Phosphatidylcholine reverses ethanol-induced increase in transepithelial endotoxin permeability and abolishes transepithelial leukocyte activation

DEFF Research Database (Denmark)

Mitscherling, K.; Volynets, V.; Parlesak, Alexandr

2009-01-01

BACKGROUND: Chronic alcohol abuse increases both intestinal bacterial overgrowth and intestinal permeability to macromolecules. Intestinal permeability of endotoxin, a component of the outer cell membrane of Gram-negative bacteria, plays a crucial role in the development of alcohol-induced liver...... disease (ALD). As impaired bile flow leads to endotoxemia and the bile component phosphatidylcholine (PC) is therapeutically active in ALD, we tested the hypothesis that conjugated primary bile salts (CPBS) and PC inhibit ethanol-enhanced transepithelial permeability of endotoxin and the subsequent...... transepithelial activation of human leukocytes. METHODS: For this purpose, we used a model in which intestinal epithelial cells (Caco-2) were basolaterally cocultivated with mononuclear leukocytes. Cells were challenged apically with endotoxin from Escherichia coli K12 and were incubated with or without...

Determination of selenium in food matrices by replicate sample neutron activation analysis

International Nuclear Information System (INIS)

Ventura, M.G.; Freitas, M.C.; Ventura, M.G.; Pacheco, A.M.G.

2009-01-01

The replicate sample instrumental neutron activation method was optimized and used for the determination of selenium in foodstuffs. The method was reliable, yielding accurate results. Lower detections limits were obtained after each successive irradiation. Different irradiation conditions were used depending on the type of sample. For samples with higher selenium contents (meat, fish, eggs), the measured selenium in the first replicate is in all cases larger than the detection limit, but a better accuracy was obtained with a larger number of replicates (2-3 replicates). For samples with extremely low selenium contents (vegetable samples), at least seven replicates were necessary to obtain a concentration value two times larger than the detection limit. (author)

Phosphatidylcholine Reverses Ethanol-Induced Increase in Transepithelial Endotoxin Permeability and Abolishes Transepithelial Leukocyte Activation

DEFF Research Database (Denmark)

Mitzscherling, Katja; Volynets, Valentina; Parlesak, Alexandr

2009-01-01

Chronic alcohol abuse increases both intestinal bacterial overgrowth and intestinal permeability to macromolecules. Intestinal permeability of endotoxin, a component of the outer cell membrane of Gram-negative bacteria, plays a crucial role in the development of alcohol-induced liver disease (ALD......). As impaired bile flow leads to endotoxemia and the bile component phosphatidylcholine (PC) is therapeutically active in ALD, we tested the hypothesis that conjugated primary bile salts (CPBS) and PC inhibit ethanol-enhanced transepithelial permeability of endotoxin and the subsequent transepithelial...... activation of human leukocytes. For this purpose, we used a model in which intestinal epithelial cells (Caco-2) were basolaterally cocultivated with mononuclear leukocytes. Cells were challenged apically with endotoxin from Escherichia coli K12 and were incubated with or without the addition of CPBS (1.5 m...

Computational Prediction of Blood-Brain Barrier Permeability Using Decision Tree Induction

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Jörg Huwyler

2012-08-01

Full Text Available Predicting blood-brain barrier (BBB permeability is essential to drug development, as a molecule cannot exhibit pharmacological activity within the brain parenchyma without first transiting this barrier. Understanding the process of permeation, however, is complicated by a combination of both limited passive diffusion and active transport. Our aim here was to establish predictive models for BBB drug permeation that include both active and passive transport. A database of 153 compounds was compiled using in vivo surface permeability product (logPS values in rats as a quantitative parameter for BBB permeability. The open source Chemical Development Kit (CDK was used to calculate physico-chemical properties and descriptors. Predictive computational models were implemented by machine learning paradigms (decision tree induction on both descriptor sets. Models with a corrected classification rate (CCR of 90% were established. Mechanistic insight into BBB transport was provided by an Ant Colony Optimization (ACO-based binary classifier analysis to identify the most predictive chemical substructures. Decision trees revealed descriptors of lipophilicity (aLogP and charge (polar surface area, which were also previously described in models of passive diffusion. However, measures of molecular geometry and connectivity were found to be related to an active drug transport component.

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.

Replication stress activates DNA repair synthesis in mitosis

DEFF Research Database (Denmark)

Minocherhomji, Sheroy; Ying, Songmin; Bjerregaard, Victoria A

2015-01-01

Oncogene-induced DNA replication stress has been implicated as a driver of tumorigenesis. Many chromosomal rearrangements characteristic of human cancers originate from specific regions of the genome called common fragile sites (CFSs). CFSs are difficult-to-replicate loci that manifest as gaps...... into mitotic prophase triggers the recruitment of MUS81 to CFSs. The nuclease activity of MUS81 then promotes POLD3-dependent DNA synthesis at CFSs, which serves to minimize chromosome mis-segregation and non-disjunction. We propose that the attempted condensation of incompletely duplicated loci in early...... mitosis serves as the trigger for completion of DNA replication at CFS loci in human cells. Given that this POLD3-dependent mitotic DNA synthesis is enhanced in aneuploid cancer cells that exhibit intrinsically high levels of chromosomal instability (CIN(+)) and replicative stress, we suggest...

Hili Inhibits HIV Replication in Activated T Cells.

Science.gov (United States)

Peterlin, B Matija; Liu, Pingyang; Wang, Xiaoyun; Cary, Daniele; Shao, Wei; Leoz, Marie; Hong, Tian; Pan, Tao; Fujinaga, Koh

2017-06-01

P-element-induced wimpy-like (Piwil) proteins restrict the replication of mobile genetic elements in the germ line. They are also expressed in many transformed cell lines. In this study, we discovered that the human Piwil 2 (Hili) protein can also inhibit HIV replication, especially in activated CD4 + T cells that are the preferred target cells for this virus in the infected host. Although resting cells did not express Hili, its expression was rapidly induced following T cell activation. In these cells and transformed cell lines, depletion of Hili increased levels of viral proteins and new viral particles. Further studies revealed that Hili binds to tRNA. Some of the tRNAs represent rare tRNA species, whose codons are overrepresented in the viral genome. Targeting tRNA Arg (UCU) with an antisense oligonucleotide replicated effects of Hili and also inhibited HIV replication. Finally, Hili also inhibited the retrotransposition of the endogenous intracysternal A particle (IAP) by a similar mechanism. Thus, Hili joins a list of host proteins that inhibit the replication of HIV and other mobile genetic elements. IMPORTANCE Piwil proteins inhibit the movement of mobile genetic elements in the germ line. In their absence, sperm does not form and male mice are sterile. This inhibition is thought to occur via small Piwi-interacting RNAs (piRNAs). However, in some species and in human somatic cells, Piwil proteins bind primarily to tRNA. In this report, we demonstrate that human Piwil proteins, especially Hili, not only bind to select tRNA species, including rare tRNAs, but also inhibit HIV replication. Importantly, T cell activation induces the expression of Hili in CD4 + T cells. Since Hili also inhibited the movement of an endogenous retrovirus (IAP), our finding shed new light on this intracellular resistance to exogenous and endogenous retroviruses as well as other mobile genetic elements. Copyright © 2017 American Society for Microbiology.

Nuclear mitochondrial DNA activates replication in Saccharomyces cerevisiae.

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Laurent Chatre

Full Text Available The nuclear genome of eukaryotes is colonized by DNA fragments of mitochondrial origin, called NUMTs. These insertions have been associated with a variety of germ-line diseases in humans. The significance of this uptake of potentially dangerous sequences into the nuclear genome is unclear. Here we provide functional evidence that sequences of mitochondrial origin promote nuclear DNA replication in Saccharomyces cerevisiae. We show that NUMTs are rich in key autonomously replicating sequence (ARS consensus motifs, whose mutation results in the reduction or loss of DNA replication activity. Furthermore, 2D-gel analysis of the mrc1 mutant exposed to hydroxyurea shows that several NUMTs function as late chromosomal origins. We also show that NUMTs located close to or within ARS provide key sequence elements for replication. Thus NUMTs can act as independent origins, when inserted in an appropriate genomic context or affect the efficiency of pre-existing origins. These findings show that migratory mitochondrial DNAs can impact on the replication of the nuclear region they are inserted in.

Using artificial intelligence to predict permeability from petrographic data

Energy Technology Data Exchange (ETDEWEB)

Maqsood Ali; Adwait Chawathe [New Mexico Petroleum Recovery Research Centre (Mexico)

2000-10-01

Petrographic data collected during thin section analysis can be invaluable for understanding the factors that control permeability distribution. Reliable prediction of permeability is important for reservoir characterization. The petrographic elements (mineralogy, porosity types, cements and clays, and pore morphology) interact with each other uniquely to generate a specific permeability distribution. It is difficult to quantify accurately this interaction and its consequent effect on permeability, emphasizing the non-linear nature of the process. To capture these non-linear interactions, neural networks were used to predict permeability from petrographic data. The neural net was used as a multivariate correlative tool because of its ability to learn the non-linear relationships between multiple input and output variables. The study was conducted on the upper Queen formation called the Shattuck Member (Permian age). The Shattuck Member is composed of very fine-grained arkosic sandstone. The core samples were available from the Sulimar Queen and South Lucky Lake fields located in Chaves County, New Mexico. Nineteen petrographic elements were collected for each permeability value using a combined minipermeameter-petrographic technique. In order to reduce noise and overfitting the permeability model, these petrographic elements were screened, and their control (ranking) with respect to permeability was determined using fuzzy logic. Since the fuzzy logic algorithm provides unbiased ranking, it was used to reduce the dimensionality of the input variables. Based on the fuzzy logic ranking, only the most influential petrographic elements were selected as inputs for permeability prediction. The neural net was trained and tested using data from Well 1-16 in the Sulimar Queen field. Relying on the ranking obtained from the fuzzy logic analysis, the net was trained using the most influential three, five, and ten petrographic elements. A fast algorithm (the scaled conjugate

Timeless links replication termination to mitotic kinase activation.

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Jayaraju Dheekollu

2011-05-01

Full Text Available The mechanisms that coordinate the termination of DNA replication with progression through mitosis are not completely understood. The human Timeless protein (Tim associates with S phase replication checkpoint proteins Claspin and Tipin, and plays an important role in maintaining replication fork stability at physical barriers, like centromeres, telomeres and ribosomal DNA repeats, as well as at termination sites. We show here that human Tim can be isolated in a complex with mitotic entry kinases CDK1, Auroras A and B, and Polo-like kinase (Plk1. Plk1 bound Tim directly and colocalized with Tim at a subset of mitotic structures in M phase. Tim depletion caused multiple mitotic defects, including the loss of sister-chromatid cohesion, loss of mitotic spindle architecture, and a failure to exit mitosis. Tim depletion caused a delay in mitotic kinase activity in vivo and in vitro, as well as a reduction in global histone H3 S10 phosphorylation during G2/M phase. Tim was also required for the recruitment of Plk1 to centromeric DNA and formation of catenated DNA structures at human centromere alpha satellite repeats. Taken together, these findings suggest that Tim coordinates mitotic kinase activation with termination of DNA replication.

The Anisotropy of Replicated Aluminum Foams

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Eugeny L. Furman

2014-01-01

Full Text Available The replication casting process gives the open-cell aluminum foams that can be used in many industrial applications as well as in filtering technology. The essential requirement for filters is the uniformity of filtering degree which is defined by the minimal pore size. However the structure of replication castings is often inhomogeneous and the minimal pore radius is decreasing in the direction of melt infiltration. The objective of this investigation is to study the dynamics of melt impregnation of the porous medium by vacuum suction to identify the possibility of reducing the anisotropy. Theoretical data illustrate the processes at the boundary between melt and gas medium. The experiments were carried out using the replication aluminum samples produced according to commercial technology. It was found that the permeability coefficient varies throughout the height of castings. A method for estimation of pressure on the line of melt movement was proposed. The resistance of NaCl layer and circular vents of the mold causes the inhomogeneity of castings. Finally the ways of minimizing the anisotropy were offered.

DNA Replication Profiling Using Deep Sequencing.

Science.gov (United States)

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

2018-01-01

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

In-Situ Air Permeability Measurements Using the Cone Permeameter at the 200 East Area of the Hanford Site

International Nuclear Information System (INIS)

Troyer, G.L.

1999-01-01

This report documents the field demonstration of the Cone Permeametertrademark (CPer) conducted at the Immobilization Low-Activity Waste (ILAW) site in the 200 East area of the Department of Energy's (DOE) Hanford facility. The demonstration was conducted using the Hanford Site Cone Penetration Platform (CPP) shown in Figure 1.1. The purpose of the technology demonstration was to (1) gather baseline data and evaluate the CPer's ability to measure air permeability in arid sands, silts and gravels; and (2) to determine the system's ability to replicate permeability profiles with multiple pushes in close proximity. The demonstration was jointly conducted by Applied Research Associates, Inc. (ARA) and Science and Engineering Associates (SEA). This report satisfies the requirements of ARA's contract No.2075 to Lockheed Martin Hanford Company. The report is organized into six major sections. This first section presents an introduction and outline to the report. Section 2 contains a discussion of the technologies used for the demonstration. Section 3 contains a brief description of the site where the demonstration was conducted. Section 4 describes the testing methodology and chronology. Section 5 presents the results obtained during the field test program. Comparisons between these results and existing site data are developed and discussed in Section 5. A conclusion and recommendation section is presented in Section 6 of the report

Variety of DNA Replication Activity Among Cyanobacteria Correlates with Distinct Respiration Activity in the Dark.

Science.gov (United States)

Ohbayashi, Ryudo; Yamamoto, Jun-Ya; Watanabe, Satoru; Kanesaki, Yu; Chibazakura, Taku; Miyagishima, Shin-Ya; Yoshikawa, Hirofumi

2017-02-01

Cyanobacteria exhibit light-dependent cell growth since most of their cellular energy is obtained by photosynthesis. In Synechococcus elongatus PCC 7942, one of the model cyanobacteria, DNA replication depends on photosynthetic electron transport. However, the critical signal for the regulatory mechanism of DNA replication has not been identified. In addition, conservation of this regulatory mechanism has not been investigated among cyanobacteria. To understand this regulatory signal and its dependence on light, we examined the regulation of DNA replication under both light and dark conditions among three model cyanobacteria, S. elongatus PCC 7942, Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120. Interestingly, DNA replication activity in Synechocystis and Anabaena was retained when cells were transferred to the dark, although it was drastically decreased in S. elongatus. Glycogen metabolism and respiration were higher in Synechocystis and Anabaena than in S. elongatus in the dark. Moreover, DNA replication activity in Synechocystis and Anabaena was reduced to the same level as that in S. elongatus by inhibition of respiratory electron transport after transfer to the dark. These results demonstrate that there is disparity in DNA replication occurring in the dark among cyanobacteria, which is caused by the difference in activity of respiratory electron transport. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Cdc7 is required throughout the yeast S phase to activate replication origins.

Science.gov (United States)

Donaldson, A D; Fangman, W L; Brewer, B J

1998-02-15

The long-standing conclusion that the Cdc7 kinase of Saccharomyces cerevisiae is required only to trigger S phase has been challenged by recent data that suggests it acts directly on individual replication origins. We tested the possibility that early- and late-activated origins have different requirements for Cdc7 activity. Cells carrying a cdc7(ts) allele were first arrested in G1 at the cdc7 block by incubation at 37 degrees C, and then were allowed to enter S phase by brief incubation at 23 degrees C. During the S phase, after return to 37 degrees C, early-firing replication origins were activated, but late origins failed to fire. Similarly, a plasmid with a late-activated origin was defective in replication. As a consequence of the origin activation defect, duplication of chromosomal sequences that are normally replicated from late origins was greatly delayed. Early-replicating regions of the genome duplicated at approximately their normal time. The requirements of early and late origins for Cdc7 appear to be temporally rather than quantitatively different, as reducing overall levels of Cdc7 by growth at semi-permissive temperature reduced activation at early and late origins approximately equally. Our results show that Cdc7 activates early and late origins separately, with late origins requiring the activity later in S phase to permit replication initiation.

DNA replication and cancer: From dysfunctional replication origin activities to therapeutic opportunities.

Science.gov (United States)

Boyer, Anne-Sophie; Walter, David; Sørensen, Claus Storgaard

2016-06-01

A dividing cell has to duplicate its DNA precisely once during the cell cycle to preserve genome integrity avoiding the accumulation of genetic aberrations that promote diseases such as cancer. A large number of endogenous impacts can challenge DNA replication and cells harbor a battery of pathways to promote genome integrity during DNA replication. This includes suppressing new replication origin firing, stabilization of replicating forks, and the safe restart of forks to prevent any loss of genetic information. Here, we describe mechanisms by which oncogenes can interfere with DNA replication thereby causing DNA replication stress and genome instability. Further, we describe cellular and systemic responses to these insults with a focus on DNA replication restart pathways. Finally, we discuss the therapeutic potential of exploiting intrinsic replicative stress in cancer cells for targeted therapy. Copyright © 2016 Elsevier Ltd. All rights reserved.

Activity-based protein profiling of the hepatitis C virus replication in Huh-7 hepatoma cells using a non-directed active site probe

Directory of Open Access Journals (Sweden)

McKay Craig S

2010-02-01

Full Text Available Abstract Background Hepatitis C virus (HCV poses a growing threat to global health as it often leads to serious liver diseases and is one of the primary causes for liver transplantation. Currently, no vaccines are available to prevent HCV infection and clinical treatments have limited success. Since HCV has a small proteome, it relies on many host cell proteins to complete its life cycle. In this study, we used a non-directed phenyl sulfonate ester probe (PS4≡ to selectively target a broad range of enzyme families that show differential activity during HCV replication in Huh-7 cells. Results The PS4≡ probe successfully targeted 19 active proteins in nine distinct protein families, some that were predominantly labeled in situ compared to the in vitro labeled cell homogenate. Nine proteins revealed altered activity levels during HCV replication. Some candidates identified, such as heat shock 70 kDa protein 8 (or HSP70 cognate, have been shown to influence viral release and abundance of cellular lipid droplets. Other differentially active PS4≡ targets, such as electron transfer flavoprotein alpha, protein disulfide isomerase A5, and nuclear distribution gene C homolog, constitute novel proteins that potentially mediate HCV propagation. Conclusions These findings demonstrate the practicality and versatility of non-directed activity-based protein profiling (ABPP to complement directed methods and accelerate the discovery of altered protein activities associated with pathological states such as HCV replication. Collectively, these results highlight the ability of in situ ABPP approaches to facilitate the identification of enzymes that are either predominantly or exclusively labeled in living cells. Several of these differentially active enzymes represent possible HCV-host interactions that could be targeted for diagnostic or therapeutic purposes.

Multiple determinants controlling activation of yeast replication origins late in S phase.

Science.gov (United States)

Friedman, K L; Diller, J D; Ferguson, B M; Nyland, S V; Brewer, B J; Fangman, W L

1996-07-01

Analysis of a 131-kb segment of the left arm of yeast chromosome XIV beginning 157 kb from the telomere reveals four highly active origins of replication that initiate replication late in S phase. Previous work has shown that telomeres act as determinants for late origin activation. However, at least two of the chromosome XIV origins maintain their late activation time when located on large circular plasmids, indicating that late replication is independent of telomeres. Analysis of the replication time of plasmid derivatives containing varying amounts of chromosome XIV DNA show that a minimum of three chromosomal elements, distinct from each tested origin, contribute to late activation time. These late determinants are functionally equivalent, because duplication of one set of contributing sequences can compensate for the removal of another set. Furthermore, insertion of an origin that is normally early activated into this domain results in a shift to late activation, suggesting that the chromosome XIV origins are not unique in their ability to respond to the late determinants.

Identifying Cancer Driver Genes Using Replication-Incompetent Retroviral Vectors

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Victor M. Bii

2016-10-01

Full Text Available Identifying novel genes that drive tumor metastasis and drug resistance has significant potential to improve patient outcomes. High-throughput sequencing approaches have identified cancer genes, but distinguishing driver genes from passengers remains challenging. Insertional mutagenesis screens using replication-incompetent retroviral vectors have emerged as a powerful tool to identify cancer genes. Unlike replicating retroviruses and transposons, replication-incompetent retroviral vectors lack additional mutagenesis events that can complicate the identification of driver mutations from passenger mutations. They can also be used for almost any human cancer due to the broad tropism of the vectors. Replication-incompetent retroviral vectors have the ability to dysregulate nearby cancer genes via several mechanisms including enhancer-mediated activation of gene promoters. The integrated provirus acts as a unique molecular tag for nearby candidate driver genes which can be rapidly identified using well established methods that utilize next generation sequencing and bioinformatics programs. Recently, retroviral vector screens have been used to efficiently identify candidate driver genes in prostate, breast, liver and pancreatic cancers. Validated driver genes can be potential therapeutic targets and biomarkers. In this review, we describe the emergence of retroviral insertional mutagenesis screens using replication-incompetent retroviral vectors as a novel tool to identify cancer driver genes in different cancer types.

Inhibition of hepatitis C virus replication through adenosine monophosphate-activated protein kinase-dependent and -independent pathways.

Science.gov (United States)

Nakashima, Kenji; Takeuchi, Kenji; Chihara, Kazuyasu; Hotta, Hak; Sada, Kiyonao

2011-11-01

Persistent infection with hepatitis C virus (HCV) is closely correlated with type 2 diabetes. In this study, replication of HCV at different glucose concentrations was investigated by using J6/JFH1-derived cell-adapted HCV in Huh-7.5 cells and the mechanism of regulation of HCV replication by AMP-activated protein kinase (AMPK) as an energy sensor of the cell analyzed. Reducing the glucose concentration in the cell culture medium from 4.5 to 1.0 g/L resulted in suppression of HCV replication, along with activation of AMPK. Whereas treatment of cells with AMPK activator 5-aminoimidazole-4-carboxamide 1-β-D-ribofuranoside (AICAR) suppressed HCV replication, compound C, a specific AMPK inhibitor, prevented AICAR's effect, suggesting that AICAR suppresses the replication of HCV by activating AMPK in Huh-7.5 cells. In contrast, compound C induced further suppression of HCV replication when the cells were cultured in low glucose concentrations or with metformin. These results suggest that low glucose concentrations and metformin have anti-HCV effects independently of AMPK activation. © 2011 The Societies and Blackwell Publishing Asia Pty Ltd.

Database Replication Prototype

OpenAIRE

Vandewall, R.

2000-01-01

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

Effect of platelet activating factor on endothelial permeability to plasma macromolecules

International Nuclear Information System (INIS)

Handley, D.A.; Arbeeny, C.M.; Lee, M.L.; Van Valen, R.G.; Saunders, R.N.

1984-01-01

The effect of intrajugular administration of platelet activating factor (PAF-C16) on vascular permeability was examined in the guinea pig. To examine the loss of selective endothelial permeability, the extravasative effect of PAF was assessed by monitoring hemoconcentration and the plasma loss of 125 I-albumin (6.7 nm), 125 I-low density lipoproteins (22.0 nm) or 125 I-very low density lipoproteins (62.1 nm). Extravasation was dose-dependent and began 1 min after PAF administration, continuing for 5-7 min. During extravasation, there was no evidence for selective plasma retention of any of the labeled plasma tracers, as measured by plasma radioactivity. These results suggest that PAF-induced extravasation is dose-dependent, with increases in vascular permeability sufficient to permit similar plasma efflux rates of albumin, low density lipoproteins and very low density lipoproteins

Hydrologic and Pollutant Removal Performance of a Full-Scale, Fully Functional Permeable Pavement Parking Lot

Science.gov (United States)

In accordance with the need for full-scale, replicated studies of permeable pavement systems used in their intended application (parking lot, roadway, etc.) across a range of climatic events, daily usage conditions, and maintenance regimes to evaluate these systems, the EPA’s Urb...

BPIFB6 Regulates Secretory Pathway Trafficking and Enterovirus Replication.

Science.gov (United States)

Morosky, Stefanie; Lennemann, Nicholas J; Coyne, Carolyn B

2016-05-15

Bactericidal/permeability-increasing protein (BPI) fold-containing family B, member 3 (BPIFB3) is an endoplasmic reticulum (ER)-localized host factor that negatively regulates coxsackievirus B (CVB) replication through its control of the autophagic pathway. Here, we show that another member of the BPIFB family, BPIFB6, functions as a positive regulator of CVB, and other enterovirus, replication by controlling secretory pathway trafficking and Golgi complex morphology. We show that similar to BPIFB3, BPIFB6 localizes exclusively to the ER, where it associates with other members of the BPIFB family. However, in contrast to our findings that RNA interference (RNAi)-mediated silencing of BPIFB3 greatly enhances CVB replication, we show that silencing of BPIFB6 expression dramatically suppresses enterovirus replication in a pan-viral manner. Mechanistically, we show that loss of BPIFB6 expression induces pronounced alterations in retrograde and anterograde trafficking, which correlate with dramatic fragmentation of the Golgi complex. Taken together, these data implicate BPIFB6 as a key regulator of secretory pathway trafficking and viral replication and suggest that members of the BPIFB family participate in diverse host cell functions to regulate virus infections. Enterovirus infections are associated with a number of severe pathologies, such as aseptic meningitis, dilated cardiomyopathy, type I diabetes, paralysis, and even death. These viruses, which include coxsackievirus B (CVB), poliovirus (PV), and enterovirus 71 (EV71), co-opt the host cell secretory pathway, which controls the transport of proteins from the endoplasmic reticulum to the Golgi complex, to facilitate their replication. Here we report on the identification of a novel regulator of the secretory pathway, bactericidal/permeability-increasing protein (BPI) fold-containing family B, member 6 (BPIFB6), whose expression is required for enterovirus replication. We show that loss of BPIFB6 expression

BPIFB6 Regulates Secretory Pathway Trafficking and Enterovirus Replication

Science.gov (United States)

Morosky, Stefanie; Lennemann, Nicholas J.

2016-01-01

ABSTRACT Bactericidal/permeability-increasing protein (BPI) fold-containing family B, member 3 (BPIFB3) is an endoplasmic reticulum (ER)-localized host factor that negatively regulates coxsackievirus B (CVB) replication through its control of the autophagic pathway. Here, we show that another member of the BPIFB family, BPIFB6, functions as a positive regulator of CVB, and other enterovirus, replication by controlling secretory pathway trafficking and Golgi complex morphology. We show that similar to BPIFB3, BPIFB6 localizes exclusively to the ER, where it associates with other members of the BPIFB family. However, in contrast to our findings that RNA interference (RNAi)-mediated silencing of BPIFB3 greatly enhances CVB replication, we show that silencing of BPIFB6 expression dramatically suppresses enterovirus replication in a pan-viral manner. Mechanistically, we show that loss of BPIFB6 expression induces pronounced alterations in retrograde and anterograde trafficking, which correlate with dramatic fragmentation of the Golgi complex. Taken together, these data implicate BPIFB6 as a key regulator of secretory pathway trafficking and viral replication and suggest that members of the BPIFB family participate in diverse host cell functions to regulate virus infections. IMPORTANCE Enterovirus infections are associated with a number of severe pathologies, such as aseptic meningitis, dilated cardiomyopathy, type I diabetes, paralysis, and even death. These viruses, which include coxsackievirus B (CVB), poliovirus (PV), and enterovirus 71 (EV71), co-opt the host cell secretory pathway, which controls the transport of proteins from the endoplasmic reticulum to the Golgi complex, to facilitate their replication. Here we report on the identification of a novel regulator of the secretory pathway, bactericidal/permeability-increasing protein (BPI) fold-containing family B, member 6 (BPIFB6), whose expression is required for enterovirus replication. We show that loss of

Developments in permeable and low permeability barriers

International Nuclear Information System (INIS)

Jefferis, S.A.; Norris, G.H.; Thomas, A.O.

1997-01-01

The concept of the reactive treatment zone whereby pollutants are attenuated as they move along a pathway in the ground has enabled a re-thinking of many of the concepts of containment. In particular it offers the potential for the control of the flux from a contaminated area by controlling the contaminant concentration in the pathway(s) as well as or instead of using a low permeability barrier. The paper outlines the basic concepts of the reactive treatment zone and the use of permeable and low permeability reactive systems. The paper then gives a case history of the installation of a permeable barrier using an in-situ reaction chamber

Dual Identity and Prejudice: The Moderating Role of Group Boundary Permeability

Science.gov (United States)

Shi, Yuanyuan; Dang, Jianning; Zheng, Wenwen; Liu, Li

2017-01-01

Past work suggested that dual identity was effective to reduce prejudice. This study extended research on dual identity and prejudice by identifying a boundary condition in this relationship, that is, group permeability. In Study 1, we replicated previous studies with Chinese individuals and found that inducing dual identity (emphasizing subgroup differences and a common nation identity), compared to the control condition, decreased the urban residents’ prejudice against rural-to-urban migrants. In Study 2, we manipulated the group boundary permeability using the Hukou system reform, and found that when the group boundary was permeable, dual identity was effective in reducing prejudice against rural-to-urban migrants. However, this effect vanished in the condition where the group boundary was impermeable. These results point to the importance of inducing dual identity under specific conditions for research on decreasing prejudice. Some practical implications of the findings for urbanization and immigration are discussed. PMID:28261130

Prediction of Hydrocarbon Reservoirs Permeability Using Support Vector Machine

Directory of Open Access Journals (Sweden)

R. Gholami

2012-01-01

Full Text Available Permeability is a key parameter associated with the characterization of any hydrocarbon reservoir. In fact, it is not possible to have accurate solutions to many petroleum engineering problems without having accurate permeability value. The conventional methods for permeability determination are core analysis and well test techniques. These methods are very expensive and time consuming. Therefore, attempts have usually been carried out to use artificial neural network for identification of the relationship between the well log data and core permeability. In this way, recent works on artificial intelligence techniques have led to introduce a robust machine learning methodology called support vector machine. This paper aims to utilize the SVM for predicting the permeability of three gas wells in the Southern Pars field. Obtained results of SVM showed that the correlation coefficient between core and predicted permeability is 0.97 for testing dataset. Comparing the result of SVM with that of a general regression neural network (GRNN revealed that the SVM approach is faster and more accurate than the GRNN in prediction of hydrocarbon reservoirs permeability.

Relationship between changed alveolar-capillary permeability and angiotensin converting enzyme activity in serum in sarcoidosis.

OpenAIRE

Eklund, A; Blaschke, E

1986-01-01

The effect of altered alveolar-capillary permeability on angiotensin converting enzyme (ACE) activity in serum (SACE) was studied in 45 patients with sarcoidosis and 21 healthy controls. In sarcoidosis increased albumin concentrations in the bronchoalveolar lavage fluid (L albumin) and increased ratios of L albumin to albumin in serum (S albumin) indicated an increased permeability of the alveolar-capillary membrane. ACE activity in the lavage fluid (LACE) was correlated with the number of al...

Activation of a yeast replication origin near a double-stranded DNA break.

Science.gov (United States)

Raghuraman, M K; Brewer, B J; Fangman, W L

1994-03-01

Irradiation in the G1 phase of the cell cycle delays the onset of DNA synthesis and transiently inhibits the activation of replication origins in mammalian cells. It has been suggested that this inhibition is the result of the loss of torsional tension in the DNA after it has been damaged. Because irradiation causes DNA damage at an undefined number of nonspecific sites in the genome, it is not known how cells respond to limited DNA damage, and how replication origins in the immediate vicinity of a damage site would behave. Using the sequence-specific HO endonuclease, we have created a defined double-stranded DNA break in a centromeric plasmid in G1-arrested cells of the yeast Saccharomyces cerevisiae. We show that replication does initiate at the origin on the cut plasmid, and that the plasmid replicates early in the S phase after linearization in vivo. These observations suggest that relaxation of a supercoiled DNA domain in yeast need not inactivate replication origins within that domain. Furthermore, these observations rule out the possibility that the late replication context associated with chromosomal termini is a consequence of DNA ends.

Hydrologic and Pollutant Removal Performance of a Full-Scale, Fully Functional Permeable Pavement Parking Lot - paper

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To meet the need for long-term, full-scale, replicated studies of permeable pavement systems used in their intended application (parking lot, roadway, etc.) across a range of climatic events, daily usage conditions, and maintenance regimes to evaluate these systems, the EPA’s Urb...

Effects of water activity and low molecular weight humectants on skin permeability and hydration dynamics - a double-blind, randomized and controlled study.

Science.gov (United States)

Albèr, C; Buraczewska-Norin, I; Kocherbitov, V; Saleem, S; Lodén, M; Engblom, J

2014-10-01

The mammalian skin is a barrier that effectively separates the water-rich interior of the body from the normally dryer exterior. Changes in the external conditions, for example ambient humidity, have been shown to affect the skin barrier properties. The prime objective of this study was to evaluate the effect of water activity of a topical formulation on skin hydration and permeability. A second objective was to gain more understanding on how two commonly used humectants, urea and glycerol, affect skin barrier function in vivo. Simple aqueous formulations were applied under occlusion to the volar forearm of healthy volunteers. Following 4-h exposure, skin water loss (by transepidermal water loss measurements), skin hydration (by Corneometry) and skin permeability (by time to vasodilation due to benzyl nicotinate exposure) were monitored. The results demonstrate that a relatively small change in the water activity of a topical formulation is sufficient to induce considerable effects on stratum corneum hydration and permeability to exogenous substances. Exposing the skin to high water activity leads to increased skin hydration and also increased permeability. Furthermore, urea and glycerol promote skin hydration and permeability even at reduced water activity of the applied formulation. These results highlight the importance of considering the water activity in topically applied formulations and the potential benefit of using humectants. The results may impact formulation optimization in how to facilitate skin hydration and to modify skin permeability by temporarily open and close the skin barrier. © 2014 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

Education: DNA replication using microscale natural convection.

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Priye, Aashish; Hassan, Yassin A; Ugaz, Victor M

2012-12-07

There is a need for innovative educational experiences that unify and reinforce fundamental principles at the interface between the physical, chemical, and life sciences. These experiences empower and excite students by helping them recognize how interdisciplinary knowledge can be applied to develop new products and technologies that benefit society. Microfluidics offers an incredibly versatile tool to address this need. Here we describe our efforts to create innovative hands-on activities that introduce chemical engineering students to molecular biology by challenging them to harness microscale natural convection phenomena to perform DNA replication via the polymerase chain reaction (PCR). Experimentally, we have constructed convective PCR stations incorporating a simple design for loading and mounting cylindrical microfluidic reactors between independently controlled thermal plates. A portable motion analysis microscope enables flow patterns inside the convective reactors to be directly visualized using fluorescent bead tracers. We have also developed a hands-on computational fluid dynamics (CFD) exercise based on modeling microscale thermal convection to identify optimal geometries for DNA replication. A cognitive assessment reveals that these activities strongly impact student learning in a positive way.

GINS complex protein Sld5 recruits SIK1 to activate MCM helicase during DNA replication.

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Joshi, Kiranmai; Shah, Varun Jayeshkumar; Maddika, Subbareddy

2016-12-01

In eukaryotes, proper loading and activation of MCM helicase at chromosomal origins plays a central role in DNA replication. Activation of MCM helicase requires its association with CDC45-GINS complex, but the mechanism of how this complex activates MCM helicase is poorly understood. Here we identified SIK1 (salt-inducible kinase 1), an AMPK related protein kinase, as a molecular link that connects GINS complex with MCM helicase activity. We demonstrated that Sld5 a component of GINS complex interacts with SIK1 and recruits it to the sites of DNA replication at the onset of S phase. Depletion of SIK1 leads to defective DNA replication. Further, we showed that SIK1 phosphorylates MCM2 at five conserved residues at its N-terminus, which is essential for the activation of MCM helicase. Collectively, our results suggest SIK1 as a novel integral component of CMG replicative helicase during eukaryotic DNA replication. Copyright © 2016 Elsevier Inc. All rights reserved.

SV40 Utilizes ATM Kinase Activity to Prevent Non-homologous End Joining of Broken Viral DNA Replication Products

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Sowd, Gregory A.; Mody, Dviti; Eggold, Joshua; Cortez, David; Friedman, Katherine L.; Fanning, Ellen

2014-01-01

Simian virus 40 (SV40) and cellular DNA replication rely on host ATM and ATR DNA damage signaling kinases to facilitate DNA repair and elicit cell cycle arrest following DNA damage. During SV40 DNA replication, ATM kinase activity prevents concatemerization of the viral genome whereas ATR activity prevents accumulation of aberrant genomes resulting from breakage of a moving replication fork as it converges with a stalled fork. However, the repair pathways that ATM and ATR orchestrate to prevent these aberrant SV40 DNA replication products are unclear. Using two-dimensional gel electrophoresis and Southern blotting, we show that ATR kinase activity, but not DNA-PKcs kinase activity, facilitates some aspects of double strand break (DSB) repair when ATM is inhibited during SV40 infection. To clarify which repair factors associate with viral DNA replication centers, we examined the localization of DSB repair proteins in response to SV40 infection. Under normal conditions, viral replication centers exclusively associate with homology-directed repair (HDR) and do not colocalize with non-homologous end joining (NHEJ) factors. Following ATM inhibition, but not ATR inhibition, activated DNA-PKcs and KU70/80 accumulate at the viral replication centers while CtIP and BLM, proteins that initiate 5′ to 3′ end resection during HDR, become undetectable. Similar to what has been observed during cellular DSB repair in S phase, these data suggest that ATM kinase influences DSB repair pathway choice by preventing the recruitment of NHEJ factors to replicating viral DNA. These data may explain how ATM prevents concatemerization of the viral genome and promotes viral propagation. We suggest that inhibitors of DNA damage signaling and DNA repair could be used during infection to disrupt productive viral DNA replication. PMID:25474690

SV40 utilizes ATM kinase activity to prevent non-homologous end joining of broken viral DNA replication products.

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Gregory A Sowd

2014-12-01

Full Text Available Simian virus 40 (SV40 and cellular DNA replication rely on host ATM and ATR DNA damage signaling kinases to facilitate DNA repair and elicit cell cycle arrest following DNA damage. During SV40 DNA replication, ATM kinase activity prevents concatemerization of the viral genome whereas ATR activity prevents accumulation of aberrant genomes resulting from breakage of a moving replication fork as it converges with a stalled fork. However, the repair pathways that ATM and ATR orchestrate to prevent these aberrant SV40 DNA replication products are unclear. Using two-dimensional gel electrophoresis and Southern blotting, we show that ATR kinase activity, but not DNA-PK(cs kinase activity, facilitates some aspects of double strand break (DSB repair when ATM is inhibited during SV40 infection. To clarify which repair factors associate with viral DNA replication centers, we examined the localization of DSB repair proteins in response to SV40 infection. Under normal conditions, viral replication centers exclusively associate with homology-directed repair (HDR and do not colocalize with non-homologous end joining (NHEJ factors. Following ATM inhibition, but not ATR inhibition, activated DNA-PK(cs and KU70/80 accumulate at the viral replication centers while CtIP and BLM, proteins that initiate 5' to 3' end resection during HDR, become undetectable. Similar to what has been observed during cellular DSB repair in S phase, these data suggest that ATM kinase influences DSB repair pathway choice by preventing the recruitment of NHEJ factors to replicating viral DNA. These data may explain how ATM prevents concatemerization of the viral genome and promotes viral propagation. We suggest that inhibitors of DNA damage signaling and DNA repair could be used during infection to disrupt productive viral DNA replication.

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

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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

Low resistivity and permeability in actively deforming shear zones on the San Andreas Fault at SAFOD

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Morrow, Carolyn A.; Lockner, David A.; Hickman, Stephen H.

2015-01-01

The San Andreas Fault Observatory at Depth (SAFOD) scientific drillhole near Parkfield, California crosses the San Andreas Fault at a depth of 2.7 km. Downhole measurements and analysis of core retrieved from Phase 3 drilling reveal two narrow, actively deforming zones of smectite-clay gouge within a roughly 200 m-wide fault damage zone of sandstones, siltstones and mudstones. Here we report electrical resistivity and permeability measurements on core samples from all of these structural units at effective confining pressures up to 120 MPa. Electrical resistivity (~10 ohm-m) and permeability (10-21 to 10-22 m2) in the actively deforming zones were one to two orders of magnitude lower than the surrounding damage zone material, consistent with broader-scale observations from the downhole resistivity and seismic velocity logs. The higher porosity of the clay gouge, 2 to 8 times greater than that in the damage zone rocks, along with surface conduction were the principal factors contributing to the observed low resistivities. The high percentage of fine-grained clay in the deforming zones also greatly reduced permeability to values low enough to create a barrier to fluid flow across the fault. Together, resistivity and permeability data can be used to assess the hydrogeologic characteristics of the fault, key to understanding fault structure and strength. The low resistivities and strength measurements of the SAFOD core are consistent with observations of low resistivity clays that are often found in the principal slip zones of other active faults making resistivity logs a valuable tool for identifying these zones.

Calcium reduces the sodium permeability of luminal membrane vesicles from toad bladder. Studies using a fast-reaction apparatus

International Nuclear Information System (INIS)

Chase, H.S. Jr.; Al-Awqati, Q.

1983-01-01

Regulation of the sodium permeability of the luminal membrane is the major mechanism by which the net rate of sodium transport across tight epithelia is varied. Previous evidence has suggested that the permeability of the luminal membrane might be regulated by changes in intracellular sodium or calcium activities. To test this directly, we isolated a fraction of the plasma membrane from the toad urinary bladder, which contains a fast, amiloride-sensitive sodium flux with characteristics similar to those of the native luminal membrane. Using a flow-quench apparatus to measure the initial rate of sodium efflux from these vesicles in the millisecond time range, we have demonstrated that the isotope exchange permeability of these vesicles is very sensitive to calcium. Calcium reduces the sodium permeability, and the half-maximal inhibitory concentration is 0.5 microM, well within the range of calcium activity found in cells. Also, the permeability of the luminal membrane vesicles is little affected by the ambient sodium concentration. These results, when taken together with studies on whole tissue, suggest that cell calcium may be an important regulator of transepithelial sodium transport by its effect on luminal sodium permeability. The effect of cell sodium on permeability may be mediated by calcium rather than by sodium itself

RPA-Binding Protein ETAA1 Is an ATR Activator Involved in DNA Replication Stress Response.

Science.gov (United States)

Lee, Yuan-Cho; Zhou, Qing; Chen, Junjie; Yuan, Jingsong

2016-12-19

ETAA1 (Ewing tumor-associated antigen 1), also known as ETAA16, was identified as a tumor-specific antigen in the Ewing family of tumors. However, the biological function of this protein remains unknown. Here, we report the identification of ETAA1 as a DNA replication stress response protein. ETAA1 specifically interacts with RPA (Replication protein A) via two conserved RPA-binding domains and is therefore recruited to stalled replication forks. Interestingly, further analysis of ETAA1 function revealed that ETAA1 participates in the activation of ATR signaling pathway via a conserved ATR-activating domain (AAD) located near its N terminus. Importantly, we demonstrate that both RPA binding and ATR activation are required for ETAA1 function at stalled replication forks to maintain genome stability. Therefore, our data suggest that ETAA1 is a new ATR activator involved in replication checkpoint control. Copyright © 2016 Elsevier Ltd. All rights reserved.

Redox-active media for permeable reactive barriers

International Nuclear Information System (INIS)

Sivavec, T.M.; Mackenzie, P.D.; Horney, D.P.; Baghel, S.S.

1997-01-01

In this paper, three classes of redox-active media are described and evaluated in terms of their long-term effectiveness in treating TCE-contaminated groundwater in permeable reactive zones. Zero-valent iron, in the form of recycled cast iron filings, the first class, has received considerable attention as a reactive media and has been used in about a dozen pilot- and full-scale subsurface wall installations. Criteria used in selecting commercial sources of granular iron, will be discussed. Two other classes of redox-active media that have not yet seen wide use in pilot- or full-scale installations will also be described: Fe(II) minerals and bimetallic systems. Fe(II) minerals, including magnetite (Fe 3 O 4 ), and ferrous sulfide (troilite, FeS), are redox-active and afford TCE reduction rates and product distributions that suggest that they react via a reductive mechanism similar to that which operates in the FeO system. Fe(II) species within the passive oxide layer coating the iron metal may act as electron transfer mediators, with FeO serving as the bulk reductant. Bimetallic systems, the third class of redox-active media, are commonly prepared by plating a second metal onto zero-valent iron (e.g., Ni/Fe and Pd/Fe) and have been shown to accelerate solvent degradation rates relative to untreated iron metal. The long-term effectiveness of this approach, however, has not yet been determined in groundwater treatability tests. The results of a Ni-plated iron column study using site groundwater indicate that a change in reduction mechanism (to catalytic dehydrohalogenation/hydrogenation) accounts for the observed rate enhancement. A significant loss in media reactivity was observed over time, attributable to Ni catalyst deactivation or poisoning. Zero-valent iron systems have not shown similar losses in reactivity in long-term laboratory, pilot or field investigations

Effect of Light-Activated Hypocrellin B on the Growth and Membrane Permeability of Gram-Negative Escherichia coli Cells

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Yuan Jiang

2014-01-01

Full Text Available Aim. To investigate the effect of light-activated hypocrellin B on the growth and membrane permeability of Gram-negative bacteria. Methods. Escherichia coli (E. coli as a model bacterium of Gram-negative bacteria was incubated with various concentrations of hypocrellin B for 60 min and was subsequently irradiated by blue light with wavelength of 470 nm at the dose of 12 J/cm2. Colony forming units were counted and the growth inhibition rate of E. coli cells was calculated after light-activated hypocrellin B. Membrane permeability was measured using flow cytometry and confocal laser scanning microscopy (CLSM with propidium iodide (PI staining. Bacterial morphology was observed using transmission electron microscopy (TEM. Reactive oxygen species in bacterial cells were measured using flow cytometry with DCFH-DA staining. Results. Significant growth inhibition rate of E. coli cells was observed after photodynamic action of hypocrellin B. Remarkable damage to the ultrastructure of E. coli was also observed by TEM. Flow cytometry and CLSM observation showed that light-activated hypocrellin B markedly increased membrane permeability of E. coli. Flow cytometry showed the intracellular ROS increase in E. coli treated by photodynamic action of hypocrellin B. Conclusion. Light-activated hypocrellin B caused intracellular ROS increase and structural damages and inhibited the growth of Gram-negative E. coli cells.

High-Resolution Replication Profiles Define the Stochastic Nature of Genome Replication Initiation and Termination

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Michelle Hawkins

2013-11-01

Full Text Available Eukaryotic genome replication is stochastic, and each cell uses a different cohort of replication origins. We demonstrate that interpreting high-resolution Saccharomyces cerevisiae genome replication data with a mathematical model allows quantification of the stochastic nature of genome replication, including the efficiency of each origin and the distribution of termination events. Single-cell measurements support the inferred values for stochastic origin activation time. A strain, in which three origins were inactivated, confirmed that the distribution of termination events is primarily dictated by the stochastic activation time of origins. Cell-to-cell variability in origin activity ensures that termination events are widely distributed across virtually the whole genome. We propose that the heterogeneity in origin usage contributes to genome stability by limiting potentially deleterious events from accumulating at particular loci.

Both DNA Polymerases δ and ε Contact Active and Stalled Replication Forks Differently

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Yu, Chuanhe; Gan, Haiyun

2017-01-01

ABSTRACT Three DNA polymerases, polymerases α, δ, and ε (Pol α, Pol δ, and Pol ε), are responsible for eukaryotic genome duplication. When DNA replication stress is encountered, DNA synthesis stalls until the stress is ameliorated. However, it is not known whether there is a difference in the association of each polymerase with active and stalled replication forks. Here, we show that each DNA polymerase has a distinct pattern of association with active and stalled replication forks. Pol α is enriched at extending Okazaki fragments of active and stalled forks. In contrast, although Pol δ contacts the nascent lagging strands of active and stalled forks, it binds to only the matured (and not elongating) Okazaki fragments of stalled forks. Pol ε has greater contact with the nascent single-stranded DNA (ssDNA) of the leading strand on active forks than on stalled forks. We propose that the configuration of DNA polymerases at stalled forks facilitates the resumption of DNA synthesis after stress removal. PMID:28784720

Use of Interface Treatment to Reduce Emissions from Residuals in Lower Permeability Zones to Groundwater flowing Through More Permeable Zones (Invited)

Science.gov (United States)

Johnson, P.; Cavanagh, B.; Clifton, L.; Daniels, E.; Dahlen, P.

2013-12-01

Many soil and groundwater remediation technologies rely on fluid flow for contaminant extraction or reactant delivery (e.g., soil vapor extraction, pump and treat, in situ chemical oxidation, air sparging, enhanced bioremediation). Given that most unconsolidated and consolidated settings have permeability contrasts, the outcome is often preferential treatment of more permeable zones and ineffective treatment of the lower permeability zones. When this happens, post-treatment contaminant emissions from low permeability zone residuals can cause unacceptable long-term impacts to groundwater in the transmissive zones. As complete remediation of the impacted lower permeability zones may not be practicable with conventional technologies, one might explore options that lead to reduction of the contaminant emissions to acceptable levels, rather than full remediation of the lower permeability layers. This could be accomplished either by creating a sustained emission reaction/attenuation zone at the high-low permeability interface, or by creating a clean soil zone extending sufficiently far into the lower permeability layer to cause the necessary reduction in contaminant concentration gradient and diffusive emission. These options are explored in proof-of-concept laboratory-scale physical model experiments. The physical models are prepared with two layers of contrasting permeability and either dissolved matrix storage or nonaqueous phase liquid (NAPL) in the lower permeability layer. A dissolved oxidant is then delivered to the interface via flow across the higher permeability layer and changes in contaminant emissions from the low permeability zone are monitored before, during, and after oxidant delivery. The use of three oxidants (dissolved oxygen, hydrogen peroxide and sodium persulfate) for treatment of emissions from petroleum hydrocarbon residuals is examined.

Groundwater protection from cadmium contamination by permeable reactive barriers

Energy Technology Data Exchange (ETDEWEB)

Di Natale, F. [Dipartimento di Ingegneria chimica, Universita di Federico II, P.le Tecchio, 80-80125 Naples (Italy)], E-mail: fdinatal@unina.it; Di Natale, M.; Greco, R. [Centro Interdipartimentale di Ricerca in Ingegneria Ambientale (CIRIAM), Dipartimento di Ingegneria Civile, Seconda Universita di Napoli, via Roma 29-81031 Aversa (Caserta) (Italy); Lancia, A. [Dipartimento di Ingegneria chimica, Universita di Federico II, P.le Tecchio, 80-80125 Naples (Italy); Laudante, C.; Musmarra, D. [Centro Interdipartimentale di Ricerca in Ingegneria Ambientale (CIRIAM), Dipartimento di Ingegneria Civile, Seconda Universita di Napoli, via Roma 29-81031 Aversa (Caserta) (Italy)

2008-12-30

This work studies the reliability of an activated carbon permeable reactive barrier in removing cadmium from a contaminated shallow aquifer. Laboratory tests have been performed to characterize the equilibrium and kinetic adsorption properties of the activated carbon in cadmium-containing aqueous solutions. A 2D numerical model has been used to describe pollutant transport within a groundwater and the pollutant adsorption on the permeable adsorbing barrier (PRB). In particular, it has been considered the case of a permeable adsorbing barrier (PAB) used to protect a river from a Cd(II) contaminated groundwater. Numerical results show that the PAB can achieve a long-term efficiency by preventing river pollution for several months.

Modeling inhomogeneous DNA replication kinetics.

Directory of Open Access Journals (Sweden)

Michel G Gauthier

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

Autophagic machinery activated by dengue virus enhances virus replication

International Nuclear Information System (INIS)

Lee, Y.-R.; Lei, H.-Y.; Liu, M.-T.; Wang, J.-R.; Chen, S.-H.; Jiang-Shieh, Y.-F.; Lin, Y.-S.; Yeh, T.-M.; Liu, C.-C.; Liu, H.-S.

2008-01-01

Autophagy is a cellular response against stresses which include the infection of viruses and bacteria. We unravel that Dengue virus-2 (DV2) can trigger autophagic process in various infected cell lines demonstrated by GFP-LC3 dot formation and increased LC3-II formation. Autophagosome formation was also observed under the transmission electron microscope. DV2-induced autophagy further enhances the titers of extracellular and intracellular viruses indicating that autophagy can promote viral replication in the infected cells. Moreover, our data show that ATG5 protein is required to execute DV2-induced autophagy. All together, we are the first to demonstrate that DV can activate autophagic machinery that is favorable for viral replication

Suitability of Torrent Permeability Tester to measure air-permeability of covercrete

Energy Technology Data Exchange (ETDEWEB)

Andrade, C.; Gonzales-Gasca, C. [Institute of Construction Sciences ' Eduardo Torroja' , Madrid (Spain); Torrent, R. [Portland Cement Institute, (Argentina)

2000-07-01

Suitability of the Torrent Permeability Tester (TPT) to measure the permeability of covercrete to air, both in the laboratory and the field, is investigated, and test results obtained in laboratory studies are discussed. The tests performed included the determination of air permeability (TPT method), oxygen permeability (Cembureau method) and capillary suction, rapid chloride permeability test (ASTM C 1202), as well as a one-year carbonation depth test. Concrete specimens of various compositions and curing regimes were used in the tests; the gas-permeability tests were repeated on the same specimens after 28 days, than again at 6 months and 12 months. Test results confirmed the suitability of the TPT as a useful tool in the characterization of the quality the of concrete cover. It was found to be sensitive to changes in concrete quality; repeatable for sensitive properties such as gas permeability ; also, it was found to correlate well with other durability-related properties. 10 refs., 8 tabs., 8 figs.

Using Replicates in Information Retrieval Evaluation.

Science.gov (United States)

Voorhees, Ellen M; Samarov, Daniel; Soboroff, Ian

2017-09-01

This article explores a method for more accurately estimating the main effect of the system in a typical test-collection-based evaluation of information retrieval systems, thus increasing the sensitivity of system comparisons. Randomly partitioning the test document collection allows for multiple tests of a given system and topic (replicates). Bootstrap ANOVA can use these replicates to extract system-topic interactions-something not possible without replicates-yielding a more precise value for the system effect and a narrower confidence interval around that value. Experiments using multiple TREC collections demonstrate that removing the topic-system interactions substantially reduces the confidence intervals around the system effect as well as increases the number of significant pairwise differences found. Further, the method is robust against small changes in the number of partitions used, against variability in the documents that constitute the partitions, and the measure of effectiveness used to quantify system effectiveness.

PKR Activation Favors Infectious Pancreatic Necrosis Virus Replication in Infected Cells

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Amr A.A. Gamil

2016-06-01

Full Text Available The double-stranded RNA-activated protein kinase R (PKR is a Type I interferon (IFN stimulated gene that has important biological and immunological functions. In viral infections, in general, PKR inhibits or promotes viral replication, but PKR-IPNV interaction has not been previously studied. We investigated the involvement of PKR during infectious pancreatic necrosis virus (IPNV infection using a custom-made rabbit antiserum and the PKR inhibitor C16. Reactivity of the antiserum to PKR in CHSE-214 cells was confirmed after IFNα treatment giving an increased protein level. IPNV infection alone did not give increased PKR levels by Western blot, while pre-treatment with PKR inhibitor before IPNV infection gave decreased eukaryotic initiation factor 2-alpha (eIF2α phosphorylation. This suggests that PKR, despite not being upregulated, is involved in eIF2α phosphorylation during IPNV infection. PKR inhibitor pre-treatment resulted in decreased virus titers, extra- and intracellularly, concomitant with reduction of cells with compromised membranes in IPNV-permissive cell lines. These findings suggest that IPNV uses PKR activation to promote virus replication in infected cells.

In vivo analysis of intestinal permeability following hemorrhagic shock

Science.gov (United States)

Alsaigh, Tom; Chang, Marisol; Richter, Michael; Mazor, Rafi; Kistler, Erik B

2015-01-01

AIM: To determine the time course of intestinal permeability changes to proteolytically-derived bowel peptides in experimental hemorrhagic shock. METHODS: We injected fluorescently-conjugated casein protein into the small bowel of anesthetized Wistar rats prior to induction of experimental hemorrhagic shock. These molecules, which fluoresce when proteolytically cleaved, were used as markers for the ability of proteolytically cleaved intestinal products to access the central circulation. Blood was serially sampled to quantify the relative change in concentration of proteolytically-cleaved particles in the systemic circulation. To provide spatial resolution of their location, particles in the mesenteric microvasculature were imaged using in vivo intravital fluorescent microscopy. The experiments were then repeated using an alternate measurement technique, fluorescein isothiocyanate (FITC)-labeled dextrans 20, to semi-quantitatively verify the ability of bowel-derived low-molecular weight molecules (< 20 kD) to access the central circulation. RESULTS: Results demonstrate a significant increase in systemic permeability to gut-derived peptides within 20 min after induction of hemorrhage (1.11 ± 0.19 vs 0.86 ± 0.07, P < 0.05) compared to control animals. Reperfusion resulted in a second, sustained increase in systemic permeability to gut-derived peptides in hemorrhaged animals compared to controls (1.2 ± 0.18 vs 0.97 ± 0.1, P < 0.05). Intravital microscopy of the mesentery also showed marked accumulation of fluorescent particles in the microcirculation of hemorrhaged animals compared to controls. These results were replicated using FITC dextrans 20 [10.85 ± 6.52 vs 3.38 ± 1.11 fluorescent intensity units (× 105, P < 0.05, hemorrhagic shock vs controls)], confirming that small bowel ischemia in response to experimental hemorrhagic shock results in marked and early increases in gut membrane permeability. CONCLUSION: Increased small bowel permeability in hemorrhagic

Evaluating the Infiltration Performance of Eight Dutch Permeable Pavements Using a New Full-Scale Infiltration Testing Method

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Floris Boogaard

2014-07-01

Full Text Available Permeable pavements are a type of sustainable urban drainage system (SUDS technique that are used around the world to infiltrate and treat urban stormwater runoff and to minimize runoff volumes. Urban stormwater runoff contains significant concentrations of suspended sediments that can cause clogging and reduce the infiltration capacity and effectiveness of permeable pavements. It is important for stormwater managers to be able to determine when the level of clogging has reached an unacceptable level, so that they can schedule maintenance or replacement activities as required. Newly-installed permeable pavements in the Netherlands must demonstrate a minimum infiltration capacity of 194 mm/h (540 l/s/ha. Other commonly used permeable pavement guidelines in the Netherlands recommend that maintenance is undertaken on permeable pavements when the infiltration falls below 0.50 m/d (20.8 mm/h. This study used a newly-developed, full-scale infiltration test procedure to evaluate the infiltration performance of eight permeable pavements in five municipalities that had been in service for over seven years in the Netherlands. The determined infiltration capacities vary between 29 and 342 mm/h. Two of the eight pavements show an infiltration capacity higher than 194 mm/h, and all infiltration capacities are higher than 20.8 mm/h. According to the guidelines, this suggests that none of the pavements tested in this study would require immediate maintenance.

Mcm10 regulates DNA replication elongation by stimulating the CMG replicative helicase.

Science.gov (United States)

Lõoke, Marko; Maloney, Michael F; Bell, Stephen P

2017-02-01

Activation of the Mcm2-7 replicative DNA helicase is the committed step in eukaryotic DNA replication initiation. Although Mcm2-7 activation requires binding of the helicase-activating proteins Cdc45 and GINS (forming the CMG complex), an additional protein, Mcm10, drives initial origin DNA unwinding by an unknown mechanism. We show that Mcm10 binds a conserved motif located between the oligonucleotide/oligosaccharide fold (OB-fold) and A subdomain of Mcm2. Although buried in the interface between these domains in Mcm2-7 structures, mutations predicted to separate the domains and expose this motif restore growth to conditional-lethal MCM10 mutant cells. We found that, in addition to stimulating initial DNA unwinding, Mcm10 stabilizes Cdc45 and GINS association with Mcm2-7 and stimulates replication elongation in vivo and in vitro. Furthermore, we identified a lethal allele of MCM10 that stimulates initial DNA unwinding but is defective in replication elongation and CMG binding. Our findings expand the roles of Mcm10 during DNA replication and suggest a new model for Mcm10 function as an activator of the CMG complex throughout DNA replication. © 2017 Lõoke et al.; Published by Cold Spring Harbor Laboratory Press.

Analysis of Fault Permeability Using Mapping and Flow Modeling, Hickory Sandstone Aquifer, Central Texas

Energy Technology Data Exchange (ETDEWEB)

Nieto Camargo, Jorge E., E-mail: jorge.nietocamargo@aramco.com; Jensen, Jerry L., E-mail: jjensen@ucalgary.ca [University of Calgary, Department of Chemical and Petroleum Engineering (Canada)

2012-09-15

Reservoir compartments, typical targets for infill well locations, are commonly created by faults that may reduce permeability. A narrow fault may consist of a complex assemblage of deformation elements that result in spatially variable and anisotropic permeabilities. We report on the permeability structure of a km-scale fault sampled through drilling a faulted siliciclastic aquifer in central Texas. Probe and whole-core permeabilities, serial CAT scans, and textural and structural data from the selected core samples are used to understand permeability structure of fault zones and develop predictive models of fault zone permeability. Using numerical flow simulation, it is possible to predict permeability anisotropy associated with faults and evaluate the effect of individual deformation elements in the overall permeability tensor. We found relationships between the permeability of the host rock and those of the highly deformed (HD) fault-elements according to the fault throw. The lateral continuity and predictable permeability of the HD fault elements enhance capability for estimating the effects of subseismic faulting on fluid flow in low-shale reservoirs.

Preliminary study of soil permeability properties using principal component analysis

Science.gov (United States)

Yulianti, M.; Sudriani, Y.; Rustini, H. A.

2018-02-01

Soil permeability measurement is undoubtedly important in carrying out soil-water research such as rainfall-runoff modelling, irrigation water distribution systems, etc. It is also known that acquiring reliable soil permeability data is rather laborious, time-consuming, and costly. Therefore, it is desirable to develop the prediction model. Several studies of empirical equations for predicting permeability have been undertaken by many researchers. These studies derived the models from areas which soil characteristics are different from Indonesian soil, which suggest a possibility that these permeability models are site-specific. The purpose of this study is to identify which soil parameters correspond strongly to soil permeability and propose a preliminary model for permeability prediction. Principal component analysis (PCA) was applied to 16 parameters analysed from 37 sites consist of 91 samples obtained from Batanghari Watershed. Findings indicated five variables that have strong correlation with soil permeability, and we recommend a preliminary permeability model, which is potential for further development.

Effect of permeability enhancers on paracellular permeability of acyclovir.

Science.gov (United States)

Ates, Muge; Kaynak, Mustafa Sinan; Sahin, Selma

2016-06-01

According to Biopharmaceutics Classification System (BCS), acyclovir is a class III (high solubility, low permeability) compound, and it is transported through paracellular route by passive diffusion. The aim of this study was to investigate the effect of various pharmaceutical excipients on the intestinal permeability of acyclovir. The single-pass in-situ intestinal perfusion (SPIP) method was used to estimate the permeability values of acyclovir and metoprolol across different intestinal segments (jejunum, ileum and colon). Permeability coefficient (Peff ) of acyclovir was determined in the absence and presence of a permeation enhancer such as dimethyl β-cyclodextrin (DM-β-CD), sodium lauryl sulfate (SLS), sodium caprate (Cap-Na) and chitosan chloride. All enhancers increased the permeability of paracellularly transported acyclovir. Although Cap-Na has the highest permeability-enhancing effect in all segments, permeation-enhancing effect of chitosan and SLS was only significant in ileum. On the other hand, DM-β-CD slightly decreased the permeability in all intestinal segments. These findings have potential implication concerning the enhancement of absorption of paracellularly transported compounds with limited oral bioavailability. In the case of acyclovir, Cap-Na either alone or in combination with SLS or chitosan has the potential to improve its absorption and bioavailability and has yet to be explored. © 2016 Royal Pharmaceutical Society.

Active role of a human genomic insert in replication of a yeast artificial chromosome.

Science.gov (United States)

van Brabant, A J; Fangman, W L; Brewer, B J

1999-06-01

Yeast artificial chromosomes (YACs) are a common tool for cloning eukaryotic DNA. The manner by which large pieces of foreign DNA are assimilated by yeast cells into a functional chromosome is poorly understood, as is the reason why some of them are stably maintained and some are not. We examined the replication of a stable YAC containing a 240-kb insert of DNA from the human T-cell receptor beta locus. The human insert contains multiple sites that serve as origins of replication. The activity of these origins appears to require the yeast ARS consensus sequence and, as with yeast origins, additional flanking sequences. In addition, the origins in the human insert exhibit a spacing, a range of activation efficiencies, and a variation in times of activation during S phase similar to those found for normal yeast chromosomes. We propose that an appropriate combination of replication origin density, activation times, and initiation efficiencies is necessary for the successful maintenance of YAC inserts.

Experimental study of very low permeability rocks using a high accuracy permeameter

International Nuclear Information System (INIS)

Larive, Elodie

2002-01-01

The measurement of fluid flow through 'tight' rocks is important to provide a better understanding of physical processes involved in several industrial and natural problems. These include deep nuclear waste repositories, management of aquifers, gas, petroleum or geothermal reservoirs, or earthquakes prevention. The major part of this work consisted of the design, construction and use of an elaborate experimental apparatus allowing laboratory permeability measurements (fluid flow) of very low permeability rocks, on samples at a centimetric scale, to constrain their hydraulic behaviour at realistic in-situ conditions. The accuracy permeameter allows the use of several measurement methods, the steady-state flow method, the transient pulse method, and the sinusoidal pore pressure oscillation method. Measurements were made with the pore pressure oscillation method, using different waveform periods, at several pore and confining pressure conditions, on different materials. The permeability of one natural standard, Westerly granite, and an artificial one, a micro-porous cement, were measured, and results obtained agreed with previous measurements made on these materials showing the reliability of the permeameter. A study of a Yorkshire sandstone shows a relationship between rock microstructure, permeability anisotropy and thermal cracking. Microstructure, porosity and permeability concepts, and laboratory permeability measurements specifications are presented, the permeameter is described, and then permeability results obtained on the investigated materials are reported [fr

Microstructure-based characterization of permeability using a random walk model

International Nuclear Information System (INIS)

Chen, F F; Yang, Y S

2012-01-01

Quantitative transport properties of materials are analysed using a random walk model, based on the microscopic compositional distribution of compositions in the materials. A material sample is defined on a simple-cubic lattice, with volume fractions specified for each composition on every volume pixel (voxel). The quantitative relation between bulk permeability and fine-scale anisotropy is investigated by assuming fully anisotropic and fully isotropic voxel morphology. Such a study has prompted an analytic approximate formulation to predict bulk permeability range for a heterogeneous multi-component system that lacks detailed microstructure information. The numerical approach is verified on synthetic structures with known permeability. The analysis technique is applied to a real-world rock sample, as illustrated by a case study detailed in this paper. The investigations show that the bulk permeability is affected significantly by fine length scale anisotropy. (paper)

Using Model Replication to Improve the Reliability of Agent-Based Models

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Zhong, Wei; Kim, Yushim

The basic presupposition of model replication activities for a computational model such as an agent-based model (ABM) is that, as a robust and reliable tool, it must be replicable in other computing settings. This assumption has recently gained attention in the community of artificial society and simulation due to the challenges of model verification and validation. Illustrating the replication of an ABM representing fraudulent behavior in a public service delivery system originally developed in the Java-based MASON toolkit for NetLogo by a different author, this paper exemplifies how model replication exercises provide unique opportunities for model verification and validation process. At the same time, it helps accumulate best practices and patterns of model replication and contributes to the agenda of developing a standard methodological protocol for agent-based social simulation.

Permeability and stress-jump effects on magnetic drug targeting in a permeable microvessel using Darcy model

Energy Technology Data Exchange (ETDEWEB)

Shaw, S., E-mail: sachinshaw@gmail.com [Department of Mathematics and Statistical Sciences, Botswana International University of Science and Technology, Private Bag 16, Palapye (Botswana); Sutradhar, A.; Murthy, PVSN [Department of Mathematics, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal (India)

2017-05-01

In the present paper, we investigated the influence of permeability of the carrier particle and stress jump condition on the porous spherical surface in magnetic drug targeting through a permeable microvessel. The nature of blood is defined by non-Newtonian Casson fluid in the core region of the microvessel and Newtonian fluid in the peripheral region which is located near the surface of the wall of the microvessel. The magnetic particles are considered as spherical and in nanosize, embedded in the carrier particle along with drug particles. A magnet is placed near the tumor position to generate a magnetic field. The relative motion of the carrier particle is the resultant of the fluidic force, magnetic force and Saffman drag force which are calculated for the spherical carrier particle. Trajectories of the carrier particle along the radial and axial direction are calculated. Effect of different parameters such as stress-jump constant, permeability of the carrier particle, pressure gradient, yield stress, Saffman force, volume fraction of the embedded magnetic nanoparticles, permeability of the microvessel wall, and the radius of the carrier particle on the trajectory of the carrier particle are discussed and displayed graphically. - Highlights: • In the present manuscript, we considered the porous carrier particle which provide a larger surface area contact with the fluid than the solid spherical carrier particle. It shows that the porous carrier particle are captured easily than the solid carrier particle. • Introduce Suffman force on the carrier particle which commences an additional resistance which acts opposite to the surface wall and helps the particles to go away from the tumor position. • Considered stress jump condition at the surface of the porous carrier particle which enhanced the tendency of the carrier particle to be capture near the tumor. • Used Darcy model to define the permeability of the wall of the microvessel.

Protein Phosphatase 1 Recruitment by Rif1 Regulates DNA Replication Origin Firing by Counteracting DDK Activity

Directory of Open Access Journals (Sweden)

Anoushka Davé

2014-04-01

Full Text Available The firing of eukaryotic origins of DNA replication requires CDK and DDK kinase activities. DDK, in particular, is involved in setting the temporal program of origin activation, a conserved feature of eukaryotes. Rif1, originally identified as a telomeric protein, was recently implicated in specifying replication timing in yeast and mammals. We show that this function of Rif1 depends on its interaction with PP1 phosphatases. Mutations of two PP1 docking motifs in Rif1 lead to early replication of telomeres in budding yeast and misregulation of origin firing in fission yeast. Several lines of evidence indicate that Rif1/PP1 counteract DDK activity on the replicative MCM helicase. Our data suggest that the PP1/Rif1 interaction is downregulated by the phosphorylation of Rif1, most likely by CDK/DDK. These findings elucidate the mechanism of action of Rif1 in the control of DNA replication and demonstrate a role of PP1 phosphatases in the regulation of origin firing.

Hepatitis C virus translation preferentially depends on active RNA replication.

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Helene Minyi Liu

Full Text Available Hepatitis C virus (HCV RNA initiates its replication on a detergent-resistant membrane structure derived from the endoplasmic reticulum (ER in the HCV replicon cells. By performing a pulse-chase study of BrU-labeled HCV RNA, we found that the newly-synthesized HCV RNA traveled along the anterograde-membrane traffic and moved away from the ER. Presumably, the RNA moved to the site of translation or virion assembly in the later steps of viral life cycle. In this study, we further addressed how HCV RNA translation was regulated by HCV RNA trafficking. When the movement of HCV RNA from the site of RNA synthesis to the Golgi complex was blocked by nocodazole, an inhibitor of ER-Golgi transport, HCV protein translation was surprisingly enhanced, suggesting that the translation of viral proteins occurred near the site of RNA synthesis. We also found that the translation of HCV proteins was dependent on active RNA synthesis: inhibition of viral RNA synthesis by an NS5B inhibitor resulted in decreased HCV viral protein synthesis even when the total amount of intracellular HCV RNA remained unchanged. Furthermore, the translation activity of the replication-defective HCV replicons or viral RNA with an NS5B mutation was greatly reduced as compared to that of the corresponding wildtype RNA. By performing live cell labeling of newly synthesized HCV RNA and proteins, we further showed that the newly synthesized HCV proteins colocalized with the newly synthesized viral RNA, suggesting that HCV RNA replication and protein translation take place at or near the same site. Our findings together indicate that the translation of HCV RNA is coupled to RNA replication and that the both processes may occur at the same subcellular membrane compartments, which we term the replicasome.

Using Replication Projects in Teaching Research Methods

Science.gov (United States)

Standing, Lionel G.; Grenier, Manuel; Lane, Erica A.; Roberts, Meigan S.; Sykes, Sarah J.

2014-01-01

It is suggested that replication projects may be valuable in teaching research methods, and also address the current need in psychology for more independent verification of published studies. Their use in an undergraduate methods course is described, involving student teams who performed direct replications of four well-known experiments, yielding…

Identification and characterization of the host protein DNAJC14 as a broadly active flavivirus replication modulator.

Directory of Open Access Journals (Sweden)

Zhigang Yi

2011-01-01

Full Text Available Viruses in the Flavivirus genus of the Flaviviridae family are arthropod-transmitted and contribute to staggering numbers of human infections and significant deaths annually across the globe. To identify cellular factors with antiviral activity against flaviviruses, we screened a cDNA library using an iterative approach. We identified a mammalian Hsp40 chaperone protein (DNAJC14 that when overexpressed was able to mediate protection from yellow fever virus (YFV-induced cell death. Further studies revealed that DNAJC14 inhibits YFV at the step of viral RNA replication. Since replication of bovine viral diarrhea virus (BVDV, a member of the related Pestivirus genus, is also known to be modulated by DNAJC14, we tested the effect of this host factor on diverse Flaviviridae family members. Flaviviruses, including the pathogenic Asibi strain of YFV, Kunjin, and tick-borne Langat virus, as well as a Hepacivirus, hepatitis C virus (HCV, all were inhibited by overexpression of DNAJC14. Mutagenesis showed that both the J-domain and the C-terminal domain, which mediates self-interaction, are required for anti-YFV activity. We found that DNAJC14 does not block YFV nor HCV NS2-3 cleavage, and using non-inhibitory mutants demonstrate that DNAJC14 is recruited to YFV replication complexes. Immunofluorescence analysis demonstrated that endogenous DNAJC14 rearranges during infection and is found in replication complexes identified by dsRNA staining. Interestingly, silencing of endogenous DNAJC14 results in impaired YFV replication suggesting a requirement for DNAJC14 in YFV replication complex assembly. Finally, the antiviral activity of overexpressed DNAJC14 occurs in a time- and dose-dependent manner. DNAJC14 overexpression may disrupt the proper stoichiometry resulting in inhibition, which can be overcome upon restoration of the optimal ratios due to the accumulation of viral nonstructural proteins. Our findings, together with previously published work

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

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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.

Prelife catalysts and replicators

OpenAIRE

Ohtsuki, Hisashi; Nowak, Martin A.

2009-01-01

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

Inhibition of dengue virus replication by novel inhibitors of RNA-dependent RNA polymerase and protease activities.

Science.gov (United States)

Pelliccia, Sveva; Wu, Yu-Hsuan; Coluccia, Antonio; La Regina, Giuseppe; Tseng, Chin-Kai; Famiglini, Valeria; Masci, Domiziana; Hiscott, John; Lee, Jin-Ching; Silvestri, Romano

2017-12-01

Dengue virus (DENV) is the leading mosquito-transmitted viral infection in the world. With more than 390 million new infections annually, and up to 1 million clinical cases with severe disease manifestations, there continues to be a need to develop new antiviral agents against dengue infection. In addition, there is no approved anti-DENV agents for treating DENV-infected patients. In the present study, we identified new compounds with anti-DENV replication activity by targeting viral replication enzymes - NS5, RNA-dependent RNA polymerase (RdRp) and NS3 protease, using cell-based reporter assay. Subsequently, we performed an enzyme-based assay to clarify the action of these compounds against DENV RdRp or NS3 protease activity. Moreover, these compounds exhibited anti-DENV activity in vivo in the ICR-suckling DENV-infected mouse model. Combination drug treatment exhibited a synergistic inhibition of DENV replication. These results describe novel prototypical small anti-DENV molecules for further development through compound modification and provide potential antivirals for treating DENV infection and DENV-related diseases.

Phosphorylation of Minichromosome Maintenance 3 (MCM3) by Checkpoint Kinase 1 (Chk1) Negatively Regulates DNA Replication and Checkpoint Activation.

Science.gov (United States)

Han, Xiangzi; Mayca Pozo, Franklin; Wisotsky, Jacob N; Wang, Benlian; Jacobberger, James W; Zhang, Youwei

2015-05-08

Mechanisms controlling DNA replication and replication checkpoint are critical for the maintenance of genome stability and the prevention or treatment of human cancers. Checkpoint kinase 1 (Chk1) is a key effector protein kinase that regulates the DNA damage response and replication checkpoint. The heterohexameric minichromosome maintenance (MCM) complex is the core component of mammalian DNA helicase and has been implicated in replication checkpoint activation. Here we report that Chk1 phosphorylates the MCM3 subunit of the MCM complex at Ser-205 under normal growth conditions. Mutating the Ser-205 of MCM3 to Ala increased the length of DNA replication track and shortened the S phase duration, indicating that Ser-205 phosphorylation negatively controls normal DNA replication. Upon replicative stress treatment, the inhibitory phosphorylation of MCM3 at Ser-205 was reduced, and this reduction was accompanied with the generation of single strand DNA, the key platform for ataxia telangiectasia mutated and Rad3-related (ATR) activation. As a result, the replication checkpoint is activated. Together, these data provide significant insights into the regulation of both normal DNA replication and replication checkpoint activation through the novel phosphorylation of MCM3 by Chk1. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

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.

Arabidopsis annexin1 mediates the radical-activated plasma membrane Ca²+- and K+-permeable conductance in root cells.

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Laohavisit, Anuphon; Shang, Zhonglin; Rubio, Lourdes; Cuin, Tracey A; Véry, Anne-Aliénor; Wang, Aihua; Mortimer, Jennifer C; Macpherson, Neil; Coxon, Katy M; Battey, Nicholas H; Brownlee, Colin; Park, Ohkmae K; Sentenac, Hervé; Shabala, Sergey; Webb, Alex A R; Davies, Julia M

2012-04-01

Plant cell growth and stress signaling require Ca²⁺ influx through plasma membrane transport proteins that are regulated by reactive oxygen species. In root cell growth, adaptation to salinity stress, and stomatal closure, such proteins operate downstream of the plasma membrane NADPH oxidases that produce extracellular superoxide anion, a reactive oxygen species that is readily converted to extracellular hydrogen peroxide and hydroxyl radicals, OH•. In root cells, extracellular OH• activates a plasma membrane Ca²⁺-permeable conductance that permits Ca²⁺ influx. In Arabidopsis thaliana, distribution of this conductance resembles that of annexin1 (ANN1). Annexins are membrane binding proteins that can form Ca²⁺-permeable conductances in vitro. Here, the Arabidopsis loss-of-function mutant for annexin1 (Atann1) was found to lack the root hair and epidermal OH•-activated Ca²⁺- and K⁺-permeable conductance. This manifests in both impaired root cell growth and ability to elevate root cell cytosolic free Ca²⁺ in response to OH•. An OH•-activated Ca²⁺ conductance is reconstituted by recombinant ANN1 in planar lipid bilayers. ANN1 therefore presents as a novel Ca²⁺-permeable transporter providing a molecular link between reactive oxygen species and cytosolic Ca²⁺ in plants.

Intestinal Permeability and Cellular Antioxidant Activity of Phenolic Compounds from Mango (Mangifera indica cv. Ataulfo) Peels.

Science.gov (United States)

Pacheco-Ordaz, Ramón; Antunes-Ricardo, Marilena; Gutiérrez-Uribe, Janet A; González-Aguilar, Gustavo A

2018-02-08

Mango ( Mangifera indica cv. Ataulfo) peel contains bound phenolics that may be released by alkaline or acid hydrolysis and may be converted into less complex molecules. Free phenolics from mango cv. Ataulfo peel were obtained using a methanolic extraction, and their cellular antioxidant activity (CAA) and permeability were compared to those obtained for bound phenolics released by alkaline or acid hydrolysis. Gallic acid was found as a simple phenolic acid after alkaline hydrolysis along with mangiferin isomers and quercetin as aglycone and glycosides. Only gallic acid, ethyl gallate, mangiferin, and quercetin were identified in the acid fraction. The acid and alkaline fractions showed the highest CAA (60.5% and 51.5%) when tested at 125 µg/mL. The value of the apparent permeability coefficient (Papp) across the Caco-2/HT-29 monolayer of gallic acid from the alkaline fraction was higher (2.61 × 10 -6 cm/s) than in the other fractions and similar to that obtained when tested pure (2.48 × 10 -6 cm/s). In conclusion, mango peels contain bound phenolic compounds that, after their release, have permeability similar to pure compounds and exert an important CAA. This finding can be applied in the development of nutraceuticals using this important by-product from the mango processing industry.

Inhibition of DNA replication, DNA repair synthesis, and DNA polymerases α and δ by butylphenyl deoxyguanosine triphosphate

International Nuclear Information System (INIS)

Dreslor, S.L.; Frattini, M.G.

1987-01-01

Semiconservative DNA replication in growing mammalian cells and ultraviolet (UV)-induced DNA repair synthesis in nongrowing mammalian cells are mediated by one or both of the aphidicolin-sensitive DNA polymerases, α and/or δ. They have studied the inhibition of replication and repair synthesis in permeable human cells by N 2 (p-n-butylphenyl)-2'-deoxyguanosine-5'-triphosphate (BuPh dGTP), an agent which inhibits polymerase α strongly and polymerase δ weakly. Both processes are inhibited by BuPh-dGTP in competition with dGTP. The K/sub i/'s are, for replication, 2-3 μM and, for repair synthesis, 3-4 μM, consistent with the involvement of the same DNA polymerase in both processes. Inhibition of isolated human polymerase α by BuPh-dGTP is also competitive with dGTP, but the K/sub i/ is approximately 10 nM, several hundred-fold lower than the K/sub i/'s of replication and repair synthesis. Isolated polymerase δ is inhibited by BuPh-dGTP at doses similar to those which inhibit replication and repair synthesis, however, attempts to determine the K/sub i/ of polymerase δ were hampered by the finding that the dependence of δ activity on deoxyribunucleotide concentration is parabolic at low doses. This behavior differs from the behavior of polymerase α and of cellular DNA replication and repair synthesis, all of which show a simple, hyperbolic relationship between activity and deoxyribonucleotide concentration. Thus, inhibition of DNA replication and UV induced DNA repair synthesis by BuPh dGTP is quantitatively similar to DNA polymerase δ, but some other characteristics of the cellular processes are more similar to those of polymerase α

Niclosamide inhibits lytic replication of Epstein-Barr virus by disrupting mTOR activation.

Science.gov (United States)

Huang, Lu; Yang, Mengtian; Yuan, Yan; Li, Xiaojuan; Kuang, Ersheng

2017-02-01

Infection with the oncogenic γ-herpesviruses Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV) cause several severe malignancies in humans. Inhibition of the lytic replication of EBV and KSHV eliminates the reservoir of persistent infection and transmission, consequently preventing the occurrence of diseases from the sources of infection. Antiviral drugs are limited in controlling these viral infectious diseases. Here, we demonstrate that niclosamide, an old anthelmintic drug, inhibits mTOR activation during EBV lytic replication. Consequently, niclosamide effectively suppresses EBV lytic gene expression, viral DNA lytic replication and virion production in EBV-infected lymphoma cells and epithelial cells. Niclosamide exhibits cytotoxicity toward lymphoma cells and induces irreversible cell cycle arrest in lytically EBV-infected cells. The ectopic overexpression of mTOR reverses the inhibition of niclosamide in EBV lytic replication. Similarly, niclosamide inhibits KSHV lytic replication. Thus, we conclude that niclosamide is a promising candidate for chemotherapy against the acute occurrence and transmission of infectious diseases of oncogenic γ-herpesviruses. Copyright © 2016 Elsevier B.V. All rights reserved.

Replicating the EnhanceFitness physical activity program in Hawai`i's multicultural population, 2007-2010.

Science.gov (United States)

Tomioka, Michiyo; Sugihara, Naomi; Braun, Kathryn L

2012-01-01

Despite evidence of the benefits of regular physical activity, many older adults are not physically active. Health professionals are challenged to replicate evidence-based programs to address low levels of physical activity among members of their communities. EnhanceFitness is an evidence-based group exercise program developed in Seattle to increase the strength, flexibility, and balance of older adults. Hawai`i's Healthy Aging Partnership supported the rural island of Kaua`i to select, adapt, implement, and evaluate EnhanceFitness to increase physical activity among older adult residents (75% Asian/Pacific Islander [API]). Evaluation measures of the replication of EnhanceFitness included fidelity of EnhanceFitness delivery and participants' attendance, satisfaction with the program, confidence to exercise regularly, and pre-post fitness check measures of physical performance (chair stands, arm curls, and the up-and-go test). Between July 2007 and December 2010, 223 Kaua`i residents enrolled in EnhanceFitness; 178 (80%) participated at least 4 months and completed the 4-month fitness checks. EnhanceFitness classes were offered with a high degree of fidelity, and both API and white participants significantly improved their physical performance (chair stands, t = -11.06, P program and instructors and high confidence to continue to exercise regularly. EnhanceFitness is replicable in Hawai`i and increased physical performance among API and white older adults. This case study outlines a replication process that other communities can follow.

Definition of herpes simplex virus type 1 helper activities for adeno-associated virus early replication events.

Directory of Open Access Journals (Sweden)

Nathalie Alazard-Dany

2009-03-01

Full Text Available The human parvovirus Adeno-Associated Virus (AAV type 2 can only replicate in cells co-infected with a helper virus, such as Adenovirus or Herpes Simplex Virus type 1 (HSV-1; whereas, in the absence of a helper virus, it establishes a latent infection. Previous studies demonstrated that the ternary HSV-1 helicase/primase (HP complex (UL5/8/52 and the single-stranded DNA-Binding Protein (ICP8 were sufficient to induce AAV-2 replication in transfected cells. We independently showed that, in the context of a latent AAV-2 infection, the HSV-1 ICP0 protein was able to activate rep gene expression. The present study was conducted to integrate these observations and to further explore the requirement of other HSV-1 proteins during early AAV replication steps, i.e. rep gene expression and AAV DNA replication. Using a cellular model that mimics AAV latency and composite constructs coding for various sets of HSV-1 genes, we first confirmed the role of ICP0 for rep gene expression and demonstrated a synergistic effect of ICP4 and, to a lesser extent, ICP22. Conversely, ICP27 displayed an inhibitory effect. Second, our analyses showed that the effect of ICP0, ICP4, and ICP22 on rep gene expression was essential for the onset of AAV DNA replication in conjunction with the HP complex and ICP8. Third, and most importantly, we demonstrated that the HSV-1 DNA polymerase complex (UL30/UL42 was critical to enhance AAV DNA replication to a significant level in transfected cells and that its catalytic activity was involved in this process. Altogether, this work represents the first comprehensive study recapitulating the series of early events taking place during HSV-1-induced AAV replication.

Evaluation of the membrane permeability (PAMPA and skin) of benzimidazoles with potential cannabinoid activity and their relation with the Biopharmaceutics Classification System (BCS).

Science.gov (United States)

Alvarez-Figueroa, M Javiera; Pessoa-Mahana, C David; Palavecino-González, M Elisa; Mella-Raipán, Jaime; Espinosa-Bustos, Cristián; Lagos-Muñoz, Manuel E

2011-06-01

The permeability of five benzimidazole derivates with potential cannabinoid activity was determined in two models of membranes, parallel artificial membrane permeability assay (PAMPA) and skin, in order to study the relationship of the physicochemical properties of the molecules and characteristics of the membranes with the permeability defined by the Biopharmaceutics Classification System. It was established that the PAMPA intestinal absorption method is a good predictor for classifying these molecules as very permeable, independent of their thermodynamic solubility, if and only if these have a Log P(oct) value permeability is conditioned on the solubility of the molecule so that it can only serve as a model for classifying the permeability of molecules that possess high solubility (class I: high solubility, high permeability; class III: high solubility, low permeability).

Replication dynamics of the yeast genome.

Science.gov (United States)

Raghuraman, M K; Winzeler, E A; Collingwood, D; Hunt, S; Wodicka, L; Conway, A; Lockhart, D J; Davis, R W; Brewer, B J; Fangman, W L

2001-10-05

Oligonucleotide microarrays were used to map the detailed topography of chromosome replication in the budding yeast Saccharomyces cerevisiae. The times of replication of thousands of sites across the genome were determined by hybridizing replicated and unreplicated DNAs, isolated at different times in S phase, to the microarrays. Origin activations take place continuously throughout S phase but with most firings near mid-S phase. Rates of replication fork movement vary greatly from region to region in the genome. The two ends of each of the 16 chromosomes are highly correlated in their times of replication. This microarray approach is readily applicable to other organisms, including humans.

Determination of filtrations and permeability of an earth dam

International Nuclear Information System (INIS)

Gomez, H.R.; Baro, G.B.; Gillen, Ricardo.

1975-11-01

The aim of this work was to measure with the aid of a radioactive tracer the speed flow of the water filtrating from Sumampa Dam in northeastern Catamarca, while being in operation, and with these data determine if the actual permeability corresponds to the projected one. Iodine-131 was used as tracer and periodical samples were taken from the down stream water in order to determine its activity concentration. In previous perforations ionic interchange resines were used so as to measure simultaneously the fixed Iodine-131. The permeability of the dam was calculated from the obtained speed based on time-concentration curves and applying Darcy formulas for permeability. (author) [es

Radiation Effects on the Cytoskeleton of Endothelial Cells and Endothelial Monolayer Permeability

International Nuclear Information System (INIS)

Gabrys, Dorota; Greco, Olga; Patel, Gaurang; Prise, Kevin M.; Tozer, Gillian M.; Kanthou, Chryso

2007-01-01

Purpose: To investigate the effects of radiation on the endothelial cytoskeleton and endothelial monolayer permeability and to evaluate associated signaling pathways, which could reveal potential mechanisms of known vascular effects of radiation. Methods and Materials: Cultured endothelial cells were X-ray irradiated, and actin filaments, microtubules, intermediate filaments, and vascular endothelial (VE)-cadherin junctions were examined by immunofluorescence. Permeability was determined by the passage of fluorescent dextran through cell monolayers. Signal transduction pathways were analyzed using RhoA, Rho kinase, and stress-activated protein kinase-p38 (SAPK2/p38) inhibitors by guanosine triphosphate-RhoA activation assay and transfection with RhoAT19N. The levels of junction protein expression and phosphorylation of myosin light chain and SAPK2/p38 were assessed by Western blotting. The radiation effects on cell death were verified by clonogenic assays. Results: Radiation induced rapid and persistent actin stress fiber formation and redistribution of VE-cadherin junctions in microvascular, but not umbilical vein endothelial cells, and microtubules and intermediate filaments remained unaffected. Radiation also caused a rapid and persistent increase in microvascular permeability. RhoA-guanosine triphosphatase and Rho kinase were activated by radiation and caused phosphorylation of downstream myosin light chain and the observed cytoskeletal and permeability changes. SAPK2/p38 was activated by radiation but did not influence either the cytoskeleton or permeability. Conclusion: This study is the first to show rapid activation of the RhoA/Rho kinase by radiation in endothelial cells and has demonstrated a link between this pathway and cytoskeletal remodeling and permeability. The results also suggest that the RhoA pathway might be a useful target for modulating the permeability and other effects of radiation for therapeutic gain

Overcoming natural replication barriers: differential helicase requirements.

Science.gov (United States)

Anand, Ranjith P; Shah, Kartik A; Niu, Hengyao; Sung, Patrick; Mirkin, Sergei M; Freudenreich, Catherine H

2012-02-01

DNA sequences that form secondary structures or bind protein complexes are known barriers to replication and potential inducers of genome instability. In order to determine which helicases facilitate DNA replication across these barriers, we analyzed fork progression through them in wild-type and mutant yeast cells, using 2-dimensional gel-electrophoretic analysis of the replication intermediates. We show that the Srs2 protein facilitates replication of hairpin-forming CGG/CCG repeats and prevents chromosome fragility at the repeat, whereas it does not affect replication of G-quadruplex forming sequences or a protein-bound repeat. Srs2 helicase activity is required for hairpin unwinding and fork progression. Also, the PCNA binding domain of Srs2 is required for its in vivo role of replication through hairpins. In contrast, the absence of Sgs1 or Pif1 helicases did not inhibit replication through structural barriers, though Pif1 did facilitate replication of a telomeric protein barrier. Interestingly, replication through a protein barrier but not a DNA structure barrier was modulated by nucleotide pool levels, illuminating a different mechanism by which cells can regulate fork progression through protein-mediated stall sites. Our analyses reveal fundamental differences in the replication of DNA structural versus protein barriers, with Srs2 helicase activity exclusively required for fork progression through hairpin structures.

Replication stress and oxidative damage contribute to aberrant constitutive activation of DNA damage signalling in human gliomas

DEFF Research Database (Denmark)

Bartkova, J; Hamerlik, P; Stockhausen, Marie

2010-01-01

brain and grade II astrocytomas, despite the degree of DDR activation was higher in grade II tumors. Markers indicative of ongoing DNA replication stress (Chk1 activation, Rad17 phosphorylation, replication protein A foci and single-stranded DNA) were present in GBM cells under high- or low...... and indicate that replication stress, rather than oxidative stress, fuels the DNA damage signalling in early stages of astrocytoma development.......Malignant gliomas, the deadliest of brain neoplasms, show rampant genetic instability and resistance to genotoxic therapies, implicating potentially aberrant DNA damage response (DDR) in glioma pathogenesis and treatment failure. Here, we report on gross, aberrant constitutive activation of DNA...

Viral hijacking of a replicative helicase loader and its implications for helicase loading control and phage replication

Energy Technology Data Exchange (ETDEWEB)

Hood, Iris V.; Berger, James M.

2016-05-31

Replisome assembly requires the loading of replicative hexameric helicases onto origins by AAA+ ATPases. How loader activity is appropriately controlled remains unclear. Here, we use structural and biochemical analyses to establish how an antimicrobial phage protein interferes with the function of theStaphylococcus aureusreplicative helicase loader, DnaI. The viral protein binds to the loader’s AAA+ ATPase domain, allowing binding of the host replicative helicase but impeding loader self-assembly and ATPase activity. Close inspection of the complex highlights an unexpected locus for the binding of an interdomain linker element in DnaI/DnaC-family proteins. We find that the inhibitor protein is genetically coupled to a phage-encoded homolog of the bacterial helicase loader, which we show binds to the host helicase but not to the inhibitor itself. These findings establish a new approach by which viruses can hijack host replication processes and explain how loader activity is internally regulated to prevent aberrant auto-association.

In vitro and in vivo activation of mitochondrial membrane permeability transition pore using triiodothyronine

Czech Academy of Sciences Publication Activity Database

Endlicher, R.; Drahota, Zdeněk; Červinková, Z.

2016-01-01

Roč. 65, č. 2 (2016), s. 321-331 ISSN 0862-8408 R&D Projects: GA ČR(CZ) GB14-36804G Institutional support: RVO:67985823 Keywords : rat liver mitochondria * membrane permeability transition pore * thyroid hormones Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.461, year: 2016

Mapping replication origins in yeast chromosomes.

Science.gov (United States)

Brewer, B J; Fangman, W L

1991-07-01

The replicon hypothesis, first proposed in 1963 by Jacob and Brenner, states that DNA replication is controlled at sites called origins. Replication origins have been well studied in prokaryotes. However, the study of eukaryotic chromosomal origins has lagged behind, because until recently there has been no method for reliably determining the identity and location of origins from eukaryotic chromosomes. Here, we review a technique we developed with the yeast Saccharomyces cerevisiae that allows both the mapping of replication origins and an assessment of their activity. Two-dimensional agarose gel electrophoresis and Southern hybridization with total genomic DNA are used to determine whether a particular restriction fragment acquires the branched structure diagnostic of replication initiation. The technique has been used to localize origins in yeast chromosomes and assess their initiation efficiency. In some cases, origin activation is dependent upon the surrounding context. The technique is also being applied to a variety of eukaryotic organisms.

Apolipoprotein L1 confers pH-switchable ion permeability to phospholipid vesicles.

Science.gov (United States)

Bruno, Jonathan; Pozzi, Nicola; Oliva, Jonathan; Edwards, John C

2017-11-03

Apolipoprotein L1 (ApoL1) is a human serum protein conferring resistance to African trypanosomes, and certain ApoL1 variants increase susceptibility to some progressive kidney diseases. ApoL1 has been hypothesized to function like a pore-forming colicin and has been reported to have permeability effects on both intracellular and plasma membranes. Here, to gain insight into how ApoL1 may function in vivo , we used vesicle-based ion permeability, direct membrane association, and intrinsic fluorescence to study the activities of purified recombinant ApoL1. We found that ApoL1 confers chloride-selective permeability to preformed phospholipid vesicles and that this selectivity is strongly pH-sensitive, with maximal activity at pH 5 and little activity above pH 7. When ApoL1 and lipid were allowed to interact at low pH and were then brought to neutral pH, chloride permeability was suppressed, and potassium permeability was activated. Both chloride and potassium permeability linearly correlated with the mass of ApoL1 in the reaction mixture, and both exhibited lipid selectivity, requiring the presence of negatively charged lipids for activity. Potassium, but not chloride, permease activity required the presence of calcium ions in both the association and activation steps. Direct assessment of ApoL1-lipid associations confirmed that ApoL1 stably associates with phospholipid vesicles, requiring low pH and the presence of negatively charged phospholipids for maximal binding. Intrinsic fluorescence of ApoL1 supported the presence of a significant structural transition when ApoL1 is mixed with lipids at low pH. This pH-switchable ion-selective permeability may explain the different effects of ApoL1 reported in intracellular and plasma membrane environments. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Permeability measuremens of brazilian Eucalyptus

Directory of Open Access Journals (Sweden)

Marcio Rogério da Silva

2010-09-01

Full Text Available The permeability of Brazilian Eucalyptus grandis and Eucalyptus citriodora wood was measured in a custom build gas analysis chamber in order to determine which species could be successfully treated with preservatives. Liquid permeability was tested using an emulsion of Neen oil and a control of distillated water. Air was used to test the gas phase permeability. For both Eucalyptus grandis and Eucalyptus citriodora, the longitudinal permeability of gas was shown to be about twice as great as the liquid phase permeability. No radial permeability was observed for either wood. The permeability of air and water through the sapwood of Eucalyptus grandis was greater than that through the sapwood of Eucalyptus citriodora. The permeability of neen oil preservative through the sapwood of Eucalyptus grandis was also greater than through the sapwood of E. Citradora, but the difference was not statistically significant. Scanning Electron Microscopy images showed that the distribution and obstruction in the vessels could be correlated with observed permeability properties. Irrespective of the causes of differences in permeability between the species, the fluid phase flux through the sapwood of both species was significant, indicating that both Eucalyptus grandis and Eucalyptus citriodora could be successfully treated with wood preservative.

A unique epigenetic signature is associated with active DNA replication loci in human embryonic stem cells.

Science.gov (United States)

Li, Bing; Su, Trent; Ferrari, Roberto; Li, Jing-Yu; Kurdistani, Siavash K

2014-02-01

The cellular epigenetic landscape changes as pluripotent stem cells differentiate to somatic cells or when differentiated cells transform to a cancerous state. These epigenetic changes are commonly correlated with differences in gene expression. Whether active DNA replication is also associated with distinct chromatin environments in these developmentally and phenotypically diverse cell types has not been known. Here, we used BrdU-seq to map active DNA replication loci in human embryonic stem cells (hESCs), normal primary fibroblasts and a cancer cell line, and correlated these maps to the epigenome. In all cell lines, the majority of BrdU peaks were enriched in euchromatin and at DNA repetitive elements, especially at microsatellite repeats, and coincided with previously determined replication origins. The most prominent BrdU peaks were shared between all cells but a sizable fraction of the peaks were specific to each cell type and associated with cell type-specific genes. Surprisingly, the BrdU peaks that were common to all cell lines were associated with H3K18ac, H3K56ac, and H4K20me1 histone marks only in hESCs but not in normal fibroblasts or cancer cells. Depletion of the histone acetyltransferases for H3K18 and H3K56 dramatically decreased the number and intensity of BrdU peaks in hESCs. Our data reveal a unique epigenetic signature that distinguishes active replication loci in hESCs from normal somatic or malignant cells.

Inflammasome Inhibition Suppresses Alveolar Cell Permeability Through Retention of Neuregulin-1 (NRG-1

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Rajanbabu Venugopal

2015-07-01

Full Text Available Background: Neuregulin (NRG-1-human epidermal receptor (HER-2 signaling pathway is a key regulator of IL-1β-mediated pulmonary inflammation and epithelial permeability. The inflammasome is a newly discovered molecular platform required for caspase-1 activation and maturation of IL-1β. However, the role of the inflammasome in NRG-1-HER2 signaling-mediated alveolar cell permeability is unknown. Methods: The inflammasome was activated or inhibited in THP-1 cells; supernatants from these cells were added to A549 cells and human small airway epithelial cells (HSAEC. The protein expression of NRG-1 and phospho-HER2 (pHER2 were measured by Western blot analysis and epithelial permeability was measured using Lucifer yellow dye. Results: Results reveal that alveolar permeability in A549 cells and HSAEC is increased when treated with supernatants of inflammasome-activated THP-1 cells. Alveolar permeability is significantly suppressed when treated with supernatant of inflammasome-inhibited THP-1 cells. Inflammasome-mediated permeability is decreased when A549 cells and HSAEC are pretreated with IL-1β receptor antagonist (IL-1βRA. In addition, HER2 kinase inhibitor AG825 or NRG-1 inhibitor TAPI inhibits inflammasome-mediated permeability in A549 cells and HSAEC demonstrating critical roles of IL-1β, NRG-1, and HER2 in inflammasome-mediated alveolar permeability. Conclusion: These findings suggest that inflammasome-induced alveolar cell permeability is mediated by NRG-1/HER2 signaling through IL-1β regulation.

Intestinal Permeability and Cellular Antioxidant Activity of Phenolic Compounds from Mango (Mangifera indica cv. Ataulfo Peels

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Ramón Pacheco-Ordaz

2018-02-01

Full Text Available Mango (Mangifera indica cv. Ataulfo peel contains bound phenolics that may be released by alkaline or acid hydrolysis and may be converted into less complex molecules. Free phenolics from mango cv. Ataulfo peel were obtained using a methanolic extraction, and their cellular antioxidant activity (CAA and permeability were compared to those obtained for bound phenolics released by alkaline or acid hydrolysis. Gallic acid was found as a simple phenolic acid after alkaline hydrolysis along with mangiferin isomers and quercetin as aglycone and glycosides. Only gallic acid, ethyl gallate, mangiferin, and quercetin were identified in the acid fraction. The acid and alkaline fractions showed the highest CAA (60.5% and 51.5% when tested at 125 µg/mL. The value of the apparent permeability coefficient (Papp across the Caco-2/HT-29 monolayer of gallic acid from the alkaline fraction was higher (2.61 × 10−6 cm/s than in the other fractions and similar to that obtained when tested pure (2.48 × 10−6 cm/s. In conclusion, mango peels contain bound phenolic compounds that, after their release, have permeability similar to pure compounds and exert an important CAA. This finding can be applied in the development of nutraceuticals using this important by-product from the mango processing industry.

Intestinal Permeability and Cellular Antioxidant Activity of Phenolic Compounds from Mango (Mangifera indica cv. Ataulfo) Peels

Science.gov (United States)

Pacheco-Ordaz, Ramón; González-Aguilar, Gustavo A.

2018-01-01

Mango (Mangifera indica cv. Ataulfo) peel contains bound phenolics that may be released by alkaline or acid hydrolysis and may be converted into less complex molecules. Free phenolics from mango cv. Ataulfo peel were obtained using a methanolic extraction, and their cellular antioxidant activity (CAA) and permeability were compared to those obtained for bound phenolics released by alkaline or acid hydrolysis. Gallic acid was found as a simple phenolic acid after alkaline hydrolysis along with mangiferin isomers and quercetin as aglycone and glycosides. Only gallic acid, ethyl gallate, mangiferin, and quercetin were identified in the acid fraction. The acid and alkaline fractions showed the highest CAA (60.5% and 51.5%) when tested at 125 µg/mL. The value of the apparent permeability coefficient (Papp) across the Caco-2/HT-29 monolayer of gallic acid from the alkaline fraction was higher (2.61 × 10−6 cm/s) than in the other fractions and similar to that obtained when tested pure (2.48 × 10−6 cm/s). In conclusion, mango peels contain bound phenolic compounds that, after their release, have permeability similar to pure compounds and exert an important CAA. This finding can be applied in the development of nutraceuticals using this important by-product from the mango processing industry. PMID:29419800

Crustal permeability

Science.gov (United States)

Gleeson, Tom; Ingebritsen, Steven E.

2016-01-01

Permeability is the primary control on fluid flow in the Earth’s crust and is key to a surprisingly wide range of geological processes, because it controls the advection of heat and solutes and the generation of anomalous pore pressures.  The practical importance of permeability – and the potential for large, dynamic changes in permeability – is highlighted by ongoing issues associated with hydraulic fracturing for hydrocarbon production (“fracking”), enhanced geothermal systems, and geologic carbon sequestration.  Although there are thousands of research papers on crustal permeability, this is the first book-length treatment.  This book bridges the historical dichotomy between the hydrogeologic perspective of permeability as a static material property and the perspective of other Earth scientists who have long recognized permeability as a dynamic parameter that changes in response to tectonism, fluid production, and geochemical reactions. 

Permeability prediction in chalks

DEFF Research Database (Denmark)

Alam, Mohammad Monzurul; Fabricius, Ida Lykke; Prasad, Manika

2011-01-01

The velocity of elastic waves is the primary datum available for acquiring information about subsurface characteristics such as lithology and porosity. Cheap and quick (spatial coverage, ease of measurement) information of permeability can be achieved, if sonic velocity is used for permeability p...... significantly using the effective specific surface as the fluid-flow concept. The FZI unit is appropriate for highly permeable sedimentary rocks such as sandstones and limestones that have small surface areas....

Usefulness of vitamin A binding protein as a marker for capillary endothelial permeability

Energy Technology Data Exchange (ETDEWEB)

Ishizaka, Akitoshi; Suzuki, Yukio; Kanazawa, Minoru; Kubo, Atsushi; Kawashiro, Takeo [Keio Univ., Tokyo (Japan). School of Medicine

1992-06-01

We performed a preliminary study to assess the usefulness of Vitamin A binding protein (VABP) as a gamma-camera marker for capillary endothelial permeability. We used a guinea pig model of endotoxin (LPS) induced acute lung injury. We calculated the concentration ratio of either {sup 125}I-albumin or {sup 125}I-VABP in lung tissue to that in plasma (tissue plasma ratio; T/P) as a parameter of capillary endothelial permeability. {sup 99m}Tc-diethylene triamine pentaacetic acid (DTPA) was used as marker for pulmonary interstitial volume. We estimated wet to dry lung weight ratio as a parameter of lung water accumulation (W/D). LPS increased the T/P of {sup 125}I-albumin and W/D, suggesting the development of permeability edema. The T/P for {sup 125}I-VABP was also increased, indicating that {sup 125}I-VABP can be used to detect elevated capillary endothelial permeability. In both groups, LPS and saline, the T/P was higher for {sup 125}I-VABP than for {sup 125}I-albumin. These data suggest that the pulmonary capillary endothelium is more permeable to VABP than albumin. (author).

Herbal medicines that benefit epidermal permeability barrier function

Directory of Open Access Journals (Sweden)

Lizhi Hu

2015-06-01

Full Text Available Epidermal permeability barrier function plays a critical role in regulating cutaneous functions. Hence, researchers have been searching for effective and affordable regimens to enhance epidermal permeability barrier function. In addition to topical stratum corneum lipids, peroxisome proliferator-activated receptor, and liver X receptor ligands, herbal medicines have been proven to benefit epidermal permeability barrier function in both normal and diseased skin, including atopic dermatitis, glucocorticoid-induced skin damage, and UVB-damaged skin. The potential mechanisms by which herbal medicines improve the permeability barrier include stimulation of epidermal differentiation, lipid production, antimicrobial peptide expression, and antioxidation. Therefore, utilization of herbal medicines could be a valuable alternative approach to enhance epidermal permeability barrier function in order to prevent and/or treat skin disorders associated with permeability barrier abnormalities.

Permeability Testing of Impacted Composite Laminates for Use on Reusable Launch Vehicles

Science.gov (United States)

Nettles, A. T.

2001-01-01

Since composite laminates are beginning to be identified for use in reusable launch vehicle propulsion systems, an understanding of their permeance is needed. A foreign object impact event can cause a localized area of permeability (leakage) in a polymer matrix composite, and it is the aim of this study to assess a method of quantifying permeability-after-impact results. A simple test apparatus is presented, and variables that could affect the measured values of permeability-after-impact were assessed. Once it was determined that valid numbers were being measured, a fiber/resin system was impacted at various impact levels and the resulting permeability measured, first with a leak check solution (qualitative) then using the new apparatus (quantitative). The results showed that as the impact level increased, so did the measured leakage. As the pressure to the specimen was increased, the leak rate was seen to increase in a nonlinear fashion for almost all the specimens tested.

Addressing the "Replication Crisis": Using Original Studies to Design Replication Studies with Appropriate Statistical Power.

Science.gov (United States)

Anderson, Samantha F; Maxwell, Scott E

2017-01-01

Psychology is undergoing a replication crisis. The discussion surrounding this crisis has centered on mistrust of previous findings. Researchers planning replication studies often use the original study sample effect size as the basis for sample size planning. However, this strategy ignores uncertainty and publication bias in estimated effect sizes, resulting in overly optimistic calculations. A psychologist who intends to obtain power of .80 in the replication study, and performs calculations accordingly, may have an actual power lower than .80. We performed simulations to reveal the magnitude of the difference between actual and intended power based on common sample size planning strategies and assessed the performance of methods that aim to correct for effect size uncertainty and/or bias. Our results imply that even if original studies reflect actual phenomena and were conducted in the absence of questionable research practices, popular approaches to designing replication studies may result in a low success rate, especially if the original study is underpowered. Methods correcting for bias and/or uncertainty generally had higher actual power, but were not a panacea for an underpowered original study. Thus, it becomes imperative that 1) original studies are adequately powered and 2) replication studies are designed with methods that are more likely to yield the intended level of power.

Magnetic permeability of stainless steel for use in accelerator beam transport systems

International Nuclear Information System (INIS)

Wilson, N.G.; Bunch, P.

1991-01-01

High-vacuum beam transport tubes are being designed for use in an accelerator under development at Los Alamos. In areas such as weld-heat-affected zones, the tubes will require localized magnetic permeability of less than 1.02. Seven austenitic stainless steel candidates, 304L, 310, 316L, 317LN, 20Cb-3, Nitronic 33, and Nitronic 40, have been evaluated to determine their permeability in cold-worked, annealed, and weld-affected zones. 310 and 20Cb-3 showed permeability after welding of less than 1.01. 1 ref., 1 fig., 1 tab

Chromium reduces the in vitro activity and fidelity of DNA replication mediated by the human cell DNA synthesome

International Nuclear Information System (INIS)

Dai Heqiao; Liu Jianying; Malkas, Linda H.; Catalano, Jennifer; Alagharu, Srilakshmi; Hickey, Robert J.

2009-01-01

Hexavalent chromium Cr(VI) is known to be a carcinogenic metal ion, with a complicated mechanism of action. It can be found within our environment in soil and water contaminated by manufacturing processes. Cr(VI) ion is readily taken up by cells, and is recognized to be both genotoxic and cytotoxic; following its reduction to the stable trivalent form of the ion, chromium(Cr(III)), within cells. This form of the ion is known to impede the activity of cellular DNA polymerase and polymerase-mediated DNA replication. Here, we report the effects of chromium on the activity and fidelity of the DNA replication process mediated by the human cell DNA synthesome. The DNA synthesome is a functional multiprotein complex that is fully competent to carry-out each phase of the DNA replication process. The IC 50 of Cr(III) toward the activity of DNA synthesome-associated DNA polymerases α, δ and ε is 15, 45 and 125 μM, respectively. Cr(III) inhibits synthesome-mediated DNA synthesis (IC 50 = 88 μM), and significantly reduces the fidelity of synthesome-mediated DNA replication. The mutation frequency induced by the different concentrations of Cr(III) ion used in our assays ranges from 2-13 fold higher than that which occurs spontaneously, and the types of mutations include single nucleotide substitutions, insertions, and deletions. Single nucleotide substitutions are the predominant type of mutation, and they occur primarily at GC base-pairs. Cr(III) ion produces a lower number of transition and a higher number of transversion mutations than occur spontaneously. Unlike Cr(III), Cr(VI) ion has little effect on the in vitro DNA synthetic activity and fidelity of the DNA synthesome, but does significantly inhibit DNA synthesis in intact cells. Cell growth and proliferation is also arrested by increasing concentrations of Cr(VI) ion. Our studies provide evidence indicating that the chromium ion induced decrease in the fidelity and activity of synthesome mediated DNA replication

DNA excision repair in permeable human fibroblasts

International Nuclear Information System (INIS)

Kaufmann, W.K.; Bodell, W.J.; Cleaver, J.E.

1983-01-01

U.v. irradiation of confluent human fibroblasts activated DNA repair, aspects of which were characterized in the cells after they were permeabilized. Incubation of intact cells for 20 min between irradiation and harvesting was necessary to obtain a maximum rate of reparative DNA synthesis. Cells harvested immediately after irradiation before repair was initiated displayed only a small stimulation of DNA synthesis, indicating that permeable cells have a reduced capacity to recognize pyrimidine dimers and activate repair. The distribution of sizes of DNA strands labeled during 10 min of reparative DNA synthesis resembled that of parental DNA. However, during a 60-min incubation of permeable cells at 37 degrees C, parental DNA and DNA labeled by reparative DNA synthesis were both cleaved to smaller sizes. Cleavage also occurred in unirradiated cells, indicating that endogenous nuclease was active during incubation. Repair patches synthesized in permeable cells displayed increased sensitivity to digestion by micrococcal nuclease. However, the change in sensitivity during a chase with unlabeled DNA precursors was small, suggesting that reassembly of nucleosome structure at sites of repair was impaired. To examine whether this deficiency was due to a preponderance of incomplete or unligated repair patches, 3H-labeled (repaired) DNA was purified, then digested with exonuclease III and nuclease S1 to probe for free 3' ends and single-stranded regions. About 85% of the [3H]DNA synthesized during a 10-min pulse resisted digestion, suggesting that a major fraction of the repair patches that were filled were also ligated. U.v. light-activated DNA synthesis in permeable cells, therefore, appears to represent the continuation of reparative gap-filling at sites of excision repair activated within intact cells. Gap-filling and ligation were comparatively efficient processes in permeable cells

An integrated approach to permeability modeling using micro-models

Energy Technology Data Exchange (ETDEWEB)

Hosseini, A.H.; Leuangthong, O.; Deutsch, C.V. [Society of Petroleum Engineers, Canadian Section, Calgary, AB (Canada)]|[Alberta Univ., Edmonton, AB (Canada)

2008-10-15

An important factor in predicting the performance of steam assisted gravity drainage (SAGD) well pairs is the spatial distribution of permeability. Complications that make the inference of a reliable porosity-permeability relationship impossible include the presence of short-scale variability in sand/shale sequences; preferential sampling of core data; and uncertainty in upscaling parameters. Micro-modelling is a simple and effective method for overcoming these complications. This paper proposed a micro-modeling approach to account for sampling bias, small laminated features with high permeability contrast, and uncertainty in upscaling parameters. The paper described the steps and challenges of micro-modeling and discussed the construction of binary mixture geo-blocks; flow simulation and upscaling; extended power law formalism (EPLF); and the application of micro-modeling and EPLF. An extended power-law formalism to account for changes in clean sand permeability as a function of macroscopic shale content was also proposed and tested against flow simulation results. There was close agreement between the model and simulation results. The proposed methodology was also applied to build the porosity-permeability relationship for laminated and brecciated facies of McMurray oil sands. Experimental data was in good agreement with the experimental data. 8 refs., 17 figs.

The permeability evolution of tuffisites and outgassing from dense rhyolitic magma

Science.gov (United States)

Heap, M. J.; Tuffen, H.; Wadsworth, F. B.; Reuschlé, T.; Castro, J. M.; Schipper, C. I.

2017-12-01

Recent observations of rhyolitic lava effusion from eruptions in Chile indicate that simultaneous pyroclastic venting facilitates outgassing. Venting from conduit-plugging lava domes is pulsatory and occurs through shallow fracture networks that deliver pyroclastic debris and exsolved gases to the surface. However, these fractures become blocked as the particulate fracture infill sinters viscously, thus drastically reducing permeability. Tuffisites, fossilized debris-filled fractures of this venting process, are abundant in pyroclastic material ejected during hybrid explosive-effusive activity. Dense tuffisite-hosting obsidian bombs ejected from Volcán Chaitén (Chile) in 2008 afford an opportunity to better understand the permeability evolution of tuffisites within low-permeability conduit plugs, wherein gas mobility is reliant upon fracture pathways. We use laboratory measurements of the permeability and porosity of tuffisites that preserve different degrees of sintering, combined with a grainsize-based sintering model and constraints on pressure-time paths from H2O diffusion, to place first-order constraints on tuffisite permeability evolution. Inferred timescales of sintering-driven tuffisite compaction and permeability loss, spanning minutes to hours, coincide with observed vent pulsations during hybrid rhyolitic activity and, more broadly, timescales of pressurization accompanying silicic lava dome extrusion. We therefore conclude that sintering exerts a first-order control on fracture-assisted outgassing from low-permeability, conduit-plugging silicic magma.

Glycerol and urea can be used to increase skin permeability in reduced hydration conditions.

Science.gov (United States)

Björklund, Sebastian; Engblom, Johan; Thuresson, Krister; Sparr, Emma

2013-12-18

The natural moisturizing factor (NMF) is a group of hygroscopic molecules that is naturally present in skin and protects from severe drying. Glycerol and urea are two examples of NMF components that are also used in skin care applications. In the present study, we investigate the influence of glycerol and urea on the permeability of a model drug (metronidazole, Mz) across excised pig skin membranes at different hydrating conditions. The degree of skin hydration is regulated by the gradient in water activity across the membrane, which in turn depends on the water activity of the formulation in contact with the skin membrane. Here, we determine the water activity of all formulations employed using an isothermal calorimetric method. Thus, the gradient in water activity is controlled by a novel experimental set-up with well-defined boundary conditions on both sides of the skin membrane. The results demonstrate that glycerol and urea can retain high steady state flux of Mz across skin membranes at dehydrating conditions, which otherwise would decrease the permeability due to dehydration. X-ray diffraction measurements are performed to give insight into the effects of glycerol and urea on SC molecular organization. The novel steady state flux results can be related to the observation that water, glycerol, and urea all affect the structural features of the SC molecular components in a similar manner. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Regulation of DNA replication in irradiated cells by trans-acting factors

International Nuclear Information System (INIS)

Wang, Y.; Huq, M.S.; Cheng, X.; Iliakis, G.

1995-01-01

We compared DNA replication activity in cytoplasmic extracts prepared from irradiated and nonirradiated HeLa cells using a simian virus 40 (SV40)-based in vitro replication assay. The assay measures semi-conservative DNA replication in a plasmid carrying the SV40 origin of replication and requires SV40 T antigen as the sole noncellular protein. The plasmid DNA used in the replication reaction is never exposed to radiation. We find that replication of plasmid DNA is significantly reduced when cytoplasmic extracts from irradiated cells are used. Since plasmid replication proceeds to completion in extracts from irradiated cells, the observed reduction in the overall replication activity is probably due to a reduction in the efficiency of initiation events. The degree of inhibition of DNA replication after exposure to 10, 30 and 50 Gy X rays as measured in vitro using this assay is similar to that measured in intact cells immediately before processing for extract preparation. These observations are compatible with the induction or activation by ionizing radiation of a factor(s) that inhibits in trans DNA replication. The results contribute to our understanding of the mechanism(s) developed by the cells to regulate DNA replication when exposed to clastogenic agents. Such processes may be of significance in the restoration of DNA integrity, and may define yet another checkpoint operating during S at the level of clusters of replicons. 26 refs., 4 figs

Pyrimidine Pool Disequilibrium Induced by a Cytidine Deaminase Deficiency Inhibits PARP-1 Activity, Leading to the Under Replication of DNA.

Directory of Open Access Journals (Sweden)

Simon Gemble

2015-07-01

Full Text Available Genome stability is jeopardized by imbalances of the dNTP pool; such imbalances affect the rate of fork progression. For example, cytidine deaminase (CDA deficiency leads to an excess of dCTP, slowing the replication fork. We describe here a novel mechanism by which pyrimidine pool disequilibrium compromises the completion of replication and chromosome segregation: the intracellular accumulation of dCTP inhibits PARP-1 activity. CDA deficiency results in incomplete DNA replication when cells enter mitosis, leading to the formation of ultrafine anaphase bridges between sister-chromatids at "difficult-to-replicate" sites such as centromeres and fragile sites. Using molecular combing, electron microscopy and a sensitive assay involving cell imaging to quantify steady-state PAR levels, we found that DNA replication was unsuccessful due to the partial inhibition of basal PARP-1 activity, rather than slower fork speed. The stimulation of PARP-1 activity in CDA-deficient cells restores replication and, thus, chromosome segregation. Moreover, increasing intracellular dCTP levels generates under-replication-induced sister-chromatid bridges as efficiently as PARP-1 knockdown. These results have direct implications for Bloom syndrome (BS, a rare genetic disease combining susceptibility to cancer and genomic instability. BS results from mutation of the BLM gene, encoding BLM, a RecQ 3'-5' DNA helicase, a deficiency of which leads to CDA downregulation. BS cells thus have a CDA defect, resulting in a high frequency of ultrafine anaphase bridges due entirely to dCTP-dependent PARP-1 inhibition and independent of BLM status. Our study describes previously unknown pathological consequences of the distortion of dNTP pools and reveals an unexpected role for PARP-1 in preventing DNA under-replication and chromosome segregation defects.

Increasing the permeability of Escherichia coli using MAC13243

DEFF Research Database (Denmark)

Muheim, Claudio; Götzke, Hansjörg; Eriksson, Anna U.

2017-01-01

molecules that make the outer membrane of Escherichia coli more permeable. We identified MAC13243, an inhibitor of the periplasmic chaperone LolA that traffics lipoproteins from the inner to the outer membrane. We observed that cells were (1) more permeable to the fluorescent probe 1-N...

The novel oral imatinib microemulsions: physical properties, cytotoxicity activities and improved Caco-2 cell permeability.

Science.gov (United States)

Gundogdu, Evren; Karasulu, Hatice Yesim; Koksal, Cinel; Karasulu, Ercüment

2013-01-01

The objective of this study was to formulate imatinib (IM) loaded to water-in-oil (w/o) microemulsions as an alternative formulation for cancer therapy and to evaluate the cytotoxic effect of microemulsions Caco-2 and MCF-7. Moreover, permeability studies were also performed with Caco-2 cells. W/o microemulsion systems were developed by using pseudo-ternary phase diagram. According to cytotoxicity studies, all formulations did not exert a cytotoxic effect on Caco-2 cells. Furthermore, all formulations had a significant cytotoxic effect on MCF-7 cells and the cytotoxic effect of M3IM was significantly more than that of other microemulsions and IM solution (p < 0.05). The permeability studies of IM across Caco-2 cells showed that permeability value from apical to basolateral was higher than permeability value of other formulations. In conclusion, the microemulsion formulations as a drug carrier, especially M3IM formulation, may be used as an effective alternative breast cancer therapy for oral delivery of IM.

Sub-core permeability and relative permeability characterization with Positron Emission Tomography

Science.gov (United States)

Zahasky, C.; Benson, S. M.

2017-12-01

This study utilizes preclinical micro-Positron Emission Tomography (PET) to image and quantify the transport behavior of pulses of a conservative aqueous radiotracer injected during single and multiphase flow experiments in a Berea sandstone core with axial parallel bedding heterogeneity. The core is discretized into streamtubes, and using the micro-PET data, expressions are derived from spatial moment analysis for calculating sub-core scale tracer flux and pore water velocity. Using the flux and velocity data, it is then possible to calculate porosity and saturation from volumetric flux balance, and calculate permeability and water relative permeability from Darcy's law. Full 3D simulations are then constructed based on this core characterization. Simulation results are compared with experimental results in order to test the assumptions of the simple streamtube model. Errors and limitations of this analysis will be discussed. These new methods of imaging and sub-core permeability and relative permeability measurements enable experimental quantification of transport behavior across scales.

Extremal dynamics in random replicator ecosystems

Energy Technology Data Exchange (ETDEWEB)

Kärenlampi, Petri P., E-mail: petri.karenlampi@uef.fi

2015-10-02

The seminal numerical experiment by Bak and Sneppen (BS) is repeated, along with computations with replicator models, including a greater amount of features. Both types of models do self-organize, and do obey power-law scaling for the size distribution of activity cycles. However species extinction within the replicator models interferes with the BS self-organized critical (SOC) activity. Speciation–extinction dynamics ruins any stationary state which might contain a steady size distribution of activity cycles. The BS-type activity appears as a dissimilar phenomenon in comparison to speciation–extinction dynamics in the replicator system. No criticality is found from the speciation–extinction dynamics. Neither are speciations and extinctions in real biological macroevolution known to contain any diverging distributions, or self-organization towards any critical state. Consequently, biological macroevolution probably is not a self-organized critical phenomenon. - Highlights: • Extremal Dynamics organizes random replicator ecosystems to two phases in fitness space. • Replicator systems show power-law scaling of activity. • Species extinction interferes with Bak–Sneppen type mutation activity. • Speciation–extinction dynamics does not show any critical phase transition. • Biological macroevolution probably is not a self-organized critical phenomenon.

Both cis and trans Activities of Foot-and-Mouth Disease Virus 3D Polymerase Are Essential for Viral RNA Replication.

Science.gov (United States)

Herod, Morgan R; Ferrer-Orta, Cristina; Loundras, Eleni-Anna; Ward, Joseph C; Verdaguer, Nuria; Rowlands, David J; Stonehouse, Nicola J

2016-08-01

The Picornaviridae is a large family of positive-sense RNA viruses that contains numerous human and animal pathogens, including foot-and-mouth disease virus (FMDV). The picornavirus replication complex comprises a coordinated network of protein-protein and protein-RNA interactions involving multiple viral and host-cellular factors. Many of the proteins within the complex possess multiple roles in viral RNA replication, some of which can be provided in trans (i.e., via expression from a separate RNA molecule), while others are required in cis (i.e., expressed from the template RNA molecule). In vitro studies have suggested that multiple copies of the RNA-dependent RNA polymerase (RdRp) 3D are involved in the viral replication complex. However, it is not clear whether all these molecules are catalytically active or what other function(s) they provide. In this study, we aimed to distinguish between catalytically active 3D molecules and those that build a replication complex. We report a novel nonenzymatic cis-acting function of 3D that is essential for viral-genome replication. Using an FMDV replicon in complementation experiments, our data demonstrate that this cis-acting role of 3D is distinct from the catalytic activity, which is predominantly trans acting. Immunofluorescence studies suggest that both cis- and trans-acting 3D molecules localize to the same cellular compartment. However, our genetic and structural data suggest that 3D interacts in cis with RNA stem-loops that are essential for viral RNA replication. This study identifies a previously undescribed aspect of picornavirus replication complex structure-function and an important methodology for probing such interactions further. Foot-and-mouth disease virus (FMDV) is an important animal pathogen responsible for foot-and-mouth disease. The disease is endemic in many parts of the world with outbreaks within livestock resulting in major economic losses. Propagation of the viral genome occurs within

Induction of UV-resistant DNA replication in Escherichia coli: Induced stable DNA replication as an SOS function

International Nuclear Information System (INIS)

Kogoma, T.; Torrey, T.A.; Connaughton, M.J.

1979-01-01

The striking similarity between the treatments that induce SOS functions and those that result in stable DNA replication (continuous DNA replication in the absence of protein synthesis) prompted us to examine the possibility of stable DNA replication being a recA + lexA + -dependent SOS function. In addition to the treatments previously reported, ultraviolet (UV) irradiation or treatment with mitomycin C was also found to induce stable DNA replication. The thermal treatment of tif-1 strains did not result in detectable levels of stable DNA replication, but nalidixic acid readily induced the activity in these strains. The induction of stable DNA replication with nalidixic acid was severely suppressed in tif-1 lex A mutant strains. The inhibitory activity of lexA3 was negated by the presence of the spr-5l mutation, an intragenic suppressor of lexA3. Induced stable DNA replication was found to be considerably more resistant to UV irradiation than normal replication both in a uvr A6 strain and a uvr + strain. The UV-resistant replication occurred mostly in the semiconservative manner. The possible roles of stable DNA replication in repair of damaged DNA are discussed. (orig.)

Evaluation of the Membrane Permeability (PAMPA and Skin) of Benzimidazoles with Potential Cannabinoid Activity and their Relation with the Biopharmaceutics Classification System (BCS)

OpenAIRE

Alvarez-Figueroa, M. Javiera; Pessoa-Mahana, C. David; Palavecino-González, M. Elisa; Mella-Raipán, Jaime; Espinosa-Bustos, Cristián; Lagos-Muñoz, Manuel E.

2011-01-01

The permeability of five benzimidazole derivates with potential cannabinoid activity was determined in two models of membranes, parallel artificial membrane permeability assay (PAMPA) and skin, in order to study the relationship of the physicochemical properties of the molecules and characteristics of the membranes with the permeability defined by the Biopharmaceutics Classification System. It was established that the PAMPA intestinal absorption method is a good predictor for classifying thes...

Recovery of ammonia and phosphate minerals from swine wastewater using gas-permeable membranes

Science.gov (United States)

Gas-permeable membrane technology is useful to recover ammonia from liquid manures. In this study, phosphorus (P) recovery via magnesium chloride precipitation was enhanced by combining it with ammonia recovery through gas-permeable membranes. Anaerobically digested swine effluent containing approx...

Evaluation of permeability and swelling pressure of compacted bentonite using a calcium hydroxide solution

International Nuclear Information System (INIS)

Aoyagi, Takayoshi; Maeda, Munehiro; Mihara, Morihiro; Tanaka, Masuhiro

1998-12-01

Tests to determine the swelling pressure, permeability, compressive strength and elastic modulus of Ca-Na exchanged bentonite, Na-bentonite and Ca-bentonite at the Power Reactor and Nuclear Fuel Development Corporation have mainly used distilled water. However, disposal facilities for TRU waste will use cementateous material for packaging, backfill as well as structural support. In this case, a large amount of calcium will dissolve in groundwater flowing through the cementateous material. Therefore, it is important to investigate the mechanical properties of bentonite in calcium-rich water as part of the disposal research program for TRU waste. In order to understand the effect of the chemical composition of water on the basic mechanical properties of bentonite - part of evaluating the disposal concepts for TRU waste disposal - we tested the permeability of compacted bentonite under saturated conditions using a calcium hydroxide solution. The aqueous solution represents water dominated by the calcium component. Na-bentonite, Ca-Na exchanged bentonite and Ca-bentonite were used for swelling pressure measurement tests and permeability testing. Measures of the maximum and equilibrium swelling pressure as well as permeability we obtained. The dry density of bentonite was varied between tests. Results show that swelling pressure and permeability are dependent on dry density. In separate tests using Ca-bentonite, the bentonite-mixing rate was varied as an independent parameter. Results show that there is little change in the swelling pressure and permeability between tests using calcium hydroxide solution and distilled water for all bentonite types. (author)

Staphylococcal SCCmec elements encode an active MCM-like helicase and thus may be replicative

Energy Technology Data Exchange (ETDEWEB)

Mir-Sanchis, Ignacio; Roman, Christina A.; Misiura, Agnieszka; Pigli, Ying Z.; Boyle-Vavra, Susan; Rice , Phoebe A. (UC)

2016-08-29

Methicillin-resistant Staphylococcus aureus (MRSA) is a public-health threat worldwide. Although the mobile genomic island responsible for this phenotype, staphylococcal cassette chromosome (SCC), has been thought to be nonreplicative, we predicted DNA-replication-related functions for some of the conserved proteins encoded by SCC. We show that one of these, Cch, is homologous to the self-loading initiator helicases of an unrelated family of genomic islands, that it is an active 3'-to-5' helicase and that the adjacent ORF encodes a single-stranded DNA–binding protein. Our 2.9-Å crystal structure of intact Cch shows that it forms a hexameric ring. Cch, like the archaeal and eukaryotic MCM-family replicative helicases, belongs to the pre–sensor II insert clade of AAA+ ATPases. Additionally, we found that SCC elements are part of a broader family of mobile elements, all of which encode a replication initiator upstream of their recombinases. Replication after excision would enhance the efficiency of horizontal gene transfer.

Permeability of gloves used in nuclear medicine departments to [(99m)Tc]-pertechnetate and [(18)F]-fluorodeoxyglucose: radiation protection considerations.

Science.gov (United States)

Ridone, S; Matheoud, R; Valzano, S; Di Martino, R; Vigna, L; Brambilla, M

2013-09-01

In order to evaluate the safety of the individual protection devices, the permeability of four different types of disposable gloves, commonly used in hospitals, was tested in relation to [(99m)Tc]-pertechnetate and to [(18)F]-fluorodeoxyglucose ([(18)F]-FDG). From these radiopharmaceutical solutions, a drop was deposited on the external surface of the glove which was opened and stretched with the external surface placed upward. The smear test technique permitted to evaluate the activity onto the inner surface of the glove at different times. The smear tests were measured in a well sodium iodide detector calibrated in efficiency for (99m)Tc and (18)F. The permeability was tested on ten samples of each type of gloves and was expressed as the ratio of the activity onto the inner surface at each time interval to the activity deposited on the external surface of the glove. For each type of gloves and for each sampling time, mean value, standard deviation and percentage coefficient of variation of permeability were evaluated. One type of gloves showed a low resistance to permeation of both radiopharmaceuticals, while another one only to pertechnetate. The other gloves were good performers. The results of this study suggest to test permeability for gloves used for handling radiopharmaceuticals, before their adoption in the clinical routine. This practice will provide a more careful service of radiation protection for nuclear medicine department staff. Copyright © 2013 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Relative Permeability of Fractured Rock

Energy Technology Data Exchange (ETDEWEB)

Mark D. Habana

2002-06-30

Contemporary understanding of multiphase flow through fractures is limited. Different studies using synthetic fractures and various fluids have yielded different relative permeability-saturation relations. This study aimed to extend the understanding of multiphase flow by conducting nitrogen-water relative permeability experiments on a naturally-fractured rock from The Geysers geothermal field. The steady-state approach was used. However, steady state was achieved only at the endpoint saturations. Several difficulties were encountered that are attributed to phase interference and changes in fracture aperture and surface roughness, along with fracture propagation/initiation. Absolute permeabilities were determined using nitrogen and water. The permeability values obtained change with the number of load cycles. Determining the absolute permeability of a core is especially important in a fractured rock. The rock may change as asperities are destroyed and fractures propagate or st rain harden as the net stresses vary. Pressure spikes occurred in water a solute permeability experiments. Conceptual models of an elastic fracture network can explain the pressure spike behavior. At the endpoint saturations the water relative permeabilities obtained are much less than the nitrogen gas relative permeabilities. Saturations were determined by weighing and by resistivity calculations. The resistivity-saturation relationship developed for the core gave saturation values that differ by 5% from the value determined by weighing. Further work is required to complete the relative permeability curve. The steady-state experimental approach encountered difficulties due to phase interference and fracture change. Steady state may not be reached until an impractical length of time. Thus, unsteady-state methods should be pursued. In unsteady-state experiments the challenge will be in quantifying rock fracture change in addition to fluid flow changes.

Reservoir rock permeability prediction using support vector regression in an Iranian oil field

International Nuclear Information System (INIS)

Saffarzadeh, Sadegh; Shadizadeh, Seyed Reza

2012-01-01

Reservoir permeability is a critical parameter for the evaluation of hydrocarbon reservoirs. It is often measured in the laboratory from reservoir core samples or evaluated from well test data. The prediction of reservoir rock permeability utilizing well log data is important because the core analysis and well test data are usually only available from a few wells in a field and have high coring and laboratory analysis costs. Since most wells are logged, the common practice is to estimate permeability from logs using correlation equations developed from limited core data; however, these correlation formulae are not universally applicable. Recently, support vector machines (SVMs) have been proposed as a new intelligence technique for both regression and classification tasks. The theory has a strong mathematical foundation for dependence estimation and predictive learning from finite data sets. The ultimate test for any technique that bears the claim of permeability prediction from well log data is the accurate and verifiable prediction of permeability for wells where only the well log data are available. The main goal of this paper is to develop the SVM method to obtain reservoir rock permeability based on well log data. (paper)

Permeability, storage and hydraulic diffusivity controlled by earthquakes

Science.gov (United States)

Brodsky, E. E.; Fulton, P. M.; Xue, L.

2016-12-01

Earthquakes can increase permeability in fractured rocks. In the farfield, such permeability increases are attributed to seismic waves and can last for months after the initial earthquake. Laboratory studies suggest that unclogging of fractures by the transient flow driven by seismic waves is a viable mechanism. These dynamic permeability increases may contribute to permeability enhancement in the seismic clouds accompanying hydraulic fracking. Permeability enhancement by seismic waves could potentially be engineered and the experiments suggest the process will be most effective at a preferred frequency. We have recently observed similar processes inside active fault zones after major earthquakes. A borehole observatory in the fault that generated the M9.0 2011 Tohoku earthquake reveals a sequence of temperature pulses during the secondary aftershock sequence of an M7.3 aftershock. The pulses are attributed to fluid advection by a flow through a zone of transiently increased permeability. Directly after the M7.3 earthquake, the newly damaged fault zone is highly susceptible to further permeability enhancement, but ultimately heals within a month and becomes no longer as sensitive. The observation suggests that the newly damaged fault zone is more prone to fluid pulsing than would be expected based on the long-term permeability structure. Even longer term healing is seen inside the fault zone of the 2008 M7.9 Wenchuan earthquake. The competition between damage and healing (or clogging and unclogging) results in dynamically controlled permeability, storage and hydraulic diffusivity. Recent measurements of in situ fault zone architecture at the 1-10 meter scale suggest that active fault zones often have hydraulic diffusivities near 10-2 m2/s. This uniformity is true even within the damage zone of the San Andreas fault where permeability and storage increases balance each other to achieve this value of diffusivity over a 400 m wide region. We speculate that fault zones

[Study on effect of pH on rectum permeability of active ingredients in Reduning suppositories in vitro].

Science.gov (United States)

Yan, Ming; Wei, Ying-chun; Meng, Jin; Xu, Dian-hong; Wu, Yun; Xiao, Wei

2015-04-01

To investigate the effect of different pH on rectum permeability of chlorogenic acid and geniposide. Four kinds of Reduning suppositories of different pH were separated and put into the rectum to study the suppositories in vitro and the content of chlorogenic acid and geniposide samples was determined by HPLC to calculate the permeation in 24 hours. With increase of pH within 2.5-7.4, the steady state flux of chlorogenic acid was increased, but the steady state flux of geniposidesamples was steady. Adjusted the pH can increase the rectum permeability of active ingredients in Reduning auppositories.

Predicting carbonate permeabilities from wireline logs using a back-propagation neural network

International Nuclear Information System (INIS)

Wiener, J.M.; Moll, R.F.; Rogers, J.A.

1991-01-01

This paper explores the applicability of using Neural Networks to aid in the determination of carbonate permeability from wireline logs. Resistivity, interval transit time, neutron porosity, and bulk density logs form Texaco's Stockyard Creek Oil field were used as input to a specially designed neural network to predict core permeabilities in this carbonate reservoir. Also of interest was the comparison of the neural network's results to those of standard statistical techniques. The process of developing the neural network for this problem has shown that a good understanding of the data is required when creating the training set from which the network learns. This network was trained to learn core permeabilities from raw and transformed log data using a hyperbolic tangent transfer function and a sum of squares global error function. Also, it required two hidden layers to solve this particular problem

Mechanisms of DNA replication termination.

Science.gov (United States)

Dewar, James M; Walter, Johannes C

2017-08-01

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

Using soft computing techniques to predict corrected air permeability using Thomeer parameters, air porosity and grain density

Science.gov (United States)

Nooruddin, Hasan A.; Anifowose, Fatai; Abdulraheem, Abdulazeez

2014-03-01

Soft computing techniques are recently becoming very popular in the oil industry. A number of computational intelligence-based predictive methods have been widely applied in the industry with high prediction capabilities. Some of the popular methods include feed-forward neural networks, radial basis function network, generalized regression neural network, functional networks, support vector regression and adaptive network fuzzy inference system. A comparative study among most popular soft computing techniques is presented using a large dataset published in literature describing multimodal pore systems in the Arab D formation. The inputs to the models are air porosity, grain density, and Thomeer parameters obtained using mercury injection capillary pressure profiles. Corrected air permeability is the target variable. Applying developed permeability models in recent reservoir characterization workflow ensures consistency between micro and macro scale information represented mainly by Thomeer parameters and absolute permeability. The dataset was divided into two parts with 80% of data used for training and 20% for testing. The target permeability variable was transformed to the logarithmic scale as a pre-processing step and to show better correlations with the input variables. Statistical and graphical analysis of the results including permeability cross-plots and detailed error measures were created. In general, the comparative study showed very close results among the developed models. The feed-forward neural network permeability model showed the lowest average relative error, average absolute relative error, standard deviations of error and root means squares making it the best model for such problems. Adaptive network fuzzy inference system also showed very good results.

A new water permeability measurement method for unsaturated tight materials using saline solutions

International Nuclear Information System (INIS)

Malinsky, Laurent; Talandier, Jean

2012-01-01

Document available in extended abstract form only. Relative water permeability of material in a radioactive waste disposal is a key parameter to simulate and predict saturation state evolution. In this paper we present a new measurement method and the results obtained for Callovo-Oxfordian (Cox) clay-stone, host rock of the underground Andra laboratory at Bure (Meuse/Haute-Marne). Relative water permeability of such a low permeability rock as Cox clay-stone has been measured up to now by an indirect method. It consists in submitting a rock sample to successive relative humidity steps imposed by saline solutions. The transient mass variation during each step and the mass at hydric equilibrium are interpreted generally by using an inverse analysis method. The water relative permeability function of water saturation is derived from water diffusion coefficient evolution and water retention curve. The proposed new method consists in directly measuring the water flux across a flat cylindrical submitted to a relative humidity gradient. Two special cells have been developed. The tightness of the lateral sample surface is insured by crushing a polyurethane ring surrounding the sample set in an aluminium device placed over a Plexiglas vessel filled with a saline solution. One of the cells is designed to allow humidity measurement in the cell. These cells can also be used to measure the relative humidity produced by a saline solution or by an unsaturated material. During a permeability measurement, the cell with the sample to be tested is continuously weighted in a Plexiglas box in which a saline solution imposes a different relative humidity at the upper sample face. The experimental set-up is shown on Figure 1. The mean permeability of the sample is proportional to the rate of mass variation when steady state is reached. The result of one test is shown on Figure 2(a). Twenty four permeability measurements have been performed on four argillite samples of 15 mm in height and

Intracellular Detection of Viral Transcription and Replication Using RNA FISH

Science.gov (United States)

2016-05-26

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

Investigation clogging dynamic of permeable pavement systems using embedded sensors

Science.gov (United States)

Permeable pavement is a stormwater control measure commonly selected in both new and retrofit applications. However, there is limited information about the clogging mechanism of these systems that effects the infiltration. A permeable pavement site located at the Seitz Elementary...

Suppressing active replication of a live attenuated simian immunodeficiency virus vaccine does not abrogate protection from challenge

Energy Technology Data Exchange (ETDEWEB)

Gabriel, Benjamin; Fiebig, Uwe; Hohn, Oliver [Robert Koch-Institut, Berlin (Germany); Plesker, Roland; Coulibaly, Cheick; Cichutek, Klaus; Mühlebach, Michael D. [Paul-Ehrlich-Institut, Langen (Germany); Bannert, Norbert; Kurth, Reinhard [Robert Koch-Institut, Berlin (Germany); Norley, Stephen, E-mail: NorleyS@rki.de [Robert Koch-Institut, Berlin (Germany)

2016-02-15

Although safety concerns preclude the use of live attenuated HIV vaccines in humans, they provide a useful system for identifying the elusive correlates of protective immunity in the SIV/macaque animal model. However, a number of pieces of evidence suggest that protection may result from prior occupancy of susceptible target cells by the vaccine virus rather than the immune response. To address this, we developed a Nef-deletion variant of an RT-SHIV whose active replication could be shut off by treatment with RT-inhibitors. Groups of macaques were inoculated with the ∆Nef-RT-SHIV and immune responses allowed to develop before antiretroviral treatment and subsequent challenge with wild-type SIVmac239. Vaccinated animals either resisted infection fully or significantly controlled the subsequent viremia. However, there was no difference between animals undergoing replication of the vaccine virus and those without. This strongly suggests that competition for available target cells does not play a role in protection. - Highlights: • A Nef-deleted RT-SHIV was used as a live attenuated vaccine in macaques. • Vaccine virus replication was shut down to investigate its role in protection. • Ongoing vaccine virus replication did not appear to be necessary for protection. • An analysis of T- and B-cell responses failed to identify a correlate of protection.

Suppressing active replication of a live attenuated simian immunodeficiency virus vaccine does not abrogate protection from challenge

International Nuclear Information System (INIS)

Gabriel, Benjamin; Fiebig, Uwe; Hohn, Oliver; Plesker, Roland; Coulibaly, Cheick; Cichutek, Klaus; Mühlebach, Michael D.; Bannert, Norbert; Kurth, Reinhard; Norley, Stephen

2016-01-01

Although safety concerns preclude the use of live attenuated HIV vaccines in humans, they provide a useful system for identifying the elusive correlates of protective immunity in the SIV/macaque animal model. However, a number of pieces of evidence suggest that protection may result from prior occupancy of susceptible target cells by the vaccine virus rather than the immune response. To address this, we developed a Nef-deletion variant of an RT-SHIV whose active replication could be shut off by treatment with RT-inhibitors. Groups of macaques were inoculated with the ∆Nef-RT-SHIV and immune responses allowed to develop before antiretroviral treatment and subsequent challenge with wild-type SIVmac239. Vaccinated animals either resisted infection fully or significantly controlled the subsequent viremia. However, there was no difference between animals undergoing replication of the vaccine virus and those without. This strongly suggests that competition for available target cells does not play a role in protection. - Highlights: • A Nef-deleted RT-SHIV was used as a live attenuated vaccine in macaques. • Vaccine virus replication was shut down to investigate its role in protection. • Ongoing vaccine virus replication did not appear to be necessary for protection. • An analysis of T- and B-cell responses failed to identify a correlate of protection.

Perturbation of DNA replication and cell cycle progression by commonly used [3H]thymidine labeling protocols

International Nuclear Information System (INIS)

Hoy, C.A.; Lewis, E.D.; Schimke, R.T.

1990-01-01

The effect of tritiated thymidine incorporation on DNA replication was studied in Chinese hamster ovary cells. Rapidly eluting (small) DNA from cells labeled with 2 microCi of [ 3 H]thymidine per ml (200 microCi/mmol) for 60 min matured to a large nonelutable size within approximately 2 to 4 h, as measured by the alkaline elution technique. However, DNA from cells exposed to 10 microCi of [ 3 H]thymidine per ml (66 microCi/mmol) was more rapidly eluting initially and did not mature to a nonelutable size during subsequent incubation. Semiconservative DNA replication measured by cesium chloride gradient analysis of bromodeoxyuridine-substituted DNA was also found to be affected by the final specific activity of the [ 3 H]thymidine used in the labeling protocol. Dramatic cell cycle perturbations accompanied these effects on DNA replication, suggesting that labeling protocols commonly used to study DNA metabolism produce aberrant DNA replication and subsequent cell cycle perturbations

Rebamipide suppresses diclofenac-induced intestinal permeability via mitochondrial protection in mice.

Science.gov (United States)

Diao, Lei; Mei, Qiao; Xu, Jian-Ming; Liu, Xiao-Chang; Hu, Jing; Jin, Juan; Yao, Qiang; Chen, Mo-Li

2012-03-14

To investigate the protective effect and mechanism of rebamipide on small intestinal permeability induced by diclofenac in mice. Diclofenac (2.5 mg/kg) was administered once daily for 3 d orally. A control group received the vehicle by gavage. Rebamipide (100 mg/kg, 200 mg/kg, 400 mg/kg) was administered intragastrically once a day for 3 d 4 h after diclofenac administration. Intestinal permeability was evaluated by Evans blue and the FITC-dextran method. The ultrastructure of the mucosal barrier was evaluated by transmission electron microscopy (TEM). Mitochondrial function including mitochondrial swelling, mitochondrial membrane potential, mitochondrial nicotinamide adenine dinucleotide-reduced (NADH) levels, succinate dehydrogenase (SDH) and ATPase activities were measured. Small intestinal mucosa was collected for assessment of malondialdehyde (MDA) content and myeloperoxidase (MPO) activity. Compared with the control group, intestinal permeability was significantly increased in the diclofenac group, which was accompanied by broken tight junctions, and significant increases in MDA content and MPO activity. Rebamipide significantly reduced intestinal permeability, improved inter-cellular tight junctions, and was associated with decreases in intestinal MDA content and MPO activity. At the mitochondrial level, rebamipide increased SDH and ATPase activities, NADH level and decreased mitochondrial swelling. Increased intestinal permeability induced by diclofenac can be attenuated by rebamipide, which partially contributed to the protection of mitochondrial function.

Clinical research on high oxygen permeable contact lens used after photorefractive keratectomy surgery

Directory of Open Access Journals (Sweden)

Hao-Jiang Yang

2013-07-01

Full Text Available AIM: To evaluate the outcome of high oxygen permeable contact lens used after photorefractive keratectomy(PRKsurgery.METHODS: Totally 95 patients(190 eyesafter PRK were included. Patients were randomly assigned to wear high oxygen permeable contact lens in one eye and normal lens in the fellow eye after surgery. The subjective symptoms and corneal epithelial status after PRK were evaluated. Uncorrected visual acuity(UCVAand haze were assessed at 6 months after PRK.RESULTS: Complaints of blurred vision, pain and photophobia were statistically more among the normal lens group than high oxygen permeable contact lens group(PPP=0.35. There was no difference in UCVA and haze 6 months after surgery(P=0.55. CONCLUSION: High oxygen permeable contact lens can significantly produce less the corneal irritated symptoms, reduce the discomfort feeling and promote healing of corneal epithelium after PRK.

DATABASE OF MIGRATION AND REPLICATION WITH ORACLE GOLDEN GATE

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Suharjito Suharjito

2014-10-01

Full Text Available The main goal of this research is to analyze and design a database configuration of migration and replication in PT Metro Batavia. Research methodologies used in this research are data collecting, analysis and design model. Data collecting method is conducted with library research and direct survey in the company. Analysis method is conducted by analyzing hangar system, migration and reflection process and the available problems. Design method is conducted by designing a prototype for migration process with the implementation of Oracle SQL Developer and replication process with implementation of Oracle Golden Gate. The result of this research is a prototype for configuration of migration and replication process by using Oracle Golden Gate, which can produce two sets of identical data for the purpose of backup and recovery, and also design a simple tool that is expected to help active-active or active-passive replication process. The conclusion of this research is migration process of MySQL database to Oracle database by using Oracle Golden Gate hasn’t been conducted, because Oracle Golden Gate still has bug related to binary log, so database of migration is conducted by using Oracle Golden Gate. However, replication of bi-directional in between database of Oracle by using Oracle SQL Developer can guarantee data availability and reduce work burden from primary database.

A 3'-end structure in RNA2 of a crinivirus is essential for viral RNA synthesis and contributes to replication-associated translation activity.

Science.gov (United States)

Mongkolsiriwattana, Chawin; Zhou, Jaclyn S; Ng, James C K

2016-10-03

The terminal ends in the genome of RNA viruses contain features that regulate viral replication and/or translation. We have identified a Y-shaped structure (YSS) in the 3' terminal regions of the bipartite genome of Lettuce chlorosis virus (LCV), a member in the genus Crinivirus (family Closteroviridae). The YSS is the first in this family of viruses to be determined using Selective 2'-Hydroxyl Acylation Analyzed by Primer Extension (SHAPE). Using luciferase constructs/replicons, in vivo and in vitro assays showed that the 5' and YSS-containing 3' terminal regions of LCV RNA1 supported translation activity. In contrast, similar regions from LCV RNA2, including those upstream of the YSS, did not. LCV RNA2 mutants with nucleotide deletions or replacements that affected the YSS were replication deficient. In addition, the YSS of LCV RNA1 and RNA2 were interchangeable without affecting viral RNA synthesis. Translation and significant replication were observed for specific LCV RNA2 replicons only in the presence of LCV RNA1, but both processes were impaired when the YSS and/or its upstream region were incomplete or altered. These results are evidence that the YSS is essential to the viral replication machinery, and contributes to replication enhancement and replication-associated translation activity in the RNA2 replicons.

AAV-mediated delivery of zinc finger nucleases targeting hepatitis B virus inhibits active replication.

Directory of Open Access Journals (Sweden)

Nicholas D Weber

Full Text Available Despite an existing effective vaccine, hepatitis B virus (HBV remains a major public health concern. There are effective suppressive therapies for HBV, but they remain expensive and inaccessible to many, and not all patients respond well. Furthermore, HBV can persist as genomic covalently closed circular DNA (cccDNA that remains in hepatocytes even during otherwise effective therapy and facilitates rebound in patients after treatment has stopped. Therefore, the need for an effective treatment that targets active and persistent HBV infections remains. As a novel approach to treat HBV, we have targeted the HBV genome for disruption to prevent viral reactivation and replication. We generated 3 zinc finger nucleases (ZFNs that target sequences within the HBV polymerase, core and X genes. Upon the formation of ZFN-induced DNA double strand breaks (DSB, imprecise repair by non-homologous end joining leads to mutations that inactivate HBV genes. We delivered HBV-specific ZFNs using self-complementary adeno-associated virus (scAAV vectors and tested their anti-HBV activity in HepAD38 cells. HBV-ZFNs efficiently disrupted HBV target sites by inducing site-specific mutations. Cytotoxicity was seen with one of the ZFNs. scAAV-mediated delivery of a ZFN targeting HBV polymerase resulted in complete inhibition of HBV DNA replication and production of infectious HBV virions in HepAD38 cells. This effect was sustained for at least 2 weeks following only a single treatment. Furthermore, high specificity was observed for all ZFNs, as negligible off-target cleavage was seen via high-throughput sequencing of 7 closely matched potential off-target sites. These results show that HBV-targeted ZFNs can efficiently inhibit active HBV replication and suppress the cellular template for HBV persistence, making them promising candidates for eradication therapy.

Relationship between intestinal permeability to [51Cr]EDTA and inflammatory activity in asymptomatic patients with Crohn's disease

International Nuclear Information System (INIS)

Pironi, L.; Miglioli, M.; Ruggeri, E.; Levorato, M.; Dallasta, M.A.; Corbelli, C.; Nibali, M.G.; Barbara, L.

1990-01-01

The relationship between intestinal permeability to an oral dose (100 mu Ci) of [51CR]EDTA and the inflammatory activity of Crohn's disease was studied in 63 adult patients (32 unresected and 31 resected) who underwent 162 evaluations. The results of the [51CR]EDTA test were compared with the serum levels of the acute-phase reactant proteins (APRP) and with the result of the [111In]leukocyte scanning, respectively, as an indirect and direct method to assess intestinal inflammation. In a group of healthy adult controls, the upper normal value for the 24-hr urinary [51CR]EDTA excretion was 3.61 (97.5% percentile) and the mean coefficient of variation was 21%. Sensitivity and specificity of the [51CR]EDTA test in identifying active inflammation expressed by increased serum levels of APRP were, respectively, 97% and 54% in the unresected group and 68% and 52% in the resected group of patients. The low specificity of the test was due to the presence of increased [51CR]EDTA urinary excretion in about half the cases with normal serum levels of APRP. The [111In]leukocyte scanning was performed in a subgroup of 11 patients (three unresected and eight resected) with normal serum levels of APRP, six with increased and five with normal [51CR]EDTA urinary excretion. All six patients with increased intestinal permeability had a positive 111In image of mild to moderate degree of activity. A positive 111In scan was present in two of the five patients with normal permeability; these were two resected patients

Compact rock material gas permeability properties

Energy Technology Data Exchange (ETDEWEB)

Wang, Huanling, E-mail: whl_hm@163.com [Key Laboratory of Coastal Disaster and Defence, Ministry of Education, Hohai University, Nanjing 210098 (China); LML, University of Lille, Cite Scientifique, 59655 Villeneuve d’Ascq (France); Xu, Weiya; Zuo, Jing [Institutes of Geotechnical Engineering, Hohai University, Nanjing 210098 (China)

2014-09-15

Natural compact rocks, such as sandstone, granite, and rock salt, are the main materials and geological environment for storing underground oil, gas, CO{sub 2,} shale gas, and radioactive waste because they have extremely low permeabilities and high mechanical strengths. Using the inert gas argon as the fluid medium, the stress-dependent permeability and porosity of monzonitic granite and granite gneiss from an underground oil storage depot were measured using a permeability and porosity measurement system. Based on the test results, models for describing the relationships among the permeability, porosity, and confining pressure of rock specimens were analyzed and are discussed. A power law is suggested to describe the relationship between the stress-dependent porosity and permeability; for the monzonitic granite and granite gneiss (for monzonitic granite (A-2), the initial porosity is approximately 4.05%, and the permeability is approximately 10{sup −19} m{sup 2}; for the granite gneiss (B-2), the initial porosity is approximately 7.09%, the permeability is approximately 10{sup −17} m{sup 2}; and the porosity-sensitivity exponents that link porosity and permeability are 0.98 and 3.11, respectively). Compared with moderate-porosity and high-porosity rocks, for which φ > 15%, low-porosity rock permeability has a relatively lower sensitivity to stress, but the porosity is more sensitive to stress, and different types of rocks show similar trends. From the test results, it can be inferred that the test rock specimens’ permeability evolution is related to the relative particle movements and microcrack closure.

Permeability During Magma Expansion and Compaction

Science.gov (United States)

Gonnermann, Helge. M.; Giachetti, Thomas; Fliedner, Céline; Nguyen, Chinh T.; Houghton, Bruce F.; Crozier, Joshua A.; Carey, Rebecca J.

2017-12-01

Plinian lapilli from the 1060 Common Era Glass Mountain rhyolitic eruption of Medicine Lake Volcano, California, were collected and analyzed for vesicularity and permeability. A subset of the samples were deformed at a temperature of 975°, under shear and normal stress, and postdeformation porosities and permeabilities were measured. Almost all undeformed samples fall within a narrow range of vesicularity (0.7-0.9), encompassing permeabilities between approximately 10-15 m2 and 10-10 m2. A percolation threshold of approximately 0.7 is required to fit the data by a power law, whereas a percolation threshold of approximately 0.5 is estimated by fitting connected and total vesicularity using percolation modeling. The Glass Mountain samples completely overlap with a range of explosively erupted silicic samples, and it remains unclear whether the erupting magmas became permeable at porosities of approximately 0.7 or at lower values. Sample deformation resulted in compaction and vesicle connectivity either increased or decreased. At small strains permeability of some samples increased, but at higher strains permeability decreased. Samples remain permeable down to vesicularities of less than 0.2, consistent with a potential hysteresis in permeability-porosity between expansion (vesiculation) and compaction (outgassing). We attribute this to retention of vesicle interconnectivity, albeit at reduced vesicle size, as well as bubble coalescence during shear deformation. We provide an equation that approximates the change in permeability during compaction. Based on a comparison with data from effusively erupted silicic samples, we propose that this equation can be used to model the change in permeability during compaction of effusively erupting magmas.

A Molecular Toolbox to Engineer Site-Specific DNA Replication Perturbation.

Science.gov (United States)

Larsen, Nicolai B; Hickson, Ian D; Mankouri, Hocine W

2018-01-01

Site-specific arrest of DNA replication is a useful tool for analyzing cellular responses to DNA replication perturbation. The E. coli Tus-Ter replication barrier can be reconstituted in eukaryotic cells as a system to engineer an unscheduled collision between a replication fork and an "alien" impediment to DNA replication. To further develop this system as a versatile tool, we describe a set of reagents and a detailed protocol that can be used to engineer Tus-Ter barriers into any locus in the budding yeast genome. Because the Tus-Ter complex is a bipartite system with intrinsic DNA replication-blocking activity, the reagents and protocols developed and validated in yeast could also be optimized to engineer site-specific replication fork barriers into other eukaryotic cell types.

A Molecular Toolbox to Engineer Site-Specific DNA Replication Perturbation

DEFF Research Database (Denmark)

Larsen, Nicolai B; Hickson, Ian D; Mankouri, Hocine W

2018-01-01

" impediment to DNA replication. To further develop this system as a versatile tool, we describe a set of reagents and a detailed protocol that can be used to engineer Tus-Ter barriers into any locus in the budding yeast genome. Because the Tus-Ter complex is a bipartite system with intrinsic DNA replication......Site-specific arrest of DNA replication is a useful tool for analyzing cellular responses to DNA replication perturbation. The E. coli Tus-Ter replication barrier can be reconstituted in eukaryotic cells as a system to engineer an unscheduled collision between a replication fork and an "alien......-blocking activity, the reagents and protocols developed and validated in yeast could also be optimized to engineer site-specific replication fork barriers into other eukaryotic cell types....

Phosphopeptide binding by Sld3 links Dbf4-dependent kinase to MCM replicative helicase activation.

Science.gov (United States)

Deegan, Tom D; Yeeles, Joseph Tp; Diffley, John Fx

2016-05-02

The initiation of eukaryotic DNA replication requires the assembly of active CMG (Cdc45-MCM-GINS) helicases at replication origins by a set of conserved and essential firing factors. This process is controlled during the cell cycle by cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK), and in response to DNA damage by the checkpoint kinase Rad53/Chk1. Here we show that Sld3, previously shown to be an essential CDK and Rad53 substrate, is recruited to the inactive MCM double hexamer in a DDK-dependent manner. Sld3 binds specifically to DDK-phosphorylated peptides from two MCM subunits (Mcm4, 6) and then recruits Cdc45. MCM mutants that cannot bind Sld3 or Sld3 mutants that cannot bind phospho-MCM or Cdc45 do not support replication. Moreover, phosphomimicking mutants in Mcm4 and Mcm6 bind Sld3 without DDK and facilitate DDK-independent replication. Thus, Sld3 is an essential "reader" of DDK phosphorylation, integrating signals from three distinct protein kinase pathways to coordinate DNA replication during S phase. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.

Intestinal permeability study of minoxidil: assessment of minoxidil as a high permeability reference drug for biopharmaceutics classification.

Science.gov (United States)

Ozawa, Makoto; Tsume, Yasuhiro; Zur, Moran; Dahan, Arik; Amidon, Gordon L

2015-01-05

The purpose of this study was to evaluate minoxidil as a high permeability reference drug for Biopharmaceutics Classification System (BCS). The permeability of minoxidil was determined in in situ intestinal perfusion studies in rodents and permeability studies across Caco-2 cell monolayers. The permeability of minoxidil was compared with that of metoprolol, an FDA reference drug for BCS classification. In rat perfusion studies, the permeability of minoxidil was somewhat higher than that of metoprolol in the jejunum, while minoxidil showed lower permeability than metoprolol in the ileum. The permeability of minoxidil was independent of intestinal segment, while the permeability of metoprolol was region-dependent. Similarly, in mouse perfusion study, the jejunal permeability of minoxidil was 2.5-fold higher than that of metoprolol. Minoxidil and metoprolol showed similar permeability in Caco-2 study at apical pH of 6.5 and basolateral pH of 7.4. The permeability of minoxidil was independent of pH, while metoprolol showed pH-dependent transport in Caco-2 study. Minoxidil exhibited similar permeability in the absorptive direction (AP-BL) in comparison with secretory direction (BL-AP), while metoprolol had higher efflux ratio (ER > 2) at apical pH of 6.5 and basolateral pH of 7.4. No concentration-dependent transport was observed for either minoxidil or metoprolol transport in Caco-2 study. Verapamil did not alter the transport of either compounds across Caco-2 cell monolayers. The permeability of minoxidil was independent of both pH and intestinal segment in intestinal perfusion studies and Caco-2 studies. Caco-2 studies also showed no involvement of carrier mediated transport in the absorption process of minoxidil. These results suggest that minoxidil may be an acceptable reference drug for BCS high permeability classification. However, minoxidil exhibited higher jejunal permeability than metoprolol and thus to use minoxidil as a reference drug would raise the

Hypoxia activates a Ca2+-permeable cation conductance sensitive to carbon monoxide and to GsMTx-4 in human and mouse sickle erythrocytes.

Science.gov (United States)

Vandorpe, David H; Xu, Chang; Shmukler, Boris E; Otterbein, Leo E; Trudel, Marie; Sachs, Frederick; Gottlieb, Philip A; Brugnara, Carlo; Alper, Seth L

2010-01-15

Deoxygenation of sickle erythrocytes activates a cation permeability of unknown molecular identity (Psickle), leading to elevated intracellular [Ca(2+)] ([Ca(2+)](i)) and subsequent activation of K(Ca) 3.1. The resulting erythrocyte volume decrease elevates intracellular hemoglobin S (HbSS) concentration, accelerates deoxygenation-induced HbSS polymerization, and increases the likelihood of cell sickling. Deoxygenation-induced currents sharing some properties of Psickle have been recorded from sickle erythrocytes in whole cell configuration. We now show by cell-attached and nystatin-permeabilized patch clamp recording from sickle erythrocytes of mouse and human that deoxygenation reversibly activates a Ca(2+)- and cation-permeable conductance sensitive to inhibition by Grammastola spatulata mechanotoxin-4 (GsMTx-4; 1 microM), dipyridamole (100 microM), DIDS (100 microM), and carbon monoxide (25 ppm pretreatment). Deoxygenation also elevates sickle erythrocyte [Ca(2+)](i), in a manner similarly inhibited by GsMTx-4 and by carbon monoxide. Normal human and mouse erythrocytes do not exhibit these responses to deoxygenation. Deoxygenation-induced elevation of [Ca(2+)](i) in mouse sickle erythrocytes did not require KCa3.1 activity. The electrophysiological and fluorimetric data provide compelling evidence in sickle erythrocytes of mouse and human for a deoxygenation-induced, reversible, Ca(2+)-permeable cation conductance blocked by inhibition of HbSS polymerization and by an inhibitor of strctch-activated cation channels. This cation permeability pathway is likely an important source of intracellular Ca(2+) for pathologic activation of KCa3.1 in sickle erythrocytes. Blockade of this pathway represents a novel therapeutic approach for treatment of sickle disease.

Hypoxia activates a Ca2+-permeable cation conductance sensitive to carbon monoxide and to GsMTx-4 in human and mouse sickle erythrocytes.

Directory of Open Access Journals (Sweden)

David H Vandorpe

2010-01-01

Full Text Available Deoxygenation of sickle erythrocytes activates a cation permeability of unknown molecular identity (Psickle, leading to elevated intracellular [Ca(2+] ([Ca(2+](i and subsequent activation of K(Ca 3.1. The resulting erythrocyte volume decrease elevates intracellular hemoglobin S (HbSS concentration, accelerates deoxygenation-induced HbSS polymerization, and increases the likelihood of cell sickling. Deoxygenation-induced currents sharing some properties of Psickle have been recorded from sickle erythrocytes in whole cell configuration.We now show by cell-attached and nystatin-permeabilized patch clamp recording from sickle erythrocytes of mouse and human that deoxygenation reversibly activates a Ca(2+- and cation-permeable conductance sensitive to inhibition by Grammastola spatulata mechanotoxin-4 (GsMTx-4; 1 microM, dipyridamole (100 microM, DIDS (100 microM, and carbon monoxide (25 ppm pretreatment. Deoxygenation also elevates sickle erythrocyte [Ca(2+](i, in a manner similarly inhibited by GsMTx-4 and by carbon monoxide. Normal human and mouse erythrocytes do not exhibit these responses to deoxygenation. Deoxygenation-induced elevation of [Ca(2+](i in mouse sickle erythrocytes did not require KCa3.1 activity.The electrophysiological and fluorimetric data provide compelling evidence in sickle erythrocytes of mouse and human for a deoxygenation-induced, reversible, Ca(2+-permeable cation conductance blocked by inhibition of HbSS polymerization and by an inhibitor of strctch-activated cation channels. This cation permeability pathway is likely an important source of intracellular Ca(2+ for pathologic activation of KCa3.1 in sickle erythrocytes. Blockade of this pathway represents a novel therapeutic approach for treatment of sickle disease.

Polymer/Silicate Nanocomposites Used to Manufacture Gas Storage Tanks With Reduced Permeability

Science.gov (United States)

Campbell, Sandi G.; Johnston, Chris

2004-01-01

Over the past decade, there has been considerable research in the area of polymer-layered silicate nanocomposites. This research has shown that the dispersion of small amounts of an organically modified layered silicate improves the polymer strength, modulus, thermal stability, and barrier properties. There have been several reports on the dispersion of layered silicates in an epoxy matrix. Potential enhancements to the barrier properties of epoxy/silicate nanocomposites make this material attractive for low permeability tankage. Polymer matrix composites (PMCs) have several advantages for cryogenic storage tanks. They are lightweight, strong, and stiff; therefore, a smaller fraction of a vehicle's potential payload capacity is used for propellant storage. Unfortunately, the resins typically used to make PMC tanks have higher gas permeability than metals. This can lead to hydrogen loss through the body of the tank instead of just at welds and fittings. One approach to eliminate this problem is to build composite tanks with thin metal liners. However, although these tanks provide good permeability performance, they suffer from a substantial mismatch in the coefficient of thermal expansion, which can lead to failure of the bond between the liner and the body of the tank. Both problems could be addressed with polymersilicate nanocomposites, which exhibit reduced hydrogen permeability, making them potential candidates for linerless PMC tanks. Through collaboration with Northrop Grumman and Michigan State University, nanocomposite test tanks were manufactured for the NASA Glenn Research Center, and the helium permeability was measured. An organically modified silicate was prepared at Michigan State University and dispersed in an epoxy matrix (EPON 826/JeffamineD230). The epoxy/silicate nanocomposites contained either 0 or 5 wt% of the organically modified silicate. The tanks were made by filament winding carbon fibers with the nanocomposite resin. Helium permeability

Permeability of porour rhyolite

Science.gov (United States)

Cashman, K.; Rust, A.; Wright, H.; Roberge, J.

2003-04-01

The development of permeability in bubble-bearing magmas determines the efficiency of volatile escape during their ascent through volcanic conduits, which, in turn, controls their explosive potential. As permeability requires bubble connectivity, relationships between permeability and porosity in silicic magmas must be controlled by the formation, growth, deformation and coalescence of their constituent bubbles. Although permeability data on porous volcanic pyroclasts are limited, the database can be greatly extended by including data for ceramic and metallic foams1. Several studies indicate that a single number does not adequately describe the permeability of a foam because inertial effects, which predominate at high flow rates, cause deviations from Darcy's law. These studies suggest that permeability is best modeled using the Forschheimer equation to determine both the Darcy permeability (k1) and the non-Darcian (k2) permeability. Importantly, at the high porosities of ceramic foams (75-95%), both k1 and k2 are strongly dependent on pore size and geometry, suggesting that measurement of these parameters provides important information on foam structure. We determined both the connected porosity (by He-pycnometry) and the permeability (k1 and k2) of rhyolitic samples having a wide range in porosity (22-85%) and vesicle textures. In general, these data support previous observations of a power law relationship between connected porosity and Darcy permeability2. In detail, variations in k1 increase at higher porosities. Similarly, k2 generally increases in both mean and standard deviation with increasing porosity. Measurements made on three mutually perpendicular cores from individual pumice clasts suggest that some of the variability can be explained by anisotropy in the vesicle structure. By comparison with ceramic foams, we suggest that the remaining variability results from differences either in average vesicle size or, more likely, in the size of apertures

Permeability testing of biomaterial membranes

Energy Technology Data Exchange (ETDEWEB)

Dreesmann, L; Hajosch, R; Nuernberger, J Vaz; Schlosshauer, B [NMI Natural and Medical Sciences Institute at University Tuebingen, Markwiesenstr. 55, D-72770 Reutlingen (Germany); Ahlers, M [GELITA AG, Gammelsbacher Str. 2, D-69412 Eberbach (Germany)], E-mail: schlosshauer@nmi.de

2008-09-01

The permeability characteristics of biomaterials are critical parameters for a variety of implants. To analyse the permeability of membranes made from crosslinked ultrathin gelatin membranes and the transmigration of cells across the membranes, we combined three technical approaches: (1) a two-chamber-based permeability assay, (2) cell culturing with cytochemical analysis and (3) biochemical enzyme electrophoresis (zymography). Based on the diffusion of a coloured marker molecule in conjunction with photometric quantification, permeability data for a gelatin membrane were determined in the presence or absence of gelatin degrading fibroblasts. Cytochemical evaluation after cryosectioning of the membranes was used to ascertain whether fibroblasts had infiltrated the membrane inside. Zymography was used to investigate the potential release of proteases from fibroblasts, which are known to degrade collagen derivatives such as gelatin. Our data show that the diffusion equilibrium of a low molecular weight dye across the selected gelatin membrane is approached after about 6-8 h. Fibroblasts increase the permeability due to cavity formation in the membrane inside without penetrating the membrane for an extended time period (>21 days in vitro). Zymography indicates that cavity formation is most likely due to the secretion of matrix metalloproteinases. In summary, the combination of the depicted methods promises to facilitate a more rational development of biomaterials, because it provides a rapid means of determining permeability characteristics and bridges the gap between descriptive methodology and the mechanistic understanding of permeability alterations due to biological degradation.

Permeability testing of biomaterial membranes

International Nuclear Information System (INIS)

Dreesmann, L; Hajosch, R; Nuernberger, J Vaz; Schlosshauer, B; Ahlers, M

2008-01-01

The permeability characteristics of biomaterials are critical parameters for a variety of implants. To analyse the permeability of membranes made from crosslinked ultrathin gelatin membranes and the transmigration of cells across the membranes, we combined three technical approaches: (1) a two-chamber-based permeability assay, (2) cell culturing with cytochemical analysis and (3) biochemical enzyme electrophoresis (zymography). Based on the diffusion of a coloured marker molecule in conjunction with photometric quantification, permeability data for a gelatin membrane were determined in the presence or absence of gelatin degrading fibroblasts. Cytochemical evaluation after cryosectioning of the membranes was used to ascertain whether fibroblasts had infiltrated the membrane inside. Zymography was used to investigate the potential release of proteases from fibroblasts, which are known to degrade collagen derivatives such as gelatin. Our data show that the diffusion equilibrium of a low molecular weight dye across the selected gelatin membrane is approached after about 6-8 h. Fibroblasts increase the permeability due to cavity formation in the membrane inside without penetrating the membrane for an extended time period (>21 days in vitro). Zymography indicates that cavity formation is most likely due to the secretion of matrix metalloproteinases. In summary, the combination of the depicted methods promises to facilitate a more rational development of biomaterials, because it provides a rapid means of determining permeability characteristics and bridges the gap between descriptive methodology and the mechanistic understanding of permeability alterations due to biological degradation

Zinc Salts Block Hepatitis E Virus Replication by Inhibiting the Activity of Viral RNA-Dependent RNA Polymerase.

Science.gov (United States)

Kaushik, Nidhi; Subramani, Chandru; Anang, Saumya; Muthumohan, Rajagopalan; Shalimar; Nayak, Baibaswata; Ranjith-Kumar, C T; Surjit, Milan

2017-11-01

Hepatitis E virus (HEV) causes an acute, self-limiting hepatitis in healthy individuals and leads to chronic disease in immunocompromised individuals. HEV infection in pregnant women results in a more severe outcome, with the mortality rate going up to 30%. Though the virus usually causes sporadic infection, epidemics have been reported in developing and resource-starved countries. No specific antiviral exists against HEV. A combination of interferon and ribavirin therapy has been used to control the disease with some success. Zinc is an essential micronutrient that plays crucial roles in multiple cellular processes. Zinc salts are known to be effective in reducing infections caused by few viruses. Here, we investigated the effect of zinc salts on HEV replication. In a human hepatoma cell (Huh7) culture model, zinc salts inhibited the replication of genotype 1 (g-1) and g-3 HEV replicons and g-1 HEV infectious genomic RNA in a dose-dependent manner. Analysis of a replication-defective mutant of g-1 HEV genomic RNA under similar conditions ruled out the possibility of zinc salts acting on replication-independent processes. An ORF4-Huh7 cell line-based infection model of g-1 HEV further confirmed the above observations. Zinc salts did not show any effect on the entry of g-1 HEV into the host cell. Furthermore, our data reveal that zinc salts directly inhibit the activity of viral RNA-dependent RNA polymerase (RdRp), leading to inhibition of viral replication. Taken together, these studies unravel the ability of zinc salts in inhibiting HEV replication, suggesting their possible therapeutic value in controlling HEV infection. IMPORTANCE Hepatitis E virus (HEV) is a public health concern in resource-starved countries due to frequent outbreaks. It is also emerging as a health concern in developed countries owing to its ability to cause acute and chronic infection in organ transplant and immunocompromised individuals. Although antivirals such as ribavirin have been used

Determination of hydrogen permeability in uncoated and coated superalloys

Science.gov (United States)

Bhattacharyya, S.; Vesely, E. J., Jr.; Hill, V. L.

1981-01-01

Hydrogen permeability, diffusivity, and solubility data were obtained for eight wrought and cast high temperature alloys over the range 650 to 815 C. Data were obtained for both uncoated alloys and wrought alloys coated with four commercially available coatings. Activation energies for permeability, diffusivity and solubility were calculated.

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.

Active Ebola Virus Replication and Heterogeneous Evolutionary Rates in EVD Survivors

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Shannon L.M. Whitmer

2018-01-01

Full Text Available Following cessation of continuous Ebola virus (EBOV transmission within Western Africa, sporadic EBOV disease (EVD cases continued to re-emerge beyond the viral incubation period. Epidemiological and genomic evidence strongly suggests that this represented transmission from EVD survivors. To investigate whether persistent infections are characterized by ongoing viral replication, we sequenced EBOV from the semen of nine EVD survivors and a subset of corresponding acute specimens. EBOV evolutionary rates during persistence were either similar to or reduced relative to acute infection rates. Active EBOV replication/transcription continued during convalescence, but decreased over time, consistent with viral persistence rather than viral latency. Patterns of genetic divergence suggest a moderate relaxation of selective constraints within the sGP carboxy-terminal tail during persistent infections, but do not support widespread diversifying selection. Altogether, our data illustrate that EBOV persistence in semen, urine, and aqueous humor is not a quiescent or latent infection.

Numerical Simulation of Hydraulic Fracturing in Low-/High-Permeability, Quasi-Brittle and Heterogeneous Rocks

Science.gov (United States)

Pakzad, R.; Wang, S. Y.; Sloan, S. W.

2018-04-01

In this study, an elastic-brittle-damage constitutive model was incorporated into the coupled fluid/solid analysis of ABAQUS to iteratively calculate the equilibrium effective stress of Biot's theory of consolidation. The Young's modulus, strength and permeability parameter of the material were randomly assigned to the representative volume elements of finite element models following the Weibull distribution function. The hydraulic conductivity of elements was associated with their hydrostatic effective stress and damage level. The steady-state permeability test results for sandstone specimens under different triaxial loading conditions were reproduced by employing the same set of material parameters in coupled transient flow/stress analyses of plane-strain models, thereby indicating the reliability of the numerical model. The influence of heterogeneity on the failure response and the absolute permeability was investigated, and the post-peak permeability was found to decrease with the heterogeneity level in the coupled analysis with transient flow. The proposed model was applied to the plane-strain simulation of the fluid pressurization of a cavity within a large-scale block under different conditions. Regardless of the heterogeneity level, the hydraulically driven fractures propagated perpendicular to the minimum principal far-field stress direction for high-permeability models under anisotropic far-field stress conditions. Scattered damage elements appeared in the models with higher degrees of heterogeneity. The partially saturated areas around propagating fractures were simulated by relating the saturation degree to the negative pore pressure in low-permeability blocks under high pressure. By replicating previously reported trends in the fracture initiation and breakdown pressure for different pressurization rates and hydraulic conductivities, the results showed that the proposed model for hydraulic fracture problems is reliable for a wide range of

Controlling DC permeability in cast steels

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Sumner, Aaran, E-mail: aaran.sumner@nottingham.ac.uk [University of Nottingham, Nottingham University Park Campus, Nottingham NG7 2RD, England (United Kingdom); Gerada, Chris, E-mail: chris.gerada@nottingham.ac.uk [Electrical Machines, University of Nottingham, Tower Building, Nottingham NG7 2RD, England (United Kingdom); Brown, Neil, E-mail: neil.brown@cummins.com [Advanced Electrical Machines Research and Technology at Cummins Power Generation, Peterborough PE2 6FZ, England (United Kingdom); Clare, Adam, E-mail: adam.clare@nottingham.ac.uk [Advanced Manufacturing, University of Nottingham, University Park Campus, Nottingham NG7 2RD, England (United Kingdom)

2017-05-01

Annealing (at multiple cooling rates) and quenching (with tempering) was performed on specimens of cast steel of varying composition. The aim was to devise a method for selecting the steel with the highest permeability, from any given range of steels, and then increasing the permeability by heat treatment. Metallographic samples were imaged using optical microscopy to show the effect of the applied heat treatments on the microstructure. Commonly cast steels can have DC permeability altered by the careful selection of a heat treatment. Increases of up to 381% were achieved by annealing using a cooling rate of 6.0 °C/min. Annealing was found to cause the carbon present in the steel to migrate from grain boundaries and from within ferrite crystals into adjacent pearlite crystals. The migration of the carbon resulted in less carbon at grain boundaries and within ferrite crystals reducing the number of pinning sites between magnetic domains. This gives rise to a higher permeability. Quenching then tempering was found to cause the formation of small ferrite crystals with the carbon content of the steel predominately held in the martensitic crystal structures. The results show that with any given range of steel compositions the highest baseline DC permeability will be found with the steel that has the highest iron content and the lowest carbon content. For the samples tested in this paper a cooling rate of 4.5 °C/min resulted in the relative permeability of the sample with the highest baseline permeability, AS4, increasing from 783 to 1479 at 0.5 T. This paper shows how heat treatments commonly applied to hypoeutectoid cast steels, to improve their mechanical performance, can be used to also enhance electromagnetic properties of these alloys. The use of cast steels allows the creation of DC components for electrical machines not possible by the widely used method of stacking of electrical grade sheet steels. - Highlights: • A range of structural steels had their

Controlling DC permeability in cast steels

International Nuclear Information System (INIS)

Sumner, Aaran; Gerada, Chris; Brown, Neil; Clare, Adam

2017-01-01

Annealing (at multiple cooling rates) and quenching (with tempering) was performed on specimens of cast steel of varying composition. The aim was to devise a method for selecting the steel with the highest permeability, from any given range of steels, and then increasing the permeability by heat treatment. Metallographic samples were imaged using optical microscopy to show the effect of the applied heat treatments on the microstructure. Commonly cast steels can have DC permeability altered by the careful selection of a heat treatment. Increases of up to 381% were achieved by annealing using a cooling rate of 6.0 °C/min. Annealing was found to cause the carbon present in the steel to migrate from grain boundaries and from within ferrite crystals into adjacent pearlite crystals. The migration of the carbon resulted in less carbon at grain boundaries and within ferrite crystals reducing the number of pinning sites between magnetic domains. This gives rise to a higher permeability. Quenching then tempering was found to cause the formation of small ferrite crystals with the carbon content of the steel predominately held in the martensitic crystal structures. The results show that with any given range of steel compositions the highest baseline DC permeability will be found with the steel that has the highest iron content and the lowest carbon content. For the samples tested in this paper a cooling rate of 4.5 °C/min resulted in the relative permeability of the sample with the highest baseline permeability, AS4, increasing from 783 to 1479 at 0.5 T. This paper shows how heat treatments commonly applied to hypoeutectoid cast steels, to improve their mechanical performance, can be used to also enhance electromagnetic properties of these alloys. The use of cast steels allows the creation of DC components for electrical machines not possible by the widely used method of stacking of electrical grade sheet steels. - Highlights: • A range of structural steels had their

Analysis of a hysteresis motor on asynchronous speed using complex permeability

International Nuclear Information System (INIS)

Horii, T.; Yuge, N.; Wakui, G.

1994-01-01

Although hysteresis motors have a comparatively small output for their mechanical dimensions compared with other types of motor, they offer the advantages of extremely low vibration and noise levels, and so are widely used as driving motors in acoustic equipment and uranium gas centrifuges. This paper deals with a method for determining the complex permeability in analysis of hysteresis motors. The method assumes that the magnetic intensity distribution is sinusoidal in the direction of rotation. Analysis of the asynchronous speed of a hysteresis motor is then performed for cylindrical coordinates, using modified Bessel functions. The results of calculations are in good agreement with experimental results, confirming the effectiveness of the proposed model and method for determining the complex permeability

Targeting DNA Replication Stress for Cancer Therapy

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Jun Zhang

2016-08-01

Full Text Available The human cellular genome is under constant stress from extrinsic and intrinsic factors, which can lead to DNA damage and defective replication. In normal cells, DNA damage response (DDR mediated by various checkpoints will either activate the DNA repair system or induce cellular apoptosis/senescence, therefore maintaining overall genomic integrity. Cancer cells, however, due to constitutive growth signaling and defective DDR, may exhibit “replication stress” —a phenomenon unique to cancer cells that is described as the perturbation of error-free DNA replication and slow-down of DNA synthesis. Although replication stress has been proven to induce genomic instability and tumorigenesis, recent studies have counterintuitively shown that enhancing replicative stress through further loosening of the remaining checkpoints in cancer cells to induce their catastrophic failure of proliferation may provide an alternative therapeutic approach. In this review, we discuss the rationale to enhance replicative stress in cancer cells, past approaches using traditional radiation and chemotherapy, and emerging approaches targeting the signaling cascades induced by DNA damage. We also summarize current clinical trials exploring these strategies and propose future research directions including the use of combination therapies, and the identification of potential new targets and biomarkers to track and predict treatment responses to targeting DNA replication stress.

The solubility-permeability interplay in using cyclodextrins as pharmaceutical solubilizers: mechanistic modeling and application to progesterone.

Science.gov (United States)

Dahan, Arik; Miller, Jonathan M; Hoffman, Amnon; Amidon, Gregory E; Amidon, Gordon L

2010-06-01

A quasi-equilibrium mass transport analysis has been developed to quantitatively explain the solubility-permeability interplay that exists when using cyclodextrins as pharmaceutical solubilizers. The model considers the effects of cyclodextrins on the membrane permeability (P(m)) as well as the unstirred water layer (UWL) permeability (P(aq)), to predict the overall effective permeability (P(eff)) dependence on cyclodextrin concentration (C(CD)). The analysis reveals that: (1) UWL permeability markedly increases with increasing C(CD) since the effective UWL thickness quickly decreases with increasing C(CD); (2) membrane permeability decreases with increasing C(CD), as a result of the decrease in the free fraction of drug; and (3) since P(aq) increases and P(m) decreases with increasing C(CD), the UWL is effectively eliminated and the overall P(eff) tends toward membrane control, that is, P(eff) approximately P(m) above a critical C(CD). Application of this transport model enabled excellent quantitative prediction of progesterone P(eff) as a function of HP beta CD concentrations in PAMPA assay, Caco-2 transepithelial studies, and in situ rat jejunal-perfusion model. This work demonstrates that when using cyclodextrins as pharmaceutical solubilizers, a trade-off exists between solubility increase and permeability decrease that must not be overlooked; the transport model presented here can aid in striking the appropriate solubility-permeability balance in order to achieve optimal overall absorption. (c) 2009 Wiley-Liss, Inc. and the American Pharmacists Association

Owner reports of attention, activity, and impulsivity in dogs: a replication study

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Iosif Ana-Maria

2010-01-01

Full Text Available Abstract Background When developing behaviour measurement tools that use third party assessments, such as parent report, it is important to demonstrate reliability of resulting scales through replication using novel cohorts. The domestic dog has been suggested as a model to investigate normal variation in attention, hyperactivity, and impulsive behaviours impaired in Attention Deficit Hyperactive Disorder (ADHD. The human ADHD Rating Scale, modified for dogs and using owner-directed surveys, was applied in a European sample. We asked whether findings would be replicated utilizing an Internet survey in a novel sample, where unassisted survey completion, participant attitudes and breeds might affect previous findings. Methods Using a slightly modified version of the prior survey, we collected responses (n = 1030, 118 breeds representing 7 breed groups primarily in the United States and Canada. This study was conducted using an Internet survey mechanism. Results Reliability analyses confirmed two scales previously identified for dogs (inattention [IA], hyperactivity-impulsivity [HA-IM]. Models including age, training status, and breed group accounted for very little variance in subscales, with no effect of gender. Conclusions The factor invariance demonstrated in these findings confirms that owner report, using this modified human questionnaire, provides dog scores according to "inattention" and "hyperactivity-impulsivity" axes. Further characterization of naturally occurring variability of attention, activity, and impulsivity in domestic dogs may provide insight into genetic backgrounds underlying behaviours impaired in attention and associated disorders.

Defining clogging potential for permeable concrete.

Science.gov (United States)

Kia, Alalea; Wong, Hong S; Cheeseman, Christopher R

2018-08-15

Permeable concrete is used to reduce urban flooding as it allows water to flow through normally impermeable infrastructure. It is prone to clogging by particulate matter and predicting the long-term performance of permeable concrete is challenging as there is currently no reliable means of characterising clogging potential. This paper reports on the performance of a range of laboratory-prepared and commercial permeable concretes, close packed glass spheres and aggregate particles of varying size, exposed to different clogging methods to understand this phenomena. New methods were developed to study clogging and define clogging potential. The tests involved applying flowing water containing sand and/or clay in cycles, and measuring the change in permeability. Substantial permeability reductions were observed in all samples, particularly when exposed to sand and clay simultaneously. Three methods were used to define clogging potential based on measuring the initial permeability decay, half-life cycle and number of cycles to full clogging. We show for the first time strong linear correlations between these parameters for a wide range of samples, indicating their use for service-life prediction. Copyright © 2018 Elsevier Ltd. All rights reserved.

Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient.

Science.gov (United States)

Yao, Jianchao; Chang, Chunqi; Salmi, Mari L; Hung, Yeung Sam; Loraine, Ann; Roux, Stanley J

2008-06-18

Currently, clustering with some form of correlation coefficient as the gene similarity metric has become a popular method for profiling genomic data. The Pearson correlation coefficient and the standard deviation (SD)-weighted correlation coefficient are the two most widely-used correlations as the similarity metrics in clustering microarray data. However, these two correlations are not optimal for analyzing replicated microarray data generated by most laboratories. An effective correlation coefficient is needed to provide statistically sufficient analysis of replicated microarray data. In this study, we describe a novel correlation coefficient, shrinkage correlation coefficient (SCC), that fully exploits the similarity between the replicated microarray experimental samples. The methodology considers both the number of replicates and the variance within each experimental group in clustering expression data, and provides a robust statistical estimation of the error of replicated microarray data. The value of SCC is revealed by its comparison with two other correlation coefficients that are currently the most widely-used (Pearson correlation coefficient and SD-weighted correlation coefficient) using statistical measures on both synthetic expression data as well as real gene expression data from Saccharomyces cerevisiae. Two leading clustering methods, hierarchical and k-means clustering were applied for the comparison. The comparison indicated that using SCC achieves better clustering performance. Applying SCC-based hierarchical clustering to the replicated microarray data obtained from germinating spores of the fern Ceratopteris richardii, we discovered two clusters of genes with shared expression patterns during spore germination. Functional analysis suggested that some of the genetic mechanisms that control germination in such diverse plant lineages as mosses and angiosperms are also conserved among ferns. This study shows that SCC is an alternative to the Pearson

A Novel Natural Product-Derived Compound, Vestaine A1, Exerts both Pro-Angiogenic and Anti-Permeability Activity via a Different Pathway from VEGF

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Yoko Ishimoto

2016-10-01

Full Text Available Background/Aims: Vascular endothelial growth factor (VEGF is a key molecule in the regulation of both angiogenesis and vascular permeability. However, it is known that overproduction of VEGF induces abnormal blood vessel formation and these vessels cause several disease pathologies, such as diabetic retinopathy. The purpose of this study was to find novel vasoactive compounds which have different properties from VEGF. Methods/Results: We screened a natural product library using a co-culture angiogenic assay of endothelial cells and fibroblasts. By focusing on morphological changes of endothelial cells, we isolated the novel compounds vestaine A1 and vestaine B1 from the cultured broth of an actinomycete strain, Streptomyces sp. SANK 63697. Vestaine A1 enhanced tube formation of endothelial cells in Matrigel and suppressed cell death induced by serum deprivation. Vestaine A1 activated both MEK1/2 and PI-3 kinase pathways independently of the VEGF pathway in a dose- and time-dependent fashion. Finally, vestaine A1 potently suppressed VEGF-induced vascular permeability both in vitro and in vivo. Conclusion: Vestaine A1 has the potential to exhibit both pro-angiogenic and anti-permeability properties, and would therefore be useful for therapeutic treatment for abnormal vascular permeability-related diseases.

Measuring the permeability of Eleana argillite from area 17, Nevada Test Site, using the transient method

International Nuclear Information System (INIS)

Lin, W.

1978-01-01

Using the transient method, we determine the permeability of high-quartz Eleana argillite from the Nevada Test Site as a function of effective pressure. By comparing calculated and observed pressure decay in the upstream reservoir, we have determined the permeability of intact and fractured specimens at effective pressures ranging from 1.0 to 24.0 MPa. Over this pressure range, Eleana argillite has a low permeability (10 -16 to 10 -19 cm 2 ) when intact and a higher permeability (10 -12 to 10 -17 cm 2 ) with one induced through-going fracture

IFN regulatory factor 1 restricts hepatitis E virus replication by activating STAT1 to induce antiviral IFN-stimulated genes.

Science.gov (United States)

Xu, Lei; Zhou, Xinying; Wang, Wenshi; Wang, Yijin; Yin, Yuebang; Laan, Luc J W van der; Sprengers, Dave; Metselaar, Herold J; Peppelenbosch, Maikel P; Pan, Qiuwei

2016-10-01

IFN regulatory factor 1 (IRF1) is one of the most important IFN-stimulated genes (ISGs) in cellular antiviral immunity. Although hepatitis E virus (HEV) is a leading cause of acute hepatitis worldwide, how ISGs counteract HEV infection is largely unknown. This study was conducted to investigate the effect of IRF1 on HEV replication. Multiple cell lines were used in 2 models that harbor HEV. In different HEV cell culture systems, IRF1 effectively inhibited HEV replication. IRF1 did not trigger IFN production, and chromatin immunoprecipitation sequencing data analysis revealed that IRF1 bound to the promoter region of signal transducers and activators of transcription 1 (STAT1). Functional assay confirmed that IRF1 could drive the transcription of STAT1, resulting in elevation of total and phosphorylated STAT1 proteins and further activating the transcription of a panel of downstream antiviral ISGs. By pharmacological inhibitors and RNAi-mediated gene-silencing approaches, we revealed that antiviral function of IRF1 is dependent on the JAK-STAT cascade. Furthermore, induction of ISGs and the anti-HEV effect of IRF1 overlapped that of IFNα, but was potentiated by ribavirin. We demonstrated that IRF1 effectively inhibits HEV replication through the activation of the JAK-STAT pathway, and the subsequent transcription of antiviral ISGs, but independent of IFN production.-Xu, L., Zhou, X., Wang, W., Wang, Y., Yin, Y., van der Laan, L. J. W., Sprengers, D., Metselaar, H. J., Peppelenbosch, M. P., Pan, Q. IFN regulatory factor 1 restricts hepatitis E virus replication by activating STAT1 to induce antiviral IFN-stimulated genes. © FASEB.

Determination of lamivudine and zidovudine permeability using a different ex vivo method in Franz cells.

Science.gov (United States)

Dezani, André Bersani; Pereira, Thaisa Marinho; Caffaro, Arthur Massabki; Reis, Juliana Mazza; Serra, Cristina Helena Dos Reis

2013-01-01

The major processes that control the absorption of orally administered drugs are dissolution and gastrointestinal permeation. These processes depend on two main properties: solubility and permeability. Based on these characteristics, the Biopharmaceutical Classification System (BCS) was proposed as a tool to assist in biowaiver and bioavailability prediction of drugs. The purpose of the present study was to evaluate the permeability of lamivudine (3TC) and zidovudine (AZT) using a different ex vivo method in Franz cells. A segment of jejunum was inserted in a Franz cells apparatus, in order to assess drug permeability in the apical-basolateral (A-B) and basolateral-apical (B-A) directions. Each drug was added to the donor chamber, collected from the acceptor chamber and analyzed by HPLC. Fluorescein (FLU) and metoprolol (METO) were used as low and high permeability markers, respectively. The apparent permeability (Papp) results for the A-B direction were: Papp FLU A-B=0.54×10(-4)cm·s(-1), Papp METO A-B=7.99×10(-4)cm·s(-1), Papp 3TC A-B=4.58×10(-4)cm·s(-1) and Papp AZT A-B=5.34×10(-4)cm·s(-1). For the B-A direction, the Papp results were: Papp FLU B-A=0.56×10(-4)cm·s(-1), Papp METO B-A=0.25×10(-4)cm·s(-1), Papp 3TC B-A=0.24×10(-4)cm·s(-1) and Papp AZT B-A=0.19×10(-4)cm·s(-1). For the A-B direction, the Papp results of fluorescein and metoprolol show low and high permeability, respectively, indicating that the membranes were appropriate for permeability studies. For the A-B direction, the Papp results of 3TC and AZT suggest that these antiretroviral drugs have permeability values close to metoprolol. Nevertheless, for the B-A direction the Papp results do not suggest efflux mechanism for any of the drugs. Thereby, the different ex vivo methods using Franz cells can be successfully applied in drug permeability studies, in particular for drug biopharmaceutical classification. Copyright © 2013 Elsevier Inc. All rights reserved.

Magnetic induction measurements and identification of the permeability of Magneto-Rheological Elastomers using finite element simulations

International Nuclear Information System (INIS)

Schubert, Gerlind; Harrison, Philip

2016-01-01

The isotropic and anisotropic magnetic permeability of Magneto-Rheological Elastomers (MREs) is identified using a simple inverse modelling approach. This involves measuring the magnetic flux density and attractive force occurring between magnets, when MRE specimens are placed in between the magnets. Tests were conducted using isotropic MREs with 10–40% and for anisotropic MREs with 10–30%, particle volume concentration. Magnetic permeabilities were then identified through inverse modelling, by simulating the system using commercially available multi-physics finite element software. As expected, the effective permeability of isotropic MREs was found to be scalar-valued; increasing with increasing particle volume concentration (from about 1.6 at 10% to 3.7 at 30% particle volume concentration). The magnetic permeability of transversely isotropic MRE was itself found to be transversely isotropic, with permeabilities in the direction of particle chain alignment from 1.6 at 10% to 4.45 at 30%, which is up to 1.07–1.25 times higher than in the transverse directions. Results of this investigation are demonstrated to show good agreement with those reported in the literature. - Highlights: • An inverse modelling approach for permeability identification of MREs. • Comparison of magnetic flux measurements with finite element simulations. • Permeability of isotropic and anisotropic MREs of varying iron content identified. • Results compare favourably with theoretical predictions. • Simple experimental setup. • Inexpensive technique that can be conducted in most mechanical test labs.

Improved permeability of acyclovir: optimization of mucoadhesive liposomes using the phospholipid vesicle-based permeation assay.

Science.gov (United States)

Naderkhani, Elenaz; Erber, Astrid; Škalko-Basnet, Nataša; Flaten, Gøril Eide

2014-02-01

The antiviral drug acyclovir (ACV) suffers from poor solubility both in lipophilic and hydrophilic environment, leading to low and highly variable bioavailability. To overcome these limitations, this study aimed at designing mucoadhesive ACV-containing liposomes to improve its permeability. Liposomes were prepared from egg phosphatidylcholine (E-PC) and E-PC/egg phosphatidylglycerol (E-PC/E-PG) and their surfaces coated with Carbopol. All liposomal formulations were fully characterized and for the first time the phospholipid vesicle-based permeation assay (PVPA) was used for testing in vitro permeability of drug from mucoadhesive liposome formulations. The negatively charged E-PC/E-PG liposomes could encapsulate more ACV than neutral E-PC liposomes. Coating with Carbopol increased the entrapment in the neutral E-PC liposomes. The incorporation of ACV into liposomes exhibited significant increase in its in vitro permeability, compared with its aqueous solution. The neutral E-PC liposomal formulations exhibited higher ACV permeability values compared with charged E-PC/E-PG formulations. Coating with Carbopol significantly enhanced the permeability from the E-PC/E-PG liposomes, as well as sonicated E-PC liposomes, which showed the highest permeability of all tested formulations. The increased permeability was according to the formulations' mucoadhesive properties. This indicates that the PVPA is suitable to distinguish between permeability of ACV from different mucoadhesive liposome formulations developed for various routes of administration. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Enhanced recovery of ammonia from swine manure anaerobic digester effluent using gas-permeable membranes and aeration

Science.gov (United States)

Atmospheric ammonia pollution from livestock wastes can be reduced using gas-permeable membrane technology by converting ammonia contained in the manure into ammonium salt for use in fertilizers. In this study, gas-permeable membrane technology was enhanced using aeration combined with nitrificatio...

Relative permeability of fractured wellbore cement: an experimental investigation using electrical resistivity monitoring for moisture content

Science.gov (United States)

Um, W.; Rod, K. A.; Strickland, C. E.

2016-12-01

Permeability is a critical parameter needed to understand flow in subsurface environments; it is particularly important in deep subsurface reservoirs where multiphase fluid flow is common, such as carbon sequestration and geothermal reservoirs. Cement is used in the annulus of wellbores due to its low permeable properties to seal aquifers, reducing leaks to adjacent strata. Extreme subsurface environments of CO2 storage and geothermal production conditions will eventually reduce the cement integrity, propagating fracture networks and increasing the permeability for air and/or water. To date, there have been no reproducible experimental investigations of relative permeability in fractured wellbore cement published. To address this gap, we conducted a series of experiments using fractured Portland cement monoliths with increasing fracture networks. The monolith cylinder sides were jacketed with heavy-duty moisture-seal heat-shrink tubing, then fractured using shear force applied via a hydraulic press. Fractures were generated with different severity for each of three monoliths. Stainless steel endcaps were fixed to the monoliths using the same shrink-wrapped jacket. Fracture characteristics were determined using X-ray microtomography and image analysis. Flow controllers were used to control flow of water and air to supply continuous water or water plus air, both of which were delivered through the influent end cap. Effluent air flow was monitored using a flow meter, and water flow was measured gravimetrically. To monitor the effective saturation of the fractures, a RCON2 concrete bulk electrical resistivity test device was attached across both endcaps and a 0.1M NaNO3 brine was used as the transport fluid to improve resistivity measurements. Water content correlated to resistivity measurements with a r2 > 0.96. Data from the experiments was evaluated using two relative permeability models, the Corey-curve, often used for modeling relative permeability in porous media

A Reconciliation of Packed Column Permeability Data: Column Permeability as a Function of Particle Porosity

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Hubert M. Quinn

2014-01-01

Full Text Available In his textbook teaching of packed bed permeability, Georges Guiochon uses mobile phase velocity as the fluid velocity term in his elaboration of the Darcy permeability equation. Although this velocity frame makes a lot of sense from a thermodynamic point of view, it is valid only with respect to permeability at a single theoretical boundary condition. In his more recent writings, however, Guiochon has departed from his long-standing mode of discussing permeability in terms of the Darcy equation and has embraced the well-known Kozeny-Blake equation. In this paper, his teaching pertaining to the constant in the Kozeny-Blake equation is examined and, as a result, a new correlation coefficient is identified and defined herein based on the velocity frame used in his teaching. This coefficient correlates pressure drop and fluid velocity as a function of particle porosity. We show that in their experimental protocols, Guiochon et al. have not adhered to a strict material balance of permeability which creates a mismatch of particle porosity and leads to erroneous conclusions regarding the value of the permeability coefficient in the Kozeny-Blake equation. By correcting the experimental data to properly reflect particle porosity we reconcile the experimental results of Guiochon and Giddings, resulting in a permeability reference chart which is presented here for the first time. This reference chart demonstrates that Guiochon’s experimental data, when properly normalized for particle porosity and other related discrepancies, corroborates the value of 267 for the constant in the Kozeny-Blake equation which was derived by Giddings in 1965.

Optical tweezers reveal how proteins alter replication

Science.gov (United States)

Chaurasiya, Kathy

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

Temperature dependence of dynamical permeability characterization of magnetic thin films using shorted microstrip line probe

International Nuclear Information System (INIS)

Li, Xiling; Li, Chengyi; Chai, Guozhi

2017-01-01

A temperature dependence microwave permeability characterization system of magnetic thin film up to 10 GHz is designed and fabricated. This system can be used at temperatures ranging from room temperature to 200 °C, and is based on a shorted microstrip probe, which is made by microwave printed circuit board. Without contacting the magnetic thin films to the probe, the microwave permeability of the film can be detected without any limitations of sample size and with almost the same accuracy, as shown by comparison with the results obtained from a shorted microstrip transmission-line fixture. The complex permeability can be deduced by an analytical approach from the measured reflection coefficient of a strip line ( S 11 ) with and without a ferromagnetic film material on it. The procedures are the same with the shorted microstrip transmission-line method. The microwave permeability of an oblique deposited CoZr thin film was investigated with this probe. The results show that the room temperature dynamic permeability of the CoZr film is in good agreement with the results obtained from the established short-circuited microstrip perturbation method. The temperature dependence permeability results fit well with the Landau–Lifshitz–Gilbert equation. Development of the temperature-dependent measurement of the magnetic properties of magnetic thin film may be useful for the high-frequency application of magnetic devices at high temperatures. (paper)

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 ...

Permeability log using new lifetime measurements

International Nuclear Information System (INIS)

Dowling, D.J.; Boyd, J.F.; Fuchs, J.A.

1975-01-01

Comparative measurements of thermal neutron decay time are obtained for a formation after irradiation with a pulsed neutron source. Chloride ions in formation fluids are concentrated by the electrosmosis effect using charged poles on a well logging sonde. The formation is irradiated with fast neutrons and a first comparative measure of the thermal neutron decay time or neutron lifetime is taken. The chloride ions are then dispersed by acoustic pumping with a magnetostrictive transducer. The formation is then again irradiated with fast neutrons and a comparative measure of neutron lifetime is taken. The comparison is a function of the variation in chloride concentration between the two measurements which is related to formation permeability

Turbulence-induced noise of a submerged cylinder using a permeable FW–H method

Directory of Open Access Journals (Sweden)

Woen-Sug Choi

2016-05-01

Full Text Available Among underwater noise sources around submerged bodies, turbulence-induced noise has not been well investigated because of the difficulty of predicting it. In computational aeroacoustics, a number of studies has been conducted using the Ffowcs Williams–Hawkings (FW–H acoustic analogy without consideration of quadrupole source term due to the unacceptable calculation cost. In this paper, turbulence-induced noise is predicted, including that due to quadrupole sources, using a large eddy simulation (LES turbulence model and a developed formulation of permeable FW–H method with an open source computational fluid dynamics (CFD tool-kit. Noise around a circular cylinder is examined and the results of using the acoustic analogy method with and without quadrupole noise are compared, i.e. the FW–H method without quadrupole noise versus the permeable FW–H method that includes quadrupole sources. The usability of the permeable FW–H method for the prediction of turbulence-noise around submerged bodies is shown.

Use of novel permeable membrane and air cathodes in acetate microbial fuel cells

Energy Technology Data Exchange (ETDEWEB)

Pant, Deepak, E-mail: deepak.pant@vito.b [Separation and Conversion Technology, VITO - Flemish Institute for Technological Research, Boeretang 200, Mol 2400 (Belgium); Van Bogaert, Gilbert; De Smet, Mark; Diels, Ludo; Vanbroekhoven, Karolien [Separation and Conversion Technology, VITO - Flemish Institute for Technological Research, Boeretang 200, Mol 2400 (Belgium)

2010-11-01

In the existing microbial fuel cells (MFCs), the use of platinized electrodes and Nafion as proton exchange membrane (PEM) leads to high costs leading to a burden for wastewater treatment. In the present study, two different novel electrode materials are reported which can replace conventional platinized electrodes and can be used as very efficient oxygen reducing cathodes. Further, a novel membrane which can be used as an ion permeable membrane (Zirfon) can replace Nafion as the membrane of choice in MFCs. The above mentioned gas porous electrodes were first tested in an electrochemical half cell configuration for their ability to reduce oxygen and later in a full MFC set up. It was observed that these non-platinized air electrodes perform very well in the presence of acetate under MFC conditions (pH 7, room temperature) for oxygen reduction. Current densities of -0.43 mA cm{sup -2} for a non-platinized graphite electrode and -0.6 mA cm{sup -2} for a non-platinized activated charcoal electrode at -200 mV vs. Ag/AgCl of applied potential were obtained. The proposed ion permeable membrane, Zirfonwas tested for its oxygen mass transfer coefficient, K{sub 0} which was compared with Nafion. The K{sub 0} for Zirfon was calculated as 1.9 x 10{sup -3} cm s{sup -1}.

Permeable reactive barrier of surface hydrophobic granular activated carbon coupled with elemental iron for the removal of 2,4-dichlorophenol in water

Energy Technology Data Exchange (ETDEWEB)

Yang Ji, E-mail: yangji@ecust.edu.cn [School of Resources and Environmental Engineering, State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai 200237 (China); Cao Limei; Guo Rui; Jia Jinping [School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240 (China)

2010-12-15

Granular activated carbon was modified with dimethyl dichlorosilane to improve its surface hydrophobicity, and therefore to improve the performance of permeable reactive barrier constructed with the modified granular activated carbon and elemental iron. X-ray photoelectron spectroscopy shows that the surface silicon concentration of the modified granular activated carbon is higher than that of the original one, leading to the increased surface hydrophobicity. Although the specific surface area decreased from 895 to 835 m{sup 2} g{sup -1}, the modified granular activated carbon could adsorb 20% more 2,4-dichlorophenol than the original one did in water. It is also proven that the permeable reactive barrier with the modified granular activated carbon is more efficient at 2,4-dichlorophenol dechlorination, in which process 2,4-dichlorophenol is transformed to 2-chlorophenol or 4-chlorophenol then to phenol, or to phenol directly.

Permeable reactive barrier of surface hydrophobic granular activated carbon coupled with elemental iron for the removal of 2,4-dichlorophenol in water

International Nuclear Information System (INIS)

Yang Ji; Cao Limei; Guo Rui; Jia Jinping

2010-01-01

Granular activated carbon was modified with dimethyl dichlorosilane to improve its surface hydrophobicity, and therefore to improve the performance of permeable reactive barrier constructed with the modified granular activated carbon and elemental iron. X-ray photoelectron spectroscopy shows that the surface silicon concentration of the modified granular activated carbon is higher than that of the original one, leading to the increased surface hydrophobicity. Although the specific surface area decreased from 895 to 835 m 2 g -1 , the modified granular activated carbon could adsorb 20% more 2,4-dichlorophenol than the original one did in water. It is also proven that the permeable reactive barrier with the modified granular activated carbon is more efficient at 2,4-dichlorophenol dechlorination, in which process 2,4-dichlorophenol is transformed to 2-chlorophenol or 4-chlorophenol then to phenol, or to phenol directly.

Notional Permeability

NARCIS (Netherlands)

Kik, R.; Van den Bos, J.P.; Maertens, J.; Verhagen, H.J.; Van der Meer, J.W.

2012-01-01

Different layer design of a rock slope and under layers has a large effect on the strengths on the rock slope itself. In the stability formula developed of VAN DER MEER [1988] this effect is represented by the term Notional Permeability with symbol P. A more open, or permeable, structure underneath

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.

Teaching about Prejudice with a Bogardus Social Distance Scale Activity: Replication and Extension

Science.gov (United States)

Maurer, Trent W.; Keim, Cassidy

2018-01-01

This study presents a three-year replication and extension of Maurer's (2013) evaluation of a classroom activity to reduce prejudice and discrimination. Students in six sections of an introductory family science course were assigned to one of three conditions and one of two target marginalized groups for a 3x2 design. Results differed…

Long-term bioventing performance in low-permeability soils

International Nuclear Information System (INIS)

Phelps, M.B.; Stanin, F.T.; Downey, D.C.

1995-01-01

Short-term and long-term bioventing treatability testing has shown that in situ air injection and extraction is a practical method for sustaining increased oxygen levels and enhancing aerobic biodegradation of petroleum hydrocarbons in low-permeability soils. At several test sites, initial physical parameter analysis of soils and air permeability tests indicated that impacted soils (fine sandy silts and clays) had low air permeabilities. Measurements of depleted soil-gas oxygen levels and increased soil-gas carbon dioxide levels indicated that the natural process of aerobic biodegradation of petroleum hydrocarbons was oxygen-limited. Initial treatability testing consisted of air permeability tests to measure the permeability of the soils to air and in situ respiration tests to measure the rates at which native microorganisms could biodegrade the contaminants when provided with sufficient oxygen. During the long-term treatment period, active air injection or extraction systems were operated for 1 year or longer. Soil gas was periodically monitored within the treatment zone to evaluate the success of the bioventing systems in increasing soil-gas oxygen levels in the low-permeability soils. Follow-up respiration tests and soil and soil-gas sampling were conducted to evaluate changes in respiration rates and contaminant concentrations with time

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

Science.gov (United States)

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

2016-08-09

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

Transcriptionally Driven DNA Replication Program of the Human Parasite Leishmania major

Directory of Open Access Journals (Sweden)

Rodrigo Lombraña

2016-08-01

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

High-permeability criterion for BCS classification: segmental/pH dependent permeability considerations.

Science.gov (United States)

Dahan, Arik; Miller, Jonathan M; Hilfinger, John M; Yamashita, Shinji; Yu, Lawrence X; Lennernäs, Hans; Amidon, Gordon L

2010-10-04

The FDA classifies a drug substance as high-permeability when the fraction of dose absorbed (F(abs)) in humans is 90% or higher. This direct correlation between human permeability and F(abs) has been recently controversial, since the β-blocker sotalol showed high F(abs) (90%) and low Caco-2 permeability. The purpose of this study was to investigate the scientific basis for this disparity between permeability and F(abs). The effective permeabilities (P(eff)) of sotalol and metoprolol, a FDA standard for the low/high P(eff) class boundary, were investigated in the rat perfusion model, in three different intestinal segments with pHs corresponding to the physiological pH in each region: (1) proximal jejunum, pH 6.5; (2) mid small intestine, pH 7.0; and (3) distal ileum, pH 7.5. Both metoprolol and sotalol showed pH-dependent permeability, with higher P(eff) at higher pH. At any given pH, sotalol showed lower permeability than metoprolol; however, the permeability of sotalol determined at pH 7.5 exceeded/matched metoprolol's at pH 6.5 and 7.0, respectively. Physicochemical analysis based on ionization, pK(a) and partitioning of these drugs predicted the same trend and clarified the mechanism behind these observed results. Experimental octanol-buffer partitioning experiments confirmed the theoretical curves. An oral dose of metoprolol has been reported to be completely absorbed in the upper small intestine; it follows, hence, that metoprolol's P(eff) value at pH 7.5 is not likely physiologically relevant for an immediate release dosage form, and the permeability at pH 6.5 represents the actual relevant value for the low/high permeability class boundary. Although sotalol's permeability is low at pH 6.5 and 7.0, at pH 7.5 it exceeds/matches the threshold of metoprolol at pH 6.5 and 7.0, most likely responsible for its high F(abs). In conclusion, we have shown that, in fact, there is no discrepancy between P(eff) and F(abs) in sotalol's absorption; the data emphasize that

Mechanisms and regulation of DNA replication initiation in eukaryotes.

Science.gov (United States)

Parker, Matthew W; Botchan, Michael R; Berger, James M

2017-04-01

Cellular DNA replication is initiated through the action of multiprotein complexes that recognize replication start sites in the chromosome (termed origins) and facilitate duplex DNA melting within these regions. In a typical cell cycle, initiation occurs only once per origin and each round of replication is tightly coupled to cell division. To avoid aberrant origin firing and re-replication, eukaryotes tightly regulate two events in the initiation process: loading of the replicative helicase, MCM2-7, onto chromatin by the origin recognition complex (ORC), and subsequent activation of the helicase by its incorporation into a complex known as the CMG. Recent work has begun to reveal the details of an orchestrated and sequential exchange of initiation factors on DNA that give rise to a replication-competent complex, the replisome. Here, we review the molecular mechanisms that underpin eukaryotic DNA replication initiation - from selecting replication start sites to replicative helicase loading and activation - and describe how these events are often distinctly regulated across different eukaryotic model organisms.

Clogging in permeable concrete: A review.

Science.gov (United States)

Kia, Alalea; Wong, Hong S; Cheeseman, Christopher R

2017-05-15

Permeable concrete (or "pervious concrete" in North America) is used to reduce local flooding in urban areas and is an important sustainable urban drainage system. However, permeable concrete exhibits reduction in permeability due to clogging by particulates, which severely limits service life. This paper reviews the clogging mechanism and current mitigating strategies in order to inform future research needs. The pore structure of permeable concrete and characteristics of flowing particulates influence clogging, which occurs when particles build-up and block connected porosity. Permeable concrete requires regular maintenance by vacuum sweeping and pressure washing, but the effectiveness and viability of these methods is questionable. The potential for clogging is related to the tortuosity of the connected porosity, with greater tortuosity resulting in increased potential for clogging. Research is required to develop permeable concrete that can be poured on-site, which produces a pore structure with significantly reduced tortuosity. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

Permeability-Porosity Relationships of Subduction Zone Sediments

Science.gov (United States)

Gamage, K.; Screaton, E.; Bekins, B.; Aiello, I.

2008-12-01

Permeability-porosity relationships for sediments from Northern Barbados, Costa Rica, Nankai, and Peru subduction zones were examined based on their sediment type and grain size distribution. Greater correlation was observed between permeability and porosity for siliciclastic sediments, diatom oozes, and nannofossil chalk than for nannofossil oozes. For siliciclastic sediments, grouping of sediments by clay content yields relationships that are generally consistent with results from other marine settings and suggest decreasing permeability for a given porosity as clay content increases. Correction of measured porosities for smectite content generally improves the quality of permeability-porosity relationships. The relationship between permeability and porosity for diatom oozes may be controlled by the amount of clay present in the ooze, causing diatom oozes to behave similarly to siliciclastic sediments. For a given porosity the nannofossil oozes have higher permeability values by 1.5 orders of magnitude than the siliciclastic sediments. However, the use of a permeability-porosity relation may not be appropriate for unconsolidated carbonates such as nannofossil oozes. This study provided insight to the effects of porosity correction for smectite, variations in lithology and grain size in permeability-porosity relationships. However, further progress in delineating controls on permeability will require more careful and better documented permeability tests on characterized samples.

Isthmin is a novel vascular permeability inducer that functions through cell-surface GRP78-mediated Src activation.

Science.gov (United States)

Venugopal, Shruthi; Chen, Mo; Liao, Wupeng; Er, Shi Yin; Wong, Wai-Shiu Fred; Ge, Ruowen

2015-07-01

Isthmin (ISM) is a recently identified 60 kDa secreted angiogenesis inhibitor. Two cell-surface receptors for ISM have been defined, the high-affinity glucose-regulated protein 78 kDa (GRP78) and the low-affinity αvβ5 integrin. As αvβ5 integrin plays an important role in pulmonary vascular permeability (VP) and ISM is highly expressed in mouse lung, we sought to clarify the role of ISM in VP. Recombinant ISM (rISM) dose-dependently enhances endothelial monolayer permeability in vitro and local dermal VP when administered intradermally in mice. Systemic rISM administration through intravenous injection leads to profound lung vascular hyperpermeability but not in other organs. Mechanistic investigations using molecular, biochemical approaches and specific chemical inhibitors revealed that ISM-GRP78 interaction triggers a direct interaction between GRP78 and Src, leading to Src activation and subsequent phosphorylation of adherens junction proteins and loss of junctional proteins from inter-endothelial junctions, resulting in enhanced VP. Dynamic studies of Src activation, VP and apoptosis revealed that ISM induces VP directly via Src activation while apoptosis contributes indirectly only after prolonged treatment. Furthermore, ISM is significantly up-regulated in lipopolysaccharide (LPS)-treated mouse lung. Blocking cell-surface GRP78 by systemic infusion of anti-GRP78 antibody significantly attenuates pulmonary vascular hyperpermeability in LPS-induced acute lung injury (ALI) in mice. ISM is a novel VP inducer that functions through cell-surface GRP78-mediated Src activation as well as induction of apoptosis. It induces a direct GRP78-Src interaction, leading to cytoplasmic Src activation. ISM contributes to pulmonary vascular hyperpermeability of LPS-induced ALI in mice. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2015. For permissions please email: journals.permissions@oup.com.

Multiple Targets for Novel Therapy of FSGS Associated with Circulating Permeability Factor

Directory of Open Access Journals (Sweden)

Virginia J. Savin

2017-01-01

Full Text Available A plasma component is responsible for altered glomerular permeability in patients with focal segmental glomerulosclerosis. Evidence includes recurrence after renal transplantation, remission after plasmapheresis, proteinuria in infants of affected mothers, transfer of proteinuria to experimental animals, and impaired glomerular permeability after exposure to patient plasma. Therapy may include decreasing synthesis of the injurious agent, removing or blocking its interaction with cells, or blocking signaling or enhancing cell defenses to restore the permeability barrier and prevent progression. Agents that may prevent the synthesis of the permeability factor include cytotoxic agents or aggressive chemotherapy. Extracorporeal therapies include plasmapheresis, immunoadsorption with protein A or anti-immunoglobulin, or lipopheresis. Oral or intravenous galactose also decreases Palb activity. Studies of glomeruli have shown that several strategies prevent the action of FSGS sera. These include blocking receptor-ligand interactions, modulating cell reactions using indomethacin or eicosanoids 20-HETE or 8,9-EET, and enhancing cytoskeleton and protein interactions using calcineurin inhibitors, glucocorticoids, or rituximab. We have identified cardiotrophin-like cytokine factor 1 (CLCF-1 as a candidate for the permeability factor. Therapies specific to CLCF-1 include potential use of cytokine receptor-like factor (CRLF-1 and inhibition of Janus kinase 2. Combined therapy using multiple modalities offers therapy to reverse proteinuria and prevent scarring.

Active RNA replication of hepatitis C virus downregulates CD81 expression.

Science.gov (United States)

Ke, Po-Yuan; Chen, Steve S-L

2013-01-01

So far how hepatitis C virus (HCV) replication modulates subsequent virus growth and propagation still remains largely unknown. Here we determine the impact of HCV replication status on the consequential virus growth by comparing normal and high levels of HCV RNA expression. We first engineered a full-length, HCV genotype 2a JFH1 genome containing a blasticidin-resistant cassette inserted at amino acid residue of 420 in nonstructural (NS) protein 5A, which allowed selection of human hepatoma Huh7 cells stably-expressing HCV. Short-term establishment of HCV stable cells attained a highly-replicating status, judged by higher expressions of viral RNA and protein as well as higher titer of viral infectivity as opposed to cells harboring the same genome without selection. Interestingly, maintenance of highly-replicating HCV stable cells led to decreased susceptibility to HCV pseudotyped particle (HCVpp) infection and downregulated cell surface level of CD81, a critical HCV entry (co)receptor. The decreased CD81 cell surface expression occurred through reduced total expression and cytoplasmic retention of CD81 within an endoplasmic reticulum -associated compartment. Moreover, productive viral RNA replication in cells harboring a JFH1 subgenomic replicon containing a similar blasticidin resistance gene cassette in NS5A and in cells robustly replicating full-length infectious genome also reduced permissiveness to HCVpp infection through decreasing the surface expression of CD81. The downregulation of CD81 surface level in HCV RNA highly-replicating cells thus interfered with reinfection and led to attenuated viral amplification. These findings together indicate that the HCV RNA replication status plays a crucial determinant in HCV growth by modulating the expression and intracellular localization of CD81.

Active RNA replication of hepatitis C virus downregulates CD81 expression.

Directory of Open Access Journals (Sweden)

Po-Yuan Ke

Full Text Available So far how hepatitis C virus (HCV replication modulates subsequent virus growth and propagation still remains largely unknown. Here we determine the impact of HCV replication status on the consequential virus growth by comparing normal and high levels of HCV RNA expression. We first engineered a full-length, HCV genotype 2a JFH1 genome containing a blasticidin-resistant cassette inserted at amino acid residue of 420 in nonstructural (NS protein 5A, which allowed selection of human hepatoma Huh7 cells stably-expressing HCV. Short-term establishment of HCV stable cells attained a highly-replicating status, judged by higher expressions of viral RNA and protein as well as higher titer of viral infectivity as opposed to cells harboring the same genome without selection. Interestingly, maintenance of highly-replicating HCV stable cells led to decreased susceptibility to HCV pseudotyped particle (HCVpp infection and downregulated cell surface level of CD81, a critical HCV entry (coreceptor. The decreased CD81 cell surface expression occurred through reduced total expression and cytoplasmic retention of CD81 within an endoplasmic reticulum -associated compartment. Moreover, productive viral RNA replication in cells harboring a JFH1 subgenomic replicon containing a similar blasticidin resistance gene cassette in NS5A and in cells robustly replicating full-length infectious genome also reduced permissiveness to HCVpp infection through decreasing the surface expression of CD81. The downregulation of CD81 surface level in HCV RNA highly-replicating cells thus interfered with reinfection and led to attenuated viral amplification. These findings together indicate that the HCV RNA replication status plays a crucial determinant in HCV growth by modulating the expression and intracellular localization of CD81.

Permeability of cork to gases.

Science.gov (United States)

Faria, David P; Fonseca, Ana L; Pereira, Helen; Teodoro, Orlando M N D

2011-04-27

The permeability of gases through uncompressed cork was investigated. More than 100 samples were assessed from different plank qualities to provide a picture of the permeability distribution. A novel technique based on a mass spectrometer leak detector was used to directly measure the helium flow through the central area of small disks 10 mm in diameter and 2 mm thick. The permeability for nitrogen, oxygen, and other gases was measured by the pressure rise technique. Boiled and nonboiled cork samples from different sections were evaluated. An asymmetric frequency distribution ranging 3 orders of magnitude (roughly from 1 to 1000 μmol/(cm·atm·day)) for selected samples without macroscopic defects was found, having a peak below 100 μmol/(cm·atm·day). Correlation was found between density and permeability: higher density samples tend to show lower permeability. However, boiled cork showed a mean lower permeability despite having a lower density. The transport mechanism of gases through cork was also examined. Calculations suggest that gases permeate uncompressed cork mainly through small channels between cells under a molecular flow regime. The diameter of such channels was estimated to be in the range of 100 nm, in agreement with the plasmodesmata size in the cork cell walls.

Captura de amonio procedente de estiercol mediante membranas permeables de gases (capture of ammonnia from turkey manure using gas-permeable membranes)

Science.gov (United States)

This paper, written in Spanish, describes the capture and recovery of gaseous ammonia from turkey manure using gas-permeable membranes technology with formation of stabilized ammonium salts. Bench experiments were carried out in Maryland using a pilot prototype system with turkey litter inside contr...

The ATM and Rad3-Related (ATR) Protein Kinase Pathway Is Activated by Herpes Simplex Virus 1 and Required for Efficient Viral Replication.

Science.gov (United States)

Edwards, Terri G; Bloom, David C; Fisher, Chris

2018-03-15

The ATM and Rad3-related (ATR) protein kinase and its downstream effector Chk1 are key sensors and organizers of the DNA damage response (DDR) to a variety of insults. Previous studies of herpes simplex virus 1 (HSV-1) showed no evidence for activation of the ATR pathway. Here we demonstrate that both Chk1 and ATR were phosphorylated by 3 h postinfection (h.p.i.). Activation of ATR and Chk1 was observed using 4 different HSV-1 strains in multiple cell types, while a specific ATR inhibitor blocked activation. Mechanistic studies point to early viral gene expression as a key trigger for ATR activation. Both pATR and pChk1 localized to the nucleus within viral replication centers, or associated with their periphery, by 3 h.p.i. Significant levels of pATR and pChk1 were also detected in the cytoplasm, where they colocalized with ICP4 and ICP0. Proximity ligation assays confirmed that pATR and pChk1 were closely and specifically associated with ICP4 and ICP0 in both the nucleus and cytoplasm by 3 h.p.i., but not with ICP8 or ICP27, presumably in a multiprotein complex. Chemically distinct ATR and Chk1 inhibitors blocked HSV-1 replication and infectious virion production, while inhibitors of ATM, Chk2, and DNA-dependent protein kinase (DNA-PK) did not. Together our data show that HSV-1 activates the ATR pathway at early stages of infection and that ATR and Chk1 kinase activities play important roles in HSV-1 replication fitness. These findings indicate that the ATR pathway may provide insight for therapeutic approaches. IMPORTANCE Viruses have evolved complex associations with cellular DNA damage response (DDR) pathways, which sense troublesome DNA structures formed during infection. The first evidence for activation of the ATR pathway by HSV-1 is presented. ATR is activated, and its downstream target Chk1 is robustly phosphorylated, during early stages of infection. Both activated proteins are found in the nucleus associated with viral replication compartments and in

Sulfolobus Replication Factor C stimulates the activity of DNA Polymerase B1

DEFF Research Database (Denmark)

Xing, Xuanxuan; Zhang, Likui; Guo, Li

2014-01-01

the hyperthermophilic archaea of the genus Sulfolobus physically interacts with DNA polymerase B1 (PolB1) and enhances both the polymerase and 3'-5' exonuclease activities of PolB1 in an ATP-independent manner. Stimulation of the PolB1 activity by RFC is independent of the ability of RFC to bind DNA but is consistent...... with the ability of RFC to facilitate DNA binding by PolB1 through protein-protein interaction. These results suggest that Sulfolobus RFC may play a role in recruiting DNA polymerase for efficient primer extension, in addition to clamp loading, during DNA replication....

Permeable reactive barrier of surface hydrophobic granular activated carbon coupled with elemental iron for the removal of 2,4-dichlorophenol in water.

Science.gov (United States)

Yang, Ji; Cao, Limei; Guo, Rui; Jia, Jinping

2010-12-15

Granular activated carbon was modified with dimethyl dichlorosilane to improve its surface hydrophobicity, and therefore to improve the performance of permeable reactive barrier constructed with the modified granular activated carbon and elemental iron. X-ray photoelectron spectroscopy shows that the surface silicon concentration of the modified granular activated carbon is higher than that of the original one, leading to the increased surface hydrophobicity. Although the specific surface area decreased from 895 to 835 m(2)g(-1), the modified granular activated carbon could adsorb 20% more 2,4-dichlorophenol than the original one did in water. It is also proven that the permeable reactive barrier with the modified granular activated carbon is more efficient at 2,4-dichlorophenol dechlorination, in which process 2,4-dichlorophenol is transformed to 2-chlorophenol or 4-chlorophenol then to phenol, or to phenol directly. Copyright © 2010 Elsevier B.V. All rights reserved.

Thromboxane A2 increases endothelial permeability through upregulation of interleukin-8

International Nuclear Information System (INIS)

Kim, Su-Ryun; Bae, Soo-Kyung; Park, Hyun-Joo; Kim, Mi-Kyoung; Kim, Koanhoi; Park, Shi-Young; Jang, Hye-Ock; Yun, Il; Kim, Yung-Jin; Yoo, Mi-Ae; Bae, Moon-Kyoung

2010-01-01

Thromboxane A 2 (TXA 2 ), a major prostanoid formed from prostaglandin H 2 by thromboxane synthase, is involved in the pathogenesis of a variety of vascular diseases. In this study, we report that TXA 2 mimetic U46619 significantly increases the endothelial permeability both in vitro and in vivo. U46619 enhanced the expression and secretion of interleukin-8 (IL-8), a major inducer of vascular permeability, in endothelial cells. Promoter analysis showed that the U46619-induced expression of IL-8 was mainly regulated by nuclear factor-κB (NF-κB). U46619 induced the activation of NF-κB through IκB kinase (IKK) activation, IκB phosphorylation and NF-κB nuclear translocation. Furthermore, the inhibition of IL-8 or blockade of the IL-8 receptor attenuated the U46619-induced endothelial cell permeability by modulating the cell-cell junctions. Overall, these results suggest that U46619 promotes vascular permeability through the production of IL-8 via NF-κB activation in endothelial cells.

Replicative Intermediates of Human Papillomavirus Type 11 in Laryngeal Papillomas: Site of Replication Initiation and Direction of Replication

Science.gov (United States)

Auborn, K. J.; Little, R. D.; Platt, T. H. K.; Vaccariello, M. A.; Schildkraut, C. L.

1994-07-01

We have examined the structures of replication intermediates from the human papillomavirus type 11 genome in DNA extracted from papilloma lesions (laryngeal papillomas). The sites of replication initiation and termination utilized in vivo were mapped by using neutral/neutral and neutral/alkaline two-dimensional agarose gel electrophoresis methods. Initiation of replication was detected in or very close to the upstream regulatory region (URR; the noncoding, regulatory sequences upstream of the open reading frames in the papillomavirus genome). We also show that replication forks proceed bidirectionally from the origin and converge 180circ opposite the URR. These results demonstrate the feasibility of analysis of replication of viral genomes directly from infected tissue.

Urban land use: Remote sensing of ground-basin permeability

Science.gov (United States)

Tinney, L. R.; Jensen, J. R.; Estes, J. E.

1975-01-01

A remote sensing analysis of the amount and type of permeable and impermeable surfaces overlying an urban recharge basin is discussed. An effective methodology for accurately generating this data as input to a safe yield study is detailed and compared to more conventional alternative approaches. The amount of area inventoried, approximately 10 sq. miles, should provide a reliable base against which automatic pattern recognition algorithms, currently under investigation for this task, can be evaluated. If successful, such approaches can significantly reduce the time and effort involved in obtaining permeability data, an important aspect of urban hydrology dynamics.

Uncoupling of Sister Replisomes during Eukaryotic DNA Replication

NARCIS (Netherlands)

Yardimci, Hasan; Loveland, Anna B.; Habuchi, Satoshi; van Oijen, Antoine M.; Walter, Johannes C.

2010-01-01

The duplication of eukaryotic genomes involves the replication of DNA from multiple origins of replication. In S phase, two sister replisomes assemble at each active origin, and they replicate DNA in opposite directions. Little is known about the functional relationship between sister replisomes.

Plasticity of DNA replication initiation in Epstein-Barr virus episomes.

Directory of Open Access Journals (Sweden)

Paolo Norio

2004-06-01

Full Text Available In mammalian cells, the activity of the sites of initiation of DNA replication appears to be influenced epigenetically, but this regulation is not fully understood. Most studies of DNA replication have focused on the activity of individual initiation sites, making it difficult to evaluate the impact of changes in initiation activity on the replication of entire genomic loci. Here, we used single molecule analysis of replicated DNA (SMARD to study the latent duplication of Epstein-Barr virus (EBV episomes in human cell lines. We found that initiation sites are present throughout the EBV genome and that their utilization is not conserved in different EBV strains. In addition, SMARD shows that modifications in the utilization of multiple initiation sites occur across large genomic regions (tens of kilobases in size. These observations indicate that individual initiation sites play a limited role in determining the replication dynamics of the EBV genome. Long-range mechanisms and the genomic context appear to play much more important roles, affecting the frequency of utilization and the order of activation of multiple initiation sites. Finally, these results confirm that initiation sites are extremely redundant elements of the EBV genome. We propose that these conclusions also apply to mammalian chromosomes.

Intestinal Permeability: The Basics

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Ingvar Bjarnason

1995-01-01

Full Text Available The authors review some of the more fundamental principles underlying the noninvasive assessment of intestinal permeability in humans, the choice of test markers and their analyses, and the practical aspects of test dose composition and how these can be changed to allow the specific assessment of regional permeability changes and other intestinal functions. The implications of increased intestinal permeability in the pathogenesis of human disease is discussed in relation to findings in patients with Crohn’s disease. A common feature of increased intestinal permeability is the development of a low grade enteropathy, and while quantitatively similar changes may be found in Crohn’s disease these seem to predict relapse of disease. Moreover, factors associated with relapse of Crohn’s disease have in common an action to increase intestinal permeability. While increased intestinal permeability does not seem to be important in the etiology of Crohn’s disease it may be a central mechanism in the clinical relapse of disease.

Predicting chemically-induced skin reactions. Part II: QSAR models of skin permeability and the relationships between skin permeability and skin sensitization

Energy Technology Data Exchange (ETDEWEB)

Alves, Vinicius M. [Laboratory of Molecular Modeling and Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO 74605-220 (Brazil); Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599 (United States); Muratov, Eugene [Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599 (United States); Laboratory of Theoretical Chemistry, A.V. Bogatsky Physical–Chemical Institute NAS of Ukraine, Odessa 65080 (Ukraine); Fourches, Denis [Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599 (United States); Strickland, Judy; Kleinstreuer, Nicole [ILS/Contractor supporting the NTP Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM), P.O. Box 13501, Research Triangle Park, NC 27709 (United States); Andrade, Carolina H. [Laboratory of Molecular Modeling and Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO 74605-220 (Brazil); Tropsha, Alexander, E-mail: alex_tropsha@unc.edu [Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599 (United States)

2015-04-15

Skin permeability is widely considered to be mechanistically implicated in chemically-induced skin sensitization. Although many chemicals have been identified as skin sensitizers, there have been very few reports analyzing the relationships between molecular structure and skin permeability of sensitizers and non-sensitizers. The goals of this study were to: (i) compile, curate, and integrate the largest publicly available dataset of chemicals studied for their skin permeability; (ii) develop and rigorously validate QSAR models to predict skin permeability; and (iii) explore the complex relationships between skin sensitization and skin permeability. Based on the largest publicly available dataset compiled in this study, we found no overall correlation between skin permeability and skin sensitization. In addition, cross-species correlation coefficient between human and rodent permeability data was found to be as low as R{sup 2} = 0.44. Human skin permeability models based on the random forest method have been developed and validated using OECD-compliant QSAR modeling workflow. Their external accuracy was high (Q{sup 2}{sub ext} = 0.73 for 63% of external compounds inside the applicability domain). The extended analysis using both experimentally-measured and QSAR-imputed data still confirmed the absence of any overall concordance between skin permeability and skin sensitization. This observation suggests that chemical modifications that affect skin permeability should not be presumed a priori to modulate the sensitization potential of chemicals. The models reported herein as well as those developed in the companion paper on skin sensitization suggest that it may be possible to rationally design compounds with the desired high skin permeability but low sensitization potential. - Highlights: • It was compiled the largest publicly-available skin permeability dataset. • Predictive QSAR models were developed for skin permeability. • No concordance between skin

Predicting chemically-induced skin reactions. Part II: QSAR models of skin permeability and the relationships between skin permeability and skin sensitization

International Nuclear Information System (INIS)

Alves, Vinicius M.; Muratov, Eugene; Fourches, Denis; Strickland, Judy; Kleinstreuer, Nicole; Andrade, Carolina H.; Tropsha, Alexander

2015-01-01

Skin permeability is widely considered to be mechanistically implicated in chemically-induced skin sensitization. Although many chemicals have been identified as skin sensitizers, there have been very few reports analyzing the relationships between molecular structure and skin permeability of sensitizers and non-sensitizers. The goals of this study were to: (i) compile, curate, and integrate the largest publicly available dataset of chemicals studied for their skin permeability; (ii) develop and rigorously validate QSAR models to predict skin permeability; and (iii) explore the complex relationships between skin sensitization and skin permeability. Based on the largest publicly available dataset compiled in this study, we found no overall correlation between skin permeability and skin sensitization. In addition, cross-species correlation coefficient between human and rodent permeability data was found to be as low as R 2 = 0.44. Human skin permeability models based on the random forest method have been developed and validated using OECD-compliant QSAR modeling workflow. Their external accuracy was high (Q 2 ext = 0.73 for 63% of external compounds inside the applicability domain). The extended analysis using both experimentally-measured and QSAR-imputed data still confirmed the absence of any overall concordance between skin permeability and skin sensitization. This observation suggests that chemical modifications that affect skin permeability should not be presumed a priori to modulate the sensitization potential of chemicals. The models reported herein as well as those developed in the companion paper on skin sensitization suggest that it may be possible to rationally design compounds with the desired high skin permeability but low sensitization potential. - Highlights: • It was compiled the largest publicly-available skin permeability dataset. • Predictive QSAR models were developed for skin permeability. • No concordance between skin sensitization and

Entrapment of active ion-permeable cyanobacteria (Anacystis nidulans) in calcium alginate

Energy Technology Data Exchange (ETDEWEB)

Papageorgiou, G.C.; Kalosaka, K.; Sotiropoulou, G.; Barbotin, J.N.; Thomasset, B.; Thomas, T.

1988-12-01

Cells of the unicellular cyanobacterium Anacystis nidulans were made permeable to ions by treating them with lysozyme and EDTA in a way that leaves the photosynthetic water-splitting function, the photoreduction of exogenous oxidants and the peptidoglycan exoskeleton of the cell virtually intact. The permeabilized cells (permeaplasts) were subsequently immobilized by entrapment in calcium alginate beads. The immobilized preparation exhibits remarkable stability both on storage and in action. On prolonged storage at room temperature in darkness, its photosynthetic activity deteriorates one-third as fast as the activity of immobilized intact cells. Illumination accelerates deactivation. Tested in prolonged runs, however, performed in an illuminated open reactor, alginate-immobilized Anacystis permeaplasts were capable of photoreducing ionic oxidants (ferricyanide) and of exporting ionic reductants (ferrocyanide) to the suspension medium continuously for more than 5 h before being totally inactivated. It is also shown that the major impediment to the photoreduction performance of immobilized permeaplasts arises from diffusion limitations, while the photonic limitation due to light reflection and scattering is approx. 7%.

The effect of microneedles on the skin permeability and antitumor activity of topical 5-fluorouracil

Directory of Open Access Journals (Sweden)

Youssef W. Naguib

2014-02-01

Full Text Available Topical 5-fluorouracil (5-FU is approved for the treatment of superficial basal cell carcinoma and actinic keratosis. However, 5-FU suffers from poor skin permeation. Microneedles have been successfully applied to improve the skin permeability of small and large molecules, and even nanoparticles, by creating micron-sized pores in the stratum corneum layer of the skin. In this report, the feasibility of using microneedles to increase the skin permeability of 5-FU was tested. Using full thickness mouse skin mounted on Franz diffusion apparatus, it was shown that the flux of 5-FU through the skin was increased by up to 4.5-fold when the skin was pretreated with microneedles (500 μm in length, 50 μm in base diameter. In a mouse model with B16-F10 mouse melanoma cells implanted in the subcutaneous space, the antitumor activity of a commercially available 5-FU topical cream (5% was significantly enhanced when the cream was applied on a skin area that was pretreated with microneedles, as compared to when the cream was simply applied on a skin area, underneath which the tumor cells were implanted, and without pretreatment of the skin with microneedles. Fluorouracil is not approved for melanoma therapy, but the clinical efficacy of topical 5-FU against tumors such as basal cell carcinoma may be improved by integrating microneedle technology into the therapy.

Class I ADP-ribosylation factors are involved in enterovirus 71 replication.

Directory of Open Access Journals (Sweden)

Jianmin Wang

Full Text Available Enterovirus 71 is one of the major causative agents of hand, foot, and mouth disease in infants and children. Replication of enterovirus 71 depends on host cellular factors. The viral replication complex is formed in novel, cytoplasmic, vesicular compartments. It has not been elucidated which cellular pathways are hijacked by the virus to create these vesicles. Here, we investigated whether proteins associated with the cellular secretory pathway were involved in enterovirus 71 replication. We used a loss-of-function assay, based on small interfering RNA. We showed that enterovirus 71 RNA replication was dependent on the activity of Class I ADP-ribosylation factors. Simultaneous depletion of ADP-ribosylation factors 1 and 3, but not three others, inhibited viral replication in cells. We also demonstrated with various techniques that the brefeldin-A-sensitive guanidine nucleotide exchange factor, GBF1, was critically important for enterovirus 71 replication. Our results suggested that enterovirus 71 replication depended on GBF1-mediated activation of Class I ADP-ribosylation factors. These results revealed a connection between enterovirus 71 replication and the cellular secretory pathway; this pathway may represent a novel target for antiviral therapies.

Class I ADP-ribosylation factors are involved in enterovirus 71 replication.

Science.gov (United States)

Wang, Jianmin; Du, Jiang; Jin, Qi

2014-01-01

Enterovirus 71 is one of the major causative agents of hand, foot, and mouth disease in infants and children. Replication of enterovirus 71 depends on host cellular factors. The viral replication complex is formed in novel, cytoplasmic, vesicular compartments. It has not been elucidated which cellular pathways are hijacked by the virus to create these vesicles. Here, we investigated whether proteins associated with the cellular secretory pathway were involved in enterovirus 71 replication. We used a loss-of-function assay, based on small interfering RNA. We showed that enterovirus 71 RNA replication was dependent on the activity of Class I ADP-ribosylation factors. Simultaneous depletion of ADP-ribosylation factors 1 and 3, but not three others, inhibited viral replication in cells. We also demonstrated with various techniques that the brefeldin-A-sensitive guanidine nucleotide exchange factor, GBF1, was critically important for enterovirus 71 replication. Our results suggested that enterovirus 71 replication depended on GBF1-mediated activation of Class I ADP-ribosylation factors. These results revealed a connection between enterovirus 71 replication and the cellular secretory pathway; this pathway may represent a novel target for antiviral therapies.

Advantageous Solubility-Permeability Interplay When Using Amorphous Solid Dispersion (ASD) Formulation for the BCS Class IV P-gp Substrate Rifaximin: Simultaneous Increase of Both the Solubility and the Permeability.

Science.gov (United States)

Beig, Avital; Fine-Shamir, Noa; Lindley, David; Miller, Jonathan M; Dahan, Arik

2017-05-01

Rifaximin is a BCS class IV (low-solubility, low-permeability) drug and also a P-gp substrate. The aims of this work were to assess the efficiency of different rifaximin amorphous solid dispersion (ASDs) formulations in achieving and maintaining supersaturation and to investigate the consequent solubility-permeability interplay. Spray-dried rifaximin ASDs were prepared with different hydrophilic polymers and their ability to achieve and maintain supersaturation was assessed. Then, rifaximin's apparent intestinal permeability was investigated as a function of increasing supersaturation both in vitro using the parallel artificial membrane permeability assay (PAMPA) and in vivo using the single-pass rat intestinal perfusion (SPIP) model. The efficiency of the different ASDs to achieve and maintain supersaturation of rifaximin was found to be highly polymer dependent, and the copovidone/HPC-SL formulation was found to be superior to the other two, allowing supersaturation of 200× that of the crystalline solubility for 20 h. In vitro, rifaximin flux was increased and the apparent permeability was constant as a function of increasing supersaturation level. In vivo, on the other hand, absorption rate coefficient (k a ) was first constant as a function of increasing supersaturation, but at 250×, the crystalline solubility k a was doubled, similar to the k a in the presence of the strong P-gp inhibitor GF120918. In conclusion, a new and favorable nature of solubility-permeability interplay was revealed in this work: delivering high supersaturation level of the BCS class IV drug rifaximin via ASD, thereby saturating the drugs' P-gp-mediated efflux transport, led to the favorable unique win-win situation, where both the solubility and the permeability increased simultaneously.

Proteasome activity is important for replication recovery, CHK1 phosphorylation and prevention of G2 arrest after low-dose formaldehyde

Energy Technology Data Exchange (ETDEWEB)

Ortega-Atienza, Sara; Green, Samantha E.; Zhitkovich, Anatoly, E-mail: anatoly_zhitkovich@brown.edu

2015-07-15

Formaldehyde (FA) is a human carcinogen with numerous sources of environmental and occupational exposures. This reactive aldehyde is also produced endogenously during metabolism of drugs and other processes. DNA–protein crosslinks (DPCs) are considered to be the main genotoxic lesions for FA. Accumulating evidence suggests that DPC repair in high eukaryotes involves proteolysis of crosslinked proteins. Here, we examined a role of the main cellular proteolytic machinery proteasomes in toxic responses of human lung cells to low FA doses. We found that transient inhibition of proteasome activity increased cytotoxicity and diminished clonogenic viability of FA-treated cells. Proteasome inactivation exacerbated suppressive effects of FA on DNA replication and increased the levels of the genotoxic stress marker γ-H2AX in normal human cells. A transient loss of proteasome activity in FA-exposed cells also caused delayed perturbations of cell cycle, which included G2 arrest and a depletion of S-phase populations at FA doses that had no effects in control cells. Proteasome activity diminished p53-Ser15 phosphorylation but was important for FA-induced CHK1 phosphorylation, which is a biochemical marker of DPC proteolysis in replicating cells. Unlike FA, proteasome inhibition had no effect on cell survival and CHK1 phosphorylation by the non-DPC replication stressor hydroxyurea. Overall, we obtained evidence for the importance of proteasomes in protection of human cells against biologically relevant doses of FA. Biochemically, our findings indicate the involvement of proteasomes in proteolytic repair of DPC, which removes replication blockage by these highly bulky lesions. - Highlights: • Proteasome inhibition enhances cytotoxicity of low-dose FA in human lung cells. • Active proteasomes diminish replication-inhibiting effects of FA. • Proteasome activity prevents delayed G2 arrest in FA-treated cells. • Proteasome inhibition exacerbates replication stress by FA in

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.

Assembly of Slx4 signaling complexes behind DNA replication forks.

Science.gov (United States)

Balint, Attila; Kim, TaeHyung; Gallo, David; Cussiol, Jose Renato; Bastos de Oliveira, Francisco M; Yimit, Askar; Ou, Jiongwen; Nakato, Ryuichiro; Gurevich, Alexey; Shirahige, Katsuhiko; Smolka, Marcus B; Zhang, Zhaolei; Brown, Grant W

2015-08-13

Obstructions to replication fork progression, referred to collectively as DNA replication stress, challenge genome stability. In Saccharomyces cerevisiae, cells lacking RTT107 or SLX4 show genome instability and sensitivity to DNA replication stress and are defective in the completion of DNA replication during recovery from replication stress. We demonstrate that Slx4 is recruited to chromatin behind stressed replication forks, in a region that is spatially distinct from that occupied by the replication machinery. Slx4 complex formation is nucleated by Mec1 phosphorylation of histone H2A, which is recognized by the constitutive Slx4 binding partner Rtt107. Slx4 is essential for recruiting the Mec1 activator Dpb11 behind stressed replication forks, and Slx4 complexes are important for full activity of Mec1. We propose that Slx4 complexes promote robust checkpoint signaling by Mec1 by stably recruiting Dpb11 within a discrete domain behind the replication fork, during DNA replication stress. © 2015 The Authors.

Rapid transient production in plants by replicating and non-replicating vectors yields high quality functional anti-HIV antibody.

Directory of Open Access Journals (Sweden)

Frank Sainsbury

2010-11-01

Full Text Available The capacity of plants and plant cells to produce large amounts of recombinant protein has been well established. Due to advantages in terms of speed and yield, attention has recently turned towards the use of transient expression systems, including viral vectors, to produce proteins of pharmaceutical interest in plants. However, the effects of such high level expression from viral vectors and concomitant effects on host cells may affect the quality of the recombinant product.To assess the quality of antibodies transiently expressed to high levels in plants, we have expressed and characterised the human anti-HIV monoclonal antibody, 2G12, using both replicating and non-replicating systems based on deleted versions of Cowpea mosaic virus (CPMV RNA-2. The highest yield (approximately 100 mg/kg wet weight leaf tissue of affinity purified 2G12 was obtained when the non-replicating CPMV-HT system was used and the antibody was retained in the endoplasmic reticulum (ER. Glycan analysis by mass-spectrometry showed that the glycosylation pattern was determined exclusively by whether the antibody was retained in the ER and did not depend on whether a replicating or non-replicating system was used. Characterisation of the binding and neutralisation properties of all the purified 2G12 variants from plants showed that these were generally similar to those of the Chinese hamster ovary (CHO cell-produced 2G12.Overall, the results demonstrate that replicating and non-replicating CPMV-based vectors are able to direct the production of a recombinant IgG similar in activity to the CHO-produced control. Thus, a complex recombinant protein was produced with no apparent effect on its biochemical properties using either high-level expression or viral replication. The speed with which a recombinant pharmaceutical with excellent biochemical characteristics can be produced transiently in plants makes CPMV-based expression vectors an attractive option for

Evolution of Database Replication Technologies for WLCG

CERN Document Server

Baranowski, Zbigniew; Blaszczyk, Marcin; Dimitrov, Gancho; Canali, Luca

2015-01-01

In this article we summarize several years of experience on database replication technologies used at WLCG and we provide a short review of the available Oracle technologies and their key characteristics. One of the notable changes and improvement in this area in recent past has been the introduction of Oracle GoldenGate as a replacement of Oracle Streams. We report in this article on the preparation and later upgrades for remote replication done in collaboration with ATLAS and Tier 1 database administrators, including the experience from running Oracle GoldenGate in production. Moreover, we report on another key technology in this area: Oracle Active Data Guard which has been adopted in several of the mission critical use cases for database replication between online and offline databases for the LHC experiments.

Feline coronavirus replication is affected by both cyclophilin A and cyclophilin B.

Science.gov (United States)

Tanaka, Yoshikazu; Sato, Yuka; Sasaki, Takashi

2017-02-01

Feline coronavirus (FCoV) causes the fatal disease feline infectious peritonitis, which is currently incurable by drug treatment, and no effective vaccines are available. Cyclosporin A (CsA), a cyclophilin (Cyp) inhibitor, inhibits the replication of FCoV in vitro and in vivo as well as the replication of human and animal coronaviruses. However, the mechanism underlying the regulation of coronavirus replication by CsA is unknown. In this study, we analysed the role of Cyps in FCoV replication using knockdown and knockout cells specific to Cyps. Inhibition of CypA and CypB reduced FCoV replication, with replication in knockout cells being much less than that in knockdown cells. Furthermore, the proteins expressed by CypA and CypB harbouring mutations in their respective predicted peptidyl-prolyl cis-transisomerase active sites, which also alter the affinities between Cyps and CsA, inhibited FCoV replication. These findings indicate that the peptidyl-prolyl cis-transisomerase active sites of Cyps might be required for FCoV replication.

A new MCM modification cycle regulates DNA replication initiation.

Science.gov (United States)

Wei, Lei; Zhao, Xiaolan

2016-03-01

The MCM DNA helicase is a central regulatory target during genome replication. MCM is kept inactive during G1, and it initiates replication after being activated in S phase. During this transition, the only known chemical change to MCM is the gain of multisite phosphorylation that promotes cofactor recruitment. Because replication initiation is intimately linked to multiple biological cues, additional changes to MCM can provide further regulatory points. Here, we describe a yeast MCM SUMOylation cycle that regulates replication. MCM subunits undergo SUMOylation upon loading at origins in G1 before MCM phosphorylation. MCM SUMOylation levels then decline as MCM phosphorylation levels rise, thus suggesting an inhibitory role of MCM SUMOylation during replication. Indeed, increasing MCM SUMOylation impairs replication initiation, partly through promoting the recruitment of a phosphatase that decreases MCM phosphorylation and activation. We propose that MCM SUMOylation counterbalances kinase-based regulation, thus ensuring accurate control of replication initiation.

Different Methods of Predicting Permeability in Shale

DEFF Research Database (Denmark)

Mbia, Ernest Ncha; Fabricius, Ida Lykke; Krogsbøll, Anette

by two to five orders of magnitudes at lower vertical effective stress below 40 MPa as the content of clay minerals increases causing heterogeneity in shale material. Indirect permeability from consolidation can give maximum and minimum values of shale permeability needed in simulating fluid flow......Permeability is often very difficult to measure or predict in shale lithology. In this work we are determining shale permeability from consolidation tests data using Wissa et al., (1971) approach and comparing the results with predicted permeability from Kozeny’s model. Core and cuttings materials...... effective stress to 9 μD at high vertical effective stress of 100 MPa. The indirect permeability calculated from consolidation tests falls in the same magnitude at higher vertical effective stress, above 40 MPa, as that of the Kozeny model for shale samples with high non-clay content ≥ 70% but are higher...

Preregistered Replication of "Affective Flexibility: Evaluative Processing Goals Shape Amygdala Activity".

Science.gov (United States)

Lumian, Daniel S; McRae, Kateri

2017-09-01

The human amygdala is sensitive to stimulus characteristics, and growing evidence suggests that it is also responsive to cognitive framing in the form of evaluative goals. To examine whether different evaluations of stimulus characteristics shape amygdala activation, we conducted a preregistered replication of Cunningham, Van Bavel, and Johnsen's (2008) study demonstrating flexible mapping of amygdala activation to stimulus characteristics, depending on evaluative goals. Participants underwent functional MRI scanning while viewing famous names under three conditions: They were asked to report their overall attitude toward each name, their positive associations only, or their negative associations only. We observed an interaction between condition and rating type, identified as the effect of interest in Cunningham et al. (2008). Specifically, postscan positivity, but not negativity, ratings predicted left amygdala activation when participants were asked to evaluate positive, but not negative, associations with the names. These results provide convergent evidence that cognitive framing, in the form of evaluative goals, can significantly alter whether amygdala activation indexes positivity or negativity.

Biostable glucose permeable polymer

DEFF Research Database (Denmark)

2017-01-01

A new biostable glucose permeable polymer has been developed which is useful, for example, in implantable glucose sensors. This biostable glucose permeable polymer has a number of advantageous characteristics and, for example, does not undergo hydrolytic cleavage and degradation, thereby providing...... a composition that facilitates long term sensor stability in vivo. The versatile characteristics of this polymer allow it to be used in a variety of contexts, for example to form the body of an implantable glucose sensor. The invention includes the polymer composition, sensor systems formed from this polymer...

Zinc binding activity of human metapneumovirus M2-1 protein is indispensable for viral replication and pathogenesis in vivo.

Science.gov (United States)

Cai, Hui; Zhang, Yu; Ma, Yuanmei; Sun, Jing; Liang, Xueya; Li, Jianrong

2015-06-01

Human metapneumovirus (hMPV) is a member of the Pneumovirinae subfamily in the Paramyxoviridae family that causes respiratory tract infections in humans. Unlike members of the Paramyxovirinae subfamily, the polymerase complex of pneumoviruses requires an additional cofactor, the M2-1 protein, which functions as a transcriptional antitermination factor. The M2-1 protein was found to incorporate zinc ions, although the specific role(s) of the zinc binding activity in viral replication and pathogenesis remains unknown. In this study, we found that the third cysteine (C21) and the last histidine (H25) in the zinc binding motif (CCCH) of hMPV M2-1 were essential for zinc binding activity, whereas the first two cysteines (C7 and C15) play only minor or redundant roles in zinc binding. In addition, the zinc binding motif is essential for the oligomerization of M2-1. Subsequently, recombinant hMPVs (rhMPVs) carrying mutations in the zinc binding motif were recovered. Interestingly, rhMPV-C21S and -H25L mutants, which lacked zinc binding activity, had delayed replication in cell culture and were highly attenuated in cotton rats. In contrast, rhMPV-C7S and -C15S strains, which retained 60% of the zinc binding activity, replicated as efficiently as rhMPV in cotton rats. Importantly, rhMPVs that lacked zinc binding activity triggered high levels of neutralizing antibody and provided complete protection against challenge with rhMPV. Taken together, these results demonstrate that zinc binding activity is indispensable for viral replication and pathogenesis in vivo. These results also suggest that inhibition of zinc binding activity may serve as a novel approach to rationally attenuate hMPV and perhaps other pneumoviruses for vaccine purposes. The pneumoviruses include many important human and animal pathogens, such as human respiratory syncytial virus (hRSV), hMPV, bovine RSV, and avian metapneumovirus (aMPV). Among these viruses, hRSV and hMPV are the leading causes of acute

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.

Transverse Chemotactic Migration of Bacteria from High to Low Permeability Regions in a Dual Permeability Porous Microfluidic Device

Science.gov (United States)

Singh, R.; Olson, M. S.

2011-12-01

Low permeability regions sandwiched between high permeability regions such as clay lenses are difficult to treat using conventional treatment methods. Trace concentrations of contaminants such as non-aqueous phase liquids (NAPLs) remain trapped in these regions and over the time diffuse out into surrounding water thereby acting as a long term source of groundwater contamination. Bacterial chemotaxis (directed migration toward a contaminant source), may be helpful in enhancing bioremediation of such contaminated sites. This study is focused on simulating a two-dimensional dual-permeability groundwater contamination scenario using microfluidic devices and evaluating transverse chemotactic migration of bacteria from high to low permeability regions. A novel bi-layer polydimethylsiloxane (PDMS) microfluidic device was fabricated using photolithography and soft lithography techniques to simulate contamination of a dual- permeability region due to leakage from an underground storage tank into a low permeability region. This device consists of a porous channel through which a bacterial suspension (Escherchia Coli HCB33) is flown and another channel for injecting contaminant/chemo-attractant (DL-aspertic acid) into the porous channel. The pore arrangement in the porous channel contains a 2-D low permeability region surrounded by high permeability regions on both sides. Experiments were performed under chemotactic and non-chemotactic (replacing attractant with buffer solution in the non porous channel) conditions. Images were captured in transverse pore throats at cross-sections 4.9, 9.8, and 19.6 mm downstream from the attractant injection point and bacteria were enumerated in the middle of each pore throat. Bacterial chemotaxis was quantified in terms of the change in relative bacterial counts in each pore throat at cross-sections 9.8 and 19.6 mm with respect to counts at the cross-section at 4.9 mm. Under non-chemotactic conditions, relative bacterial count was observed

An Experimental Study of Micron-Size Zero-Valent Iron Emplacement in Permeable Porous Media Using Polymer-Enhanced Fluids

Energy Technology Data Exchange (ETDEWEB)

Oostrom, Mart; Wietsma, Thomas W.; Covert, Matthew A.; Vermeul, Vince R.

2005-12-22

At the Hanford Site, an extensive In Situ Redox Manipulation (ISRM) permeable reactive barrier was installed to prevent chromate from reaching the Columbia River. However, chromium has been detected in several wells, indicating a premature loss of the reductive capacity in the aquifer. One possible cause for premature chromate breakthrough is associated with the presence of high-permeability zones in the aquifer. In these zones, groundwater moves relatively fast and is able to oxidize iron more rapidly. There is also a possibility that the high-permeability flow paths are deficient in reducing equivalents (e.g. reactive iron), required for barrier performance. One way enhancement of the current barrier reductive capacity can be achieved is by the addition of micron-scale zero-valent iron to the high-permeability zones within the aquifer. The potential emplacement of zero-valent iron (Fe0) into high-permeability Hanford sediments (Ringold Unit E gravels) using shear-thinning fluids containing polymers was investigated in three-dimensional wedge-shaped aquifer models. Polymers were used to create a suspension viscous enough to keep the Fe0 in solution for extended time periods to improve colloid movement into the porous media without causing a permanent detrimental decrease in hydraulic conductivity. Porous media were packed in the wedge-shaped flow cell to create either a heterogeneous layered system with a high-permeability zone in between two low-permeability zones or a high-permeability channel surrounded by low-permeability materials. The injection flow rate, polymer type, polymer concentration, and injected pore volumes were determined based on preliminary short- and long-column experiments.

Database Replication

CERN Document Server

Kemme, Bettina

2010-01-01

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

Predicting chemically-induced skin reactions. Part II: QSAR models of skin permeability and the relationships between skin permeability and skin sensitization

Science.gov (United States)

Alves, Vinicius M.; Muratov, Eugene; Fourches, Denis; Strickland, Judy; Kleinstreuer, Nicole; Andrade, Carolina H.; Tropsha, Alexander

2015-01-01

Skin permeability is widely considered to be mechanistically implicated in chemically-induced skin sensitization. Although many chemicals have been identified as skin sensitizers, there have been very few reports analyzing the relationships between molecular structure and skin permeability of sensitizers and non-sensitizers. The goals of this study were to: (i) compile, curate, and integrate the largest publicly available dataset of chemicals studied for their skin permeability; (ii) develop and rigorously validate QSAR models to predict skin permeability; and (iii) explore the complex relationships between skin sensitization and skin permeability. Based on the largest publicly available dataset compiled in this study, we found no overall correlation between skin permeability and skin sensitization. In addition, cross-species correlation coefficient between human and rodent permeability data was found to be as low as R2=0.44. Human skin permeability models based on the random forest method have been developed and validated using OECD-compliant QSAR modeling workflow. Their external accuracy was high (Q2ext = 0.73 for 63% of external compounds inside the applicability domain). The extended analysis using both experimentally-measured and QSAR-imputed data still confirmed the absence of any overall concordance between skin permeability and skin sensitization. This observation suggests that chemical modifications that affect skin permeability should not be presumed a priori to modulate the sensitization potential of chemicals. The models reported herein as well as those developed in the companion paper on skin sensitization suggest that it may be possible to rationally design compounds with the desired high skin permeability but low sensitization potential. PMID:25560673

Initiation preference at a yeast origin of replication.

Science.gov (United States)

Brewer, B J; Fangman, W L

1994-04-12

Replication origins in the yeast Saccharomyces cerevisiae are identified as autonomous replication sequence (ARS) elements. To examine the effect of origin density on replication initiation, we have analyzed the replication of a plasmid that contains two copies of the same origin, ARS1. The activation of origins and the direction that replication forks move through flanking sequences can be physically determined by analyzing replication intermediates on two-dimensional agarose gels. We find that only one of the two identical ARSs on the plasmid initiates replication on any given plasmid molecule; that is, this close spacing of ARSs results in an apparent interference between the potential origins. Moreover, in the particular plasmid that we constructed, one of the two identical copies of ARS1 is used four times more frequently than the other one. These results show that the plasmid context is critical for determining the preferred origin. This origin preference is also exhibited when the tandem copies of ARS1 are introduced into a yeast chromosome. The sequences responsible for establishing the origin preference have been identified by deletion analysis and are found to reside in a portion of the yeast URA3 gene.

Gene organization inside replication domains in mammalian genomes

Science.gov (United States)

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

2012-11-01

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

Integrating Electrokinetic and Bioremediation Process for Treating Oil Contaminated Low Permeability Soil

Science.gov (United States)

Ramadan, Bimastyaji Surya; Effendi, Agus Jatnika; Helmy, Qomarudin

2018-02-01

Traditional oil mining activities always ignores environmental regulation which may cause contamination in soil and environment. Crude oil contamination in low-permeability soil complicates recovery process because it requires substantial energy for excavating and crushing the soil. Electrokinetic technology can be used as an alternative technology to treat contaminated soil and improve bioremediation process (biostimulation) through transfer of ions and nutrient that support microorganism growth. This study was conducted using a combination of electrokinetic and bioremediation processes. Result shows that the application of electrokinetic and bioremediation in low permeability soils can provide hydrocarbon removal efficiency up to 46,3% in 7 days operation. The highest amount of microorganism can be found in 3-days operation, which is 2x108 CFU/ml using surfactant as flushing fluid for solubilizing hydrocarbon molecules. Enhancing bioremediation using electrokinetic process is very potential to recover oil contaminated low permeability soil in the future.

Insights into the Initiation of Eukaryotic DNA Replication.

Science.gov (United States)

Bruck, Irina; Perez-Arnaiz, Patricia; Colbert, Max K; Kaplan, Daniel L

2015-01-01

The initiation of DNA replication is a highly regulated event in eukaryotic cells to ensure that the entire genome is copied once and only once during S phase. The primary target of cellular regulation of eukaryotic DNA replication initiation is the assembly and activation of the replication fork helicase, the 11-subunit assembly that unwinds DNA at a replication fork. The replication fork helicase, called CMG for Cdc45-Mcm2-7, and GINS, assembles in S phase from the constituent Cdc45, Mcm2-7, and GINS proteins. The assembly and activation of the CMG replication fork helicase during S phase is governed by 2 S-phase specific kinases, CDK and DDK. CDK stimulates the interaction between Sld2, Sld3, and Dpb11, 3 initiation factors that are each required for the initiation of DNA replication. DDK, on the other hand, phosphorylates the Mcm2, Mcm4, and Mcm6 subunits of the Mcm2-7 complex. Sld3 recruits Cdc45 to Mcm2-7 in a manner that depends on DDK, and recent work suggests that Sld3 binds directly to Mcm2-7 and also to single-stranded DNA. Furthermore, recent work demonstrates that Sld3 and its human homolog Treslin substantially stimulate DDK phosphorylation of Mcm2. These data suggest that the initiation factor Sld3/Treslin coordinates the assembly and activation of the eukaryotic replication fork helicase by recruiting Cdc45 to Mcm2-7, stimulating DDK phosphorylation of Mcm2, and binding directly to single-stranded DNA as the origin is melted.

The use of tracers in the study of the ionic permeability of the nerve

International Nuclear Information System (INIS)

Guinnebault, M.

1961-01-01

The use of the radioactive tracers 24 Na and 42 K, and the electrophysiological fine study carried out on the plant Cephalopods nervous cells have made it possible, during ten years, to study the relationships between the electrical phenomena observed during the propagation of the nervous impulse and the ionic movements which occur at the cell membrane between the intra- and extra-cellular media. In the state of rest, the nerve fibres present a certain permeability towards sodium and potassium, a permeability which allows the renewal, from the extra-cellular medium, of the cations contained in the cytoplasm. At the moment of the passage of the nervous impulse, it is possible to demonstrate a temporary increase in the permeability towards the sodium which causes the entry of Na + ions into the nerve fibre, whilst, a few milliseconds later, the increase in the potassium permeability causes the departure of an equivalent quantity of K + ions. A recovery phase follows the passage of the nervous impulse, during which the original ionic conditions are re-established. If the potassium movements can be considered as passive, the expulsion of Na + requires, on the part of the cell, the use of a part of the metabolic energy. (author) [fr

Replication stress and oxidative damage contribute to aberrant constitutive activation of DNA damage signalling in human gliomas

DEFF Research Database (Denmark)

Bartkova, J; Hamerlik, P; Stockhausen, Marie

2010-01-01

damage signalling in low- and high-grade human gliomas, and analyze the sources of such endogenous genotoxic stress. Based on analyses of human glioblastoma multiforme (GBM) cell lines, normal astrocytes and clinical specimens from grade II astrocytomas (n=41) and grade IV GBM (n=60), we conclude...... that the DDR machinery is constitutively activated in gliomas, as documented by phosphorylated histone H2AX (gammaH2AX), activation of the ATM-Chk2-p53 pathway, 53BP1 foci and other markers. Oxidative DNA damage (8-oxoguanine) was high in some GBM cell lines and many GBM tumors, while it was low in normal...... brain and grade II astrocytomas, despite the degree of DDR activation was higher in grade II tumors. Markers indicative of ongoing DNA replication stress (Chk1 activation, Rad17 phosphorylation, replication protein A foci and single-stranded DNA) were present in GBM cells under high- or low...

In-situ infiltration performance of different permeable pavements in a employee used parking lot--A four-year study.

Science.gov (United States)

Kumar, Kuldip; Kozak, Joseph; Hundal, Lakhwinder; Cox, Albert; Zhang, Heng; Granato, Thomas

2016-02-01

Permeable pavements are being adopted as a green solution in many parts of the world to manage urban stormwater quantity and quality. This paper reports on the measured in-situ infiltration performance over a four-year period since construction and use of three permeable parking sections (permeable pavers, permeable concrete and permeable asphalt) of an employee car parking lot. There was only a marginal decline in infiltration rates of all three pavements after one year of use. However, between years two to four, the infiltration rates declined significantly due to clogging of pores either by dry deposition of particles and/or shear stress of vehicles driving and degrading the permeable surfaces; during the last two years, a greater decline was also observed in driving areas of the parking lots compared to parking slots, where minimal wear and tear are expected. Maintenance strategies were employed to reclaim some of the lost infiltration rate of the permeable pavements to limited success. Despite this decline, the infiltration rates were still four to five times higher than average rainstorm intensity in the region. Thus, these permeable pavement parking lots may have significant ecological importance due to their ability to infiltrate rainwater quickly, reduce the runoff in the catchment area, and also dampen runoff peak flows that could otherwise enter the collection system for treatment in a combined sewer area. Copyright © 2015 Elsevier Ltd. All rights reserved.

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.

Spacetime Replication of Quantum Information Using (2 , 3) Quantum Secret Sharing and Teleportation

Science.gov (United States)

Wu, Yadong; Khalid, Abdullah; Davijani, Masoud; Sanders, Barry

The aim of this work is to construct a protocol to replicate quantum information in any valid configuration of causal diamonds and assess resources required to physically realize spacetime replication. We present a set of codes to replicate quantum information along with a scheme to realize these codes using continuous-variable quantum optics. We use our proposed experimental realizations to determine upper bounds on the quantum and classical resources required to simulate spacetime replication. For four causal diamonds, our implementation scheme is more efficient than the one proposed previously. Our codes are designed using a decomposition algorithm for complete directed graphs, (2 , 3) quantum secret sharing, quantum teleportation and entanglement swapping. These results show the simulation of spacetime replication of quantum information is feasible with existing experimental methods. Alberta Innovates, NSERC, China's 1000 Talent Plan and the Institute for Quantum Information and Matter, which is an NSF Physics Frontiers Center (NSF Grant PHY-1125565) with support of the Gordon and Betty Moore Foundation (GBMF-2644).

Principal permeability determination from multiple horizontal well tests

Energy Technology Data Exchange (ETDEWEB)

Economides, M. [Texas A and M Univ., TX (United States); Munoz, A.; Ehlig-Economides, C.

1998-12-31

A method for obtaining principal permeability magnitudes and direction that requires only the linear flow regime from transient tests in three horizontal wells oriented in three distinct and arbitrary directions, is described. Well design optimization strategies require knowledge of both the principal permeability orientation as well as the horizontal permeability magnitudes. When the degree of horizontal permeability anisotropy (i.e. permeability in the bedding plane with respect to direction) is significant, the productivity of a long horizontal well will depend greatly on its direction, especially when the well is first brought into production. Productivities have been found to deviate substantially among wells in the same reservoir and this deviation has been attributed to differences in well orientation. In view of this fact, measuring permeability anisotropy becomes a compelling necessity. The success of the proposed method is illustrated by a case study in which the principal permeability magnitudes and direction from three wells were used to predict the productivity of a fourth well within 10 per cent. Use of the computed principal permeabilities from the case study, it was possible to forecast the cumulative production to show the significance of well trajectory optimization on the discounted cash flow and the net present value. 20 refs., 3 figs.

Data from Investigating Variation in Replicability: A “Many Labs” Replication Project

Directory of Open Access Journals (Sweden)

Richard A. Klein

2014-04-01

Full Text Available This dataset is from the Many Labs Replication Project in which 13 effects were replicated across 36 samples and over 6,000 participants. Data from the replications are included, along with demographic variables about the participants and contextual information about the environment in which the replication was conducted. Data were collected in-lab and online through a standardized procedure administered via an online link. The dataset is stored on the Open Science Framework website. These data could be used to further investigate the results of the included 13 effects or to study replication and generalizability more broadly.

Phosphoproteomic Analysis of KSHV-Infected Cells Reveals Roles of ORF45-Activated RSK during Lytic Replication.

Directory of Open Access Journals (Sweden)

Denis Avey

2015-07-01

Full Text Available Kaposi's Sarcoma-Associated Herpesvirus (KSHV is an oncogenic virus which has adapted unique mechanisms to modulate the cellular microenvironment of its human host. The pathogenesis of KSHV is intimately linked to its manipulation of cellular signaling pathways, including the extracellular signal-regulated kinase (ERK mitogen-activated protein kinase (MAPK pathway. We have previously shown that KSHV ORF45 contributes to the sustained activation of both ERK and p90 ribosomal S6 kinase (RSK, a major functional mediator of ERK/MAPK signaling during KSHV lytic replication. ORF45-activated RSK is required for optimal KSHV lytic gene expression and progeny virion production, though the underlying mechanisms downstream of this activation are still unclear. We hypothesized that the activation of RSK by ORF45 causes differential phosphorylation of cellular and viral substrates, affecting biological processes essential for efficient KSHV lytic replication. Accordingly, we observed widespread and significant differences in protein phosphorylation upon induction of lytic replication. Mass-spectrometry-based phosphoproteomic screening identified putative substrates of ORF45-activated RSK in KSHV-infected cells. Bioinformatic analyses revealed that nuclear proteins, including several transcriptional regulators, were overrepresented among these candidates. We validated the ORF45/RSK-dependent phosphorylation of several putative substrates by employing KSHV BAC mutagenesis, kinase inhibitor treatments, and/or CRISPR-mediated knockout of RSK in KSHV-infected cells. Furthermore, we assessed the consequences of knocking out these substrates on ORF45/RSK-dependent regulation of gene expression and KSHV progeny virion production. Finally, we show data to support that ORF45 regulates the translational efficiency of a subset of viral/cellular genes with complex secondary structure in their 5' UTR. Altogether, these data shed light on the mechanisms by which KSHV ORF45

Direct Binding to Replication Protein A (RPA)-coated Single-stranded DNA Allows Recruitment of the ATR Activator TopBP1 to Sites of DNA Damage*

Science.gov (United States)

Acevedo, Julyana; Yan, Shan; Michael, W. Matthew

2016-01-01

A critical event for the ability of cells to tolerate DNA damage and replication stress is activation of the ATR kinase. ATR activation is dependent on the BRCT (BRCA1 C terminus) repeat-containing protein TopBP1. Previous work has shown that recruitment of TopBP1 to sites of DNA damage and stalled replication forks is necessary for downstream events in ATR activation; however, the mechanism for this recruitment was not known. Here, we use protein binding assays and functional studies in Xenopus egg extracts to show that TopBP1 makes a direct interaction, via its BRCT2 domain, with RPA-coated single-stranded DNA. We identify a point mutant that abrogates this interaction and show that this mutant fails to accumulate at sites of DNA damage and that the mutant cannot activate ATR. These data thus supply a mechanism for how the critical ATR activator, TopBP1, senses DNA damage and stalled replication forks to initiate assembly of checkpoint signaling complexes. PMID:27129245

Physically based model for extracting dual permeability parameters using non-Newtonian fluids

Science.gov (United States)

Abou Najm, M. R.; Basset, C.; Stewart, R. D.; Hauswirth, S.

2017-12-01

Dual permeability models are effective for the assessment of flow and transport in structured soils with two dominant structures. The major challenge to those models remains in the ability to determine appropriate and unique parameters through affordable, simple, and non-destructive methods. This study investigates the use of water and a non-Newtonian fluid in saturated flow experiments to derive physically-based parameters required for improved flow predictions using dual permeability models. We assess the ability of these two fluids to accurately estimate the representative pore sizes in dual-domain soils, by determining the effective pore sizes of macropores and micropores. We developed two sub-models that solve for the effective macropore size assuming either cylindrical (e.g., biological pores) or planar (e.g., shrinkage cracks and fissures) pore geometries, with the micropores assumed to be represented by a single effective radius. Furthermore, the model solves for the percent contribution to flow (wi) corresponding to the representative macro and micro pores. A user-friendly solver was developed to numerically solve the system of equations, given that relevant non-Newtonian viscosity models lack forms conducive to analytical integration. The proposed dual-permeability model is a unique attempt to derive physically based parameters capable of measuring dual hydraulic conductivities, and therefore may be useful in reducing parameter uncertainty and improving hydrologic model predictions.

Epigenetically-inherited centromere and neocentromere DNA replicates earliest in S-phase.

Directory of Open Access Journals (Sweden)

Amnon Koren

2010-08-01

Full Text Available Eukaryotic centromeres are maintained at specific chromosomal sites over many generations. In the budding yeast Saccharomyces cerevisiae, centromeres are genetic elements defined by a DNA sequence that is both necessary and sufficient for function; whereas, in most other eukaryotes, centromeres are maintained by poorly characterized epigenetic mechanisms in which DNA has a less definitive role. Here we use the pathogenic yeast Candida albicans as a model organism to study the DNA replication properties of centromeric DNA. By determining the genome-wide replication timing program of the C. albicans genome, we discovered that each centromere is associated with a replication origin that is the first to fire on its respective chromosome. Importantly, epigenetic formation of new ectopic centromeres (neocentromeres was accompanied by shifts in replication timing, such that a neocentromere became the first to replicate and became associated with origin recognition complex (ORC components. Furthermore, changing the level of the centromere-specific histone H3 isoform led to a concomitant change in levels of ORC association with centromere regions, further supporting the idea that centromere proteins determine origin activity. Finally, analysis of centromere-associated DNA revealed a replication-dependent sequence pattern characteristic of constitutively active replication origins. This strand-biased pattern is conserved, together with centromere position, among related strains and species, in a manner independent of primary DNA sequence. Thus, inheritance of centromere position is correlated with a constitutively active origin of replication that fires at a distinct early time. We suggest a model in which the distinct timing of DNA replication serves as an epigenetic mechanism for the inheritance of centromere position.

Human Parvovirus B19 Utilizes Cellular DNA Replication Machinery for Viral DNA Replication.

Science.gov (United States)

Zou, Wei; Wang, Zekun; Xiong, Min; Chen, Aaron Yun; Xu, Peng; Ganaie, Safder S; Badawi, Yomna; Kleiboeker, Steve; Nishimune, Hiroshi; Ye, Shui Qing; Qiu, Jianming

2018-03-01

Human parvovirus B19 (B19V) infection of human erythroid progenitor cells (EPCs) induces a DNA damage response and cell cycle arrest at late S phase, which facilitates viral DNA replication. However, it is not clear exactly which cellular factors are employed by this single-stranded DNA virus. Here, we used microarrays to systematically analyze the dynamic transcriptome of EPCs infected with B19V. We found that DNA metabolism, DNA replication, DNA repair, DNA damage response, cell cycle, and cell cycle arrest pathways were significantly regulated after B19V infection. Confocal microscopy analyses revealed that most cellular DNA replication proteins were recruited to the centers of viral DNA replication, but not the DNA repair DNA polymerases. Our results suggest that DNA replication polymerase δ and polymerase α are responsible for B19V DNA replication by knocking down its expression in EPCs. We further showed that although RPA32 is essential for B19V DNA replication and the phosphorylated forms of RPA32 colocalized with the replicating viral genomes, RPA32 phosphorylation was not necessary for B19V DNA replication. Thus, this report provides evidence that B19V uses the cellular DNA replication machinery for viral DNA replication. IMPORTANCE Human parvovirus B19 (B19V) infection can cause transient aplastic crisis, persistent viremia, and pure red cell aplasia. In fetuses, B19V infection can result in nonimmune hydrops fetalis and fetal death. These clinical manifestations of B19V infection are a direct outcome of the death of human erythroid progenitors that host B19V replication. B19V infection induces a DNA damage response that is important for cell cycle arrest at late S phase. Here, we analyzed dynamic changes in cellular gene expression and found that DNA metabolic processes are tightly regulated during B19V infection. Although genes involved in cellular DNA replication were downregulated overall, the cellular DNA replication machinery was tightly

A DNA sequence element that advances replication origin activation time in Saccharomyces cerevisiae.

Science.gov (United States)

Pohl, Thomas J; Kolor, Katherine; Fangman, Walton L; Brewer, Bonita J; Raghuraman, M K

2013-11-06

Eukaryotic origins of DNA replication undergo activation at various times in S-phase, allowing the genome to be duplicated in a temporally staggered fashion. In the budding yeast Saccharomyces cerevisiae, the activation times of individual origins are not intrinsic to those origins but are instead governed by surrounding sequences. Currently, there are two examples of DNA sequences that are known to advance origin activation time, centromeres and forkhead transcription factor binding sites. By combining deletion and linker scanning mutational analysis with two-dimensional gel electrophoresis to measure fork direction in the context of a two-origin plasmid, we have identified and characterized a 19- to 23-bp and a larger 584-bp DNA sequence that are capable of advancing origin activation time.

Abatement of ammonia emissions from digested manure using gas-permeable membranes

Science.gov (United States)

A new strategy to avoid ammonia emissions from anaerobically digested swine manure was tested using the gas-permeable membrane process. Evaluation of the efficiency of ammonia recovery from digestate as well as mitigation of ammonia emissions to the atmosphere were carried out. Digestate was colle...

Chronic DNA Replication Stress Reduces Replicative Lifespan of Cells by TRP53-Dependent, microRNA-Assisted MCM2-7 Downregulation.

Directory of Open Access Journals (Sweden)

Gongshi Bai

2016-01-01

Full Text Available Circumstances that compromise efficient DNA replication, such as disruptions to replication fork progression, cause a state known as DNA replication stress (RS. Whereas normally proliferating cells experience low levels of RS, excessive RS from intrinsic or extrinsic sources can trigger cell cycle arrest and senescence. Here, we report that a key driver of RS-induced senescence is active downregulation of the Minichromosome Maintenance 2-7 (MCM2-7 factors that are essential for replication origin licensing and which constitute the replicative helicase core. Proliferating cells produce high levels of MCM2-7 that enable formation of dormant origins that can be activated in response to acute, experimentally-induced RS. However, little is known about how physiological RS levels impact MCM2-7 regulation. We found that chronic exposure of primary mouse embryonic fibroblasts (MEFs to either genetically-encoded or environmentally-induced RS triggered gradual MCM2-7 repression, followed by inhibition of replication and senescence that could be accelerated by MCM hemizygosity. The MCM2-7 reduction in response to RS is TRP53-dependent, and involves a group of Trp53-dependent miRNAs, including the miR-34 family, that repress MCM expression in replication-stressed cells before they undergo terminal cell cycle arrest. miR-34 ablation partially rescued MCM2-7 downregulation and genomic instability in mice with endogenous RS. Together, these data demonstrate that active MCM2-7 repression is a physiologically important mechanism for RS-induced cell cycle arrest and genome maintenance on an organismal level.

Enhancing the intestinal membrane permeability of zanamivir: a carrier mediated prodrug approach.

Science.gov (United States)

Gupta, Sheeba Varghese; Gupta, Deepak; Sun, Jing; Dahan, Arik; Tsume, Yasuhiro; Hilfinger, John; Lee, Kyung-Dall; Amidon, Gordon L

2011-12-05

The purpose of this study was to improve the membrane permeability and oral absorption of the poorly permeable anti-influenza agent, zanamivir. The poor oral bioavailability is attributed to the high polarity (cLogP ∼ -5) resulting from the polar and zwitterionic nature of zanamivir. In order to improve the permeability of zanamivir, prodrugs with amino acids were developed to target the intestinal membrane transporter, hPepT1. Several acyloxy ester prodrugs of zanamivir conjugated with amino acids were synthesized and characterized. The prodrugs were evaluated for their chemical stability in buffers at various pHs and for their transport and tissue activation by enzymes. The acyloxy ester prodrugs of zanamivir were shown to competitively inhibit [(3)H]Gly-Sar uptake in Caco-2 cells (IC(50): 1.19 ± 0.33 mM for L-valyl prodrug of zanamivir). The L-valyl prodrug of zanamivir exhibited ∼3-fold higher uptake in transfected HeLa/hPepT1 cells compared to wild type HeLa cells, suggesting, at least in part, carrier mediated transport by the hPepT1 transporter. Further, enhanced transcellular permeability of prodrugs across Caco-2 monolayer compared to the parent drug (P(app) = 2.24 × 10(-6) ± 1.33 × 10(-7) cm/s for L-valyl prodrug of zanamivir), with only parent zanamivir appearing in the receiver compartment, indicates that the prodrugs exhibited both enhanced transport and activation in intestinal mucosal cells. Most significantly, several of these prodrugs exhibited high intestinal jejunal membrane permeability, similar to metoprolol, in the in situ rat intestinal perfusion system, a system highly correlated with human jejunal permeability. In summary, this mechanistic targeted prodrug strategy, to enhance oral absorption via intestinal membrane carriers such as hPepT1, followed by activation to parent drug (active pharmaceutical ingredient or API) in the mucosal cell, significantly improves the intestinal epithelial cell permeability of zanamivir and has the

Thioredoxin 80-Activated-Monocytes (TAMs) Inhibit the Replication of Intracellular Pathogens

DEFF Research Database (Denmark)

Cortes-Bratti, Ximena; Brasseres, Eugenie; Herrera-Rodriquez, Fabiola

2011-01-01

Background: Thioredoxin 80 (Trx80) is an 80 amino acid natural cleavage product of Trx, produced primarily by monocytes. Trx80 induces differentiation of human monocytes into a novel cell type, named Trx80-activated-monocytes (TAMs). Principal Findings: In this investigation we present evidence...... for a role of TAMs in the control of intracellular bacterial infections. As model pathogens we have chosen Listeria monocytogenes and Brucella abortus which replicate in the cytosol and the endoplasmic reticulum respectively. Our data indicate that TAMs efficiently inhibit intracellular growth of both L...... in TAMs compared to that observed in control cells 24 h post-infection, indicating that TAMs kill bacteria by preventing their escape from the endosomal compartments, which progress into a highly degradative phagolysosome. Significance: Our results show that Trx80 potentiates the bactericidal activities...

Viral replication. Structural basis for RNA replication by the hepatitis C virus polymerase.

Science.gov (United States)

Appleby, Todd C; Perry, Jason K; Murakami, Eisuke; Barauskas, Ona; Feng, Joy; Cho, Aesop; Fox, David; Wetmore, Diana R; McGrath, Mary E; Ray, Adrian S; Sofia, Michael J; Swaminathan, S; Edwards, Thomas E

2015-02-13

Nucleotide analog inhibitors have shown clinical success in the treatment of hepatitis C virus (HCV) infection, despite an incomplete mechanistic understanding of NS5B, the viral RNA-dependent RNA polymerase. Here we study the details of HCV RNA replication by determining crystal structures of stalled polymerase ternary complexes with enzymes, RNA templates, RNA primers, incoming nucleotides, and catalytic metal ions during both primed initiation and elongation of RNA synthesis. Our analysis revealed that highly conserved active-site residues in NS5B position the primer for in-line attack on the incoming nucleotide. A β loop and a C-terminal membrane-anchoring linker occlude the active-site cavity in the apo state, retract in the primed initiation assembly to enforce replication of the HCV genome from the 3' terminus, and vacate the active-site cavity during elongation. We investigated the incorporation of nucleotide analog inhibitors, including the clinically active metabolite formed by sofosbuvir, to elucidate key molecular interactions in the active site. Copyright © 2015, American Association for the Advancement of Science.

Promotion of Hendra Virus Replication by MicroRNA 146a

Science.gov (United States)

Marsh, Glenn A.; Jenkins, Kristie A.; Gantier, Michael P.; Tizard, Mark L.; Middleton, Deborah; Lowenthal, John W.; Haining, Jessica; Izzard, Leonard; Gough, Tamara J.; Deffrasnes, Celine; Stambas, John; Robinson, Rachel; Heine, Hans G.; Pallister, Jackie A.; Foord, Adam J.; Bean, Andrew G.; Wang, Lin-Fa

2013-01-01

Hendra virus is a highly pathogenic zoonotic paramyxovirus in the genus Henipavirus. Thirty-nine outbreaks of Hendra virus have been reported since its initial identification in Queensland, Australia, resulting in seven human infections and four fatalities. Little is known about cellular host factors impacting Hendra virus replication. In this work, we demonstrate that Hendra virus makes use of a microRNA (miRNA) designated miR-146a, an NF-κB-responsive miRNA upregulated by several innate immune ligands, to favor its replication. miR-146a is elevated in the blood of ferrets and horses infected with Hendra virus and is upregulated by Hendra virus in human cells in vitro. Blocking miR-146a reduces Hendra virus replication in vitro, suggesting a role for this miRNA in Hendra virus replication. In silico analysis of miR-146a targets identified ring finger protein (RNF)11, a member of the A20 ubiquitin editing complex that negatively regulates NF-κB activity, as a novel component of Hendra virus replication. RNA interference-mediated silencing of RNF11 promotes Hendra virus replication in vitro, suggesting that increased NF-κB activity aids Hendra virus replication. Furthermore, overexpression of the IκB superrepressor inhibits Hendra virus replication. These studies are the first to demonstrate a host miRNA response to Hendra virus infection and suggest an important role for host miRNAs in Hendra virus disease. PMID:23345523

DNA replication machinery is required for development in Drosophila.

Science.gov (United States)

Kohzaki, Hidetsugu; Asano, Maki; Murakami, Yota

2018-01-01

 In Drosophila , some factors involved in chromosome replication seem to be involved in gene amplification and endoreplication, which are actively utilized in particular tissue development, but direct evidence has not been shown. Therefore, we examined the effect of depletion of replication factors on these processes. First, we confirmed RNAi knockdown can be used for the depletion of replication factors by comparing the phenotypes of RNAi knockdown and deletion or point mutants of the components of DNA licensing factor, MCM2, MCM4 and Cdt1. Next, we found that tissue-specific RNAi knockdown of replication factors caused tissue-specific defects, probably due to defects in DNA replication. In particular, we found that depletion inhibited gene amplification of the chorion gene in follicle cells and endoreplication in salivary glands, showing that chromosomal DNA replication factors are required for these processes. Finally, using RNAi, we screened the genes for chromosomal DNA replication that affected tissue development. Interestingly, wing specific knockdown of Mcm10 induced wing formation defects. These results suggest that some components of chromosomal replication machinery are directly involved in tissue development.

Integrating Electrokinetic and Bioremediation Process for Treating Oil Contaminated Low Permeability Soil

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Surya Ramadan Bimastyaji

2018-01-01

Full Text Available Traditional oil mining activities always ignores environmental regulation which may cause contamination in soil and environment. Crude oil contamination in low-permeability soil complicates recovery process because it requires substantial energy for excavating and crushing the soil. Electrokinetic technology can be used as an alternative technology to treat contaminated soil and improve bioremediation process (biostimulation through transfer of ions and nutrient that support microorganism growth. This study was conducted using a combination of electrokinetic and bioremediation processes. Result shows that the application of electrokinetic and bioremediation in low permeability soils can provide hydrocarbon removal efficiency up to 46,3% in 7 days operation. The highest amount of microorganism can be found in 3-days operation, which is 2x108 CFU/ml using surfactant as flushing fluid for solubilizing hydrocarbon molecules. Enhancing bioremediation using electrokinetic process is very potential to recover oil contaminated low permeability soil in the future.

Murine leukemia virus (MLV replication monitored with fluorescent proteins

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Bittner Alexandra

2004-12-01

Full Text Available Abstract Background Cancer gene therapy will benefit from vectors that are able to replicate in tumor tissue and cause a bystander effect. Replication-competent murine leukemia virus (MLV has been described to have potential as cancer therapeutics, however, MLV infection does not cause a cytopathic effect in the infected cell and viral replication can only be studied by immunostaining or measurement of reverse transcriptase activity. Results We inserted the coding sequences for green fluorescent protein (GFP into the proline-rich region (PRR of the ecotropic envelope protein (Env and were able to fluorescently label MLV. This allowed us to directly monitor viral replication and attachment to target cells by flow cytometry. We used this method to study viral replication of recombinant MLVs and split viral genomes, which were generated by replacement of the MLV env gene with the red fluorescent protein (RFP and separately cloning GFP-Env into a retroviral vector. Co-transfection of both plasmids into target cells resulted in the generation of semi-replicative vectors, and the two color labeling allowed to determine the distribution of the individual genomes in the target cells and was indicative for the occurrence of recombination events. Conclusions Fluorescently labeled MLVs are excellent tools for the study of factors that influence viral replication and can be used to optimize MLV-based replication-competent viruses or vectors for gene therapy.

Stabilization of Reversed Replication Forks by Telomerase Drives Telomere Catastrophe.

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Margalef, Pol; Kotsantis, Panagiotis; Borel, Valerie; Bellelli, Roberto; Panier, Stephanie; Boulton, Simon J

2018-01-25

Telomere maintenance critically depends on the distinct activities of telomerase, which adds telomeric repeats to solve the end replication problem, and RTEL1, which dismantles DNA secondary structures at telomeres to facilitate replisome progression. Here, we establish that reversed replication forks are a pathological substrate for telomerase and the source of telomere catastrophe in Rtel1 -/- cells. Inhibiting telomerase recruitment to telomeres, but not its activity, or blocking replication fork reversal through PARP1 inhibition or depleting UBC13 or ZRANB3 prevents the rapid accumulation of dysfunctional telomeres in RTEL1-deficient cells. In this context, we establish that telomerase binding to reversed replication forks inhibits telomere replication, which can be mimicked by preventing replication fork restart through depletion of RECQ1 or PARG. Our results lead us to propose that telomerase inappropriately binds to and inhibits restart of reversed replication forks within telomeres, which compromises replication and leads to critically short telomeres. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

ATR prohibits replication catastrophe by preventing global exhaustion of RPA.

Science.gov (United States)

Toledo, Luis Ignacio; Altmeyer, Matthias; Rask, Maj-Britt; Lukas, Claudia; Larsen, Dorthe Helena; Povlsen, Lou Klitgaard; Bekker-Jensen, Simon; Mailand, Niels; Bartek, Jiri; Lukas, Jiri

2013-11-21

ATR, activated by replication stress, protects replication forks locally and suppresses origin firing globally. Here, we show that these functions of ATR are mechanistically coupled. Although initially stable, stalled forks in ATR-deficient cells undergo nucleus-wide breakage after unscheduled origin firing generates an excess of single-stranded DNA that exhausts the nuclear pool of RPA. Partial reduction of RPA accelerated fork breakage, and forced elevation of RPA was sufficient to delay such "replication catastrophe" even in the absence of ATR activity. Conversely, unscheduled origin firing induced breakage of stalled forks even in cells with active ATR. Thus, ATR-mediated suppression of dormant origins shields active forks against irreversible breakage via preventing exhaustion of nuclear RPA. This study elucidates how replicating genomes avoid destabilizing DNA damage. Because cancer cells commonly feature intrinsically high replication stress, this study also provides a molecular rationale for their hypersensitivity to ATR inhibitors. Copyright © 2013 Elsevier Inc. All rights reserved.

Hyperthermia stimulates HIV-1 replication.

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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.

Permeability Tests on Eastern Scheldt Sand

DEFF Research Database (Denmark)

Jakobsen, Kim Parsberg

on the characteristics of the soil matrix, the permeability is determined for different void ratios. All tests are performed on reconstituted specimens of Eastern Scheldt Sand. The permeability is determined by use of a falling head apparatus. Finally the test results are briefly summarised and a relationship between......The flow through porous media plays an important role in various engineering disciplines, as for example in ground water hydrology and soil mechanics. In the present study the permeability is determined for a fine, saturated sand. As the flow through a porous media strongly depends...

Gas permeability and thermal behavior of polypropylene films used for packaging minimally processed fresh-cut potatoes: a case study.

Science.gov (United States)

Siracusa, Valentina; Blanco, Ignazio; Romani, Santina; Tylewicz, Urszula; Dalla Rosa, Marco

2012-10-01

This work reports an experimental study on the permeability and thermal behavior of commercial polypropylene (PP) film used for fresh-cut potatoes packaging. The permeability was tested using oxygen, carbon dioxide, nitrogen, mix of these 3 gases, normally used for modified atmosphere packaging (MAP) and Air, to understand if it would be possible to extend the shelf life of this food product designed for the catering field in respect to the packaging behavior. The temperature influence on permeability data, from 5 to 40 °C, was analyzed, before and after 4, 8, 12, 15, and 20 d of food contact, pointing out the dependence between temperature and gas transmission rate (GTR), solubility (S), diffusion coefficient (D), and time lag (t(L)) parameters. The activation energies (E) of the permeation process were determined with the different gases used in the experiments. The thermal behavior of PP film was studied by differential scanning calorimetry (DSC) and thermogravimetric analysis (TG) to well understand its thermal stability. Fourier transformed-infrared with attenuated total reflectance (FT-IR/ATR) spectroscopy was also performed in order to study the influence of the food contact on the chemical characteristics of the polymer film. The results obtained were discussed and compared each other. Studied samples showed, for all investigated gases, an increase of gas permeability and S values at higher temperature. Heat resistance classification among the sample as it is and stored in modified atmospheres was made. Finally all performed experiments have showed good polymer stability for the shelf-life storage potatoes under study. Study of packaging material was performed in a range of temperature, which can simulate the service condition to assess the suitability of a commercial polymer film for modified atmosphere packaging of fresh-cut potatoes minimally processed designed for catering purpose. © 2012 Institute of Food Technologists®

Registered Replication Report

DEFF Research Database (Denmark)

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

2017-01-01

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

The Role of miR-330-3p/PKC-α Signaling Pathway in Low-Dose Endothelial-Monocyte Activating Polypeptide-II Increasing the Permeability of Blood-Tumor Barrier

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Jiahui Liu

2017-12-01

Full Text Available This study was performed to determine whether EMAP II increases the permeability of the blood-tumor barrier (BTB by affecting the expression of miR-330-3p as well as its possible mechanisms. We determined the over-expression of miR-330-3p in glioma microvascular endothelial cells (GECs by Real-time PCR. Endothelial monocyte-activating polypeptide-II (EMAP-II significantly decreased the expression of miR-330-3p in GECs. Pre-miR-330-3p markedly decreased the permeability of BTB and increased the expression of tight junction (TJ related proteins ZO-1, occludin and claudin-5, however, anti-miR-330-3p had the opposite effects. Anti-miR-330-3p could enhance the effect of EMAP-II on increasing the permeability of BTB, however, pre-miR-330-3p partly reversed the effect of EMAP-II on that. Similarly, anti-miR-330-3p improved the effects of EMAP-II on increasing the expression levels of PKC-α and p-PKC-α in GECs and pre-miR-330-3p partly reversed the effects. MiR-330-3p could target bind to the 3′UTR of PKC-α. The results of in vivo experiments were similar to those of in vitro experiments. These suggested that EMAP-II could increase the permeability of BTB through inhibiting miR-330-3p which target negative regulation of PKC-α. Pre-miR-330-3p and PKC-α inhibitor decreased the BTB permeability and up-regulated the expression levels of ZO-1, occludin and claudin-5 while anti-miR-330-3p and PKC-α activator brought the reverse effects. Compared with EMAP-II, anti-miR-330-3p and PKC-α activator alone, the combination of the three combinations significantly increased the BTB permeability. EMAP-II combined with anti-miR-330-3p and PKCα activator could enhance the DOX’s effects on inhibiting the cell viabilities and increasing the apoptosis of U87 glioma cells. Our studies suggest that low-dose EMAP-II up-regulates the expression of PKC-α and increases the activity of PKC-α by inhibiting the expression of miR-330-3p, reduces the expression of ZO-1

DNA replication origins—where do we begin?

Science.gov (United States)

Prioleau, Marie-Noëlle; MacAlpine, David M.

2016-01-01

For more than three decades, investigators have sought to identify the precise locations where DNA replication initiates in mammalian genomes. The development of molecular and biochemical approaches to identify start sites of DNA replication (origins) based on the presence of defining and characteristic replication intermediates at specific loci led to the identification of only a handful of mammalian replication origins. The limited number of identified origins prevented a comprehensive and exhaustive search for conserved genomic features that were capable of specifying origins of DNA replication. More recently, the adaptation of origin-mapping assays to genome-wide approaches has led to the identification of tens of thousands of replication origins throughout mammalian genomes, providing an unprecedented opportunity to identify both genetic and epigenetic features that define and regulate their distribution and utilization. Here we summarize recent advances in our understanding of how primary sequence, chromatin environment, and nuclear architecture contribute to the dynamic selection and activation of replication origins across diverse cell types and developmental stages. PMID:27542827

Accurate control testing for clay liner permeability

Energy Technology Data Exchange (ETDEWEB)

Mitchell, R J

1991-08-01

Two series of centrifuge tests were carried out to evaluate the use of centrifuge modelling as a method of accurate control testing of clay liner permeability. The first series used a large 3 m radius geotechnical centrifuge and the second series a small 0.5 m radius machine built specifically for research on clay liners. Two permeability cells were fabricated in order to provide direct data comparisons between the two methods of permeability testing. In both cases, the centrifuge method proved to be effective and efficient, and was found to be free of both the technical difficulties and leakage risks normally associated with laboratory permeability testing of fine grained soils. Two materials were tested, a consolidated kaolin clay having an average permeability coefficient of 1.2{times}10{sup -9} m/s and a compacted illite clay having a permeability coefficient of 2.0{times}10{sup -11} m/s. Four additional tests were carried out to demonstrate that the 0.5 m radius centrifuge could be used for linear performance modelling to evaluate factors such as volumetric water content, compaction method and density, leachate compatibility and other construction effects on liner leakage. The main advantages of centrifuge testing of clay liners are rapid and accurate evaluation of hydraulic properties and realistic stress modelling for performance evaluations. 8 refs., 12 figs., 7 tabs.

Escherichia coli DnaE Polymerase Couples Pyrophosphatase Activity to DNA Replication.

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Fabio Lapenta

Full Text Available DNA Polymerases generate pyrophosphate every time they catalyze a step of DNA elongation. This elongation reaction is generally believed as thermodynamically favoured by the hydrolysis of pyrophosphate, catalyzed by inorganic pyrophosphatases. However, the specific action of inorganic pyrophosphatases coupled to DNA replication in vivo was never demonstrated. Here we show that the Polymerase-Histidinol-Phosphatase (PHP domain of Escherichia coli DNA Polymerase III α subunit features pyrophosphatase activity. We also show that this activity is inhibited by fluoride, as commonly observed for inorganic pyrophosphatases, and we identified 3 amino acids of the PHP active site. Remarkably, E. coli cells expressing variants of these catalytic residues of α subunit feature aberrant phenotypes, poor viability, and are subject to high mutation frequencies. Our findings indicate that DNA Polymerases can couple DNA elongation and pyrophosphate hydrolysis, providing a mechanism for the control of DNA extension rate, and suggest a promising target for novel antibiotics.

Synchronization of DNA array replication kinetics

Science.gov (United States)

Manturov, Alexey O.; Grigoryev, Anton V.

2016-04-01

In the present work we discuss the features of the DNA replication kinetics at the case of multiplicity of simultaneously elongated DNA fragments. The interaction between replicated DNA fragments is carried out by free protons that appears at the every nucleotide attachment at the free end of elongated DNA fragment. So there is feedback between free protons concentration and DNA-polymerase activity that appears as elongation rate dependence. We develop the numerical model based on a cellular automaton, which can simulate the elongation stage (growth of DNA strands) for DNA elongation process with conditions pointed above and we study the possibility of the DNA polymerases movement synchronization. The results obtained numerically can be useful for DNA polymerase movement detection and visualization of the elongation process in the case of massive DNA replication, eg, under PCR condition or for DNA "sequencing by synthesis" sequencing devices evaluation.

FBH1 Catalyzes Regression of Stalled Replication Forks

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Kasper Fugger

2015-03-01

Full Text Available DNA replication fork perturbation is a major challenge to the maintenance of genome integrity. It has been suggested that processing of stalled forks might involve fork regression, in which the fork reverses and the two nascent DNA strands anneal. Here, we show that FBH1 catalyzes regression of a model replication fork in vitro and promotes fork regression in vivo in response to replication perturbation. Cells respond to fork stalling by activating checkpoint responses requiring signaling through stress-activated protein kinases. Importantly, we show that FBH1, through its helicase activity, is required for early phosphorylation of ATM substrates such as CHK2 and CtIP as well as hyperphosphorylation of RPA. These phosphorylations occur prior to apparent DNA double-strand break formation. Furthermore, FBH1-dependent signaling promotes checkpoint control and preserves genome integrity. We propose a model whereby FBH1 promotes early checkpoint signaling by remodeling of stalled DNA replication forks.

Replication of Merkel cell polyomavirus induces reorganization of promyelocytic leukemia nuclear bodies.

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Neumann, Friederike; Czech-Sioli, Manja; Dobner, Thomas; Grundhoff, Adam; Schreiner, Sabrina; Fischer, Nicole

2016-11-01

Merkel cell polyomavirus (MCPyV) is associated with Merkel cell carcinoma (MCC), a rare but aggressive skin cancer. The virus is highly prevalent: 60-80 % of adults are seropositive; however, cells permissive for MCPyV infection are unknown. Consequently, very little information about the MCPyV life cycle is available. Until recently, MCPyV replication could only be studied using a semi-permissive in vitro replication system (Neumann et al., 2011; Feng et al., 2011, Schowalter et al., 2011). MCPyV replication most likely depends on subnuclear structures such as promyelocytic leukemia protein nuclear bodies (PML-NBs), which are known to play regulatory roles in the infection of many DNA viruses. Here, we investigated PML-NB components as candidate host factors to control MCPyV DNA replication. We showed that PML-NBs change in number and size in cells actively replicating MCPyV proviral DNA. We observed a significant increase in PML-NBs in cells positive for MCPyV viral DNA replication. Interestingly, a significant amount of cells actively replicating MCPyV did not show any Sp100 expression. While PML and Daxx had no effect on MCPyV DNA replication, MCPyV replication was increased in cells depleted for Sp100, strongly suggesting that Sp100 is a negative regulator of MCPyV DNA replication.

Centromere replication timing determines different forms of genomic instability in Saccharomyces cerevisiae checkpoint mutants during replication stress.

Science.gov (United States)

Feng, Wenyi; Bachant, Jeff; Collingwood, David; Raghuraman, M K; Brewer, Bonita J

2009-12-01

Yeast replication checkpoint mutants lose viability following transient exposure to hydroxyurea, a replication-impeding drug. In an effort to understand the basis for this lethality, we discovered that different events are responsible for inviability in checkpoint-deficient cells harboring mutations in the mec1 and rad53 genes. By monitoring genomewide replication dynamics of cells exposed to hydroxyurea, we show that cells with a checkpoint deficient allele of RAD53, rad53K227A, fail to duplicate centromeres. Following removal of the drug, however, rad53K227A cells recover substantial DNA replication, including replication through centromeres. Despite this recovery, the rad53K227A mutant fails to achieve biorientation of sister centromeres during recovery from hydroxyurea, leading to secondary activation of the spindle assembly checkpoint (SAC), aneuploidy, and lethal chromosome segregation errors. We demonstrate that cell lethality from this segregation defect could be partially remedied by reinforcing bipolar attachment. In contrast, cells with the mec1-1 sml1-1 mutations suffer from severely impaired replication resumption upon removal of hydroxyurea. mec1-1 sml1-1 cells can, however, duplicate at least some of their centromeres and achieve bipolar attachment, leading to abortive segregation and fragmentation of incompletely replicated chromosomes. Our results highlight the importance of replicating yeast centromeres early and reveal different mechanisms of cell death due to differences in replication fork progression.

Zonulin as prehaptoglobin2 regulates lung permeability and activates the complement system.

Science.gov (United States)

Rittirsch, Daniel; Flierl, Michael A; Nadeau, Brian A; Day, Danielle E; Huber-Lang, Markus S; Grailer, Jamison J; Zetoune, Firas S; Andjelkovic, Anuska V; Fasano, Alessio; Ward, Peter A

2013-06-15

Zonulin is a protein involved in the regulation of tight junctions (TJ) in epithelial or endothelial cells. Zonulin is known to affect TJ in gut epithelial cells, but little is known about its influences in other organs. Prehaptoglobin2 has been identified as zonulin and is related to serine proteases (MASPs, C1qrs) that activate the complement system. The current study focused on the role of zonulin in development of acute lung injury (ALI) in C57BL/6 male mice following intrapulmonary deposition of IgG immune complexes. A zonulin antagonist (AT-1001) and a related peptide with permeability agonist activities (AT-1002) were employed and given intratracheally or intravenously. Also, zonulin was blocked in lung with a neutralizing antibody. In a dose-dependent manner, AT-1001 or zonulin neutralizing antibody attenuated the intensity of ALI (as quantitated by albumin leak, neutrophil accumulation, and proinflammatory cytokines). A similar pattern was found using the bacterial lipopolysaccharide model of ALI. Using confocal microscopy on sections of injured lungs, staining patterns for TJ proteins were discontinuous, reduced, and fragmented. As expected, the leak of blood products into the alveolar space confirmed the passage of 3 and 20 kDa dextran, and albumin. In contrast to AT-1001, application of the zonulin agonist AT-1002 intensified ALI. Zonulin both in vitro and in vivo induced generation of complement C3a and C5a. Collectively, these data suggest that zonulin facilitates development of ALI both by enhancing albumin leak and complement activation as well as increased buildup of neutrophils and cytokines during development of ALI.

Rescue from replication stress during mitosis.

Science.gov (United States)

Fragkos, Michalis; Naim, Valeria

2017-04-03

Genomic instability is a hallmark of cancer and a common feature of human disorders, characterized by growth defects, neurodegeneration, cancer predisposition, and aging. Recent evidence has shown that DNA replication stress is a major driver of genomic instability and tumorigenesis. Cells can undergo mitosis with under-replicated DNA or unresolved DNA structures, and specific pathways are dedicated to resolving these structures during mitosis, suggesting that mitotic rescue from replication stress (MRRS) is a key process influencing genome stability and cellular homeostasis. Deregulation of MRRS following oncogene activation or loss-of-function of caretaker genes may be the cause of chromosomal aberrations that promote cancer initiation and progression. In this review, we discuss the causes and consequences of replication stress, focusing on its persistence in mitosis as well as the mechanisms and factors involved in its resolution, and the potential impact of incomplete replication or aberrant MRRS on tumorigenesis, aging and disease.

Demonstrations of Magnetic Phenomena: Measuring the Air Permeability Using Tablets

Science.gov (United States)

Lara, V. O. M.; Amaral, D. F.; Faria, D.; Vieira, L. P.

2014-01-01

We use a tablet to experimentally determine the dependencies of the magnetic field (B) on the electrical current and the axial distance from a coil (z). Our data shows good precision on the inverse cubic dependence of the magnetic field on the axial distance, B?z[superscript -3]. We obtain the value of air permeability µ[subscript air] with good…

Magnetic field extraction of trap-based electron beams using a high-permeability grid

International Nuclear Information System (INIS)

Hurst, N. C.; Danielson, J. R.; Surko, C. M.

2015-01-01

A method to form high quality electrostatically guided lepton beams is explored. Test electron beams are extracted from tailored plasmas confined in a Penning-Malmberg trap. The particles are then extracted from the confining axial magnetic field by passing them through a high magnetic permeability grid with radial tines (a so-called “magnetic spider”). An Einzel lens is used to focus and analyze the beam properties. Numerical simulations are used to model non-adiabatic effects due to the spider, and the predictions are compared with the experimental results. Improvements in beam quality are discussed relative to the use of a hole in a high permeability shield (i.e., in lieu of the spider), and areas for further improvement are described

The low/high BCS permeability class boundary: physicochemical comparison of metoprolol and labetalol.

Science.gov (United States)

Zur, Moran; Gasparini, Marisa; Wolk, Omri; Amidon, Gordon L; Dahan, Arik

2014-05-05

Although recognized as overly conservative, metoprolol is currently the common low/high BCS permeability class boundary reference compound, while labetalol was suggested as a potential alternative. The purpose of this study was to identify the various characteristics that the optimal marker should exhibit, and to investigate the suitability of labetalol as the permeability class reference drug. Labetalol's BCS solubility class was determined, and its physicochemical properties and intestinal permeability were thoroughly investigated, both in vitro and in vivo in rats, considering the complexity of the whole of the small intestine. Labetalol was found to be unequivocally a high-solubility compound. In the pH range throughout the small intestine (6.5-7.5), labetalol exhibited pH-dependent permeability, with higher permeability at higher pH values. While in vitro octanol-buffer partitioning (Log D) values of labetalol were significantly higher than those of metoprolol, the opposite was evident in the in vitro PAMPA permeability assay. The results of the in vivo perfusion studies in rats lay between the two contradictory in vitro studies; metoprolol was shown to have moderately higher rat intestinal permeability than labetalol. Theoretical distribution of the ionic species of the drugs was in corroboration with the experimental in vitro and the in vivo data. We propose three characteristics that the optimal permeability class reference drug should exhibit: (1) fraction dose absorbed in the range of 90%; (2) the optimal marker drug should be absorbed largely via passive transcellular permeability, with no/negligible carrier-mediated active intestinal transport (influx or efflux); and (3) the optimal marker drug should preferably be nonionizable. The data presented in this paper demonstrate that neither metoprolol nor labetalol can be regarded as optimal low/high-permeability class boundary standard. While metoprolol is too conservative due to its complete absorption

Recovery of ammonia and production of high-grade phosphates from side-stream digester effluents using gas-permeable membranes

Science.gov (United States)

Phosphorus recovery was combined with ammonia recovery using gas-permeable membranes. In a first step, the ammonia and alkalinity were removed from municipal side-stream wastewater using low-rate aeration and a gas-permeable membrane manifold. In a second step, the phosphorus was removed using magne...

Investigation clogging dynamic of permeable pavement systems using embedded sensors

Science.gov (United States)

Razzaghmanesh, Mostafa; Borst, Michael

2018-02-01

Permeable pavement is a stormwater control measure commonly selected in both new and retrofit applications. However, there is limited information about the clogging mechanism of these systems that effects the infiltration. A permeable pavement site located at the Seitz Elementary School, on Fort Riley, Kansas was selected for this study. An 80-space parking lot was built behind the school as part of an EPA collaboration with the U.S. Army. The parking lot design includes a permeable interlocking concrete pavement section along the downgradient edge. This study monitored the clogging progress of the pavement section using twelve water content reflectometers and three buried tipping bucket rain gauges. This clogging dynamic investigation was divided into three stages namely pre-clogged, transitional, and clogged. Recorded initial relative water content of all three stages were significantly and negatively correlated to antecedent dry weather periods with stronger correlations during clogged conditions. The peak relative water content correlation with peak rainfall 10-min intensity was significant for the water content reflectometers located on the western edge away from the eastern edge; this correlation was strongest during transition stage. Once clogged, rainfall measurements no longer correlated with the buried tipping bucket rain gauges. Both water content reflectometers and buried tipping bucket rain gauges showed the progress of surface clogging. For every 6 mm of rain, clogging advanced 1 mm across the surface. The results generally support the hypothesis that the clogging progresses from the upgradient to the downgradient edge. The magnitude of the contributing drainage area and rainfall characteristics are effective factors on rate and progression of clogging.

Evaluation of permeability of compacted bentonite ground considering heterogeneity by geostatistics

International Nuclear Information System (INIS)

Tanaka, Yukihisa; Nakamura, Kunihiko; Kudo, Kohji; Hironaga, Michihiko; Nakagami, Motonori; Niwase, Kazuhito; Komatsu, Shin-ichi

2007-01-01

The permeability of the bentonite ground as an engineered barrier is possibly designed to the value which is lower than that determined in terms of required performance because of heterogeneous distribution of permeability in the ground, which might be considerable when the ground is created by the compaction method. The effect of heterogeneity in the ground on the permeability of the bentonite ground should be evaluated by overall permeability of the ground, whereas in practice, the effect is evaluated by the distribution of permeability in the ground. Thus, in this study, overall permeability of the bentonite ground is evaluated from the permeability of the bentonite ground is evaluated from the permeability distribution determined using the geostatistical method with the dry density data as well as permeability data of the undisturbed sample recovered from the bentonite ground. Consequently, it was proved through this study that possibility of overestimation of permeability of the bentonite ground can be reduced if the overall permeability is used. (author)

Constitutively Active MAVS Inhibits HIV-1 Replication via Type I Interferon Secretion and Induction of HIV-1 Restriction Factors.

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Sachin Gupta

Full Text Available Type I interferon is known to inhibit HIV-1 replication through the induction of interferon stimulated genes (ISG, including a number of HIV-1 restriction factors. To better understand interferon-mediated HIV-1 restriction, we constructed a constitutively active form of the RIG-I adapter protein MAVS. Constitutive MAVS was generated by fusion of full length MAVS to a truncated form of the Epstein Barr virus protein LMP1 (ΔLMP1. Supernatant from ΔLMP1-MAVS-transfected 293T cells contained high levels of type I interferons and inhibited HIV replication in both TZM-bl and primary human CD4+ T cells. Supernatant from ΔLMP1-MAVS-transfected 293T cells also inhibited replication of VSV-G pseudotyped single cycle SIV in TZM-bl cells, suggesting restriction was post-entry and common to both HIV and SIV. Gene array analysis of ΔLMP1-MAVS-transfected 293T cells and trans-activated CD4+ T cells showed significant upregulation of ISG, including previously characterized HIV restriction factors Viperin, Tetherin, MxB, and ISG56. Interferon blockade studies implicated interferon-beta in this response. In addition to direct viral inhibition, ΔLMP1-MAVS markedly enhanced secretion of IFN-β and IL-12p70 by dendritic cells and the activation and maturation of dendritic cells. Based on this immunostimulatory activity, an adenoviral vector (Ad5 expressing ΔLMP1-MAVS was tested as a molecular adjuvant in an HIV vaccine mouse model. Ad5-Gag antigen combined with Ad5-ΔLMP1-MAVS enhanced control of vaccinia-gag replication in a mouse challenge model, with 4/5 animals showing undetectable virus following challenge. Overall, ΔLMP1-MAVS is a promising reagent to inhibit HIV-1 replication in infected tissues and enhance vaccine-mediated immune responses, while avoiding toxicity associated with systemic type I interferon administration.

Evaluation of permeable fractures in rock aquifers

Science.gov (United States)

Bok Lee, Hang

2015-04-01

In this study, the practical usefulness and fundamental applicability of a self-potential (SP) method for identifying the permeable fractures were evaluated by a comparison of SP methods with other geophysical logging methods and hydraulic tests. At a 10 m-shallow borehole in the study site, the candidates of permeable fractures crossing the borehole were first determined by conventional geophysical methods such as an acoustic borehole televiwer, temperature, electrical conductivity and gamma-gamma loggings, which was compared to the analysis by the SP method. Constant pressure injection and recovery tests were conducted for verification of the hydraulic properties of the fractures identified by various logging methods. The acoustic borehole televiwer and gamma-gamma loggings detected the open space or weathering zone within the borehole, but they cannot prove the possibility of a groundwater flow through the detected fractures. The temperature and electrical conductivity loggings had limitations to detect the fractured zones where groundwater in the borehole flows out to the surrounding rock aquifers. Comparison of results from different methods showed that there is a best correlation between the distribution of hydraulic conductivity and the variation of the SP signals, and the SP logging can estimate accurately the hydraulic activity as well as the location of permeable fractures. Based on the results, the SP method is recommended for determining the hydraulically-active fractures rather than other conventional geophysical loggings. This self-potential method can be effectively applied in the initial stage of a site investigation which selects the optimal location and evaluates the hydrogeological property of fractures in target sites for the underground structure including the geothermal reservoir and radioactive waste disposal.

A drainage data-based calculation method for coalbed permeability

International Nuclear Information System (INIS)

Lai, Feng-peng; Li, Zhi-ping; Fu, Ying-kun; Yang, Zhi-hao

2013-01-01

This paper establishes a drainage data-based calculation method for coalbed permeability. The method combines material balance and production equations. We use a material balance equation to derive the average pressure of the coalbed in the production process. The dimensionless water production index is introduced into the production equation for the water production stage. In the subsequent stage, which uses both gas and water, the gas and water production ratio is introduced to eliminate the effect of flush-flow radius, skin factor, and other uncertain factors in the calculation of coalbed methane permeability. The relationship between permeability and surface cumulative liquid production can be described as a single-variable cubic equation by derivation. The trend shows that the permeability initially declines and then increases after ten wells in the southern Qinshui coalbed methane field. The results show an exponential relationship between permeability and cumulative water production. The relationship between permeability and cumulative gas production is represented by a linear curve and that between permeability and surface cumulative liquid production is represented by a cubic polynomial curve. The regression result of the permeability and surface cumulative liquid production agrees with the theoretical mathematical relationship. (paper)

Capsid protein VP4 of human rhinovirus induces membrane permeability by the formation of a size-selective multimeric pore.

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Anusha Panjwani

2014-08-01

Full Text Available Non-enveloped viruses must deliver their viral genome across a cell membrane without the advantage of membrane fusion. The mechanisms used to achieve this remain poorly understood. Human rhinovirus, a frequent cause of the common cold, is a non-enveloped virus of the picornavirus family, which includes other significant pathogens such as poliovirus and foot-and-mouth disease virus. During picornavirus cell entry, the small myristoylated capsid protein VP4 is released from the virus, interacts with the cell membrane and is implicated in the delivery of the viral RNA genome into the cytoplasm to initiate replication. In this study, we have produced recombinant C-terminal histidine-tagged human rhinovirus VP4 and shown it can induce membrane permeability in liposome model membranes. Dextran size-exclusion studies, chemical crosslinking and electron microscopy demonstrated that VP4 forms a multimeric membrane pore, with a channel size consistent with transfer of the single-stranded RNA genome. The membrane permeability induced by recombinant VP4 was influenced by pH and was comparable to permeability induced by infectious virions. These findings present a molecular mechanism for the involvement of VP4 in cell entry and provide a model system which will facilitate exploration of VP4 as a novel antiviral target for the picornavirus family.

Distributional Replication

OpenAIRE

Beare, Brendan K.

2009-01-01

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

Fractal Theory for Permeability Prediction, Venezuelan and USA Wells

Science.gov (United States)

Aldana, Milagrosa; Altamiranda, Dignorah; Cabrera, Ana

2014-05-01

Inferring petrophysical parameters such as permeability, porosity, water saturation, capillary pressure, etc, from the analysis of well logs or other available core data has always been of critical importance in the oil industry. Permeability in particular, which is considered to be a complex parameter, has been inferred using both empirical and theoretical techniques. The main goal of this work is to predict permeability values on different wells using Fractal Theory, based on a method proposed by Pape et al. (1999). This approach uses the relationship between permeability and the geometric form of the pore space of the rock. This method is based on the modified equation of Kozeny-Carman and a fractal pattern, which allows determining permeability as a function of the cementation exponent, porosity and the fractal dimension. Data from wells located in Venezuela and the United States of America are analyzed. Employing data of porosity and permeability obtained from core samples, and applying the Fractal Theory method, we calculated the prediction equations for each well. At the beginning, this was achieved by training with 50% of the data available for each well. Afterwards, these equations were tested inferring over 100% of the data to analyze possible trends in their distribution. This procedure gave excellent results in all the wells in spite of their geographic distance, generating permeability models with the potential to accurately predict permeability logs in the remaining parts of the well for which there are no core samples, using even porority logs. Additionally, empirical models were used to determine permeability and the results were compared with those obtained by applying the fractal method. The results indicated that, although there are empirical equations that give a proper adjustment, the prediction results obtained using fractal theory give a better fit to the core reference data.

Chromatin Immunoprecipitation of Replication Factors Moving with the Replication Fork

OpenAIRE

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

2009-01-01

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

Permeability Barrier Generation in the Martian Lithosphere

Science.gov (United States)

Schools, Joe; Montési, Laurent

2015-11-01

Permeability barriers develop when a magma produced in the interior of a planet rises into the cooler lithosphere and crystallizes more rapidly than the lithosphere can deform (Sparks and Parmentier, 1991). Crystallization products may then clog the porous network in which melt is propagating, reducing the permeability to almost zero, i.e., forming a permeability barrier. Subsequent melts cannot cross the barrier. Permeability barriers have been useful to explain variations in crustal thickness at mid-ocean ridges on Earth (Magde et al., 1997; Hebert and Montési, 2011; Montési et al., 2011). We explore here under what conditions permeability barriers may form on Mars.We use the MELTS thermodynamic calculator (Ghiorso and Sack, 1995; Ghiorso et al., 2002; Asimow et al., 2004) in conjunction with estimated Martian mantle compositions (Morgan and Anders, 1979; Wänke and Dreibus, 1994; Lodders and Fegley, 1997; Sanloup et al., 1999; Taylor 2013) to model the formation of permeability barriers in the lithosphere of Mars. In order to represent potential past and present conditions of Mars, we vary the lithospheric thickness, mantle potential temperature (heat flux), oxygen fugacity, and water content.Our results show that permeability layers can develop in the thermal boundary layer of the simulated Martian lithosphere if the mantle potential temperature is higher than ~1500°C. The various Martian mantle compositions yield barriers in the same locations, under matching variable conditions. There is no significant difference in barrier location over the range of accepted Martian oxygen fugacity values. Water content is the most significant influence on barrier development as it reduces the temperature of crystallization, allowing melt to rise further into the lithosphere. Our lower temperature and thicker lithosphere model runs, which are likely the most similar to modern Mars, show no permeability barrier generation. Losing the possibility of having a permeability

Automation of cell-based drug absorption assays in 96-well format using permeable support systems.

Science.gov (United States)

Larson, Brad; Banks, Peter; Sherman, Hilary; Rothenberg, Mark

2012-06-01

Cell-based drug absorption assays, such as Caco-2 and MDCK-MDR1, are an essential component of lead compound ADME/Tox testing. The permeability and transport data they provide can determine whether a compound continues in the drug discovery process. Current methods typically incorporate 24-well microplates and are performed manually. Yet the need to generate absorption data earlier in the drug discovery process, on an increasing number of compounds, is driving the use of higher density plates. A simple, more efficient process that incorporates 96-well permeable supports and proper instrumentation in an automated process provides more reproducible data compared to manual methods. Here we demonstrate the ability to perform drug permeability and transport assays using Caco-2 or MDCKII-MDR1 cells. The assay procedure was automated in a 96-well format, including cell seeding, media and buffer exchanges, compound dispense, and sample removal using simple robotic instrumentation. Cell monolayer integrity was confirmed via transepithelial electrical resistance and Lucifer yellow measurements. Proper cell function was validated by analyzing apical-to-basolateral and basolateral-to-apical movement of rhodamine 123, a known P-glycoprotein substrate. Apparent permeability and efflux data demonstrate how the automated procedure provides a less variable method than manual processing, and delivers a more accurate assessment of a compound's absorption characteristics.

Individual and Contextual Factors Influencing Engagement in Learning Activities after Errors at Work: A Replication Study in a German Retail Bank

Science.gov (United States)

Leicher, Veronika; Mulder, Regina H.

2016-01-01

Purpose: The purpose of this replication study is to identify relevant individual and contextual factors influencing learning from errors at work and to determine if the predictors for learning activities are the same for the domains of nursing and retail banking. Design/methodology/approach: A cross-sectional replication study was carried out in…

Hydroxyurea-Induced Replication Stress

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Kenza Lahkim Bennani-Belhaj

2010-01-01

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

CRISPR-mediated control of the bacterial initiation of replication.

Science.gov (United States)

Wiktor, Jakub; Lesterlin, Christian; Sherratt, David J; Dekker, Cees

2016-05-05

Programmable control of the cell cycle has been shown to be a powerful tool in cell-biology studies. Here, we develop a novel system for controlling the bacterial cell cycle, based on binding of CRISPR/dCas9 to the origin-of-replication locus. Initiation of replication of bacterial chromosomes is accurately regulated by the DnaA protein, which promotes the unwinding of DNA at oriC We demonstrate that the binding of CRISPR/dCas9 to any position within origin or replication blocks the initiation of replication. Serial-dilution plating, single-cell fluorescence microscopy, and flow-cytometry experiments show that ongoing rounds of chromosome replication are finished upon CRISPR/dCas9 binding, but no new rounds are initiated. Upon arrest, cells stay metabolically active and accumulate cell mass. We find that elevating the temperature from 37 to 42°C releases the CRISR/dCas9 replication inhibition, and we use this feature to recover cells from the arrest. Our simple and robust method of controlling the bacterial cell cycle is a useful asset for synthetic biology and DNA-replication studies in particular. The inactivation of CRISPR/dCas9 binding at elevated temperatures may furthermore be of wide interest for CRISPR/Cas9 applications in genomic engineering. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Replication Catastrophe

DEFF Research Database (Denmark)

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

2017-01-01

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

Calculation of large scale relative permeabilities from stochastic properties of the permeability field and fluid properties

Energy Technology Data Exchange (ETDEWEB)

Lenormand, R.; Thiele, M.R. [Institut Francais du Petrole, Rueil Malmaison (France)

1997-08-01

The paper describes the method and presents preliminary results for the calculation of homogenized relative permeabilities using stochastic properties of the permeability field. In heterogeneous media, the spreading of an injected fluid is mainly sue to the permeability heterogeneity and viscosity fingering. At large scale, when the heterogeneous medium is replaced by a homogeneous one, we need to introduce a homogenized (or pseudo) relative permeability to obtain the same spreading. Generally, is derived by using fine-grid numerical simulations (Kyte and Berry). However, this operation is time consuming and cannot be performed for all the meshes of the reservoir. We propose an alternate method which uses the information given by the stochastic properties of the field without any numerical simulation. The method is based on recent developments on homogenized transport equations (the {open_quotes}MHD{close_quotes} equation, Lenormand SPE 30797). The MHD equation accounts for the three basic mechanisms of spreading of the injected fluid: (1) Dispersive spreading due to small scale randomness, characterized by a macrodispersion coefficient D. (2) Convective spreading due to large scale heterogeneities (layers) characterized by a heterogeneity factor H. (3) Viscous fingering characterized by an apparent viscosity ration M. In the paper, we first derive the parameters D and H as functions of variance and correlation length of the permeability field. The results are shown to be in good agreement with fine-grid simulations. The are then derived a function of D, H and M. The main result is that this approach lead to a time dependent . Finally, the calculated are compared to the values derived by history matching using fine-grid numerical simulations.

Suppressions of Serotonin-Induced Increased Vascular Permeability and Leukocyte Infiltration by Bixa orellana Leaf Extract

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Yoke Keong Yong

2013-01-01

Full Text Available The aim of the present study was to evaluate the anti-inflammatory activities of aqueous extract of Bixa orellana (AEBO leaves and its possible mechanisms in animal models. The anti-inflammatory activity of the extract was evaluated using serotonin-induced rat paw edema, increased peritoneal vascular permeability, and leukocyte infiltrations in an air-pouch model. Nitric oxide (NO, indicated by the sum of nitrites and nitrates, and vascular growth endothelial growth factor (VEGF were measured in paw tissues of rats to determine their involvement in the regulation of increased permeability. Pretreatments with AEBO (50 and 150 mg kg−1 prior to serotonin inductions resulted in maximum inhibitions of 56.2% of paw volume, 45.7% of Evans blue dye leakage in the peritoneal vascular permeability model, and 83.9% of leukocyte infiltration in the air-pouch model. 57.2% maximum inhibition of NO and 27% of VEGF formations in rats’ paws were observed with AEBO at the dose of 150 mg kg−1. Pharmacological screening of the extract showed significant (P<0.05 anti-inflammatory activity, indicated by the suppressions of increased vascular permeability and leukocyte infiltration. The inhibitions of these inflammatory events are probably mediated via inhibition of NO and VEGF formation and release.

Tuning Liposome Membrane Permeability by Competitive Peptide Dimerization and Partitioning-Folding Interactions Regulated by Proteolytic Activity

Science.gov (United States)

Lim, Seng Koon; Sandén, Camilla; Selegård, Robert; Liedberg, Bo; Aili, Daniel

2016-02-01

Membrane active peptides are of large interest for development of drug delivery vehicles and therapeutics for treatment of multiple drug resistant infections. Lack of specificity can be detrimental and finding routes to tune specificity and activity of membrane active peptides is vital for improving their therapeutic efficacy and minimize harmful side effects. We describe a de novo designed membrane active peptide that partition into lipid membranes only when specifically and covalently anchored to the membrane, resulting in pore-formation. Dimerization with a complementary peptide efficiently inhibits formation of pores. The effect can be regulated by proteolytic digestion of the inhibitory peptide by the matrix metalloproteinase MMP-7, an enzyme upregulated in many malignant tumors. This system thus provides a precise and specific route for tuning the permeability of lipid membranes and a novel strategy for development of recognition based membrane active peptides and indirect enzymatically controlled release of liposomal cargo.

Activation of nucleotide oligomerization domain 2 (NOD2 by human cytomegalovirus initiates innate immune responses and restricts virus replication.

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Arun Kapoor

Full Text Available Nucleotide-binding oligomerization domain 2 (NOD2 is an important innate immune sensor of bacterial pathogens. Its induction results in activation of the classic NF-κB pathway and alternative pathways including type I IFN and autophagy. Although the importance of NOD2 in recognizing RNA viruses has recently been identified, its role in sensing DNA viruses has not been studied. We report that infection with human cytomegalovirus (HCMV results in significant induction of NOD2 expression, beginning as early as 2 hours post infection and increasing steadily 24 hours post infection and afterwards. Infection with human herpesvirus 1 and 2 does not induce NOD2 expression. While the HCMV-encoded glycoprotein B is not required for NOD2 induction, a replication competent virion is necessary. Lentivirus-based NOD2 knockdown in human foreskin fibroblasts (HFFs and U373 glioma cells leads to enhanced HCMV replication along with decreased levels of interferon beta (IFN-β and the pro-inflammatory cytokine, IL8. NOD2 induction in HCMV-infected cells activates downstream NF-κB and interferon pathways supported by reduced nuclear localization of NF-κB and pIRF3 in NOD2 knockdown HFFs. Stable overexpression of NOD2 in HFFs restricts HCMV replication in association with increased levels of IFN-β and IL8. Similarly, transient overexpression of NOD2 in U373 cells or its downstream kinase, RIPK2, results in decreased HCMV replication and enhanced cytokine responses. However, overexpression of a mutant NOD2, 3020insC, associated with severe Crohn's disease, results in enhanced HCMV replication and decreased levels of IFN-β in U373 cells. These results show for the first time that NOD2 plays a significant role in HCMV replication and may provide a model for studies of HCMV recognition by the host cell and HCMV colitis in Crohn's disease.

DNA replication origins-where do we begin?

Science.gov (United States)

Prioleau, Marie-Noëlle; MacAlpine, David M

2016-08-01

For more than three decades, investigators have sought to identify the precise locations where DNA replication initiates in mammalian genomes. The development of molecular and biochemical approaches to identify start sites of DNA replication (origins) based on the presence of defining and characteristic replication intermediates at specific loci led to the identification of only a handful of mammalian replication origins. The limited number of identified origins prevented a comprehensive and exhaustive search for conserved genomic features that were capable of specifying origins of DNA replication. More recently, the adaptation of origin-mapping assays to genome-wide approaches has led to the identification of tens of thousands of replication origins throughout mammalian genomes, providing an unprecedented opportunity to identify both genetic and epigenetic features that define and regulate their distribution and utilization. Here we summarize recent advances in our understanding of how primary sequence, chromatin environment, and nuclear architecture contribute to the dynamic selection and activation of replication origins across diverse cell types and developmental stages. © 2016 Prioleau and MacAlpine; Published by Cold Spring Harbor Laboratory Press.

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.

Fast Laplace solver approach to pore-scale permeability

Science.gov (United States)

Arns, C. H.; Adler, P. M.

2018-02-01

We introduce a powerful and easily implemented method to calculate the permeability of porous media at the pore scale using an approximation based on the Poiseulle equation to calculate permeability to fluid flow with a Laplace solver. The method consists of calculating the Euclidean distance map of the fluid phase to assign local conductivities and lends itself naturally to the treatment of multiscale problems. We compare with analytical solutions as well as experimental measurements and lattice Boltzmann calculations of permeability for Fontainebleau sandstone. The solver is significantly more stable than the lattice Boltzmann approach, uses less memory, and is significantly faster. Permeabilities are in excellent agreement over a wide range of porosities.

Late-replicating X-chromosome: replication patterns in mammalian females

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Tunin Karen

2002-01-01

Full Text Available The GTG-banding and 5-BrdU incorporation patterns of the late-replicating X-chromosome were studied in female dogs and cattle, and compared to human female patterns. The replication patterns of the short arm of the X-chromosomes did not show any difference between human, dog and cattle females. As to the long arm, some bands showed differences among the three studied species regarding the replication kinetics pattern. These differences were observed in a restricted region of the X-chromosome, delimited by Xq11 -> q25 in humans, by Xq1 -> q8 in dogs, and by Xq12 -> q32 in cattle. In an attempt to find out if these differences in the replication kinetics could be a reflection of differences in the localization of genes in that region of the X-chromosome, we used the probe for the human androgen receptor gene (AR localized at Xq12, which is in the region where we observed differences among the three studied species. We did not, however, observe hybridization signals. Our study goes on, using other human probes for genes located in the region Xq11 -> Xq25.

Control of BTEX migration using a biologically enhanced permeable barrier

International Nuclear Information System (INIS)

Borden, R.C.; Goin, R.T.; Kao, C.M.

1997-01-01

A permeable barrier system, consisting of a line of closely spaced wells, was installed perpendicular to ground water flow to control the migration of a dissolved hydrocarbon plume. The wells were charged with concrete briquets that release oxygen and nitrate at a controlled rate, enhancing aerobic biodegradation in the downgradient aquifer. Laboratory batch reactor experiments were conducted to identify concrete mixtures that slowly released oxygen over an extended time period. A full-scale permeable barrier system using ORC was constructed at a gasoline-spill site. During the first 242 days of operation, total BTEX decreased from 17 to 3.4 mg/L and dissolved oxygen increased from 0.4 to 1.8 mg/L during transport through the barrier. Over time, BTEX treatment efficiencies declined, indicating the barrier system had become less effective in releasing oxygen and nutrients to the highly contaminated portion of the aquifer. Point dilution tests and sediment analyses performed at the conclusion of the project indicated that the aquifer in the vicinity of the remediation wells had been clogged by precipitation with iron minerals

Electrokinetic effects and fluid permeability

International Nuclear Information System (INIS)

Berryman, J.G.

2003-01-01

Fluid permeability of porous media depends mainly on connectivity of the pore space and two physical parameters: porosity and a pertinent length-scale parameter. Electrical imaging methods typically establish connectivity and directly measure electrical conductivity, which can then often be related to porosity by Archie's law. When electrical phase measurements are made in addition to the amplitude measurements, information about the pertinent length scale can then be obtained. Since fluid permeability controls the ability to flush unwanted fluid contaminants from the subsurface, inexpensive maps of permeability could improve planning strategies for remediation efforts. Detailed knowledge of fluid permeability is also important for oil field exploitation, where knowledge of permeability distribution in three dimensions is a common requirement for petroleum reservoir simulation and analysis, as well as for estimates on the economics of recovery

Understanding how replication processes can maintain systems away from equilibrium using Algorithmic Information Theory.

Science.gov (United States)

Devine, Sean D

2016-02-01

Replication can be envisaged as a computational process that is able to generate and maintain order far-from-equilibrium. Replication processes, can self-regulate, as the drive to replicate can counter degradation processes that impact on a system. The capability of replicated structures to access high quality energy and eject disorder allows Landauer's principle, in conjunction with Algorithmic Information Theory, to quantify the entropy requirements to maintain a system far-from-equilibrium. Using Landauer's principle, where destabilising processes, operating under the second law of thermodynamics, change the information content or the algorithmic entropy of a system by ΔH bits, replication processes can access order, eject disorder, and counter the change without outside interventions. Both diversity in replicated structures, and the coupling of different replicated systems, increase the ability of the system (or systems) to self-regulate in a changing environment as adaptation processes select those structures that use resources more efficiently. At the level of the structure, as selection processes minimise the information loss, the irreversibility is minimised. While each structure that emerges can be said to be more entropically efficient, as such replicating structures proliferate, the dissipation of the system as a whole is higher than would be the case for inert or simpler structures. While a detailed application to most real systems would be difficult, the approach may well be useful in understanding incremental changes to real systems and provide broad descriptions of system behaviour. Copyright © 2016 The Author. Published by Elsevier Ireland Ltd.. All rights reserved.

Determination of hydrogen permeability in commercial and modified superalloys

Science.gov (United States)

Bhattacharyya, S.; Peterman, W.

1983-01-01

The results of hydrogen permeability measurements on several iron- and cobalt-base alloys as well as on two long-ranged ordered alloys over the range of 705 to 870 C (1300 to 1600 F) are summarized. The test alloys included wrought alloys N-155, IN 800, A-286, 19-9DL, and 19-9DL modifications with aluminum, niobium, and misch metal. In addition, XF-818, CRM-6D, SA-F11, and HS-31 were evaluated. Two wrought long-range ordered alloys, Ni3Al and (Fe,Ni)3(V,Al) were also evaluated. All tests were conducted at 20.7 MPa pressure in either pure and/or 1% CO2-doped H2 for test periods as long as 133 h. Detailed analyses were conducted to determine the relative permeability rankings of these alloys and the effect of doping, exit surface oxidation, specimen design variations, and test duration on permeability coefficient, and permeation activation energies were determined. The two long-range ordered alloys had the lowest permeability coefficients in pure H2 when compared with the eight commercial alloys and their modifications. With CO2 doping, significant decrease in permeability was observed in commercial alloys--no doped tests were conducted with the long-range ordered alloys.

Transparent anodes for polymer photovoltaics: Oxygen permeability of PEDOT

DEFF Research Database (Denmark)

Andersen, M.; Carlé, Jon Eggert; Cruys-Bagger, N.

2007-01-01

The oxygen permeability of the transparent organic anode poly(3,4,-ethylene dioxythiophene) with paratoluenesulphonate as the anion (PEDOT:pTS) was determined to be 2.5 +/- 0.7 x 10(-15) cm(3) (STP) CM cm(-2) S-1 Pa-1, and is thus comparable in magnitude to the oxygen permeability of polyethylene......The oxygen permeability of the transparent organic anode poly(3,4,-ethylene dioxythiophene) with paratoluenesulphonate as the anion (PEDOT:pTS) was determined to be 2.5 +/- 0.7 x 10(-15) cm(3) (STP) CM cm(-2) S-1 Pa-1, and is thus comparable in magnitude to the oxygen permeability...... of polyethyleneterephthalate (PET). The oxygen diffusion through bilayers of polyethylene (PE) and PEDOT:pTS and bilayers of PET and PEDOT:pTS was established. The bilayer structures were applied as the carrier substrate and the transparent anode in polymer-based photovoltaic devices employing a mixture of poly(1-methoxy-4......-(2-ethylhexyloxy)-p-phenylenevinylene) (MEH-PPV) and [6,6]-phenyt-C-61-butanoicacidmethylester (PCBM) as the active layer and aluminium as the cathode. The oxygen permeability of the layers and the aluminium cathode was correlated with the lifetime of the solar cell devices. It was found that the performance...

The measurement of water vapor permeability of glove materials using dilute tritiated water

International Nuclear Information System (INIS)

Doughty, D.H.

1982-01-01

As fusion technology progresses, there will be an increasing need to handle tritium and tritiated compounds. Protective clothing, especially drybox gloves, must be an effective barrier to minimize worker exposure. The water vapor permeability of glove materials and finished glove constructions is a crucial property of drybox gloves and is not sufficiently well characterized. We have built an apparatus that measures water vapor permeability of elastomers using dilute tritiated water. The technique is more sensitive than other methods currently available and allows us to make measurements on materials and under conditions previously inaccessible. In particular, we present results on laminated drybox gloves for which data is not currently available. (orig.)

Experimentally-induced immune activation in natural hosts of SIV induces significant increases in viral replication and CD4+ T cell depletion

Energy Technology Data Exchange (ETDEWEB)

Ribeiro, Ruy M [Los Alamos National Laboratory

2008-01-01

Chronically SIVagm-infected African green monkeys (AGMs) have a remarkably stable non-pathogenic disease course, with levels of immune activation in chronic SIVagm infection similar to those observed in uninfected monkeys and stable viral loads (VLs) for long periods of time. In vivo administration of lipopolysaccharide (LPS) or an IL-2/diphtheria toxin fusion protein (Ontak) to chronically SIVagm-infected AGMs triggered increases in immune activation and subsequently of viral replication and depletion of intestinal CD4{sup +} T cells. Our study indicates that circulating microbial products can increase viral replication by inducing immune activation and increasing the number of viral target cells, thus demonstrating that immune activation and T cell prolifeation are key factors in AIDS pathogenesis.

/sup 51/Cr-EDTA//sup 14/C-mannitol intestinal permeability test. Clinical use in screening for coeliac disease

Energy Technology Data Exchange (ETDEWEB)

Fotherby, K.J.; Wraight, E.P.; Neale, G.

1988-01-01

An intestinal permeability test with a combination of /sup 51/Cr-EDTA and /sup 14/C-mannitol was performed under routine conditions on 176 occasions in 161 adult patients. Of these patients, 116 were under investigation for possible coeliac disease, 33 were known to have coeliac disease, and 12 had inflammatory bowel disease. Small-bowel biopsies were performed in 61 patients. Expressing the results as the ratio of the 6-h urinary recoveries of the two probes was as sensitive as 95%, but more specific for histological mucosal abnormality (62% versus 46%) than measuring the urinary recovery of /sup 51/Cr-EDTA alone. All but two of the patients with active inflammatory bowel disease, whether Crohn's disease or ulcerative colitis, had an abnormal ratio. The /sup 51/Cr-EDTA//sup 14/C-mannitol intestinal permeablity test with a 6-h urine collection is a rapid and simple test of small-intestinal function suitable for routine use. 19 refs.

Improving enzymatic activities and thermostability of a tri-functional enzyme with SOD, catalase and cell-permeable activities.

Science.gov (United States)

Luangwattananun, Piriya; Eiamphungporn, Warawan; Songtawee, Napat; Bülow, Leif; Isarankura Na Ayudhya, Chartchalerm; Prachayasittikul, Virapong; Yainoy, Sakda

2017-04-10

Synergistic action of major antioxidant enzymes, e.g., superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPx) is known to be more effective than the action of any single enzyme. Recently, we have engineered a tri-functional enzyme, 6His-MnSOD-TAT/CAT-MnSOD (M-TAT/CM), with SOD, CAT and cell-permeable activities. The protein actively internalized into the cells and showed superior protection against oxidative stress-induced cell death over native enzymes fused with TAT. To improve its molecular size, enzymatic activity and stability, in this study, MnSOD portions of the engineered protein were replaced by CuZnSOD, which is the smallest and the most heat resistant SOD isoform. The newly engineered protein, CAT-CuZnSOD/6His-CuZnSOD-TAT (CS/S-TAT), had a 42% reduction in molecular size and an increase in SOD and CAT activities by 22% and 99%, respectively. After incubation at 70°C for 10min, the CS/S-TAT retained residual SOD activity up to 54% while SOD activity of the M-TAT/CM was completely abolished. Moreover, the protein exhibited a 5-fold improvement in half-life at 70°C. Thus, this work provides insights into the design and synthesis of a smaller but much more stable multifunctional antioxidant enzyme with ability to enter mammalian cells for further application as protective/therapeutic agent against oxidative stress-related conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

Osmotic regulation of the mitochondrial permeability transition pore investigated by light scattering, fluorescence and electron microscopy techniques.

Science.gov (United States)

Baev, Artyom Y; Elustondo, Pia A; Negoda, Alexander; Pavlov, Evgeny V

2017-07-08

Mitochondrial permeability transition (PT) is a phenomenon of an increase of the inner membrane permeability in response to an excessive matrix calcium accumulation. PTP is caused by the opening of the large weakly selective channel. Molecular composition and regulation of permeability transition pore (PTP) are not well understood. Here we used isolated mitochondria to investigate dependence of PTP activation on the osmotic pressure. We found that in low osmotic strength solution calcium-induced PTP is significantly inhibited. We propose that this effect is linked to the changes in the curvature of the mitochondrial inner membrane. This interpretation is consistent with the idea about the importance of ATP synthase dimerization in modulation of the PTP activity. Copyright © 2017. Published by Elsevier Inc.

Replicating Health Economic Models: Firm Foundations or a House of Cards?

Science.gov (United States)

Bermejo, Inigo; Tappenden, Paul; Youn, Ji-Hee

2017-11-01

Health economic evaluation is a framework for the comparative analysis of the incremental health gains and costs associated with competing decision alternatives. The process of developing health economic models is usually complex, financially expensive and time-consuming. For these reasons, model development is sometimes based on previous model-based analyses; this endeavour is usually referred to as model replication. Such model replication activity may involve the comprehensive reproduction of an existing model or 'borrowing' all or part of a previously developed model structure. Generally speaking, the replication of an existing model may require substantially less effort than developing a new de novo model by bypassing, or undertaking in only a perfunctory manner, certain aspects of model development such as the development of a complete conceptual model and/or comprehensive literature searching for model parameters. A further motivation for model replication may be to draw on the credibility or prestige of previous analyses that have been published and/or used to inform decision making. The acceptability and appropriateness of replicating models depends on the decision-making context: there exists a trade-off between the 'savings' afforded by model replication and the potential 'costs' associated with reduced model credibility due to the omission of certain stages of model development. This paper provides an overview of the different levels of, and motivations for, replicating health economic models, and discusses the advantages, disadvantages and caveats associated with this type of modelling activity. Irrespective of whether replicated models should be considered appropriate or not, complete replicability is generally accepted as a desirable property of health economic models, as reflected in critical appraisal checklists and good practice guidelines. To this end, the feasibility of comprehensive model replication is explored empirically across a small

The potential of permeability damage during thermal recovery of Cold Lake bitumen

Energy Technology Data Exchange (ETDEWEB)

Zhou, Z.; Wiwchar, B.; Gunter, W. D. [Alberta Research Council, Devon, AB (Canada); Dudley, J. S. [Imperial Oil Resources, Calgary, AB (Canada)

1999-09-01

Methods and results of coreflood tests designed to evaluate permeability damage caused by Clearwater formation clays in the Cold Lake area of Alberta are described. Three periods of permeability damage were encountered, the first during and shortly after the core was heated to 250 degrees C. Experimental evidence suggests that thermally activated grain crushing and subsequent fines migration were responsible for this initial permeability loss. The second period of damage was a gradual process which resulted in 65 per cent and 78 percent of permeability loss for the two corefloods, respectively. This phase of the permeability damage was considered to have been the result of hydrothermal reactions (berthierine to Fe-saponite). The third period of permeability damage occurred when fresh water was injected into the core. This was attributed to osmotic swelling of the Fe-saponite. A comparison of field evidence with experimental results revealed certain discrepancies, suspected to be due to the kinetics of the reaction, including disruption of berthierine grain coats and permeability damage due to subsequent fines migration. To err on the safe side, it is recommended that thermal recovery wells should be completed away from berthierine-rich zones. 15 refs., 2 tabs., 7 figs.

The role of Vif oligomerization and RNA chaperone activity in HIV-1 replication.

Science.gov (United States)

Batisse, Julien; Guerrero, Santiago; Bernacchi, Serena; Sleiman, Dona; Gabus, Caroline; Darlix, Jean-Luc; Marquet, Roland; Tisné, Carine; Paillart, Jean-Christophe

2012-11-01

The viral infectivity factor (Vif) is essential for the productive infection and dissemination of HIV-1 in non-permissive cells that involve most natural HIV-1 target cells. Vif counteracts the packaging of two cellular cytidine deaminases named APOBEC3G (A3G) and A3F by diverse mechanisms including the recruitment of an E3 ubiquitin ligase complex and the proteasomal degradation of A3G/A3F, the inhibition of A3G mRNA translation or by a direct competition mechanism. In addition, Vif appears to be an active partner of the late steps of viral replication by participating in virus assembly and Gag processing, thus regulating the final stage of virion formation notably genomic RNA dimerization and by inhibiting the initiation of reverse transcription. Vif is a small pleiotropic protein with multiple domains, and recent studies highlighted the importance of Vif conformation and flexibility in counteracting A3G and in binding RNA. In this review, we will focus on the oligomerization and RNA chaperone properties of Vif and show that the intrinsic disordered nature of some Vif domains could play an important role in virus assembly and replication. Experimental evidence demonstrating the RNA chaperone activity of Vif will be presented. Copyright © 2012 Elsevier B.V. All rights reserved.

DNA Replication in Engineered Escherichia coli Genomes with Extra Replication Origins.

Science.gov (United States)

Milbredt, Sarah; Farmani, Neda; Sobetzko, Patrick; Waldminghaus, Torsten

2016-10-21

The standard outline of bacterial genomes is a single circular chromosome with a single replication origin. From the bioengineering perspective, it appears attractive to extend this basic setup. Bacteria with split chromosomes or multiple replication origins have been successfully constructed in the last few years. The characteristics of these engineered strains will largely depend on the respective DNA replication patterns. However, the DNA replication has not been investigated systematically in engineered bacteria with multiple origins or split replicons. Here we fill this gap by studying a set of strains consisting of (i) E. coli strains with an extra copy of the native replication origin (oriC), (ii) E. coli strains with an extra copy of the replication origin from the secondary chromosome of Vibrio cholerae (oriII), and (iii) a strain in which the E. coli chromosome is split into two linear replicons. A combination of flow cytometry, microarray-based comparative genomic hybridization (CGH), and modeling revealed silencing of extra oriC copies and differential timing of ectopic oriII copies compared to the native oriC. The results were used to derive construction rules for future multiorigin and multireplicon projects.

Permeability enhancement by shock cooling

Science.gov (United States)

Griffiths, Luke; Heap, Michael; Reuschlé, Thierry; Baud, Patrick; Schmittbuhl, Jean

2015-04-01

The permeability of an efficient reservoir, e.g. a geothermal reservoir, should be sufficient to permit the circulation of fluids. Generally speaking, permeability decreases over the life cycle of the geothermal system. As a result, is usually necessary to artificially maintain and enhance the natural permeability of these systems. One of the methods of enhancement -- studied here -- is thermal stimulation (injecting cold water at low pressure). This goal of this method is to encourage new thermal cracks within the reservoir host rocks, thereby increasing reservoir permeability. To investigate the development of thermal microcracking in the laboratory we selected two granites: a fine-grained (Garibaldi Grey granite, grain size = 0.5 mm) and a course-grained granite (Lanhelin granite, grain size = 2 mm). Both granites have an initial porosity of about 1%. Our samples were heated to a range of temperatures (100-1000 °C) and were either cooled slowly (1 °C/min) or shock cooled (100 °C/s). A systematic microstructural (2D crack area density, using standard stereological techniques, and 3D BET specific surface area measurements) and rock physical property (porosity, P-wave velocity, uniaxial compressive strength, and permeability) analysis was undertaken to understand the influence of slow and shock cooling on our reservoir granites. Microstructurally, we observe that the 2D crack surface area per unit volume and the specific surface area increase as a result of thermal stressing, and, for the same maximum temperature, crack surface area is higher in the shock cooled samples. This observation is echoed by our rock physical property measurements: we see greater changes for the shock cooled samples. We can conclude that shock cooling is an extremely efficient method of generating thermal microcracks and modifying rock physical properties. Our study highlights that thermal treatments are likely to be an efficient method for the "matrix" permeability enhancement of

Genome-wide alterations of the DNA replication program during tumor progression

Science.gov (United States)

Arneodo, A.; Goldar, A.; Argoul, F.; Hyrien, O.; Audit, B.

2016-08-01

Oncogenic stress is a major driving force in the early stages of cancer development. Recent experimental findings reveal that, in precancerous lesions and cancers, activated oncogenes may induce stalling and dissociation of DNA replication forks resulting in DNA damage. Replication timing is emerging as an important epigenetic feature that recapitulates several genomic, epigenetic and functional specificities of even closely related cell types. There is increasing evidence that chromosome rearrangements, the hallmark of many cancer genomes, are intimately associated with the DNA replication program and that epigenetic replication timing changes often precede chromosomic rearrangements. The recent development of a novel methodology to map replication fork polarity using deep sequencing of Okazaki fragments has provided new and complementary genome-wide replication profiling data. We review the results of a wavelet-based multi-scale analysis of genomic and epigenetic data including replication profiles along human chromosomes. These results provide new insight into the spatio-temporal replication program and its dynamics during differentiation. Here our goal is to bring to cancer research, the experimental protocols and computational methodologies for replication program profiling, and also the modeling of the spatio-temporal replication program. To illustrate our purpose, we report very preliminary results obtained for the chronic myelogeneous leukemia, the archetype model of cancer. Finally, we discuss promising perspectives on using genome-wide DNA replication profiling as a novel efficient tool for cancer diagnosis, prognosis and personalized treatment.

The replicative DNA polymerase of herpes simplex virus 1 exhibits apurinic/apyrimidinic and 5′-deoxyribose phosphate lyase activities

Science.gov (United States)

Bogani, Federica; Boehmer, Paul E.

2008-01-01

Base excision repair (BER) is essential for maintaining genome stability both to counter the accumulation of unusual bases and to protect from base loss in the DNA. Herpes simplex virus 1 (HSV-1) is a large dsDNA virus that encodes its own DNA replication machinery, including enzymes involved in nucleotide metabolism. We report on a replicative family B and a herpesvirus-encoded DNA Pol that possesses DNA lyase activity. We have discovered that the catalytic subunit of the HSV-1 DNA polymerase (Pol) (UL30) exhibits apurinic/apyrimidinic (AP) and 5′-deoxyribose phosphate (dRP) lyase activities. These activities are integral to BER and lead to DNA cleavage on the 3′ side of abasic sites and 5′-dRP residues that remain after cleavage by 5′-AP endonuclease. The UL30-catalyzed reaction occurs independently of divalent cation and proceeds via a Schiff base intermediate, indicating that it occurs via a lyase mechanism. Partial proteolysis of the Schiff base shows that the DNA lyase activity resides in the Pol domain of UL30. These observations together with the presence of a virus-encoded uracil DNA glycosylase indicates that HSV-1 has the capacity to perform critical steps in BER. These findings have implications on the role of BER in viral genome maintenance during lytic replication and reactivation from latency. PMID:18695225

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.

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.

Do the recommended standards for in vitro biopharmaceutic classification of drug permeability meet the "passive transport" criterion for biowaivers?

Science.gov (United States)

Žakelj, Simon; Berginc, Katja; Roškar, Robert; Kraljič, Bor; Kristl, Albin

2013-01-01

BCS based biowaivers are recognized by major regulatory agencies. An application for a biowaiver can be supported by or even based on "in vitro" measurements of drug permeability. However, guidelines limit the application of biowaivers to drug substances that are transported only by passive mechanisms. Regarding published permeability data as well as measurements obtained in our institution, one can rarely observe drug substances that conform to this very strict criterion. Therefore, we measured the apparent permeability coefficients of 13 drugs recommended by FDA's Guidance to be used as standards for "in vitro" permeability classification. The asymmetry of permeability data determined for both directions (mucosal-to-serosal and serosalto- mucosal) through the rat small intestine revealed significant active transport for four out of the nine high-permeability standards and for all four low-permeability standard drugs. As could be expected, this asymmetry was abolished at 4°C on rat intestine. The permeability of all nine high-permeability, but none of the low permeability standards, was also much lower when measured with intestinal tissue, Caco-2 cell monolayers or artificial membranes at 4°C compared to standard conditions (37°C). Additionally, concurrent testing of several standard drugs revealed that membrane transport can be affected by the use of internal permeability standards. The implications of the results are discussed regarding the regulatory aspects of biopharmaceutical classification, good practice in drug permeability evaluation and regarding the general relevance of transport proteins with broad specificity in drug absorption.

Permeable pavement study (Edison)

Data.gov (United States)

U.S. Environmental Protection Agency — While permeable pavement is increasingly being used to control stormwater runoff, field-based, side-by-side investigations on the effects different pavement types...

Permeability of EVOH Barrier Material Used in Automotive Applications: Metrology Development for Model Fuel Mixtures

Directory of Open Access Journals (Sweden)

Zhao Jing

2015-02-01

Full Text Available EVOH (Ethylene-Vinyl Alcohol materials are widely used in automotive applications in multi-layer fuel lines and tanks owing to their excellent barrier properties to aromatic and aliphatic hydrocarbons. These barrier materials are essential to limit environmental fuel emissions and comply with the challenging requirements of fast changing international regulations. Nevertheless, the measurement of EVOH permeability to model fuel mixtures or to their individual components is particularly difficult due to the complexity of these systems and their very low permeability, which can vary by several orders of magnitude depending on the permeating species and their relative concentrations. This paper describes the development of a new automated permeameter capable of taking up the challenge of measuring minute quantities as low as 1 mg/(m2.day for partial fluxes for model fuel mixtures containing ethanol, i-octane and toluene at 50°C. The permeability results are discussed as a function of the model fuel composition and the importance of EVOH preconditioning is emphasized for accurate permeability measurements. The last part focuses on the influence of EVOH conditioning on its mechanical properties and its microstructure, and further illustrates the specific behavior of EVOH in presence of ethanol oxygenated fuels. The new metrology developed in this work offers a new insight in the permeability properties of a leading barrier material and will help prevent the consequences of (bioethanol addition in fuels on environmental emissions through fuel lines and tanks.

Stress dependence of permeability of intact and fractured shale cores.

Science.gov (United States)

van Noort, Reinier; Yarushina, Viktoriya

2016-04-01

Whether a shale acts as a caprock, source rock, or reservoir, understanding fluid flow through shale is of major importance for understanding fluid flow in geological systems. Because of the low permeability of shale, flow is thought to be largely confined to fractures and similar features. In fracking operations, fractures are induced specifically to allow for hydrocarbon exploration. We have constructed an experimental setup to measure core permeabilities, using constant flow or a transient pulse. In this setup, we have measured the permeability of intact and fractured shale core samples, using either water or supercritical CO2 as the transporting fluid. Our measurements show decreasing permeability with increasing confining pressure, mainly due to time-dependent creep. Furthermore, our measurements show that for a simple splitting fracture, time-dependent creep will also eliminate any significant effect of this fracture on permeability. This effect of confinement on fracture permeability can have important implications regarding the effects of fracturing on shale permeability, and hence for operations depending on that.

ATPase activity measurement of DNA replicative helicase from Bacillus stearothermophilus by malachite green method.

Science.gov (United States)

Yang, Mu; Wang, Ganggang

2016-09-15

The DnaB helicase from Bacillus stearothermophilus (DnaBBst) was a model protein for studying the bacterial DNA replication. In this work, a non-radioactive method for measuring ATPase activity of DnaBBst helicase was described. The working parameters and conditions were optimized. Furthermore, this method was applied to investigate effects of DnaG primase, ssDNA and helicase loader protein (DnaI) on ATPase activity of DnaBBst. Our results showed this method was sensitive and efficient. Moreover, it is suitable for the investigation of functional interaction between DnaB and related factors. Copyright © 2016 Elsevier Inc. All rights reserved.

Permeability of skin and oral mucosa to water and horseradish peroxidase as related to the thickness of the permeability barrier

International Nuclear Information System (INIS)

Squier, C.A.; Hall, B.K.

1985-01-01

The permeability of porcine skin and keratinized and nonkeratinized oral mucosa to tritium-labeled water and horseradish peroxidase (HRPO) was determined using perfusion chambers. Small blocks from each tissue were also incubated with HRPO and the extent of penetration visualized microscopically; this enabled measurements to be made of the thickness of the permeability barrier to this water-soluble tracer. Results obtained after inverting the oral mucosa in the chambers or adding metabolic inhibitors indicated that both compounds diffuse across the tissue. The permeability constants derived directly in the study showed that skin was less permeable than oral mucosa and that the floor of the mouth was significantly more permeable than all other regions. When these constants were normalized in terms of a standard permeability barrier thickness and the different tissues compared, the values obtained for skin were again less than those of the oral regions but, of these, the buccal mucosa was significantly higher. The difference in permeability between epidermis and keratinized oral epithelium may be due to differences in the volume density of membrane-coating granules known to exist between the tissues; differences between the oral mucosal regions may reflect differences in the nature of the intercellular barrier material

Pressure tube replication techniques using the advanced NDE system

International Nuclear Information System (INIS)

Isherwood, A.; Jarron, D.; Travers, J.; Hanley, K.

2006-01-01

Periodic and in-service inspections of fuel channels are essential for the proper assessment of the structural integrity of these vital components. The arrival of new delivery devices for fuel channel inspections has driven new tooling for gathering and analyzing NDE data. The Advanced Non-Destructive Examination (ANDE) Replication System has been designed to compliment the ANDE Inspection System by providing a two plate replica system. These plates deliver a compound that makes a positive 3D mould of known ID flaws to gather information for flaw assessment. The two plate system, and the ability to retrieve and recharge the moulds in the reactor vault allows for gathering defect information with minimal critical path time. The ANDE Replication System was built on the foundation of CIGAR experience by a solid design team familiar with 3D CAD and manufacturing techniques. The tooling and controls went through a series of integration stages in the laboratory and then later with the Universal Delivery Machine (UDM) before being used on reactor starting in 2003. Once the inspection phase of an outage has been completed, the analysis team provides a list of flaw candidates that require 'root radius' information to complete the flaw assessment. This is a measure of how sharp the corners are in the defect. This data is used as part of the stress calculation that ultimately determines how many shutdown cycles that the reactor can have before that flaw must be re-inspected. The inspection tool is then swapped out of the delivery machine in the reactor vault using the versatile connectorized umbilical. The replication tool is loaded on the machine, charged with replica compound on each of the two plates, and then sent to the target channel(s). On channel, the operators use the same console as the ANDE Inspection System, but have a separate control system with a graphical display of the tool that shows its position in the channel with respect to the E-face. The axial and

Inhibition of in vitro SV40 DNA replication by ultraviolet light

International Nuclear Information System (INIS)

Gough, G.; Wood, R.W.

1989-01-01

Ultraviolet light-induced DNA damage was found to inhibit SV40 origin-dependent DNA synthesis carried out by soluble humancell extracts. Replication of SV40-based plasmids was reduced to approx. 35% of that in unirradiated controls after irradiation with 50-100 J/m 2 germicidal ultraviolet light, where an average of 3-6 pyrimidine dimer photoproducts were formed per plasmid circle. Inhibition of the DNA helicase activity of T antigen (required for initiation of replication in the in vitro system) was also investigated, and was only significant after much higher fluences, 1000-5000 J/m 2 . The data indicate that DNA damage by ultraviolet light inhibits DNA synthesis in cell-free extracts principally by affecting components of the replication complex other than the DNA helicase activity of T antigen. The soluble system could be used to biochemically investigate the possible bypass or tolerance of DNA damage during replication (author). 21 refs.; 2 figs

REPLICATION TOOL AND METHOD OF PROVIDING A REPLICATION TOOL

DEFF Research Database (Denmark)

2016-01-01

The invention relates to a replication tool (1, 1a, 1b) for producing a part (4) with a microscale textured replica surface (5a, 5b, 5c, 5d). The replication tool (1, 1a, 1b) comprises a tool surface (2a, 2b) defining a general shape of the item. The tool surface (2a, 2b) comprises a microscale...... energy directors on flange portions thereof uses the replication tool (1, 1a, 1b) to form an item (4) with a general shape as defined by the tool surface (2a, 2b). The formed item (4) comprises a microscale textured replica surface (5a, 5b, 5c, 5d) with a lateral arrangement of polydisperse microscale...

Centromeric DNA replication reconstitution reveals DNA loops and ATR checkpoint suppression.

Science.gov (United States)

Aze, Antoine; Sannino, Vincenzo; Soffientini, Paolo; Bachi, Angela; Costanzo, Vincenzo

2016-06-01

Half of the human genome is made up of repetitive DNA. However, mechanisms underlying replication of chromosome regions containing repetitive DNA are poorly understood. We reconstituted replication of defined human chromosome segments using bacterial artificial chromosomes in Xenopus laevis egg extract. Using this approach we characterized the chromatin assembly and replication dynamics of centromeric alpha-satellite DNA. Proteomic analysis of centromeric chromatin revealed replication-dependent enrichment of a network of DNA repair factors including the MSH2-6 complex, which was required for efficient centromeric DNA replication. However, contrary to expectations, the ATR-dependent checkpoint monitoring DNA replication fork arrest could not be activated on highly repetitive DNA due to the inability of the single-stranded DNA binding protein RPA to accumulate on chromatin. Electron microscopy of centromeric DNA and supercoil mapping revealed the presence of topoisomerase I-dependent DNA loops embedded in a protein matrix enriched for SMC2-4 proteins. This arrangement suppressed ATR signalling by preventing RPA hyper-loading, facilitating replication of centromeric DNA. These findings have important implications for our understanding of repetitive DNA metabolism and centromere organization under normal and stressful conditions.

Permeability After Impact Testing of Composite Laminates

Science.gov (United States)

Nettles, Alan T.

2003-01-01

Since composite laminates are beginning to be identified for use in reusable launch vehicle propulsion systems, an understanding of their permeance is needed. A foreign object impact event can cause a localized area of permeability (leakage) in a polymer matrix composite and it is the aim of this study to assess a method of quantifying permeability-after-impact results. A simple test apparatus is presented and variables that could affect the measured values of permeability-after-impact were assessed. Once it was determined that valid numbers were being measured, a fiber/resin system was impacted at various impact levels and the resulting permeability measured, first with a leak check solution (qualitative) then using the new apparatus (quantitative). The results showed that as the impact level increased, so did the measured leakage. As the pressure to the specimen was increased, the leak rate was seen to increase in a non-linear fashion for almost all of the specimens tested.

Synthetic Rock Analogue for Permeability Studies of Rock Salt with Mudstone

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Hongwu Yin

2017-09-01

Full Text Available Knowledge about the permeability of surrounding rock (salt rock and mudstone interlayer is an important topic, which acts as a key parameter to characterize the tightness of gas storage. The goal of experiments that test the permeability of gas storage facilities in rock salt is to develop a synthetic analogue to use as a permeability model. To address the permeability of a mudstone/salt layered and mixed rock mass in Jintan, Jiangsu Province, synthetic mixed and layered specimens using the mudstone and the salt were fabricated for permeability testing. Because of the gas “slippage effect”, test results are corrected by the Klinkenberg method, and the permeability of specimens is obtained by regression fitting. The results show that the permeability of synthetic pure rock salt is 6.9 × 10−20 m2, and its porosity is 3.8%. The permeability of synthetic mudstone rock is 2.97 × 10−18 m2, with a porosity 17.8%. These results are close to those obtained from intact natural specimens. We also find that with the same mudstone content, the permeability of mixed specimens is about 40% higher than for the layered specimens, and with an increase in the mudstone content, the Klinkenberg permeability increases for both types of specimens. The permeability and mudstone content have a strong exponential relationship. When the mudstone content is below 40%, the permeability increases only slightly with mudstone content, whereas above this threshold, the permeability increases rapidly with mudstone content. The results of the study are of use in the assessment of the tightness of natural gas storage facilities in mudstone-rich rock salt formations in China.

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

Energy Technology Data Exchange (ETDEWEB)

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

2017-04-18

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

Permeability Tests on Silkeborg Sand No. 0000

DEFF Research Database (Denmark)

Lund, Willy; Jakobsen, Kim Parsberg

on the characteristics of the soil matrix, the permeability is determined for different void ratios. All tests are performed on reconstituted specimens of Silkeborg Sand No. 0000. The permeability is determined by use of a falling head apparatus. The apparatus, test procedures and the analysis method are described......The flow through porous media plays an important role in various engineering disciplines, as for example in ground water hydrology and soil mechanics. In the present study the permeability is determined for a fine, saturated sand. As the flow through a porous media strongly depends...

Checkpoint responses to replication stalling: inducing tolerance and preventing mutagenesis

Energy Technology Data Exchange (ETDEWEB)

Kai, Mihoko; Wang, Teresa S.-F

2003-11-27

Replication mutants often exhibit a mutator phenotype characterized by point mutations, single base frameshifts, and the deletion or duplication of sequences flanked by homologous repeats. Mutation in genes encoding checkpoint proteins can significantly affect the mutator phenotype. Here, we use fission yeast (Schizosaccharomyces pombe) as a model system to discuss the checkpoint responses to replication perturbations induced by replication mutants. Checkpoint activation induced by a DNA polymerase mutant, aside from delay of mitotic entry, up-regulates the translesion polymerase DinB (Pol{kappa}). Checkpoint Rad9-Rad1-Hus1 (9-1-1) complex, which is loaded onto chromatin by the Rad17-Rfc2-5 checkpoint complex in response to replication perturbation, recruits DinB onto chromatin to generate the point mutations and single nucleotide frameshifts in the replication mutator. This chain of events reveals a novel checkpoint-induced tolerance mechanism that allows cells to cope with replication perturbation, presumably to make possible restarting stalled replication forks. Fission yeast Cds1 kinase plays an essential role in maintaining DNA replication fork stability in the face of DNA damage and replication fork stalling. Cds1 kinase is known to regulate three proteins that are implicated in maintaining replication fork stability: Mus81-Eme1, a hetero-dimeric structure-specific endonuclease complex; Rqh1, a RecQ-family helicase involved in suppressing inappropriate recombination during replication; and Rad60, a protein required for recombinational repair during replication. These Cds1-regulated proteins are thought to cooperatively prevent mutagenesis and maintain replication fork stability in cells under replication stress. These checkpoint-regulated processes allow cells to survive replication perturbation by preventing stalled replication forks from degenerating into deleterious DNA structures resulting in genomic instability and cancer development.

Checkpoint responses to replication stalling: inducing tolerance and preventing mutagenesis

International Nuclear Information System (INIS)

Kai, Mihoko; Wang, Teresa S.-F.

2003-01-01

Replication mutants often exhibit a mutator phenotype characterized by point mutations, single base frameshifts, and the deletion or duplication of sequences flanked by homologous repeats. Mutation in genes encoding checkpoint proteins can significantly affect the mutator phenotype. Here, we use fission yeast (Schizosaccharomyces pombe) as a model system to discuss the checkpoint responses to replication perturbations induced by replication mutants. Checkpoint activation induced by a DNA polymerase mutant, aside from delay of mitotic entry, up-regulates the translesion polymerase DinB (Polκ). Checkpoint Rad9-Rad1-Hus1 (9-1-1) complex, which is loaded onto chromatin by the Rad17-Rfc2-5 checkpoint complex in response to replication perturbation, recruits DinB onto chromatin to generate the point mutations and single nucleotide frameshifts in the replication mutator. This chain of events reveals a novel checkpoint-induced tolerance mechanism that allows cells to cope with replication perturbation, presumably to make possible restarting stalled replication forks. Fission yeast Cds1 kinase plays an essential role in maintaining DNA replication fork stability in the face of DNA damage and replication fork stalling. Cds1 kinase is known to regulate three proteins that are implicated in maintaining replication fork stability: Mus81-Eme1, a hetero-dimeric structure-specific endonuclease complex; Rqh1, a RecQ-family helicase involved in suppressing inappropriate recombination during replication; and Rad60, a protein required for recombinational repair during replication. These Cds1-regulated proteins are thought to cooperatively prevent mutagenesis and maintain replication fork stability in cells under replication stress. These checkpoint-regulated processes allow cells to survive replication perturbation by preventing stalled replication forks from degenerating into deleterious DNA structures resulting in genomic instability and cancer development

Replicating animal mitochondrial DNA

Directory of Open Access Journals (Sweden)

Emily A. McKinney

2013-01-01

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

The Replication Recipe: What makes for a convincing replication?

NARCIS (Netherlands)

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

2014-01-01

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

The replication recipe : What makes for a convincing replication?

NARCIS (Netherlands)

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

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

Permeability analysis of Asbuton material used as core layers of water resistance in the body of dam

Science.gov (United States)

Rahim, H.; Tjaronge, M. W.; Thaha, A.; Djamaluddin, R.

2017-11-01

In order to increase consumption of the local materials and national products, large reserves of Asbuton material about 662.960 million tons in the Buton Islands became an alternative as a waterproof core layer in the body of dam. The Asbuton material was used in this research is Lawele Granular Asphalt (LGA). This study was an experimental study conducted in the laboratory by conducting density testing (content weight) and permeability on Asbuton material. Testing of the Asbuton material used Falling Head method to find out the permeability value of Asbuton material. The data of test result to be analyzed are the relation between compaction energy and density value also relation between density value and permeability value of Asbuton material. The result shows that increases the number of blow apply to the Asbuton material at each layer will increase the density of the Asbuton material. The density value of Asbuton material that satisfies the requirements for use as an impermeable core layer in the dam body is 1.53 grams/cm3. The increase the density value (the weight of the contents) of the Asbuton material will reduce its permeability value of the Asbuton material.

Predicting permeability and electrical conductivity of sedimentary rocks from microgeometry

International Nuclear Information System (INIS)

Schlueter, E.M.; Cook, N.G.W.

1991-02-01

The determination of hydrologic parameters that characterize fluid flow through rock masses on a large scale (e.g., hydraulic conductivity, capillary pressure, and relative permeability) is crucial to activities such as the planning and control of enhanced oil recovery operations, and the design of nuclear waste repositories. Hydraulic permeability and electrical conductivity of sedimentary rocks are predicted from the microscopic geometry of the pore space. The cross-sectional areas and perimeters of the individual pores are estimated from two-dimensional scanning electron micrographs of rock sections. The hydraulic and electrical conductivities of the individual pores are determined from these geometrical parameters, using Darcy's law and Ohm's law. Account is taken of the fact that the cross-sections are randomly oriented with respect to the channel axes, and for possible variation of cross-sectional area along the length of the pores. The effective medium theory from solid-state physics is then used to determine an effective average conductance of each pore. Finally, the pores are assumed to be arranged on a cubic lattice, which allows the calculation of overall macroscopic values for the permeability and the electrical conductivity. Preliminary results using Berea, Boise, Massilon and Saint-Gilles sandstones show reasonably close agreement between the predicted and measured transport properties. 12 refs., 5 figs., 1 tab

A permeability model for coal and other fractured, sorptive-elastic media

Energy Technology Data Exchange (ETDEWEB)

Robertson, E.P.; Christiansen, R.L. [Marathon Oil Co., Houston, TX (United States). Research & Development Facility

2008-09-15

This paper describes the derivation of a new equation that can be used to model the permeability behavior of a fractured, sorptive-elastic medium, such as coal, under variable stress conditions. The equation is applicable to confinement pressure schemes commonly used during the collection of permeability data in the laboratory. The model is derived for cubic geometry under biaxial or hydrostatic confining pressures. The model is designed to handle changes in permeability caused by adsorption and desorption of gases onto and from the matrix blocks in fractured media. The model equations can be used to calculate permeability changes caused by the production of methane (CH{sub 4}) from coal as well as the injection of gases, such as carbon dioxide, for sequestration in coal. Sensitivity analysis of the model found that each of the input variables can have a significant impact on the outcome of the permeability forecast as a function of changing pore pressure, thus, accurate input data are essential. The permeability model also can be used as a tool to determine input parameters for field simulations by curve fitting laboratory-generated permeability data. The new model is compared to two other widely used coal-permeability models using a hypothetical coal with average properties.

Permeability model of sintered porous media: analysis and experiments

Science.gov (United States)

Flórez Mera, Juan Pablo; Chiamulera, Maria E.; Mantelli, Marcia B. H.

2017-11-01

In this paper, the permeability of porous media fabricated from copper powder sintering process was modeled and measured, aiming the use of the porosity as input parameter for the prediction of the permeability of sintering porous media. An expression relating the powder particle mean diameter with the permeability was obtained, based on an elementary porous media cell, which is physically represented by a duct formed by the arrangement of spherical particles forming a simple or orthorhombic packing. A circular duct with variable section was used to model the fluid flow within the porous media, where the concept of the hydraulic diameter was applied. Thus, the porous is modeled as a converging-diverging duct. The electrical circuit analogy was employed to determine two hydraulic resistances of the cell: based on the Navier-Stokes equation and on the Darcýs law. The hydraulic resistances are compared between themselves and an expression to determine the permeability as function of average particle diameter is obtained. The atomized copper powder was sifted to reduce the size dispersion of the particles. The porosities and permeabilities of sintered media fabricated from powders with particle mean diameters ranging from 20 to 200 microns were measured, by means of the image analysis method and using an experimental apparatus. The permeability data of a porous media, made of copper powder and saturated with distilled water, was used to compare with the permeability model. Permeability literature models, which considers that powder particles have the same diameter and include porosity data as input parameter, were compared with the present model and experimental data. This comparison showed to be quite good.

The replicative DNA polymerase of herpes simplex virus 1 exhibits apurinic/apyrimidinic and 5′-deoxyribose phosphate lyase activities

OpenAIRE

Bogani, Federica; Boehmer, Paul E.

2008-01-01

Base excision repair (BER) is essential for maintaining genome stability both to counter the accumulation of unusual bases and to protect from base loss in the DNA. Herpes simplex virus 1 (HSV-1) is a large dsDNA virus that encodes its own DNA replication machinery, including enzymes involved in nucleotide metabolism. We report on a replicative family B and a herpesvirus-encoded DNA Pol that possesses DNA lyase activity. We have discovered that the catalytic subunit of the HSV-1 DNA polymeras...

Estimation of permeability and permeability anisotropy in horizontal wells through numerical simulation of mud filtrate invasion

Energy Technology Data Exchange (ETDEWEB)

Pereira, Nelson [PETROBRAS S.A., Rio de Janeiro, RJ (Brazil). Exploracao e Producao; Altman, Raphael; Rasmus, John; Oliveira, Jansen [Schlumberger Servicos de Petroleo Ltda., Rio de Janeiro, RJ (Brazil)

2008-07-01

This paper describes how permeability and permeability anisotropy is estimated in horizontal wells using LWD (logging-while-drilling) laterolog resistivity data. Laterolog-while-drilling resistivity passes of while-drilling and timelapse (while reaming) were used to capture the invasion process. Radial positions of water based mud invasion fronts were calculated from while-drilling and reaming resistivity data. The invasion process was then recreated by constructing forward models with a fully implicit, near-wellbore numerical simulation such that the invasion front at a given time was consistent with the position of the front predicted by resistivity inversions. The radial position of the invasion front was shown to be sensitive to formation permeability. The while-drilling environment provides a fertile scenario to investigate reservoir dynamic properties because mud cake integrity and growth is not fully developed which means that the position of the invasion front at a particular point in time is more sensitive to formation permeability. The estimation of dynamic formation properties in horizontal wells is of particular value in marginal fields and deep-water offshore developments where running wireline and obtaining core is not always feasible, and where the accuracy of reservoir models can reduce the risk in field development decisions. (author)

Detection of semi-volatile organic compounds in permeable pavement infiltrate

Science.gov (United States)

Abstract The Edison Environmental Center (EEC) performs research on green infrastructure (GI) treatment options. One such treatment option is the use of permeable pavements. EEC constructed a parking lot comprised of three different permeable systems: permeable asphalt, porous ...

Adiponectin, a downstream target gene of peroxisome proliferator-activated receptor γ, controls hepatitis B virus replication

International Nuclear Information System (INIS)

Yoon, Sarah; Jung, Jaesung; Kim, Taeyeung; Park, Sun; Chwae, Yong-Joon; Shin, Ho-Joon; Kim, Kyongmin

2011-01-01

In this study, HepG2-hepatitis B virus (HBV)-stable cells that did not overexpress HBx and HBx-deficient mutant-transfected cells were analyzed for their expression of HBV-induced, upregulated adipogenic and lipogenic genes. The mRNAs of CCAAT enhancer binding protein α (C/EBPα), peroxisome proliferator-activated receptor γ (PPARγ), adiponectin, liver X receptor α (LXRα), sterol regulatory element binding protein 1c (SREBP1c), and fatty acid synthase (FAS) were expressed at higher levels in HepG2-HBV and lamivudine-treated stable cells and HBx-deficient mutant-transfected cells than in the HepG2 cells. Lamivudine treatment reduced the mRNA levels of PPARγ and C/EBPα. Conversely, HBV replication was upregulated by adiponectin and PPARγ agonist rosiglitazone treatments and was downregulated by adiponectin siRNAs. Collectively, our results demonstrate that HBV replication and/or protein expression, even in the absence of HBx, upregulated adipogenic or lipogenic genes, and that the control of adiponectin might prove useful as a therapeutic modality for the treatment of chronic hepatitis B.

Investigation clogging dynamic of permeable pavement systems using embeded sensors

Data.gov (United States)

U.S. Environmental Protection Agency — Permeable pavement is a stormwater control measure commonly selected in both new and retrofit applications. However, there is limited information about the clogging...

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

Science.gov (United States)

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

2012-01-01

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

Acute inactivation of the replicative helicase in human cells triggers MCM8-9-dependent DNA synthesis

DEFF Research Database (Denmark)

Natsume, Toyoaki; Nishimura, Kohei; Minocherhomji, Sheroy

2017-01-01

stemming from replisome dissociation during DNA replication perturbation, we used a degron-based system for inducible proteolysis of a subunit of the replicative helicase. We show that MCM2-depleted cells activate a DNA damage response pathway and generate replication-associated DNA double-strand breaks...

Propofol and magnesium attenuate isoflurane-induced caspase-3 activation via inhibiting mitochondrial permeability transition pore

Directory of Open Access Journals (Sweden)

Zhang Yiying

2012-08-01

Full Text Available Abstract Background The inhalation anesthetic isoflurane has been shown to open the mitochondrial permeability transition pore (mPTP and induce caspase activation and apoptosis, which may lead to learning and memory impairment. Cyclosporine A, a blocker of mPTP opening might attenuate the isoflurane-induced mPTP opening, lessening its ripple effects. Magnesium and anesthetic propofol are also mPTP blockers. We therefore set out to determine whether propofol and magnesium can attenuate the isoflurane-induced caspase activation and mPTP opening. Methods We investigated the effects of magnesium sulfate (Mg2+, propofol, and isoflurane on the opening of mPTP and caspase activation in H4 human neuroglioma cells stably transfected to express full-length human amyloid precursor protein (APP (H4 APP cells and in six day-old wild-type mice, employing Western blot analysis and flowcytometry. Results Here we show that Mg2+ and propofol attenuated the isoflurane-induced caspase-3 activation in H4-APP cells and mouse brain tissue. Moreover, Mg2+ and propofol, the blockers of mPTP opening, mitigated the isoflurane-induced mPTP opening in the H4-APP cells. Conclusion These data illustrate that Mg2+ and propofol may ameliorate the isoflurane-induced neurotoxicity by inhibiting its mitochondrial dysfunction. Pending further studies, these findings may suggest the use of Mg2+ and propofol in preventing and treating anesthesia neurotoxicity.

Initiation of Replication in Escherichia coli

DEFF Research Database (Denmark)

Frimodt-Møller, Jakob

The circular chromosome of Escherichia coli is replicated by two replisomes assembled at the unique origin and moving in the opposite direction until they meet in the less well defined terminus. The key protein in initiation of replication, DnaA, facilitates the unwinding of double-stranded DNA...... to single-stranded DNA in oriC. Although DnaA is able to bind both ADP and ATP, DnaA is only active in initiation when bound to ATP. Although initiation of replication, and the regulation of this, is thoroughly investigated it is still not fully understood. The overall aim of the thesis was to investigate...... the regulation of initiation, the effect on the cell when regulation fails, and if regulation was interlinked to chromosomal organization. This thesis uncovers that there exists a subtle balance between chromosome replication and reactive oxygen species (ROS) inflicted DNA damage. Thus, failure in regulation...

In vivo human buccal permeability of nicotine

DEFF Research Database (Denmark)

Adrian, Charlotte L; Olin, Helle B D; Dalhoff, Kim

2006-01-01

The aim was to examine the in vivo buccal pH-dependent permeability of nicotine in humans and furthermore compare the in vivo permeability of nicotine to previous in vitro permeability data. The buccal permeability of nicotine was examined in a three-way cross-over study in eight healthy non......-smokers using a buccal perfusion cell. The disappearance of nicotine from perfusion solutions with pH 6.0, 7.4, and 8.1 was studied for 3h. The apparent permeability of nicotine (P(app)) was determined at each pH value. Parotid saliva was collected in an attempt to assess systemic levels of nicotine....... The disappearance rate of nicotine increased significantly as the pH increased, which resulted in P(app) values of 0.57+/-0.55 x 10(-4), 2.10+/-0.23 x 10(-4), and 3.96+/-0.54 x 10(-4)cms(-1) (mean+/-S.D.) at pH 6.0, 7.4, and 8.1, respectively. A linear relationship (R(2)=0.993) was obtained between the P...

Optimizing solubility and permeability of a biopharmaceutics classification system (BCS) class 4 antibiotic drug using lipophilic fragments disturbing the crystal lattice.

Science.gov (United States)

Tehler, Ulrika; Fagerberg, Jonas H; Svensson, Richard; Larhed, Mats; Artursson, Per; Bergström, Christel A S

2013-03-28

Esterification was used to simultaneously increase solubility and permeability of ciprofloxacin, a biopharmaceutics classification system (BCS) class 4 drug (low solubility/low permeability) with solid-state limited solubility. Molecular flexibility was increased to disturb the crystal lattice, lower the melting point, and thereby improve the solubility, whereas lipophilicity was increased to enhance the intestinal permeability. These structural changes resulted in BCS class 1 analogues (high solubility/high permeability) emphasizing that simple medicinal chemistry may improve both these properties.

BRPF3-HBO1 regulates replication origin activation and histone H3K14 acetylation

DEFF Research Database (Denmark)

Feng, Yunpeng; Vlassis, Arsenios; Roques, Céline

2016-01-01

implicated in replication control by measuring RPA accumulation upon replication stress. We identify six factors required for normal rates of DNA replication and characterize a function of the bromodomain and PHD finger-containing protein 3 (BRPF3) in replication initiation. BRPF3 forms a complex with HBO1...

DNA Copy-Number Control through Inhibition of Replication Fork Progression

Directory of Open Access Journals (Sweden)

Jared T. Nordman

2014-11-01

Full Text Available Proper control of DNA replication is essential to ensure faithful transmission of genetic material and prevent chromosomal aberrations that can drive cancer progression and developmental disorders. DNA replication is regulated primarily at the level of initiation and is under strict cell-cycle regulation. Importantly, DNA replication is highly influenced by developmental cues. In Drosophila, specific regions of the genome are repressed for DNA replication during differentiation by the SNF2 domain-containing protein SUUR through an unknown mechanism. We demonstrate that SUUR is recruited to active replication forks and mediates the repression of DNA replication by directly inhibiting replication fork progression instead of functioning as a replication fork barrier. Mass spectrometry identification of SUUR-associated proteins identified the replicative helicase member CDC45 as a SUUR-associated protein, supporting a role for SUUR directly at replication forks. Our results reveal that control of eukaryotic DNA copy number can occur through the inhibition of replication fork progression.

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

Durable Suit Bladder with Improved Water Permeability for Pressure and Environment Suits

Science.gov (United States)

Bue, Grant C.; Kuznetz, Larry; Orndoff, Evelyne; Tang, Henry; Aitchison, Lindsay; Ross, Amy

2009-01-01

Water vapor permeability is shown to be useful in rejecting heat and managing moisture accumulation in launch-and-entry pressure suits. Currently this is accomplished through a porous Gortex layer in the Advanced Crew and Escape Suit (ACES) and in the baseline design of the Constellation Suit System Element (CSSE) Suit 1. Non-porous dense monolithic membranes (DMM) that are available offer potential improvements for water vapor permeability with reduced gas leak. Accordingly, three different pressure bladder materials were investigated for water vapor permeability and oxygen leak: ElasthaneTM 80A (thermoplastic polyether urethane) provided from stock polymer material and two custom thermoplastic polyether urethanes. Water vapor, carbon dioxide and oxygen permeability of the DMM's was measured in a 0.13 mm thick stand-alone layer, a 0.08 mm and 0.05 mm thick layer each bonded to two different nylon and polyester woven reinforcing materials. Additional water vapor permeability and mechanical compression measurements were made with the reinforced 0.05 mm thick layers, further bonded with a polyester wicking and overlaid with moistened polyester fleece thermal underwear .This simulated the pressure from a supine crew person. The 0.05 mm thick nylon reinforced sample with polyester wicking layer was further mechanically tested for wear and abrasion. Concepts for incorporating these materials in launch/entry and Extravehicular Activity pressure suits are presented.

Gas and Water Permeability of Concrete

Energy Technology Data Exchange (ETDEWEB)

Villar, M. V.; Martin, P. L.; Romero, F. J.; Gutierrez-Rodirgo, V.; Barcala, J. M.

2012-11-01

The gas pressure of concrete samples was measured in an unsteady-state equipment working under low injection pressures and in a newly fine tuned steady-state setup working under different pressures. These measurements allowed the estimation of the intrinsic and relative gas permeability of the concrete and of the effect of boundary conditions on them. Permeability decreased with water content, but it was also greatly affected by the hydraulic history of concrete, i.e. if it had been previously dried or wetted. In particular, and for a given degree of saturation, the gas permeability of concrete previously saturated was lower than if the concrete had been just air dried or saturated after air drying. In any case, the gas permeability was about two orders of magnitude higher than the liquid water permeability (10-16 vs. 10-18 m2), probably due to the chemical reactions taking place during saturation (carbonation). The relative gas permeability of concrete increased sharply for water degrees of saturation smaller than 50%. The boundary conditions also affected the gas permeability, which seemed to be mostly conditioned by the back pressure and the confining pressure, increasing as the former increased and decreasing as the latter increased, i.e. decreasing as the effective pressure increased. Overall the increase of pressure head or injection pressure implied a decrease in gas permeability. External,microcracking during air-drying could not be ruled out as responsible for the decrease of permeability with confining pressure. The apparent permeability obtained applying the Klinkenberg method for a given effective pressure was only slightly smaller than the average of all the values measured for the same confining pressure range. For this reason it is considered that the Klinkenberg effect was not relevant in the range of pressures applied. (Author) 37 refs.

From structure to mechanism—understanding initiation of DNA replication

Science.gov (United States)

Riera, Alberto; Barbon, Marta; Noguchi, Yasunori; Reuter, L. Maximilian; Schneider, Sarah; Speck, Christian

2017-01-01

DNA replication results in the doubling of the genome prior to cell division. This process requires the assembly of 50 or more protein factors into a replication fork. Here, we review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. We focus on the minichromosome maintenance (MCM2–7) proteins, which form the core of the eukaryotic replication fork, as this complex undergoes major structural rearrangements in order to engage with DNA, regulate its DNA-unwinding activity, and maintain genome stability. PMID:28717046

Simple clinical means of documenting increased pulmonary endothelial permeability to protein

Energy Technology Data Exchange (ETDEWEB)

Mishkin, F.S.; Niden, A.; Kumar, A.; Thomas, A.; Reese, I.C.; Vasinrapee, P.

1987-02-20

The authors investigated a simple method that can be used at the bedside for documenting the net accumulation of albumin in the lung. The technique employs measurement with a computer-linked gamma camera of the activity ratio in an area of the right lung compared with the same-sized area in the heart at 20 minutes and three hours following intravenous injection of technetium Tc 99m albumin. They applied this measurement to three groups of patients: a control group and patients with roentgenographic evidence of edema classified according to clinically available criteria as either hydrostatic edema or permeability edema to see if they could document differences among these groups. In control patients this ratio did not increase by more than seven units between the 20-minute and three-hour measurements. Of 18 patients classified by other routine clinical means as having hydrostatic pulmonary edema, 89% showed no increase in lung albumin accumulation. In 29 patients with permeability edema associated with the so-called adult respiratory distress syndrome, 31% showed evidence of net pulmonary albumin accumulation. These findings suggest that some patients otherwise classified as having hydrostatic edema have concomitant permeability changes in the microvasculature and that permeability edema represents a spectrum of endothelial damage.

Simple clinical means of documenting increased pulmonary endothelial permeability to protein

International Nuclear Information System (INIS)

Mishkin, F.S.; Niden, A.; Kumar, A.; Thomas, A.; Reese, I.C.; Vasinrapee, P.

1987-01-01

The authors investigated a simple method that can be used at the bedside for documenting the net accumulation of albumin in the lung. The technique employs measurement with a computer-linked gamma camera of the activity ratio in an area of the right lung compared with the same-sized area in the heart at 20 minutes and three hours following intravenous injection of technetium Tc 99m albumin. They applied this measurement to three groups of patients: a control group and patients with roentgenographic evidence of edema classified according to clinically available criteria as either hydrostatic edema or permeability edema to see if they could document differences among these groups. In control patients this ratio did not increase by more than seven units between the 20-minute and three-hour measurements. Of 18 patients classified by other routine clinical means as having hydrostatic pulmonary edema, 89% showed no increase in lung albumin accumulation. In 29 patients with permeability edema associated with the so-called adult respiratory distress syndrome, 31% showed evidence of net pulmonary albumin accumulation. These findings suggest that some patients otherwise classified as having hydrostatic edema have concomitant permeability changes in the microvasculature and that permeability edema represents a spectrum of endothelial damage

Gadolinium prevents high airway pressure-induced permeability increases in isolated rat lungs.

Science.gov (United States)

Parker, J C; Ivey, C L; Tucker, J A

1998-04-01

To determine the initial signaling event in the vascular permeability increase after high airway pressure injury, we compared groups of lungs ventilated at different peak inflation pressures (PIPs) with (gadolinium group) and without (control group) infusion of 20 microM gadolinium chloride, an inhibitor of endothelial stretch-activated cation channels. Microvascular permeability was assessed by using the capillary filtration coefficient (Kfc), a measure of capillary hydraulic conductivity. Kfc was measured after ventilation for 30-min periods with 7, 20, and 30 cmH2O PIP with 3 cmH2O positive end-expiratory pressure and with 35 cmH2O PIP with 8 cmH2O positive end-expiratory pressure. In control lungs, Kfc increased significantly to 1.8 and 3.7 times baseline after 30 and 35 cmH2O PIP, respectively. In the gadolinium group, Kfc was unchanged from baseline (0.060 +/- 0.010 ml . min-1 . cmH2O-1 . 100 g-1) after any PIP ventilation period. Pulmonary vascular resistance increased significantly from baseline in both groups before the last Kfc measurement but was not different between groups. These results suggest that microvascular permeability is actively modulated by a cellular response to mechanical injury and that stretch-activated cation channels may initiate this response through increases in intracellular calcium concentration.

Drug-like properties and the causes of poor solubility and poor permeability.

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Lipinski, C A

2000-01-01

There are currently about 10000 drug-like compounds. These are sparsely, rather than uniformly, distributed through chemistry space. True diversity does not exist in experimental combinatorial chemistry screening libraries. Absorption, distribution, metabolism, and excretion (ADME) and chemical reactivity-related toxicity is low, while biological receptor activity is higher dimensional in chemistry space, and this is partly explainable by evolutionary pressures on ADME to deal with endobiotics and exobiotics. ADME is hard to predict for large data sets because current ADME experimental screens are multi-mechanisms, and predictions get worse as more data accumulates. Currently, screening for biological receptor activity precedes or is concurrent with screening for properties related to "drugability." In the future, "drugability" screening may precede biological receptor activity screening. The level of permeability or solubility needed for oral absorption is related to potency. The relative importance of poor solubility and poor permeability towards the problem of poor oral absorption depends on the research approach used for lead generation. A "rational drug design" approach as exemplified by Merck advanced clinical candidates leads to time-dependent higher molecular weight, higher H-bonding properties, unchanged lipophilicity, and, hence, poorer permeability. A high throughput screening (HTS)-based approach as exemplified by unpublished data on Pfizer (Groton, CT) early candidates leads to higher molecular weight, unchanged H-bonding properties, higher lipophilicity, and, hence, poorer aqueous solubility.

Use of digital image analysis to estimate fluid permeability of porous materials: Application of two-point correlation functions

International Nuclear Information System (INIS)

Berryman, J.G.; Blair, S.C.

1986-01-01

Scanning electron microscope images of cross sections of several porous specimens have been digitized and analyzed using image processing techniques. The porosity and specific surface area may be estimated directly from measured two-point spatial correlation functions. The measured values of porosity and image specific surface were combined with known values of electrical formation factors to estimate fluid permeability using one version of the Kozeny-Carman empirical relation. For glass bead samples with measured permeability values in the range of a few darcies, our estimates agree well ( +- 10--20%) with the measurements. For samples of Ironton-Galesville sandstone with a permeability in the range of hundreds of millidarcies, our best results agree with the laboratory measurements again within about 20%. For Berea sandstone with still lower permeability (tens of millidarcies), our predictions from the images agree within 10--30%. Best results for the sandstones were obtained by using the porosities obtained at magnifications of about 100 x (since less resolution and better statistics are required) and the image specific surface obtained at magnifications of about 500 x (since greater resolution is required)

Effect of leukotriene receptor antagonists on vascular permeability during endotoxic shock

International Nuclear Information System (INIS)

Cook, J.A.; Li, E.J.; Spicer, K.M.; Wise, W.C.; Halushka, P.V.

1990-01-01

Evidence has accumulated that sulfidopeptide leukotrienes are significant pathogenic mediators of certain hematologic and hemodynamic sequelae of endotoxic shock. In the present study, the effects of a selective LTD4/E4 receptor antagonist, LY171883 (LY), or a selective LTD4 receptor antagonist, SKF-104353 (SKF), were assessed on splanchnic and pulmonary localization of 99mTechnetium-labeled human serum albumin (99mTc-HSA) in acute endotoxic shock in the rat. Dynamic gamma camera imaging of heart (H), midabdominal (GI), and lung regions of interest generated time activity curves for baseline and at 5-35 min after Salmonella enteritidis endotoxin (10 mg/kg, i.v.). Slopes of GI/H and lung/H activity (permeability index, GI/H or lung/H X 10(-3)/min) provided indices of intestinal and lung localization. Rats received LY (30 mg/kg, i.v.), LY vehicle (LY Veh), SKF (10 mg/kg), or SKF vehicle (SK Veh) 10 min prior to endotoxin or endotoxin vehicle. In rats receiving the LY Veh and endotoxin (n = 8) or SKF Veh and endotoxin (n = 12), the splanchnic permeability indices to 99mTc-HSA were increased 11.2-fold and 5.1-fold, respectively (P less than 0.05) compared to vehicle control groups not given endotoxin (n = 5). Pulmonary permeability index for 99mTc-HSA was increased (P less than 0.05) to a lesser extent (3.2-fold) by endotoxin compared to vehicle controls. Pretreatment with SKF reduced the mesenteric permeability index to control levels (P less than 0.05) during the 5-35 min time interval post-endotoxin. LY reduced the mesenteric permeability index by 70%. Pulmonary relative permeability to 99mTc-HSA was not affected by LY pretreatment. Both splanchnic and lung relative permeability to the isotope was transient; at 135-225 min post-endotoxin, splanchnic localization of 99mTc-HSA (n = 4) was not significantly different from vehicle controls in these vascular beds

Biomarkers of replicative senescence revisited

DEFF Research Database (Denmark)

Nehlin, Jan

2016-01-01

Biomarkers of replicative senescence can be defined as those ultrastructural and physiological variations as well as molecules whose changes in expression, activity or function correlate with aging, as a result of the gradual exhaustion of replicative potential and a state of permanent cell cycle...... arrest. The biomarkers that characterize the path to an irreversible state of cell cycle arrest due to proliferative exhaustion may also be shared by other forms of senescence-inducing mechanisms. Validation of senescence markers is crucial in circumstances where quiescence or temporary growth arrest may...... be triggered or is thought to be induced. Pre-senescence biomarkers are also important to consider as their presence indicate that induction of aging processes is taking place. The bona fide pathway leading to replicative senescence that has been extensively characterized is a consequence of gradual reduction...

36 CFR 910.64 - Replication.

Science.gov (United States)

2010-07-01

... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Replication. 910.64 Section 910.64 Parks, Forests, and Public Property PENNSYLVANIA AVENUE DEVELOPMENT CORPORATION GENERAL... DEVELOPMENT AREA Glossary of Terms § 910.64 Replication. Replication means the process of using modern methods...

Hydrogels with precisely controlled integrin activation dictate vascular patterning and permeability

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