slices and LUTs. The experiments show that serial bubble sort r...

  11. Negative wake behind bubbles in non-newtonian liquids

    DEFF Research Database (Denmark)

    Hassager, Ole

    1979-01-01

    Gas bubbles rising by gravity in non-Newtonian elastic liquids are different to gas bubbles in viscous Newtonian fluids in at least two ways. First, the bubbles in the non-Newtonian liquids often have a peculiar tip at the rear pole, and second, the terminal rise velocity versus volume curve ofte...

  12. Gas pressure in bubble attached to tube circular outlet

    OpenAIRE

    Salonen, A; Gay, Cyprien; Maestro, A; Drenckhan, W; Rio, Emmanuelle

    2016-01-01

    In the present Supplementary notes to our work ``Arresting bubble coarsening: A two-bubble experiment to investigate grain growth in presence of surface elasticity'' (accepted in EPL), we derive the expression of the gas pressure inside a bubble located above and attached to the circular outlet of a vertical tube.

  13. The Milky Way Project: A Census of Small Bubbles

    Science.gov (United States)

    Arvidsson, Kim; Wolf-Chase, G. A.; Way Project, Milky

    2013-01-01

    The first data release (DR1) from the Milky Way Project (MWP) contains 1362 visually identified small bubbles drawn by users. These small infrared bubbles typically have diameters MSX6C point source catalog; >90% of all small bubbles are MSX point sources.

  14. Adhesion of solid particles to gas bubbles. Part 2: Experimental

    NARCIS (Netherlands)

    Omota, Florin; Dimian, Alexandre C.; Bliek, A.

    2006-01-01

    In slurry bubble columns, the adhesion of solid catalyst particles to bubbles may significantly affect the G–L mass transfer and bubble size distribution. This feature may be exploited in design by modifying the hydrophilic or hydrophobic nature of the particles used. Previously we have proposed a

  15. Optical measurement of bubbles: System design and application

    NARCIS (Netherlands)

    Leifer, I.; Leeuw, G.de; Cohen, L.H.

    2003-01-01

    Affordable high quality charge-coupled device (CCD) video cameras and image processing software are powerful tools for bubble measurements. Because of the wide variation between bubble populations, different bubble measurement systems (BMSs) are required depending upon the application. Two BMSs are

  16. Numerical simulation of single bubble dynamics under acoustic travelling waves.

    Science.gov (United States)

    Ma, Xiaojian; Huang, Biao; Li, Yikai; Chang, Qing; Qiu, Sicong; Su, Zheng; Fu, Xiaoying; Wang, Guoyu

    2018-04-01

    The objective of this paper is to apply CLSVOF method to investigate the single bubble dynamics in acoustic travelling waves. The Naiver-Stokes equation considering the acoustic radiation force is proposed and validated to capture the bubble behaviors. And the CLSVOF method, which can capture the continuous geometric properties and satisfies mass conservation, is applied in present work. Firstly, the regime map, depending on the dimensionless acoustic pressure amplitude and acoustic wave number, is constructed to present different bubble behaviors. Then, the time evolution of the bubble oscillation is investigated and analyzed. Finally, the effect of the direction and the damping coefficient of acoustic wave propagation on the bubble behavior are also considered. The numerical results show that the bubble presents distinct oscillation types in acoustic travelling waves, namely, volume oscillation, shape oscillation, and splitting oscillation. For the splitting oscillation, the formation of jet, splitting of bubble, and the rebound of sub-bubbles may lead to substantial increase in pressure fluctuations on the boundary. For the shape oscillation, the nodes and antinodes of the acoustic pressure wave contribute to the formation of the "cross shape" of the bubble. It should be noted that the direction of the bubble translation and bubble jet are always towards the direction of wave propagation. In addition, the damping coefficient causes bubble in shape oscillation to be of asymmetry in shape and inequality in size, and delays the splitting process. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Bubbles as a means for the deaeration of water bodies

    NARCIS (Netherlands)

    Zhang, Yuhang; Zhou, Gedi; Prosperetti, Andrea

    2017-01-01

    Occasional dissolved-air supersaturation - such as may occur, for instance, downstream of dams - is harmful to fish because it causes gas bubble disease. A counterintuitive but effective means of reducing dissolved air content is the injection of bubbles in the supersaturated water. The bubbles

  18. Nasal continuous positive airway pressure: does bubbling improve gas exchange?

    Science.gov (United States)

    Morley, C J; Lau, R; De Paoli, A; Davis, P G

    2005-07-01

    In a randomised crossover trial, 26 babies, treated with Hudson prong continuous positive airway pressure (CPAP) from a bubbling bottle, received vigorous, high amplitude, or slow bubbling for 30 minutes. Pulse oximetry, transcutaneous carbon dioxide, and respiratory rate were recorded. The bubbling rates had no effect on carbon dioxide, oxygenation, or respiratory rate.

  19. A mathematical definition of the financial bubbles and crashes

    Science.gov (United States)

    Watanabe, Kota; Takayasu, Hideki; Takayasu, Misako

    2007-09-01

    We check the validity of the mathematical method of detecting financial bubbles or crashes, which is based on a data fitting with an exponential function. We show that the period of a bubble can be determined nearly uniquely independent of the precision of data. The method is widely applicable for stock market data such as the Internet bubble.

  20. Air bubble migration is a random event post embryo transfer.

    Science.gov (United States)

    Confino, E; Zhang, J; Risquez, F

    2007-06-01

    Air bubble location following embryo transfer (ET) is the presumable placement spot of embryos. The purpose of this study was to document endometrial air bubble position and migration following embryo transfer. Multicenter prospective case study. Eighty-eight embryo transfers were performed under abdominal ultrasound guidance in two countries by two authors. A single or double air bubble was loaded with the embryos using a soft, coaxial, end opened catheters. The embryos were slowly injected 10-20 mm from the fundus. Air bubble position was recorded immediately, 30 minutes later and when the patient stood up. Bubble marker location analysis revealed a random distribution without visible gravity effect when the patients stood up. The bubble markers demonstrated splitting, moving in all directions and dispersion. Air bubbles move and split frequently post ET with the patient in the horizontal position, suggestive of active uterine contractions. Bubble migration analysis supports a rather random movement of the bubbles and possibly the embryos. Standing up changed somewhat bubble configuration and distribution in the uterine cavity. Gravity related bubble motion was uncommon, suggesting that horizontal rest post ET may not be necessary. This report challenges the common belief that a very accurate ultrasound guided embryo placement is mandatory. The very random bubble movement observed in this two-center study suggests that a large "window" of embryo placement maybe present.

  1. The interaction between multiple bubbles and the free surface

    International Nuclear Information System (INIS)

    Zhang Aman; Yao Xiongliang

    2008-01-01

    The flow is assumed to be potential, and a boundary integral method is used to solve the Laplace equation for the velocity potential to investigate the shape and the position of the bubble. A 3D code to study the bubble dynamics is developed, and the calculation results agree well with the experimental data. Numerical analyses are carried out for the interaction between multiple bubbles near the free surface including in-phase and out-of-phase bubbles. The calculation result shows that the bubble period increases with the decrease of the distance between bubble centres because of the depression effect between multiple bubbles. The depression has no relationship with the free surface and it is more apparent for out-of-phase bubbles. There are great differences in dynamic behaviour between the in-phase bubbles and the out-of-phase bubbles due to the depression effect. Furthermore, the interaction among eight bubbles is simulated with a three-dimensional model, and the evolving process and the relevant physical phenomena are presented. These phenomena can give a reference to the future work on the power of bubbles induced by multiple charges exploding simultaneously or continuously

  2. The transcriptional landscape

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2011-01-01

    The application of new and less biased methods to study the transcriptional output from genomes, such as tiling arrays and deep sequencing, has revealed that most of the genome is transcribed and that there is substantial overlap of transcripts derived from the two strands of DNA. In protein coding...... regions, the map of transcripts is very complex due to small transcripts from the flanking ends of the transcription unit, the use of multiple start and stop sites for the main transcript, production of multiple functional RNA molecules from the same primary transcript, and RNA molecules made...... by independent transcription from within the unit. In genomic regions separating those that encode proteins or highly abundant RNA molecules with known function, transcripts are generally of low abundance and short-lived. In most of these cases, it is unclear to what extent a function is related to transcription...

  3. Making continuous bubble type polyethylene foam incombustible

    International Nuclear Information System (INIS)

    Kaji, Kanako; Hatada, Motoyoshi; Yoshizawa, Iwao; Komai, Kuniaki; Kohara, Choji.

    1989-01-01

    Since continuous bubble type plastic foam has excellent compression characteristics and sound absorption characteristics, it has been widely used as cushion material, sealing material, sound insulating material and so on. However, the most part of plastic foam is taken by air, therefore at the time of fires, it becomes a very dangerous material. At present, the material used mostly as the seat cushions for airliners, railroad coaches, automobiles and others is polyurethane foam, but since it contains C-N couples in its molecules, it is feared to generate cyanic gas according to the condition of combustion. As the plastic foam that does not generate harmful gas at the time of fires, there is continuous bubble type polyethylene which is excellent in its weathering property and chemical resistance. A reactive, phosphorus-containing oligomer has large molecular weight and two or more double couplings in a molecule, therefore, it does not enter the inside of polyethylene, and polymerizes and crosslinks on the surfaces of bubble walls in the foam, accordingly it is expected that the apparent graft polymerization is carried out, and it is very effective for making polyethylene foam incombustible. The method of making graft foam, the properties of graft foam and so on are reported. When the graft polymerization of this oligomer to continuous bubble type polyethylene foam was tried, highly incombustible polyethylene foam was obtained. (K.I.)

  4. Bubbles in piezo-acoustic inkjet printing

    NARCIS (Netherlands)

    Lohse, D.; Jeurissen, R.J.M.; de Jong, J.; Versluis, M.; Wijshoff, H.M.A.; van den Berg, M.; Reinten, H.

    2008-01-01

    Ink-jet printing is considered as the hitherto most successful application of microfluidics. A notorious problem in piezo-acoustic ink-jet systems is the formation of air bubbles during operation. They seriously disturb the acoustics and can cause the droplet formation to stop. We could show by a

  5. Non-Abelian bubbles in microstate geometries

    Energy Technology Data Exchange (ETDEWEB)

    Ramírez, Pedro F. [Instituto de Física Teórica UAM/CSIC,C/ Nicolás Cabrera, 13-15, C.University Cantoblanco, E-28049 Madrid (Spain); Institut de Physique Théorique, Université Paris Saclay, CEA, CNRS,Orme des Merisiers bâtiment 774, F-91191 Gif-sur-Yvette (France)

    2016-11-24

    We find the first smooth bubbling microstate geometries with non-Abelian fields. The solutions constitute an extension of the BPS three-charge smooth microstates. These consist in general families of regular supersymmetric solutions with non-trivial topology, i.e. bubbles, of N=1, d=5 Super-Einstein-Yang-Mills theory, having the asymptotic charges of a black hole or black ring but with no horizon. The non-Abelian fields make their presence at the very heart of the microstate structure: the physical size of the bubbles is affected by the non-Abelian topological charge they carry, which combines with the Abelian flux threading the bubbles to hold them up. Interestingly the non-Abelian fields carry a set of adjustable continuous parameters that do not alter the asymptotics of the solutions but modify the local geometry. This feature can be used to obtain a classically infinite number of microstate solutions with the asymptotics of a single black hole or black ring.

  6. Customized bubble continuous positive airway pressure (BCPAP ...

    African Journals Online (AJOL)

    owner

    2013-02-09

    Feb 9, 2013 ... our institution, we modified the existing Bubble CPAP devise using readily available but far less expensive materials. The resultant product is cheap, easily assem- .... Hurd SS, Bryan MH, Cotton RB,. Epstein MF et al. is chronic lung disease in low birth weight infants preventable? Pediatrics 1987; 9. (1):26- ...

  7. Bubble and Drop Nonlinear Dynamics (BDND)

    Science.gov (United States)

    Trinh, E. H.; Leal, L. Gary; Thomas, D. A.; Crouch, R. K.

    1998-01-01

    Free drops and bubbles are weakly nonlinear mechanical systems that are relatively simple to characterize experimentally in 1-G as well as in microgravity. The understanding of the details of their motion contributes to the fundamental study of nonlinear phenomena and to the measurement of the thermophysical properties of freely levitated melts. The goal of this Glovebox-based experimental investigation is the low-gravity assessment of the capabilities of a modular apparatus based on ultrasonic resonators and on the pseudo- extinction optical method. The required experimental task is the accurate measurements of the large-amplitude dynamics of free drops and bubbles in the absence of large biasing influences such as gravity and levitation fields. A single-axis levitator used for the positioning of drops in air, and an ultrasonic water-filled resonator for the trapping of air bubbles have been evaluated in low-gravity and in 1-G. The basic feasibility of drop positioning and shape oscillations measurements has been verified by using a laptop-interfaced automated data acquisition and the optical extinction technique. The major purpose of the investigation was to identify the salient technical issues associated with the development of a full-scale Microgravity experiment on single drop and bubble dynamics.

  8. THE AGE OF THE LOCAL INTERSTELLAR BUBBLE

    International Nuclear Information System (INIS)

    Abt, Helmut A.

    2011-01-01

    The Local Interstellar Bubble is an irregular region from 50 to 150 pc from the Sun in which the interstellar gas density is 10 -2 -10 -3 of that outside the bubble and the interstellar temperature is 10 6 K. Evidently most of the gas was swept out by one or more supernovae. I explored the stellar contents and ages of the region from visual double stars, spectroscopic doubles, single stars, open clusters, emission regions, X-ray stars, planetary nebulae, and pulsars. The bubble has three sub-regions. The region toward the galactic center has stars as early as O9.5 V and with ages of 2-4 M yr. It also has a pulsar (PSRJ1856-3754) with a spin-down age of 3.76 Myr. That pulsar is likely to be the remnant of the supernova that drove away most of the gas. The central lobe has stars as early as B7 V and therefore an age of about 160 Myr or less. The Pleiades lobe has stars as early as B3 and therefore an age of about 50 Myr. There are no obvious pulsars that resulted from the supernovae that cleared out those areas. As found previously by Welsh and Lallement, the bubble has five B stars along its perimeter that show high-temperature ions of O VI and C II along their lines of sight, confirming its high interstellar temperature.

  9. The bubble distribution in glass refining channels

    Czech Academy of Sciences Publication Activity Database

    Němec, Lubomír; Cincibusová, P.

    2005-01-01

    Roč. 49, č. 4 (2005), s. 269-277 ISSN 0862-5468 Institutional research plan: CEZ:AV0Z40320502 Keywords : glass fining * bubble distribution s models * horizontal channel Subject RIV: CA - Inorganic Chemistry Impact factor: 0.463, year: 2005

  10. Argonne Bubble Experiment Thermal Model Development II

    Energy Technology Data Exchange (ETDEWEB)

    Buechler, Cynthia Eileen [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-07-01

    This report describes the continuation of the work reported in “Argonne Bubble Experiment Thermal Model Development”. The experiment was performed at Argonne National Laboratory (ANL) in 2014. A rastered 35 MeV electron beam deposited power in a solution of uranyl sulfate, generating heat and radiolytic gas bubbles. Irradiations were performed at three beam power levels, 6, 12 and 15 kW. Solution temperatures were measured by thermocouples, and gas bubble behavior was observed. This report will describe the Computational Fluid Dynamics (CFD) model that was developed to calculate the temperatures and gas volume fractions in the solution vessel during the irradiations. The previous report described an initial analysis performed on a geometry that had not been updated to reflect the as-built solution vessel. Here, the as-built geometry is used. Monte-Carlo N-Particle (MCNP) calculations were performed on the updated geometry, and these results were used to define the power deposition profile for the CFD analyses, which were performed using Fluent, Ver. 16.2. CFD analyses were performed for the 12 and 15 kW irradiations, and further improvements to the model were incorporated, including the consideration of power deposition in nearby vessel components, gas mixture composition, and bubble size distribution. The temperature results of the CFD calculations are compared to experimental measurements.

  11. Organization of bubble chamber image processing

    International Nuclear Information System (INIS)

    Gritsaenko, I.A.; Petrovykh, L.P.; Petrovykh, Yu.L.; Fenyuk, A.B.

    1985-01-01

    A programme of bubble chamber image processing is described. The programme is written in FORTRAN, it is developed for the DEC-10 computer and is designed for operation of semi-automation processing-measurement projects PUOS-2 and PUOS-4. Fornalization of the image processing permits to use it for different physical experiments

  12. Ultrasound induced by CW laser cavitation bubbles

    International Nuclear Information System (INIS)

    Korneev, N; Montero, P Rodriguez; Ramos-Garcia, R; Ramirez-San-Juan, J C; Padilla-Martinez, J P

    2011-01-01

    The generation of ultrasound by a collapsing single cavitation bubble in a strongly absorbing liquid illuminated with a moderate power CW laser is described. The ultrasound shock wave is detected with hydrophone and interferometric device. To obtain a stronger pulse it is necessary to adjust a liquid absorption and a beam diameter. Their influence can be qualitatively understood with a simple model.

  13. Heat transport in bubbling turbulent convection.

    Science.gov (United States)

    Lakkaraju, Rajaram; Stevens, Richard J A M; Oresta, Paolo; Verzicco, Roberto; Lohse, Detlef; Prosperetti, Andrea

    2013-06-04

    Boiling is an extremely effective way to promote heat transfer from a hot surface to a liquid due to numerous mechanisms, many of which are not understood in quantitative detail. An important component of the overall process is that the buoyancy of the bubble compounds with that of the liquid to give rise to a much-enhanced natural convection. In this article, we focus specifically on this enhancement and present a numerical study of the resulting two-phase Rayleigh-Bénard convection process in a cylindrical cell with a diameter equal to its height. We make no attempt to model other aspects of the boiling process such as bubble nucleation and detachment. The cell base and top are held at temperatures above and below the boiling point of the liquid, respectively. By keeping this difference constant, we study the effect of the liquid superheat in a Rayleigh number range that, in the absence of boiling, would be between 2 × 10(6) and 5 × 10(9). We find a considerable enhancement of the heat transfer and study its dependence on the number of bubbles, the degree of superheat of the hot cell bottom, and the Rayleigh number. The increased buoyancy provided by the bubbles leads to more energetic hot plumes detaching from the cell bottom, and the strength of the circulation in the cell is significantly increased. Our results are in general agreement with recent experiments on boiling Rayleigh-Bénard convection.

  14. Is there a Housing Bubble in Turkey?

    Directory of Open Access Journals (Sweden)

    Coskun Yener

    2017-03-01

    Full Text Available There was a notable housing price inflation in aggregate/local levels in Turkey during the last few years. Although the country’s economic fundamentals remain strong, the probability of a housing bubble is a heated debate among market participants. This timely investigation brings greater clarity to whether the Turkish housing market is in a bubble. The study uses a multi-strand approach to dissect the bubble over the period of Jan. 2010 - Dec. 2014. First, monthly/annual price-to-income and monthly price-to-rent ratios are examined for the national Turkish as well as regional Istanbul, Izmir and Ankara housing markets. Second, an extended CASE and SHILLER (2003 model is applied assessing the interdependence between housing prices and a series of explanatory variables. Lastly, the Right Tail Augmented Dickey-Fuller (Rtadf test is performed to support the overall analysis. This study finds that neither affordability ratios nor regression estimates support the existence of the bubble in Turkey.

  15. Condensation of vapor bubble in subcooled pool

    Science.gov (United States)

    Horiuchi, K.; Koiwa, Y.; Kaneko, T.; Ueno, I.

    2017-02-01

    We focus on condensation process of vapor bubble exposed to a pooled liquid of subcooled conditions. Two different geometries are employed in the present research; one is the evaporation on the heated surface, that is, subcooled pool boiling, and the other the injection of vapor into the subcooled pool. The test fluid is water, and all series of the experiments are conducted under the atmospheric pressure condition. The degree of subcooling is ranged from 10 to 40 K. Through the boiling experiment, unique phenomenon known as microbubble emission boiling (MEB) is introduced; this phenomenon realizes heat flux about 10 times higher than the critical heat flux. Condensation of the vapor bubble is the key phenomenon to supply ambient cold liquid to the heated surface. In order to understand the condensing process in the MEB, we prepare vapor in the vapor generator instead of the evaporation on the heated surface, and inject the vapor to expose the vapor bubble to the subcooled liquid. Special attention is paid to the dynamics of the vapor bubble detected by the high-speed video camera, and on the enhancement of the heat transfer due to the variation of interface area driven by the condensation.

  16. Radiolytic and thermolytic bubble gas hydrogen composition

    Energy Technology Data Exchange (ETDEWEB)

    Woodham, W. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2017-12-11

    This report describes the development of a mathematical model for the estimation of the hydrogen composition of gas bubbles trapped in radioactive waste. The model described herein uses a material balance approach to accurately incorporate the rates of hydrogen generation by a number of physical phenomena and scale the aforementioned rates in a manner that allows calculation of the final hydrogen composition.

  17. Is Education Facing a "Tech Bubble"?

    Science.gov (United States)

    Davis, Michelle R.

    2013-01-01

    Educational technology companies and entrepreneurs may face the risk of a "tech bubble," similar to the massive boom-and-bust that rocked the technology market in the late 1990s, according to market analysts and a recently released paper. A relatively new focus on K-12 educational technology as an investment vehicle, a surge of investors looking…

  18. Image digitizer system for bubble chamber laser

    International Nuclear Information System (INIS)

    Haggerty, H.

    1986-01-01

    An IBM PC-based image digitizer system has been assembled to monitor the laser flash used for holography at the 15 foot bubble chamber. The hardware and the operating software are outlined. For an operational test of the system, an array of LEDs was flashed with a 10 microsecond pulse and the image was grabbed by one of the operating programs and processed

  19. Bubbles That Change the Speed of Sound

    Science.gov (United States)

    Planinsic, Gorazd; Etkina, Eugenia

    2012-01-01

    The influence of bubbles on sound has long attracted the attention of physicists. In his 1920 book Sir William Bragg described sound absorption caused by foam in a glass of beer tapped by a spoon. Frank S. Crawford described and analyzed the change in the pitch of sound in a similar experiment and named the phenomenon the "hot chocolate effect."…

  20. BUBBLE - an urban boundary layer meteorology project

    DEFF Research Database (Denmark)

    Rotach, M.W.; Vogt, R.; Bernhofer, C.

    2005-01-01

    ground truth, as well as on urban turbulence and profiling (sodar, RASS, tethered balloon) were performed. Also tracer experiments with near-roof-level release and sampling were performed. In parallel to the experimental activities within BUBBLE, a meso-scale numerical atmospheric model, which contains...

  1. On Stability of a Bubble Column

    Czech Academy of Sciences Publication Activity Database

    Růžička, Marek

    2013-01-01

    Roč. 91, č. 2 (2013), s. 191-203 ISSN 0263-8762 R&D Projects: GA ČR GA104/07/1110 Institutional support: RVO:67985858 Keywords : bubble column * flow regimes * steady solution Subject RIV: CI - Industrial Chemistry, Chemical Engineering Impact factor: 2.281, year: 2013

  2. Heat transport in bubbling turbulent convection

    NARCIS (Netherlands)

    Lakkaraju, R.; Stevens, Richard Johannes Antonius Maria; Oresta, P.; Verzicco, Roberto; Lohse, Detlef; Prosperetti, Andrea

    2013-01-01

    Boiling is an extremely effective way to promote heat transfer from a hot surface to a liquid due to numerous mechanisms, many of which are not understood in quantitative detail. An important component of the overall process is that the buoyancy of the bubble compounds with that of the liquid to

  3. Partial coalescence from bubbles to drops

    KAUST Repository

    Zhang, F. H.; Thoraval, Marie-Jean; Thoroddsen, Sigurdur T; Taborek, P.

    2015-01-01

    the travel time of this wave mode on the bubble surface, we also show that the model is consistent with the experiments. This wavenumber is determined by both the global drainage as well as the interface shapes during the rapid coalescence in the neck

  4. Drop impact entrapment of bubble rings

    KAUST Repository

    Thoraval, M.-J.; Takehara, K.; Etoh, T.G.; Thoroddsen, Sigurdur T

    2013-01-01

    We use ultra-high-speed video imaging to look at the initial contact of a drop impacting on a liquid layer. We observe experimentally the vortex street and the bubble-ring entrapments predicted numerically, for high impact velocities, by Thoraval et

  5. Detailed modeling of hydrodynamics mass transfer and chemical reactions in a bubble column using a discrete bubble model

    NARCIS (Netherlands)

    Darmana, D.; Deen, N.G.; Kuipers, J.A.M.

    2005-01-01

    A 3D discrete bubble model is adopted to investigate complex behavior involving hydrodynamics, mass transfer and chemical reactions in a gas¿liquid bubble column reactor. In this model a continuum description is adopted for the liquid phase and additionally each individual bubble is tracked in a

  6. Modeling of mass transfer and chemical reactions in a bubble column reactor using a discrete bubble model

    NARCIS (Netherlands)

    Darmana, D.; Deen, N.G.; Kuipers, J.A.M.

    2004-01-01

    A 3D discrete bubble model is adopted to investigate complex behavior involving hydrodynamics, mass transfer and chemical reactions in a gas-liquid bubble column reactor. In this model a continuum description is adopted for the liquid phase and additionally each individual bubble is tracked in a

  7. Detailed modeling of hydrodynamics mass transfer and chemical reactions in a bubble column using a discrete bubble model

    NARCIS (Netherlands)

    Darmana, D.; Deen, N.G.; Kuipers, J.A.M.

    2005-01-01

    A 3D discrete bubble model is adopted to investigate complex behavior involving hydrodynamics, mass transfer and chemical reactions in a gas–liquid bubble column reactor. In this model a continuum description is adopted for the liquid phase and additionally each individual bubble is tracked in a

  8. Cap Bubble Drift Velocity in a Confined Test Section

    International Nuclear Information System (INIS)

    Xiaodong Sun; Seungjin Kim; Mamoru Ishii; Lincoln, Frank W.; Beus, Stephen G.

    2002-01-01

    In the two-group interfacial area transport equation, bubbles are categorized into two groups, i.e., spherical/distorted bubbles as group 1 and cap/slug/churn-turbulent bubbles as group 2. The bubble rise velocities for both groups of bubbles may be estimated by the drift flux model by applying different distribution parameters and drift velocities for both groups. However, the drift velocity for group 2 bubbles is not always applicable (when the wall effect becomes important) as in the current test loop of interest where the flow channel is confined by two parallel flat walls, with a dimension of 200-mm in width and 10-mm in gap. The previous experiments indicated that no stable slug flow existed in this test section, which was designed to permit visualization of the flow patterns and bubble characteristics without the distortion associated with curved surfaces. In fact, distorted cap bubbly and churn-turbulent flow was observed. Therefore, it is essential to developed a correlation for cap bubble drift velocity in this confined flow channel. Since the rise velocity of a cap bubble depends on its size, a high-speed movie camera is used to capture images of cap bubbles to obtain the bubble size information. Meanwhile, the rise velocity of cap and elongated bubbles (called cap bubbles hereafter) is investigated by examining the captured images frame by frame. As a result, the conventional correlation of drift velocity for slug bubbles is modified and acceptable agreements between the measurements and correlation estimation are achieved

  9. Bubbles with shock waves and ultrasound: a review.

    Science.gov (United States)

    Ohl, Siew-Wan; Klaseboer, Evert; Khoo, Boo Cheong

    2015-10-06

    The study of the interaction of bubbles with shock waves and ultrasound is sometimes termed 'acoustic cavitation'. It is of importance in many biomedical applications where sound waves are applied. The use of shock waves and ultrasound in medical treatments is appealing because of their non-invasiveness. In this review, we present a variety of acoustics-bubble interactions, with a focus on shock wave-bubble interaction and bubble cloud phenomena. The dynamics of a single spherically oscillating bubble is rather well understood. However, when there is a nearby surface, the bubble often collapses non-spherically with a high-speed jet. The direction of the jet depends on the 'resistance' of the boundary: the bubble jets towards a rigid boundary, splits up near an elastic boundary, and jets away from a free surface. The presence of a shock wave complicates the bubble dynamics further. We shall discuss both experimental studies using high-speed photography and numerical simulations involving shock wave-bubble interaction. In biomedical applications, instead of a single bubble, often clouds of bubbles appear (consisting of many individual bubbles). The dynamics of such a bubble cloud is even more complex. We shall show some of the phenomena observed in a high-intensity focused ultrasound (HIFU) field. The nonlinear nature of the sound field and the complex inter-bubble interaction in a cloud present challenges to a comprehensive understanding of the physics of the bubble cloud in HIFU. We conclude the article with some comments on the challenges ahead.

  10. A derivation of the stable cavitation threshold accounting for bubble-bubble interactions.

    Science.gov (United States)

    Guédra, Matthieu; Cornu, Corentin; Inserra, Claude

    2017-09-01

    The subharmonic emission of sound coming from the nonlinear response of a bubble population is the most used indicator for stable cavitation. When driven at twice their resonance frequency, bubbles can exhibit subharmonic spherical oscillations if the acoustic pressure amplitude exceeds a threshold value. Although various theoretical derivations exist for the subharmonic emission by free or coated bubbles, they all rest on the single bubble model. In this paper, we propose an analytical expression of the subharmonic threshold for interacting bubbles in a homogeneous, monodisperse cloud. This theory predicts a shift of the subharmonic resonance frequency and a decrease of the corresponding pressure threshold due to the interactions. For a given sonication frequency, these results show that an optimal value of the interaction strength (i.e. the number density of bubbles) can be found for which the subharmonic threshold is minimum, which is consistent with recently published experiments conducted on ultrasound contrast agents. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Study of droplet entrainment from bubbling surface in a bubble column

    International Nuclear Information System (INIS)

    Ramirez de Santiago, M.

    1991-05-01

    In a bubble column droplets are ejected from the free surface by bubble bursting or splashing. Depending on their size, the droplets are partly carried away by the streaming gas or fall back to the bubbling surface by gravity force. Experiments have been carried out to determine the void fraction in the column by means of an optical probe. In the interfacial zone the bubble bursting process was captured with a high-speed video camera. Simultaneous measurements were made of size and velocity of droplets at several distances from the bubbling surface with a Phase-Doppler Anemometry. The bubble column can be divided into three regions: A lower zone with a flat profile of the local void fraction, a central zone where the flow regime is steady and an upper zone where the local void fraction grows rapidly. A two-parameter log-normal distribution function was proposed in order to describe the polydisperse distribution of droplet-size. Results were obtained concerning the entrainment, concentration, volume fraction and interfacial area of droplets. Finally, it was found that the turbulence intensity affects the droplet terminal velocity for droplets smaller than the Kolmogorov microscale [fr

  12. Electron microscopic analysis of rotavirus assembly-replication intermediates

    International Nuclear Information System (INIS)

    Boudreaux, Crystal E.; Kelly, Deborah F.; McDonald, Sarah M.

    2015-01-01

    Rotaviruses (RVs) replicate their segmented, double-stranded RNA genomes in tandem with early virion assembly. In this study, we sought to gain insight into the ultrastructure of RV assembly-replication intermediates (RIs) using transmission electron microscopy (EM). Specifically, we examined a replicase-competent, subcellular fraction that contains all known RV RIs. Three never-before-seen complexes were visualized in this fraction. Using in vitro reconstitution, we showed that ~15-nm doughnut-shaped proteins in strings were nonstructural protein 2 (NSP2) bound to viral RNA transcripts. Moreover, using immunoaffinity-capture EM, we revealed that ~20-nm pebble-shaped complexes contain the viral RNA polymerase (VP1) and RNA capping enzyme (VP3). Finally, using a gel purification method, we demonstrated that ~30–70-nm electron-dense, particle-shaped complexes represent replicase-competent core RIs, containing VP1, VP3, and NSP2 as well as capsid proteins VP2 and VP6. The results of this study raise new questions about the interactions among viral proteins and RNA during the concerted assembly–replicase process. - Highlights: • Rotaviruses replicate their genomes in tandem with early virion assembly. • Little is known about rotavirus assembly-replication intermediates. • Assembly-replication intermediates were imaged using electron microscopy

  13. Electron microscopic analysis of rotavirus assembly-replication intermediates

    Energy Technology Data Exchange (ETDEWEB)

    Boudreaux, Crystal E.; Kelly, Deborah F. [Virginia Tech Carilion School of Medicine and Research Institute, Roanoke, VA (United States); McDonald, Sarah M., E-mail: mcdonaldsa@vtc.vt.edu [Virginia Tech Carilion School of Medicine and Research Institute, Roanoke, VA (United States); Department of Biomedical Sciences and Pathobiology, Virginia—Maryland Regional College of Veterinary Medicine, Blacksburg, VA (United States)

    2015-03-15

    Rotaviruses (RVs) replicate their segmented, double-stranded RNA genomes in tandem with early virion assembly. In this study, we sought to gain insight into the ultrastructure of RV assembly-replication intermediates (RIs) using transmission electron microscopy (EM). Specifically, we examined a replicase-competent, subcellular fraction that contains all known RV RIs. Three never-before-seen complexes were visualized in this fraction. Using in vitro reconstitution, we showed that ~15-nm doughnut-shaped proteins in strings were nonstructural protein 2 (NSP2) bound to viral RNA transcripts. Moreover, using immunoaffinity-capture EM, we revealed that ~20-nm pebble-shaped complexes contain the viral RNA polymerase (VP1) and RNA capping enzyme (VP3). Finally, using a gel purification method, we demonstrated that ~30–70-nm electron-dense, particle-shaped complexes represent replicase-competent core RIs, containing VP1, VP3, and NSP2 as well as capsid proteins VP2 and VP6. The results of this study raise new questions about the interactions among viral proteins and RNA during the concerted assembly–replicase process. - Highlights: • Rotaviruses replicate their genomes in tandem with early virion assembly. • Little is known about rotavirus assembly-replication intermediates. • Assembly-replication intermediates were imaged using electron microscopy.

  14. Champagne experiences various rhythmical bubbling regimes in a flute.

    Science.gov (United States)

    Liger-Belair, Gérard; Tufaile, Alberto; Jeandet, Philippe; Sartorelli, José-Carlos

    2006-09-20

    Bubble trains are seen rising gracefully from a few points on the glass wall (called nucleation sites) whenever champagne is poured into a glass. As time passes during the gas-discharging process, the careful observation of some given bubble columns reveals that the interbubble distance may change suddenly, thus revealing different rhythmical bubbling regimes. Here, it is reported that the transitions between the different bubbling regimes of some nucleation sites during gas discharging is a process which may be ruled by a strong interaction between tiny gas pockets trapped inside the nucleation site and/or also by an interaction between the tiny bubbles just blown from the nucleation site.

  15. Observation of high-temperature bubbles in an ECR plasma

    Science.gov (United States)

    Terasaka, K.; Yoshimura, S.; Tanaka, M. Y.

    2018-05-01

    Creation and annihilation of high-temperature bubbles have been observed in an electron cyclotron resonance plasma. The electron temperature in the bubble core is three times higher than that in the ambient region, and the size perpendicular to the magnetic field is much smaller than the plasma diameter. Formation of a bubble accompanies large negative spikes in the floating potential of a Langmuir probe, and the spatiotemporal behavior of the bubble has been visualized with a high-impedance wire grid detector. It is found that the bubble is in a prolate spheroidal shape with the axis along the magnetic field and occurs randomly in time and independently in space.

  16. Investigation of the condensing vapor bubble behavior through CFD simulation

    International Nuclear Information System (INIS)

    Sablania, Sidharth; Verma, Akash; Goyal, P.; Dutta, Anu; Singh, R.K.

    2013-09-01

    In nuclear systems the sub-cooled boiling flow is an important problem due to the behavior of condensing vapor bubble which has a large effect on the heat transfer characteristics as well as pressure drops and flow instability. The sub-cooled boiling flows become very complex and dynamic phenomena by the vapor bubble-water interaction. This happens due to the boiling/condensation, break-up, and coalescence of the bubble and needs to be addressed for characterizing the above mentioned flow parameters. There have been many researches to analyze the behavior of bubble experimentally and analytically. However, it is very difficult to get complete information about the behavior of bubble because of ever changing interface between vapor and water phase due to bubble condensation/evaporation Therefore, it is necessary to carry out a CFD simulation for better understanding the complex phenomenon of the bubble behavior. The present work focuses on the simulation of condensing bubble in subcooled boiling flow using (Volume of Fluid) VOF method in the CFD code CFD-ACE+. In order to simulate the heat and mass transfer through the bubble interface, CFD modeling for the bubble condensation was developed by modeling the source terms in the governing equations of VOF model using the User-Defined Function (UDF) in CFD-ACE+ code. The effect of condensation on bubble behavior was analyzed by comparing the behavior of condensing bubble with that of adiabatic bubble. It was observed that the behavior of condensing bubble was different from that of non condensing bubble in respect of bubble shape, diameter, velocity etc. The results obtained from the present simulation in terms of various parameters such as bubble velocity, interfacial area and bubble volume agreed well with the reported experimental results verified with FLUENT code in available literature. Hence, this CFD-ACE+ simulation of single bubble condensation will be a useful computational fluid dynamics tool for analyzing the

  17. The effect of ion irradiation on inert gas bubble mobility

    International Nuclear Information System (INIS)

    Alexander, D.E.; Birtcher, R.C.

    1991-09-01

    The effect of Al ion irradiation on the mobility of Xe gas bubbles in Al thin films was investigated. Transmission electron microscopy was used to determine bubble diffusivities in films irradiated and/or annealed at 673K, 723K and 773K. Irradiation increased bubble diffusivity by a factor of 2--9 over that due to thermal annealing alone. The Arrhenius behavior and dose rate dependence of bubble diffusivity are consistent with a radiation enhanced diffusion phenomenon affecting a volume diffusion mechanism of bubble transport. 9 refs., 3 figs., 2 tabs

  18. Exploding and Imaging of Electron Bubbles in Liquid Helium

    Science.gov (United States)

    Yadav, Neha; Vadakkumbatt, Vaisakh; Maris, Humphrey J.; Ghosh, Ambarish

    2017-06-01

    An electron bubble in liquid helium-4 under the saturated vapor pressure becomes unstable and explodes if the pressure becomes more negative than -1.9 bars. In this paper, we use focused ultrasound to explode electron bubbles. We then image at 30,000 frames per second the growth and subsequent collapse of the bubbles. We find that bubbles can grow to as large as 1 mm in diameter within 2 ms after the cavitation event. We examine the relation between the maximum size of the bubble and the lifetime and find good agreement with the experimental results.

  19. REPLICATION TOOL AND METHOD OF PROVIDING A REPLICATION TOOL

    DEFF Research Database (Denmark)

    2016-01-01

    The invention relates to a replication tool (1, 1a, 1b) for producing a part (4) with a microscale textured replica surface (5a, 5b, 5c, 5d). The replication tool (1, 1a, 1b) comprises a tool surface (2a, 2b) defining a general shape of the item. The tool surface (2a, 2b) comprises a microscale...... energy directors on flange portions thereof uses the replication tool (1, 1a, 1b) to form an item (4) with a general shape as defined by the tool surface (2a, 2b). The formed item (4) comprises a microscale textured replica surface (5a, 5b, 5c, 5d) with a lateral arrangement of polydisperse microscale...

  20. Activation-induced deoxycytidine deaminase (AID) co-transcriptional scanning at single-molecule resolution

    Science.gov (United States)

    Senavirathne, Gayan; Bertram, Jeffrey G.; Jaszczur, Malgorzata; Chaurasiya, Kathy R.; Pham, Phuong; Mak, Chi H.; Goodman, Myron F.; Rueda, David

    2015-12-01

    Activation-induced deoxycytidine deaminase (AID) generates antibody diversity in B cells by initiating somatic hypermutation (SHM) and class-switch recombination (CSR) during transcription of immunoglobulin variable (IgV) and switch region (IgS) DNA. Using single-molecule FRET, we show that AID binds to transcribed dsDNA and translocates unidirectionally in concert with RNA polymerase (RNAP) on moving transcription bubbles, while increasing the fraction of stalled bubbles. AID scans randomly when constrained in an 8 nt model bubble. When unconstrained on single-stranded (ss) DNA, AID moves in random bidirectional short slides/hops over the entire molecule while remaining bound for ~5 min. Our analysis distinguishes dynamic scanning from static ssDNA creasing. That AID alone can track along with RNAP during transcription and scan within stalled transcription bubbles suggests a mechanism by which AID can initiate SHM and CSR when properly regulated, yet when unregulated can access non-Ig genes and cause cancer.

  1. Analysis of JC virus DNA replication using a quantitative and high-throughput assay

    International Nuclear Information System (INIS)

    Shin, Jong; Phelan, Paul J.; Chhum, Panharith; Bashkenova, Nazym; Yim, Sung; Parker, Robert; Gagnon, David; Gjoerup, Ole; Archambault, Jacques; Bullock, Peter A.

    2014-01-01

    Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCV DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. - Highlights: • Development of a high-throughput screening assay for JCV DNA replication using C33A cells. • Evidence that T-ag fails to accumulate in the nuclei of established glioma cell lines. • Evidence that NF-1 directly promotes JCV DNA replication in C33A cells. • Proof-of-concept that the HTS assay can be used to identify pharmacological inhibitor of JCV DNA replication

  2. Analysis of JC virus DNA replication using a quantitative and high-throughput assay

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Jong; Phelan, Paul J.; Chhum, Panharith; Bashkenova, Nazym; Yim, Sung; Parker, Robert [Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111 (United States); Gagnon, David [Institut de Recherches Cliniques de Montreal (IRCM), 110 Pine Avenue West, Montreal, Quebec, Canada H2W 1R7 (Canada); Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec (Canada); Gjoerup, Ole [Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA 02111 (United States); Archambault, Jacques [Institut de Recherches Cliniques de Montreal (IRCM), 110 Pine Avenue West, Montreal, Quebec, Canada H2W 1R7 (Canada); Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec (Canada); Bullock, Peter A., E-mail: Peter.Bullock@tufts.edu [Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111 (United States)

    2014-11-15

    Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCV DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. - Highlights: • Development of a high-throughput screening assay for JCV DNA replication using C33A cells. • Evidence that T-ag fails to accumulate in the nuclei of established glioma cell lines. • Evidence that NF-1 directly promotes JCV DNA replication in C33A cells. • Proof-of-concept that the HTS assay can be used to identify pharmacological inhibitor of JCV DNA replication.

  3. Measurement of micro Bubbles generated by a pressurized dissolution method

    Energy Technology Data Exchange (ETDEWEB)

    Hosokawa, S; Tanaka, K; Tomiyama, A [Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501 (Japan); Maeda, Y; Yamaguchi, S; Ito, Y, E-mail: hosokawa@mech.kobe-u.ac.j [Panasonic Electric Works Co., Ltd., 1048 Kadoma, Osaka 571-8686 (Japan)

    2009-02-01

    Diameters of micro-bubbles are apt to range from about one mm to several-hundred mm, and therefore, it is difficult to measure a correct diameter distribution using a single measurement method. In this study, diameters of bubbles generated by a pressurized dissolution method are measured by using phase Doppler anemometry (PDA) and an image processing method, which is based on the Sobel filter and Hough transform. The diameter distribution and the Sauter mean diameter of micro bubbles are evaluated based on the diameters measured by both methods. Experiments are conducted for several mass flow rates of dissolved gas and of air bubbles entrained in the upstream of the decompression nozzle to examine effects of the entrained bubbles on bubble diameter. As a result, the following conclusions are obtained: (1) Diameter distribution of micro bubbles can be accurately measured for a wide range of diameter by using PDA and the image processing method. (2) The mean diameter of micro-bubbles generated by gasification of dissolved gas is smaller than that generated by breakup of air bubbles entrained in the upstream of the decompression nozzle. (3) The mean bubble diameter increases with the entrainment of air bubbles in the upstream of the decompression nozzle at a constant mass flow rate of dissolved gas.

  4. Measurement of micro Bubbles generated by a pressurized dissolution method

    International Nuclear Information System (INIS)

    Hosokawa, S; Tanaka, K; Tomiyama, A; Maeda, Y; Yamaguchi, S; Ito, Y

    2009-01-01

    Diameters of micro-bubbles are apt to range from about one mm to several-hundred mm, and therefore, it is difficult to measure a correct diameter distribution using a single measurement method. In this study, diameters of bubbles generated by a pressurized dissolution method are measured by using phase Doppler anemometry (PDA) and an image processing method, which is based on the Sobel filter and Hough transform. The diameter distribution and the Sauter mean diameter of micro bubbles are evaluated based on the diameters measured by both methods. Experiments are conducted for several mass flow rates of dissolved gas and of air bubbles entrained in the upstream of the decompression nozzle to examine effects of the entrained bubbles on bubble diameter. As a result, the following conclusions are obtained: (1) Diameter distribution of micro bubbles can be accurately measured for a wide range of diameter by using PDA and the image processing method. (2) The mean diameter of micro-bubbles generated by gasification of dissolved gas is smaller than that generated by breakup of air bubbles entrained in the upstream of the decompression nozzle. (3) The mean bubble diameter increases with the entrainment of air bubbles in the upstream of the decompression nozzle at a constant mass flow rate of dissolved gas.

  5. Ignition modes of nanosecond discharge with bubbles in distilled water

    International Nuclear Information System (INIS)

    Hamdan, Ahmad; Cha, Min Suk

    2015-01-01

    Here, we present the microscopic physical characteristics of nanosecond discharges with an array of bubbles in distilled water. In particular, applying a single high-voltage pulse, four delayed intensified charge-coupled device cameras successfully visualized four successive images during a single discharge event. We identified three distinctive modes of ignition inside a bubble, depending on the relative location of the bubble with respect to pin-to-hollow needle electrodes when a single bubble was located in an inter-electrode gap of 1 mm: anode-driven ignition, cathode-driven ignition, and co-ignition near both electrodes. Anode- and cathode-driven ignitions evolved into either a complete propagation of the streamer or an incomplete propagation, which were limited in location by proximity to an ignition location, while co-ignitions consistently showed complete propagation. When we increased the gap to 2 mm to accommodate multiple bubbles in the gap, an ignited bubble near the cathode was able to cause the ignition of an upper adjacent bubble. Bubble–bubble interface zones can also be spots of ignition, such that we observed simultaneous co-ignitions in the zones of bubble–bubble interfaces and near electrodes with triple bubbles. We compared the experimental results of discharge propagation with different ignition modes between Ar, He, and N 2 bubbles. In addition, numerical simulations for static electric fields reasonably supported observed ignition behavior such that field intensity was locally enhanced. (paper)

  6. Inertial collapse of bubble pairs near a solid surface

    Science.gov (United States)

    Alahyari Beig, Shahaboddin; Johnsen, Eric

    2017-11-01

    Cavitation occurs in a variety of applications ranging from naval structures to biomedical ultrasound. One important consequence is structural damage to neighboring surfaces following repeated inertial collapse of vapor bubbles. Although the mechanical loading produced by the collapse of a single bubble has been widely investigated, less is known about the detailed dynamics of the collapse of multiple bubbles. In such a problem, the bubble-bubble interactions typically affect the dynamics, e.g., by increasing the non-sphericity of the bubbles and amplifying/hindering the collapse intensity depending on the flow parameters. Here, we quantify the effects of bubble-bubble interactions on the bubble dynamics, as well as the pressures/temperatures produced by the collapse of a pair of gas bubbles near a rigid surface. We perform high-resolution simulations of this problem by solving the three-dimensional compressible Navier-Stokes equations for gas/liquid flows. The results are used to investigate the non-spherical bubble dynamics and characterize the pressure and temperature fields based on the relevant parameters entering the problem: stand-off distance, geometrical configuration (angle, relative size, distance), collapse strength. This research was supported in part by ONR Grant N00014-12-1-0751 and NSF Grant CBET 1253157.

  7. On the mobility of fission-gas bubbles

    International Nuclear Information System (INIS)

    Nichols, F.A.; Ronchi, C.

    1986-01-01

    The importance of bubble migration in fuel swelling and fission-product release remains a controversial topic in spite of a great deal of research. For steady state analyses some authors ignore bubble motion totally, whereas others use mobilities (based on out-of-pile measurements) which are far below the theoretical diffusion-control predictions. Under transient conditions some continue to use zero or low bubble mobilities, whereas others invoke higher mobilities. Experimental information on mobility of bubbles under irradiation conditions is very limited, but supports the theoretical values for bubble sizes above 1 μm. The authors discuss here some interesting new results which may provide direct evidence for in-pile mobilities comparable with surface-diffusion control predictions for much smaller bubbles (<20nm), where out-of-pile studies indicate greatly reduced mobilities. A brief summary is presented of information available for bubble mobilities, both in- and out-of-pile

  8. Dynamics of micro-bubble sonication inside a phantom vessel

    KAUST Repository

    Qamar, Adnan; Samtaney, Ravi; Bull, Joseph L.

    2013-01-01

    A model for sonicated micro-bubble oscillations inside a phantom vessel is proposed. The model is not a variant of conventional Rayleigh-Plesset equation and is obtained from reduced Navier-Stokes equations. The model relates the micro-bubble oscillation dynamics with geometric and acoustic parameters in a consistent manner. It predicts micro-bubble oscillation dynamics as well as micro-bubble fragmentation when compared to the experimental data. For large micro-bubble radius to vessel diameter ratios, predictions are damped, suggesting breakdown of inherent modeling assumptions for these cases. Micro-bubble response with acoustic parameters is consistent with experiments and provides physical insight to the micro-bubble oscillation dynamics.

  9. Gas transport into a cavitation bubble during the explosion

    International Nuclear Information System (INIS)

    Oldenziel, D.M.

    1976-01-01

    When considering cavitation bubbles exploding from small stream nuclei the surface tension plays an important role, and mostly negative pressures exist in the surroundings of such a bubble. During the short explosion time, the gas and vapor pressure in the bubble plays no important role in the dynamic process. The high radial velocity of the bubble wall introduces a steep gradient in the concentration of dissolved air near it, which results in some enforced gas transport into the bubble. During the bubble implosion it is necessary to take into account the amount of gas in the bubble, as it certainly plays an important role in exploring the cavitation erosion. In this survey the solution of a mathematical model for the gas diffusion process is compared with some experimental results

  10. Numerical simulation of high Reynolds number bubble motion

    Energy Technology Data Exchange (ETDEWEB)

    McLaughlin, J.B. [Clarkson Univ., Potsdam, NY (United States)

    1995-12-31

    This paper presents the results of numerical simulations of bubble motion. All the results are for single bubbles in unbounded fluids. The liquid phase is quiescent except for the motion created by the bubble, which is axisymmetric. The main focus of the paper is on bubbles that are of order 1 mm in diameter in water. Of particular interest is the effect of surfactant molecules on bubble motion. Results for the {open_quotes}insoluble surfactant{close_quotes} model will be presented. These results extend research by other investigators to finite Reynolds numbers. The results indicate that, by assuming complete coverage of the bubble surface, one obtains good agreement with experimental observations of bubble motion in tap water. The effect of surfactant concentration on the separation angle is discussed.

  11. Dynamics of micro-bubble sonication inside a phantom vessel

    KAUST Repository

    Qamar, Adnan

    2013-01-10

    A model for sonicated micro-bubble oscillations inside a phantom vessel is proposed. The model is not a variant of conventional Rayleigh-Plesset equation and is obtained from reduced Navier-Stokes equations. The model relates the micro-bubble oscillation dynamics with geometric and acoustic parameters in a consistent manner. It predicts micro-bubble oscillation dynamics as well as micro-bubble fragmentation when compared to the experimental data. For large micro-bubble radius to vessel diameter ratios, predictions are damped, suggesting breakdown of inherent modeling assumptions for these cases. Micro-bubble response with acoustic parameters is consistent with experiments and provides physical insight to the micro-bubble oscillation dynamics.

  12. Numerical simulation of superheated vapor bubble rising in stagnant liquid

    Science.gov (United States)

    Samkhaniani, N.; Ansari, M. R.

    2017-09-01

    In present study, the rising of superheated vapor bubble in saturated liquid is simulated using volume of fluid method in OpenFOAM cfd package. The surface tension between vapor-liquid phases is considered using continuous surface force method. In order to reduce spurious current near interface, Lafaurie smoothing filter is applied to improve curvature calculation. Phase change is considered using Tanasawa mass transfer model. The variation of saturation temperature in vapor bubble with local pressure is considered with simplified Clausius-Clapeyron relation. The couple velocity-pressure equation is solved using PISO algorithm. The numerical model is validated with: (1) isothermal bubble rising and (2) one-dimensional horizontal film condensation. Then, the shape and life time history of single superheated vapor bubble are investigated. The present numerical study shows vapor bubble in saturated liquid undergoes boiling and condensation. It indicates bubble life time is nearly linear proportional with bubble size and superheat temperature.

  13. Interaction of equal-size bubbles in shear flow.

    Science.gov (United States)

    Prakash, Jai; Lavrenteva, Olga M; Byk, Leonid; Nir, Avinoam

    2013-04-01

    The inertia-induced forces on two identical spherical bubbles in a simple shear flow at small but finite Reynolds number, for the case when the bubbles are within each other's inner viscous region, are calculated making use of the reciprocal theorem. This interaction force is further employed to model the dynamics of air bubbles injected to a viscous fluid sheared in a Couette device at the first shear flow instability where the bubbles are trapped inside the stable Taylor vortex. It was shown that, during a long time scale, the inertial interaction between the bubbles in the primary shear flow drives them away from each other and, as a result, equal-size bubbles eventually assume an ordered string with equal separation distances between all neighbors. We report on experiments showing the dynamic evolution of various numbers of bubbles. The results of the theory are in good agreement with the experimental observations.

  14. Eternal inflation, bubble collisions, and the persistence of memory

    International Nuclear Information System (INIS)

    Garriga, Jaume; Guth, Alan H.; Vilenkin, Alexander

    2007-01-01

    A 'bubble universe' nucleating in an eternally inflating false vacuum will experience, in the course of its expansion, collisions with an infinite number of other bubbles. In an idealized model, we calculate the rate of collisions around an observer inside a given reference bubble. We show that the collision rate violates both the homogeneity and the isotropy of the bubble universe. Each bubble has a center which can be related to 'the beginning of inflation' in the parent false vacuum, and any observer not at the center will see an anisotropic bubble collision rate that peaks in the outward direction. Surprisingly, this memory of the onset of inflation persists no matter how much time elapses before the nucleation of the reference bubble

  15. Comparison of cavitation bubbles evolution in viscous media

    Directory of Open Access Journals (Sweden)

    Jasikova Darina

    2018-01-01

    Full Text Available There have been tried many types of liquids with different ranges of viscosity values that have been tested to form a single cavitation bubble. The purpose of these experiments was to observe the behaviour of cavitation bubbles in media with different ranges of absorbance. The most of the method was based on spark to induced superheat limit of liquid. Here we used arrangement of the laser-induced breakdown (LIB method. There were described the set cavitation setting that affects the size bubble in media with different absorbance. We visualized the cavitation bubble with a 60 kHz high speed camera. We used here shadowgraphy setup for the bubble visualization. There were observed time development and bubble extinction in various media, where the size of the bubble in the silicone oil was extremely small, due to the absorbance size of silicon oil.

  16. Insulated hsp70B' promoter: stringent heat-inducible activity in replication-deficient, but not replication-competent adenoviruses.

    Science.gov (United States)

    Rohmer, Stanimira; Mainka, Astrid; Knippertz, Ilka; Hesse, Andrea; Nettelbeck, Dirk M

    2008-04-01

    Key to the realization of gene therapy is the development of efficient and targeted gene transfer vectors. Therapeutic gene transfer by replication-deficient or more recently by conditionally replication-competent/oncolytic adenoviruses has shown much promise. For specific applications, however, it will be advantageous to provide vectors that allow for external control of gene expression. The efficient cellular heat shock system in combination with available technology for focused and controlled hyperthermia suggests heat-regulated transcription control as a promising tool for this purpose. We investigated the feasibility of a short fragment of the human hsp70B' promoter, with and without upstream insulator elements, for the regulation of transgene expression by replication-deficient or oncolytic adenoviruses. Two novel adenoviral vectors with an insulated hsp70B' promoter were developed and showed stringent heat-inducible gene expression with induction ratios up to 8000-fold. In contrast, regulation of gene expression from the hsp70B' promoter without insulation was suboptimal. In replication-competent/oncolytic adenoviruses regulation of the hsp70B' promoter was lost specifically during late replication in permissive cells and could not be restored by the insulators. We developed novel adenovirus gene transfer vectors that feature improved and stringent regulation of transgene expression from the hsp70B' promoter using promoter insulation. These vectors have potential for gene therapy applications that benefit from external modulation of therapeutic gene expression or for combination therapy with hyperthermia. Furthermore, our study reveals that vector replication can deregulate inserted cellular promoters, an observation which is of relevance for the development of replication-competent/oncolytic gene transfer vectors. (c) 2008 John Wiley & Sons, Ltd.

  17. Measurements of fast neutrons by bubble detectors

    Energy Technology Data Exchange (ETDEWEB)

    Castillo, F.; Martinez, H. [Laboratorio de Espectroscopia, Instituto de Ciencias Fisicas, Universidad Nacional Autonoma de Mexico, Apartado Postal 48-3, 62251, Cuernavaca Morelos (Mexico); Leal, B. [Instituto de Ciencias Nucleares, Universidad Nacional Autonoma de Mexico, Apartado Postal 70-543, 04510, Ciudad Universitaria, Mexico D. F. (Mexico); Rangel, J. [Instituto de Ciencias Nucleares, Universidad Nacional Autonoma de Mexico, Apartado Postal 70-543, 04510, Ciudad Universitaria, Mexico D. F (Mexico); Reyes, P. G. [Facultad de Ciencias, Universidad Autonoma del Estado de Mexico, Instituto Literario 100, Col. Centro, 50000, Toluca Estado de Mexico (Mexico)

    2013-07-03

    Neutron bubble detectors have been studied using Am-Be and D-D neuron sources, which give limited energy information. The Bubble Detector Spectrometer (BDS) have six different energy thresholds ranging from 10 KeV to 10 Mev. The number of bubbles obtained in each measurement is related to the dose (standardized response R) equivalent neutrons through sensitivity (b / {mu}Sv) and also with the neutron flux (neutrons per unit area) through a relationship that provided by the manufacturer. Bubble detectors were used with six different answers (0.11 b/ {mu}Sv, 0093 b/{mu}Sv, 0.14 b/{mu}Sv, 0.17 b/{mu}Sv, 0051 b/{mu}Sv). To test the response of the detectors (BDS) radiate a set of six of them with different energy threshold, with a source of Am-Be, placing them at a distance of one meter from it for a few minutes. Also, exposed to dense plasma focus Fuego Nuevo II (FN-II FPD) of ICN-UNAM, apparatus which produces fusion plasma, generating neutrons by nuclear reactions of neutrons whose energy emitting is 2.45 MeV. In this case the detectors were placed at a distance of 50 cm from the pinch at 90 Degree-Sign this was done for a certain number of shots. In both cases, the standard response is reported (Dose in {mu}Sv) for each of the six detectors representing an energy range, this response is given by the expression R{sub i}= B{sub i} / S{sub i} where B{sub i} is the number of bubbles formed in each and the detector sensitivity (S{sub i}) is given for each detector in (b / {mu}Sv). Also, reported for both cases, the detected neutron flux (n cm{sup -2}), by a given ratio and the response involves both standardized R, as the average cross section sigma. The results obtained have been compared with the spectrum of Am-Be source. From these measurements it can be concluded that with a combination of bubble detectors, with different responses is possible to measure the equivalent dose in a range of 10 to 100 {mu}Sv fields mixed neutron and gamma, and pulsed generated fusion

  18. Three-dimensional one-way bubble tracking method for the prediction of developing bubble-slug flows in a vertical pipe. 1st report, models and demonstration

    International Nuclear Information System (INIS)

    Tamai, Hidesada; Tomiyama, Akio

    2004-01-01

    A three-dimensional one-way bubble tracking method is one of the most promising numerical methods for the prediction of a developing bubble flow in a vertical pipe, provided that several constitutive models are prepared. In this study, a bubble shape, an equation of bubble motion, a liquid velocity profile, a pressure field, turbulent fluctuation and bubble coalescence are modeled based on available knowledge on bubble dynamics. Bubble shapes are classified into four types in terms of bubble equivalent diameter. A wake velocity model is introduced to simulate approaching process among bubbles due to wake entrainment. Bubble coalescence is treated as a stochastic phenomenon with the aid of coalescence probabilities that depend on the sizes of two interacting bubbles. The proposed method can predict time-spatial evolution of flow pattern in a developing bubble-slug flow. (author)

  19. Transcription as a Threat to Genome Integrity.

    Science.gov (United States)

    Gaillard, Hélène; Aguilera, Andrés

    2016-06-02

    Genomes undergo different types of sporadic alterations, including DNA damage, point mutations, and genome rearrangements, that constitute the basis for evolution. However, these changes may occur at high levels as a result of cell pathology and trigger genome instability, a hallmark of cancer and a number of genetic diseases. In the last two decades, evidence has accumulated that transcription constitutes an important natural source of DNA metabolic errors that can compromise the integrity of the genome. Transcription can create the conditions for high levels of mutations and recombination by its ability to open the DNA structure and remodel chromatin, making it more accessible to DNA insulting agents, and by its ability to become a barrier to DNA replication. Here we review the molecular basis of such events from a mechanistic perspective with particular emphasis on the role of transcription as a genome instability determinant.

  20. A physiological model of the interaction between tissue bubbles and the formation of blood-borne bubbles under decompression

    International Nuclear Information System (INIS)

    Chappell, M A; Payne, S J

    2006-01-01

    Under decompression, bubbles can form in the human body, and these can be found both within the body tissues and the bloodstream. Mathematical models for the growth of both types of bubbles have previously been presented, but they have not been coupled together. This work thus explores the interaction between the growth of tissue and blood-borne bubbles under decompression, specifically looking at the extent to which they compete for the common resource of inert gas held in solution in the tissues. The influence of tissue bubbles is found to be significant for densities as low as 10 ml -1 for tissues which are poorly perfused. However, the effects of formation of bubbles in the blood are not found until the density of bubble production sites reaches 10 6 ml -1 . From comparison of the model predictions with experimental evidence for bubbles produced in animals and man under decompression, it is concluded that the density of tissue bubbles is likely to have a significant effect on the number of bubbles produced in the blood. However, the density of nucleation sites in the blood is unlikely to be sufficiently high in humans for the formation of bubbles in the blood to have a significant impact on the growth of the bubbles in the tissue

  1. DNA replication is an integral part of the mouse oocyte's reprogramming machinery.

    Directory of Open Access Journals (Sweden)

    Bingyuan Wang

    Full Text Available Many of the structural and mechanistic requirements of oocyte-mediated nuclear reprogramming remain elusive. Previous accounts that transcriptional reprogramming of somatic nuclei in mouse zygotes may be complete in 24-36 hours, far more rapidly than in other reprogramming systems, raise the question of whether the mere exposure to the activated mouse ooplasm is sufficient to enact reprogramming in a nucleus. We therefore prevented DNA replication and cytokinesis, which ensue after nuclear transfer, in order to assess their requirement for transcriptional reprogramming of the key pluripotency genes Oct4 (Pou5f1 and Nanog in cloned mouse embryos. Using transcriptome and allele-specific analysis, we observed that hundreds of mRNAs, but not Oct4 and Nanog, became elevated in nucleus-transplanted oocytes without DNA replication. Progression through the first round of DNA replication was essential but not sufficient for transcriptional reprogramming of Oct4 and Nanog, whereas cytokinesis and thereby cell-cell interactions were dispensable for transcriptional reprogramming. Responses similar to clones also were observed in embryos produced by fertilization in vitro. Our results link the occurrence of reprogramming to a previously unappreciated requirement of oocyte-mediated nuclear reprogramming, namely DNA replication. Nuclear transfer alone affords no immediate transition from a somatic to a pluripotent gene expression pattern unless DNA replication is also in place. This study is therefore a resource to appreciate that the quest for always faster reprogramming methods may collide with a limit that is dictated by the cell cycle.

  2. Biomarkers of replicative senescence revisited

    DEFF Research Database (Denmark)

    Nehlin, Jan

    2016-01-01

    Biomarkers of replicative senescence can be defined as those ultrastructural and physiological variations as well as molecules whose changes in expression, activity or function correlate with aging, as a result of the gradual exhaustion of replicative potential and a state of permanent cell cycle...... arrest. The biomarkers that characterize the path to an irreversible state of cell cycle arrest due to proliferative exhaustion may also be shared by other forms of senescence-inducing mechanisms. Validation of senescence markers is crucial in circumstances where quiescence or temporary growth arrest may...... be triggered or is thought to be induced. Pre-senescence biomarkers are also important to consider as their presence indicate that induction of aging processes is taking place. The bona fide pathway leading to replicative senescence that has been extensively characterized is a consequence of gradual reduction...

  3. Regulation of beta cell replication

    DEFF Research Database (Denmark)

    Lee, Ying C; Nielsen, Jens Høiriis

    2008-01-01

    Beta cell mass, at any given time, is governed by cell differentiation, neogenesis, increased or decreased cell size (cell hypertrophy or atrophy), cell death (apoptosis), and beta cell proliferation. Nutrients, hormones and growth factors coupled with their signalling intermediates have been...... suggested to play a role in beta cell mass regulation. In addition, genetic mouse model studies have indicated that cyclins and cyclin-dependent kinases that determine cell cycle progression are involved in beta cell replication, and more recently, menin in association with cyclin-dependent kinase...... inhibitors has been demonstrated to be important in beta cell growth. In this review, we consider and highlight some aspects of cell cycle regulation in relation to beta cell replication. The role of cell cycle regulation in beta cell replication is mostly from studies in rodent models, but whether...

  4. Post-transcription cleavage generates the 3' end of F17R transcripts in vaccinia virus

    International Nuclear Information System (INIS)

    D'Costa, Susan M.; Antczak, James B.; Pickup, David J.; Condit, Richard C.

    2004-01-01

    Most vaccinia virus intermediate and late mRNAs possess 3' ends that are extremely heterogeneous in sequence. However, late mRNAs encoding the cowpox A-type inclusion protein (ATI), the second largest subunit of the RNA polymerase, and the late telomeric transcripts possess homogeneous 3' ends. In the case of the ATI mRNA, it has been shown that the homogeneous 3' end is generated by a post-transcriptional endoribonucleolytic cleavage event. We have determined that the F17R gene also produces homogeneous transcripts generated by a post-transcriptional cleavage event. Mapping of in vivo mRNA shows that the major 3' end of the F17R transcript maps 1262 nt downstream of the F17R translational start site. In vitro transcripts spanning the in vivo 3' end are cleaved in an in vitro reaction using extracts from virus infected cells, and the site of cleavage is the same both in vivo and in vitro. Cleavage is not observed using extract from cells infected in the presence of hydroxyurea; therefore, the cleavage factor is either virus-coded or virus-induced during the post-replicative phase of virus replication. The cis-acting sequence responsible for cleavage is orientation specific and the factor responsible for cleavage activity has biochemical properties similar to the factor required for cleavage of ATI transcripts. Partially purified cleavage factor generates cleavage products of expected size when either the ATI or F17R substrates are used in vitro, strongly suggesting that cleavage of both transcripts is mediated by the same factor

  5. Personality and Academic Motivation: Replication, Extension, and Replication

    Science.gov (United States)

    Jones, Martin H.; McMichael, Stephanie N.

    2015-01-01

    Previous work examines the relationships between personality traits and intrinsic/extrinsic motivation. We replicate and extend previous work to examine how personality may relate to achievement goals, efficacious beliefs, and mindset about intelligence. Approximately 200 undergraduates responded to the survey with a 150 participants replicating…

  6. Effects of Interferon-α/β on HBV Replication Determined by Viral Load

    Science.gov (United States)

    Tian, Yongjun; Chen, Wen-ling; Ou, Jing-hsiung James

    2011-01-01

    Interferons α and β (IFN-α/β) are type I interferons produced by the host to control microbial infections. However, the use of IFN-α to treat hepatitis B virus (HBV) patients generated sustained response to only a minority of patients. By using HBV transgenic mice as a model and by using hydrodynamic injection to introduce HBV DNA into the mouse liver, we studied the effect of IFN-α/β on HBV in vivo. Interestingly, our results indicated that IFN-α/β could have opposite effects on HBV: they suppressed HBV replication when viral load was high and enhanced HBV replication when viral load was low. IFN-α/β apparently suppressed HBV replication via transcriptional and post-transcriptional regulations. In contrast, IFN-α/β enhanced viral replication by inducing the transcription factor HNF3γ and activating STAT3, which together stimulated HBV gene expression and replication. Further studies revealed an important role of IFN-α/β in stimulating viral growth and prolonging viremia when viral load is low. This use of an innate immune response to enhance its replication and persistence may represent a novel strategy that HBV uses to enhance its growth and spread in the early stage of viral infection when the viral level is low. PMID:21829354

  7. Sp100 colocalizes with HPV replication foci and restricts the productive stage of the infectious cycle.

    Directory of Open Access Journals (Sweden)

    Wesley H Stepp

    2017-10-01

    Full Text Available We have shown previously that Sp100 (a component of the ND10 nuclear body represses transcription, replication and establishment of incoming human papillomavirus (HPV DNA in the early stages of infection. In this follow up study, we show that Sp100 does not substantially regulate viral infection in the maintenance phase, however at late stages of infection Sp100 interacts with amplifying viral genomes to repress viral processes. We find that Sp100 localizes to HPV16 replication foci generated in primary keratinocytes, to HPV31 replication foci that form in differentiated cells, and to HPV16 replication foci in CIN 1 cervical biopsies. To analyze this further, Sp100 was down regulated by siRNA treatment of differentiating HPV31 containing cells and levels of viral transcription and replication were assessed. This revealed that Sp100 represses viral transcription and replication in differentiated cells. Analysis of Sp100 binding to viral chromatin showed that Sp100 bound across the viral genome, and that binding increased at late stages of infection. Therefore, Sp100 represses the HPV life cycle at both early and late stages of infection.

  8. CS EMISSION NEAR MIR-BUBBLES

    International Nuclear Information System (INIS)

    Watson, C.; Devine, Kathryn; Quintanar, N.; Candelaria, T.

    2016-01-01

    We survey 44 young stellar objects located near the edges of mid-IR-identified bubbles in CS (1–0) using the Green Bank Telescope. We detect emission in 18 sources, indicating young protostars that are good candidates for being triggered by the expansion of the bubble. We calculate CS column densities and abundances. Three sources show evidence of infall through non-Gaussian line-shapes. Two of these sources are associated with dark clouds and are promising candidates for further exploration of potential triggered star formation. We obtained on-the-fly maps in CS (1–0) of three sources, showing evidence of significant interactions between the sources and the surrounding environment

  9. Computational analysis of ozonation in bubble columns

    International Nuclear Information System (INIS)

    Quinones-Bolanos, E.; Zhou, H.; Otten, L.

    2002-01-01

    This paper presents a new computational ozonation model based on the principle of computational fluid dynamics along with the kinetics of ozone decay and microbial inactivation to predict the performance of ozone disinfection in fine bubble columns. The model can be represented using a mixture two-phase flow model to simulate the hydrodynamics of the water flow and using two transport equations to track the concentration profiles of ozone and microorganisms along the height of the column, respectively. The applicability of this model was then demonstrated by comparing the simulated ozone concentrations with experimental measurements obtained from a pilot scale fine bubble column. One distinct advantage of this approach is that it does not require the prerequisite assumptions such as plug flow condition, perfect mixing, tanks-in-series, uniform radial or longitudinal dispersion in predicting the performance of disinfection contactors without carrying out expensive and tedious tracer studies. (author)

  10. The Recent Financial Bubble: an Overview

    Directory of Open Access Journals (Sweden)

    Thalassinos E.

    2009-12-01

    Full Text Available The main aim of this paper is to analyse the recent financial crisis and to make recommendations how to handle it in the best possible way. Financial bubbles, since the great depression, have been analysed and some recommendations have been made taking into account the internationalization of the world economy which behaves like a domino. The recent financial crisis in the sub-prime mortgage market creates new problems in the world market with unforeseen continuances. Deflation has been referred to as a possible continuance after a financial bubble because often but not always deflation follows. Deflation often results in financial and economic crises. Financial and economic crises affect the architecture of the monetary system, while a change in the system may affect the role of the dollar, the euro and the yen.

  11. Bubbling surface operators and S-duality

    International Nuclear Information System (INIS)

    Gomis, Jaume; Matsuura, Shunji

    2007-01-01

    We construct smooth asymptotically /ADS solutions of Type IIB supergravity corresponding to all the half-BPS surface operators in N = 4 SYM. All the parameters labeling a half-BPS surface operator are identified in the corresponding bubbling geometry. We use the supergravity description of surface operators to study the action of the SL(2,Z) duality group of N 4 SYM on the parameters of the surface operator, and find that it coincides with the recent proposal by Gukov and Witten in the framework of the gauge theory approach to the geometrical Langlands with ramification. We also show that whenever a bubbling geometry becomes singular that the path integral description of the corresponding surface operator also becomes singular

  12. Hydrodynamics of ultra-relativistic bubble walls

    Directory of Open Access Journals (Sweden)

    Leonardo Leitao

    2016-04-01

    Full Text Available In cosmological first-order phase transitions, gravitational waves are generated by the collisions of bubble walls and by the bulk motions caused in the fluid. A sizeable signal may result from fast-moving walls. In this work we study the hydrodynamics associated to the fastest propagation modes, namely, ultra-relativistic detonations and runaway solutions. We compute the energy injected by the phase transition into the fluid and the energy which accumulates in the bubble walls. We provide analytic approximations and fits as functions of the net force acting on the wall, which can be readily evaluated for specific models. We also study the back-reaction of hydrodynamics on the wall motion, and we discuss the extrapolation of the friction force away from the ultra-relativistic limit. We use these results to estimate the gravitational wave signal from detonations and runaway walls.

  13. Hydrodynamics of ultra-relativistic bubble walls

    Energy Technology Data Exchange (ETDEWEB)

    Leitao, Leonardo, E-mail: lleitao@mdp.edu.ar; Mégevand, Ariel, E-mail: megevand@mdp.edu.ar

    2016-04-15

    In cosmological first-order phase transitions, gravitational waves are generated by the collisions of bubble walls and by the bulk motions caused in the fluid. A sizeable signal may result from fast-moving walls. In this work we study the hydrodynamics associated to the fastest propagation modes, namely, ultra-relativistic detonations and runaway solutions. We compute the energy injected by the phase transition into the fluid and the energy which accumulates in the bubble walls. We provide analytic approximations and fits as functions of the net force acting on the wall, which can be readily evaluated for specific models. We also study the back-reaction of hydrodynamics on the wall motion, and we discuss the extrapolation of the friction force away from the ultra-relativistic limit. We use these results to estimate the gravitational wave signal from detonations and runaway walls.

  14. Hydrodynamic models for slurry bubble column reactors

    Energy Technology Data Exchange (ETDEWEB)

    Gidaspow, D. [IIT Center, Chicago, IL (United States)

    1995-12-31

    The objective of this investigation is to convert a {open_quotes}learning gas-solid-liquid{close_quotes} fluidization model into a predictive design model. This model is capable of predicting local gas, liquid and solids hold-ups and the basic flow regimes: the uniform bubbling, the industrially practical churn-turbulent (bubble coalescence) and the slugging regimes. Current reactor models incorrectly assume that the gas and the particle hold-ups (volume fractions) are uniform in the reactor. They must be given in terms of empirical correlations determined under conditions that radically differ from reactor operation. In the proposed hydrodynamic approach these hold-ups are computed from separate phase momentum balances. Furthermore, the kinetic theory approach computes the high slurry viscosities from collisions of the catalyst particles. Thus particle rheology is not an input into the model.

  15. CS EMISSION NEAR MIR-BUBBLES

    Energy Technology Data Exchange (ETDEWEB)

    Watson, C. [Manchester University, Department of Physics, 604 E. College Ave., North Manchester, IN 46962 (United States); Devine, Kathryn [College of Idaho, Department of Physics, 2112 Cleveland Blvd, Caldwell, ID 83605 (United States); Quintanar, N. [Texas A and M University, Department of Nuclear Engineering, 401 Joe Routt Blvd, College Station, TX 77843 (United States); Candelaria, T., E-mail: cwatson@manchester.edu, E-mail: KDevine@collegeofidaho.edu, E-mail: nrquintanar@tamu.edu, E-mail: tcandela@nmt.edu [New Mexico Institute of Mining and Technology, Department of Physics, 801 Leroy Place, Socorro, NM 87801 (United States)

    2016-02-10

    We survey 44 young stellar objects located near the edges of mid-IR-identified bubbles in CS (1–0) using the Green Bank Telescope. We detect emission in 18 sources, indicating young protostars that are good candidates for being triggered by the expansion of the bubble. We calculate CS column densities and abundances. Three sources show evidence of infall through non-Gaussian line-shapes. Two of these sources are associated with dark clouds and are promising candidates for further exploration of potential triggered star formation. We obtained on-the-fly maps in CS (1–0) of three sources, showing evidence of significant interactions between the sources and the surrounding environment.

  16. Rapid-Cycling Bubble-Chamber, details

    CERN Multimedia

    CERN PhotoLab

    1980-01-01

    Parts of the hydraulic expansion system of the Rapid-Cycling Bubble-Chamber (RCBC). RCBC was the largest of 3 rapid-cycling bubble-chambers (the others were LEBC and HOLEBC), used as target- and vertex-detectors within the European Hybrid Spectrometer (EHS) in the SPS North Area (EHN1). RCBC contained 250 l of liquid hydrogen and was located inside a 3 T superconducting magnet. It was designed for 30 expansions/s (100 times faster than BEBC), the system shown here allowed 50 expansions/s. RCBC operated from 1981 to 1983 for experiments NA21, NA22 and NA23 at a rate of 15 expansions/s, clocking up a total of over 4 million. In the rear, at left, is bearded Lucien Veillet; Augustin Didona is at the right. See also 8001009. The installation of the piston assembly in the RCBC chamber body is shown in the Annual Report 1980, p.65.

  17. Chromosome replication, cell growth, division and shape: a personal perspective

    Directory of Open Access Journals (Sweden)

    Arieh eZaritsky

    2015-08-01

    Full Text Available The origins of Molecular Biology and Bacterial Physiology are reviewed, from our personal standpoints, emphasizing the coupling between bacterial growth, chromosome replication and cell division, dimensions and shape. Current knowledge is discussed with historical perspective, summarizing past and present achievements and enlightening ideas for future studies. An interactive simulation program of the Bacterial Cell Division Cycle (BCD, described as The Central Dogma in Bacteriology, is briefly represented. The coupled process of transcription/translation of genes encoding membrane proteins and insertion into the membrane (so-called transertion is invoked as the functional relationship between the only two unique macromolecules in the cell, DNA and peptidoglycan embodying the nucleoid and the sacculus respectively. We envision that nucleoid complexity, defined as the weighted-mean DNA content associated with the replication terminus, is directly related to cell shape through the transertion process. Accordingly, the primary signal for cell division transmitted by DNA dynamics (replication, transcription and segregation to the peptidoglycan biosynthetic machinery is of a physico-chemical nature, eg stress in the plasma membrane, relieving nucleoid occlusion in the cell's center hence enabling the divisome to assemble and function between segregated daughter nucleoids.

  18. The Bern Infinitesimal Bubble Chamber (BIBC)

    CERN Multimedia

    CERN PhotoLab

    1977-01-01

    The chamber body was machined from a block of aluminium. The visible volume was cylindrical with 65 mm diameter and 35 mm depth. It was filled with propane or freon. It was meant as vertex detector in the search of short-lived particles. It was also used with in-line holography resulting in 8 µm bubble size and 9 cm depth of the field. See E. Ramseyer, B. Hahn and E. Hugentobler, Nucl. Instrum. Methods 201 (1982) 335.

  19. Expendable bubble tiltmeter for geophysical monitoring

    OpenAIRE

    Westphal, J. A.; Carr, M. A.; Miller, W. F.; Dzurisin, Daniel

    1983-01-01

    An unusually rugged highly sensitive and inexpensive bubble tiltmeter has been designed, tested, and built in quantity. These tiltmeters are presently used on two volcanoes and an Alaskan glacier, where they continuously monitor surface tilts of geological interest. This paper discusses the mechanical, thermal, and electric details of the meter, and illustrates its performance characteristics in both large ( > 10^(-4) radian) and small ( < 10^(-6) radian) tilt environments. The meter's ult...

  20. On the shape of giant soap bubbles

    NARCIS (Netherlands)

    Cohen, C.; Darbois Texier, B.; Reyssat, E.; Snoeijer, Jacobus Hendrikus; Quere, D.; Clanet, Christophe

    2017-01-01

    We study the effect of gravity on giant soap bubbles and show that it becomes dominant above the critical size ℓ=a2/e0ℓ=a2/e0, where e0e0 is the mean thickness of the soap film and a=γb/ρg−√a=γb/ρg is the capillary length ( γbγb stands for vapor–liquid surface tension, and ρρ stands for the liquid