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.

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....

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...

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....

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.

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

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.

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.

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.

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.

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.

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.

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.

Ancient mtDNA genetic variants modulate mtDNA transcription and replication.

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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

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

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

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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.

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.

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...

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 ...

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.

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.

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

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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.

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

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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.

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.

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.

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

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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.

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

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

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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.

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.

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.

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

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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.

Pinch-off Scaling Law of Soap Bubbles

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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.

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

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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.

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

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

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

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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.

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

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

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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

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...

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

Gene organization inside replication domains in mammalian genomes

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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.

Activation-induced deoxycytidine deaminase (AID) co-transcriptional scanning at single-molecule resolution

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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.

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

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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.

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

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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

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.

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.

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.

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

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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

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

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

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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.

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

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)

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

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....

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

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

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

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

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.

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

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.

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.

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

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.

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.

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.

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.

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.

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.

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

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

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.

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....

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.

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.

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.

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

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)

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.

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)

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.

Calcein represses human papillomavirus 16 E1-E2 mediated DNA replication via blocking their binding to the viral origin of replication.

Science.gov (United States)

Das, Dipon; Smith, Nathan W; Wang, Xu; Richardson, Stacie L; Hartman, Matthew C T; Morgan, Iain M

2017-08-01

Human papillomaviruses are causative agents in several human diseases ranging from genital warts to ano-genital and oropharyngeal cancers. Currently only symptoms of HPV induced disease are treated; there are no antivirals available that directly target the viral life cycle. Previously, we determined that the cellular protein TopBP1 interacts with the HPV16 replication/transcription factor E2. This E2-TopBP1 interaction is essential for optimal E1-E2 DNA replication and for the viral life cycle. The drug calcein disrupts the interaction of TopBP1 with itself and other host proteins to promote cell death. Here we demonstrate that calcein blocks HPV16 E1-E2 DNA replication via blocking the viral replication complex forming at the origin of replication. This occurs at non-toxic levels of calcein and demonstrates specificity as it does not block the ability of E2 to regulate transcription. We propose that calcein or derivatives could be developed as an anti-HPV therapeutic. Copyright © 2017 Elsevier Inc. All rights reserved.

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....

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)

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, ...

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...

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.

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

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

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.

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...

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.

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.

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.

Selective recruitment of nuclear factors to productively replicating herpes simplex virus genomes.

Science.gov (United States)

Dembowski, Jill A; DeLuca, Neal A

2015-05-01

Much of the HSV-1 life cycle is carried out in the cell nucleus, including the expression, replication, repair, and packaging of viral genomes. Viral proteins, as well as cellular factors, play essential roles in these processes. Isolation of proteins on nascent DNA (iPOND) was developed to label and purify cellular replication forks. We adapted aspects of this method to label viral genomes to both image, and purify replicating HSV-1 genomes for the identification of associated proteins. Many viral and cellular factors were enriched on viral genomes, including factors that mediate DNA replication, repair, chromatin remodeling, transcription, and RNA processing. As infection proceeded, packaging and structural components were enriched to a greater extent. Among the more abundant proteins that copurified with genomes were the viral transcription factor ICP4 and the replication protein ICP8. Furthermore, all seven viral replication proteins were enriched on viral genomes, along with cellular PCNA and topoisomerases, while other cellular replication proteins were not detected. The chromatin-remodeling complexes present on viral genomes included the INO80, SWI/SNF, NURD, and FACT complexes, which may prevent chromatinization of the genome. Consistent with this conclusion, histones were not readily recovered with purified viral genomes, and imaging studies revealed an underrepresentation of histones on viral genomes. RNA polymerase II, the mediator complex, TFIID, TFIIH, and several other transcriptional activators and repressors were also affinity purified with viral DNA. The presence of INO80, NURD, SWI/SNF, mediator, TFIID, and TFIIH components is consistent with previous studies in which these complexes copurified with ICP4. Therefore, ICP4 is likely involved in the recruitment of these key cellular chromatin remodeling and transcription factors to viral genomes. Taken together, iPOND is a valuable method for the study of viral genome dynamics during infection and

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.

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.

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.

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.

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).

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.

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)

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

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.

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.

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.

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...

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.

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

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

PRC1 Prevents Replication Stress during Chondrogenic Transit Amplification

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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.

Segment-specific terminal sequences of Bunyamwera bunyavirus regulate genome replication

International Nuclear Information System (INIS)

Barr, John N.; Elliott, Richard M.; Dunn, Ewan F.; Wertz, Gail W.

2003-01-01

Bunyamwera virus (BUNV) is the prototype of both the Orthobunyavirus genus and the Bunyaviridae family of segmented negative sense RNA viruses. The tripartite BUNV genome consists of small (S), medium (M), and large (L) segments that are transcribed to give a single mRNA and replicated to generate an antigenome that is the template for synthesis of further genomic RNA strands. We modified an existing cDNA-derived RNA synthesis system to allow identification of BUNV RNA replication and transcription products by direct metabolic labeling. Direct RNA analysis allowed us to distinguish between template activities that affected either RNA replication or mRNA transcription, an ability that was not possible using previous reporter gene expression assays. We generated genome analogs containing the entire nontranslated terminal sequences of the S, M, and L BUNV segments surrounding a common sequence. Analysis of RNAs synthesized from these templates revealed that the relative abilities of BUNV segments to perform RNA replication was M > L > S. Exchange of segment-specific terminal nucleotides identified a 12-nt region located within both the 3' and 5' termini of the M segment that correlated with its high replication ability

Transcription profiling suggests that mitochondrial topoisomerase IB acts as a topological barrier and regulator of mitochondrial DNA transcription.

Science.gov (United States)

Dalla Rosa, Ilaria; Zhang, Hongliang; Khiati, Salim; Wu, Xiaolin; Pommier, Yves

2017-12-08

Mitochondrial DNA (mtDNA) is essential for cell viability because it encodes subunits of the respiratory chain complexes. Mitochondrial topoisomerase IB (TOP1MT) facilitates mtDNA replication by removing DNA topological tensions produced during mtDNA transcription, but it appears to be dispensable. To test whether cells lacking TOP1MT have aberrant mtDNA transcription, we performed mitochondrial transcriptome profiling. To that end, we designed and implemented a customized tiling array, which enabled genome-wide, strand-specific, and simultaneous detection of all mitochondrial transcripts. Our technique revealed that Top1mt KO mouse cells process the mitochondrial transcripts normally but that protein-coding mitochondrial transcripts are elevated. Moreover, we found discrete long noncoding RNAs produced by H-strand transcription and encompassing the noncoding regulatory region of mtDNA in human and murine cells and tissues. Of note, these noncoding RNAs were strongly up-regulated in the absence of TOP1MT. In contrast, 7S DNA, produced by mtDNA replication, was reduced in the Top1mt KO cells. We propose that the long noncoding RNA species in the D-loop region are generated by the extension of H-strand transcripts beyond their canonical stop site and that TOP1MT acts as a topological barrier and regulator for mtDNA transcription and D-loop formation.

Selective recruitment of nuclear factors to productively replicating herpes simplex virus genomes.

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Jill A Dembowski

2015-05-01

Full Text Available Much of the HSV-1 life cycle is carried out in the cell nucleus, including the expression, replication, repair, and packaging of viral genomes. Viral proteins, as well as cellular factors, play essential roles in these processes. Isolation of proteins on nascent DNA (iPOND was developed to label and purify cellular replication forks. We adapted aspects of this method to label viral genomes to both image, and purify replicating HSV-1 genomes for the identification of associated proteins. Many viral and cellular factors were enriched on viral genomes, including factors that mediate DNA replication, repair, chromatin remodeling, transcription, and RNA processing. As infection proceeded, packaging and structural components were enriched to a greater extent. Among the more abundant proteins that copurified with genomes were the viral transcription factor ICP4 and the replication protein ICP8. Furthermore, all seven viral replication proteins were enriched on viral genomes, along with cellular PCNA and topoisomerases, while other cellular replication proteins were not detected. The chromatin-remodeling complexes present on viral genomes included the INO80, SWI/SNF, NURD, and FACT complexes, which may prevent chromatinization of the genome. Consistent with this conclusion, histones were not readily recovered with purified viral genomes, and imaging studies revealed an underrepresentation of histones on viral genomes. RNA polymerase II, the mediator complex, TFIID, TFIIH, and several other transcriptional activators and repressors were also affinity purified with viral DNA. The presence of INO80, NURD, SWI/SNF, mediator, TFIID, and TFIIH components is consistent with previous studies in which these complexes copurified with ICP4. Therefore, ICP4 is likely involved in the recruitment of these key cellular chromatin remodeling and transcription factors to viral genomes. Taken together, iPOND is a valuable method for the study of viral genome dynamics

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)

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.

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.

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)

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.

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.

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

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

Crystallization and preliminary X-ray characterization of the eukaryotic replication terminator Reb1-Ter DNA complex.

Science.gov (United States)

Jaiswal, Rahul; Singh, Samarendra K; Bastia, Deepak; Escalante, Carlos R

2015-04-01

The Reb1 protein from Schizosaccharomyces pombe is a member of a family of proteins that control programmed replication termination and/or transcription termination in eukaryotic cells. These events occur at naturally occurring replication fork barriers (RFBs), where Reb1 binds to termination (Ter) DNA sites and coordinates the polar arrest of replication forks and transcription approaching in opposite directions. The Reb1 DNA-binding and replication-termination domain was expressed in Escherichia coli, purified and crystallized in complex with a 26-mer DNA Ter site. Batch crystallization under oil was required to produce crystals of good quality for data collection. Crystals grew in space group P2₁, with unit-cell parameters a = 68.9, b = 162.9, c = 71.1 Å, β = 94.7°. The crystals diffracted to a resolution of 3.0 Å. The crystals were mosaic and required two or three cycles of annealing. This study is the first to yield structural information about this important family of proteins and will provide insights into the mechanism of replication and transcription termination.

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. ...

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.

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.

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.

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.

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.

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

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.

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.

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.)

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

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.

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.

Inhibition of spring viraemia of carp virus replication in an Epithelioma papulosum cyprini cell line by RNAi

Science.gov (United States)

Gotesman, M; Soliman, H; Besch, R; El-Matbouli, M

2015-01-01

Spring viraemia of carp virus (SVCV) is an aetiological agent of a serious disease affecting carp farms in Europe and is a member of the Rhabdoviridae family of viruses. The genome of SVCV codes for five proteins: nucleoprotein (N), phosphoprotein (P), matrix protein (M), glycoprotein (G) and RNA-dependent RNA polymerase (L). RNA-mediated interference (RNAi) by small interfering RNAs (siRNAs) is a powerful tool to inhibit gene transcription and is used to study genes important for viral replication. In previous studies regarding another member of Rhabdoviridae, siRNA inhibition of the rabies virus nucleoprotein gene provided in vitro and in vivo protection against rabies. In this study, synthetic siRNA molecules were designed to target SVCV-N and SVCV-P transcripts to inhibit SVCV replication and were tested in an epithelioma papulosum cyprini (EPC) cell line. Inhibition of gene transcription was measured by real-time quantitative reverse-transcription PCR (RT-qPCR). The efficacy of using siRNA for inhibition of viral replication was analysed by RT-qPCR measurement of a reporter gene (glycoprotein) expression and by virus endpoint titration. Inhibition of nucleoprotein and phosphoprotein gene expression by siRNA reduced SVCV replication. However, use of tandem siRNAs that target phosphoprotein and nucleoprotein worked best at reducing SVCV replication. PMID:24460815

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)

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.

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.

Evidence for gene-specific rather than transcription rate-dependent histone H3 exchange in yeast coding regions.

Science.gov (United States)

Gat-Viks, Irit; Vingron, Martin

2009-02-01

In eukaryotic organisms, histones are dynamically exchanged independently of DNA replication. Recent reports show that different coding regions differ in their amount of replication-independent histone H3 exchange. The current paradigm is that this histone exchange variability among coding regions is a consequence of transcription rate. Here we put forward the idea that this variability might be also modulated in a gene-specific manner independently of transcription rate. To that end, we study transcription rate-independent replication-independent coding region histone H3 exchange. We term such events relative exchange. Our genome-wide analysis shows conclusively that in yeast, relative exchange is a novel consistent feature of coding regions. Outside of replication, each coding region has a characteristic pattern of histone H3 exchange that is either higher or lower than what was expected by its RNAPII transcription rate alone. Histone H3 exchange in coding regions might be a way to add or remove certain histone modifications that are important for transcription elongation. Therefore, our results that gene-specific coding region histone H3 exchange is decoupled from transcription rate might hint at a new epigenetic mechanism of transcription regulation.

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

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.

Dynamics of bubble-bubble interaction in sheared low-viscosity magma imaged by X-ray computed micro-tomography

Science.gov (United States)

Helo, C.; Flaws, A.; Hess, K.-U.; Franz, A.; Clague, D. A.; Dingwell, D. B.

2012-04-01

X-ray computed tomography of vesicles in basaltic pyroclastic glass fragments has been used to investigate the syn-eruptive shear environment and resulting bubble-bubble interaction during mild pyroclastic eruptions in a mid-ocean ridge environment. We have imaged vesicles present in two different types of pyroclastic fragments produced by mildly explosive activity on Axial Seamount, limu o Pele, that is, thin glass films often described as bubble walls, and tube scoria fragments. Rapid quenching of the glass has prevented extensive bubble relaxation preserving the syn-eruptive geometry of the bubbles in these fragments. Isolated, ellipsoid-shaped vesicles in low-vesicular limu o Pele indicate deformation in a simple shear environment. Under these shear conditions higher vesiculated parts of the erupting magma show strong bubble-bubble interactions partially leading to coalscence and formation of tubular vesicles. These tubular vesicles can reach significant lengths, exceeding the dimensions of the small glass fragments (2 mm). Their unreformed radius can be more then one order of magnitude larger than that of the isolated vesicles in the limu o Pele fragments. We can distinguish two principle modes of interaction based on the relative orientation of the bubbles. Interaction along the sidewalls of two bubbles, and tip-to-tip interaction. At interdistances of less than a few tens of micrometre, interaction of the sidewalls results in deformation of the bubbles to more irregular shapes, with depressions caused by close, small bubbles or in some cases bubbles being partially mantled around tubular bubbles. This often leads to a more close packing of bubbles. At distances of less than a few microns, the melt films between the bubbles destabilize leading to coalescence. This mechanism appears to involve a bulging of the larger bubble into the smaller, followed by melt film rapture and coalescence. The complete digestion of one bubble by the other is the slow rate

Fermi Bubble: Giant Gamma-Ray Bubbles in the Milky Way

Science.gov (United States)

Su, Meng

Data from the Fermi-LAT reveal two gigantic gamma-ray emitting bubble structures (known as the Fermibubbles), extending˜50° above and below the Galactic center symmetric about the Galactic plane, with a width of˜40∘ in longitude. The gamma-ray emission associated with these bubbles has a significantly harder spectrum ({dN}/{dE} ˜ {E}^{-2}) than the inverse Compton emission from known cosmic ray electrons in the Galactic disk, or the gamma-rays produced by decay of pions from proton-ISM collisions. The bubbles are spatially correlated with the hard-spectrum microwave excess known as the WMAPhaze; the edges of the bubbles also line up with features in the ROSATsoft X-ray maps at 1.5-2keV. The Fermibubble is most likely created by some large episode of energy injection in the Galactic center, such as past accretion events onto the central massive black hole, or a nuclear starburst in the last˜10Myr. Study of the origin and evolution of the bubbles also has the potential to improve our understanding of recent energetic events in the inner Galaxy and the high-latitude cosmic ray population.

Intragenic origins due to short G1 phases underlie oncogene-induced DNA replication stress.

Science.gov (United States)

Macheret, Morgane; Halazonetis, Thanos D

2018-03-01

Oncogene-induced DNA replication stress contributes critically to the genomic instability that is present in cancer. However, elucidating how oncogenes deregulate DNA replication has been impeded by difficulty in mapping replication initiation sites on the human genome. Here, using a sensitive assay to monitor nascent DNA synthesis in early S phase, we identified thousands of replication initiation sites in cells before and after induction of the oncogenes CCNE1 and MYC. Remarkably, both oncogenes induced firing of a novel set of DNA replication origins that mapped within highly transcribed genes. These ectopic origins were normally suppressed by transcription during G1, but precocious entry into S phase, before all genic regions had been transcribed, allowed firing of origins within genes in cells with activated oncogenes. Forks from oncogene-induced origins were prone to collapse, as a result of conflicts between replication and transcription, and were associated with DNA double-stranded break formation and chromosomal rearrangement breakpoints both in our experimental system and in a large cohort of human cancers. Thus, firing of intragenic origins caused by premature S phase entry represents a mechanism of oncogene-induced DNA replication stress that is relevant for genomic instability in human cancer.

Opposite replication polarities of transcribed and nontranscribed histone H5 genes

International Nuclear Information System (INIS)

Trempe, J.P.; Lindstrom, Y.I.; Leffak, M.

1988-01-01

The authors used an in vitro nuclear runoff replication assay to analyze the direction of replication of the active and inactive histone H5 genes in avian cells. In embryonic erythrocytes the transcribed histone H5 gene displayed sensitivity to endogenous nuclease cleavage. In contrast, this gene was insensitive to endogenous nuclease digestion under the same conditions in nuclei of the lymphoblastoid cell line MSB-1, and histone H5 gene transcripts were not detectable by dot-blot analysis of MSB-1 cell RNA. When nuclei were isolated from embryonic erythrocyctes and incubated with bromodeoxyuridine triphosphate, runoff replication from endogenous nuclease cleavage sites led to a relative enrichment for fragments near the 3' end of the histone H5 gene in the density-labeled DNA. In nuclei of MSB-1 cells or chicken embryo fibroblasts, however, runoff replication from restriction enzyme-cut sites (or induced endogenous nuclease-cut sites in MSB-1 nuclei) led to a relative enrichment for fragments near the 5' end of the H5 gene in dense DNA. Based on the enhanced incorporation of bromodeoxyuridine into origin-distal regions of DNA during the in vitro runoff replication assay, the authors conclude that the active histone H5 gene in embryonic erythrocytes is preferentially replicated in the transcriptional direction from an origin in the 5'-flanking DNA, whereas its inactive counterparts in MSB-1 cells and chicken embryo fibroblasts are preferentially replicated in the opposite direction

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.

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...

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...

Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation.

Science.gov (United States)

Glyde, Robert; Ye, Fuzhou; Darbari, Vidya Chandran; Zhang, Nan; Buck, Martin; Zhang, Xiaodong

2017-07-06

Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DNA is delivered to the RNAP active site. Using a bacterial RNAP containing the alternative σ 54 factor and cryoelectron microscopy, we determined structures of RPc and the activator-bound intermediate complex en route to RPo at 3.8 and 5.8 Å. Our structures show how RNAP-σ 54 interacts with promoter DNA to initiate the DNA distortions required for transcription bubble formation, and how the activator interacts with RPc, leading to significant conformational changes in RNAP and σ 54 that promote RPo formation. We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Iron chelators ICL670 and 311 inhibit HIV-1 transcription

International Nuclear Information System (INIS)

Debebe, Zufan; Ammosova, Tatyana; Jerebtsova, Marina; Kurantsin-Mills, Joseph; Niu, Xiaomei; Charles, Sharroya; Richardson, Des R.; Ray, Patricio E.; Gordeuk, Victor R.; Nekhai, Sergei

2007-01-01

HIV-1 replication is induced by an excess of iron and iron chelation by desferrioxamine (DFO) inhibits viral replication by reducing proliferation of infected cells. Treatment of cells with DFO and 2-hydroxy-1-naphthylaldehyde isonicotinoyl hydrazone (311) inhibit expression of proteins that regulate cell-cycle progression, including cycle-dependent kinase 2 (CDK2). Our recent studies showed that CDK2 participates in HIV-1 transcription and viral replication suggesting that inhibition of CDK2 by iron chelators might also affect HIV-1 transcription. Here we evaluated the effect of a clinically approved orally effective iron chelator, 4-[3,5-bis-(hydroxyphenyl)-1,2,4-triazol-1-yl]-benzoic acid (ICL670) and 311 on HIV-1 transcription. Both ICL670 and 311 inhibited Tat-induced HIV-1 transcription in CEM-T cells, 293T and HeLa cells. Neither ICL670 nor 311 induced cytotoxicity at concentrations that inhibited HIV-1 transcription. The chelators decreased cellular activity of CDK2 and reduced HIV-1 Tat phosphorylation by CDK2. Neither ICL670A or 311 decreased CDK9 protein level but significantly reduced association of CDK9 with cyclin T1 and reduced phosphorylation of Ser-2 residues of RNA polymerase II C-terminal domain. In conclusion, our findings add to the evidence that iron chelators can inhibit HIV-1 transcription by deregulating CDK2 and CDK9. Further consideration should be given to the development of iron chelators for future anti-retroviral therapeutics

Inhibition of spring viraemia of carp virus replication in an Epithelioma papulosum cyprini cell line by RNAi.

Science.gov (United States)

Gotesman, M; Soliman, H; Besch, R; El-Matbouli, M

2015-02-01

Spring viraemia of carp virus (SVCV) is an aetiological agent of a serious disease affecting carp farms in Europe and is a member of the Rhabdoviridae family of viruses. The genome of SVCV codes for five proteins: nucleoprotein (N), phosphoprotein (P), matrix protein (M), glycoprotein (G) and RNA-dependent RNA polymerase (L). RNA-mediated interference (RNAi) by small interfering RNAs (siRNAs) is a powerful tool to inhibit gene transcription and is used to study genes important for viral replication. In previous studies regarding another member of Rhabdoviridae, siRNA inhibition of the rabies virus nucleoprotein gene provided in vitro and in vivo protection against rabies. In this study, synthetic siRNA molecules were designed to target SVCV-N and SVCV-P transcripts to inhibit SVCV replication and were tested in an epithelioma papulosum cyprini (EPC) cell line. Inhibition of gene transcription was measured by real-time quantitative reverse-transcription PCR (RT-qPCR). The efficacy of using siRNA for inhibition of viral replication was analysed by RT-qPCR measurement of a reporter gene (glycoprotein) expression and by virus endpoint titration. Inhibition of nucleoprotein and phosphoprotein gene expression by siRNA reduced SVCV replication. However, use of tandem siRNAs that target phosphoprotein and nucleoprotein worked best at reducing SVCV replication. © 2014 The Authors. Journal of Fish Diseases published by John Wiley & Sons Ltd.

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.

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.

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.

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...

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

Bubble propagation on a rail: a concept for sorting bubbles by size

Science.gov (United States)

Franco-Gómez, Andrés; Thompson, Alice B.; Hazel, Andrew L.; Juel, Anne

We demonstrate experimentally that the introduction of a rail, a small height constriction, within the cross-section of a rectangular channel could be used as a robust passive sorting device in two-phase fluid flows. Single air bubbles carried within silicone oil are generally transported on one side of the rail. However, for flow rates marginally larger than a critical value, a narrow band of bubble sizes can propagate (stably) over the rail, while bubbles of other sizes segregate to the side of the rail. The width of this band of bubble sizes increases with flow rate and the size of the most stable bubble can be tuned by varying the rail width. We present a complementary theoretical analysis based on a depth-averaged theory, which is in qualitative agreement with the experiments. The theoretical study reveals that the mechanism relies on a non-trivial interaction between capillary and viscous forces that is fully dynamic, rather than being a simple modification of capillary static solutions.

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...

Zika Virus RNA Replication and Persistence in Brain and Placental Tissue

Science.gov (United States)

Rabeneck, Demi B.; Martines, Roosecelis B.; Reagan-Steiner, Sarah; Ermias, Yokabed; Estetter, Lindsey B.C.; Suzuki, Tadaki; Ritter, Jana; Keating, M. Kelly; Hale, Gillian; Gary, Joy; Muehlenbachs, Atis; Lambert, Amy; Lanciotti, Robert; Oduyebo, Titilope; Meaney-Delman, Dana; Bolaños, Fernando; Saad, Edgar Alberto Parra; Shieh, Wun-Ju; Zaki, Sherif R.

2017-01-01

Zika virus is causally linked with congenital microcephaly and may be associated with pregnancy loss. However, the mechanisms of Zika virus intrauterine transmission and replication and its tropism and persistence in tissues are poorly understood. We tested tissues from 52 case-patients: 8 infants with microcephaly who died and 44 women suspected of being infected with Zika virus during pregnancy. By reverse transcription PCR, tissues from 32 (62%) case-patients (brains from 8 infants with microcephaly and placental/fetal tissues from 24 women) were positive for Zika virus. In situ hybridization localized replicative Zika virus RNA in brains of 7 infants and in placentas of 9 women who had pregnancy losses during the first or second trimester. These findings demonstrate that Zika virus replicates and persists in fetal brains and placentas, providing direct evidence of its association with microcephaly. Tissue-based reverse transcription PCR extends the time frame of Zika virus detection in congenital and pregnancy-associated infections. PMID:27959260

Checkpoint-dependent RNR induction promotes fork restart after replicative stress.

Science.gov (United States)

Morafraile, Esther C; Diffley, John F X; Tercero, José Antonio; Segurado, Mónica

2015-01-20

The checkpoint kinase Rad53 is crucial to regulate DNA replication in the presence of replicative stress. Under conditions that interfere with the progression of replication forks, Rad53 prevents Exo1-dependent fork degradation. However, although EXO1 deletion avoids fork degradation in rad53 mutants, it does not suppress their sensitivity to the ribonucleotide reductase (RNR) inhibitor hydroxyurea (HU). In this case, the inability to restart stalled forks is likely to account for the lethality of rad53 mutant cells after replication blocks. Here we show that Rad53 regulates replication restart through the checkpoint-dependent transcriptional response, and more specifically, through RNR induction. Thus, in addition to preventing fork degradation, Rad53 prevents cell death in the presence of HU by regulating RNR-expression and localization. When RNR is induced in the absence of Exo1 and RNR negative regulators, cell viability of rad53 mutants treated with HU is increased and the ability of replication forks to restart after replicative stress is restored.

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

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

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

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.

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.

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

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.

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.

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

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)

A test of the transcription model for biased inheritance of yeast mitochondrial DNA.

Science.gov (United States)

Lorimer, H E; Brewer, B J; Fangman, W L

1995-09-01

Two strand-specific origins of replication appear to be required for mammalian mitochondrial DNA (mtDNA) replication. Structural equivalents of these origins are found in the rep sequences of Saccharomyces cerevisiae mtDNA. These striking similarities have contributed to a universal model for the initiation of mtDNA replication in which a primer is created by cleavage of an origin region transcript. Consistent with this model are the properties of deletion mutants of yeast mtDNA ([rho-]) with a high density of reps (HS [rho-]). These mutant mtDNAs are preferentially inherited by the progeny resulting from the mating of HS [rho-] cells with cells containing wild-type mtDNA ([rho+]). This bias is presumed to result from a replication advantage conferred on HS [rho-] mtDNA by the high density of rep sequences acting as origins. To test whether transcription is indeed required for the preferential inheritance of HS [rho-] mtDNA, we deleted the nuclear gene (RPO41) for the mitochondrial RNA polymerase, reducing transcripts by at least 1000-fold. Since [rho-] genomes, but not [rho+] genomes, are stable when RPO41 is deleted, we examined matings between HS [rho-] and neutral [rho-] cells. Neutral [rho-] mtDNAs lack rep sequences and are not preferentially inherited in [rho-] x [rho+] crosses. In HS [rho-] x neutral [rho-] matings, the HS [rho-] mtDNA was preferentially inherited whether both parents were wild type or both were deleted for RPO41. Thus, transcription from the rep promoter does not appear to be necessary for biased inheritance. Our results, and analysis of the literature, suggest that priming by transcription is not a universal mechanism for mtDNA replication initiation.

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

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...

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.)

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

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.

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

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.

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)

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

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.

Transcription of Small Surface Structures in Injection Moulding - An Experimental Study

DEFF Research Database (Denmark)

Arlø, Uffe Rolf; Kjær, Erik Michael

2000-01-01

The ability to replicate the surface roughness from mold wall to the plastic part in injection moldning has many functional and cosmetic important implications from medical use to designer products. Generally the understanding of surface transcription i.e the the replication of the surface...... structure from the mould to plastic part, also relates to micro injection moulding and moulding of parts with specific micro structures on the surface such as optical parts. The present study concerns transcription of surface roughness as a function of process parameters. The study is carried out...

Transcription of Small Surface Structures in Injection Molding - an Experimental Study

DEFF Research Database (Denmark)

Arlø, Uffe Rolf; Kjær, Erik Michael

2001-01-01

The ability to replicate the surface roughness from mold wall to the plastic part in injection moldning has many functional and cosmetic important implications from medical use to designer products. Generally the understanding of surface transcription i.e the the replication of the surface...... structure from the mould to plastic part, also relates to micro injection moulding and moulding of parts with specific micro structures on the surface such as optical parts. The present study concerns transcription of surface roughness as a function of process parameters. The study is carried out...

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

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

Cytology of DNA Replication Reveals Dynamic Plasticity of Large-Scale Chromatin Fibers.

Science.gov (United States)

Deng, Xiang; Zhironkina, Oxana A; Cherepanynets, Varvara D; Strelkova, Olga S; Kireev, Igor I; Belmont, Andrew S

2016-09-26

In higher eukaryotic interphase nuclei, the 100- to >1,000-fold linear compaction of chromatin is difficult to reconcile with its function as a template for transcription, replication, and repair. It is challenging to imagine how DNA and RNA polymerases with their associated molecular machinery would move along the DNA template without transient decondensation of observed large-scale chromatin "chromonema" fibers [1]. Transcription or "replication factory" models [2], in which polymerases remain fixed while DNA is reeled through, are similarly difficult to conceptualize without transient decondensation of these chromonema fibers. Here, we show how a dynamic plasticity of chromatin folding within large-scale chromatin fibers allows DNA replication to take place without significant changes in the global large-scale chromatin compaction or shape of these large-scale chromatin fibers. Time-lapse imaging of lac-operator-tagged chromosome regions shows no major change in the overall compaction of these chromosome regions during their DNA replication. Improved pulse-chase labeling of endogenous interphase chromosomes yields a model in which the global compaction and shape of large-Mbp chromatin domains remains largely invariant during DNA replication, with DNA within these domains undergoing significant movements and redistribution as they move into and then out of adjacent replication foci. In contrast to hierarchical folding models, this dynamic plasticity of large-scale chromatin organization explains how localized changes in DNA topology allow DNA replication to take place without an accompanying global unfolding of large-scale chromatin fibers while suggesting a possible mechanism for maintaining epigenetic programming of large-scale chromatin domains throughout DNA replication. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

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...

The mitochondrial transcription factor A functions in mitochondrial base excision repair

DEFF Research Database (Denmark)

Canugovi, Chandrika; Maynard, Scott; Bayne, Anne-Cécile V

2010-01-01

Mitochondrial transcription factor A (TFAM) is an essential component of mitochondrial nucleoids. TFAM plays an important role in mitochondrial transcription and replication. TFAM has been previously reported to inhibit nucleotide excision repair (NER) in vitro but NER has not yet been detected i...

Peretinoin, an Acyclic Retinoid, Inhibits Hepatitis B Virus Replication by Suppressing Sphingosine Metabolic Pathway In Vitro

Directory of Open Access Journals (Sweden)

Kazuhisa Murai

2018-01-01

Full Text Available Hepatocellular carcinoma (HCC frequently develops from hepatitis C virus (HCV and hepatitis B virus (HBV infection. We previously reported that peretinoin, an acyclic retinoid, inhibits HCV replication. This study aimed to examine the influence of peretinoin on the HBV lifecycle. HBV-DNA and covalently closed circular DNA (cccDNA were evaluated by a qPCR method in HepG2.2.15 cells. Peretinoin significantly reduced the levels of intracellular HBV-DNA, nuclear cccDNA, and HBV transcript at a concentration that did not induce cytotoxicity. Conversely, other retinoids, such as 9-cis, 13-cis retinoic acid (RA, and all-trans-retinoic acid (ATRA, had no effect or rather increased HBV replication. Mechanistically, although peretinoin increased the expression of HBV-related transcription factors, as observed for other retinoids, peretinoin enhanced the binding of histone deacetylase 1 (HDAC1 to cccDNA in the nucleus and negatively regulated HBV transcription. Moreover, peretinoin significantly inhibited the expression of SPHK1, a potential inhibitor of HDAC activity, and might be involved in hepatic inflammation, fibrosis, and HCC. SPHK1 overexpression in cells cancelled the inhibition of HBV replication induced by peretinoin. This indicates that peretinoin activates HDAC1 and thereby suppresses HBV replication by inhibiting the sphingosine metabolic pathway. Therefore, peretinoin may be a novel therapeutic agent for HBV replication and chemoprevention against HCC.

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.

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.

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.

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.

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

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

Heterochromatin Reorganization during Early Mouse Development Requires a Single-Stranded Noncoding Transcript

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Miguel Casanova

2013-09-01

Full Text Available The equalization of pericentric heterochromatin from distinct parental origins following fertilization is essential for genome function and development. The recent implication of noncoding transcripts in this process raises questions regarding the connection between RNA and the nuclear organization of distinct chromatin environments. Our study addresses the interrelationship between replication and transcription of the two parental pericentric heterochromatin (PHC domains and their reorganization during early embryonic development. We demonstrate that the replication of PHC is dispensable for its clustering at the late two-cell stage. In contrast, using parthenogenetic embryos, we show that pericentric transcripts are essential for this reorganization independent of the chromatin marks associated with the PHC domains. Finally, our discovery that only reverse pericentric transcripts are required for both the nuclear reorganization of PHC and development beyond the two-cell stage challenges current views on heterochromatin organization.

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.

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 ...

Spherical Solutions of an Underwater Explosion Bubble

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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.

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

Review on fiber morphology obtained by bubble electrospinning and blown bubble spinning

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He Ji-Huan

2012-01-01

Full Text Available Here we show an intriguing phenomenon in the bubble electrospinning process that the ruptured film might be stripped upwards by an electronic force to form a very thin and long plate-like strip, which might been received in the metal receiver as discontinuous backbone-like wrinkled materials, rather than smooth nano-fibers or microspheres. The processes are called the bubble electrospinning. The electronic force can be replaced by a blowing air, and the process is called as the blown bubble spinning. We demonstrate that the size and thickness of the ruptured film are the crucial parameters that are necessary to understand the various observations including beads and nanoporous materials. We identify the conditions required for a ruptured film to form discontinuous structure, and a critical width of the ruptured film to form a cylindrical fiber, above which a long and thin plate-like strip might be obtained, and a criterion for oscillatory jet diameter, which leads to bead morphology of the obtained fibers. The space of the adjacent beads depends on the fiber size. We anticipate our assay to be a starting point for more sophisticated study of the bubble electrospinning and the blown bubble spinning and for mass-production of both nanofibers and nanoscale discontinuous materials.

Influence of drag closures and inlet conditions on bubble dynamics and flow behavior inside a bubble column

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Amjad Asad

2017-01-01

Full Text Available In this paper, the hydrodynamics of a bubble column is investigated numerically using the discrete bubble model, which tracks the dispersed bubbles individually in a liquid column. The discrete bubble model is combined with the volume of fluid approach to account for a proper free surface boundary condition at the liquid–gas interface. This improves describing the backflow region, which takes place close to the wall region. The numerical simulation is conducted by means of the open source computational fluid dynamics library OpenFOAM®. In order to validate the numerical model, experimental results of a bubble column are used. The numerical prediction shows an overall good agreement compared to the experimental data. The effect of injection conditions and the influence of the drag closures on bubble dynamics are investigated in the current paper. Here, the significant effect of injection boundary conditions on bubble dynamics and flow velocity in the studied cavity is revealed. Moreover, the impact of the choice of the drag closure on the liquid velocity field and on bubble behavior is indicated by comparing three drag closures derived from former studies.

Determination of size distribution of bubbles in a bubbly column two phase flows by ultrasound and neural networks

Energy Technology Data Exchange (ETDEWEB)

Baroni, Douglas B.; Lamy, Carlos A.; Bittencourt, Marcelo S.Q.; Pereira, Claudio M.N.A., E-mail: douglasbaroni@ien.gov.b, E-mail: lamy@ien.gov.b, E-mail: bittenc@ien.gov.b, E-mail: cmnap@ien.gov.b [Instituto de Engenharia Nuclear (IEN/CNEN-RJ), Rio de Janeiro, RJ (Brazil); Cunha Filho, Jurandyr S. [Escola Tecnica Estadual Visconde de Maua (ETEVM/RJ), Rio de Janeiro, RJ (Brazil); Motta, Mauricio S., E-mail: mmotta@cefet-rj.b [Centro Federal de Educacao Tecnologica Celso Suckow da Fonseca (CEFET/RJ), Rio de Janeiro, RJ (Brazil)

2011-07-01

The development of advanced nuclear reactor conceptions depends largely on the amount of available data to the designer. Non invasive ultrasonic techniques can contribute to the evaluation of gas-liquid two-phase regimes in the nuclear thermo-hydraulic circuits. A key-point for success of those techniques is the interpretation of the ultrasonic signal. In this work, a methodology based in artificial neural networks (ANN) is proposed to predict size distribution of bubbles in a bubbly flow. To accomplish that, an air feed system control was used to obtain specific bubbly flows in an experimental system utilizing a Plexiglas vertical bubbly column. Four different size distribution of bubbles were generated. The bubbles were photographed and measured. To evaluate the different size distribution of bubbles it was used the ultrasonic reflected echo on the opposite wall of the column. Then, an ANN has been developed for predicting size distribution of bubbles by using the frequency spectra of the ultrasonic signal as input. A trained artificial neural network using ultrasonic signal in the frequency domain can evaluate with a good precision the size distribution of bubbles generated in this system. (author)

Determination of size distribution of bubbles in a bubbly column two phase flows by ultrasound and neural networks

International Nuclear Information System (INIS)

Baroni, Douglas B.; Lamy, Carlos A.; Bittencourt, Marcelo S.Q.; Pereira, Claudio M.N.A.; Cunha Filho, Jurandyr S.; Motta, Mauricio S.

2011-01-01

The development of advanced nuclear reactor conceptions depends largely on the amount of available data to the designer. Non invasive ultrasonic techniques can contribute to the evaluation of gas-liquid two-phase regimes in the nuclear thermo-hydraulic circuits. A key-point for success of those techniques is the interpretation of the ultrasonic signal. In this work, a methodology based in artificial neural networks (ANN) is proposed to predict size distribution of bubbles in a bubbly flow. To accomplish that, an air feed system control was used to obtain specific bubbly flows in an experimental system utilizing a Plexiglas vertical bubbly column. Four different size distribution of bubbles were generated. The bubbles were photographed and measured. To evaluate the different size distribution of bubbles it was used the ultrasonic reflected echo on the opposite wall of the column. Then, an ANN has been developed for predicting size distribution of bubbles by using the frequency spectra of the ultrasonic signal as input. A trained artificial neural network using ultrasonic signal in the frequency domain can evaluate with a good precision the size distribution of bubbles generated in this system. (author)

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)

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.

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

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

DNA template dependent accuracy variation of nucleotide selection in transcription.

Directory of Open Access Journals (Sweden)

Harriet Mellenius

Full Text Available It has been commonly assumed that the effect of erroneous transcription of DNA genes into messenger RNAs on peptide sequence errors are masked by much more frequent errors of mRNA translation to protein. We present a theoretical model of transcriptional accuracy. It uses experimentally estimated standard free energies of double-stranded DNA and RNA/DNA hybrids and predicts a DNA template dependent transcriptional accuracy variation spanning several orders of magnitude. The model also identifies high-error as well a high-accuracy transcription motifs. The source of the large accuracy span is the context dependent variation of the stacking free energy of pairs of correct and incorrect base pairs in the ever moving transcription bubble. Our model predictions have direct experimental support from recent single molecule based identifications of transcriptional errors in the C. elegans transcriptome. Our conclusions challenge the general view that amino acid substitution errors in proteins are mainly caused by translational errors. It suggests instead that transcriptional error hotspots are the dominating source of peptide sequence errors in some DNA template contexts, while mRNA translation is the major cause of protein errors in other contexts.

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.

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.

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

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

Study of Bubble Size, Void Fraction, and Mass Transport in a Bubble Column under High Amplitude Vibration

Directory of Open Access Journals (Sweden)

Shahrouz Mohagheghian

2018-04-01

Full Text Available Vertical vibration is known to cause bubble breakup, clustering and retardation in gas-liquid systems. In a bubble column, vibration increases the mass transfer ratio by increasing the residence time and phase interfacial area through introducing kinetic buoyancy force (Bjerknes effect and bubble breakup. Previous studies have explored the effect of vibration frequency (f, but minimal effort has focused on the effect of amplitude (A on mass transfer intensification. Thus, the current work experimentally examines bubble size, void fraction, and mass transfer in a bubble column under relatively high amplitude vibration (1.5 mm < A <9.5 mm over a frequency range of 7.5–22.5 Hz. Results of the present work were compared with past studies. The maximum stable bubble size under vibration was scaled using Hinze theory for breakage. Results of this work indicate that vibration frequency exhibits local maxima in both mass transfer and void fraction. Moreover, an optimum amplitude that is independent of vibration frequency was found for mass transfer enhancements. Finally, this work suggests physics-based models to predict void fraction and mass transfer in a vibrating bubble column.

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

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

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

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

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.

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

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

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)

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

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.

Influences of non-uniform pressure field outside bubbles on the propagation of acoustic waves in dilute bubbly liquids.

Science.gov (United States)

Zhang, Yuning; Du, Xiaoze

2015-09-01

Predictions of the propagation of the acoustic waves in bubbly liquids is of great importance for bubble dynamics and related applications (e.g. sonochemistry, sonochemical reactor design, biomedical engineering). In the present paper, an approach for modeling the propagation of the acoustic waves in dilute bubbly liquids is proposed through considering the non-uniform pressure field outside the bubbles. This approach is validated through comparing with available experimental data in the literature. Comparing with the previous models, our approach mainly improves the predictions of the attenuation of acoustic waves in the regions with large kR0 (k is the wave number and R0 is the equilibrium bubble radius). Stability of the oscillating bubbles under acoustic excitation are also quantitatively discussed based on the analytical solution. Copyright © 2015 Elsevier B.V. All rights reserved.

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.

DNA Replication Is Required for Circadian Clock Function by Regulating Rhythmic Nucleosome Composition.

Science.gov (United States)

Liu, Xiao; Dang, Yunkun; Matsu-Ura, Toru; He, Yubo; He, Qun; Hong, Christian I; Liu, Yi

2017-07-20

Although the coupling between circadian and cell cycles allows circadian clocks to gate cell division and DNA replication in many organisms, circadian clocks were thought to function independently of cell cycle. Here, we show that DNA replication is required for circadian clock function in Neurospora. Genetic and pharmacological inhibition of DNA replication abolished both overt and molecular rhythmicities by repressing frequency (frq) gene transcription. DNA replication is essential for the rhythmic changes of nucleosome composition at the frq promoter. The FACT complex, known to be involved in histone disassembly/reassembly, is required for clock function and is recruited to the frq promoter in a replication-dependent manner to promote replacement of histone H2A.Z by H2A. Finally, deletion of H2A.Z uncoupled the dependence of the circadian clock on DNA replication. Together, these results establish circadian clock and cell cycle as interdependent coupled oscillators and identify DNA replication as a critical process in the circadian mechanism. Published by Elsevier Inc.

Analysis of JC virus DNA replication using a quantitative and high-throughput assay

Science.gov (United States)

Shin, Jong; Phelan, Paul J.; Chhum, Panharith; Bashkenova, Nazym; Yim, Sung; Parker, Robert; Gagnon, David; Gjoerup, Ole; Archambault, Jacques; Bullock, Peter A.

2015-01-01

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. PMID:25155200

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.

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

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.

A bubble detection system for propellant filling pipeline

Energy Technology Data Exchange (ETDEWEB)

Wen, Wen; Zong, Guanghua; Bi, Shusheng [Robotics Institute, Beihang University, 100191 Beijing (China)

2014-06-15

This paper proposes a bubble detection system based on the ultrasound transmission method, mainly for probing high-speed bubbles in the satellite propellant filling pipeline. First, three common ultrasonic detection methods are compared and the ultrasound transmission method is used in this paper. Then, the ultrasound beam in a vertical pipe is investigated, suggesting that the width of the beam used for detection is usually smaller than the internal diameter of the pipe, which means that when bubbles move close to the pipe wall, they may escape from being detected. A special device is designed to solve this problem. It can generate the spiral flow to force all the bubbles to ascend along the central line of the pipe. In the end, experiments are implemented to evaluate the performance of this system. Bubbles of five different sizes are generated and detected. Experiment results show that the sizes and quantity of bubbles can be estimated by this system. Also, the bubbles of different radii can be distinguished from each other. The numerical relationship between the ultrasound attenuation and the bubble radius is acquired and it can be utilized for estimating the unknown bubble size and measuring the total bubble volume.

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.

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.

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.

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 ...

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.

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.

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.

A Bubble-Based Drag Model at the Local-Grid Level for Eulerian Simulation of Bubbling Fluidized Beds

Directory of Open Access Journals (Sweden)

Kun Hong

2016-01-01

Full Text Available A bubble-based drag model at the local-grid level is proposed to simulate gas-solid flows in bubbling fluidized beds of Geldart A particles. In this model, five balance equations are derived from the mass and the momentum conservation. This set of equations along with necessary correlations for bubble diameter and voidage of emulsion phase is solved to obtain seven local structural parameters (uge, upe, εe, δb, ub, db, and ab which describe heterogeneous flows of bubbling fluidized beds. The modified drag coefficient obtained from the above-mentioned structural parameters is then incorporated into the two-fluid model to simulate the hydrodynamics of Geldart A particles in a lab-scale bubbling fluidized bed. The comparison between experimental and simulation results for the axial and radial solids concentration profiles is promising.

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 ...

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

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...

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

The Hepatitis B Virus (HBV) HBx Protein Activates AKT To Simultaneously Regulate HBV Replication and Hepatocyte Survival

Science.gov (United States)

Rawat, Siddhartha

2014-01-01

ABSTRACT Chronic infection with hepatitis B virus (HBV) is a risk factor for developing liver diseases such as hepatocellular carcinoma (HCC). HBx is a multifunctional protein encoded by the HBV genome; HBx stimulates HBV replication and is thought to play an important role in the development of HBV-associated HCC. HBx can activate the phosphatidylinositol 3-kinase (PI3K)/AKT signaling pathway in some cell lines; however, whether HBx regulates PI3K/AKT signaling in normal hepatocytes has not been evaluated. In studies described here, we assessed HBx activation of PI3K/AKT signaling in an ex vivo model of cultured primary hepatocytes and determined how this HBx activity affects HBV replication. We report that HBx activates AKT in primary hepatocytes and that the activation of AKT decreases HBV replication and HBV mRNA and core protein levels. We show that the transcription factor hepatocyte nuclear factor 4α (HNF4α) is a target of HBx-regulated AKT, and we link HNF4α to HBx-regulated AKT modulation of HBV transcription and replication. Although we and others have shown that HBx stimulates and is likely required for HBV replication, we now report that HBx also activates signals that can diminish the overall level of HBV replication. While this may seem counterintuitive, we show that an important effect of HBx activation of AKT is inhibition of apoptosis. Consequently, our studies suggest that HBx balances HBV replication and cell survival by stimulating signaling pathways that enhance hepatocyte survival at the expense of higher levels of HBV replication. IMPORTANCE Chronic hepatitis B virus (HBV) infection is a common cause of the development of liver cancer. Regulation of cell signaling pathways by the HBV HBx protein is thought to influence the development of HBV-associated liver cancer. HBx stimulates, and may be essential for, HBV replication. We show that HBx activates AKT in hepatocytes to reduce HBV replication. While this seems contradictory to an

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…

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

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.

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

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

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

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

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.

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)

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.

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.

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

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.

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

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)

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)

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)

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

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

Structural organization of poliovirus RNA replication is mediated by viral proteins of the P2 genomic region

International Nuclear Information System (INIS)

Bienz, K.; Egger, D.; Troxler, M.; Pasamontes, L.

1990-01-01

Transcriptionally active replication complexes bound to smooth membrane vesicles were isolated from poliovirus-infected cells. In electron microscopic, negatively stained preparations, the replication complex appeared as an irregularly shaped, oblong structure attached to several virus-induced vesicles of a rosettelike arrangement. Electron microscopic immunocytochemistry of such preparations demonstrated that the poliovirus replication complex contains the proteins coded by the P2 genomic region (P2 proteins) in a membrane-associated form. In addition, the P2 proteins are also associated with viral RNA, and they can be cross-linked to viral RNA by UV irradiation. Guanidine hydrochloride prevented the P2 proteins from becoming membrane bound but did not change their association with viral RNA. The findings allow the conclusion that the protein 2C or 2C-containing precursor(s) is responsible for the attachment of the viral RNA to the vesicular membrane and for the spatial organization of the replication complex necessary for its proper functioning in viral transcription. A model for the structure of the viral replication complex and for the function of the 2C-containing P2 protein(s) and the vesicular membranes is proposed

Inclusion bodies are a site of ebolavirus replication.

Science.gov (United States)

Hoenen, Thomas; Shabman, Reed S; Groseth, Allison; Herwig, Astrid; Weber, Michaela; Schudt, Gordian; Dolnik, Olga; Basler, Christopher F; Becker, Stephan; Feldmann, Heinz

2012-11-01

Inclusion bodies are a characteristic feature of ebolavirus infections in cells. They contain large numbers of preformed nucleocapsids, but their biological significance has been debated, and they have been suggested to be aggregates of viral proteins without any further biological function. However, recent data for other viruses that produce similar structures have suggested that inclusion bodies might be involved in genome replication and transcription. In order to study filovirus inclusion bodies, we fused mCherry to the ebolavirus polymerase L, which is found in inclusion bodies. The resulting L-mCherry fusion protein was functional in minigenome assays and incorporated into virus-like particles. Importantly, L-mCherry fluorescence in transfected cells was readily detectable and distributed in a punctate pattern characteristic for inclusion bodies. A recombinant ebolavirus encoding L-mCherry instead of L was rescued and showed virtually identical growth kinetics and endpoint titers to those for wild-type virus. Using this virus, we showed that the onset of inclusion body formation corresponds to the onset of viral genome replication, but that viral transcription occurs prior to inclusion body formation. Live-cell imaging further showed that inclusion bodies are highly dynamic structures and that they can undergo dramatic reorganization during cell division. Finally, by labeling nascent RNAs using click technology we showed that inclusion bodies are indeed the site of viral RNA synthesis. Based on these data we conclude that, rather than being inert aggregates of nucleocapsids, ebolavirus inclusion bodies are in fact complex and dynamic structures and an important site at which viral RNA replication takes place.

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

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

Shock waves from non-spherically collapsing cavitation bubbles

Science.gov (United States)

Supponen, Outi; Obreschkow, Danail; Farhat, Mohamed

2017-11-01

Combining simultaneous high-speed imaging and hydrophone measurements, we uncover details of the multiple shock wave emission from laser-induced cavitation bubbles collapsing in a non-spherical way. For strongly deformed bubbles collapsing near a free surface, we identify the distinct shock waves caused by the jet impact onto the opposite bubble wall and by the individual collapses of the remaining bubble segments. The energy carried by each of these shocks depends on the level of bubble deformation, quantified by the anisotropy parameter ζ, the dimensionless equivalent of the Kelvin impulse. For jetting bubbles, at ζ water hammer as ph = 0.45 (ρc2 Δp) 1 / 2ζ-1 .

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...

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.

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.

Enterovirus type 71 2A protease functions as a transcriptional activator in yeast

Directory of Open Access Journals (Sweden)

Lai Meng-Jiun

2010-08-01

Full Text Available Abstract Enterovirus type 71 (EV71 2A protease exhibited strong transcriptional activity in yeast cells. The transcriptional activity of 2A protease was independent of its protease activity. EV71 2A protease retained its transcriptional activity after truncation of 40 amino acids at the N-terminus but lost this activity after truncation of 60 amino acids at the N-terminus or deletion of 20 amino acids at the C-terminus. Thus, the acidic domain at the C-terminus of this protein is essential for its transcriptional activity. Indeed, deletion of amino acids from 146 to 149 (EAME in this acidic domain lost the transcriptional activity of EV71 2A protein though still retained its protease activity. EV71 2A protease was detected both in the cytoplasm and nucleus using confocal microscopy analysis. Coxsackie virus B3 2A protease also exhibited transcriptional activity in yeast cells. As expected, an acidic domain in the C-terminus of Coxsackie virus B3 2A protease was also identified. Truncation of this acidic domain resulted in the loss of transcriptional activity. Interestingly, this acidic region of poliovirus 2A protease is critical for viral RNA replication. The transcriptional activity of the EV71 or Coxsackie virus B3 2A protease should play a role in viral replication and/or pathogenesis.

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

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)

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...

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.

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

H4K20me0 marks post-replicative chromatin and recruits the TONSL–MMS22L DNA repair complex

DEFF Research Database (Denmark)

Saredi, Giulia; Huang, Hongda; Hammond, Colin M

2016-01-01

After DNA replication, chromosomal processes including DNA repair and transcription take place in the context of sister chromatids. While cell cycle regulation can guide these processes globally, mechanisms to distinguish pre- and post-replicative states locally remain unknown. Here we reveal...

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.

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

From Rising Bubble to RNA/DNA and Bacteria

Science.gov (United States)

Marks, Roman; Cieszyńska, Agata; Wereszka, Marzena; Borkowski, Wojciech

2017-04-01

In this study we have focused on the movement of rising bubbles in a salty water body. Experiments reviled that free buoyancy movement of bubbles forces displacement of ions, located on the outer side of the bubble wall curvatures. During the short moment of bubble passage, all ions in the vicinity of rising bubble, are separated into anions that are gathered on the bubble upper half sphere and cations that slip along the bottom concave half-sphere of a bubble and develop a sub-bubble vortex. The principle of ions separation bases on the differences in displacement resistance. In this way, relatively heavier and larger, thus more resistant to displacement anions are gathered on the rising bubble upper half sphere, while smaller and lighter cations are assembled on the bottom half sphere and within the sub-bubble vortex. The acceleration of motion generates antiparallel rotary of bi-ionic domains, what implies that anions rotate in clockwise (CW) and cationic in counter-clockwise (CCW) direction. Then, both rotational systems may undergo splicing and extreme condensing by bi-pirouette narrowing of rotary. It is suggested that such double helix motion of bi-ionic domains creates RNA/DNA molecules. Finally, when the bubble reaches the water surface it burst and the preprocessed RNA/DNA matter is ejected into the droplets. Since that stage, droplet is suspended in positively charged troposphere, thus the cationic domain is located in the droplet center, whilst negative ions are attracted to configure the outer areola. According to above, the present study implies that the rising bubbles in salty waters may incept synergistic processing of matter resulting in its rotational/spherical organization that led to assembly of RNA/DNA molecules and bacteria cells.

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

Sonar gas flux estimation by bubble insonification: application to methane bubble flux from seep areas in the outer Laptev Sea

Science.gov (United States)

Leifer, Ira; Chernykh, Denis; Shakhova, Natalia; Semiletov, Igor

2017-06-01

Sonar surveys provide an effective mechanism for mapping seabed methane flux emissions, with Arctic submerged permafrost seepage having great potential to significantly affect climate. We created in situ engineered bubble plumes from 40 m depth with fluxes spanning 0.019 to 1.1 L s-1 to derive the in situ calibration curve (Q(σ)). These nonlinear curves related flux (Q) to sonar return (σ) for a multibeam echosounder (MBES) and a single-beam echosounder (SBES) for a range of depths. The analysis demonstrated significant multiple bubble acoustic scattering - precluding the use of a theoretical approach to derive Q(σ) from the product of the bubble σ(r) and the bubble size distribution where r is bubble radius. The bubble plume σ occurrence probability distribution function (Ψ(σ)) with respect to Q found Ψ(σ) for weak σ well described by a power law that likely correlated with small-bubble dispersion and was strongly depth dependent. Ψ(σ) for strong σ was largely depth independent, consistent with bubble plume behavior where large bubbles in a plume remain in a focused core. Ψ(σ) was bimodal for all but the weakest plumes. Q(σ) was applied to sonar observations of natural arctic Laptev Sea seepage after accounting for volumetric change with numerical bubble plume simulations. Simulations addressed different depths and gases between calibration and seep plumes. Total mass fluxes (Qm) were 5.56, 42.73, and 4.88 mmol s-1 for MBES data with good to reasonable agreement (4-37 %) between the SBES and MBES systems. The seepage flux occurrence probability distribution function (Ψ(Q)) was bimodal, with weak Ψ(Q) in each seep area well described by a power law, suggesting primarily minor bubble plumes. The seepage-mapped spatial patterns suggested subsurface geologic control attributing methane fluxes to the current state of subsea permafrost.

Theoretical aspects of appearing of bubbles in economy

Directory of Open Access Journals (Sweden)

Pronoza Pavlo V.

2014-01-01

Full Text Available The article considers theoretical aspects of appearing of bubbles in economy. It analyses vies of scientists regarding the essence of this phenomenon and, with the help of content analysis, specifies the essence of the bubble notion in economy. It considers main stages of appearance of such bubbles. It offers classification of their types. It analyses pre-requisites of appearance of bubbles in economy and their features. It considers main existing approaches to detection and modelling appearance of bubbles. It proves that bubbles negatively influence economy of the countries, that is why, the problem of their detection and prevention is one of the central problems in the process of development of policy of state regulation of economy.

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.

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.)

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

Gas fluxing of aluminum: a bubble probe for optimization of bubbles/bubble distribution and minimization of splashing/droplet formation

International Nuclear Information System (INIS)

James W. Evans; Auitumn Fjeld

2006-01-01

Aluminum is one of our most important materials and finds major use in transportation (e.g. aircraft) and packaging (e.g. beverage cans). According to International Aluminium Institute statistics (www.world-aluminium.org) 23.46 million metric tons of aluminum were produced last year in the electrolytic cells used to make this metal, continuing an increase seen over the previous four years and sustained for the first half of this year. 23% of this ?primary? production was in North America. A smaller, yet important, source of the nation?s aluminum is ''secondary production'', that is the recycling of aluminum products such as beverage cans. The Aluminum Association reports that 51.4 billion beverage cans were recycled in the U.S. last year (compared to 98.9 billion new cans shipped). Whether from primary or secondary production, it is typically necessary to treat the aluminum to remove small quantities of impurities or unwanted alloying agents before the metal can be further processed and sold. In the case of primary aluminum it is the removal of trace impurities such as sodium that is needed; in the case of recycled aluminum it is the removal of alloy constituents, such as magnesium which is, after aluminum, the principal metal used in beverage cans. The procedure commonly used is known as ''gas fluxing'' and entails bubbling a reactive mixture of chlorine and argon through the molten metal. The intent is that the chlorine react with the impurities to form compounds that can easily separate from the aluminum. Unfortunately a fraction of the chlorine forms volatile aluminum chloride that leaves the fluxing unit. This represents a loss of aluminum product; furthermore the aluminum chloride can react with atmospheric moisture to form hydrogen chloride gas with impact on workers and the environment. Some of these emissions are controlled by bag houses but some escape. For example EPA's Toxic Release Inventory for 1997 has stack emissions of chlorides and chlorine

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.

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.

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

Dynamics of bubble formation in highly viscous liquids.

Science.gov (United States)

Pancholi, Ketan; Stride, Eleanor; Edirisinghe, Mohan

2008-04-15

There has recently been considerable interest in the development of devices for the preparation of monodisperse microbubble suspensions for use as ultrasound contrast agents and drug delivery vehicles. These applications require not only a high degree of bubble uniformity but also a maximum bubble size of 8 mum, and this provides a strong motivation for developing an improved understanding of the process of bubble formation in a given device. The aim of this work was to investigate bubble formation in a T-junction device and determine the influence of the different processing parameters upon bubble size, in particular, liquid viscosity. Images of air bubble formation in a specially designed T-junction were recorded using a high-speed camera for different ratios of liquid to gas flow rate (Ql/Qg) and different liquid viscosities (microl). It was found that theoretical predictions of the flow profile in the focal region based on analysis of axisymmetric Stokes flow were accurate to within 6% when compared with the experimental data, indicating that this provided a suitable means of describing the bubble formation process. Both the theoretical and experimental results showed that Ql/Qg and mul had a significant influence upon bubble formation and eventual size, with higher flow rates and higher viscosities producing smaller bubbles. There were, however, found to be limiting values of Ql/Qg and mul beyond which no further reduction in bubble size was achieved.

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.

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.

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

Inhibition of Cell Division and DNA Replication Impair Mouse-Naïve Pluripotency Exit.

Science.gov (United States)

Waisman, Ariel; Vazquez Echegaray, Camila; Solari, Claudia; Cosentino, María Soledad; Martyn, Iain; Deglincerti, Alessia; Ozair, Mohammad Zeeshan; Ruzo, Albert; Barañao, Lino; Miriuka, Santiago; Brivanlou, Ali; Guberman, Alejandra

2017-09-01

The cell cycle has gained attention as a key determinant for cell fate decisions, but the contribution of DNA replication and mitosis in stem cell differentiation has not been extensively studied. To understand if these processes act as "windows of opportunity" for changes in cell identity, we established synchronized cultures of mouse embryonic stem cells as they exit the ground state of pluripotency. We show that initial transcriptional changes in this transition do not require passage through mitosis and that conversion to primed pluripotency is linked to lineage priming in the G1 phase. Importantly, we demonstrate that impairment of DNA replication severely blocks transcriptional switch to primed pluripotency, even in the absence of p53 activity induced by the DNA damage response. Our data suggest an important role for DNA replication during mouse embryonic stem cell differentiation, which could shed light on why pluripotent cells are only receptive to differentiation signals during G1, that is, before the S phase. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

Bubble gate for in-plane flow control.

Science.gov (United States)

Oskooei, Ali; Abolhasani, Milad; Günther, Axel

2013-07-07

We introduce a miniature gate valve as a readily implementable strategy for actively controlling the flow of liquids on-chip, within a footprint of less than one square millimetre. Bubble gates provide for simple, consistent and scalable control of liquid flow in microchannel networks, are compatible with different bulk microfabrication processes and substrate materials, and require neither electrodes nor moving parts. A bubble gate consists of two microchannel sections: a liquid-filled channel and a gas channel that intercepts the liquid channel to form a T-junction. The open or closed state of a bubble gate is determined by selecting between two distinct gas pressure levels: the lower level corresponds to the "open" state while the higher level corresponds to the "closed" state. During closure, a gas bubble penetrates from the gas channel into the liquid, flanked by a column of equidistantly spaced micropillars on each side, until the flow of liquid is completely obstructed. We fabricated bubble gates using single-layer soft lithographic and bulk silicon micromachining procedures and evaluated their performance with a combination of theory and experimentation. We assessed the dynamic behaviour during more than 300 open-and-close cycles and report the operating pressure envelope for different bubble gate configurations and for the working fluids: de-ionized water, ethanol and a biological buffer. We obtained excellent agreement between the experimentally determined bubble gate operational envelope and a theoretical prediction based on static wetting behaviour. We report case studies that serve to illustrate the utility of bubble gates for liquid sampling in single and multi-layer microfluidic devices. Scalability of our strategy was demonstrated by simultaneously addressing 128 bubble gates.

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.

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)

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.

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.

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

Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes

Directory of Open Access Journals (Sweden)

Hsiung Chao

2011-10-01

Full Text Available Abstract Background Changes in transcriptional orientation (“CTOs” occur frequently in prokaryotic genomes. Such changes usually result from genomic inversions, which may cause a conflict between the directions of replication and transcription and an increase in mutation rate. However, CTOs do not always lead to the replication-transcription confrontation. Furthermore, CTOs may cause deleterious disruptions of operon structure and/or gene regulations. The currently existing CTOs may indicate relaxation of selection pressure. Therefore, it is of interest to investigate whether CTOs have an independent effect on the evolutionary rates of the affected genes, and whether these genes are subject to any type of selection pressure in prokaryotes. Methods Three closely related enterbacteria, Escherichia coli, Klebsiella pneumoniae and Salmonella enterica serovar Typhimurium, were selected for comparisons of synonymous (dS and nonsynonymous (dN substitution rate between the genes that have experienced changes in transcriptional orientation (changed-orientation genes, “COGs” and those that do not (same-orientation genes, “SOGs”. The dN/dS ratio was also derived to evaluate the selection pressure on the analyzed genes. Confounding factors in the estimation of evolutionary rates, such as gene essentiality, gene expression level, replication-transcription confrontation, and decreased dS at gene terminals were controlled in the COG-SOG comparisons. Results We demonstrate that COGs have significantly higher dN and dS than SOGs when a series of confounding factors are controlled. However, the dN/dS ratios are similar between the two gene groups, suggesting that the increase in dS can sufficiently explain the increase in dN in COGs. Therefore, the increases in evolutionary rates in COGs may be mainly mutation-driven. Conclusions Here we show that CTOs can increase the evolutionary rates of the affected genes. This effect is independent of the

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

Nuclear Trafficking of Retroviral RNAs and Gag Proteins during Late Steps of Replication

Directory of Open Access Journals (Sweden)

Matthew S. Stake

2013-11-01

Full Text Available Retroviruses exploit nuclear trafficking machinery at several distinct stages in their replication cycles. In this review, we will focus primarily on nucleocytoplasmic trafficking events that occur after the completion of reverse transcription and proviral integration. First, we will discuss nuclear export of unspliced viral RNA transcripts, which serves two essential roles: as the mRNA template for the translation of viral structural proteins and as the genome for encapsidation into virions. These full-length viral RNAs must overcome the cell’s quality control measures to leave the nucleus by co-opting host factors or encoding viral proteins to mediate nuclear export of unspliced viral RNAs. Next, we will summarize the most recent findings on the mechanisms of Gag nuclear trafficking and discuss potential roles for nuclear localization of Gag proteins in retrovirus replication.

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.

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

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

Raman Spectral Band Oscillations in Large Graphene Bubbles

Science.gov (United States)

Huang, Yuan; Wang, Xiao; Zhang, Xu; Chen, Xianjue; Li, Baowen; Wang, Bin; Huang, Ming; Zhu, Chongyang; Zhang, Xuewei; Bacsa, Wolfgang S.; Ding, Feng; Ruoff, Rodney S.

2018-05-01

Raman spectra of large graphene bubbles showed size-dependent oscillations in spectral intensity and frequency, which originate from optical standing waves formed in the vicinity of the graphene surface. At a high laser power, local heating can lead to oscillations in the Raman frequency and also create a temperature gradient in the bubble. Based on Raman data, the temperature distribution within the graphene bubble was calculated, and it is shown that the heating effect of the laser is reduced when moving from the center of a bubble to its edge. By studying graphene bubbles, both the thermal conductivity and chemical reactivity of graphene were assessed. When exposed to hydrogen plasma, areas with bubbles are found to be more reactive than flat graphene.

Two types of nonlinear wave equations for diffractive beams in bubbly liquids with nonuniform bubble number density.

Science.gov (United States)

Kanagawa, Tetsuya

2015-05-01

This paper theoretically treats the weakly nonlinear propagation of diffracted sound beams in nonuniform bubbly liquids. The spatial distribution of the number density of the bubbles, initially in a quiescent state, is assumed to be a slowly varying function of the spatial coordinates; the amplitude of variation is assumed to be small compared to the mean number density. A previous derivation method of nonlinear wave equations for plane progressive waves in uniform bubbly liquids [Kanagawa, Yano, Watanabe, and Fujikawa (2010). J. Fluid Sci. Technol. 5(3), 351-369] is extended to handle quasi-plane beams in weakly nonuniform bubbly liquids. The diffraction effect is incorporated by adding a relation that scales the circular sound source diameter to the wavelength into the original set of scaling relations composed of nondimensional physical parameters. A set of basic equations for bubbly flows is composed of the averaged equations of mass and momentum, the Keller equation for bubble wall, and supplementary equations. As a result, two types of evolution equations, a nonlinear Schrödinger equation including dissipation, diffraction, and nonuniform effects for high-frequency short-wavelength case, and a Khokhlov-Zabolotskaya-Kuznetsov equation including dispersion and nonuniform effects for low-frequency long-wavelength case, are derived from the basic set.

Approaching behavior of a pair of spherical bubbles in quiescent liquids

Science.gov (United States)

Sanada, Toshiyuki; Kusuno, Hiroaki

2015-11-01

Some unique motions related bubble-bubble interaction, such as equilibrium distance, wake induced lift force, have been proposed by theoretical analysis or numerical simulations. These motions are different from the solid spheres like DKT model (Drafting, Kissing and Tumbling). However, there is a lack of the experimental verification. In this study, we experimentally investigated the motion of a pair of bubbles initially positioned in-line configuration in ultrapure water or an aqueous surfactant solution. The bubble motion were observed by two high speed video cameras. The bubbles Reynolds number was ranged from 50 to 300 and bubbles hold the spherical shape in this range. In ultrapure water, initially the trailing bubble deviated from the vertical line on the leading bubble owing to the wake of the leading bubble. And then, the slight difference of the bubble radius changed the relative motion. When the trailing bubble slightly larger than the leading bubble, the trailing bubble approached to the leading bubble due to it's buoyancy difference. The bubbles attracted and collided only when the bubbles rising approximately side by side configuration. In addition, we will also discuss the motion of bubbles rising in an aqueous surfactant solution.

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

Methane emission by bubbling from Gatun Lake, Panama

Science.gov (United States)

Keller, Michael; Stallard, Robert F.

1994-01-01

We studied methane emission by bubbling from Gatun Lake, Panama, at water depths of less than 1 m to about 10 m. Gas bubbles were collected in floating traps deployed during 12- to 60-hour observation periods. Comparison of floating traps and floating chambers showed that about 98% of methane emission occurred by bubbling and only 2% occurred by diffusion. Average methane concentration of bubbles at our sites varied from 67% to 77%. Methane emission by bubbling occurred episodically, with greatest rates primarily between the hours of 0800 and 1400 LT. Events appear to be triggered by wind. The flux of methane associated with bubbling was strongly anticorrelated with water depth. Seasonal changes in water depth caused seasonal variation of methane emission. Bubble methane fluxes through the lake surface into the atmosphere measured during 24-hour intervals were least (10-200 mg/m2/d) at deeper sites (greater than 7 m) and greatest (300-2000 mg/m2/d) at shallow sites (less than 2 m).

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.

Bubbly flows around a two-dimensional circular cylinder

Science.gov (United States)

Lee, Jubeom; Park, Hyungmin

2016-11-01

Two-phase cross flows around a bluff body occur in many thermal-fluid systems like steam generators, heat exchangers and nuclear reactors. However, our current knowledge on the interactions among bubbles, bubble-induced flows and the bluff body are limited. In the present study, the gas-liquid bubbly flows around a solid circular cylinder are experimentally investigated while varying the mean void fraction from 5 to 27%. The surrounding liquid (water) is initially static and the liquid flow is only induced by the air bubbles. For the measurements, we use the high-speed two-phase particle image velocimetry techniques. First, depending on the mean void fraction, two regimes are classified with different preferential concentration of bubbles in the cylinder wake, which are explained in terms of hydrodynamic force balances acting on rising bubbles. Second, the differences between the two-phase and single-phase flows (while matching their Reynolds numbers) around a circular cylinder will be discussed in relation to effects of bubble dynamics and the bubble-induced turbulence on the cylinder wake. Supported by a Grant (MPSS-CG-2016-02) through the Disaster and Safety Management Institute funded by Ministry of Public Safety and Security of Korean government.

Modeling of the evolution of bubble size distribution of gas-liquid flow inside a large vertical pipe. Influence of bubble coalescence and breakup models

International Nuclear Information System (INIS)

Liao, Yixiang; Lucas, Dirk

2011-01-01

The range of gas-liquid flow applications in today's technology is immensely wide. Important examples can be found in chemical reactors, boiling and condensation equipments as well as nuclear reactors. In gas-liquid flows, the bubble size distribution plays an important role in the phase structure and interfacial exchange behaviors. It is therefore necessary to take into account the dynamic change of the bubble size distribution to get good predictions in CFD. An efficient 1D Multi-Bubble-Size-Class Test Solver was introduced in Lucas et al. (2001) for the simulation of the development of the flow structure along a vertical pipe. The model considers a large number of bubble classes. It solves the radial profiles of liquid and gas velocities, bubble-size class resolved gas fraction profiles as well as turbulence parameters on basis of the bubble size distribution present at the given axial position. The evolution of the flow along the height is assumed to be solely caused by the progress of bubble coalescence and break-up resulting in a bubble size distribution changing in the axial direction. In this model, the bubble coalescence and breakup models are very important for reasonable predictions of the bubble size distribution. Many bubble coalescence and breakup models have been proposed in the literature. However, some obvious discrepancies exist in the models; for example, the daughter bubble size distributions are greatly different from different bubble breakup models, as reviewed in our previous publication (Liao and Lucas, 2009a; 2010). Therefore, it is necessary to compare and evaluate typical bubble coalescence and breakup models that have been commonly used in the literature. Thus, this work is aimed to make a comparison of several typical bubble coalescence and breakup models and to discuss in detail the ability of the Test Solver to predict the evolution of bubble size distribution. (orig.)

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

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.

Two-fluid model LES of a bubble column

International Nuclear Information System (INIS)

Brahma N Reddy Vanga; Martin A Lopez de Bertodano; Eckhard Krepper; Alexandr Zaruba; Horst-Michael Prasser

2005-01-01

The hydrodynamics of a rectangular bubble column operating in the dispersed bubbly regime has been numerically investigated using a two-fluid model Large Eddy Simulation (LES). Experimental data were obtained to validate the model. LES computational fluid dynamic calculations of the transient flow for the bubble column were performed to account for the turbulence in the liquid phase. The computational mesh is of the same scale as the bubble size. The sub grid-scale Reynolds stresses were calculated with the Smagorinsky model. Furthermore, the effect of the bubbles on the turbulence in the continuous phase was modeled using Sato's eddy viscosity model for bubble-induced turbulence. Mean quantities were computed by averaging over a time period that was longer than the dynamic time scales of the turbulence, in particular the void fraction and the average velocity of the bubbles. A systematic analysis of the effect of the interfacial momentum transfer terms on these quantities has been conducted. The bubble column was locally aerated using a sparger located in the center of the bottom plate. The experimental studies involve wire-mesh tomography measurements for void fraction and bubble size distributions and digital image processing of high speed camera images for estimation of bubble velocities, size distributions and flow patterns. Experiments were performed for various aspect ratios (height of water column to width ratio) and superficial gas velocities. It was found that the non-drag bubble forces play a very prominent role in the predicting the correct flow pattern and void fraction distributions. In the calculations, the lift force and the wall force were considered. A 'wall peak' in the time averaged void fraction distribution has been experimentally observed and this cannot be predicted without including these non-drag forces in the numerical calculations. In this paper, experimental data are compared with the results of the numerical simulations. (authors)

Numerical investigation of interaction between rising bubbles in a viscous liquid

Energy Technology Data Exchange (ETDEWEB)

Yoon, Ik Roh [Korea Institute of Marine Science and Technology Promotion, Seoul (Korea, Republic of); Shin Seung Won [Hongik University, Seoul (Korea, Republic of)

2016-07-15

The rising behavior of bubbles undergoing bubble-bubble interaction in a viscous liquid is studied using a two-dimensional direct numerical simulation. Level contour reconstruction method (LCRM), one of the connectivity-free front tracking methods, is applied to describe a moving interface accurately under highly deformable conditions. This work focuses on the effects of bubble size on the interaction of two bubbles rising side-by-side in a stagnant liquid. Several characteristics of bubble-bubble interaction are analyzed quantitatively as supported by energy analysis. The results showed clear differences between small and large bubbles with respect to their interaction behavior in terms of lateral movement, vortex intensity, suppression of surface deformation, and viscous dissipation rate. Distributions of vorticity and viscous dissipation rate near the bubble interfaces also differed depending on the size of the bubbles. Strong vortices from large bubbles triggered oscillation in bubble-bubble interaction and played a dominant role in the interaction process as the size of bubbles increases.

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.

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.

Photothermally controlled Marangoni flow around a micro bubble

International Nuclear Information System (INIS)

Namura, Kyoko; Nakajima, Kaoru; Kimura, Kenji; Suzuki, Motofumi

2015-01-01

We have experimentally investigated the control of Marangoni flow around a micro bubble using photothermal conversion. Using a focused laser spot acting as a highly localized heat source on Au nanoparticles/dielectric/Ag mirror thin film enables us to create a micro bubble and to control the temperature gradient around the bubble at a micrometer scale. When we irradiate the laser next to the bubble, a strong main flow towards the bubble and two symmetric rotation flows on either side of it develop. The shape of this rotation flow shows a significant transformation depending on the relative position of the bubble and the laser spot. Using this controllable rotation flow, we have demonstrated sorting of the polystyrene spheres with diameters of 2 μm and 0.75 μm according to their size

Photothermally controlled Marangoni flow around a micro bubble

Science.gov (United States)

Namura, Kyoko; Nakajima, Kaoru; Kimura, Kenji; Suzuki, Motofumi

2015-01-01

We have experimentally investigated the control of Marangoni flow around a micro bubble using photothermal conversion. Using a focused laser spot acting as a highly localized heat source on Au nanoparticles/dielectric/Ag mirror thin film enables us to create a micro bubble and to control the temperature gradient around the bubble at a micrometer scale. When we irradiate the laser next to the bubble, a strong main flow towards the bubble and two symmetric rotation flows on either side of it develop. The shape of this rotation flow shows a significant transformation depending on the relative position of the bubble and the laser spot. Using this controllable rotation flow, we have demonstrated sorting of the polystyrene spheres with diameters of 2 μm and 0.75 μm according to their size.

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....

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.

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

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).

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.

Bubble shape in horizontal and near horizontal intermittent flow

International Nuclear Information System (INIS)

Gu, Hanyang; Guo, Liejin

2015-01-01

Highlights: • The bubble shapes in intermittent flows are presented experimentally. • The nose-tail inversion phenomenon appears at a low Froude number in downward pipe. • Transition from plug to slug flow occurs when the bubble tail changes from staircase pattern to hydraulic jump. - Abstract: This paper presents an experimental study of the shape of isolated bubbles in horizontal and near horizontal intermittent flows. It is found that the shapes of the nose and body of bubble depend on the Froude number defined by gas/liquid mixture velocity in a pipe, whereas the shape of the back of bubble region depends on both the Froude number and bubble length. The photographic studies show that the transition from plug to slug flow occurs when the back of the bubble changes from staircase pattern to hydraulic jump with the increase of the Froude number and bubble length. The effect of pipe inclination on characteristics of bubble is significant: The bubble is inversely located in a downwardly inclined pipe when the Froude number is low, and the transition from plug flow to slug flow in an upward inclined pipe is more ready to occur compared with that in a downwardly inclined pipe

The influence of bubbles on the perception carbonation bite.

Directory of Open Access Journals (Sweden)

Paul M Wise

Full Text Available Although many people naively assume that the bite of carbonation is due to tactile stimulation of the oral cavity by bubbles, it has become increasingly clear that carbonation bite comes mainly from formation of carbonic acid in the oral mucosa. In Experiment 1, we asked whether bubbles were in fact required to perceive carbonation bite. Subjects rated oral pungency from several concentrations of carbonated water both at normal atmospheric pressure (at which bubbles could form and at 2.0 atmospheres pressure (at which bubbles did not form. Ratings of carbonation bite under the two pressure conditions were essentially identical, indicating that bubbles are not required for pungency. In Experiment 2, we created controlled streams of air bubbles around the tongue in mildly pungent CO2 solutions to determine how tactile stimulation from bubbles affects carbonation bite. Since innocuous sensations like light touch and cooling often suppress pain, we predicted that bubbles might reduce rated bite. Contrary to prediction, air bubbles flowing around the tongue significantly enhanced rated bite, without inducing perceived bite in blank (un-carbonated solutions. Accordingly, though bubbles are clearly not required for carbonation bite, they may well modulate perceived bite. More generally, the results show that innocuous tactile stimulation can enhance chemogenic pain. Possible physiological mechanisms are discussed.

Hydrodynamic interaction on large-Reynolds-number aligned bubbles: Drag effects

International Nuclear Information System (INIS)

Ramirez-Munoz, J.; Salinas-Rodriguez, E.; Soria, A.; Gama-Goicochea, A.

2011-01-01

Graphical abstract: Display Omitted Highlights: → The hydrodynamic interaction of a pair aligned equal-sized bubbles is analyzed. → The leading bubble wake decreases the drag on the trailing bubble. → A new semi-analytical model for the trailing bubble's drag is presented. → The equilibrium distance between bubbles is predicted. - Abstract: The hydrodynamic interaction of two equal-sized spherical gas bubbles rising along a vertical line with a Reynolds number (Re) between 50 and 200 is analyzed. An approach to estimate the trailing bubble drag based on the search of a proper reference fluid velocity is proposed. Our main result is a new, simple semi-analytical model for the trailing bubble drag. Additionally, the equilibrium separation distance between bubbles is predicted. The proposed models agree quantitatively up to small distances between bubbles, with reported data for 50 ≤ Re ≤ 200. The relative average error for the trailing bubble drag, Er, is found to be in the range 1.1 ≤ Er ≤ 1.7, i.e., it is of the same order of the analytical predictions in the literature.

Hydrodynamic interaction on large-Reynolds-number aligned bubbles: Drag effects

Energy Technology Data Exchange (ETDEWEB)

Ramirez-Munoz, J., E-mail: jrm@correo.azc.uam.mx [Departamento de Energia, Universidad Autonoma Metropolitana-Azcapotzalco, Av. San Pablo 180, Col. Reynosa Tamaulipas, 02200 Mexico D.F. (Mexico); Centro de Investigacion en Polimeros, Marcos Achar Lobaton No. 2, Tepexpan, 55885 Acolman, Edo. de Mexico (Mexico); Salinas-Rodriguez, E.; Soria, A. [Departamento de IPH, Universidad Autonoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, 09340 Mexico D.F. (Mexico); Gama-Goicochea, A. [Centro de Investigacion en Polimeros, Marcos Achar Lobaton No. 2, Tepexpan, 55885 Acolman, Edo. de Mexico (Mexico)

2011-07-15

Graphical abstract: Display Omitted Highlights: > The hydrodynamic interaction of a pair aligned equal-sized bubbles is analyzed. > The leading bubble wake decreases the drag on the trailing bubble. > A new semi-analytical model for the trailing bubble's drag is presented. > The equilibrium distance between bubbles is predicted. - Abstract: The hydrodynamic interaction of two equal-sized spherical gas bubbles rising along a vertical line with a Reynolds number (Re) between 50 and 200 is analyzed. An approach to estimate the trailing bubble drag based on the search of a proper reference fluid velocity is proposed. Our main result is a new, simple semi-analytical model for the trailing bubble drag. Additionally, the equilibrium separation distance between bubbles is predicted. The proposed models agree quantitatively up to small distances between bubbles, with reported data for 50 {<=} Re {<=} 200. The relative average error for the trailing bubble drag, Er, is found to be in the range 1.1 {<=} Er {<=} 1.7, i.e., it is of the same order of the analytical predictions in the literature.

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

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)

Bubble behavior characteristics based on virtual binocular stereo vision

Science.gov (United States)

Xue, Ting; Xu, Ling-shuang; Zhang, Shang-zhen

2018-01-01

The three-dimensional (3D) behavior characteristics of bubble rising in gas-liquid two-phase flow are of great importance to study bubbly flow mechanism and guide engineering practice. Based on the dual-perspective imaging of virtual binocular stereo vision, the 3D behavior characteristics of bubbles in gas-liquid two-phase flow are studied in detail, which effectively increases the projection information of bubbles to acquire more accurate behavior features. In this paper, the variations of bubble equivalent diameter, volume, velocity and trajectory in the rising process are estimated, and the factors affecting bubble behavior characteristics are analyzed. It is shown that the method is real-time and valid, the equivalent diameter of the rising bubble in the stagnant water is periodically changed, and the crests and troughs in the equivalent diameter curve appear alternately. The bubble behavior characteristics as well as the spiral amplitude are affected by the orifice diameter and the gas volume flow.

Jet formation in shock-heavy gas bubble interaction

Institute of Scientific and Technical Information of China (English)

Zhi-Gang Zhai; Ting Si; Li-Yong Zou; Xi-Sheng Luo

2013-01-01

The influences of the acoustic impedance and shock strength on the jet formation in shock-heavy gas bubble interaction are numerically studied in this work.The process of a shock interacting with a krypton or a SF6 bubble is studied by the numerical method VAS2D.As a validation,the experiments of a SF6 bubble accelerated by a planar shock were performed.The results indicate that,due to the mismatch of acoustic impedance,the way of jet formation in heavy gas bubble with different species is diversified under the same initial condition.With respect to the same bubble,the manner of jet formation is also distinctly different under different shock strengths.The disparities of the acoustic impedance result in different effects of shock focusing in the bubble,and different behaviors of shock wave inside and outside the bubble.The analyses of the wave pattern and the pressure variation indicate that the jet formation is closely associated with the pressure perturbation.Moreover,the analysis of the vorticity deposition,and comparisons of circulation and baroclinic torque show that the baroclinic vorticity also contributes to the jet formation.It is concluded that the pressure perturbation and baroclinic vorticity deposition are the two dominant factors for the jet formation in shock-heavy gas bubble interaction.

Can airborne ultrasound monitor bubble size in chocolate?

International Nuclear Information System (INIS)

Watson, N; Hazlehurst, T; Povey, M; Vieira, J; Sundara, R; Sandoz, J-P

2014-01-01

Aerated chocolate products consist of solid chocolate with the inclusion of bubbles and are a popular consumer product in many countries. The volume fraction and size distribution of the bubbles has an effect on their sensory properties and manufacturing cost. For these reasons it is important to have an online real time process monitoring system capable of measuring their bubble size distribution. As these products are eaten by consumers it is desirable that the monitoring system is non contact to avoid food contaminations. In this work we assess the feasibility of using an airborne ultrasound system to monitor the bubble size distribution in aerated chocolate bars. The experimental results from the airborne acoustic experiments were compared with theoretical results for known bubble size distributions using COMSOL Multiphysics. This combined experimental and theoretical approach is used to develop a greater understanding of how ultrasound propagates through aerated chocolate and to assess the feasibility of using airborne ultrasound to monitor bubble size distribution in these systems. The results indicated that a smaller bubble size distribution would result in an increase in attenuation through the product

Can airborne ultrasound monitor bubble size in chocolate?

Science.gov (United States)

Watson, N.; Hazlehurst, T.; Povey, M.; Vieira, J.; Sundara, R.; Sandoz, J.-P.

2014-04-01

Aerated chocolate products consist of solid chocolate with the inclusion of bubbles and are a popular consumer product in many countries. The volume fraction and size distribution of the bubbles has an effect on their sensory properties and manufacturing cost. For these reasons it is important to have an online real time process monitoring system capable of measuring their bubble size distribution. As these products are eaten by consumers it is desirable that the monitoring system is non contact to avoid food contaminations. In this work we assess the feasibility of using an airborne ultrasound system to monitor the bubble size distribution in aerated chocolate bars. The experimental results from the airborne acoustic experiments were compared with theoretical results for known bubble size distributions using COMSOL Multiphysics. This combined experimental and theoretical approach is used to develop a greater understanding of how ultrasound propagates through aerated chocolate and to assess the feasibility of using airborne ultrasound to monitor bubble size distribution in these systems. The results indicated that a smaller bubble size distribution would result in an increase in attenuation through the product.

THREE-DIMENSIONAL MAGNETOHYDRODYNAMIC SIMULATIONS OF BUOYANT BUBBLES IN GALAXY CLUSTERS

International Nuclear Information System (INIS)

O'Neill, S. M.; De Young, D. S.; Jones, T. W.

2009-01-01

We report results of three-dimensional magnetohydrodynamic simulations of the dynamics of buoyant bubbles in magnetized galaxy cluster media. The simulations are three-dimensional extensions of two-dimensional calculations reported by Jones and De Young. Initially, spherical bubbles and briefly inflated spherical bubbles all with radii a few times smaller than the intracluster medium (ICM) scale height were followed as they rose through several ICM scale heights. Such bubbles quickly evolve into a toroidal form that, in the absence of magnetic influences, is stable against fragmentation in our simulations. This ring formation results from (commonly used) initial conditions that cause ICM material below the bubbles to drive upwards through the bubble, creating a vortex ring; that is, hydrostatic bubbles develop into 'smoke rings', if they are initially not very much smaller or very much larger than the ICM scale height. Even modest ICM magnetic fields with β = P gas /P mag ∼ 3 can influence the dynamics of the bubbles, provided the fields are not tangled on scales comparable to or smaller than the size of the bubbles. Quasi-uniform, horizontal fields with initial β ∼ 10 2 bifurcated our bubbles before they rose more than about a scale height of the ICM, and substantially weaker fields produced clear distortions. These behaviors resulted from stretching and amplification of ICM fields trapped in irregularities along the top surface of the young bubbles. On the other hand, tangled magnetic fields with similar, modest strengths are generally less easily amplified by the bubble motions and are thus less influential in bubble evolution. Inclusion of a comparably strong, tangled magnetic field inside the initial bubbles had little effect on our bubble evolution, since those fields were quickly diminished through expansion of the bubble and reconnection of the initial field.

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

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)

Dynamics of diffusive bubble growth and pressure recovery in a bubbly rhyolitic melt embedded in an elastic solid

Science.gov (United States)

Chouet, Bernard A.; Dawson, Phillip B.; Nakano, Masaru

2006-01-01

We present a model of gas exsolution and bubble expansion in a melt supersaturated in response to a sudden pressure drop. In our model, the melt contains a suspension of gas bubbles of identical sizes and is encased in a penny-shaped crack embedded in an elastic solid. The suspension is modeled as a three-dimensional lattice of spherical cells with slight overlap, where each elementary cell consists of a gas bubble surrounded by a shell of volatile-rich melt. The melt is then subjected to a step drop in pressure, which induces gas exsolution and bubble expansion, resulting in the compression of the melt and volumetric expansion of the crack. The dynamics of diffusion-driven bubble growth and volumetric crack expansion span 9 decades in time. The model demonstrates that the speed of the crack response depends strongly on volatile diffusivity in the melt and bubble number density and is markedly sensitive to the ratio of crack thickness to crack radius and initial bubble radius but is relatively insensitive to melt viscosity. The net drop in gas concentration in the melt after pressure recovery represents only a small fraction of the initial concentration prior to the drop, suggesting the melt may undergo numerous pressure transients before becoming significantly depleted of gases. The magnitude of pressure and volume recovery in the crack depends sensitively on the size of the input-pressure transient, becoming relatively larger for smaller-size transients in a melt containing bubbles with initial radii less than 10-5 m. Amplification of the input transient may be large enough to disrupt the crack wall and induce brittle failure in the rock matrix surrounding the crack. Our results provide additional basis for the interpretation of volume changes in the magma conduit under Popocatépetl Volcano during Vulcanian degassing bursts in its eruptive activity in April–May 2000.

Energy cascading by triple-bubble interactions via time-delayed control

International Nuclear Information System (INIS)

Lin, Yen-Liang; Chang, Chia-Ming; Tseng, Fan-Gang; Yang, I-Da; Chieng, Ching-Chang

2012-01-01

The triple-bubble interaction controlled by a precise time-delayed technique was investigated in detail with respect to different ignition times, heater spaces and sequential firing modes to promote efficient energy cascading and concentration. The target bubble, which was generated under a specific delay time with two auxiliary bubbles, can have a volume that is two or almost three times larger than that of a single bubble. This result overcomes the limitation of energy usage on an explosive microbubble under a constant heat flux. As the heater space decreases, stronger bubble–bubble interactions were obtained due to the hydrodynamic effect and the intensive pressure wave emission, resulting in highly enhancing and depressing bubble dynamics. Other interesting phenomena, such as bubble shifting, mushroom-shape bubble, rod-shape bubble and bubble extension among heaters, were also recorded by a high-speed phase-averaged stroboscopic technique, displaying special non-spherical bubble dynamics. Artificial manipulation of bubble behavior was further conducted in a two-level sequential firing process. Using various volumetric combinations, the adjustable multi-level fluid transportation can be realized by a digital time-delayed control. The above-mentioned information can be applied to not only the design and operation of inkjet printheads but also cavitation research and fluid pumping in microdevices. (paper)

Helium bubbles aggravated defects production in self-irradiated copper

Science.gov (United States)

Wu, FengChao; Zhu, YinBo; Wu, Qiang; Li, XinZhu; Wang, Pei; Wu, HengAn

2017-12-01

Under the environment of high radiation, materials used in fission and fusion reactors will internally accumulate numerous lattice defects and bubbles. With extensive studies focused on bubble resolution under irradiation, the mutually effects between helium bubbles and displacement cascades in irradiated materials remain unaddressed. Therefore, the defects production and microstructure evolution under self-irradiation events in vicinity of helium bubbles are investigated by preforming large scale molecular dynamics simulations in single-crystal copper. When subjected to displacement cascades, distinguished bubble resolution categories dependent on bubble size are observed. With the existence of bubbles, radiation damage is aggravated with the increasing bubble size, represented as the promotion of point defects and dislocations. The atomic mechanisms of heterogeneous dislocation structures are attributed to different helium-vacancy cluster modes, transforming from the resolved gas trapped with vacancies to the biased absorption of vacancies by the over-pressured bubble. In both cases, helium impedes the recombination of point defects, leading to the accelerated formation of interstitial loops. The results and insight obtained here might contribute to understand the underlying mechanism of transmutant solute on the long-term evolution of irradiated materials.

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

Neutron Imaging study of bubble behaviors in Nanofluid Through Engineered Orifices

International Nuclear Information System (INIS)

Seo, Seok Bin; Bang, In Cheol; Kim, Tae Joo

2014-01-01

Most studies focused on the change of surface parameters through deposited nanoparticles, while Vafaei and Wen firstly discussed modification of bubble dynamics by dispersed nanoparticles in fluid as well as deposited ones. The boiling mechanism, as an effective heat transfer mode, includes bubble generation, growth, departure, and coalescence. Therefore the change of bubble dynamics can lead to the change of boiling heat transfer condition. That is, not only surface characteristics but the dispersed nanoparticles would be the essential parameters of boiling mechanism in terms of bubble dynamics. For advanced visualization of opaque fluids, the neutron imaging technique is introduced. In the present study, the bubble dynamics in nanofluid through engineered orifices was studied. The main parameters of engineered orifices are size and geometry. Photographic analysis of bubble departure frequency and averaged bubble departure volume provides as follows: With increasing orifice diameter, averaged bubble departure volume increases, while bubble departure frequency decreases. The results are attributed to enhanced capillary force by increasing contact perimeter. Averaged bubble departure volume and bubble departure frequency remain similar for three different types of orifices. But edges of the triangle and square orifice produce small bubbles which interrupts bubble generation. The converged triple contact line due to the edge may be a reason for the emerged baby bubbles. Nanofluid shows less averaged bubble departure volume and higher bubble departure frequency. Considering little change in physical properties of the fluid, interaction between bubble interface and nanoparticles may be in charge of the results

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)

Turbulence modulation induced by bubble swarm in oscillating-grid turbulence

International Nuclear Information System (INIS)

Morikawa, Koichi; Urano, Shigeyuki; Saito, Takayuki

2007-01-01

In the present study, liquid-phase turbulence modulation induced by a bubble swarm ascending in arbitrary turbulence was experimentally investigated. Liquid-phase homogeneous isotropic turbulence was formed using an oscillating grid in a cylindrical acrylic vessel of 149 mm in inner diameter. A bubble swarm consisting of 19 bubbles of 2.8 mm in equivalent diameter was examined; the bubble size and launching time were completely controlled using a bubble launching device through audio speakers. This bubble launching device was able to repeatedly control the bubble swarm arbitrarily and precisely. The bubble swarm was launched at a frequency of 4 Hz. The liquid phase motion was measured via two LDA (Laser Doppler Anemometer) probes. The turbulence intensity, spatial correlation and integral scale were calculated from LDA data obtained by the two spatially-separate-point measurement. When the bubble swarm was added, the turbulence intensity dramatically changed. The original isotropic turbulence was modulated to the anisotropic turbulence by the mutual interference between the bubble swarm and ambient isotropic turbulence. The integral scales were calculated from the spatial correlation function. The effects of the bubble swarm on the integral scales showed the tendencies similar to those on turbulence intensity. (author)

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.

Gas Bubble Migration and Trapping in Porous Media: Pore-Scale Simulation

Science.gov (United States)

Mahabadi, Nariman; Zheng, Xianglei; Yun, Tae Sup; van Paassen, Leon; Jang, Jaewon

2018-02-01

Gas bubbles can be naturally generated or intentionally introduced in sediments. Gas bubble migration and trapping affect the rate of gas emission into the atmosphere or modify the sediment properties such as hydraulic and mechanical properties. In this study, the migration and trapping of gas bubbles are simulated using the pore-network model extracted from the 3D X-ray image of in situ sediment. Two types of bubble size distribution (mono-sized and distributed-sized cases) are used in the simulation. The spatial and statistical bubble size distribution, residual gas saturation, and hydraulic conductivity reduction due to the bubble trapping are investigated. The results show that the bubble size distribution becomes wider during the gas bubble migration due to bubble coalescence for both mono-sized and distributed-sized cases. And the trapped bubble fraction and the residual gas saturation increase as the bubble size increases. The hydraulic conductivity is reduced as a result of the gas bubble trapping. The reduction in hydraulic conductivity is apparently observed as bubble size and the number of nucleation points increase.

Modeling of bubble break-up in stirred tanks

Directory of Open Access Journals (Sweden)

Živković Goran

2004-01-01

Full Text Available The Lagrangian code LAG3D for dispersed phase flow modeling was implemented with the introduction of bubble break-up model. The research was restricted on bubbles with diameter less than 2 mm, i.e. bubbles which could be treated as spheres. The model was developed according to the approach of Martinez-Bazan model. It was rearranged and adjusted for the use in the particular problem of flow in stirred tanks. Developed model is stochastic one, based on the assumption that shear in the flow induces the break of the bubble. As a dominant parameter a dissipation of the turbulent kinetic energy was used. Computations were performed for two different types of the stirrer: Rushton turbine, and Pitch blade turbine. The geometry of the tank was kept constant (four blades. Two different types of liquids with very big difference in viscosity were used, i.e. silicon oil and dimethylsulfoxide, in order to enable computation of the flow in turbulent regime as well. As a parameter of the flow, the number of rotations of the stirrer was varying. As a result of the computation the fields of velocity of both phases were got, as well as the fields of bubble concentration bubble mean diameter and bubble Sauter diameter. To estimate the influence of the break-up model on the processes in the stirred tank a computations with and without this model were performed and compared. A considerable differences were found not only in the field of bubble diameter, but also in the field of bubble concentration. That confirmed a necessity of the introduction of such model. A comparison with the experiments performed with phase Doppler anemometry technique showed very good agreement in velocity and concentration profiles of the gas phase. The results for the average bubble diameter are qualitatively the same, but in almost all computations about 20% smaller bubble diameter was got than in the measurements.

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

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.

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)

Formation and repair of DNA-protein cross-links (DPCs) in newly replicated DNA

International Nuclear Information System (INIS)

Chiu, S.; Friedman, L.R.; Oleinick, N.L.

1987-01-01

DPCs preferentially involve proteins of the nuclear matrix, the site of replication and transcription. To elucidate the relationship with replication, the formation and repair of DPCs has been studied in newly replicated DNA. Log-phase V79 cells were pulsed with /sup 3/H-TdR (10-20 μCi/ml) for 30-90 sec at 22 0 followed by up to a 60 min chase at 37 0 . Irradiation (0-100 Gy) immediately after the pulse increases the labeled DNA in DPCs with a dose-dependence that is unaffected by the initial level of labeled DPC or by chase time. When cells are irradiated before the pulse, DNA synthesis is inhibited; however, release of pulse-labeled DPCs appears normal. The data suggest that during replication, DNA is cross-linked to (matrix) protein, contributing to background DPCs

Laser controllable generation and manipulation of micro-bubbles in water

Science.gov (United States)

Angelsky, O. V.; Bekshaev, A. Ya.; Maksimyak, P. P.; Maksimyak, A. P.; Hanson, S. G.; Kontush, S. M.

2018-01-01

Micrometer-sized vapor bubbles are formed due to local heating of the water suspension containing absorptive pigment particles of 100 nm diameter. The heating is performed by the CW near-infrared laser radiation. By changing the laser power, four regimes are realized: (1) bubble generation, (2) stable growth of the existing bubbles; (3) stationary existence of the bubbles and (4) bubbles' shrinkage and collapse. The generation and evolution of single bubbles and ensembles of bubbles with controllable sizes and numbers is demonstrated. The bubbles are grouped within the laserilluminated region. They can be easily moved and transported together with the focal spot. The results can be useful for applications associated with the precise manipulation and the species delivery in nano- and micro-engineering problems.

Inertial manipulation of bubbles in rectangular microfluidic channels.

Science.gov (United States)

Hadikhani, Pooria; Hashemi, S Mohammad H; Balestra, Gioele; Zhu, Lailai; Modestino, Miguel A; Gallaire, François; Psaltis, Demetri

2018-03-27

Inertial microfluidics is an active field of research that deals with crossflow positioning of the suspended entities in microflows. Until now, the majority of the studies have focused on the behavior of rigid particles in order to provide guidelines for microfluidic applications such as sorting and filtering. Deformable entities such as bubbles and droplets are considered in fewer studies despite their importance in multiphase microflows. In this paper, we show that the trajectory of bubbles flowing in rectangular and square microchannels can be controlled by tuning the balance of forces acting on them. A T-junction geometry is employed to introduce bubbles into a microchannel and analyze their lateral equilibrium position in a range of Reynolds (1 < Re < 40) and capillary numbers (0.1 < Ca < 1). We find that the Reynolds number (Re), the capillary number (Ca), the diameter of the bubble (D[combining macron]), and the aspect ratio of the channel are the influential parameters in this phenomenon. For instance, at high Re, the flow pushes the bubble towards the wall while large Ca or D[combining macron] moves the bubble towards the center. Moreover, in the shallow channels, having aspect ratios higher than one, the bubble moves towards the narrower sidewalls. One important outcome of this study is that the equilibrium position of bubbles in rectangular channels is different from that of solid particles. The experimental observations are in good agreement with the performed numerical simulations and provide insights into the dynamics of bubbles in laminar flows which can be utilized in the design of flow based multiphase flow reactors.

Structure of positive streamers inside gaseous bubbles immersed in liquids

International Nuclear Information System (INIS)

Babaeva, Natalia Yu; Kushner, Mark J

2009-01-01

Electric discharges and streamers in liquids typically proceed through vapour phase channels produced by the streamer or in gaseous bubbles. The bubbles can originate by enthalpy changes produced by the discharge or can be artificially injected into the liquid. Experiments on streamers in bubbles immersed in liquids have shown that the discharge propagates either along the surface of the bubble or through the volume of the bubble as in conventional streamer propagation in air. In this paper we report on results of a computational investigation of streamer propagation through bubbles immersed in liquids. We found that the dielectric constant of the liquid in large part determines the path the streamer takes. Streamers in bubbles immersed in a liquid with a high permittivity preferentially propagate along the surface of the bubble. Liquids with low permittivity can result in the streamer propagating along the axis of the bubble. The permittivity at which this transition occurs is a function of the applied voltage, size of the bubble and the conductivity of the liquid. (fast track communication)

Expansion of a vapor bubble and aerosols transfer

International Nuclear Information System (INIS)

Breton, J.P.; Lapicore, A.; Porrachia, A.; Natta, M.; Amblard, M.; Berthoud, G.

1979-08-01

Experimental results on the expansion and collapse of two phase vapor bubble, and on the aerosols transport outside the tank are presented. Two facilities using small source of hot water (2 cm 3 ) or bigger ones (1000 cm 3 ) were used and are described. Two models are developped to analyze the results on the bubble. They show the heat and mass transfer from the bubble to the surroundings and the following reduction in the mechanical energy delivered by the bubble, and the decrease in this reduction due to noncondensables and to scale effect. The models developed or the aerosol transfer show that most particles are likely transported from the bubble to the cover gas

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

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

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.

Bubble coalescence dynamics and supersaturation in electrolytic gas evolution

Energy Technology Data Exchange (ETDEWEB)

Stover, R.L. [Univ. of California, Berkeley, CA (United States). Dept. of Chemical Engineering]|[Lawrence Berkeley National Lab., CA (United States). Energy and Environment Div.

1996-08-01

The apparatus and procedures developed in this research permit the observation of electrolytic bubble coalescence, which heretofore has not been possible. The influence of bubble size, electrolyte viscosity, surface tension, gas type, and pH on bubble coalescence was examined. The Navier-Stokes equations with free surface boundary conditions were solved numerically for the full range of experimental variables that were examined. Based on this study, the following mechanism for bubble coalescence emerges: when two gas bubbles coalesce, the surface energy decreases as the curvature and surface area of the resultant bubble decrease, and the energy is imparted into the surrounding liquid. The initial motion is driven by the surface tension and slowed by the inertia and viscosity of the surrounding fluid. The initial velocity of the interface is approximately proportional to the square root of the surface tension and inversely proportional to the square root of the bubble radius. Fluid inertia sustains the oblate/prolate oscillations of the resultant bubble. The period of the oscillations varies with the bubble radius raised to the 3/2 power and inversely with the square root of the surface tension. Viscous resistance dampens the oscillations at a rate proportional to the viscosity and inversely proportional to the square of the bubble radius. The numerical simulations were consistent with most of the experimental results. The differences between the computed and measured saddle point decelerations and periods suggest that the surface tension in the experiments may have changed during each run. By adjusting the surface tension in the simulation, a good fit was obtained for the 150-{micro}m diameter bubbles. The simulations fit the experiments on larger bubbles with very little adjustment of surface tension. A more focused analysis should be done to elucidate the phenomena that occur in the receding liquid film immediately following rupture.

Convection in a volcanic conduit recorded by bubbles

Science.gov (United States)

Carey, Rebecca J.; Manga, Michael; Degruyter, Wim; Gonnermann, Helge M.; Swanson, Donald; Houghton, Bruce F.; Orr, Tim R.; Patrick, Matthew R.

2013-01-01

Microtextures of juvenile pyroclasts from Kīlauea’s (Hawai‘i) early A.D. 2008 explosive activity record the velocity and depth of convection within the basaltic magma-filled conduit. We use X-ray microtomography (μXRT) to document the spatial distribution of bubbles. We find small bubbles (radii from 5 μm to 70 μm) in a halo surrounding larger millimeter-size bubbles. This suggests that dissolved water was enriched around the larger bubbles—the opposite of what is expected if bubbles grow as water diffuses into the bubble. Such volatile enrichment implies that the volatiles within the large bubbles were redissolving into the melt as they descended into the conduit by the downward motion of convecting magma within the lava lake. The thickness of the small bubble halo is ∼100–150 μm, consistent with water diffusing into the melt on time scales on the order of 103 s. Eruptions, triggered by rockfall, rapidly exposed this magma to lower pressures, and the haloes of melt with re-dissolved water became sufficiently supersaturated to cause nucleation of the population of smaller bubbles. The required supersaturation pressures are consistent with a depth of a few hundred meters and convection velocities of the order of 0.1 m s−1, similar to the circulation velocity observed on the surface of the Halema‘uma‘u lava lake.

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.

Environmental stress speeds up DNA replication in Pseudomonas putida in chemostat cultivations.

Science.gov (United States)

Lieder, Sarah; Jahn, Michael; Koepff, Joachim; Müller, Susann; Takors, Ralf

2016-01-01

Cellular response to different types of stress is the hallmark of the cell's strategy for survival. How organisms adjust their cell cycle dynamics to compensate for changes in environmental conditions is an important unanswered question in bacterial physiology. A cell using binary fission for reproduction passes through three stages during its cell cycle: a stage from cell birth to initiation of replication, a DNA replication phase and a period of cell division. We present a detailed analysis of durations of cell cycle phases, investigating their dynamics under environmental stress conditions. Applying continuous steady state cultivations (chemostats), the DNA content of a Pseudomonas putida KT2440 population was quantified with flow cytometry at distinct growth rates. Data-driven modeling revealed that under stress conditions, such as oxygen deprivation, solvent exposure and decreased iron availability, DNA replication was accelerated correlated to the severity of the imposed stress (up to 1.9-fold). Cells maintained constant growth rates by balancing the shortened replication phase with extended cell cycle phases before and after replication. Transcriptome data underpin the transcriptional upregulation of crucial genes of the replication machinery. Hence adaption of DNA replication speed appears to be an important strategy to withstand environmental stress. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Can we use volatility to diagnose financial bubbles? lessons from 40historical bubbles

Directory of Open Access Journals (Sweden)

Didier Sornette

2018-03-01

Full Text Available We inspect the price volatility before, during, and after financial asset bubbles in orderto uncover possible commonalities and check empirically whether volatility might be used as anindicator or an early warning signal of an unsustainable price increase and the associated crash. Someresearchers and finance practitioners believe that historical and/or implied volatility increase beforea crash, but we do not see this as a consistent behavior. We examine forty well-known bubbles and,using creative graphical representations to capture robustly the transient dynamics of the volatility, findthat the dynamics of the volatility would not have been a useful predictor of the subsequent crashes.In approximately two-third of the studied bubbles, the crash follows a period of lower volatility,reminiscent of the idiom of a “lull before the storm”. This paradoxical behavior, from the lensesof traditional asset pricing models, further questions the general relationship between risk and return.

DNA-binding proteins regulating pIP501 transfer and replication

Directory of Open Access Journals (Sweden)

Elisabeth Grohmann

2016-08-01

Full Text Available pIP501 is a Gram-positive broad-host-range model plasmid intensively used for studying plasmid replication and conjugative transfer. It is a multiple antibiotic resistance plasmid frequently found in clinical Enterococcus faecalis and Enterococcus faecium isolates. Replication of pIP501 proceeds unidirectionally by a theta mechanism. The minimal replicon of pIP501 is composed of the repR gene encoding the essential rate-limiting replication initiator protein RepR and the origin of replication, oriR, located downstream of repR. RepR is similar to RepE of related streptococcal plasmid pAMβ1, which has been shown to possess RNase activity cleaving free RNA molecules in close proximity of the initiation site of DNA synthesis. Replication of pIP501 is controlled by the concerted action of a small protein, CopR, and an antisense RNA, RNAIII. CopR has a dual role: It acts as transcriptional repressor at the repR promoter and prevents convergent transcription of RNAIII and repR mRNA (RNAII, thereby indirectly increasing RNAIII synthesis. CopR binds asymmetrically as a dimer at two consecutive binding sites upstream of and overlapping with the repR promoter. RNAIII induces transcriptional attenuation within the leader region of the repR mRNA (RNAII. Deletion of either control component causes a 10- to 20-fold increase of plasmid copy number, while simultaneous deletions have no additional effect. Conjugative transfer of pIP501 depends on a type IV secretion system (T4SS encoded in a single operon. Its transfer host-range is considerably broad, as it has been transferred to virtually all Gram-positive bacteria including filamentous streptomycetes and even the Gram-negative Escherichia coli. Expression of the 15 genes encoding the T4SS is tightly controlled by binding of the relaxase TraA, the transfer initiator protein, to the operon promoter, which overlaps with the origin of transfer (oriT. The T4SS operon encodes the DNA-binding proteins TraJ (VirD4

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

Three-dimensional reacting shock–bubble interaction

NARCIS (Netherlands)

Diegelmann, Felix; Hickel, S.; Adams, Nikolaus A.

2017-01-01

We investigate a reacting shock–bubble interaction through three-dimensional numerical simulations with detailed chemistry. The convex shape of the bubble focuses the shock and generates regions of high pressure and temperature, which are sufficient to ignite the diluted stoichiometric

A method for bubble volume calculating in vertical two-phase flow

International Nuclear Information System (INIS)

Wang, H Y; Dong, F

2009-01-01

The movement of bubble is a basic subject in gas-liquid two-phase flow research. A method for calculating bubble volume which is one of the most important characters in bubble motion research was proposed. A suit of visualized experimental device was designed and set up. Single bubble rising in stagnant liquid in a rectangular tank was studied using the high-speed video system. Bubbles generated by four orifice with different diameter (1mm, 2mm, 3mm, 4mm) were recorded respectively. Sequences of recorded high-speed images were processed by digital image processing method, such as image noise remove, binary image transform, bubble filling, and so on. then, Several parameters could be obtained from the processed image. Bubble area, equivalent diameter, bubble velocity, bubble acceleration are all indispensable in bubble volume calculating. In order to get the force balance equation, forces that work on bubble along vertical direction, including drag force, virtual mass force, buoyancy, gravity and liquid thrust, were analyzed. Finally, the bubble volume formula could be derived from the force balance equation and bubble parameters. Examples were given to shown the computing process and results. Comparison of the bubble volume calculated by geomettic method and the present method have shown the superiority of the proposed method in this paper.

Experimental study of bubbly flow using image processing techniques

Energy Technology Data Exchange (ETDEWEB)

Fu, Yucheng, E-mail: ycfu@vt.edu; Liu, Yang, E-mail: liu130@vt.edu

2016-12-15

This paper presents an experimental study of bubbly flows at relatively high void fractions using an advanced image processing method. Bubble overlapping is a common problem in such flows and the past studies often treat the overlapping bubbles as a whole, which introduces considerable measurement uncertainties. In this study, a hybrid method combining intersection point detection and watershed segmentation is used to separate the overlapping bubbles. In order to reconstruct bubbles from separated segments, a systematic procedure is developed which can preserve more features captured in the raw image compared to the simple ellipse fitting method. The distributions of void fraction, interfacial area concentration, number density and velocity are obtained from the extracted bubble information. High-speed images of air-water bubbly flows are acquired and processed for eight test runs conducted in a 30 mm × 10 mm rectangular channel. The developed image processing scheme can effectively separate overlapping bubbles and the results compare well with the measurements by the gas flow meter and double-sensor conductivity probe. The development of flows in transverse and mainstream directions are analyzed and compared with the prediction made by the one-dimensional interfacial area transport equation (IATE) and the bubble number density transport equation.

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)

ATAD2 is an epigenetic reader of newly synthesized histone marks during DNA replication.

Science.gov (United States)

Koo, Seong Joo; Fernández-Montalván, Amaury E; Badock, Volker; Ott, Christopher J; Holton, Simon J; von Ahsen, Oliver; Toedling, Joern; Vittori, Sarah; Bradner, James E; Gorjánácz, Mátyás

2016-10-25

ATAD2 (ATPase family AAA domain-containing protein 2) is a chromatin regulator harboring an AAA+ ATPase domain and a bromodomain, previously proposed to function as an oncogenic transcription co-factor. Here we suggest that ATAD2 is also required for DNA replication. ATAD2 is co-expressed with genes involved in DNA replication in various cancer types and predominantly expressed in S phase cells where it localized on nascent chromatin (replication sites). Our extensive biochemical and cellular analyses revealed that ATAD2 is recruited to replication sites through a direct interaction with di-acetylated histone H4 at K5 and K12, indicative of newly synthesized histones during replication-coupled chromatin reassembly. Similar to ATAD2-depletion, ectopic expression of ATAD2 mutants that are deficient in binding to these di-acetylation marks resulted in reduced DNA replication and impaired loading of PCNA onto chromatin, suggesting relevance of ATAD2 in DNA replication. Taken together, our data show a novel function of ATAD2 in cancer and for the first time identify a reader of newly synthesized histone di-acetylation-marks during replication.

Analysis of classical swine fever virus RNA replication determinants using replicons

DEFF Research Database (Denmark)

Risager, Peter Christian; Fahnøe, Ulrik; Gullberg, Maria

2013-01-01

Self-replicating RNAs (replicons), with or without reporter gene sequences, derived from the genome of the Paderborn strain of classical swine fever virus (CSFV) have been produced. The full-length viral cDNA, propagated within a bacterial artificial chromosome (BAC), was modified by targeted...... recombination within E. coli. RNA transcripts were produced in vitro and introduced into cells by electroporation. The translation and replication of the replicon RNAs could be followed by the accumulation of luciferase (from Renilla reniformis or Gaussia princeps) protein expression (where appropriate......), as well as by detection of the CSFV NS3 protein production within the cells. Inclusion of the viral E2 coding region within the replicon was advantageous for the replication efficiency. Production of chimeric RNAs, substituting the NS2 and NS3 coding regions (as a unit) from the Paderborn strain...