Does altercentric interference rely on mentalizing?: Results from two level-1 perspective-taking tasks

PubMed Central

Gollwitzer, Anton; Santos, Laurie R.

2018-01-01

Considerable debate has focused on whether adults possess an implicit system for representing others’ mental states. Some argue that people automatically represent the perspective of others using evidence from altercentric interference—cases in which another agent’s perspective affects the speed with which one can report one’s own perspective. Others have argued that altercentric interference is not always specific to social stimuli and thus may represent a simpler process such as submentalizing. To distinguish between these positions, Study 1 developed a novel measure of altercentric interference—a “sandbox” measure—that allowed us to more sensitively assess altercentric interference across social and non-social conditions. We replicated previous findings showing that participants experience both egocentric and altercentric interference, but we found that these effects emerge equally in social and non-social conditions. To further test whether altercentric interference emerges in social perspective-taking situations, Study 2 conducted a conceptual replication of a study which used a novel “goggle” paradigm to assess whether individuals implicitly represent others’ perspectives. Although we failed to find evidence of altercentric interference in response times, participants’ accuracy reflected the possibility of interference from others’ perspectives. We argue that these findings provide support for the idea that altercentric interference in response to social stimuli (an avatar) is driven by perspective-taking mechanisms, while such interference in response to non-social stimuli (an arrow) is driven by attention-cuing mechanisms. PMID:29566019

Replication, randomization, and treatment design concepts for on-farm research

USDA-ARS?s Scientific Manuscript database

For most agronomists, randomization and replication are fundamental concepts that have a nearly sacred or spiritual status. They are an integral part of nearly all of our field-based activities. Some on-farm research falls into this category, simply because it is driven and designed by researchers w...

Why people stereotype affects how they stereotype: the differential influence of comprehension goals and self-enhancement goals on stereotyping.

PubMed

van den Bos, Arne; Stapel, Diederik A

2009-01-01

In four studies, the authors examined the hypothesis that the way people stereotype is determined by the motives that instigate it. Study 1 measured and demonstrated the effectiveness of a commonly used priming technique to manipulate comprehension and self-enhancement goals. Study 2 demonstrated that why people stereotype determines how they stereotype: When a comprehension goal was salient, positive as well as negative stereotypes were applied, whereas a salient self-enhancement goal led to the application of negative but not positive stereotypes. Study 3 replicated these effects with different stereotypes. Study 4 replicated these effects and gave more insight in the consequences of goal fulfillment on stereotyping. Results indicated the fulfillment of a salient self-enhancement or comprehension goal led to the reduction of stereotyping. These effects were goal specific: Fulfillment of a self-enhancement goal decreased enhancement-driven but not comprehension-driven stereotyping; fulfillment of a comprehension goal decreased comprehension-driven but not enhancement-driven stereotyping.

A plasma deflagration accelerator as a platform for laboratory astrophysics

NASA Astrophysics Data System (ADS)

Underwood, Thomas C.; Loebner, Keith T. K.; Cappelli, Mark A.

2017-06-01

The replication of astrophysical flows in the laboratory is critical for isolating particular phenomena and dynamics that appear in complex, highly-coupled natural systems. In particular, plasma jets are observed in astrophysical contexts at a variety of scales, typically at high magnetic Reynolds number and driven by internal currents. In this paper, we present detailed measurements of the plasma parameters within deflagration-produced plasma jets, the scaling of these parameters against both machine operating conditions and the corresponding astrophysical phenomena. Using optical and spectroscopic diagnostics, including Schlieren cinematography, we demonstrate the production of current-driven plasma jets of ∼100 km/s and magnetic Reynolds numbers of ∼100, and discuss the dynamics of their acceleration into vacuum. The results of this study will contribute to the reproduction of various types of astrophysical jets in the laboratory and indicate the ability to further probe active research areas such as jet collimation, stability, and interaction.

Stochastic variation in telomere shortening rate causes heterogeneity of human fibroblast replicative life span.

PubMed

Martin-Ruiz, Carmen; Saretzki, Gabriele; Petrie, Joanne; Ladhoff, Juliane; Jeyapalan, Jessie; Wei, Wenyi; Sedivy, John; von Zglinicki, Thomas

2004-04-23

The replicative life span of human fibroblasts is heterogeneous, with a fraction of cells senescing at every population doubling. To find out whether this heterogeneity is due to premature senescence, i.e. driven by a nontelomeric mechanism, fibroblasts with a senescent phenotype were isolated from growing cultures and clones by flow cytometry. These senescent cells had shorter telomeres than their cycling counterparts at all population doubling levels and both in mass cultures and in individual subclones, indicating heterogeneity in the rate of telomere shortening. Ectopic expression of telomerase stabilized telomere length in the majority of cells and rescued them from early senescence, suggesting a causal role of telomere shortening. Under standard cell culture conditions, there was a minor fraction of cells that showed a senescent phenotype and short telomeres despite active telomerase. This fraction increased under chronic mild oxidative stress, which is known to accelerate telomere shortening. It is possible that even high telomerase activity cannot fully compensate for telomere shortening in all cells. The data show that heterogeneity of the human fibroblast replicative life span can be caused by significant stochastic cell-to-cell variation in telomere shortening.

An integrated chemical biology approach reveals the mechanism of action of HIV replication inhibitors.

PubMed

Pagano, Nicholas; Teriete, Peter; Mattmann, Margrith E; Yang, Li; Snyder, Beth A; Cai, Zhaohui; Heil, Marintha L; Cosford, Nicholas D P

2017-12-01

Continuous flow (microfluidic) chemistry was employed to prepare a small focused library of dihydropyrimidinone (DHPM) derivatives. Compounds in this class have been reported to exhibit activity against the human immunodeficiency virus (HIV), but their molecular target had not been identified. We tested the initial set of DHPMs in phenotypic assays providing a hit (1i) that inhibited the replication of the human immunodeficiency virus HIV in cells. Flow chemistry-driven optimization of 1i led to the identification of HIV replication inhibitors such as 1l with cellular potency comparable with the clinical drug nevirapine (NVP). Mechanism of action (MOA) studies using cellular and biochemical assays coupled with 3D fingerprinting and in silico modeling demonstrated that these drug-like probe compounds exert their effects by inhibiting the viral reverse transcriptase polymerase (RT). This led to the design and synthesis of the novel DHPM 1at that inhibits the replication of drug resistant strains of HIV. Our work demonstrates that combining flow chemistry-driven analogue refinement with phenotypic assays, in silico modeling and MOA studies is a highly effective strategy for hit-to-lead optimization applicable to the discovery of future therapeutic agents. Copyright © 2017. Published by Elsevier Ltd.

Intersubtype Differences in the Effect of a Rare p24 Gag Mutation on HIV-1 Replicative Fitness

PubMed Central

Chopera, Denis R.; Cotton, Laura A.; Zawaira, Alexander; Mann, Jaclyn K.; Ngandu, Nobubelo K.; Ntale, Roman; Carlson, Jonathan M.; Mlisana, Koleka; Woodman, Zenda; de Assis Rosa, Debra; Martin, Eric; Miura, Toshiyuki; Pereyra, Florencia; Walker, Bruce D.; Gray, Clive M.; Martin, Darren P.; Ndung'u, Thumbi; Brockman, Mark A.; Karim, Salim Abdool

2012-01-01

Certain immune-driven mutations in HIV-1, such as those arising in p24Gag, decrease viral replicative capacity. However, the intersubtype differences in the replicative consequences of such mutations have not been explored. In HIV-1 subtype B, the p24Gag M250I mutation is a rare variant (0.6%) that is enriched among elite controllers (7.2%) (P = 0.0005) and appears to be a rare escape variant selected by HLA-B58 supertype alleles (P < 0.01). In contrast, in subtype C, it is a relatively common minor polymorphic variant (10 to 15%) whose appearance is not associated with a particular HLA allele. Using site-directed mutant viruses, we demonstrate that M250I reduces in vitro viral replicative capacity in both subtype B and subtype C sequences. However, whereas in subtype C downstream compensatory mutations at p24Gag codons 252 and 260 reduce the adverse effects of M250I, fitness costs in subtype B appear difficult to restore. Indeed, patient-derived subtype B sequences harboring M250I exhibited in vitro replicative defects, while those from subtype C did not. The structural implications of M250I were predicted by protein modeling to be greater in subtype B versus C, providing a potential explanation for its lower frequency and enhanced replicative defects in subtype B. In addition to accounting for genetic differences between HIV-1 subtypes, the design of cytotoxic-T-lymphocyte-based vaccines may need to account for differential effects of host-driven viral evolution on viral fitness. PMID:23015721

Complete regression of human malignant mesothelioma xenografts following local injection of midkine promoter-driven oncolytic adenovirus

PubMed Central

Kubo, Shuji; Kawasaki, Yoshiko; Yamaoka, Norie; Tagawa, Masatoshi; Kasahara, Noriyuki; Terada, Nobuyuki; Okamura, Haruki

2010-01-01

Background Malignant mesothelioma is a highly aggressive tumor with poor prognosis. Conventional therapies for mesothelioma are generally non-curative, and new treatment paradigms are urgently needed. We hypothesized that the tumor-specific midkine (Mdk) promoter could confer transcriptional targeting to oncolytic adenoviruses for effective treatment of malignant mesothelioma. Methods We analyzed Mdk expression by quantitative RT-PCR in six human mesothelioma cell lines, and tested Mdk promoter activity by luciferase reporter assay. Based on these data, we constructed a replication-selective oncolytic adenovirus, designated AdMdk-E1-iresTK, which contains an Mdk promoter-driven adenoviral E1 gene and HSV-thymidine kinase (TK) suicide gene, and CMV promoter-driven green fluorescent protein (GFP) marker gene. Selectivity of viral replication and cytolysis were characterized in normal vs. mesothelioma cells in vitro, and intratumoral spread and antitumor efficacy were investigated in vivo. Results Mdk promoter activity was restricted in normal cells, but highly activated in mesothelioma cell lines. AdMdk-E1-iresTK was seen to efficiently replicate, produce viral progeny, and spread in multiple mesothelioma cell lines. Lytic spread of AdMdk-E1-iresTK mediated efficient killing of these mesothelioma cells, and its in vitro cytocidal effect was significantly enhanced by treatment with the prodrug, ganciclovir. Intratumoral injection of AdMdk-E1-iresTK caused complete regression of MESO4 and MSTO human mesothelioma xenografts in athymic mice. In vivo fluorescence imaging demonstrated intratumoral spread of AdMdk-E1-iresTK-derived signals, which vanished after tumor eradication. Conclusions These data indicate that transcriptional targeting of viral replication by the Mdk promoter represents a promising general strategy for oncolytic virotherapy of cancers with upregulated Mdk expression, including malignant mesothelioma. PMID:20635326

Autonomous model protocell division driven by molecular replication.

PubMed

Taylor, J W; Eghtesadi, S A; Points, L J; Liu, T; Cronin, L

2017-08-10

The coupling of compartmentalisation with molecular replication is thought to be crucial for the emergence of the first evolvable chemical systems. Minimal artificial replicators have been designed based on molecular recognition, inspired by the template copying of DNA, but none yet have been coupled to compartmentalisation. Here, we present an oil-in-water droplet system comprising an amphiphilic imine dissolved in chloroform that catalyses its own formation by bringing together a hydrophilic and a hydrophobic precursor, which leads to repeated droplet division. We demonstrate that the presence of the amphiphilic replicator, by lowering the interfacial tension between droplets of the reaction mixture and the aqueous phase, causes them to divide. Periodic sampling by a droplet-robot demonstrates that the extent of fission is increased as the reaction progresses, producing more compartments with increased self-replication. This bridges a divide, showing how replication at the molecular level can be used to drive macroscale droplet fission.Coupling compartmentalisation and molecular replication is essential for the development of evolving chemical systems. Here the authors show an oil-in-water droplet containing a self-replicating amphiphilic imine that can undergo repeated droplet division.

Consequences of HLA-B*13-Associated Escape Mutations on HIV-1 Replication and Nef Function

PubMed Central

Shahid, Aniqa; Olvera, Alex; Anmole, Gursev; Kuang, Xiaomei T.; Cotton, Laura A.; Plana, Montserrat; Brander, Christian; Brockman, Mark A.

2015-01-01

ABSTRACT HLA-B*13 is associated with superior in vivo HIV-1 viremia control. Protection is thought to be mediated by sustained targeting of key cytotoxic T lymphocyte (CTL) epitopes and viral fitness costs of CTL escape in Gag although additional factors may contribute. We assessed the impact of 10 published B*13-associated polymorphisms in Gag, Pol, and Nef, in 23 biologically relevant combinations, on HIV-1 replication capacity and Nef-mediated reduction of cell surface CD4 and HLA class I expression. Mutations were engineered into HIV-1NL4.3, and replication capacity was measured using a green fluorescent protein (GFP) reporter T cell line. Nef-mediated CD4 and HLA-A*02 downregulation was assessed by flow cytometry, and T cell recognition of infected target cells was measured via coculture with an HIV-specific luciferase reporter cell line. When tested individually, only Gag-I147L and Gag-I437L incurred replicative costs (5% and 17%, respectively), consistent with prior reports. The Gag-I437L-mediated replication defect was rescued to wild-type levels by the adjacent K436R mutation. A novel B*13 epitope, comprising 8 residues and terminating at Gag147, was identified in p24Gag (GQMVHQAIGag140–147). No other single or combination Gag, Pol, or Nef mutant impaired viral replication. Single Nef mutations did not affect CD4 or HLA downregulation; however, the Nef double mutant E24Q-Q107R showed 40% impairment in HLA downregulation with no evidence of Nef stability defects. Moreover, target cells infected with HIV-1-NefE24Q-Q107R were recognized better by HIV-specific T cells than those infected with HIV-1NL4.3 or single Nef mutants. Our results indicate that CTL escape in Gag and Nef can be functionally costly and suggest that these effects may contribute to long-term HIV-1 control by HLA-B*13. IMPORTANCE Protective effects of HLA-B*13 on HIV-1 disease progression are mediated in part by fitness costs of CTL escape mutations in conserved Gag epitopes, but other mechanisms remain incompletely known. We extend our knowledge of the impact of B*13-driven escape on HIV-1 replication by identifying Gag-K436R as a compensatory mutation for the fitness-costly Gag-I437L. We also identify Gag-I147L, the most rapidly and commonly selected B*13-driven substitution in HIV-1, as a putative C-terminal anchor residue mutation in a novel B*13 epitope. Most notably, we identify a novel escape-driven fitness defect: B*13-driven substitutions E24Q and Q107R in Nef, when present together, substantially impair this protein's ability to downregulate HLA class I. This, in turn, increases the visibility of infected cells to HIV-specific T cells. Our results suggest that B*13-associated escape mutations impair HIV-1 replication by two distinct mechanisms, that is, by reducing Gag fitness and dampening Nef immune evasion function. PMID:26355081

157 Pathogenesis of Epstein-Barr Virus-driven lymphomas of HIV+ patients: new insights of potential clinical relevance

PubMed Central

Dolcetti, Riccardo

2014-01-01

Human Immunodeficiency Virus (HIV)+ patients have an increased risk to develop lymphomas, including a significant fraction of histotypes associated with Epstein-Barr Virus (EBV) infection. Although restoration of EBV-specific T-cell function induced by HAART has led to a decreased incidence of the more immunogenic EBV-associated lymphomas, such as immunoblastic and primary central nervous system lymphomas, other EBV+ histotypes are still prevalent in the HAART era, particularly Hodgkin’s lymphoma. Therefore, factors other than HIV-induced immune suppression are probably required for the development of EBV-related lymphomas in this setting. Particular attention is being given to the identification of microenvironmental stimuli able to up-regulate critical EBV latency proteins or to induce/enhance EBV replication. In fact, recent evidence indicates that, although latency programs predominate in EBV-driven tumors, lytic EBV replication may also be of pathogenic relevance, at least in the early phases of cell transformation. This is particularly relevant for HIV-related lymphomagenesis since the underlying impairment of immune responses may favour uncontrolled activation of EBV lytic replication in latently-infected B lymphocytes. Available data indicate that local expression of distinct cytokines, including IL-4 and IL-13, may up-regulate the expression of the LMP-1 oncoprotein in B cells, thus favoring lymphomagenesis. In the search of microenvironmental factors that may promote the development of EBV-driven lymphomas in HIV+ patients, we obtained evidence supporting a pathogenic role for HIV matrix protein p17, which accumulates in lymphoid tissues of HIV+ individuals, even during HAART. Our findings support a direct contribution of HIV p17 to the development of EBV-driven lymphomagenesis and may provide the rationale for new strategies of clinical intervention in this setting.

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

PubMed

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.

The HARP domain dictates the annealing helicase activity of HARP/SMARCAL1.

PubMed

Ghosal, Gargi; Yuan, Jingsong; Chen, Junjie

2011-06-01

Mutations in HepA-related protein (HARP, or SMARCAL1) cause Schimke immunoosseous dysplasia (SIOD). HARP has ATP-dependent annealing helicase activity, which helps to stabilize stalled replication forks and facilitate DNA repair during replication. Here, we show that the conserved tandem HARP (2HP) domain dictates this annealing helicase activity. Furthermore, chimeric proteins generated by fusing the 2HP domain of HARP with the SNF2 domain of BRG1 or HELLS show annealing helicase activity in vitro and, when targeted to replication forks, mimic the functions of HARP in vivo. We propose that the HARP domain endows HARP with this ATP-driven annealing helicase activity.

A Necessary Condition for Coexistence of Autocatalytic Replicators in a Prebiotic Environment

PubMed Central

Hernandez, Andres F.; Grover, Martha A.

2013-01-01

A necessary, but not sufficient, mathematical condition for the coexistence of short replicating species is presented here. The mathematical condition is obtained for a prebiotic environment, simulated as a fed-batch reactor, which combines monomer recycling, variable reaction order and a fixed monomer inlet flow with two replicator types and two monomer types. An extensive exploration of the parameter space in the model validates the robustness and efficiency of the mathematical condition, with nearly 1.7% of parameter sets meeting the condition and half of those exhibiting sustained coexistence. The results show that it is possible to generate a condition of coexistence, where two replicators sustain a linear growth simultaneously for a wide variety of chemistries, under an appropriate environment. The presence of multiple monomer types is critical to sustaining the coexistence of multiple replicator types. PMID:25369813

A necessary condition for coexistence of autocatalytic replicators in a prebiotic environment.

PubMed

Hernandez, Andres F; Grover, Martha A

2013-07-24

A necessary, but not sufficient, mathematical condition for the coexistence of short replicating species is presented here. The mathematical condition is obtained for a prebiotic environment, simulated as a fed-batch reactor, which combines monomer recycling, variable reaction order and a fixed monomer inlet flow with two replicator types and two monomer types. An extensive exploration of the parameter space in the model validates the robustness and efficiency of the mathematical condition, with nearly 1.7% of parameter sets meeting the condition and half of those exhibiting sustained coexistence. The results show that it is possible to generate a condition of coexistence, where two replicators sustain a linear growth simultaneously for a wide variety of chemistries, under an appropriate environment. The presence of multiple monomer types is critical to sustaining the coexistence of multiple replicator types.

Computational Trials: Unraveling Motility Phenotypes, Progression Patterns, and Treatment Options for Glioblastoma Multiforme

PubMed Central

Raman, Fabio; Scribner, Elizabeth; Saut, Olivier; Wenger, Cornelia; Colin, Thierry; Fathallah-Shaykh, Hassan M.

2016-01-01

Glioblastoma multiforme is a malignant brain tumor with poor prognosis and high morbidity due to its invasiveness. Hypoxia-driven motility and concentration-driven motility are two mechanisms of glioblastoma multiforme invasion in the brain. The use of anti-angiogenic drugs has uncovered new progression patterns of glioblastoma multiforme associated with significant differences in overall survival. Here, we apply a mathematical model of glioblastoma multiforme growth and invasion in humans and design computational trials using agents that target angiogenesis, tumor replication rates, or motility. The findings link highly-dispersive, moderately-dispersive, and hypoxia-driven tumors to the patterns observed in glioblastoma multiforme treated by anti-angiogenesis, consisting of progression by Expanding FLAIR, Expanding FLAIR + Necrosis, and Expanding Necrosis, respectively. Furthermore, replication rate-reducing strategies (e.g. Tumor Treating Fields) appear to be effective in highly-dispersive and moderately-dispersive tumors but not in hypoxia-driven tumors. The latter may respond to motility-reducing agents. In a population computational trial, with all three phenotypes, a correlation was observed between the efficacy of the rate-reducing agent and the prolongation of overall survival times. This research highlights the potential applications of computational trials and supports new hypotheses on glioblastoma multiforme phenotypes and treatment options. PMID:26756205

Variance stabilization and normalization for one-color microarray data using a data-driven multiscale approach.

PubMed

Motakis, E S; Nason, G P; Fryzlewicz, P; Rutter, G A

2006-10-15

Many standard statistical techniques are effective on data that are normally distributed with constant variance. Microarray data typically violate these assumptions since they come from non-Gaussian distributions with a non-trivial mean-variance relationship. Several methods have been proposed that transform microarray data to stabilize variance and draw its distribution towards the Gaussian. Some methods, such as log or generalized log, rely on an underlying model for the data. Others, such as the spread-versus-level plot, do not. We propose an alternative data-driven multiscale approach, called the Data-Driven Haar-Fisz for microarrays (DDHFm) with replicates. DDHFm has the advantage of being 'distribution-free' in the sense that no parametric model for the underlying microarray data is required to be specified or estimated; hence, DDHFm can be applied very generally, not just to microarray data. DDHFm achieves very good variance stabilization of microarray data with replicates and produces transformed intensities that are approximately normally distributed. Simulation studies show that it performs better than other existing methods. Application of DDHFm to real one-color cDNA data validates these results. The R package of the Data-Driven Haar-Fisz transform (DDHFm) for microarrays is available in Bioconductor and CRAN.

Technical Challenges in the Development of a NASA Synthetic Vision System Concept

NASA Technical Reports Server (NTRS)

Bailey, Randall E.; Parrish, Russell V.; Kramer, Lynda J.; Harrah, Steve; Arthur, J. J., III

2002-01-01

Within NASA's Aviation Safety Program, the Synthetic Vision Systems Project is developing display system concepts to improve pilot terrain/situation awareness by providing a perspective synthetic view of the outside world through an on-board database driven by precise aircraft positioning information updating via Global Positioning System-based data. This work is aimed at eliminating visibility-induced errors and low visibility conditions as a causal factor to civil aircraft accidents, as well as replicating the operational benefits of clear day flight operations regardless of the actual outside visibility condition. Synthetic vision research and development activities at NASA Langley Research Center are focused around a series of ground simulation and flight test experiments designed to evaluate, investigate, and assess the technology which can lead to operational and certified synthetic vision systems. The technical challenges that have been encountered and that are anticipated in this research and development activity are summarized.

DigOut: viewing differential expression genes as outliers.

PubMed

Yu, Hui; Tu, Kang; Xie, Lu; Li, Yuan-Yuan

2010-12-01

With regards to well-replicated two-conditional microarray datasets, the selection of differentially expressed (DE) genes is a well-studied computational topic, but for multi-conditional microarray datasets with limited or no replication, the same task is not properly addressed by previous studies. This paper adopts multivariate outlier analysis to analyze replication-lacking multi-conditional microarray datasets, finding that it performs significantly better than the widely used limit fold change (LFC) model in a simulated comparative experiment. Compared with the LFC model, the multivariate outlier analysis also demonstrates improved stability against sample variations in a series of manipulated real expression datasets. The reanalysis of a real non-replicated multi-conditional expression dataset series leads to satisfactory results. In conclusion, a multivariate outlier analysis algorithm, like DigOut, is particularly useful for selecting DE genes from non-replicated multi-conditional gene expression dataset.

c-MYC—Making Liver Sick: Role of c-MYC in Hepatic Cell Function, Homeostasis and Disease

PubMed Central

Zheng, Kang; Cubero, Francisco Javier; Nevzorova, Yulia A.

2017-01-01

Over 35 years ago, c-MYC, a highly pleiotropic transcription factor that regulates hepatic cell function, was identified. In recent years, a considerable increment in the number of publications has significantly shifted the way that the c-MYC function is perceived. Overexpression of c-MYC alters a wide range of roles including cell proliferation, growth, metabolism, DNA replication, cell cycle progression, cell adhesion and differentiation. The purpose of this review is to broaden the understanding of the general functions of c-MYC, to focus on c-MYC-driven pathogenesis in the liver, explain its mode of action under basal conditions and during disease, and discuss efforts to target c-MYC as a plausible therapy for liver disease. PMID:28422055

Order-splitting and long-memory in an order-driven market

NASA Astrophysics Data System (ADS)

Yamamoto, R.; LeBaron, B.

2010-01-01

Recent empirical research has documented long-memories of trading volume, volatility, and order-signs in stock markets. We conjecture that traders' order-splitting is related to these empirical features. This study conducts simulations on an order-driven economy where agents split their orders into small pieces and execute piece by piece to reduce price impact. We demonstrate that we can replicate the long-memories in our order-splitting economy and conclude that order-splitting can be a possible cause for these empirical properties.

Flow pumping system for physiological waveforms.

PubMed

Tsai, William; Savaş, Omer

2010-02-01

A pulsatile flow pumping system is developed to replicate flow waveforms with reasonable accuracy for experiments simulating physiological blood flows at numerous points in the body. The system divides the task of flow waveform generation between two pumps: a gear pump generates the mean component and a piston pump generates the oscillatory component. The system is driven by two programmable servo controllers. The frequency response of the system is used to characterize its operation. The system has been successfully tested in vascular flow experiments where sinusoidal, carotid, and coronary flow waveforms are replicated.

Modeling noisy resonant system response

NASA Astrophysics Data System (ADS)

Weber, Patrick Thomas; Walrath, David Edwin

2017-02-01

In this paper, a theory-based model replicating empirical acoustic resonant signals is presented and studied to understand sources of noise present in acoustic signals. Statistical properties of empirical signals are quantified and a noise amplitude parameter, which models frequency and amplitude-based noise, is created, defined, and presented. This theory-driven model isolates each phenomenon and allows for parameters to be independently studied. Using seven independent degrees of freedom, this model will accurately reproduce qualitative and quantitative properties measured from laboratory data. Results are presented and demonstrate success in replicating qualitative and quantitative properties of experimental data.

Dynamic Architecture of Eukaryotic DNA Replication Forks In Vivo, Visualized by Electron Microscopy.

PubMed

Zellweger, Ralph; Lopes, Massimo

2018-01-01

The DNA replication process can be heavily perturbed by several different conditions of genotoxic stress, particularly relevant for cancer onset and therapy. The combination of psoralen crosslinking and electron microscopy has proven instrumental to reveal the fine architecture of in vivo DNA replication intermediates and to uncover their remodeling upon specific conditions of genotoxic stress. The replication structures are stabilized in vivo (by psoralen crosslinking) prior to extraction and enrichment procedures, allowing their visualization at the transmission electron microscope. This chapter outlines the procedures required to visualize and interpret in vivo replication intermediates of eukaryotic genomic DNA, and includes an improved method for enrichment of replication intermediates, compared to previously used BND-cellulose columns.

Human Adipose‐Derived Stem Cells Expanded Under Ambient Oxygen Concentration Accumulate Oxidative DNA Lesions and Experience Procarcinogenic DNA Replication Stress

PubMed Central

Renoud, Marie‐Laure; Hoede, Claire; Gonzalez, Ignacio; Jones, Natalie; Longy, Michel; Sensebé, Luc; Cazaux, Christophe

2016-01-01

Abstract Adipose‐derived stem cells (ADSCs) have led to growing interest in cell‐based therapy because they can be easily harvested from an abundant tissue. ADSCs must be expanded in vitro before transplantation. This essential step causes concerns about the safety of adult stem cells in terms of potential transformation. Tumorigenesis is driven in its earliest step by DNA replication stress, which is characterized by the accumulation of stalled DNA replication forks and activation of the DNA damage response. Thus, to evaluate the safety of ADSCs during ex vivo expansion, we monitored DNA replication under atmospheric (21%) or physiologic (1%) oxygen concentration. Here, by combining immunofluorescence and DNA combing, we show that ADSCs cultured under 21% oxygen accumulate endogenous oxidative DNA lesions, which interfere with DNA replication by increasing fork stalling events, thereby leading to incomplete DNA replication and fork collapse. Moreover, we found by RNA sequencing (RNA‐seq) that culture of ADSCs under atmospheric oxygen concentration leads to misexpression of cell cycle and DNA replication genes, which could contribute to DNA replication stress. Finally, analysis of acquired small nucleotide polymorphism shows that expansion of ADSCs under 21% oxygen induces a mutational bias toward deleterious transversions. Overall, our results suggest that expanding ADSCs at a low oxygen concentration could reduce the risk for DNA replication stress‐associated transformation, as occurs in neoplastic tissues. Stem Cells Translational Medicine 2017;6:68–76 PMID:28170194

When the research is not reproducible: The importance of author-initiated and institution-driven responses and investigations.

PubMed

Tang, Bor Luen

2018-05-20

Important and potentially useful findings in the sciences are under more intense public scrutiny now more than ever. Other researchers in the field dive into replicating and expanding the findings while the media swamps the community and the public with peripheral reporting and analyses. How should authors and the hosting/funding institutions respond when other workers in the field could not reproduce or replicate their published results? To illustrate the importance of author-initiated and institution-driven investigations in response to outcries of research irreproducibility, I draw on comparisons between three recent and well-publicized cases in the life sciences: betatrophin, STAP cells, and NgAgo. Swift, transparent responses and investigations facilitate activation of the self-correcting mechanism of science and are likely also critical in preserving the community's resources, public trust, and the reputation of the institutions and individuals concerned. Operational guidelines for "author and institutional responses" towards external reports of irreproducibility should therefore be in place for all research intensive institutions.

A mitosis-specific and R loop-driven ATR pathway promotes faithful chromosome segregation.

PubMed

Kabeche, Lilian; Nguyen, Hai Dang; Buisson, Rémi; Zou, Lee

2018-01-05

The ataxia telangiectasia mutated and Rad3-related (ATR) kinase is crucial for DNA damage and replication stress responses. Here, we describe an unexpected role of ATR in mitosis. Acute inhibition or degradation of ATR in mitosis induces whole-chromosome missegregation. The effect of ATR ablation is not due to altered cyclin-dependent kinase 1 (CDK1) activity, DNA damage responses, or unscheduled DNA synthesis but to loss of an ATR function at centromeres. In mitosis, ATR localizes to centromeres through Aurora A-regulated association with centromere protein F (CENP-F), allowing ATR to engage replication protein A (RPA)-coated centromeric R loops. As ATR is activated at centromeres, it stimulates Aurora B through Chk1, preventing formation of lagging chromosomes. Thus, a mitosis-specific and R loop-driven ATR pathway acts at centromeres to promote faithful chromosome segregation, revealing functions of R loops and ATR in suppressing chromosome instability. Copyright © 2018, American Association for the Advancement of Science.

Major evolutionary transitions in individuality

PubMed Central

West, Stuart A.; Fisher, Roberta M.; Gardner, Andy; Kiers, E. Toby

2015-01-01

The evolution of life on earth has been driven by a small number of major evolutionary transitions. These transitions have been characterized by individuals that could previously replicate independently, cooperating to form a new, more complex life form. For example, archaea and eubacteria formed eukaryotic cells, and cells formed multicellular organisms. However, not all cooperative groups are en route to major transitions. How can we explain why major evolutionary transitions have or haven’t taken place on different branches of the tree of life? We break down major transitions into two steps: the formation of a cooperative group and the transformation of that group into an integrated entity. We show how these steps require cooperation, division of labor, communication, mutual dependence, and negligible within-group conflict. We find that certain ecological conditions and the ways in which groups form have played recurrent roles in driving multiple transitions. In contrast, we find that other factors have played relatively minor roles at many key points, such as within-group kin discrimination and mechanisms to actively repress competition. More generally, by identifying the small number of factors that have driven major transitions, we provide a simpler and more unified description of how life on earth has evolved. PMID:25964342

Automatic processing influences free recall: converging evidence from the process dissociation procedure and remember-know judgments.

PubMed

McCabe, David P; Roediger, Henry L; Karpicke, Jeffrey D

2011-04-01

Dual-process theories of retrieval suggest that controlled and automatic processing contribute to memory performance. Free recall tests are often considered pure measures of recollection, assessing only the controlled process. We report two experiments demonstrating that automatic processes also influence free recall. Experiment 1 used inclusion and exclusion tasks to estimate recollection and automaticity in free recall, adopting a new variant of the process dissociation procedure. Dividing attention during study selectively reduced the recollection estimate but did not affect the automatic component. In Experiment 2, we replicated the results of Experiment 1, and subjects additionally reported remember-know-guess judgments during recall in the inclusion condition. In the latter task, dividing attention during study reduced remember judgments for studied items, but know responses were unaffected. Results from both methods indicated that free recall is partly driven by automatic processes. Thus, we conclude that retrieval in free recall tests is not driven solely by conscious recollection (or remembering) but also by automatic influences of the same sort believed to drive priming on implicit memory tests. Sometimes items come to mind without volition in free recall.

Primary Role for Toll-Like Receptor-Driven Tumor Necrosis Factor Rather than Cytosolic Immune Detection in Restricting Coxiella burnetii Phase II Replication within Mouse Macrophages

PubMed Central

Bradley, William P.; Boyer, Mark A.; Nguyen, Hieu T.; Birdwell, L. Dillon; Yu, Janet; Ribeiro, Juliana M.; Roy, Craig R.

2016-01-01

Coxiella burnetii replicates within permissive host cells by employing a Dot/Icm type IV secretion system (T4SS) to translocate effector proteins that direct the formation of a parasitophorous vacuole. C57BL/6 mouse macrophages restrict the intracellular replication of the C. burnetii Nine Mile phase II (NMII) strain. However, eliminating Toll-like receptor 2 (TLR2) permits bacterial replication, indicating that the restriction of bacterial replication is immune mediated. Here, we examined whether additional innate immune pathways are employed by C57BL/6 macrophages to sense and restrict NMII replication. In addition to the known role of TLR2 in detecting and restricting NMII infection, we found that TLR4 also contributes to cytokine responses but is not required to restrict bacterial replication. Furthermore, the TLR signaling adaptors MyD88 and Trif are required for cytokine responses and restricting bacterial replication. The C. burnetii NMII T4SS translocates bacterial products into C57BL/6 macrophages. However, there was little evidence of cytosolic immune sensing of NMII, as there was a lack of inflammasome activation, T4SS-dependent cytokine responses, and robust type I interferon (IFN) production, and these pathways were not required to restrict bacterial replication. Instead, endogenous tumor necrosis factor (TNF) produced upon TLR sensing of C. burnetii NMII was required to control bacterial replication. Therefore, our findings indicate a primary role for TNF produced upon immune detection of C. burnetii NMII by TLRs, rather than cytosolic PRRs, in enabling C57BL/6 macrophages to restrict bacterial replication. PMID:26787725

DEIsoM: a hierarchical Bayesian model for identifying differentially expressed isoforms using biological replicates

PubMed Central

Peng, Hao; Yang, Yifan; Zhe, Shandian; Wang, Jian; Gribskov, Michael; Qi, Yuan

2017-01-01

Abstract Motivation High-throughput mRNA sequencing (RNA-Seq) is a powerful tool for quantifying gene expression. Identification of transcript isoforms that are differentially expressed in different conditions, such as in patients and healthy subjects, can provide insights into the molecular basis of diseases. Current transcript quantification approaches, however, do not take advantage of the shared information in the biological replicates, potentially decreasing sensitivity and accuracy. Results We present a novel hierarchical Bayesian model called Differentially Expressed Isoform detection from Multiple biological replicates (DEIsoM) for identifying differentially expressed (DE) isoforms from multiple biological replicates representing two conditions, e.g. multiple samples from healthy and diseased subjects. DEIsoM first estimates isoform expression within each condition by (1) capturing common patterns from sample replicates while allowing individual differences, and (2) modeling the uncertainty introduced by ambiguous read mapping in each replicate. Specifically, we introduce a Dirichlet prior distribution to capture the common expression pattern of replicates from the same condition, and treat the isoform expression of individual replicates as samples from this distribution. Ambiguous read mapping is modeled as a multinomial distribution, and ambiguous reads are assigned to the most probable isoform in each replicate. Additionally, DEIsoM couples an efficient variational inference and a post-analysis method to improve the accuracy and speed of identification of DE isoforms over alternative methods. Application of DEIsoM to an hepatocellular carcinoma (HCC) dataset identifies biologically relevant DE isoforms. The relevance of these genes/isoforms to HCC are supported by principal component analysis (PCA), read coverage visualization, and the biological literature. Availability and implementation The software is available at https://github.com/hao-peng/DEIsoM Contact pengh@alumni.purdue.edu Supplementary information Supplementary data are available at Bioinformatics online. PMID:28595376

A Machine LearningFramework to Forecast Wave Conditions

NASA Astrophysics Data System (ADS)

Zhang, Y.; James, S. C.; O'Donncha, F.

2017-12-01

Recently, significant effort has been undertaken to quantify and extract wave energy because it is renewable, environmental friendly, abundant, and often close to population centers. However, a major challenge is the ability to accurately and quickly predict energy production, especially across a 48-hour cycle. Accurate forecasting of wave conditions is a challenging undertaking that typically involves solving the spectral action-balance equation on a discretized grid with high spatial resolution. The nature of the computations typically demands high-performance computing infrastructure. Using a case-study site at Monterey Bay, California, a machine learning framework was trained to replicate numerically simulated wave conditions at a fraction of the typical computational cost. Specifically, the physics-based Simulating WAves Nearshore (SWAN) model, driven by measured wave conditions, nowcast ocean currents, and wind data, was used to generate training data for machine learning algorithms. The model was run between April 1st, 2013 and May 31st, 2017 generating forecasts at three-hour intervals yielding 11,078 distinct model outputs. SWAN-generated fields of 3,104 wave heights and a characteristic period could be replicated through simple matrix multiplications using the mapping matrices from machine learning algorithms. In fact, wave-height RMSEs from the machine learning algorithms (9 cm) were less than those for the SWAN model-verification exercise where those simulations were compared to buoy wave data within the model domain (>40 cm). The validated machine learning approach, which acts as an accurate surrogate for the SWAN model, can now be used to perform real-time forecasts of wave conditions for the next 48 hours using available forecasted boundary wave conditions, ocean currents, and winds. This solution has obvious applications to wave-energy generation as accurate wave conditions can be forecasted with over a three-order-of-magnitude reduction in computational expense. The low computational cost (and by association low computer-power requirement) means that the machine learning algorithms could be installed on a wave-energy converter as a form of "edge computing" where a device could forecast its own 48-hour energy production.

Sleeping Beauty transposon-based system for rapid generation of HBV-replicating stable cell lines.

PubMed

Wu, Yong; Zhang, Tian-Ying; Fang, Lin-Lin; Chen, Zi-Xuan; Song, Liu-Wei; Cao, Jia-Li; Yang, Lin; Yuan, Quan; Xia, Ning-Shao

2016-08-01

The stable HBV-replicating cell lines, which carry replication-competent HBV genome stably integrated into the genome of host cell, are widely used to evaluate the effects of antiviral agents. However, current methods to generate HBV-replicating cell lines, which are mostly dependent on random integration of foreign DNA via plasmid transfection, are less-efficient and time-consuming. To address this issue, we constructed an all-in-one Sleeping Beauty transposon system (denoted pTSMP-HBV vector) for robust generation of stable cell lines carrying replication-competent HBV genome of different genotype. This vector contains a Sleeping Beauty transposon containing HBV 1.3-copy genome with an expression cassette of the SV40 promoter driving red fluorescent protein (mCherry) and self-cleaving P2A peptide linked puromycin resistance gene (PuroR). In addition, a PGK promoter-driven SB100X hyperactive transposase cassette is placed in the outside of the transposon in the same plasmid.The HBV-replicating stable cells could be obtained from pTSMP-HBV transfected HepG2 cells by red fluorescence-activated cell sorting and puromycin resistant cell selection within 4-week. Using this system, we successfully constructed four cell lines carrying replication-competent HBV genome of genotypes A-D. The replication and viral protein expression profiles of these cells were systematically characterized. In conclusion, our study provides a high-efficiency strategy to generate HBV-replicating stable cell lines, which may facilitate HBV-related virological study. Copyright © 2016. Published by Elsevier B.V.

DNA polymerases eta and kappa exchange with the polymerase delta holoenzyme to complete common fragile site synthesis.

PubMed

Barnes, Ryan P; Hile, Suzanne E; Lee, Marietta Y; Eckert, Kristin A

2017-09-01

Common fragile sites (CFSs) are inherently unstable genomic loci that are recurrently altered in human tumor cells. Despite their instability, CFS are ubiquitous throughout the human genome and associated with large tumor suppressor genes or oncogenes. CFSs are enriched with repetitive DNA sequences, one feature postulated to explain why these loci are inherently difficult to replicate, and sensitive to replication stress. We have shown that specialized DNA polymerases (Pols) η and κ replicate CFS-derived sequences more efficiently than the replicative Pol δ. However, we lacked an understanding of how these enzymes cooperate to ensure efficient CFS replication. Here, we designed a model of lagging strand replication with RFC loaded PCNA that allows for maximal activity of the four-subunit human Pol δ holoenzyme, Pol η, and Pol κ in polymerase mixing assays. We discovered that Pol η and κ are both able to exchange with Pol δ stalled at repetitive CFS sequences, enhancing Normalized Replication Efficiency. We used this model to test the impact of PCNA mono-ubiquitination on polymerase exchange, and found no change in polymerase cooperativity in CFS replication compared with unmodified PCNA. Finally, we modeled replication stress in vitro using aphidicolin and found that Pol δ holoenzyme synthesis was significantly inhibited in a dose-dependent manner, preventing any replication past the CFS. Importantly, Pol η and κ were still proficient in rescuing this stalled Pol δ synthesis, which may explain, in part, the CFS instability phenotype of aphidicolin-treated Pol η and Pol κ-deficient cells. In total, our data support a model wherein Pol δ stalling at CFSs allows for free exchange with a specialized polymerase that is not driven by PCNA. Copyright © 2017 Elsevier B.V. All rights reserved.

Using surface-enhanced Raman spectroscopy and electrochemically driven melting to discriminate Yersinia pestis from Y. pseudotuberculosis based on single nucleotide polymorphisms within unpurified polymerase chain reaction amplicons.

PubMed

Papadopoulou, Evanthia; Goodchild, Sarah A; Cleary, David W; Weller, Simon A; Gale, Nittaya; Stubberfield, Michael R; Brown, Tom; Bartlett, Philip N

2015-02-03

The development of sensors for the detection of pathogen-specific DNA, including relevant species/strain level discrimination, is critical in molecular diagnostics with major impacts in areas such as bioterrorism and food safety. Herein, we use electrochemically driven denaturation assays monitored by surface-enhanced Raman spectroscopy (SERS) to target single nucleotide polymorphisms (SNPs) that distinguish DNA amplicons generated from Yersinia pestis, the causative agent of plague, from the closely related species Y. pseudotuberculosis. Two assays targeting SNPs within the groEL and metH genes of these two species have been successfully designed. Polymerase chain reaction (PCR) was used to produce Texas Red labeled single-stranded DNA (ssDNA) amplicons of 262 and 251 bases for the groEL and metH targets, respectively. These amplicons were used in an unpurified form to hybridize to immobilized probes then subjected to electrochemically driven melting. In all cases electrochemically driven melting was able to discriminate between fully homologous DNA and that containing SNPs. The metH assay was particularly challenging due to the presence of only a single base mismatch in the middle of the 251 base long PCR amplicon. However, manipulation of assay conditions (conducting the electrochemical experiments at 10 °C) resulted in greater discrimination between the complementary and mismatched DNA. Replicate data were collected and analyzed for each duplex on different days, using different batches of PCR product and different sphere segment void (SSV) substrates. Despite the variability introduced by these differences, the assays are shown to be reliable and robust providing a new platform for strain discrimination using unpurified PCR samples.

Awe, uncertainty, and agency detection.

PubMed

Valdesolo, Piercarlo; Graham, Jesse

2014-01-01

Across five studies, we found that awe increases both supernatural belief (Studies 1, 2, and 5) and intentional-pattern perception (Studies 3 and 4)-two phenomena that have been linked to agency detection, or the tendency to interpret events as the consequence of intentional and purpose-driven agents. Effects were both directly and conceptually replicated, and mediational analyses revealed that these effects were driven by the influence of awe on tolerance for uncertainty. Experiences of awe decreased tolerance for uncertainty, which, in turn, increased the tendency to believe in nonhuman agents and to perceive human agency in random events.

Constructing a community-level amenity index

Treesearch

Joanna Paulson Ganning; Courtney G. Flint

2010-01-01

The study of amenity-driven regional change has proliferated in recent years, especially in the American West. While methods of quantifying amenity levels have progressed, they usually rely on traditional and inflexible methods of creating indices. This research note describes a method of manual indexing that allows a flexible and replicable way of assessing amenity...

Quantitation & Case-Study-Driven Inquiry to Enhance Yeast Fermentation Studies

ERIC Educational Resources Information Center

Grammer, Robert T.

2012-01-01

We propose a procedure for the assay of fermentation in yeast in microcentrifuge tubes that is simple and rapid, permitting assay replicates, descriptive statistics, and the preparation of line graphs that indicate reproducibility. Using regression and simple derivatives to determine initial velocities, we suggest methods to compare the effects of…

A plasmid-based reverse genetics system for influenza A virus.

PubMed Central

Pleschka, S; Jaskunas, R; Engelhardt, O G; Zürcher, T; Palese, P; García-Sastre, A

1996-01-01

A reverse genetics system for negative-strand RNA viruses was first successfully developed for influenza viruses. This technology involved the transfection of in vitro-reconstituted ribonucleoprotein (RNP) complexes into influenza virus-infected cells. We have now developed a method that allows intracellular reconstitution of RNP complexes from plasmid-based expression vectors. Expression of a viral RNA-like transcript is achieved from a plasmid containing a truncated human polymerase I (polI) promoter and a ribozyme sequence that generates the desired 3' end by autocatalytic cleavage. The polI-driven plasmid is cotransfected into human 293 cells with polII-responsive plasmids that express the viral PB1, PB2, PA, and NP proteins. This exclusively plasmid-driven system results in the efficient transcription and replication of the viral RNA-like reporter and allows the study of cis- and trans-acting signals involved in the transcription and replication of influenza virus RNAs. Using this system, we have also been able to rescue a synthetic neuraminidase gene into a recombinant influenza virus. This method represents a convenient alternative to the previously established RNP transfection system. PMID:8648766

A 4-study replication of the moderating effects of greed on socioeconomic status and unethical behaviour.

PubMed

Balakrishnan, Anjana; Palma, Paolo A; Patenaude, Joshua; Campbell, Lorne

2017-01-31

Four replications of Piff and colleagues' study examined the moderating effects of greed attitudes on the relationship between socio-economic status (SES) and unethical behaviour (Study 7). In the original study, the researchers found that both greed and SES predicted increased propensity to engage in unethical behavior. Furthermore, this association was moderated such that the effects of SES on unethical behaviour were no longer present in the greed prime condition versus the neutral condition. In replication 1 of the original study main effects of greed attitudes and SES were found, but no interaction was found. Main effects for greed emerged in replications 3 and 4. However no main effects for SES or interactions emerged for replications 2-4. A meta-analysis was conducted with all replications and the original study, and found no moderating effect of greed on the relationship between SES and unethical behavior.

A 4-study replication of the moderating effects of greed on socioeconomic status and unethical behaviour

PubMed Central

Balakrishnan, Anjana; Palma, Paolo A.; Patenaude, Joshua; Campbell, Lorne

2017-01-01

Four replications of Piff and colleagues’ study examined the moderating effects of greed attitudes on the relationship between socio-economic status (SES) and unethical behaviour (Study 7). In the original study, the researchers found that both greed and SES predicted increased propensity to engage in unethical behavior. Furthermore, this association was moderated such that the effects of SES on unethical behaviour were no longer present in the greed prime condition versus the neutral condition. In replication 1 of the original study main effects of greed attitudes and SES were found, but no interaction was found. Main effects for greed emerged in replications 3 and 4. However no main effects for SES or interactions emerged for replications 2–4. A meta-analysis was conducted with all replications and the original study, and found no moderating effect of greed on the relationship between SES and unethical behavior. PMID:28140396

DNA replication stress restricts ribosomal DNA copy number.

PubMed

Salim, Devika; Bradford, William D; Freeland, Amy; Cady, Gillian; Wang, Jianmin; Pruitt, Steven C; Gerton, Jennifer L

2017-09-01

Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100-200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how "normal" copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a "normal" rDNA copy number.

Identification of proteins that may directly interact with human RPA.

PubMed

Nakaya, Ryou; Takaya, Junichiro; Onuki, Takeshi; Moritani, Mariko; Nozaki, Naohito; Ishimi, Yukio

2010-11-01

RPA, which consisted of three subunits (RPA1, 2 and 3), plays essential roles in DNA transactions. At the DNA replication forks, RPA binds to single-stranded DNA region to stabilize the structure and to assemble other replication proteins. Interactions between RPA and several replication proteins have been reported but the analysis is not comprehensive. We systematically performed the qualitative analysis to identify RPA interaction partners to understand the protein-protein interaction at the replication forks. We expressed in insect cells the three subunits of human RPA, together with one replication protein, which is present at the forks under normal conditions and/or under the replication stress conditions, to examine the interaction. Among 30 proteins examined in total, it was found that at least 14 proteins interacted with RPA. RPA interacted with MCM3-7, MCM-BP and CDC45 proteins among the proteins that play roles in the initiation and the elongation of the DNA replication. RPA bound with TIPIN, CLASPIN and RAD17, which are involved in the DNA replication checkpoint functions. RPA also bound with cyclin-dependent kinases and an amino-terminal fragment of Rb protein that negatively regulates DNA replication. These results suggest that RPA interacts with the specific proteins among those that play roles in the regulation of the replication fork progression.

Drawing ability in typical and atypical development; colour cues and the effect of oblique lines.

PubMed

Farran, E K; Dodd, G F

2015-06-01

Individuals with Williams syndrome (WS) have poor drawing ability. Here, we investigated whether colour could be used as a facilitation cue during a drawing task. Participants with WS and non-verbal ability matched typically developing (TD) children were shown line figures presented on a 3 by 3 dot matrix, and asked to replicate the figures by drawing on an empty dot matrix. The dots of the matrix were either all black (control condition), or nine different coloured dots (colour condition). In a third condition, which also used coloured dots, participants were additionally asked to verbalise the colours of the dots prior to replicating the line drawings (colour-verbal condition). Performance was stronger in both WS and TD groups on the two coloured conditions, compared with the control condition. However, the facilitation effect of colour was significantly weaker in the WS group than in the TD group. Replication of oblique line segments was less successful than replication of non-oblique line segments for both groups; this effect was reduced by colour facilitation in the TD group only. Verbalising the colours had no additional impact on performance in either group. We suggest that colour acted as a cue to individuate the dots, thus enabling participants to better ascertain the spatial relationships between the parts of each figure, to determine the start and end points of component lines, and to determine the correspondence between the model and their replication. The reduced facilitation in the WS group is discussed in relation to the effect of oblique versus non-oblique lines, the use of atypical drawing strategies, and reduced attention to the model when drawing the replication. © 2014 MENCAP and International Association of the Scientific Study of Intellectual and Developmental Disabilities and John Wiley & Sons Ltd.

Polyamines and Hypusination Are Required for Ebolavirus Gene Expression and Replication

PubMed Central

Olsen, Michelle E.; Filone, Claire Marie; Rozelle, Dan; Mire, Chad E.; Agans, Krystle N.; Hensley, Lisa

2016-01-01

ABSTRACT Ebolavirus (EBOV) is an RNA virus that is known to cause severe hemorrhagic fever in humans and other primates. EBOV successfully enters and replicates in many cell types. This replication is dependent on the virus successfully coopting a number of cellular factors. Many of these factors are currently unidentified but represent potential targets for antiviral therapeutics. Here we show that cellular polyamines are critical for EBOV replication. We found that small-molecule inhibitors of polyamine synthesis block gene expression driven by the viral RNA-dependent RNA polymerase. Short hairpin RNA (shRNA) knockdown of the polyamine pathway enzyme spermidine synthase also resulted in reduced EBOV replication. These findings led us to further investigate spermidine, a polyamine that is essential for the hypusination of eukaryotic initiation factor 5A (eIF5A). Blocking the hypusination of eIF5A (and thereby inhibiting its function) inhibited both EBOV gene expression and viral replication. The mechanism appears to be due to the importance of hypusinated eIF5A for the accumulation of VP30, an essential component of the viral polymerase. The same reduction in hypusinated eIF5A did not alter the accumulation of other viral polymerase components. This action makes eIF5A function an important gate for proper EBOV polymerase assembly and function through the control of a single virus protein. PMID:27460797

Quantitative multi-target RNA profiling in Epstein-Barr virus infected tumor cells.

PubMed

Greijer, A E; Ramayanti, O; Verkuijlen, S A W M; Novalić, Z; Juwana, H; Middeldorp, J M

2017-03-01

Epstein-Barr virus (EBV) is etiologically linked to multiple acute, chronic and malignant diseases. Detection of EBV-RNA transcripts in tissues or biofluids besides EBV-DNA can help in diagnosing EBV related syndromes. Sensitive EBV transcription profiling yields new insights on its pathogenic role and may be useful for monitoring virus targeted therapy. Here we describe a multi-gene quantitative RT-PCR profiling method that simultaneously detects a broad spectrum (n=16) of crucial latent and lytic EBV transcripts. These transcripts include (but are not restricted to), EBNA1, EBNA2, LMP1, LMP2, BARTs, EBER1, BARF1 and ZEBRA, Rta, BGLF4 (PK), BXLF1 (TK) and BFRF3 (VCAp18) all of which have been implicated in EBV-driven oncogenesis and viral replication. With this method we determine the amount of RNA copies per infected (tumor) cell in bulk populations of various origin. While we confirm the expected RNA profiles within classic EBV latency programs, this sensitive quantitative approach revealed the presence of rare cells undergoing lytic replication. Inducing lytic replication in EBV tumor cells supports apoptosis and is considered as therapeutic approach to treat EBV-driven malignancies. This sensitive multi-primed quantitative RT-PCR approach can provide broader understanding of transcriptional activity in latent and lytic EBV infection and is suitable for monitoring virus-specific therapy responses in patients with EBV associated cancers. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

DNA Damage and Genomic Instability Induced by Inappropriate DNA Re-replication

DTIC Science & Technology

2006-04-01

replication in yeast cells. In the prior reporting period we demonstrated that re-replication induces a rapid and significant decrease in cell viability...repair, DNA replication, checkpoint, cell cycle, yeast , RAD9 16. SECURITY CLASSIFICATION OF: 18. NUMBER OF PAGES 19a. NAME OF RESPONSIBLE PERSON...initiation, our laboratory has been able to conditionally induce varying amounts of re- replication in yeast cells. Effectively, cells enter, but do not

EEG Beta Power but Not Background Music Predicts the Recall Scores in a Foreign-Vocabulary Learning Task.

PubMed

Küssner, Mats B; de Groot, Annette M B; Hofman, Winni F; Hillen, Marij A

2016-01-01

As tantalizing as the idea that background music beneficially affects foreign vocabulary learning may seem, there is-partly due to a lack of theory-driven research-no consistent evidence to support this notion. We investigated inter-individual differences in the effects of background music on foreign vocabulary learning. Based on Eysenck's theory of personality we predicted that individuals with a high level of cortical arousal should perform worse when learning with background music compared to silence, whereas individuals with a low level of cortical arousal should be unaffected by background music or benefit from it. Participants were tested in a paired-associate learning paradigm consisting of three immediate word recall tasks, as well as a delayed recall task one week later. Baseline cortical arousal assessed with spontaneous EEG measurement in silence prior to the learning rounds was used for the analyses. Results revealed no interaction between cortical arousal and the learning condition (background music vs. silence). Instead, we found an unexpected main effect of cortical arousal in the beta band on recall, indicating that individuals with high beta power learned more vocabulary than those with low beta power. To substantiate this finding we conducted an exact replication of the experiment. Whereas the main effect of cortical arousal was only present in a subsample of participants, a beneficial main effect of background music appeared. A combined analysis of both experiments suggests that beta power predicts the performance in the word recall task, but that there is no effect of background music on foreign vocabulary learning. In light of these findings, we discuss whether searching for effects of background music on foreign vocabulary learning, independent of factors such as inter-individual differences and task complexity, might be a red herring. Importantly, our findings emphasize the need for sufficiently powered research designs and exact replications of theory-driven experiments when investigating effects of background music and inter-individual variation on task performance.

EEG Beta Power but Not Background Music Predicts the Recall Scores in a Foreign-Vocabulary Learning Task

PubMed Central

de Groot, Annette M. B.; Hofman, Winni F.; Hillen, Marij A.

2016-01-01

As tantalizing as the idea that background music beneficially affects foreign vocabulary learning may seem, there is—partly due to a lack of theory-driven research—no consistent evidence to support this notion. We investigated inter-individual differences in the effects of background music on foreign vocabulary learning. Based on Eysenck’s theory of personality we predicted that individuals with a high level of cortical arousal should perform worse when learning with background music compared to silence, whereas individuals with a low level of cortical arousal should be unaffected by background music or benefit from it. Participants were tested in a paired-associate learning paradigm consisting of three immediate word recall tasks, as well as a delayed recall task one week later. Baseline cortical arousal assessed with spontaneous EEG measurement in silence prior to the learning rounds was used for the analyses. Results revealed no interaction between cortical arousal and the learning condition (background music vs. silence). Instead, we found an unexpected main effect of cortical arousal in the beta band on recall, indicating that individuals with high beta power learned more vocabulary than those with low beta power. To substantiate this finding we conducted an exact replication of the experiment. Whereas the main effect of cortical arousal was only present in a subsample of participants, a beneficial main effect of background music appeared. A combined analysis of both experiments suggests that beta power predicts the performance in the word recall task, but that there is no effect of background music on foreign vocabulary learning. In light of these findings, we discuss whether searching for effects of background music on foreign vocabulary learning, independent of factors such as inter-individual differences and task complexity, might be a red herring. Importantly, our findings emphasize the need for sufficiently powered research designs and exact replications of theory-driven experiments when investigating effects of background music and inter-individual variation on task performance. PMID:27537520

Conflict-driven adaptive control is enhanced by integral negative emotion on a short time scale.

PubMed

Yang, Qian; Pourtois, Gilles

2018-02-05

Negative emotion influences cognitive control, and more specifically conflict adaptation. However, discrepant results have often been reported in the literature. In this study, we broke down negative emotion into integral and incidental components using a modern motivation-based framework, and assessed whether the former could change conflict adaptation. In the first experiment, we manipulated the duration of the inter-trial-interval (ITI) to assess the actual time-scale of this effect. Integral negative emotion was induced by using loss-related feedback contingent on task performance, and measured at the subjective and physiological levels. Results showed that conflict-driven adaptive control was enhanced when integral negative emotion was elicited, compared to a control condition without changes in defensive motivation. Importantly, this effect was only found when a short, as opposed to long ITI was used, suggesting that it had a short time scale. In the second experiment, we controlled for effects of feature repetition and contingency learning, and replicated an enhanced conflict adaptation effect when integral negative emotion was elicited and a short ITI was used. We interpret these new results against a standard cognitive control framework assuming that integral negative emotion amplifies specific control signals transiently, and in turn enhances conflict adaptation.

Management of fluorescent lamps in controlled environment chambers

NASA Technical Reports Server (NTRS)

Romer, Mark

1994-01-01

Management of fluorescent lights is recommended to (1) maintain uniformity of light intensity over time and (2) permit reproducibility of lighting conditions during experimental replications. At the McGill Phytotron, the lighting intensity can be controlled to desired level because any individual pair of the 40 lamps in each chamber can be set to be 'on' at any particular time. A lamp canopy service history is maintained for each experiment permitting accurate replication of lighting conditions for subsequent replicate trials.

A Framework for Understanding Community Colleges' Organizational Capacity for Data Use: A Convergent Parallel Mixed Methods Study

ERIC Educational Resources Information Center

Kerrigan, Monica Reid

2014-01-01

This convergent parallel design mixed methods case study of four community colleges explores the relationship between organizational capacity and implementation of data-driven decision making (DDDM). The article also illustrates purposive sampling using replication logic for cross-case analysis and the strengths and weaknesses of quantitizing…

Regional contingencies in the relationship between aboveground biomass and litter in the world’s grasslands

Treesearch

L.R. O' Halloran; E.T. Borer; E.W. Seabloom; A.S. MacDougall; E.E. Cleland; R.L. McCulley; S. Hobbie; S. Harpole; N.M. DeCrappeo; C.-J. Chu; J.D. Bakker; K.F. Davies; G. Du; J. Firn; N. Hagenah; K.S. Hofmockel; J.M.H. Knops; W. Li; B.A. Melbourne; J.W. Morgan; J.L. Orrock; S.M. Prober; C.J. Stevens

2013-01-01

Based on regional-scale studies, aboveground production and litter decomposition are thought to positively covary, because they are driven by shared biotic and climatic factors. Until now we have been unable to test whether production and decomposition are generally coupled across climatically dissimilar regions, because we lacked replicated data collected within a...

Business Spanish in the Real World: A Task-Based Needs Analysis

ERIC Educational Resources Information Center

Martin, Alexandra; Adrada-Rafael, Sergio

2017-01-01

The growing demand for Spanish for Specific Purposes (SSP) courses at universities in the United States in the last two decades (Klee, 2015) has brought to light the need for more theoretically driven research in this field, which can inform pedagogical decisions and materials design. The present study conceptually replicates Serafini and Torres…

Accelerated Self-Replication under Non-Equilibrium, Periodic Energy Delivery

NASA Astrophysics Data System (ADS)

Zhang, Rui; Olvera de La Cruz, Monica

2014-03-01

Self-replication is a remarkable phenomenon in nature that has fascinated scientists for decades. In a self-replicating system, the original units are attracted to a template, which induce their binding. In equilibrium, the energy required to disassemble the newly assembled copy from the mother template is supplied by thermal energy. The possibility of optimizing self-replication is explored by controlling the frequency at which energy is supplied to the system. A model system inspired by a class of light switchable colloids is considered where light is used to control the interactions. Conditions under which self-replication can be significantly more effective under non-equilibrium, cyclic energy delivery than under equilibrium constant energy conditions are identified. Optimal self-replication does not require constant energy expenditure. Instead, the proper timing at which energy is delivered to the system is an essential controllable parameter to induce high replication rates. This work was supported by the Non-Equilibrium Energy Research Center (NERC), which is an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0000989.

Reduced genetic distance and high replication levels increase the RNA recombination rate of hepatitis delta virus.

PubMed

Lin, Chia-Chi; Yang, Zhi-Wei; Iang, Shan-Bei; Chao, Mei

2015-01-02

Hepatitis delta virus (HDV) replication is carried out by host RNA polymerases. Since homologous inter-genotypic RNA recombination is known to occur in HDV, possibly via a replication-dependent process, we hypothesized that the degree of sequence homology and the replication level should be related to the recombination frequency in cells co-expressing two HDV sequences. To confirm this, we separately co-transfected cells with three different pairs of HDV genomic RNAs and analyzed the obtained recombinants by RT-PCR followed by restriction fragment length polymorphism and sequencing analyses. The sequence divergence between the clones ranged from 24% to less than 0.1%, and the difference in replication levels was as high as 100-fold. As expected, significant differences were observed in the recombination frequencies, which ranged from 0.5% to 47.5%. Furthermore, varying the relative amounts of parental RNA altered the dominant recombinant species produced, suggesting that template switching occurs frequently during the synthesis of genomic HDV RNA. Taken together, these data suggest that during the host RNA polymerase-driven RNA recombination of HDV, both inter- and intra-genotypic recombination events are important in shaping the genetic diversity of HDV. Copyright © 2014 Elsevier B.V. All rights reserved.

Accessory genes confer a high replication rate to virulent feline immunodeficiency virus.

PubMed

Troyer, Ryan M; Thompson, Jesse; Elder, John H; VandeWoude, Sue

2013-07-01

Feline immunodeficiency virus (FIV) is a lentivirus that causes AIDS in domestic cats, similar to human immunodeficiency virus (HIV)/AIDS in humans. The FIV accessory protein Vif abrogates the inhibition of infection by cat APOBEC3 restriction factors. FIV also encodes a multifunctional OrfA accessory protein that has characteristics similar to HIV Tat, Vpu, Vpr, and Nef. To examine the role of vif and orfA accessory genes in FIV replication and pathogenicity, we generated chimeras between two FIV molecular clones with divergent disease potentials: a highly pathogenic isolate that replicates rapidly in vitro and is associated with significant immunopathology in vivo, FIV-C36 (referred to here as high-virulence FIV [HV-FIV]), and a less-pathogenic strain, FIV-PPR (referred to here as low-virulence FIV [LV-FIV]). Using PCR-driven overlap extension, we produced viruses in which vif, orfA, or both genes from virulent HV-FIV replaced equivalent genes in LV-FIV. The generation of these chimeras is more straightforward in FIV than in primate lentiviruses, since FIV accessory gene open reading frames have very little overlap with other genes. All three chimeric viruses exhibited increased replication kinetics in vitro compared to the replication kinetics of LV-FIV. Chimeras containing HV-Vif or Vif/OrfA had replication rates equivalent to those of the virulent HV-FIV parental virus. Furthermore, small interfering RNA knockdown of feline APOBEC3 genes resulted in equalization of replication rates between LV-FIV and LV-FIV encoding HV-FIV Vif. These findings demonstrate that Vif-APOBEC interactions play a key role in controlling the replication and pathogenicity of this immunodeficiency-inducing virus in its native host species and that accessory genes act as mediators of lentiviral strain-specific virulence.

Right ventrolateral prefrontal cortex mediates individual differences in conflict-driven cognitive control

PubMed Central

Egner, Tobias

2013-01-01

Conflict adaptation – a conflict-triggered improvement in the resolution of conflicting stimulus or response representations – has become a widely used probe of cognitive control processes in both healthy and clinical populations. Previous functional magnetic resonance imaging (fMRI) studies have localized activation foci associated with conflict resolution to dorsolateral prefrontal cortex (dlPFC). The traditional group-analysis approach employed in these studies highlights regions that are, on average, activated during conflict resolution, but does not necessarily reveal areas mediating individual differences in conflict resolution, because between-subject variance is treated as noise. Here, we employed a complementary approach in order to elucidate the neural bases of variability in the proficiency of conflict-driven cognitive control. We analyzed two independent fMRI data sets of face-word Stroop tasks by using individual variability in the behavioral expression of conflict adaptation as the metric against which brain activation was regressed, while controlling for individual differences in mean reaction time and Stroop interference. Across the two experiments, a replicable neural substrate of individual variation in conflict adaptation was found in ventrolateral prefrontal cortex (vlPFC), specifically, in the right inferior frontal gyrus, pars orbitalis (BA 47). Unbiased regression estimates showed that variability in activity in this region accounted for ~40% of the variance in behavioral expression of conflict adaptation across subjects, thus documenting a heretofore unsuspected key role for vlPFC in mediating conflict-driven adjustments in cognitive control. We speculate that vlPFC plays a primary role in conflict control that is supplemented by dlPFC recruitment under conditions of suboptimal performance. PMID:21568631

Right ventrolateral prefrontal cortex mediates individual differences in conflict-driven cognitive control.

PubMed

Egner, Tobias

2011-12-01

Conflict adaptation--a conflict-triggered improvement in the resolution of conflicting stimulus or response representations--has become a widely used probe of cognitive control processes in both healthy and clinical populations. Previous fMRI studies have localized activation foci associated with conflict resolution to dorsolateral PFC (dlPFC). The traditional group analysis approach employed in these studies highlights regions that are, on average, activated during conflict resolution, but does not necessarily reveal areas mediating individual differences in conflict resolution, because between-subject variance is treated as noise. Here, we employed a complementary approach to elucidate the neural bases of variability in the proficiency of conflict-driven cognitive control. We analyzed two independent fMRI data sets of face-word Stroop tasks by using individual variability in the behavioral expression of conflict adaptation as the metric against which brain activation was regressed while controlling for individual differences in mean RT and Stroop interference. Across the two experiments, a replicable neural substrate of individual variation in conflict adaptation was found in ventrolateral PFC (vlPFC), specifically, in the right inferior frontal gyrus, pars orbitalis (BA 47). Unbiased regression estimates showed that variability in activity in this region accounted for ∼ 40% of the variance in behavioral expression of conflict adaptation across subjects, thus documenting a heretofore unsuspected key role for vlPFC in mediating conflict-driven adjustments in cognitive control. We speculate that vlPFC plays a primary role in conflict control that is supplemented by dlPFC recruitment under conditions of suboptimal performance.

Matrix Conditions and KLF2-Dependent Induction of Heme Oxygenase-1 Modulate Inhibition of HCV Replication by Fluvastatin

PubMed Central

Singethan, Katrin; Sirma, Hüseyin; Keller, Amelie Dorothea; Rosal, Sergio René Perez; Schrader, Jörg; Loscher, Christine; Volz, Tassilo; Bartenschlager, Ralf; Lohmann, Volker; Protzer, Ulrike; Dandri, Maura; Lohse, Ansgar W.; Tiegs, Gisa; Sass, Gabriele

2014-01-01

Background & Aims HMG-CoA-reductase-inhibitors (statins) have been shown to interfere with HCV replication in vitro. We investigated the mechanism, requirements and contribution of heme oxygenase-1(HO-1)-induction by statins to interference with HCV replication. Methods HO-1-induction by fluva-, simva-, rosuva-, atorva- or pravastatin was correlated to HCV replication, using non-infectious replicon systems as well as the infectious cell culture system. The mechanism of HO-1-induction by statins as well as its relevance for interference with HCV replication was investigated using transient or permanent knockdown cell lines. Polyacrylamide(PAA) gels of different density degrees or the Rho-kinase-inhibitor Hydroxyfasudil were used in order to mimic matrix conditions corresponding to normal versus fibrotic liver tissue. Results All statins used, except pravastatin, decreased HCV replication and induced HO-1 expression, as well as interferon response in vitro. HO-1-induction was mediated by reduction of Bach1 expression and induction of the Nuclear factor (erythroid-derived 2)-like 2 (NRF2) cofactor Krueppel-like factor 2 (KLF2). Knockdown of KLF2 or HO-1 abrogated effects of statins on HCV replication. HO-1-induction and anti-viral effects of statins were more pronounced under cell culture conditions mimicking advanced stages of liver disease. Conclusions Statin-mediated effects on HCV replication seem to require HO-1-induction, which is more pronounced in a microenvironment resembling fibrotic liver tissue. This implicates that certain statins might be especially useful to support HCV therapy of patients at advanced stages of liver disease. PMID:24801208

Meiotic recombination counteracts male-biased mutation (male-driven evolution).

PubMed

Mawaribuchi, Shuuji; Ito, Michihiko; Ogata, Mitsuaki; Oota, Hiroki; Katsumura, Takafumi; Takamatsu, Nobuhiko; Miura, Ikuo

2016-01-27

Meiotic recombination is believed to produce greater genetic variation despite the fact that deoxyribonucleic acid (DNA)-replication errors are a major source of mutations. In some vertebrates, mutation rates are higher in males than in females, which developed the theory of male-driven evolution (male-biased mutation). However, there is little molecular evidence regarding the relationships between meiotic recombination and male-biased mutation. Here we tested the theory using the frog Rana rugosa, which has both XX/XY- and ZZ/ZW-type sex-determining systems within the species. The male-to-female mutation-rate ratio (α) was calculated from homologous sequences on the X/Y or Z/W sex chromosomes, which supported male-driven evolution. Surprisingly, each α value was notably higher in the XX/XY-type group than in the ZZ/ZW-type group, although α should have similar values within a species. Interestingly, meiotic recombination between homologous chromosomes did not occur except at terminal regions in males of this species. Then, by subdividing α into two new factors, a replication-based male-to-female mutation-rate ratio (β) and a meiotic recombination-based XX-to-XY/ZZ-to-ZW mutation-rate ratio (γ), we constructed a formula describing the relationship among a nucleotide-substitution rate and the two factors, β and γ. Intriguingly, the β- and γ-values were larger and smaller than 1, respectively, indicating that meiotic recombination might reduce male-biased mutations. © 2016 The Author(s).

Human embryonic stem cells fail to activate CHK1 and commit to apoptosis in response to DNA replication stress.

PubMed

Desmarais, Joëlle A; Hoffmann, Michele J; Bingham, Gregg; Gagou, Mary E; Meuth, Mark; Andrews, Peter W

2012-07-01

Pluripotent cells of the early embryo, to which embryonic stem cells (ESCs) correspond, give rise to all the somatic cells of the developing fetus. Any defects that occur in their genome or epigenome would have devastating consequences. Genetic and epigenetic change in human ESCs appear to be an inevitable consequence of long-term culture, driven by selection of variant cells that have a higher propensity for self-renewal rather than either differentiation or death. Mechanisms underlying the potentially separate events of mutation and subsequent selection of variants are poorly understood. Here, we show that human ESCs and their malignant counterpart, embryonal carcinoma (EC) cells, both fail to activate critical S-phase checkpoints when exposed to DNA replication inhibitors and commit to apoptosis instead. Human ESCs and EC cells also fail to form replication protein A, γH2AX, or RAD51 foci or load topoisomerase (DNA) II binding protein 1 onto chromatin in response to replication inhibitors. Furthermore, direct measurements of single-stranded DNA (ssDNA) show that these cells fail to generate the ssDNA regions in response to replication stress that are necessary for the activation of checkpoints and the initiation of homologous recombination repair to protect replication fork integrity and restart DNA replication. Taken together, our data suggest that pluripotent cells control genome integrity by the elimination of damaged cells through apoptosis rather than DNA repair, and therefore, mutations or epigenetic modifications resulting in an imbalance in cell death control could lead to genetic instability. Copyright © 2012 AlphaMed Press.

Accommodation Responds to Optical Vergence and Not Defocus Blur Alone.

PubMed

Del Águila-Carrasco, Antonio J; Marín-Franch, Iván; Bernal-Molina, Paula; Esteve-Taboada, José J; Kruger, Philip B; Montés-Micó, Robert; López-Gil, Norberto

2017-03-01

To determine whether changes in wavefront spherical curvature (optical vergence) are a directional cue for accommodation. Nine subjects participated in this experiment. The accommodation response to a monochromatic target was measured continuously with a custom-made adaptive optics system while astigmatism and higher-order aberrations were corrected in real time. There were two experimental open-loop conditions: vergence-driven condition, where the deformable mirror provided sinusoidal changes in defocus at the retina between -1 and +1 diopters (D) at 0.2 Hz; and blur-driven condition, in which the level of defocus at the retina was always 0 D, but a sinusoidal defocus blur between -1 and +1 D at 0.2 Hz was simulated in the target. Right before the beginning of each trial, the target was moved to an accommodative demand of 2 D. Eight out of nine subjects showed sinusoidal responses for the vergence-driven condition but not for the blur-driven condition. Their average (±SD) gain for the vergence-driven condition was 0.50 (±0.28). For the blur-driven condition, average gain was much smaller at 0.07 (±0.03). The ninth subject showed little to no response for both conditions, with average gain <0.08. Vergence-driven condition gain was significantly different from blur-driven condition gain (P = 0.004). Accommodation responds to optical vergence, even without feedback, and not to changes in defocus blur alone. These results suggest the presence of a retinal mechanism that provides a directional cue for accommodation from optical vergence.

DNA replication stress restricts ribosomal DNA copy number

PubMed Central

Salim, Devika; Bradford, William D.; Freeland, Amy; Cady, Gillian; Wang, Jianmin

2017-01-01

Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100–200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how “normal” copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a “normal” rDNA copy number. PMID:28915237

Conditional analysis identifies three novel major histocompatibility complex loci associated with psoriasis.

PubMed

Knight, Jo; Spain, Sarah L; Capon, Francesca; Hayday, Adrian; Nestle, Frank O; Clop, Alex; Barker, Jonathan N; Weale, Michael E; Trembath, Richard C

2012-12-01

Psoriasis is a common, chronic, inflammatory skin disorder. A number of genetic loci have been shown to confer risk for psoriasis. Collectively, these offer an integrated model for the inherited basis for susceptibility to psoriasis that combines altered skin barrier function together with the dysregulation of innate immune pathogen sensing and adap-tive immunity. The major histocompatibility complex (MHC) harbours the psoriasis susceptibility region which exhibits the largest effect size, driven in part by variation contained on the HLA-Cw*0602 allele. However, the resolution of the number and genomic location of potential independent risk loci are hampered by extensive linkage disequilibrium across the region. We leveraged the power of large psoriasis case and control data sets and the statistical approach of conditional analysis to identify potential further association signals distributed across the MHC. In addition to the major loci at HLA-C (P = 2.20 × 10(-236)), we observed and replicated four additional independent signals for disease association, three of which are novel. We detected evidence for association at SNPs rs2507971 (P = 6.73 × 10(-14)), rs9260313 (P = 7.93 × 10(-09)), rs66609536 (P = 3.54 × 10(-07)) and rs380924 (P = 6.24 × 10(-06)), located within the class I region of the MHC, with each observation replicated in an independent sample (P ≤ 0.01). The previously identified locus is close to MICA, the other three lie near MICB, HLA-A and HCG9 (a non-coding RNA gene). The identification of disease associations with both MICA and MICB is particularly intriguing, since each encodes an MHC class I-related protein with potent immunological function.

Asymmetrical Responses of Ecosystem Processes to Positive Versus Negative Precipitation Extremes: a Replicated Regression Experimental Approach

NASA Astrophysics Data System (ADS)

Felton, A. J.; Smith, M. D.

2016-12-01

Heightened climatic variability due to atmospheric warming is forecast to increase the frequency and severity of climate extremes. In particular, changes to interannual variability in precipitation, characterized by increases in extreme wet and dry years, are likely to impact virtually all terrestrial ecosystem processes. However, to date experimental approaches have yet to explicitly test how ecosystem processes respond to multiple levels of climatic extremity, limiting our understanding of how ecosystems will respond to forecast increases in the magnitude of climate extremes. Here we report the results of a replicated regression experimental approach, in which we imposed 9 and 11 levels of growing season precipitation amount and extremity in mesic grassland during 2015 and 2016, respectively. Each level corresponded to a specific percentile of the long-term record, which produced a large gradient of soil moisture conditions that ranged from extreme wet to extreme dry. In both 2015 and 2016, asymptotic responses to water availability were observed for soil respiration. This asymmetry was driven in part by transitions between soil moisture versus temperature constraints on respiration as conditions became increasingly dry versus increasingly wet. In 2015, aboveground net primary production (ANPP) exhibited asymmetric responses to precipitation that largely mirrored those of soil respiration. In total, our results suggest that in this mesic ecosystem, these two carbon cycle processes were more sensitive to extreme drought than to extreme wet years. Future work will assess ANPP responses for 2016, soil nutrient supply and physiological responses of the dominant plant species. Future efforts are needed to compare our findings across a diverse array of ecosystem types, and in particular how the timing and magnitude of precipitation events may modify the response of ecosystem processes to increasing magnitudes of precipitation extremes.

Biliary Tree Stem Cells, Precursors to Pancreatic Committed Progenitors: Evidence for Possible Life-long Pancreatic Organogenesis

PubMed Central

Wang, Yunfang; Lanzoni, Giacomo; Carpino, Guido; Cui, Cai-Bin; Dominguez-Bendala, Juan; Wauthier, Eliane; Cardinale, Vincenzo; Oikawa, Tsunekazu; Pileggi, Antonello; Gerber, David; Furth, Mark E.; Alvaro, Domenico; Gaudio, Eugenio; Inverardi, Luca; Reid, Lola M.

2013-01-01

Peribiliary glands (PBGs) in bile duct walls, and pancreatic duct glands (PDGs) associated with pancreatic ducts, in humans of all ages, contain a continuous, ramifying network of cells in overlapping maturational lineages. We show that proximal (PBGs)-to-distal (PDGs) maturational lineages start near the duodenum with cells expressing markers of pluripotency (NANOG,OCT4,SOX2), proliferation (Ki67), self-replication (SALL4), and early hepato-pancreatic commitment (SOX9,SOX17,PDX1,LGR5), transitioning to PDG cells with no expression of pluripotency or self-replication markers, maintenance of pancreatic genes (PDX1), and expression of markers of pancreatic endocrine maturation (NGN3,MUC6,insulin). Radial-axis lineages start in PBGs near the ducts’ fibromuscular layers with stem cells and end at the ducts’ lumens with cells devoid of stem cell traits and positive for pancreatic endocrine genes. Biliary tree-derived cells behaved as stem cells in culture under expansion conditions, culture plastic and serum-free Kubota’s Medium, proliferating for months as undifferentiated cells, whereas pancreas-derived cells underwent only ∼8-10 divisions, then partially differentiated towards an islet fate. Biliary tree-derived cells proved precursors of pancreas’ committed progenitors. Both could be driven by 3-dimensional conditions, islet-derived matrix components and a serum-free, hormonally defined medium for an islet fate (HDM-P), to form spheroids with ultrastructural, electrophysiological and functional characteristics of neoislets, including glucose regulatability. Implantation of these neoislets into epididymal fat pads of immuno-compromised mice, chemically rendered diabetic, resulted in secretion of human C-peptide, regulatable by glucose, and able to alleviate hyperglycemia in hosts. The biliary tree-derived stem cells and their connections to pancreatic committed progenitors constitute a biological framework for life-long pancreatic organogenesis. PMID:23847135

Detection of neuroendocrine tumors using promoter-specific secreted Gaussia luciferase.

PubMed

Tseng, Alan Wei-Shun; Akerstrom, Victoria; Chen, Chiachen; Breslin, Mary B; Lan, Michael S

2016-01-01

Accurate detection of neuroendocrine (NE) tumors is critically important for better prognosis and treatment outcomes in patients. To demonstrate the efficacy of using an adenoviral vector for the detection of NE tumors, we have constructed a pair of adenoviral vectors which, in combination, can conditionally replicate and release Gaussia luciferase into the circulation after infecting the NE tumors. The expression of these two vectors is regulated upstream by an INSM1-promoter (insulinoma-associated-1) that is specifically active in NE tumors and developing NE tissues, but silenced in normal adult tissues. In order to retain the tumor-specificity of the INSM1 promoter, we have modified the promoter using the core insulator sequence from the chicken β-globin HS4 insulator and the neuronal restrictive silencing element (NRSE). This modified INSM1-promoter can retain NE tumor specificity in an adenoviral construct while driving a mutated adenovirus E1A gene (∆24E1A), the Metridia, or Gaussia luciferase gene. The in vitro cell line and mouse xenograft human tumor studies revealed the NE specificity of the INSM1-promoter in NE lung cancer, neuroblastoma, medulloblastoma, retinoblastoma, and insulinoma. When we combined the INSM1-promoter driven Gaussia luciferase with ∆24E1A, the co-infected NE tumor secreted higher levels of Gaussia luciferase as compared to the INSM1p-Gaussia virus alone. In a mouse subcutaneous xenograft tumor model, the combination viruses secreted detectable level of Gaussia luciferase after infecting an INSM1-positive NE lung tumor for ≥12 days. Therefore, the INSM1-promoter specific conditional replicating adenovirus represents a sensitive diagnostic tool to aid clinicians in the detection of NE tumors.

Distinct functions of human RecQ helicases during DNA replication.

PubMed

Urban, Vaclav; Dobrovolna, Jana; Janscak, Pavel

2017-06-01

DNA replication is the most vulnerable process of DNA metabolism in proliferating cells and therefore it is tightly controlled and coordinated with processes that maintain genomic stability. Human RecQ helicases are among the most important factors involved in the maintenance of replication fork integrity, especially under conditions of replication stress. RecQ helicases promote recovery of replication forks being stalled due to different replication roadblocks of either exogenous or endogenous source. They prevent generation of aberrant replication fork structures and replication fork collapse, and are involved in proper checkpoint signaling. The essential role of human RecQ helicases in the genome maintenance during DNA replication is underlined by association of defects in their function with cancer predisposition. Copyright © 2016 Elsevier B.V. All rights reserved.

Nanobacteria: Fact or Fiction? Characteristics, Detection and Medical Importance of Novel Self-Replicating, Calcifying Nanoparticles

NASA Technical Reports Server (NTRS)

Ciftcioglu, Neva; Mckay, David S.; Mathew, Grace; Kajander, E. Olavi

2006-01-01

There is some debate in microbiology as to whether Nanobacteria (NB) are alive. This paper reviews some aspects of NB. In summary, Nanobacteria is a perfect model for studying biogenic mineralization/calcification because NB a) are self-replicating particles and have less complicated metabolic pathways b) accumulate calcium and phosphate under physiological conditions, c)produce a calcium phosphate mineral similar to bone, d) exist in physical conditions (pH, gravity, temperature, etc) that are easy to manipulate, and which can be replicated for the physiological model.

Identifying impact of software dependencies on replicability of biomedical workflows.

PubMed

Miksa, Tomasz; Rauber, Andreas; Mina, Eleni

2016-12-01

Complex data driven experiments form the basis of biomedical research. Recent findings warn that the context in which the software is run, that is the infrastructure and the third party dependencies, can have a crucial impact on the final results delivered by a computational experiment. This implies that in order to replicate the same result, not only the same data must be used, but also it must be run on an equivalent software stack. In this paper we present the VFramework that enables assessing replicability of workflows. It identifies whether any differences in software dependencies among two executions of the same workflow exist and whether they have impact on the produced results. We also conduct a case study in which we investigate the impact of software dependencies on replicability of Taverna workflows used in biomedical research of Huntington's disease. We re-execute analysed workflows in environments differing in operating system distribution and configuration. The results show that the VFramework can be used to identify the impact of software dependencies on the replicability of biomedical workflows. Furthermore, we observe that despite the fact that the workflows are executed in a controlled environment, they still depend on specific tools installed in the environment. The context model used by the VFramework improves the deficiencies of provenance traces and documents also such tools. Based on our findings we define guidelines for workflow owners that enable them to improve replicability of their workflows. Copyright © 2016 Elsevier Inc. All rights reserved.

Antiretroviral Agents Effectively Block HIV Replication after Cell-to-Cell Transfer

PubMed Central

Permanyer, Marc; Ballana, Ester; Ruiz, Alba; Badia, Roger; Riveira-Munoz, Eva; Gonzalo, Encarna; Clotet, Bonaventura

2012-01-01

Cell-to-cell transmission of HIV has been proposed as a mechanism contributing to virus escape to the action of antiretrovirals and a mode of HIV persistence during antiretroviral therapy. Here, cocultures of infected HIV-1 cells with primary CD4+ T cells or lymphoid cells were used to evaluate virus transmission and the effect of known antiretrovirals. Transfer of HIV antigen from infected to uninfected cells was resistant to the reverse transcriptase inhibitors (RTIs) zidovudine (AZT) and tenofovir, but was blocked by the attachment inhibitor IgGb12. However, quantitative measurement of viral DNA production demonstrated that all anti-HIV agents blocked virus replication with similar potency to cell-free virus infections. Cell-free and cell-associated infections were equally sensitive to inhibition of viral replication when HIV-1 long terminal repeat (LTR)-driven green fluorescent protein (GFP) expression in target cells was measured. However, detection of GFP by flow cytometry may incorrectly estimate the efficacy of antiretrovirals in cell-associated virus transmission, due to replication-independent Tat-mediated LTR transactivation as a consequence of cell-to-cell events that did not occur in short-term (48-h) cell-free virus infections. In conclusion, common markers of virus replication may not accurately correlate and measure infectivity or drug efficacy in cell-to-cell virus transmission. When accurately quantified, active drugs blocked proviral DNA and virus replication in cell-to-cell transmission, recapitulating the efficacy of antiretrovirals in cell-free virus infections and in vivo. PMID:22696642

Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression.

PubMed

Lemieux, Sébastien

2006-08-25

The identification of differentially expressed genes (DEGs) from Affymetrix GeneChips arrays is currently done by first computing expression levels from the low-level probe intensities, then deriving significance by comparing these expression levels between conditions. The proposed PL-LM (Probe-Level Linear Model) method implements a linear model applied on the probe-level data to directly estimate the treatment effect. A finite mixture of Gaussian components is then used to identify DEGs using the coefficients estimated by the linear model. This approach can readily be applied to experimental design with or without replication. On a wholly defined dataset, the PL-LM method was able to identify 75% of the differentially expressed genes within 10% of false positives. This accuracy was achieved both using the three replicates per conditions available in the dataset and using only one replicate per condition. The method achieves, on this dataset, a higher accuracy than the best set of tools identified by the authors of the dataset, and does so using only one replicate per condition.

Primate Lentiviruses Modulate NF-κB Activity by Multiple Mechanisms to Fine-Tune Viral and Cellular Gene Expression

PubMed Central

Heusinger, Elena; Kirchhoff, Frank

2017-01-01

The transcription factor nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) plays a complex role during the replication of primate lentiviruses. On the one hand, NF-κB is essential for induction of efficient proviral gene expression. On the other hand, this transcription factor contributes to the innate immune response and induces expression of numerous cellular antiviral genes. Recent data suggest that primate lentiviruses cope with this challenge by boosting NF-κB activity early during the replication cycle to initiate Tat-driven viral transcription and suppressing it at later stages to minimize antiviral gene expression. Human and simian immunodeficiency viruses (HIV and SIV, respectively) initially exploit their accessory Nef protein to increase the responsiveness of infected CD4+ T cells to stimulation. Increased NF-κB activity initiates Tat expression and productive replication. These events happen quickly after infection since Nef is rapidly expressed at high levels. Later during infection, Nef proteins of HIV-2 and most SIVs exert a very different effect: by down-modulating the CD3 receptor, an essential factor for T cell receptor (TCR) signaling, they prevent stimulation of CD4+ T cells via antigen-presenting cells and hence suppress further induction of NF-κB and an effective antiviral immune response. Efficient LTR-driven viral transcription is maintained because it is largely independent of NF-κB in the presence of Tat. In contrast, human immunodeficiency virus type 1 (HIV-1) and its simian precursors have lost the CD3 down-modulation function of Nef and use the late viral protein U (Vpu) to inhibit NF-κB activity by suppressing its nuclear translocation. In this review, we discuss how HIV-1 and other primate lentiviruses might balance viral and antiviral gene expression through a tight temporal regulation of NF-κB activity throughout their replication cycle. PMID:28261165

Scoping Report: AI-Driven Wargame Replicator

DTIC Science & Technology

2010-12-01

Evans, 2003 Without training involving external input Responsive to verbal instructions Clark & Karmiloff-Smith, 1993 Associative Rule-based Sloman...Applied to Clustering. Online available on January 21, 2010, at http://laboratorios.fi.uba.ar/lsi/rgm/ comunicaciones /c-AGsclustering-ORLANDO96.pdf...systems for associative recall and recognition. Psychological Review, 91:281-294. [214] Polk, T.A. and Newell, A. (1995). Deduction as verbal reasoning

Replicating the Relationship between Teachers' Data Use and Student Achievement: The Urban Data Study and the Data Dashboard Usage Study

ERIC Educational Resources Information Center

Faria, Ann-Marie; Greenberg, Ariela; Meakin, John; Bichay, Krystal; Heppen, Jessica

2014-01-01

Educators have long used test scores to make educational decisions, but only within the last decade has the availability of data been systematic (Abelman, Elmore, Even, Kenyon, & Marshall, 1999). In recent years, interest has spiked in data-driven decision making in education (Marsh, Pane, & Hamilton, 2006). With technological advances and…

Replication of Salmonella enterica Serovar Typhimurium in Human Monocyte-Derived Macrophages

PubMed Central

Lathrop, Stephanie K.; Binder, Kelsey A.; Starr, Tregei; Cooper, Kendal G.; Chong, Audrey; Carmody, Aaron B.

2015-01-01

Salmonella enterica serovar Typhimurium is a common cause of food-borne gastrointestinal illness, but additionally it causes potentially fatal bacteremia in some immunocompromised patients. In mice, systemic spread and replication of the bacteria depend upon infection of and replication within macrophages, but replication in human macrophages is not widely reported or well studied. In order to assess the ability of Salmonella Typhimurium to replicate in human macrophages, we infected primary monocyte-derived macrophages (MDM) that had been differentiated under conditions known to generate different phenotypes. We found that replication in MDM depends greatly upon the phenotype of the cells, as M1-skewed macrophages did not allow replication, while M2a macrophages and macrophages differentiated with macrophage colony-stimulating factor (M-CSF) alone (termed M0) did. We describe how additional conditions that alter the macrophage phenotype or the gene expression of the bacteria affect the outcome of infection. In M0 MDM, the temporal expression of representative genes from Salmonella pathogenicity islands 1 and 2 (SPI1 and SPI2) and the importance of the PhoP/Q two-component regulatory system are similar to what has been shown in mouse macrophages. However, in contrast to mouse macrophages, where replication is SPI2 dependent, we observed early SPI2-independent replication in addition to later SPI2-dependent replication in M0 macrophages. Only SPI2-dependent replication was associated with death of the host cell at later time points. Altogether, our results reveal a very nuanced interaction between Salmonella and human macrophages. PMID:25895967

Replication of Salmonella enterica Serovar Typhimurium in Human Monocyte-Derived Macrophages.

PubMed

Lathrop, Stephanie K; Binder, Kelsey A; Starr, Tregei; Cooper, Kendal G; Chong, Audrey; Carmody, Aaron B; Steele-Mortimer, Olivia

2015-07-01

Salmonella enterica serovar Typhimurium is a common cause of food-borne gastrointestinal illness, but additionally it causes potentially fatal bacteremia in some immunocompromised patients. In mice, systemic spread and replication of the bacteria depend upon infection of and replication within macrophages, but replication in human macrophages is not widely reported or well studied. In order to assess the ability of Salmonella Typhimurium to replicate in human macrophages, we infected primary monocyte-derived macrophages (MDM) that had been differentiated under conditions known to generate different phenotypes. We found that replication in MDM depends greatly upon the phenotype of the cells, as M1-skewed macrophages did not allow replication, while M2a macrophages and macrophages differentiated with macrophage colony-stimulating factor (M-CSF) alone (termed M0) did. We describe how additional conditions that alter the macrophage phenotype or the gene expression of the bacteria affect the outcome of infection. In M0 MDM, the temporal expression of representative genes from Salmonella pathogenicity islands 1 and 2 (SPI1 and SPI2) and the importance of the PhoP/Q two-component regulatory system are similar to what has been shown in mouse macrophages. However, in contrast to mouse macrophages, where replication is SPI2 dependent, we observed early SPI2-independent replication in addition to later SPI2-dependent replication in M0 macrophages. Only SPI2-dependent replication was associated with death of the host cell at later time points. Altogether, our results reveal a very nuanced interaction between Salmonella and human macrophages. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Bacterial dynamics in steady-state biofilters: beyond functional stability.

PubMed

Cabrol, Léa; Malhautier, Luc; Poly, Franck; Lepeuple, Anne-Sophie; Fanlo, Jean-Louis

2012-01-01

The spatial and temporal dynamics of microbial community structure and function were surveyed in duplicated woodchip-biofilters operated under constant conditions for 231 days. The contaminated gaseous stream for treatment was representative of composting emissions, included ammonia, dimethyl disulfide and a mixture of five oxygenated volatile organic compounds. The community structure and diversity were investigated by denaturing gradient gel electrophoresis on 16S rRNA gene fragments. During the first 42 days, microbial acclimatization revealed the influence of operating conditions and contaminant loading on the biofiltration community structure and diversity, as well as the limited impact of inoculum compared to the greater persistence of the endogenous woodchip community. During long-term operation, a high and stable removal efficiency was maintained despite a highly dynamic microbial community, suggesting the probable functional redundancy of the community. Most of the contaminant removal occurred in the first compartment, near the gas inlet, where the microbial diversity was the highest. The stratification of the microbial structures along the filter bed was statistically correlated to the longitudinal distribution of environmental conditions (selective pressure imposed by contaminant concentrations) and function (contaminant elimination capacity), highlighting the central role of the bacterial community. The reproducibility of microbial succession in replicates suggests that the community changes were presumably driven by a deterministic process.

Mechanisms of bacterial DNA replication restart

PubMed Central

Windgassen, Tricia A; Wessel, Sarah R; Bhattacharyya, Basudeb

2018-01-01

Abstract Multi-protein DNA replication complexes called replisomes perform the essential process of copying cellular genetic information prior to cell division. Under ideal conditions, replisomes dissociate only after the entire genome has been duplicated. However, DNA replication rarely occurs without interruptions that can dislodge replisomes from DNA. Such events produce incompletely replicated chromosomes that, if left unrepaired, prevent the segregation of full genomes to daughter cells. To mitigate this threat, cells have evolved ‘DNA replication restart’ pathways that have been best defined in bacteria. Replication restart requires recognition and remodeling of abandoned replication forks by DNA replication restart proteins followed by reloading of the replicative DNA helicase, which subsequently directs assembly of the remaining replisome subunits. This review summarizes our current understanding of the mechanisms underlying replication restart and the proteins that drive the process in Escherichia coli (PriA, PriB, PriC and DnaT). PMID:29202195

Abortive replication of Bombyx mori nucleopolyhedrovirus in Sf9 and High Five cells: Defective nuclear transport of the virions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Katou, Yasuhiro; Ikeda, Motoko; Kobayashi, Michihiro

2006-04-10

Despite close genetic relationship, Bombyx mori nucleopolyhedrovirus (BmNPV) and Autographa californica multicapsid NPV (AcMNPV) display a distinct host range property. Here, BmNPV replication was examined in Sf9 and High Five cells that were nonproductive for BmNPV infection but supported high titers of AcMNPV replication. Recombinant BmNPV, vBm/gfp/lac, containing bm-ie1 promoter-driven egfp showed that few Sf9 and High Five cells infected with vBm/gfp/lac expressed EGFP, while large proportion of EGFP-expressing cells was observed when transfected with vBm/gfp/lac DNA. Immunocytochemical analysis showed that BmNPV was not imported into the nucleus of these two cell lines, while recombinant BmNPV, vBm{delta}64/ac-gp64 possessing AcMNPV gp64more » was imported into the nucleus, yielding progeny virions in High Five cells, but not Sf9 cells. These results indicate that the defective nuclear import of infected virions due to insufficient BmNPV GP64 function is involved in the restricted BmNPV replication in Sf9 and High Five cells.« less

A functional analysis of social reinforcement in vicarious verbal conditioning.

PubMed

Donohue, G B; Tryon, W W

1985-01-01

This article reports the results of 629 subjects in three experiments designed to replicate and extend the phenomenon of vicarious verbal conditioning. Experiment I replicated the finding that subjects who responded most to vicarious verbal conditioning were aware of the contingency involved. Experiment II attempted to examine the effects of prior history with the verbal reinforcer on vicarious verbal conditioning by providing seven groups of subjects with varying classic conditioning histories prior to vicarious verbal conditioning. The null results associated with this experiment were hypothesized to be due to the fact that the vicarious verbal conditioning took place in a language laboratory where the subjects could hear but not see the model. Experiment III replicated Experiment II in a live group context as was done in Experiment I. The results showed that vicarious verbal conditioning was again found to take place, that associating the verbal reinforcer with a tone or tone plus money via forward classic conditioning potentiated the effects of the verbal reinforcer, that backward classic conditioning did not potentiate the reinforcer, d) nor did either of two sensitization procedures potentiate the effects of the verbal reinforcer. Both aware and unaware subjects evidenced vicarious verbal conditioning.

MERS-CoV Accessory ORFs Play Key Role for Infection and Pathogenesis

PubMed Central

Menachery, Vineet D.; Mitchell, Hugh D.; Cockrell, Adam S.; Gralinski, Lisa E.; Yount, Boyd L.; Graham, Rachel L.; McAnarney, Eileen T.; Douglas, Madeline G.; Scobey, Trevor; Beall, Anne; Dinnon, Kenneth; Kocher, Jacob F.; Hale, Andrew E.; Stratton, Kelly G.; Waters, Katrina M.

2017-01-01

ABSTRACT While dispensable for viral replication, coronavirus (CoV) accessory open reading frame (ORF) proteins often play critical roles during infection and pathogenesis. Utilizing a previously generated mutant, we demonstrate that the absence of all four Middle East respiratory syndrome CoV (MERS-CoV) accessory ORFs (deletion of ORF3, -4a, -4b, and -5 [dORF3-5]) has major implications for viral replication and pathogenesis. Importantly, attenuation of the dORF3-5 mutant is primarily driven by dysregulated host responses, including disrupted cell processes, augmented interferon (IFN) pathway activation, and robust inflammation. In vitro replication attenuation also extends to in vivo models, allowing use of dORF3-5 as a live attenuated vaccine platform. Finally, examination of ORF5 implicates a partial role in modulation of NF-κB-mediated inflammation. Together, the results demonstrate the importance of MERS-CoV accessory ORFs for pathogenesis and highlight them as potential targets for surveillance and therapeutic treatments moving forward. PMID:28830941

An Inadvertent Concurrent Replication: Same Roadmap, Different Journey

ERIC Educational Resources Information Center

Lemons, Christopher J.; King, Seth A.; Davidson, Kimberly A.; Berryessa, Teresa L.; Gajjar, Shimul A.; Sacks, Lia H.

2016-01-01

Replication is a critical aspect of scientific inquiry that presents a variety of challenges to researchers, even under the best of conditions. We conducted a review of replication rates in special education journals similar to the review conducted by Makel et al. in this issue. Unknowingly conducting independent reviews allowed for an unexpected…

Self-consistent asset pricing models

NASA Astrophysics Data System (ADS)

Malevergne, Y.; Sornette, D.

2007-08-01

We discuss the foundations of factor or regression models in the light of the self-consistency condition that the market portfolio (and more generally the risk factors) is (are) constituted of the assets whose returns it is (they are) supposed to explain. As already reported in several articles, self-consistency implies correlations between the return disturbances. As a consequence, the alphas and betas of the factor model are unobservable. Self-consistency leads to renormalized betas with zero effective alphas, which are observable with standard OLS regressions. When the conditions derived from internal consistency are not met, the model is necessarily incomplete, which means that some sources of risk cannot be replicated (or hedged) by a portfolio of stocks traded on the market, even for infinite economies. Analytical derivations and numerical simulations show that, for arbitrary choices of the proxy which are different from the true market portfolio, a modified linear regression holds with a non-zero value αi at the origin between an asset i's return and the proxy's return. Self-consistency also introduces “orthogonality” and “normality” conditions linking the betas, alphas (as well as the residuals) and the weights of the proxy portfolio. Two diagnostics based on these orthogonality and normality conditions are implemented on a basket of 323 assets which have been components of the S&P500 in the period from January 1990 to February 2005. These two diagnostics show interesting departures from dynamical self-consistency starting about 2 years before the end of the Internet bubble. Assuming that the CAPM holds with the self-consistency condition, the OLS method automatically obeys the resulting orthogonality and normality conditions and therefore provides a simple way to self-consistently assess the parameters of the model by using proxy portfolios made only of the assets which are used in the CAPM regressions. Finally, the factor decomposition with the self-consistency condition derives a risk-factor decomposition in the multi-factor case which is identical to the principal component analysis (PCA), thus providing a direct link between model-driven and data-driven constructions of risk factors. This correspondence shows that PCA will therefore suffer from the same limitations as the CAPM and its multi-factor generalization, namely lack of out-of-sample explanatory power and predictability. In the multi-period context, the self-consistency conditions force the betas to be time-dependent with specific constraints.

Insights into the structure and assembly of the Bacillus subtilis clamp-loader complex and its interaction with the replicative helicase

PubMed Central

Afonso, José P.; Chintakayala, Kiran; Suwannachart, Chatrudee; Sedelnikova, Svetlana; Giles, Kevin; Hoyes, John B.; Soultanas, Panos; Rafferty, John B.; Oldham, Neil J.

2013-01-01

The clamp-loader complex plays a crucial role in DNA replication by loading the β-clamp onto primed DNA to be used by the replicative polymerase. Relatively little is known about the stoichiometry, structure and assembly pathway of this complex, and how it interacts with the replicative helicase, in Gram-positive organisms. Analysis of full and partial complexes by mass spectrometry revealed that a hetero-pentameric τ3-δ-δ′ Bacillus subtilis clamp-loader assembles via multiple pathways, which differ from those exhibited by the Gram-negative model Escherichia coli. Based on this information, a homology model of the B. subtilis τ3-δ-δ′ complex was constructed, which revealed the spatial positioning of the full C-terminal τ domain. The structure of the δ subunit was determined by X-ray crystallography and shown to differ from that of E. coli in the nature of the amino acids comprising the τ and δ′ binding regions. Most notably, the τ-δ interaction appears to be hydrophilic in nature compared with the hydrophobic interaction in E. coli. Finally, the interaction between τ3 and the replicative helicase DnaB was driven by ATP/Mg2+ conformational changes in DnaB, and evidence is provided that hydrolysis of one ATP molecule by the DnaB hexamer is sufficient to stabilize its interaction with τ3. PMID:23525462

Stronger enhancer II/core promoter activities of hepatitis B virus isolates of B2 subgenotype than those of C2 subgenotype

PubMed Central

Qin, Yanli; Zhou, Xueshi; Jia, Haodi; Chen, Chaoyang; Zhao, Weifeng; Zhang, Jiming; Tong, Shuping

2016-01-01

Hepatitis B virus (HBV) genotype C causes prolonged chronic infection and increased risk for liver cancer than genotype B. Our previous work revealed lower replication capacity of wild-type genotype C2 than B2 isolates. HBV DNA replication is driven by pregenomic RNA, which is controlled by core promoter (CP) and further augmented by enhancer I (ENI) and enhancer II (ENII). DNA fragments covering these regulatory elements were amplified from B2 and C2 isolates to generate luciferase reporter constructs. As ENII is fully embedded in CP, we inserted HBV DNA fragments in the sense orientation to determine their combined activities, and in the antisense orientation to measure enhancer activities alone. Genotype B2 isolates displayed higher ENI+ENII+CP, ENII+CP, and ENII activities, but not ENI or ENI+ENII activity, than C2 isolates. The higher ENII+CP activity was partly attributable to 4 positions displaying genotype-specific variability. Exchanging CP region was sufficient to revert the replication phenotypes of several B2 and C2 clones tested. These results suggest that a weaker ENII and/or CP at least partly accounts for the lower replication capacities of wild-type C2 isolates, which could drive the subsequent acquisition of CP mutations. Such mutations increase genome replication and are implicated in liver cancer development. PMID:27461034

Stronger enhancer II/core promoter activities of hepatitis B virus isolates of B2 subgenotype than those of C2 subgenotype.

PubMed

Qin, Yanli; Zhou, Xueshi; Jia, Haodi; Chen, Chaoyang; Zhao, Weifeng; Zhang, Jiming; Tong, Shuping

2016-07-27

Hepatitis B virus (HBV) genotype C causes prolonged chronic infection and increased risk for liver cancer than genotype B. Our previous work revealed lower replication capacity of wild-type genotype C2 than B2 isolates. HBV DNA replication is driven by pregenomic RNA, which is controlled by core promoter (CP) and further augmented by enhancer I (ENI) and enhancer II (ENII). DNA fragments covering these regulatory elements were amplified from B2 and C2 isolates to generate luciferase reporter constructs. As ENII is fully embedded in CP, we inserted HBV DNA fragments in the sense orientation to determine their combined activities, and in the antisense orientation to measure enhancer activities alone. Genotype B2 isolates displayed higher ENI+ENII+CP, ENII+CP, and ENII activities, but not ENI or ENI+ENII activity, than C2 isolates. The higher ENII+CP activity was partly attributable to 4 positions displaying genotype-specific variability. Exchanging CP region was sufficient to revert the replication phenotypes of several B2 and C2 clones tested. These results suggest that a weaker ENII and/or CP at least partly accounts for the lower replication capacities of wild-type C2 isolates, which could drive the subsequent acquisition of CP mutations. Such mutations increase genome replication and are implicated in liver cancer development.

Life as a cosmic imperative?

PubMed

de Duve, Christian

2011-02-13

The origin of life on Earth may be divided into two stages separated by the first appearance of replicable molecules, most probably of RNA. The first stage depended exclusively on chemistry. The second stage likewise involved chemistry, but with the additional participation of selection, a necessary concomitant of inevitable replication accidents. Consideration of these two processes suggests that the origin of life may have been close to obligatory under the physical-chemical conditions that prevailed at the site of its birth. Thus, an extrasolar planet in which those conditions were replicated appears as a probable site for the appearance of extra-terrestrial life.

Defining life: connecting robotics and chemistry.

PubMed

Brack, André; Troublé, Michel

2010-04-01

Life is commonly referred as open systems driven by organic chemistry capable to self reproduce and to evolve. The notion of life has also been extended to non chemical systems such as robots. The key characteristics of living systems, i.e. autonomy, self-replication, self-reproduction, self-organization, self-aggregation, autocatalysis, as defined in chemistry and in robotics, are compared in a dialogue between a chemist and a robotitian.

Input Skewedness, Consistency, and Order of Frequent Verbs in Frequency-Driven Second Language Construction Learning: A Replication and Extension of Casenhiser and Goldberg (2005) to Adult Second Language Acquisition

ERIC Educational Resources Information Center

Nakamura, Daisuke

2012-01-01

Recent usage-based models of language acquisition research has found that three frequency manipulations; (1) skewed input (Casenhiser & Goldberg 2005), (2) input consistency (Childers & Tomasello 2001), and (3) order of frequent verbs (Goldberg, Casenhiser, & White 2007) facilitated construction learning in children. The present paper addresses…

Facile Method to Study Catalytic Oxygen Evolution Using a Dissolved Oxygen Optical Probe: An Undergraduate Chemistry Laboratory to Appreciate Artificial Photosynthesis

ERIC Educational Resources Information Center

Renderos, Genesis; Aquino, Tawanda; Gutierrez, Kristian; Badiei, Yosra M.

2017-01-01

Artificial photosynthesis (AP) is a synthetic chemical process that replicates natural photosynthesis to mass produce hydrogen as a clean fuel from sunlight-driven water splitting (2H[subscript 2]O [right arrow] O[subscript 2] + H[subscript 2]). In both natural and artificial photosynthesis, an oxygen-evolving catalyst (OEC) is needed to catalyze…

Attentional capture under high perceptual load.

PubMed

Cosman, Joshua D; Vecera, Shaun P

2010-12-01

Attentional capture by abrupt onsets can be modulated by several factors, including the complexity, or perceptual load, of a scene. We have recently demonstrated that observers are less likely to be captured by abruptly appearing, task-irrelevant stimuli when they perform a search that is high, as opposed to low, in perceptual load (Cosman & Vecera, 2009), consistent with perceptual load theory. However, recent results indicate that onset frequency can influence stimulus-driven capture, with infrequent onsets capturing attention more often than did frequent onsets. Importantly, in our previous task, an abrupt onset was present on every trial, and consequently, attentional capture might have been affected by both onset frequency and perceptual load. In the present experiment, we examined whether onset frequency influences attentional capture under conditions of high perceptual load. When onsets were presented frequently, we replicated our earlier results; attentional capture by onsets was modulated under conditions of high perceptual load. Importantly, however, when onsets were presented infrequently, we observed robust capture effects. These results conflict with a strong form of load theory and, instead, suggest that exposure to the elements of a task (e.g., abrupt onsets) combines with high perceptual load to modulate attentional capture by task-irrelevant information.

Origin of life. Primordial genetics: Information transfer in a pre-RNA world based on self-replicating beta-sheet amyloid conformers.

PubMed

Maury, Carl Peter J

2015-10-07

The question of the origin of life on Earth can largely be reduced to the question of what was the first molecular replicator system that was able to replicate and evolve under the presumably very harsh conditions on the early Earth. It is unlikely that a functional RNA could have existed under such conditions and it is generally assumed that some other kind of information system preceded the RNA world. Here, I present an informational molecular system that is stable, self-replicative, environmentally responsive, and evolvable under conditions characterized by high temperatures, ultraviolet and cosmic radiation. This postulated pregenetic system is based on the amyloid fold, a functionally unique polypeptide fold characterized by a cross beta-sheet structure in which the beta strands are arranged perpendicular to the fiber axis. Beside an extraordinary structural robustness, the amyloid fold possesses a unique ability to transmit information by a three-dimensional templating mechanism. In amyloidogenesis short peptide monomers are added one by one to the growing end of the fiber. From the same monomeric subunits several structural variants of amyloid may be formed. Then, in a self-replicative mode, a specific amyloid conformer can act as a template and confer its spatially encoded information to daughter molecular entities in a repetitive way. In this process, the specific conformational information, the spatially changed organization, is transmitted; the coding element is the steric zipper structure, and recognition occurs by amino acid side chain complementarity. The amyloid information system fulfills several basic requirements of a primordial evolvable replicator system: (i) it is stable under the presumed primitive Earth conditions, (ii) the monomeric building blocks of the informational polymer can be formed from available prebiotic compounds, (iii) the system is self-assembling and self-replicative and (iv) it is adaptive to changes in the environment and evolvable. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

Structure and Dynamics of Replication-Mutation Systems

NASA Astrophysics Data System (ADS)

Schuster, Peter

1987-03-01

The kinetic equations of polynucleotide replication can be brought into fairly simple form provided certain environmental conditions are fulfilled. Two flow reactors, the continuously stirred tank reactor (CSTR) and a special dialysis reactor are particularly suitable for the analysis of replication kinetics. An experimental setup to study the chemical reaction network of RNA synthesis was derived from the bacteriophage Qβ. It consists of a virus specific RNA polymerase, Qβ replicase, the activated ribonucleosides GTP, ATP, CTP and UTP as well as a template suitable for replication. The ordinary differential equations for replication and mutation under the conditions of the flow reactors were analysed by the qualitative methods of bifurcation theory as well as by numerical integration. The various kinetic equations are classified according to their dynamical properties: we distinguish "quasilinear systems" which have uniquely stable point attractors and "nonlinear systems" with inherent nonlinearities which lead to multiple steady states, Hopf bifuractions, Feigenbaum-like sequences and chaotic dynamics for certain parameter ranges. Some examples which are relevant in molecular evolution and population genetics are discussed in detail.

Measuring DNA Replication in Hypoxic Conditions.

PubMed

Foskolou, Iosifina P; Biasoli, Deborah; Olcina, Monica M; Hammond, Ester M

2016-01-01

It is imperative that dividing cells maintain replication fork integrity in order to prevent DNA damage and cell death. The investigation of DNA replication is of high importance as alterations in this process can lead to genomic instability, a known causative factor of tumor development. A simple, sensitive, and informative technique which enables the study of DNA replication, is the DNA fiber assay, an adaptation of which is described in this chapter. The DNA fiber method is a powerful tool, which allows the quantitative and qualitative analysis of DNA replication at the single molecule level. The sequential pulse labeling of live cells with two thymidine analogues and the subsequent detection with specific antibodies and fluorescence imaging allows direct examination of sites of DNA synthesis. In this chapter, we describe how this assay can be performed in conditions of low oxygen levels (hypoxia)-a physiologically relevant stress that occurs in most solid tumors. Moreover, we suggest ways on how to overcome the technical problems that arise while using the hypoxic chambers.

Bio-amplifier with Driven Shield Inputs to Reduce Electrical Noise and its Application to Laboratory Teaching of Electrophysiology

PubMed Central

Matsuzaka, Yoshiya; Ichihara, Toshiaki; Abe, Toshihiko; Mushiake, Hajime

2012-01-01

We describe a custom-designed bio-amplifier and its use in teaching neurophysiology to undergraduate students. The amplifier has the following features: 1) differential amplification with driven shield inputs, which makes it workable even in electrically unshielded environments, 2) high input impedance to allow recordings of small signals through high signal source impedance, 3) dual fixed frequency bandpass filters (1–340Hz for surface EMG, EEG, local field potential etc and 320Hz – 3.4kHz for neuronal action potential recording) and independent gain controllers (up to x107,000) to allow the recording of different signals from the same source (e.g., local field potential and spiking activity of neurons), and 4) printed circuit board technology for easy replication with consistent quality. We compared its performance with a commercial amplifier in an electrically noisy environment. Even without any electrostatic shield, it recorded clear electromyographic activity with little interference from other electric appliances. In contrast, the commercial amplifier’s performance severely deteriorated under the same condition. We used this amplifier to build a computer-controlled stimulation and measurement system for electroencephalographic recordings by undergraduate students. The students successfully recorded various sensory evoked potentials with clarity that otherwise would have required costly instruments. This amplifier is a low-cost yet reliable instrument for electro-physiological recording both in education and research. PMID:23504543

Force-driven unbinding of proteins HU and Fis from DNA quantified using a thermodynamic Maxwell relation

PubMed Central

Xiao, Botao; Zhang, Houyin; Johnson, Reid C.; Marko, John F.

2011-01-01

Determining numbers of proteins bound to large DNAs is important for understanding their chromosomal functions. Protein numbers may be affected by physical factors such as mechanical forces generated in DNA, e.g. by transcription or replication. We performed single-DNA stretching experiments with bacterial nucleoid proteins HU and Fis, verifying that the force–extension measurements were in thermodynamic equilibrium. We, therefore, could use a thermodynamic Maxwell relation to deduce the change of protein number on a single DNA due to varied force. For the binding of both HU and Fis under conditions studied, numbers of bound proteins decreased as force was increased. Our experiments showed that most of the bound HU proteins were driven off the DNA at 6.3 pN for HU concentrations lower than 150 nM; our HU data were fit well by a statistical-mechanical model of protein-induced bending of DNA. In contrast, a significant amount of Fis proteins could not be forced off the DNA at forces up to 12 pN and Fis concentrations up to 20 nM. This thermodynamic approach may be applied to measure changes in numbers of a wide variety of molecules bound to DNA or other polymers. Force-dependent DNA binding by proteins suggests mechano-chemical mechanisms for gene regulation. PMID:21427084

Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size

PubMed Central

Lamarre, Sophie; Frasse, Pierre; Zouine, Mohamed; Labourdette, Delphine; Sainderichin, Elise; Hu, Guojian; Le Berre-Anton, Véronique; Bouzayen, Mondher; Maza, Elie

2018-01-01

RNA-Seq is a widely used technology that allows an efficient genome-wide quantification of gene expressions for, for example, differential expression (DE) analysis. After a brief review of the main issues, methods and tools related to the DE analysis of RNA-Seq data, this article focuses on the impact of both the replicate number and library size in such analyses. While the main drawback of previous relevant studies is the lack of generality, we conducted both an analysis of a two-condition experiment (with eight biological replicates per condition) to compare the results with previous benchmark studies, and a meta-analysis of 17 experiments with up to 18 biological conditions, eight biological replicates and 100 million (M) reads per sample. As a global trend, we concluded that the replicate number has a larger impact than the library size on the power of the DE analysis, except for low-expressed genes, for which both parameters seem to have the same impact. Our study also provides new insights for practitioners aiming to enhance their experimental designs. For instance, by analyzing both the sensitivity and specificity of the DE analysis, we showed that the optimal threshold to control the false discovery rate (FDR) is approximately 2−r, where r is the replicate number. Furthermore, we showed that the false positive rate (FPR) is rather well controlled by all three studied R packages: DESeq, DESeq2, and edgeR. We also analyzed the impact of both the replicate number and library size on gene ontology (GO) enrichment analysis. Interestingly, we concluded that increases in the replicate number and library size tend to enhance the sensitivity and specificity, respectively, of the GO analysis. Finally, we recommend to RNA-Seq practitioners the production of a pilot data set to strictly analyze the power of their experimental design, or the use of a public data set, which should be similar to the data set they will obtain. For individuals working on tomato research, on the basis of the meta-analysis, we recommend at least four biological replicates per condition and 20 M reads per sample to be almost sure of obtaining about 1000 DE genes if they exist. PMID:29491871

Proteasome-dependent degradation of replisome components regulates faithful DNA replication.

PubMed

Roseaulin, Laura C; Noguchi, Chiaki; Noguchi, Eishi

2013-08-15

The replication machinery, or the replisome, collides with a variety of obstacles during the normal process of DNA replication. In addition to damaged template DNA, numerous chromosome regions are considered to be difficult to replicate owing to the presence of DNA secondary structures and DNA-binding proteins. Under these conditions, the replication fork stalls, generating replication stress. Stalled forks are prone to collapse, posing serious threats to genomic integrity. It is generally thought that the replication checkpoint functions to stabilize the replisome and replication fork structure upon replication stress. This is important in order to allow DNA replication to resume once the problem is solved. However, our recent studies demonstrated that some replisome components undergo proteasome-dependent degradation during DNA replication in the fission yeast Schizosaccharomyces pombe. Our investigation has revealed the involvement of the SCF(Pof3) (Skp1-Cullin/Cdc53-F-box) ubiquitin ligase in replisome regulation. We also demonstrated that forced accumulation of the replisome components leads to abnormal DNA replication upon replication stress. Here we review these findings and present additional data indicating the importance of replisome degradation for DNA replication. Our studies suggest that cells activate an alternative pathway to degrade replisome components in order to preserve genomic integrity.

Self-replication: Nanostructure evolution

NASA Astrophysics Data System (ADS)

Simmel, Friedrich C.

2017-10-01

DNA origami nanostructures were utilized to replicate a seed pattern that resulted in the growth of populations of nanostructures. Exponential growth could be controlled by environmental conditions depending on the preferential requirements of each population.

SEE locomotor behavior test discriminates C57BL/6J and DBA/2J mouse inbred strains across laboratories and protocol conditions.

PubMed

Kafkafi, Neri; Lipkind, Dina; Benjamini, Yoav; Mayo, Cheryl L; Elmer, Gregory I; Golani, Ilan

2003-06-01

Conventional tests of behavioral phenotyping frequently have difficulties differentiating certain genotypes and replicating these differences across laboratories and protocol conditions. This study explores the hypothesis that automated tests can be designed to quantify ethologically relevant behavior patterns that more readily characterize heritable and replicable phenotypes. It used SEE (Strategy for the Exploration of Exploration) to phenotype the locomotor behavior of the C57BL/6 and DBA/2 mouse inbred strains across 3 laboratories. The 2 genotypes differed in 15 different measures of behavior, none of which had a significant genotype-laboratory interaction. Within the same laboratory, most of these differences were replicated in additional experiments despite the test photoperiod phase being changed and saline being injected. Results suggest that well-designed tests may considerably enhance replicability across laboratories.

Synchronization of DNA array replication kinetics

NASA Astrophysics Data System (ADS)

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.

Do We Know What We Think We Know? On the Importance of Replication in Instructional Communication Research. Forum: The Future of Instructional Communication

ERIC Educational Resources Information Center

Kaufmann, Renee; Tatum, Nicholas T.

2017-01-01

Replication is a fundamental principle of social science, enabling researchers to verify the accuracy of empirical findings, clarify the conditions under which phenomena occur, and further validate the social significance of research (Brandt et al., 2014). However, a lack of replication research has been published in instructional communication…

Kis antitoxin couples plasmid R1 replication and parD (kis,kid) maintenance modules.

PubMed

López-Villarejo, Juan; Diago-Navarro, Elizabeth; Hernández-Arriaga, Ana María; Díaz-Orejas, Ramón

2012-03-01

The coupling between the replication and parD (kis, kid) maintenance modules of R1 has been revisited here by the isolation of a significant collection of conditional replication mutants in the pKN1562 mini-R1 plasmid, and in its derivative, pJLV01, specifically affected in the RNase activity of the Kid toxin. This new analysis aims to identify key factors in this coupling. For this purpose we have quantified and characterized the restriction introduced by parD to isolate conditional replication mutants of this plasmid, a signature of the modular coupling. This restriction depends on the RNase activity of the Kid toxin and it is relieved by either over-expression of the Kis antitoxin or by preventing its degradation by Lon and ClpAP proteases. Based on these data and on the correlation between copy numbers and parD transcriptional levels obtained in the different mutants, it is proposed that a reduction of Kis antitoxin levels in response to inefficient plasmid replication is the key factor for coupling plasmid replication and parD modules. Copyright © 2012 Elsevier Inc. All rights reserved.

Heat shock protein 72 expression allows permissive replication of oncolytic adenovirus dl1520 (ONYX-015) in rat glioblastoma cells

PubMed Central

Madara, Jonathan; Krewet, James A; Shah, Maulik

2005-01-01

In this study we have made novel observations with regards to potentiation of the tumoricidal activity of the oncolytic adenovirus, dl1520 (ONYX-015) in rat glioblastoma cell lines expressing heat shock protein 72 (HSP72) due to permissive virus replication. ONYX-015 is a conditionally replicating adenovirus that is deleted for the E1B 55 kDA gene product whose normal function is to interact with cell-cycle regulatory proteins to permit virus replication. However, many murine and rodent cell lines are not permissive for adenovirus replication. Previously, it has been reported that the heat shock response is necessary for adenovirus replication and that induction of heat shock proteins is mediated by E1 region gene products. Therefore, we hypothesized that HSP72 expression may allow for permissive replication of ONYX-015 in previously non-permissive cells. Rat glioma cell lines 9L and RT2 were transfected with a plasmids expressing HSP72 or GFP. After infection with ONYX-015, no tumoricidal activity is observed in GFP expressing cell lines despite adequate transduction. In contrast, HSP72 transfected cells show cytopathic effects by 72 hours and greater than 75% loss of viability by 96 hours. Burst assays show active virus replication in the HSP72 expressing cell lines. Therefore, 9L-HSP72 and RT2-HSP72 are ideal models to evaluate the efficacy of ONYX-015 in an immunocompetent rat model. Our study has implications for creating rodent tumor models for pre-clinical studies with E1 region deleted conditionally replicating adenovirus. PMID:15762988

How does achievement motivation influence mental effort mobilization? Physiological evidence of deteriorative effects of negative affects on the level of engagement.

PubMed

Capa, Rémi L; Audiffren, Michel

2009-12-01

We tested whether the effect of achievement motivation on effort is modulated by two possible factors of the motivational intensity theory (Wright and Kirby, 2001): perceived difficulty and maximally justified effort. Approach-driven (N=16) and avoidance-driven (N=16) participants were first instructed to perform a reaction time task to the best of their abilities. Next, the participants were instructed to consistently beat their performance standard established in the first condition. Approach-driven participants showed a stronger decrease of midfrequency band of heart rate variability, which was used as an index of mental effort, than avoidance-driven participants in the second instruction condition. Moreover, avoidance-driven participants showed a higher corrugator supercilii reactivity, which was used as an index of negative affects, than approach-driven participants in the second instruction condition. No difference of perceived difficulty between groups was observed. Results suggested that avoidance-driven participants developed negative affects in the second instruction condition decreasing the maximally justified effort and their level of engagement.

Subtle shifts in microbial communities occur alongside the release of carbon induced by drought and rewetting in contrasting peatland ecosystems.

PubMed

Potter, Caitlin; Freeman, Chris; Golyshin, Peter N; Ackermann, Gail; Fenner, Nathalie; McDonald, James E; Ehbair, Abdassalam; Jones, Timothy G; Murphy, Loretta M; Creer, Simon

2017-09-12

Peat represents a globally significant pool of sequestered carbon. However, peatland carbon stocks are highly threatened by anthropogenic climate change, including drought, which leads to a large release of carbon dioxide. Although the enzymatic mechanisms underlying drought-driven carbon release are well documented, the effect of drought on peatland microbial communities has been little studied. Here, we carried out a replicated and controlled drought manipulation using intact peat 'mesocosm cores' taken from bog and fen habitats, and used a combination of community fingerprinting and sequencing of marker genes to identify community changes associated with drought. Community composition varied with habitat and depth. Moreover, community differences between mesocosm cores were stronger than the effect of the drought treatment, emphasising the importance of replication in microbial marker gene studies. While the effect of drought on the overall composition of prokaryotic and eukaryotic communities was weak, a subset of the microbial community did change in relative abundance, especially in the fen habitat at 5 cm depth. 'Drought-responsive' OTUs were disproportionately drawn from the phyla Bacteroidetes and Proteobacteria. Collectively, the data provide insights into the microbial community changes occurring alongside drought-driven carbon release from peatlands, and suggest a number of novel avenues for future research.

Biological evolution of replicator systems: towards a quantitative approach.

PubMed

Martin, Osmel; Horvath, J E

2013-04-01

The aim of this work is to study the features of a simple replicator chemical model of the relation between kinetic stability and entropy production under the action of external perturbations. We quantitatively explore the different paths leading to evolution in a toy model where two independent replicators compete for the same substrate. To do that, the same scenario described originally by Pross (J Phys Org Chem 17:312-316, 2004) is revised and new criteria to define the kinetic stability are proposed. Our results suggest that fast replicator populations are continually favored by the effects of strong stochastic environmental fluctuations capable to determine the global population, the former assumed to be the only acting evolution force. We demonstrate that the process is continually driven by strong perturbations only, and that population crashes may be useful proxies for these catastrophic environmental fluctuations. As expected, such behavior is particularly enhanced under very large scale perturbations, suggesting a likely dynamical footprint in the recovery patterns of new species after mass extinction events in the Earth's geological past. Furthermore, the hypothesis that natural selection always favors the faster processes may give theoretical support to different studies that claim the applicability of maximum principles like the Maximum Metabolic Flux (MMF) or Maximum Entropy Productions Principle (MEPP), seen as the main goal of biological evolution.

Biological Evolution of Replicator Systems: Towards a Quantitative Approach

NASA Astrophysics Data System (ADS)

Martin, Osmel; Horvath, J. E.

2013-04-01

The aim of this work is to study the features of a simple replicator chemical model of the relation between kinetic stability and entropy production under the action of external perturbations. We quantitatively explore the different paths leading to evolution in a toy model where two independent replicators compete for the same substrate. To do that, the same scenario described originally by Pross (J Phys Org Chem 17:312-316, 2004) is revised and new criteria to define the kinetic stability are proposed. Our results suggest that fast replicator populations are continually favored by the effects of strong stochastic environmental fluctuations capable to determine the global population, the former assumed to be the only acting evolution force. We demonstrate that the process is continually driven by strong perturbations only, and that population crashes may be useful proxies for these catastrophic environmental fluctuations. As expected, such behavior is particularly enhanced under very large scale perturbations, suggesting a likely dynamical footprint in the recovery patterns of new species after mass extinction events in the Earth's geological past. Furthermore, the hypothesis that natural selection always favors the faster processes may give theoretical support to different studies that claim the applicability of maximum principles like the Maximum Metabolic Flux (MMF) or Maximum Entropy Productions Principle (MEPP), seen as the main goal of biological evolution.

Cluster-cluster aggregation with particle replication and chemotaxy: a simple model for the growth of animal cells in culture

NASA Astrophysics Data System (ADS)

Alves, S. G.; Martins, M. L.

2010-09-01

Aggregation of animal cells in culture comprises a series of motility, collision and adhesion processes of basic relevance for tissue engineering, bioseparations, oncology research and in vitro drug testing. In the present paper, a cluster-cluster aggregation model with stochastic particle replication and chemotactically driven motility is investigated as a model for the growth of animal cells in culture. The focus is on the scaling laws governing the aggregation kinetics. Our simulations reveal that in the absence of chemotaxy the mean cluster size and the total number of clusters scale in time as stretched exponentials dependent on the particle replication rate. Also, the dynamical cluster size distribution functions are represented by a scaling relation in which the scaling function involves a stretched exponential of the time. The introduction of chemoattraction among the particles leads to distribution functions decaying as power laws with exponents that decrease in time. The fractal dimensions and size distributions of the simulated clusters are qualitatively discussed in terms of those determined experimentally for several normal and tumoral cell lines growing in culture. It is shown that particle replication and chemotaxy account for the simplest cluster size distributions of cellular aggregates observed in culture.

Changes in DnaA-dependent gene expression contribute to the transcriptional and developmental response of Bacillus subtilis to manganese limitation in Luria-Bertani medium.

PubMed

Hoover, Sharon E; Xu, Weihong; Xiao, Wenzhong; Burkholder, William F

2010-08-01

The SOS response to DNA damage in bacteria is a well-known component of the complex transcriptional responses to genotoxic environmental stresses such as exposure to reactive oxygen species, alkylating agents, and many of the antibiotics targeting DNA replication. However, bacteria such as Bacillus subtilis also respond to conditions that perturb DNA replication via a transcriptional response mediated by the replication initiation protein DnaA. In addition to regulating the initiation of DNA replication, DnaA directly regulates the transcription of specific genes. Conditions that perturb DNA replication can trigger the accumulation of active DnaA, activating or repressing the transcription of genes in the DnaA regulon. We report here that simply growing B. subtilis in LB medium altered DnaA-dependent gene expression in a manner consistent with the accumulation of active DnaA and that this was part of a general transcriptional response to manganese limitation. The SOS response to DNA damage was not induced under these conditions. One of the genes positively regulated by DnaA in Bacillus subtilis encodes a protein that inhibits the initiation of sporulation, Sda. Sda expression was induced as cells entered stationary phase in LB medium but not in LB medium supplemented with manganese, and the induction of Sda inhibited sporulation-specific gene expression and the onset of spore morphogenesis. In the absence of Sda, manganese-limited cells initiated spore development but failed to form mature spores. These data highlight that DnaA-dependent gene expression may influence the response of bacteria to a range of environmental conditions, including conditions that are not obviously associated with genotoxic stress.

Changes in DnaA-Dependent Gene Expression Contribute to the Transcriptional and Developmental Response of Bacillus subtilis to Manganese Limitation in Luria-Bertani Medium▿ †

PubMed Central

Hoover, Sharon E.; Xu, Weihong; Xiao, Wenzhong; Burkholder, William F.

2010-01-01

The SOS response to DNA damage in bacteria is a well-known component of the complex transcriptional responses to genotoxic environmental stresses such as exposure to reactive oxygen species, alkylating agents, and many of the antibiotics targeting DNA replication. However, bacteria such as Bacillus subtilis also respond to conditions that perturb DNA replication via a transcriptional response mediated by the replication initiation protein DnaA. In addition to regulating the initiation of DNA replication, DnaA directly regulates the transcription of specific genes. Conditions that perturb DNA replication can trigger the accumulation of active DnaA, activating or repressing the transcription of genes in the DnaA regulon. We report here that simply growing B. subtilis in LB medium altered DnaA-dependent gene expression in a manner consistent with the accumulation of active DnaA and that this was part of a general transcriptional response to manganese limitation. The SOS response to DNA damage was not induced under these conditions. One of the genes positively regulated by DnaA in Bacillus subtilis encodes a protein that inhibits the initiation of sporulation, Sda. Sda expression was induced as cells entered stationary phase in LB medium but not in LB medium supplemented with manganese, and the induction of Sda inhibited sporulation-specific gene expression and the onset of spore morphogenesis. In the absence of Sda, manganese-limited cells initiated spore development but failed to form mature spores. These data highlight that DnaA-dependent gene expression may influence the response of bacteria to a range of environmental conditions, including conditions that are not obviously associated with genotoxic stress. PMID:20511500

CDK activity provides temporal and quantitative cues for organizing genome duplication

PubMed Central

Perrot, Anthony; Millington, Christopher Lee; Gómez-Escoda, Blanca; Schausi-Tiffoche, Diane

2018-01-01

In eukaryotes, the spatial and temporal organization of genome duplication gives rise to distinctive profiles of replication origin usage along the chromosomes. While it has become increasingly clear that these programs are important for cellular physiology, the mechanisms by which they are determined and modulated remain elusive. Replication initiation requires the function of cyclin-dependent kinases (CDKs), which associate with various cyclin partners to drive cell proliferation. Surprisingly, although we possess detailed knowledge of the CDK regulators and targets that are crucial for origin activation, little is known about whether CDKs play a critical role in establishing the genome-wide pattern of origin selection. We have addressed this question in the fission yeast, taking advantage of a simplified cell cycle network in which cell proliferation is driven by a single cyclin-CDK module. This system allows us to precisely control CDK activity in vivo using chemical genetics. First, in contrast to previous reports, our results clearly show that distinct cyclin-CDK pairs are not essential for regulating specific subsets of origins and for establishing a normal replication program. Importantly, we then demonstrate that the timing at which CDK activity reaches the S phase threshold is critical for the organization of replication in distinct efficiency domains, while the level of CDK activity at the onset of S phase is a dose-dependent modulator of overall origin efficiencies. Our study therefore implicates these different aspects of CDK regulation as versatile mechanisms for shaping the architecture of DNA replication across the genome. PMID:29466359

Evolution of DNA Replication Protein Complexes in Eukaryotes and Archaea

PubMed Central

Chia, Nicholas; Cann, Isaac; Olsen, Gary J.

2010-01-01

Background The replication of DNA in Archaea and eukaryotes requires several ancillary complexes, including proliferating cell nuclear antigen (PCNA), replication factor C (RFC), and the minichromosome maintenance (MCM) complex. Bacterial DNA replication utilizes comparable proteins, but these are distantly related phylogenetically to their archaeal and eukaryotic counterparts at best. Methodology/Principal Findings While the structures of each of the complexes do not differ significantly between the archaeal and eukaryotic versions thereof, the evolutionary dynamic in the two cases does. The number of subunits in each complex is constant across all taxa. However, they vary subtly with regard to composition. In some taxa the subunits are all identical in sequence, while in others some are homologous rather than identical. In the case of eukaryotes, there is no phylogenetic variation in the makeup of each complex—all appear to derive from a common eukaryotic ancestor. This is not the case in Archaea, where the relationship between the subunits within each complex varies taxon-to-taxon. We have performed a detailed phylogenetic analysis of these relationships in order to better understand the gene duplications and divergences that gave rise to the homologous subunits in Archaea. Conclusion/Significance This domain level difference in evolution suggests that different forces have driven the evolution of DNA replication proteins in each of these two domains. In addition, the phylogenies of all three gene families support the distinctiveness of the proposed archaeal phylum Thaumarchaeota. PMID:20532250

Phage Lambda P Protein: Trans-Activation, Inhibition Phenotypes and their Suppression

PubMed Central

Hayes, Sidney; Erker, Craig; Horbay, Monique A.; Marciniuk, Kristen; Wang, Wen; Hayes, Connie

2013-01-01

The initiation of bacteriophage λ replication depends upon interactions between the oriλ DNA site, phage proteins O and P, and E. coli host replication proteins. P exhibits a high affinity for DnaB, the major replicative helicase for unwinding double stranded DNA. The concept of P-lethality relates to the hypothesis that P can sequester DnaB and in turn prevent cellular replication initiation from oriC. Alternatively, it was suggested that P-lethality does not involve an interaction between P and DnaB, but is targeted to DnaA. P-lethality is assessed by examining host cells for transformation by ColE1-type plasmids that can express P, and the absence of transformants is attributed to a lethal effect of P expression. The plasmid we employed enabled conditional expression of P, where under permissive conditions, cells were efficiently transformed. We observed that ColE1 replication and plasmid establishment upon transformation is extremely sensitive to P, and distinguish this effect from P-lethality directed to cells. We show that alleles of dnaB protect the variant cells from P expression. P-dependent cellular filamentation arose in ΔrecA or lexA[Ind-] cells, defective for SOS induction. Replication propagation and restart could represent additional targets for P interference of E. coli replication, beyond the oriC-dependent initiation step. PMID:23389467

SCF(FBXW7α) modulates the intra-S-phase DNA-damage checkpoint by regulating Polo like kinase-1 stability.

PubMed

Giráldez, Servando; Herrero-Ruiz, Joaquín; Mora-Santos, Mar; Japón, Miguel Á; Tortolero, Maria; Romero, Francisco

2014-06-30

The intra-S-checkpoint is essential to control cell progression through S phase under normal conditions and in response to replication stress. When DNA lesions are detected, replication fork progression is blocked allowing time for repair to avoid genomic instability and the risk of cancer. DNA replication initiates at many origins of replication in eukaryotic cells, where a series of proteins form pre-replicative complexes (pre-RCs) that are activated to become pre-initiation complexes and ensure a single round of replication in each cell cycle. PLK1 plays an important role in the regulation of DNA replication, contributing to the regulation of pre-RCs formation by phosphorylating several proteins, under both normal and stress conditions. Here we report that PLK1 is ubiquitinated and degraded by SCFFBXW7α/proteasome. Moreover, we identified a new Cdc4 phosphodegron in PLK1, conserved from yeast to humans, whose mutation prevents PLK1 destruction. We established that endogenous SCFFBXW7α degrades PLK1 in the G1 and S phases of an unperturbed cell cycle and in S phase following UV irradiation. Furthermore, we showed that FBXW7α overexpression or UV irradiation prevented the loading of proteins onto chromatin to form pre-RCs and, accordingly, reduced cell proliferation. We conclude that PLK1 degradation mediated by SCFFBXW7α modulates the intra-S-phase checkpoint.

SCFFBXW7α modulates the intra-S-phase DNA-damage checkpoint by regulating Polo like kinase-1 stability

PubMed Central

Giráldez, Servando; Herrero-Ruiz, Joaquín; Mora-Santos, Mar; Japón, Miguel Á.; Tortolero, Maria; Romero, Francisco

2014-01-01

The intra-S-checkpoint is essential to control cell progression through S phase under normal conditions and in response to replication stress. When DNA lesions are detected, replication fork progression is blocked allowing time for repair to avoid genomic instability and the risk of cancer. DNA replication initiates at many origins of replication in eukaryotic cells, where a series of proteins form pre-replicative complexes (pre-RCs) that are activated to become pre-initiation complexes and ensure a single round of replication in each cell cycle. PLK1 plays an important role in the regulation of DNA replication, contributing to the regulation of pre-RCs formation by phosphorylating several proteins, under both normal and stress conditions. Here we report that PLK1 is ubiquitinated and degraded by SCFFBXW7α/proteasome. Moreover, we identified a new Cdc4 phosphodegron in PLK1, conserved from yeast to humans, whose mutation prevents PLK1 destruction. We established that endogenous SCFFBXW7α degrades PLK1 in the G1 and S phases of an unperturbed cell cycle and in S phase following UV irradiation. Furthermore, we showed that FBXW7α overexpression or UV irradiation prevented the loading of proteins onto chromatin to form pre-RCs and, accordingly, reduced cell proliferation. We conclude that PLK1 degradation mediated by SCFFBXW7α modulates the intra-S-phase checkpoint. PMID:24970797

Suppression of the Escherichia coli dnaA46 mutation by changes in the activities of the pyruvate-acetate node links DNA replication regulation to central carbon metabolism.

PubMed

Tymecka-Mulik, Joanna; Boss, Lidia; Maciąg-Dorszyńska, Monika; Matias Rodrigues, João F; Gaffke, Lidia; Wosinski, Anna; Cech, Grzegorz M; Szalewska-Pałasz, Agnieszka; Węgrzyn, Grzegorz; Glinkowska, Monika

2017-01-01

To ensure faithful transmission of genetic material to progeny cells, DNA replication is tightly regulated, mainly at the initiation step. Escherichia coli cells regulate the frequency of initiation according to growth conditions. Results of the classical, as well as the latest studies, suggest that the DNA replication in E. coli starts at a predefined, constant cell volume per chromosome but the mechanisms coordinating DNA replication with cell growth are still not fully understood. Results of recent investigations have revealed a role of metabolic pathway proteins in the control of cell division and a direct link between metabolism and DNA replication has also been suggested both in Bacillus subtilis and E. coli cells. In this work we show that defects in the acetate overflow pathway suppress the temperature-sensitivity of a defective replication initiator-DnaA under acetogenic growth conditions. Transcriptomic and metabolic analyses imply that this suppression is correlated with pyruvate accumulation, resulting from alterations in the pyruvate dehydrogenase (PDH) activity. Consequently, deletion of genes encoding the pyruvate dehydrogenase subunits likewise resulted in suppression of the thermal-sensitive growth of the dnaA46 strain. We propose that the suppressor effect may be directly related to the PDH complex activity, providing a link between an enzyme of the central carbon metabolism and DNA replication.

Conditionally replicative adenovirus for gastrointestinal cancers.

PubMed

Yamamoto, Masato

2004-08-01

The clinical outcome of advanced gastrointestinal (GI) cancers (especially pancreatic and oesophageal cancers) is dismal, despite the advance of conventional therapeutic strategies. Cancer gene therapy is a category of new therapeutics, among which conditionally replicative adenovirus (CRAd) is one promising strategy to overcome existing obstacles of cancer gene therapy. Various CRAds have been developed for GI cancer treatment by taking advantage of the replication biology of adenovirus. Some CRAds have already been tested in clinical trials, but have fallen short of initial expectations. Concerns for clinical applicability include therapeutic potency, replication selectivity and interval end points in clinical trials. In addition, improvement of experimental animal models is needed for a deeper understanding of CRAd biology. Despite these obstacles, CRAds continue to be an exciting area of investigation with great potential for clinical utility. Further virological and oncological research will eventually lead to full realisation of the therapeutic potential of CRAds in the field of GI cancers.

Replicates in high dimensions, with applications to latent variable graphical models.

PubMed

Tan, Kean Ming; Ning, Yang; Witten, Daniela M; Liu, Han

2016-12-01

In classical statistics, much thought has been put into experimental design and data collection. In the high-dimensional setting, however, experimental design has been less of a focus. In this paper, we stress the importance of collecting multiple replicates for each subject in this setting. We consider learning the structure of a graphical model with latent variables, under the assumption that these variables take a constant value across replicates within each subject. By collecting multiple replicates for each subject, we are able to estimate the conditional dependence relationships among the observed variables given the latent variables. To test the null hypothesis of conditional independence between two observed variables, we propose a pairwise decorrelated score test. Theoretical guarantees are established for parameter estimation and for this test. We show that our proposal is able to estimate latent variable graphical models more accurately than some existing proposals, and apply the proposed method to a brain imaging dataset.

In vitro fertilization experiments using sockeye salmon reveal that bigger eggs are more fertilizable under sperm limitation

PubMed Central

Macfarlane, Christopher P.; Hoysak, Drew J.; Liley, N. Robin; Gage, Matthew J.G.

2009-01-01

Although theory and widespread evidence show that the evolution of egg size is driven primarily by offspring and maternal fitness demands, an additional explanation invokes sperm limitation as a selective force that could also influence egg size optima. Levitan proposed that constraints from gamete encounter in external fertilization environments could select for enlargement of ova to increase the physical size of the fertilization target. We test this theory using in vitro fertilization experiments in an externally fertilizing fish. Sockeye salmon (Onchorhyncus nerka) females show considerable between-individual variation in ovum size, and we explored the consequences of this natural variation for the fertilization success of individual eggs under conditions of sperm limitation. By engineering consistent conditions where in vitro fertilization rate was always intermediate, we were able to compare the sizes of fertilized and unfertilized eggs across 20 fertilization replicates. After controlling for any changes in volume through incubation, results showed that successfully fertilized eggs were significantly larger than the eggs that failed to achieve fertilization. Under conditions without sperm limitation, fertility was unaffected by egg size. Our findings therefore support Levitan's theory, demonstrating empirically that some element of egg size variation could be selected by fertilization demands under sperm limitation. However, further research on sperm limitation in natural spawnings is required to assess the selective importance of these results. PMID:19364734

In vitro fertilization experiments using sockeye salmon reveal that bigger eggs are more fertilizable under sperm limitation.

PubMed

Macfarlane, Christopher P; Hoysak, Drew J; Liley, N Robin; Gage, Matthew J G

2009-07-07

Although theory and widespread evidence show that the evolution of egg size is driven primarily by offspring and maternal fitness demands, an additional explanation invokes sperm limitation as a selective force that could also influence egg size optima. Levitan proposed that constraints from gamete encounter in external fertilization environments could select for enlargement of ova to increase the physical size of the fertilization target. We test this theory using in vitro fertilization experiments in an externally fertilizing fish. Sockeye salmon (Onchorhyncus nerka) females show considerable between-individual variation in ovum size, and we explored the consequences of this natural variation for the fertilization success of individual eggs under conditions of sperm limitation. By engineering consistent conditions where in vitro fertilization rate was always intermediate, we were able to compare the sizes of fertilized and unfertilized eggs across 20 fertilization replicates. After controlling for any changes in volume through incubation, results showed that successfully fertilized eggs were significantly larger than the eggs that failed to achieve fertilization. Under conditions without sperm limitation, fertility was unaffected by egg size. Our findings therefore support Levitan's theory, demonstrating empirically that some element of egg size variation could be selected by fertilization demands under sperm limitation. However, further research on sperm limitation in natural spawnings is required to assess the selective importance of these results.

Trade-offs between driving nodes and time-to-control in complex networks

PubMed Central

Pequito, Sérgio; Preciado, Victor M.; Barabási, Albert-László; Pappas, George J.

2017-01-01

Recent advances in control theory provide us with efficient tools to determine the minimum number of driving (or driven) nodes to steer a complex network towards a desired state. Furthermore, we often need to do it within a given time window, so it is of practical importance to understand the trade-offs between the minimum number of driving/driven nodes and the minimum time required to reach a desired state. Therefore, we introduce the notion of actuation spectrum to capture such trade-offs, which we used to find that in many complex networks only a small fraction of driving (or driven) nodes is required to steer the network to a desired state within a relatively small time window. Furthermore, our empirical studies reveal that, even though synthetic network models are designed to present structural properties similar to those observed in real networks, their actuation spectra can be dramatically different. Thus, it supports the need to develop new synthetic network models able to replicate controllability properties of real-world networks. PMID:28054597

Trade-offs between driving nodes and time-to-control in complex networks

NASA Astrophysics Data System (ADS)

Pequito, Sérgio; Preciado, Victor M.; Barabási, Albert-László; Pappas, George J.

2017-01-01

Recent advances in control theory provide us with efficient tools to determine the minimum number of driving (or driven) nodes to steer a complex network towards a desired state. Furthermore, we often need to do it within a given time window, so it is of practical importance to understand the trade-offs between the minimum number of driving/driven nodes and the minimum time required to reach a desired state. Therefore, we introduce the notion of actuation spectrum to capture such trade-offs, which we used to find that in many complex networks only a small fraction of driving (or driven) nodes is required to steer the network to a desired state within a relatively small time window. Furthermore, our empirical studies reveal that, even though synthetic network models are designed to present structural properties similar to those observed in real networks, their actuation spectra can be dramatically different. Thus, it supports the need to develop new synthetic network models able to replicate controllability properties of real-world networks.

Utility of Respondent Driven Sampling to Reach Disadvantaged Emerging Adults for Assessment of Substance Use, Weight, and Sexual Behaviors.

PubMed

Tucker, Jalie A; Simpson, Cathy A; Chandler, Susan D; Borch, Casey A; Davies, Susan L; Kerbawy, Shatomi J; Lewis, Terri H; Crawford, M Scott; Cheong, JeeWon; Michael, Max

2016-01-01

Emerging adulthood often entails heightened risk-taking with potential life-long consequences, and research on risk behaviors is needed to guide prevention programming, particularly in under-served and difficult to reach populations. This study evaluated the utility of Respondent Driven Sampling (RDS), a peer-driven methodology that corrects limitations of snowball sampling, to reach at-risk African American emerging adults from disadvantaged urban communities. Initial "seed" participants from the target group recruited peers, who then recruited their peers in an iterative process (110 males, 234 females; M age = 18.86 years). Structured field interviews assessed common health risk factors, including substance use, overweight/obesity, and sexual behaviors. Established gender-and age-related associations with risk factors were replicated, and sample risk profiles and prevalence estimates compared favorably with matched samples from representative U.S. national surveys. Findings supported the use of RDS as a sampling method and grassroots platform for research and prevention with community-dwelling risk groups.

Artificial muscles driven by the cooperative actuation of electrochemical molecular machines. Persistent discrepancies and challenges

NASA Astrophysics Data System (ADS)

Otero

2017-10-01

Here we review the persisting conceptual discrepancies between different research groups working on artificial muscles based on conducting polymers and other electroactive material. The basic question is if they can be treated as traditional electro-mechanical (physical) actuators driven by electric fields and described by some adaptation of their physical models or if, replicating natural muscles, they are electro-chemo-mechanical actuators driven by electrochemical reaction of the constitutive molecular machines: the polymeric chains. In that case the charge consumed by the reaction will control the volume variation of the muscular material and the motor displacement, following the basic and single Faraday's laws: the charge consumed by the reaction determines the number of exchanged ions and solvent, the film volume variation to lodge/expel them and the amplitude of the movement. Deviations from the linear relationships are due to the osmotic exchange of solvent and to the presence of parallel reactions from the electrolyte, which originate creeping effects. Challenges and limitations are underlined.

Loss of maintenance DNA methylation results in abnormal DNA origin firing during DNA replication.

PubMed

Haruta, Mayumi; Shimada, Midori; Nishiyama, Atsuya; Johmura, Yoshikazu; Le Tallec, Benoît; Debatisse, Michelle; Nakanishi, Makoto

2016-01-22

The mammalian maintenance methyltransferase DNMT1 [DNA (cytosine-5-)-methyltransferase 1] mediates the inheritance of the DNA methylation pattern during replication. Previous studies have shown that depletion of DNMT1 causes a severe growth defect and apoptosis in differentiated cells. However, the detailed mechanisms behind this phenomenon remain poorly understood. Here we show that conditional ablation of Dnmt1 in murine embryonic fibroblasts (MEFs) resulted in an aberrant DNA replication program showing an accumulation of late-S phase replication and causing severely defective growth. Furthermore, we found that the catalytic activity and replication focus targeting sequence of DNMT1 are required for a proper DNA replication program. Taken together, our findings suggest that the maintenance of DNA methylation by DNMT1 plays a critical role in proper regulation of DNA replication in mammalian cells. Copyright © 2015 Elsevier Inc. All rights reserved.

The effect of DNA replication on mutation of the Saccharomyces cerevisiae CDC8 gene.

PubMed

Zaborowska, D; Zuk, J

1990-04-01

Incubation in YPD medium under permissive conditions when DNA replication is going on, strongly stimulates the induction of cdc+ colonies of UV-irradiated cells of yeast strains HB23 (cdc8-1/cdc8-3), HB26 (cdc8-3/cdc8-3) and HB7 (cdc8-1/cdc8-1). Inhibition of DNA replication by hydroxyurea, araCMP, cycloheximide or caffeine or else by incubation in phosphate buffer pH 7.0, abolishes this stimulation. Thus the replication of DNA is strongly correlated with the high induction of cdc+ colonies by UV irradiation. It is postulated that these UV-induced cdc+ colonies arise as the result infidelity in DNA replication.

Novel Chromosome Organization Pattern in Actinomycetales-Overlapping Replication Cycles Combined with Diploidy.

PubMed

Böhm, Kati; Meyer, Fabian; Rhomberg, Agata; Kalinowski, Jörn; Donovan, Catriona; Bramkamp, Marc

2017-06-06

Bacteria regulate chromosome replication and segregation tightly with cell division to ensure faithful segregation of DNA to daughter generations. The underlying mechanisms have been addressed in several model species. It became apparent that bacteria have evolved quite different strategies to regulate DNA segregation and chromosomal organization. We have investigated here how the actinobacterium Corynebacterium glutamicum organizes chromosome segregation and DNA replication. Unexpectedly, we found that C. glutamicum cells are at least diploid under all of the conditions tested and that these organisms have overlapping C periods during replication, with both origins initiating replication simultaneously. On the basis of experimental data, we propose growth rate-dependent cell cycle models for C. glutamicum IMPORTANCE Bacterial cell cycles are known for few model organisms and can vary significantly between species. Here, we studied the cell cycle of Corynebacterium glutamicum , an emerging cell biological model organism for mycolic acid-containing bacteria, including mycobacteria. Our data suggest that C. glutamicum carries two pole-attached chromosomes that replicate with overlapping C periods, thus initiating a new round of DNA replication before the previous one is terminated. The newly replicated origins segregate to midcell positions, where cell division occurs between the two new origins. Even after long starvation or under extremely slow-growth conditions, C. glutamicum cells are at least diploid, likely as an adaptation to environmental stress that may cause DNA damage. The cell cycle of C. glutamicum combines features of slow-growing organisms, such as polar origin localization, and fast-growing organisms, such as overlapping C periods. Copyright © 2017 Böhm et al.

Evaluative Priming in the Pronunciation Task.

PubMed

Klauer, Karl Christoph; Becker, Manuel; Spruyt, Adriaan

2016-01-01

We replicated and extended a study by Spruyt and Hermans (2008) in which picture primes engendered an evaluative-priming effect on the pronunciation of target words. As preliminary steps, we assessed data reproducibility of the original study, conducted Pilot Study I to identify highly semantically related prime-target pairs, reanalyzed the original data excluding such pairs, conducted Pilot Study II to demonstrate that we can replicate traditional associative priming effects in the pronunciation task, and conducted Pilot Study III to generate relatively unrelated sets of prime pictures and target words. The main study comprised three between-participants conditions: (1) a close replication of the original study, (2) the same condition excluding highly related prime-target pairs, and (3) a condition based on the relatively unrelated sets of prime pictures and target words developed in Pilot Study III. There was little evidence for an evaluative priming effect independent of semantic relatedness.

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

PubMed

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

2015-01-20

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

The Alleged Crisis and the Illusion of Exact Replication.

PubMed

Stroebe, Wolfgang; Strack, Fritz

2014-01-01

There has been increasing criticism of the way psychologists conduct and analyze studies. These critiques as well as failures to replicate several high-profile studies have been used as justification to proclaim a "replication crisis" in psychology. Psychologists are encouraged to conduct more "exact" replications of published studies to assess the reproducibility of psychological research. This article argues that the alleged "crisis of replicability" is primarily due to an epistemological misunderstanding that emphasizes the phenomenon instead of its underlying mechanisms. As a consequence, a replicated phenomenon may not serve as a rigorous test of a theoretical hypothesis because identical operationalizations of variables in studies conducted at different times and with different subject populations might test different theoretical constructs. Therefore, we propose that for meaningful replications, attempts at reinstating the original circumstances are not sufficient. Instead, replicators must ascertain that conditions are realized that reflect the theoretical variable(s) manipulated (and/or measured) in the original study. © The Author(s) 2013.

The Flavivirus Protease As a Target for Drug Discovery

PubMed Central

Brecher, Matthew; Zhang, Jing; Li, Hongmin

2014-01-01

Many flaviviruses are significant human pathogens causing considerable disease burdens, including encephalitis and hemorrhagic fever, in the regions in which they are endemic. A paucity of treatments for flaviviral infections has driven interest in drug development targeting proteins essential to flavivirus replication, such as the viral protease. During viral replication, the flavivirus genome is translated as a single polyprotein precursor, which must be cleaved into individual proteins by a complex of the viral protease, NS3, and its cofactor, NS2B. Because this cleavage is an obligate step of the viral life-cycle, the flavivirus protease is an attractive target for antiviral drug development. In this review, we will survey recent drug development studies targeting the NS3 active site, as well as studies targeting an NS2B/NS3 interaction site determined from flavivirus protease crystal structures. PMID:24242363

The flavivirus protease as a target for drug discovery.

PubMed

Brecher, Matthew; Zhang, Jing; Li, Hongmin

2013-12-01

Many flaviviruses are significant human pathogens causing considerable disease burdens, including encephalitis and hemorrhagic fever, in the regions in which they are endemic. A paucity of treatments for flaviviral infections has driven interest in drug development targeting proteins essential to flavivirus replication, such as the viral protease. During viral replication, the flavivirus genome is translated as a single polyprotein precursor, which must be cleaved into individual proteins by a complex of the viral protease, NS3, and its cofactor, NS2B. Because this cleavage is an obligate step of the viral life-cycle, the flavivirus protease is an attractive target for antiviral drug development. In this review, we will survey recent drug development studies targeting the NS3 active site, as well as studies targeting an NS2B/NS3 interaction site determined from flavivirus protease crystal structures.

Variation of HPV Subtypes with Focus on HPV-Infection and Cancer in the Head and Neck Region.

PubMed

Wichmann, Gunnar

The human papillomavirus (HPV) comprises a heterogeneous group of double-strand DNA viruses with variable potential to infect human epithelial cells and trigger neoplastic transformation. Its 8 kb genome encodes proteins required for virus replication and self-organized formation of infectious particles but also for early proteins E6 and E7 able to trigger neoplastic transformation. E6 and E7 of high-risk (HR) HPV subtypes can bind to p53 or release E2F and abrogate replication control. Due to variable amino acid sequence (AAS) in the binding sites of E6 and E7 particular HR-HPV variants within subtypes are essentially heterogeneous in efficacy triggering neoplastic transformation and cancer development. This could explain differences in the clinical course of HPV-driven head and neck cancer.

Impact of the Hayflick Limit on T cell responses to infection: lessons from aging and HIV disease.

PubMed

Effros, Rita B

2004-02-01

Aging and HIV disease show certain immunological similarities. In both situations, control over viral infection is diminished, and there is an increase in certain types of cancer. The immune cell type responsible for controlling viral infections and cancer is the so-called CD8 or cytotoxic T cell. In elderly persons and individuals chronically infected with HIV, there are high proportions of CD8 T cells that resemble cells that reach the end stage of replicative senescence in cell culture after repeated rounds of antigen-driven proliferation. Senescent cultures are characterized by irreversible cell cycle arrest, shortened telomeres, inability to upregulate telomerase, loss of CD28 expression, and apoptosis resistance. Strategies that retard replicative senescence may, therefore, provide novel approaches to enhancing immune function during aging and HIV disease.

Control of pore geometry in soil microcosms and its effect on the growth and spread of Pseudomonas and Bacillus sp.

NASA Astrophysics Data System (ADS)

Otten, Wilfred; Juyal, Archana; Eickhorst, Thilo; Falconer, Ruth; Spiers, Andrew; Baveye, Philippe

2017-04-01

The way micro-organisms access C and interact with each other in heterogeneous environments is key to our understanding of soil processes. Growth and mobility of bacteria is crucial aspect of these processes in particular how this is affected by complicated pathways of water and air-filled pores. Simplified experimental systems, often referred to with the term microcosms, have played a central role in the development of modern ecological thinking ranging from competitive exclusion to examination of spatial resources and competitive mechanisms, with important model driven insights to the field. However, in the majority of cases these do not include detailed description of the soil physical conditions and hence there is still little insight in how soil structure affects these processes. Recent advances in the use of Xray CT now allow for a different approach to this as we can obtain quantitative insight in to the pathways of interaction and how these are controlled in microcosms. In the current presentation we therefor ask the following questions: - To what extent can we control the pore geometry in microcosm studies through manipulation of common variables such as density and aggregate size? Are replicated microcosms really replicated at the microscale? - What is the effect of pore geometry on the growth dynamics of bacteria following introduction into soil? - What is the effect of pore geometry on the rate and extent of spread of bacteria in soil? We focus on Pseudomonas sp. and Bacillus sp. Both species are abundantly present in the rhizosphere and bulk-soil, frequently studied for their growth promoting ability, yet there is still very little knowledge available on how the growth and spread is affected by soil physical conditions such as pore geometry and wetness. We show how pore geometry, connectivity and interface areas are affected by the way soil is packed into microcosms and how this affects growth and spread of both species. We emphasize that microscopic heterogeneity has significant impact on bacterial dynamics and that soil physical conditions need to be considered in greater detail in microcosm studies to ensure generalisation of results.

The mammalian INO80 chromatin remodeling complex is required for replication stress recovery

PubMed Central

Vassileva, Ivelina; Yanakieva, Iskra; Peycheva, Michaela; Gospodinov, Anastas; Anachkova, Boyka

2014-01-01

A number of studies have implicated the yeast INO80 chromatin remodeling complex in DNA replication, but the function of the human INO80 complex during S phase remains poorly understood. Here, we have systematically investigated the involvement of the catalytic subunit of the human INO80 complex during unchallenged replication and under replication stress by following the effects of its depletion on cell survival, S-phase checkpoint activation, the fate of individual replication forks, and the consequences of fork collapse. We report that INO80 was specifically needed for efficient replication elongation, while it was not required for initiation of replication. In the absence of the Ino80 protein, cells became hypersensitive to hydroxyurea and displayed hyperactive ATR-Chk1 signaling. Using bulk and fiber labeling of DNA, we found that cells deficient for Ino80 and Arp8 had impaired replication restart after treatment with replication inhibitors and accumulated double-strand breaks as evidenced by the formation of γ-H2AX and Rad51 foci. These data indicate that under conditions of replication stress mammalian INO80 protects stalled forks from collapsing and allows their subsequent restart. PMID:25016522

Loss of maintenance DNA methylation results in abnormal DNA origin firing during DNA replication

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haruta, Mayumi; Shimada, Midori, E-mail: midorism@med.nagoya-cu.ac.jp; Nishiyama, Atsuya

The mammalian maintenance methyltransferase DNMT1 [DNA (cytosine-5-)-methyltransferase 1] mediates the inheritance of the DNA methylation pattern during replication. Previous studies have shown that depletion of DNMT1 causes a severe growth defect and apoptosis in differentiated cells. However, the detailed mechanisms behind this phenomenon remain poorly understood. Here we show that conditional ablation of Dnmt1 in murine embryonic fibroblasts (MEFs) resulted in an aberrant DNA replication program showing an accumulation of late-S phase replication and causing severely defective growth. Furthermore, we found that the catalytic activity and replication focus targeting sequence of DNMT1 are required for a proper DNA replication program.more » Taken together, our findings suggest that the maintenance of DNA methylation by DNMT1 plays a critical role in proper regulation of DNA replication in mammalian cells. - Highlights: • DNMT1 depletion results in an abnormal DNA replication program. • Aberrant DNA replication is independent of the DNA damage checkpoint in DNMT1cKO. • DNMT1 catalytic activity and RFT domain are required for proper DNA replication. • DNMT1 catalytic activity and RFT domain are required for cell proliferation.« less

Apigenin Restricts FMDV Infection and Inhibits Viral IRES Driven Translational Activity

PubMed Central

Qian, Suhong; Fan, Wenchun; Qian, Ping; Zhang, Dong; Wei, Yurong; Chen, Huanchun; Li, Xiangmin

2015-01-01

Foot-and-mouth disease (FMD) is a highly contagious disease of domestic and wild ruminants that is caused by FMD virus (FMDV). FMD outbreaks have occurred in livestock-containing regions worldwide. Apigenin, which is a flavonoid naturally existing in plant, possesses various pharmacological effects, including anti-inflammatory, anticancer, antioxidant and antiviral activities. Results show that apigenin can inhibit FMDV-mediated cytopathogenic effect and FMDV replication in vitro. Further studies demonstrate the following: (i) apigenin inhibits FMDV infection at the viral post-entry stage; (ii) apigenin does not exhibit direct extracellular virucidal activity; and (iii) apigenin interferes with the translational activity of FMDV driven by internal ribosome entry site. Studies on applying apigein in vivo are required for drug development and further identification of potential drug targets against FDMV infection. PMID:25835532

Apigenin restricts FMDV infection and inhibits viral IRES driven translational activity.

PubMed

Qian, Suhong; Fan, Wenchun; Qian, Ping; Zhang, Dong; Wei, Yurong; Chen, Huanchun; Li, Xiangmin

2015-03-31

Foot-and-mouth disease (FMD) is a highly contagious disease of domestic and wild ruminants that is caused by FMD virus (FMDV). FMD outbreaks have occurred in livestock-containing regions worldwide. Apigenin, which is a flavonoid naturally existing in plant, possesses various pharmacological effects, including anti-inflammatory, anticancer, antioxidant and antiviral activities. Results show that apigenin can inhibit FMDV-mediated cytopathogenic effect and FMDV replication in vitro. Further studies demonstrate the following: (i) apigenin inhibits FMDV infection at the viral post-entry stage; (ii) apigenin does not exhibit direct extracellular virucidal activity; and (iii) apigenin interferes with the translational activity of FMDV driven by internal ribosome entry site. Studies on applying apigein in vivo are required for drug development and further identification of potential drug targets against FDMV infection.

A comparison of methods for teaching receptive labeling to children with autism spectrum disorders: a systematic replication.

PubMed

Grow, Laura L; Kodak, Tiffany; Carr, James E

2014-01-01

Previous research has demonstrated that the conditional-only method (starting with a multiple-stimulus array) is more efficient than the simple-conditional method (progressive incorporation of more stimuli into the array) for teaching receptive labeling to children with autism spectrum disorders (Grow, Carr, Kodak, Jostad, & Kisamore,). The current study systematically replicated the earlier study by comparing the 2 approaches using progressive prompting with 2 boys with autism. The results showed that the conditional-only method was a more efficient and reliable teaching procedure than the simple-conditional method. The results further call into question the practice of teaching simple discriminations to facilitate acquisition of conditional discriminations. © Society for the Experimental Analysis of Behavior.

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

PubMed

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

2005-05-01

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

Comparing Visible and Invisible Social Support: Non-evaluative Support Buffers Cardiovascular Responses to Stress.

PubMed

Kirsch, Julie A; Lehman, Barbara J

2015-12-01

Previous research suggests that in contrast to invisible social support, visible social support produces exaggerated negative emotional responses. Drawing on work by Bolger and colleagues, this study disentangled social support visibility from negative social evaluation in an examination of the effects of social support on negative emotions and cardiovascular responses. As part of an anticipatory speech task, 73 female participants were randomly assigned to receive no social support, invisible social support, non-confounded visible social support or visible social support as delivered in a 2007 study by Bolger and Amarel. Twelve readings, each for systolic blood pressure, diastolic blood pressure and heart rate were taken at 5-min intervals throughout the periods of baseline, reactivity and recovery. Cardiovascular outcomes were tested by incorporating a series of theoretically driven planned contrasts into tests of stress reactivity conducted through piecewise growth curve modelling. Linear and quadratic trends established cardiovascular reactivity to the task. Further, in comparison to the control and replication conditions, the non-confounded visible and invisible social support conditions attenuated cardiovascular reactivity over time. Pre- and post-speech negative emotional responses were not affected by the social support manipulations. These results suggest that appropriately delivered visible social support may be as beneficial as invisible social support. Copyright © 2014 John Wiley & Sons, Ltd.

Effect of exposure to petroleum hydrocarbons upon cardio-respiratory function in the common sole (Solea solea).

PubMed

Claireaux, Guy; Davoodi, Fariba

2010-06-10

The long term consequences of oil exposure upon marine populations are still poorly evaluated. One particular missing piece of information relates to the link between oil exposure, individuals' ability to face environmental contingencies and populations' production and dynamics. In that context, the present paper investigates the impact of oil exposure upon fish cardio-respiratory performance, this performance being viewed as a key determinant of individual fitness. Experimental conditions replicated the contamination conditions observed during the weeks that immediately followed the Erika oil spill (west coast of France; December 1999). Sole (Solea solea), were exposed to number-2 oil for 5 days and were then challenged with an acute rise in temperature (from 15 to 30 degrees C at 1.5 degrees Ch(-1)). Oxygen consumption, cardiac output, heart rate and stroke volume were monitored throughout. Experimental results showed that compared to uncontaminated control animals, oil-exposed sole displayed impaired cardio-respiratory responses and were unable to meet the temperature-driven increase in tissues oxygen demand. The relationship between oxygen consumption and cardiac output indicated that oil-exposed fish had recourse to venous oxygen stores very early in the thermal challenge (20 degrees C). In control fish there was no evidence for depletion of venous oxygen store until above 25 degrees C.

Replicative age induces mitotic recombination in the ribosomal RNA gene cluster of Saccharomyces cerevisiae.

PubMed

Lindstrom, Derek L; Leverich, Christina K; Henderson, Kiersten A; Gottschling, Daniel E

2011-03-01

Somatic mutations contribute to the development of age-associated disease. In earlier work, we found that, at high frequency, aging Saccharomyces cerevisiae diploid cells produce daughters without mitochondrial DNA, leading to loss of respiration competence and increased loss of heterozygosity (LOH) in the nuclear genome. Here we used the recently developed Mother Enrichment Program to ask whether aging cells that maintain the ability to produce respiration-competent daughters also experience increased genomic instability. We discovered that this population exhibits a distinct genomic instability phenotype that primarily affects the repeated ribosomal RNA gene array (rDNA array). As diploid cells passed their median replicative life span, recombination rates between rDNA arrays on homologous chromosomes progressively increased, resulting in mutational events that generated LOH at >300 contiguous open reading frames on the right arm of chromosome XII. We show that, while these recombination events were dependent on the replication fork block protein Fob1, the aging process that underlies this phenotype is Fob1-independent. Furthermore, we provide evidence that this aging process is not driven by mechanisms that modulate rDNA recombination in young cells, including loss of cohesion within the rDNA array or loss of Sir2 function. Instead, we suggest that the age-associated increase in rDNA recombination is a response to increasing DNA replication stress generated in aging cells.

Novel Chromosome Organization Pattern in Actinomycetales—Overlapping Replication Cycles Combined with Diploidy

PubMed Central

Böhm, Kati; Meyer, Fabian; Rhomberg, Agata; Kalinowski, Jörn; Donovan, Catriona

2017-01-01

ABSTRACT Bacteria regulate chromosome replication and segregation tightly with cell division to ensure faithful segregation of DNA to daughter generations. The underlying mechanisms have been addressed in several model species. It became apparent that bacteria have evolved quite different strategies to regulate DNA segregation and chromosomal organization. We have investigated here how the actinobacterium Corynebacterium glutamicum organizes chromosome segregation and DNA replication. Unexpectedly, we found that C. glutamicum cells are at least diploid under all of the conditions tested and that these organisms have overlapping C periods during replication, with both origins initiating replication simultaneously. On the basis of experimental data, we propose growth rate-dependent cell cycle models for C. glutamicum. PMID:28588128

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

PubMed

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.

Registered Replication Report: Dijksterhuis and van Knippenberg (1998).

PubMed

O'Donnell, Michael; Nelson, Leif D; Ackermann, Evi; Aczel, Balazs; Akhtar, Athfah; Aldrovandi, Silvio; Alshaif, Nasseem; Andringa, Ronald; Aveyard, Mark; Babincak, Peter; Balatekin, Nursena; Baldwin, Scott A; Banik, Gabriel; Baskin, Ernest; Bell, Raoul; Białobrzeska, Olga; Birt, Angie R; Boot, Walter R; Braithwaite, Scott R; Briggs, Jessie C; Buchner, Axel; Budd, Desiree; Budzik, Kathryn; Bullens, Lottie; Bulley, Richard L; Cannon, Peter R; Cantarero, Katarzyna; Cesario, Joseph; Chambers, Stephanie; Chartier, Christopher R; Chekroun, Peggy; Chong, Clara; Cleeremans, Axel; Coary, Sean P; Coulthard, Jacob; Cramwinckel, Florien M; Denson, Thomas F; Díaz-Lago, Marcos; DiDonato, Theresa E; Drummond, Aaron; Eberlen, Julia; Ebersbach, Titus; Edlund, John E; Finnigan, Katherine M; Fisher, Justin; Frankowska, Natalia; García-Sánchez, Efraín; Golom, Frank D; Graves, Andrew J; Greenberg, Kevin; Hanioti, Mando; Hansen, Heather A; Harder, Jenna A; Harrell, Erin R; Hartanto, Andree; Inzlicht, Michael; Johnson, David J; Karpinski, Andrew; Keller, Victor N; Klein, Olivier; Koppel, Lina; Krahmer, Emiel; Lantian, Anthony; Larson, Michael J; Légal, Jean-Baptiste; Lucas, Richard E; Lynott, Dermot; Magaldino, Corey M; Massar, Karlijn; McBee, Matthew T; McLatchie, Neil; Melia, Nadhilla; Mensink, Michael C; Mieth, Laura; Moore-Berg, Samantha; Neeser, Geraldine; Newell, Ben R; Noordewier, Marret K; Ali Özdoğru, Asil; Pantazi, Myrto; Parzuchowski, Michał; Peters, Kim; Philipp, Michael C; Pollmann, Monique M H; Rentzelas, Panagiotis; Rodríguez-Bailón, Rosa; Philipp Röer, Jan; Ropovik, Ivan; Roque, Nelson A; Rueda, Carolina; Rutjens, Bastiaan T; Sackett, Katey; Salamon, Janos; Sánchez-Rodríguez, Ángel; Saunders, Blair; Schaafsma, Juliette; Schulte-Mecklenbeck, Michael; Shanks, David R; Sherman, Martin F; Steele, Kenneth M; Steffens, Niklas K; Sun, Jessie; Susa, Kyle J; Szaszi, Barnabas; Szollosi, Aba; Tamayo, Ricardo M; Tinghög, Gustav; Tong, Yuk-Yue; Tweten, Carol; Vadillo, Miguel A; Valcarcel, Deisy; Van der Linden, Nicolas; van Elk, Michiel; van Harreveld, Frenk; Västfjäll, Daniel; Vazire, Simine; Verduyn, Philippe; Williams, Matt N; Willis, Guillermo B; Wood, Sarah E; Yang, Chunliang; Zerhouni, Oulmann; Zheng, Robert; Zrubka, Mark

2018-03-01

Dijksterhuis and van Knippenberg (1998) reported that participants primed with a category associated with intelligence ("professor") subsequently performed 13% better on a trivia test than participants primed with a category associated with a lack of intelligence ("soccer hooligans"). In two unpublished replications of this study designed to verify the appropriate testing procedures, Dijksterhuis, van Knippenberg, and Holland observed a smaller difference between conditions (2%-3%) as well as a gender difference: Men showed the effect (9.3% and 7.6%), but women did not (0.3% and -0.3%). The procedure used in those replications served as the basis for this multilab Registered Replication Report. A total of 40 laboratories collected data for this project, and 23 of these laboratories met all inclusion criteria. Here we report the meta-analytic results for those 23 direct replications (total N = 4,493), which tested whether performance on a 30-item general-knowledge trivia task differed between these two priming conditions (results of supplementary analyses of the data from all 40 labs, N = 6,454, are also reported). We observed no overall difference in trivia performance between participants primed with the "professor" category and those primed with the "hooligan" category (0.14%) and no moderation by gender.

Dataset of red light induced pupil constriction superimposed on post-illumination pupil response.

PubMed

Lei, Shaobo; Goltz, Herbert C; Sklar, Jaime C; Wong, Agnes M F

2016-09-01

We collected and analyzed pupil diameter data from of 7 visually normal participants to compare the maximum pupil constriction (MPC) induced by "Red Only" vs. "Blue+Red" visual stimulation conditions. The "Red Only" condition consisted of red light (640±10 nm) stimuli of variable intensity and duration presented to dark-adapted eyes with pupils at resting state. This condition stimulates the cone-driven activity of the intrinsically photosensitive retinal ganglion cells (ipRGC). The "Blue+Red" condition consisted of the same red light stimulus presented during ongoing blue (470±17 nm) light-induced post-illumination pupil response (PIPR), representing the cone-driven ipRGC activity superimposed on the melanopsin-driven intrinsic activity of the ipRGCs ("The Absence of Attenuating Effect of Red light Exposure on Pre-existing Melanopsin-Driven Post-illumination Pupil Response" Lei et al. (2016) [1]). MPC induced by the "Red Only" condition was compared with the MPC induced by the "Blue+Red" condition by multiple paired sample t -tests with Bonferroni correction.

Resistance of Adenoviral DNA Replication to Aphidicolin Is Dependent on the 72-Kilodalton DNA-Binding Protein

PubMed Central

Foster, David A.; Hantzopoulos, Petros; Zubay, Geoffrey

1982-01-01

Aphidicolin is a highly specific inhibitor of DNA polymerase α and has been most useful for assessing the role of this enzyme in various replication processes (J. A. Huberman, Cell 23:647-648, 1981). Both nuclear DNA replication and simian virus 40 DNA replication are highly sensitive to this drug (Krokan et al., Biochemistry 18:4431-4443, 1979), whereas mitochondrial DNA synthesis is completely insensitive (Zimmerman et al., J. Biol. Chem. 255:11847-11852, 1980). Adenovirus DNA replication is sensitive to aphidicolin, but only at much higher concentrations. These patterns of sensitivity are seen both in vivo and in vitro (Krokan et al., Biochemistry 18:4431-4443, 1979). A temperature-sensitive mutant of adenovirus type 5 known as H5ts125 is able to complete but not initiate new rounds of replication at nonpermissive temperatures (P. C. van der Vliet and J. S. Sussenbach, Virology 67:415-426, 1975). When cells infected with H5ts125 were shifted from permissive (33°C) to nonpermissive (41°C) conditions, the residual DNA synthesis (elongation) showed a striking increase in sensitivity to aphidicolin. The temperature-sensitive mutation of H5ts125 is in the gene for the 72-kilodalton single-stranded DNA-binding protein. This demonstrated that the increased resistance to aphidicolin shown by adenovirus DNA replication was dependent on that protein. It also supports an elongation role for both DNA polymerase α and the 72-kilodalton single-stranded DNA-binding protein in adenovirus DNA replication. Further support for an elongation role of DNA polymerase α came from experiments with permissive temperature conditions and inhibiting levels of aphidicolin in which it was shown that newly initiated strands failed to elongate to completion. Images PMID:6809958

Mu-driven transposition of recombinant mini-Mu unit DNA in the Corynebacterium glutamicum chromosome.

PubMed

Gorshkova, Natalya V; Lobanova, Juliya S; Tokmakova, Irina L; Smirnov, Sergey V; Akhverdyan, Valerii Z; Krylov, Alexander A; Mashko, Sergey V

2018-03-01

A dual-component Mu-transposition system was modified for the integration/amplification of genes in Corynebacterium. The system consists of two types of plasmids: (i) a non-replicative integrative plasmid that contains the transposing mini-Mu(LR) unit bracketed by the L/R Mu ends or the mini-Mu(LER) unit, which additionally contains the enhancer element, E, and (ii) an integration helper plasmid that expresses the transposition factor genes for MuA and MuB. Efficient transposition in the C. glutamicum chromosome (≈ 2 × 10 -4 per cell) occurred mainly through the replicative pathway via cointegrate formation followed by possible resolution. Optimizing the E location in the mini-Mu unit significantly increased the efficiency of Mu-driven intramolecular transposition-amplification in C. glutamicum as well as in gram-negative bacteria. The new C. glutamicum genome modification strategy that was developed allows the consequent independent integration/amplification/fixation of target genes at high copy numbers. After integration/amplification of the first mini-Mu(LER) unit in the C. glutamicum chromosome, the E-element, which is bracketed by lox-like sites, is excised by Cre-mediated fashion, thereby fixing the truncated mini-Mu(LR) unit in its position for the subsequent integration/amplification of new mini-Mu(LER) units. This strategy was demonstrated using the genes for the citrine and green fluorescent proteins, yECitrine and yEGFP, respectively.

Actin dynamics affect mitochondrial quality control and aging in budding yeast.

PubMed

Higuchi, Ryo; Vevea, Jason D; Swayne, Theresa C; Chojnowski, Robert; Hill, Vanessa; Boldogh, Istvan R; Pon, Liza A

2013-12-02

Actin cables of budding yeast are bundles of F-actin that extend from the bud tip or neck to the mother cell tip, serve as tracks for bidirectional cargo transport, and undergo continuous movement from buds toward mother cells [1]. This movement, retrograde actin cable flow (RACF), is similar to retrograde actin flow in lamellipodia, growth cones, immunological synapses, dendritic spines, and filopodia [2-5]. In all cases, actin flow is driven by the push of actin polymerization and assembly at the cell cortex, and myosin-driven pulling forces deeper within the cell [6-10]. Therefore, for movement and inheritance from mothers to buds, mitochondria must "swim upstream" against the opposing force of RACF [11]. We find that increasing RACF rates results in increased fitness of mitochondria inherited by buds and that the increase in mitochondrial fitness leads to extended replicative lifespan and increased cellular healthspan. The sirtuin SIR2 is required for normal RACF and mitochondrial fitness, and increasing RACF rates in sir2Δ cells increases mitochondrial fitness and cellular healthspan but does not affect replicative lifespan. These studies support the model that RACF serves as a filter for segregation of fit from less-fit mitochondria during inheritance, which controls cellular lifespan and healthspan. They also support a role for Sir2p in these processes. Copyright © 2013 Elsevier Ltd. All rights reserved.

CEO summit. The new delivery & financing realities. Part III of III.

PubMed

Becker, B F; Cramer, H; Easley, D; Nathanson, P; Neeson, R; Raney, J; Samuelson, C; Ummel, S

1994-08-20

In cooperation with McManis Associates Inc., Washington, Hospitals & Health Networks recently convened a summit on the integration of financing and delivery in health care. This installment is the third of a three-part series on lessons learned by those on the front lines of integration activity. The session was designed and facilitated by senior associates at McManis. Among the issues summit participants discussed in the second segment: What level of understanding do purchasers have of the factors that differentiate quality in health care services? Can provider-driven integrated delivery systems compete with insurer-driven ones? And what happens when a large integrated delivery system merges with a dominant insurer, as happened in the Philadelphia market? Can that model be successfully replicated in other markets? In this final segment, participants talk about whether providers' deep connections to their communities will add value in a reformed delivery system; how incentives might be aligned among all the players in integrated networks and organizations; how the concept of community focus might be redefined under systems integration; and the process involved in preparing for constant, accelerated change. The second segment concluded with comments about the assets providers and insurers bring to integrated health systems, and whether the merger experience of Graduate Health System and QCC/Independence Blue Cross could be replicated in other markets or not.

Novel electric power-driven hydrodynamic injection system for gene delivery: safety and efficacy of human factor IX delivery in rats.

PubMed

Yokoo, T; Kamimura, K; Suda, T; Kanefuji, T; Oda, M; Zhang, G; Liu, D; Aoyagi, Y

2013-08-01

The development of a safe and reproducible gene delivery system is an essential step toward the clinical application of the hydrodynamic gene delivery (HGD) method. For this purpose, we have developed a novel electric power-driven injection system called the HydroJector-EM, which can replicate various time-pressure curves preloaded into the computer program before injection. The assessment of the reproducibility and safety of gene delivery system in vitro and in vivo demonstrated the precise replication of intravascular time-pressure curves and the reproducibility of gene delivery efficiency. The highest level of luciferase expression (272 pg luciferase per mg of proteins) was achieved safely using the time-pressure curve, which reaches 30 mm Hg in 10 s among various curves tested. Using this curve, the sustained expression of a therapeutic level of human factor IX protein (>500 ng ml(-1)) was maintained for 2 months after the HGD of the pBS-HCRHP-FIXIA plasmid. Other than a transient increase in liver enzymes that recovered in a few days, no adverse events were seen in rats. These results confirm the effectiveness of the HydroJector-EM for reproducible gene delivery and demonstrate that long-term therapeutic gene expression can be achieved by automatic computer-controlled hydrodynamic injection that can be performed by anyone.

Preneoplastic lesion growth driven by the death of adjacent normal stem cells

PubMed Central

Chao, Dennis L.; Eck, J. Thomas; Brash, Douglas E.; Maley, Carlo C.; Luebeck, E. Georg

2008-01-01

Clonal expansion of premalignant lesions is an important step in the progression to cancer. This process is commonly considered to be a consequence of sustaining a proliferative mutation. Here, we investigate whether the growth trajectory of clones can be better described by a model in which clone growth does not depend on a proliferative advantage. We developed a simple computer model of clonal expansion in an epithelium in which mutant clones can only colonize space left unoccupied by the death of adjacent normal stem cells. In this model, competition for space occurs along the frontier between mutant and normal territories, and both the shapes and the growth rates of lesions are governed by the differences between mutant and normal cells' replication or apoptosis rates. The behavior of this model of clonal expansion along a mutant clone's frontier, when apoptosis of both normal and mutant cells is included, matches the growth of UVB-induced p53-mutant clones in mouse dorsal epidermis better than a standard exponential growth model that does not include tissue architecture. The model predicts precancer cell mutation and death rates that agree with biological observations. These results support the hypothesis that clonal expansion of premalignant lesions can be driven by agents, such as ionizing or nonionizing radiation, that cause cell killing but do not directly stimulate cell replication. PMID:18815380

Rotating Arc Jet Test Model: Time-Accurate Trajectory Heat Flux Replication in a Ground Test Environment

NASA Technical Reports Server (NTRS)

Laub, Bernard; Grinstead, Jay; Dyakonov, Artem; Venkatapathy, Ethiraj

2011-01-01

Though arc jet testing has been the proven method employed for development testing and certification of TPS and TPS instrumentation, the operational aspects of arc jets limit testing to selected, but constant, conditions. Flight, on the other hand, produces timevarying entry conditions in which the heat flux increases, peaks, and recedes as a vehicle descends through an atmosphere. As a result, we are unable to "test as we fly." Attempts to replicate the time-dependent aerothermal environment of atmospheric entry by varying the arc jet facility operating conditions during a test have proven to be difficult, expensive, and only partially successful. A promising alternative is to rotate the test model exposed to a constant-condition arc jet flow to yield a time-varying test condition at a point on a test article (Fig. 1). The model shape and rotation rate can be engineered so that the heat flux at a point on the model replicates the predicted profile for a particular point on a flight vehicle. This simple concept will enable, for example, calibration of the TPS sensors on the Mars Science Laboratory (MSL) aeroshell for anticipated flight environments.

Bed Load Variability and Morphology of Gravel Bed Rivers Subject to Unsteady Flow: A Laboratory Investigation

NASA Astrophysics Data System (ADS)

Redolfi, M.; Bertoldi, W.; Tubino, M.; Welber, M.

2018-02-01

Measurement and estimation of bed load transport in gravel bed rivers are highly affected by its temporal fluctuations. Such variability is primarily driven by the flow regime but is also associated with a variety of inherent channel processes, such as flow turbulence, grain entrainment, and bed forms migration. These internal and external controls often act at comparable time scales, and are therefore difficult to disentangle, thus hindering the study of bed load variability under unsteady flow regime. In this paper, we report on laboratory experiments performed in a large, mobile bed flume where typical hydromorphological conditions of gravel bed rivers were reproduced. Data from a large number of replicated runs, including triangular and square-wave hydrographs, were used to build a statistically sound description of sediment transport processes. We found that the inherent variability of bed load flux strongly depends on the sampling interval, and it is significantly higher in complex, wandering or braided channels. This variability can be filtered out by computing the mean response over the experimental replicates, which allows us to highlight two distinctive phenomena: (i) an overshooting (undershooting) response of the mean bed load flux to a sudden increase (decrease) of discharge, and (ii) a clockwise hysteresis in the sediment rating curve. We then provide an interpretation of these findings through a conceptual mathematical model, showing how both phenomena are associated with a lagging morphological adaptation to unsteady flow. Overall, this work provides basic information for evaluating, monitoring, and managing gravel transport in morphologically active rivers.

The influence of data-driven versus conceptually-driven processing on the development of PTSD-like symptoms.

PubMed

Kindt, Merel; van den Hout, Marcel; Arntz, Arnoud; Drost, Jolijn

2008-12-01

Ehlers and Clark [(2000). A cognitive model of posttraumatic stress disorder. Behaviour Research and Therapy, 38, 319-345] propose that a predominance of data-driven processing during the trauma predicts subsequent PTSD. We wondered whether, apart from data-driven encoding, sustained data-driven processing after the trauma is also crucial for the development of PTSD. Both hypotheses were tested in two analogue experiments. Experiment 1 demonstrated that relative to conceptually-driven processing (n=20), data-driven processing after the film (n=14), resulted in more intrusions. Experiment 2 demonstrated that relative to the neutral condition (n=24) and the data-driven encoding condition (n=24), conceptual encoding (n=25) reduced suppression of intrusions and a trend emerged for memory fragmentation. The difference between the two encoding styles was due to the beneficial effect of induced conceptual encoding and not to the detrimental effect of data-driven encoding. The data support the viability of the distinction between data-driven/conceptually-driven processing for the understanding of the development of PTSD.

Contingency and statistical laws in replicate microbial closed ecosystems.

PubMed

Hekstra, Doeke R; Leibler, Stanislas

2012-05-25

Contingency, the persistent influence of past random events, pervades biology. To what extent, then, is each course of ecological or evolutionary dynamics unique, and to what extent are these dynamics subject to a common statistical structure? Addressing this question requires replicate measurements to search for emergent statistical laws. We establish a readily replicated microbial closed ecosystem (CES), sustaining its three species for years. We precisely measure the local population density of each species in many CES replicates, started from the same initial conditions and kept under constant light and temperature. The covariation among replicates of the three species densities acquires a stable structure, which could be decomposed into discrete eigenvectors, or "ecomodes." The largest ecomode dominates population density fluctuations around the replicate-average dynamics. These fluctuations follow simple power laws consistent with a geometric random walk. Thus, variability in ecological dynamics can be studied with CES replicates and described by simple statistical laws. Copyright © 2012 Elsevier Inc. All rights reserved.

Reflections on "Replicating Milgram" (Burger, 2009)

ERIC Educational Resources Information Center

Miller, Arthur G.

2009-01-01

In "Replicating Milgram: Would People Still Obey Today?" Jerry M. Burger (see record 2008-19206-001) reported a high base rate of obedience, comparable to that observed by Stanley Milgram (1974). Another condition, involving a defiant confederate, failed to significantly reduce obedience. This commentary discusses the primary contributions of…

Sustainability of a Compartmentalized Host-Parasite Replicator System under Periodic Washout-Mixing Cycles

PubMed Central

Furubayashi, Taro

2018-01-01

The emergence and dominance of parasitic replicators are among the major hurdles for the proliferation of primitive replicators. Compartmentalization of replicators is proposed to relieve the parasite dominance; however, it remains unclear under what conditions simple compartmentalization uncoupled with internal reaction secures the long-term survival of a population of primitive replicators against incessant parasite emergence. Here, we investigate the sustainability of a compartmentalized host-parasite replicator (CHPR) system undergoing periodic washout-mixing cycles, by constructing a mathematical model and performing extensive simulations. We describe sustainable landscapes of the CHPR system in the parameter space and elucidate the mechanism of phase transitions between sustainable and extinct regions. Our findings revealed that a large population size of compartments, a high mixing intensity, and a modest amount of nutrients are important factors for the robust survival of replicators. We also found two distinctive sustainable phases with different mixing intensities. These results suggest that a population of simple host–parasite replicators assumed before the origin of life can be sustained by a simple compartmentalization with periodic washout-mixing processes. PMID:29373536

Prereplicative events involving simian virus 40 DNA in permissive cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rinaldy, A.; Feunteun, J.; Rosenberg, B.H.

1982-01-01

Simian virus 40 DNA molecules were found to be unable to replicate for 9 h after infection, even in cells that were already replicating the DNA of preinfecting simian virus 40; after 9 h, the ability of the DNA to replicate began to rise sharply. The kinetics of activation indicated that each DNA molecule undergoes a series of slow consecutive reactions, not involving T-antigen, before it can replicate. These pre-replicative molecular transformations probably involve configurational changes; their nature and their relation to the initiation of viral DNA synthesis is discussed. Observation of the replicative behavior of one viral DNA inmore » the presence of another was made possible by the use of two different mutants with distinguishable DNAs: a viable deletion mutant containing DNA insensitive to TaqI restriction enzyme was used to provide viral functions required for replication, and is a tsA mutant with TaqI-sensitive DNA was introduced at various times as a probe to determine the ability of the DNA to replicate under different conditions.« less

Centromeric DNA replication reconstitution reveals DNA loops and ATR checkpoint suppression

PubMed Central

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

2016-01-01

Half of human genome is made 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 (BACs) in Xenopus laevis egg extract. Using this approach we characterized 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 among which 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 inability of 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 on our understanding of repetitive DNA metabolism and centromere organization under normal and stressful conditions. PMID:27111843

Host-parasite oscillation dynamics and evolution in a compartmentalized RNA replication system.

PubMed

Bansho, Yohsuke; Furubayashi, Taro; Ichihashi, Norikazu; Yomo, Tetsuya

2016-04-12

To date, various cellular functions have been reconstituted in vitro such as self-replication systems using DNA, RNA, and proteins. The next important challenges include the reconstitution of the interactive networks of self-replicating species and investigating how such interactions generate complex ecological behaviors observed in nature. Here, we synthesized a simple replication system composed of two self-replicating host and parasitic RNA species. We found that the parasitic RNA eradicates the host RNA under bulk conditions; however, when the system is compartmentalized, a continuous oscillation pattern in the population dynamics of the two RNAs emerges. The oscillation pattern changed as replication proceeded mainly owing to the evolution of the host RNA. These results demonstrate that a cell-like compartment plays an important role in host-parasite ecological dynamics and suggest that the origin of the host-parasite coevolution might date back to the very early stages of the evolution of life.

Aggregate and individual replication probability within an explicit model of the research process.

PubMed

Miller, Jeff; Schwarz, Wolf

2011-09-01

We study a model of the research process in which the true effect size, the replication jitter due to changes in experimental procedure, and the statistical error of effect size measurement are all normally distributed random variables. Within this model, we analyze the probability of successfully replicating an initial experimental result by obtaining either a statistically significant result in the same direction or any effect in that direction. We analyze both the probability of successfully replicating a particular experimental effect (i.e., the individual replication probability) and the average probability of successful replication across different studies within some research context (i.e., the aggregate replication probability), and we identify the conditions under which the latter can be approximated using the formulas of Killeen (2005a, 2007). We show how both of these probabilities depend on parameters of the research context that would rarely be known in practice. In addition, we show that the statistical uncertainty associated with the size of an initial observed effect would often prevent accurate estimation of the desired individual replication probability even if these research context parameters were known exactly. We conclude that accurate estimates of replication probability are generally unattainable.

Replication of DNA containing apurinic sites in human and mouse cells probed with parvoviruses MVM and H-1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vos, J.M.; Rommelaere, J.

We studied the effect of apurinic sites on DNA replication in mouse and human cells, using parvoviruses MVM (minute virus of mice) and H-1 as probes. Although apurinic sites are efficient blocks to the replication of these single-stranded DNA viruses in vivo, depurinated parvoviruses can be reactivated if host cells have been preexposed to a subtoxic dose of UV light. The target of this conditional reactivation process is the conversion of depurinated input DNA into double-stranded replicative forms; the concomitant increase in viral mutagenesis strongly suggests that apurinic sites can be bypassed in mammalian cells.

Phosphorylated STAT5 directly facilitates parvovirus B19 DNA replication in human erythroid progenitors through interaction with the MCM complex.

PubMed

Ganaie, Safder S; Zou, Wei; Xu, Peng; Deng, Xuefeng; Kleiboeker, Steve; Qiu, Jianming

2017-05-01

Productive infection of human parvovirus B19 (B19V) exhibits high tropism for burst forming unit erythroid (BFU-E) and colony forming unit erythroid (CFU-E) progenitor cells in human bone marrow and fetal liver. This exclusive restriction of the virus replication to human erythroid progenitor cells is partly due to the intracellular factors that are essential for viral DNA replication, including erythropoietin signaling. Efficient B19V replication also requires hypoxic conditions, which upregulate the signal transducer and activator of transcription 5 (STAT5) pathway, and phosphorylated STAT5 is essential for virus replication. In this study, our results revealed direct involvement of STAT5 in B19V DNA replication. Consensus STAT5-binding elements were identified adjacent to the NS1-binding element within the minimal origins of viral DNA replication in the B19V genome. Phosphorylated STAT5 specifically interacted with viral DNA replication origins both in vivo and in vitro, and was actively recruited within the viral DNA replication centers. Notably, STAT5 interacted with minichromosome maintenance (MCM) complex, suggesting that STAT5 directly facilitates viral DNA replication by recruiting the helicase complex of the cellular DNA replication machinery to viral DNA replication centers. The FDA-approved drug pimozide dephosphorylates STAT5, and it inhibited B19V replication in ex vivo expanded human erythroid progenitors. Our results demonstrated that pimozide could be a promising antiviral drug for treatment of B19V-related diseases.

Formal design and verification of a reliable computing platform for real-time control. Phase 1: Results

NASA Technical Reports Server (NTRS)

Divito, Ben L.; Butler, Ricky W.; Caldwell, James L.

1990-01-01

A high-level design is presented for a reliable computing platform for real-time control applications. Design tradeoffs and analyses related to the development of the fault-tolerant computing platform are discussed. The architecture is formalized and shown to satisfy a key correctness property. The reliable computing platform uses replicated processors and majority voting to achieve fault tolerance. Under the assumption of a majority of processors working in each frame, it is shown that the replicated system computes the same results as a single processor system not subject to failures. Sufficient conditions are obtained to establish that the replicated system recovers from transient faults within a bounded amount of time. Three different voting schemes are examined and proved to satisfy the bounded recovery time conditions.

Metaresearch for Evaluating Reproducibility in Ecology and Evolution.

PubMed

Fidler, Fiona; Chee, Yung En; Wintle, Bonnie C; Burgman, Mark A; McCarthy, Michael A; Gordon, Ascelin

2017-03-01

Recent replication projects in other disciplines have uncovered disturbingly low levels of reproducibility, suggesting that those research literatures may contain unverifiable claims. The conditions contributing to irreproducibility in other disciplines are also present in ecology. These include a large discrepancy between the proportion of "positive" or "significant" results and the average statistical power of empirical research, incomplete reporting of sampling stopping rules and results, journal policies that discourage replication studies, and a prevailing publish-or-perish research culture that encourages questionable research practices. We argue that these conditions constitute sufficient reason to systematically evaluate the reproducibility of the evidence base in ecology and evolution. In some cases, the direct replication of ecological research is difficult because of strong temporal and spatial dependencies, so here, we propose metaresearch projects that will provide proxy measures of reproducibility.

When can the cause of a population decline be determined?

PubMed

Hefley, Trevor J; Hooten, Mevin B; Drake, John M; Russell, Robin E; Walsh, Daniel P

2016-11-01

Inferring the factors responsible for declines in abundance is a prerequisite to preventing the extinction of wild populations. Many of the policies and programmes intended to prevent extinctions operate on the assumption that the factors driving the decline of a population can be determined. Exogenous factors that cause declines in abundance can be statistically confounded with endogenous factors such as density dependence. To demonstrate the potential for confounding, we used an experiment where replicated populations were driven to extinction by gradually manipulating habitat quality. In many of the replicated populations, habitat quality and density dependence were confounded, which obscured causal inference. Our results show that confounding is likely to occur when the exogenous factors that are driving the decline change gradually over time. Our study has direct implications for wild populations, because many factors that could drive a population to extinction change gradually through time. © 2016 John Wiley & Sons Ltd/CNRS.

When can the cause of a population decline be determined?

USGS Publications Warehouse

Hefley, Trevor J.; Hooten, Mevin B.; Drake, John M.; Russell, Robin E.; Walsh, Daniel P.

2016-01-01

Inferring the factors responsible for declines in abundance is a prerequisite to preventing the extinction of wild populations. Many of the policies and programmes intended to prevent extinctions operate on the assumption that the factors driving the decline of a population can be determined. Exogenous factors that cause declines in abundance can be statistically confounded with endogenous factors such as density dependence. To demonstrate the potential for confounding, we used an experiment where replicated populations were driven to extinction by gradually manipulating habitat quality. In many of the replicated populations, habitat quality and density dependence were confounded, which obscured causal inference. Our results show that confounding is likely to occur when the exogenous factors that are driving the decline change gradually over time. Our study has direct implications for wild populations, because many factors that could drive a population to extinction change gradually through time.

Across-Task Conflict Regulation: A Replication Failure

ERIC Educational Resources Information Center

Runger, Dennis; Schwager, Sabine; Frensch, Peter A.

2010-01-01

Fernandez-Duque and Knight (2008, Experiment 4) described an across-task effect of endogenously generated, anticipatory control: A cue that predicted conflict in an upcoming Eriksen flanker task modulated conflict regulation in a subsequent number Stroop task. In 3 experiments, 1 of which included an exact replication condition, we failed to…

Identification of a high-efficiency baculovirus DNA replication origin that functions in insect and mammalian cells.

PubMed

Wu, Yueh-Lung; Wu, Carol-P; Huang, Yu-Hui; Huang, Sheng-Ping; Lo, Huei-Ru; Chang, Hao-Shuo; Lin, Pi-Hsiu; Wu, Ming-Cheng; Chang, Chia-Jung; Chao, Yu-Chan

2014-11-01

The p143 gene from Autographa californica multinucleocapsid nucleopolyhedrovirus (AcMNPV) has been found to increase the expression of luciferase, which is driven by the polyhedrin gene promoter, in a plasmid with virus coinfection. Further study indicated that this is due to the presence of a replication origin (ori) in the coding region of this gene. Transient DNA replication assays showed that a specific fragment of the p143 coding sequence, p143-3, underwent virus-dependent DNA replication in Spodoptera frugiperda IPLB-Sf-21 (Sf-21) cells. Deletion analysis of the p143-3 fragment showed that subfragment p143-3.2a contained the essential sequence of this putative ori. Sequence analysis of this region revealed a unique distribution of imperfect palindromes with high AT contents. No sequence homology or similarity between p143-3.2a and any other known ori was detected, suggesting that it is a novel baculovirus ori. Further study showed that the p143-3.2a ori can replicate more efficiently in infected Sf-21 cells than baculovirus homologous regions (hrs), the major baculovirus ori, or non-hr oris during virus replication. Previously, hr on its own was unable to replicate in mammalian cells, and for mammalian viral oris, viral proteins are generally required for their proper replication in host cells. However, the p143-3.2a ori was, surprisingly, found to function as an efficient ori in mammalian cells without the need for any viral proteins. We conclude that p143 contains a unique sequence that can function as an ori to enhance gene expression in not only insect cells but also mammalian cells. Baculovirus DNA replication relies on both hr and non-hr oris; however, so far very little is known about the latter oris. Here we have identified a new non-hr ori, the p143 ori, which resides in the coding region of p143. By developing a novel DNA replication-enhanced reporter system, we have identified and located the core region required for the p143 ori. This ori contains a large number of imperfect inverted repeats and is the most active ori in the viral genome during virus infection in insect cells. We also found that it is a unique ori that can replicate in mammalian cells without the assistance of baculovirus gene products. The identification of this ori should contribute to a better understanding of baculovirus DNA replication. Also, this ori is very useful in assisting with gene expression in mammalian cells. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Necessary conditions for the emergence of homochirality via autocatalytic self-replication

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stich, Michael; Ribó, Josep M.; Blackmond, Donna G., E-mail: blackmond@scripps.edu

We analyze a recent proposal for spontaneous mirror symmetry breaking based on the coupling of first-order enantioselective autocatalysis and direct production of the enantiomers that invokes a critical role for intrinsic reaction noise. For isolated systems, the racemic state is the unique stable outcome for both stochastic and deterministic dynamics when the system is in compliance with the constraints dictated by the thermodynamics of chemical reaction processes. In open systems, the racemic outcome also results for both stochastic and deterministic dynamics when driving the autocatalysis unidirectionally by external reagents. Nonracemic states can result in the latter only if the reversemore » reactions are strictly zero: these are kinetically controlled outcomes for small populations and volumes, and can be simulated by stochastic dynamics. However, the stability of the thermodynamic limit proves that the racemic outcome is the unique stable state for strictly irreversible externally driven autocatalysis. These findings contradict the suggestion that the inhibition requirement of the Frank autocatalytic model for the emergence of homochirality may be relaxed in a noise-induced mechanism.« less

ISABEL Triggering Sustainable Biogas Energy Communities through Social Innovation

NASA Astrophysics Data System (ADS)

Baumgarten, Wibke; Piedra Garcia, Diego

2017-04-01

The Horizon 2020 funding project ISABEL (Triggering Sustainable Biogas Energy Communities through Social Innovation) is all about promoting, supporting and developing community biogas in Europe. The project is set on providing all the framework conditions for biogas communities to shape, develop and thrive. It works on all angles to pave the way for the transition from traditional supply chains to community ownership and take full advantage of the ample societal benefits of regional community-driven biogas systems, fuelled and inspired by Social Innovation principles. The biogas communities emerge in three targeted ISABEL regions, Baden-Württemberg in Germany, Central and Eastern Macedonia and Thrace in Greece and Yorkshire, Lincolnshire and the Humber in UK. To realize this vision ISABEL is employing its "5E strategy" with the following objectives: Educate: Re-position biogas energy by re-branding it as a "public good". Engage: Enable the development of regional Biogas Communities. Empower: Utilize the created momentum through Social Innovation and Public Participation Evaluate: Assess the local interventions and drafting lessons and guidelines Expand: Maximise impact through transfer and replication

Modelling the dynamics of scarlet fever epidemics in the 19th century.

PubMed

Duncan, S R; Scott, S; Duncan, C J

2000-01-01

Annual deaths from scarlet fever in Liverpool, UK during 1848-1900 have been used as a model system for studying the historical dynamics of the epidemics. Mathematical models are developed which include the growth of the population and the death rate from scarlet fever. Time-series analysis of the results shows that there were two distinct phases to the disease (i) 1848-1880: regular epidemics (wavelength = 3.7 years) consistent with the system being driven by an oscillation in the transmission coefficient (deltabeta) at its resonant frequency, probably associated with dry conditions in winter (ii) 1880-1900: an undriven SEIR system with a falling endemic level and decaying epidemics. This period was associated with improved nutritive levels. There is also evidence from time-series analysis that raised wheat prices in pregnancy caused increased susceptibility in the subsequent children. The pattern of epidemics and the demographic characteristics of the population can be replicated in the modelling which provides insights into the detailed epidemiology of scarlet fever in this community in the 19th century.

Timing of host feeding drives rhythms in parasite replication

PubMed Central

Cumnock, Katherine; Schneider, David; Subudhi, Amit; Savill, Nicholas J.

2018-01-01

Circadian rhythms enable organisms to synchronise the processes underpinning survival and reproduction to anticipate daily changes in the external environment. Recent work shows that daily (circadian) rhythms also enable parasites to maximise fitness in the context of ecological interactions with their hosts. Because parasite rhythms matter for their fitness, understanding how they are regulated could lead to innovative ways to reduce the severity and spread of diseases. Here, we examine how host circadian rhythms influence rhythms in the asexual replication of malaria parasites. Asexual replication is responsible for the severity of malaria and fuels transmission of the disease, yet, how parasite rhythms are driven remains a mystery. We perturbed feeding rhythms of hosts by 12 hours (i.e. diurnal feeding in nocturnal mice) to desynchronise the host’s peripheral oscillators from the central, light-entrained oscillator in the brain and their rhythmic outputs. We demonstrate that the rhythms of rodent malaria parasites in day-fed hosts become inverted relative to the rhythms of parasites in night-fed hosts. Our results reveal that the host’s peripheral rhythms (associated with the timing of feeding and metabolism), but not rhythms driven by the central, light-entrained circadian oscillator in the brain, determine the timing (phase) of parasite rhythms. Further investigation reveals that parasite rhythms correlate closely with blood glucose rhythms. In addition, we show that parasite rhythms resynchronise to the altered host feeding rhythms when food availability is shifted, which is not mediated through rhythms in the host immune system. Our observations suggest that parasites actively control their developmental rhythms. Finally, counter to expectation, the severity of disease symptoms expressed by hosts was not affected by desynchronisation of their central and peripheral rhythms. Our study at the intersection of disease ecology and chronobiology opens up a new arena for studying host-parasite-vector coevolution and has broad implications for applied bioscience. PMID:29481559

An efficient, reliable and inexpensive device for the rapid homogenization of multiple tissue samples by centrifugation.

PubMed

Ilyin, S E; Plata-Salamán, C R

2000-02-15

Homogenization of tissue samples is a common first step in the majority of current protocols for RNA, DNA, and protein isolation. This report describes a simple device for centrifugation-mediated homogenization of tissue samples. The method presented is applicable to RNA, DNA, and protein isolation, and we show examples where high quality total cell RNA, DNA, and protein were obtained from brain and other tissue samples. The advantages of the approach presented include: (1) a significant reduction in time investment relative to hand-driven or individual motorized-driven pestle homogenization; (2) easy construction of the device from inexpensive parts available in any laboratory; (3) high replicability in the processing; and (4) the capacity for the parallel processing of multiple tissue samples, thus allowing higher efficiency, reliability, and standardization.

Effects of a randomized gratitude intervention on death-related fear of recurrence in breast cancer survivors.

PubMed

Otto, Amy K; Szczesny, Elana C; Soriano, Emily C; Laurenceau, Jean-Philippe; Siegel, Scott D

2016-12-01

Among the most prevalent and distressing concerns endorsed by breast cancer survivors is fear of cancer recurrence (FOR), and one of the most salient facets is the worry that a recurrence of cancer could cause one's death. The primary goal of the present study was to test the effects of a brief, low-cost gratitude intervention on overall FOR and death-related FOR, positing pursuit of meaningful goals as a theoretically driven putative mediator. To replicate published tests of similar gratitude-eliciting interventions, positive affect (PA) was also considered as an outcome. Sixty-seven women with early stage breast cancer were randomly assigned to either a 6-week online gratitude intervention or a 6-week online control condition. Outcomes were assessed at pre- and posttreatment, as well as 1 month and 3 months after the end of treatment. The mediator, meaningful goal pursuit, was measured via assessments over the 6-week intervention period. Results revealed that patients in the gratitude intervention experienced a significant decrease in death-related FOR compared to the control condition. Moreover, this effect was significantly mediated by meaningful goal pursuit (and not by PA). The gratitude intervention was also found to prevent declines in PA observed in the control condition. Overall, findings support the notion that a brief gratitude intervention can promote well-being and psychological adaptation to cancer by stimulating the pursuit of meaningful goals and subsequently reducing death-related FOR. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

New perspectives on adolescent motivated behavior: attention and conditioning

PubMed Central

Ernst, Monique; Daniele, Teresa; Frantz, Kyle

2011-01-01

Adolescence is a critical transition period, during which fundamental changes prepare the adolescent for becoming an adult. Heuristic models of the neurobiology of adolescent behavior have emerged, promoting the central role of reward and motivation, coupled with cognitive immaturities. Here, we bring focus to two basic sets of processes, attention and conditioning, which are essential for adaptive behavior. Using the dual-attention model developed by Corbetta and Shulman (2002), which identifies a stimulus-driven and a goal-driven attention network, we propose a balance that favors stimulus-driven attention over goal-driven attention in youth. Regarding conditioning, we hypothesize that stronger associations tend to be made between environmental cues and appetitive stimuli, and weaker associations with aversive stimuli, in youth relative to adults. An attention system geared to prioritize stimulus-driven attention, together with more powerful associative learning with appetitive incentives, contribute to shape patterns of adolescent motivated behavior. This proposed bias in attention and conditioning function could facilitate the impulsive, novelty-seeking and risk-taking behavior that is typical of many adolescents. PMID:21977221

General Relativistic Effects on Neutrino-driven Winds from Young, Hot Neutron Stars and r-Process Nucleosynthesis

NASA Astrophysics Data System (ADS)

Otsuki, Kaori; Tagoshi, Hideyuki; Kajino, Toshitaka; Wanajo, Shin-ya

2000-04-01

Neutrino-driven winds from young hot neutron stars, which are formed by supernova explosions, are the most promising candidate site for r-process nucleosynthesis. We study general relativistic effects on this wind in Schwarzschild geometry in order to look for suitable conditions for successful r-process nucleosynthesis. It is quantitatively demonstrated that general relativistic effects play a significant role in increasing the entropy and decreasing the dynamic timescale of the neutrino-driven wind. Exploring the wide parameter region that determines the expansion dynamics of the wind, we find interesting physical conditions that lead to successful r-process nucleosynthesis. The conditions that we found are realized in a neutrino-driven wind with a very short dynamic timescale, τdyn~6 ms, and a relatively low entropy, S~140. We carry out α-process and r-process nucleosynthesis calculations on these conditions with our single network code, which includes over 3000 isotopes, and confirm quantitatively that the second and third r-process abundance peaks are produced in neutrino-driven winds.

Convergence of service, policy, and science toward consumer-driven mental health care.

PubMed

Carroll, Christopher D; Manderscheid, Ronald W; Daniels, Allen S; Compagni, Amelia

2006-12-01

A common theme is emerging in sentinel reports on the United States health care system. Consumer relevance and demands on service systems and practices are influencing how mental health care is delivered and how systems will be shaped in the future. The present report seeks to assemble a confluence of consumer-driven themes from noteworthy reports on the state of the mental health system in the U.S. It also explores innovative efforts, promising practices, collaborative efforts, as well as identification of barriers to consumer-directed care, with possible solutions. The report reviews the relevant public mental health policy and data used in published work. The findings indicate an increasing public and private interest in promoting consumer-driven care, even though historical systems of care predominate, and often create, barriers to wide-spread redesign of a consumer-centered mental health care system. Innovative consumer-driven practices are increasing as quality, choice, and self-determination become integral parts of a redesigned U.S. mental health care system. The use of consumer-driven approaches in mental health is limited at best. These programs challenge industry norms and traditional practices. Limitations include the need for additional and thorough evaluations of effectiveness (cost and clinical) and replicability of consumer-directed programs. Consumer-driven services indicate that mental health consumers are expecting to be more participative in their mental health care. This expectation will influence how traditional mental health services and providers become more consumer-centric and meet the demand. Public and private interest in consumer-driven health care range from creating cost-conscious consumers to individualized control of recovery. The health care sector should seek to invest more resources in the provision of consumer-driven health care programs. The results of this study have implications and are informative for other countries where consumer-directed care is delivered in either the private or public health care systems. More research is needed to obtain further evidence on the use of consumer-driven services and their overall effectiveness.

Three-dimensional architecture of tick-borne encephalitis virus replication sites and trafficking of the replicated RNA.

PubMed

Miorin, Lisa; Romero-Brey, Inés; Maiuri, Paolo; Hoppe, Simone; Krijnse-Locker, Jacomine; Bartenschlager, Ralf; Marcello, Alessandro

2013-06-01

Flavivirus replication is accompanied by the rearrangement of cellular membranes that may facilitate viral genome replication and protect viral components from host cell responses. The topological organization of viral replication sites and the fate of replicated viral RNA are not fully understood. We exploited electron microscopy to map the organization of tick-borne encephalitis virus (TBEV) replication compartments in infected cells and in cells transfected with a replicon. Under both conditions, 80-nm vesicles were seen within the lumen of the endoplasmic reticulum (ER) that in infected cells also contained virions. By electron tomography, the vesicles appeared as invaginations of the ER membrane, displaying a pore that could enable release of newly synthesized viral RNA into the cytoplasm. To track the fate of TBEV RNA, we took advantage of our recently developed method of viral RNA fluorescent tagging for live-cell imaging combined with bleaching techniques. TBEV RNA was found outside virus-induced vesicles either associated to ER membranes or free to move within a defined area of juxtaposed ER cisternae. From our results, we propose a biologically relevant model of the possible topological organization of flavivirus replication compartments composed of replication vesicles and a confined extravesicular space where replicated viral RNA is retained. Hence, TBEV modifies the ER membrane architecture to provide a protected environment for viral replication and for the maintenance of newly replicated RNA available for subsequent steps of the virus life cycle.

Diminished medial prefrontal cortex activation during the recollection of stressful events is an acquired characteristic of PTSD.

PubMed

Dahlgren, M K; Laifer, L M; VanElzakker, M B; Offringa, R; Hughes, K C; Staples-Bradley, L K; Dubois, S J; Lasko, N B; Hinojosa, C A; Orr, S P; Pitman, R K; Shin, L M

2018-05-01

Previous research has shown relatively diminished medial prefrontal cortex activation and heightened psychophysiological responses during the recollection of personal events in post-traumatic stress disorder (PTSD), but the origin of these abnormalities is unknown. Twin studies provide the opportunity to determine whether such abnormalities reflect familial vulnerabilities, result from trauma exposure, or are acquired characteristics of PTSD. In this case-control twin study, 26 male identical twin pairs (12 PTSD; 14 non-PTSD) discordant for PTSD and combat exposure recalled and imagined trauma-unrelated stressful and neutral life events using a standard script-driven imagery paradigm during functional magnetic resonance imaging and concurrent skin conductance measurement. Diminished activation in the medial prefrontal cortex during Stressful v. Neutral script-driven imagery was observed in the individuals with PTSD, relative to other groups. Diminished medial prefrontal cortex activation during Stressful v. Neutral script-driven imagery may be an acquired characteristic of PTSD. If replicated, this finding could be used prospectively to inform diagnosis and the assessment of treatment response.

The `Henry Problem' of `density-driven' groundwater flow versus Tothian `groundwater flow systems' with variable density: A review of the influential Biscayne aquifer data.

NASA Astrophysics Data System (ADS)

Weyer, K. U.

2017-12-01

Coastal groundwater flow investigations at the Biscayne Bay, south of Miami, Florida, gave rise to the concept of density-driven flow of seawater into coastal aquifers creating a saltwater wedge. Within that wedge, convection-driven return flow of seawater and a dispersion zone were assumed by Cooper et al. (1964) to be the cause of the Biscayne aquifer `sea water wedge'. This conclusion was based on the chloride distribution within the aquifer and on an analytical model concept assuming convection flow within a confined aquifer without taking non-chemical field data into consideration. This concept was later labelled the `Henry Problem', which any numerical variable density flow program must be able to simulate to be considered acceptable. Both, `density-driven flow' and Tothian `groundwater flow systems' (with or without variable density conditions) are driven by gravitation. The difference between the two are the boundary conditions. 'Density-driven flow' occurs under hydrostatic boundary conditions while Tothian `groundwater flow systems' occur under hydrodynamic boundary conditions. Revisiting the Cooper et al. (1964) publication with its record of piezometric field data (heads) showed that the so-called sea water wedge has been caused by discharging deep saline groundwater driven by gravitational flow and not by denser sea water. Density driven flow of seawater into the aquifer was not found reflected in the head measurements for low and high tide conditions which had been taken contemporaneously with the chloride measurements. These head measurements had not been included in the flow interpretation. The very same head measurements indicated a clear dividing line between shallow local fresh groundwater flow and saline deep groundwater flow without the existence of a dispersion zone or a convection cell. The Biscayne situation emphasizes the need for any chemical interpretation of flow pattern to be supported by head data as energy indicators of flow fields. At the Biscayne site density-driven flow of seawater did and does not exist. Instead this site and the Florida coast line in general are the end points of local fresh and regional saline groundwater flow systems driven by gravity forces and not by density differences.

A person-centred segmentation study in elderly care: towards efficient demand-driven care.

PubMed

Eissens van der Laan, M R; van Offenbeek, M A G; Broekhuis, H; Slaets, J P J

2014-07-01

Providing patients with more person-centred care without increasing costs is a key challenge in healthcare. A relevant but often ignored hindrance to delivering person-centred care is that the current segmentation of the population and the associated organization of healthcare supply are based on diseases. A person-centred segmentation, i.e., based on persons' own experienced difficulties in fulfilling needs, is an elementary but often overlooked first step in developing efficient demand-driven care. This paper describes a person-centred segmentation study of elderly, a large and increasing target group confronted with heterogeneous and often interrelated difficulties in their functioning. In twenty-five diverse healthcare and welfare organizations as well as elderly associations in the Netherlands, data were collected on the difficulties in biopsychosocial functioning experienced by 2019 older adults. Data were collected between March 2010 and January 2011 and sampling took place based on their (temporarily) living conditions. Factor Mixture Model was conducted to categorize the respondents into segments with relatively similar experienced difficulties concerning their functioning. First, the analyses show that older adults can be empirically categorized into five meaningful segments: feeling vital; difficulties with psychosocial coping; physical and mobility complaints; difficulties experienced in multiple domains; and feeling extremely frail. The categorization seems robust as it was replicated in two population-based samples in the Netherlands. The segmentation's usefulness is discussed and illustrated through an evaluation of the alignment between a segment's unfulfilled biopsychosocial needs and current healthcare utilization. The set of person-centred segmentation variables provides healthcare providers the option to perform a more comprehensive first triage step than only a disease-based one. The outcomes of this first step could guide a focused and, therefore, more efficient second triage step. On a local or regional level, this person-centred segmentation provides input information to policymakers and care providers for the demand-driven allocation of resources. Copyright © 2014 Elsevier Ltd. All rights reserved.

Classical conditioning of sexual response in women: a replication study.

PubMed

Both, Stephanie; Brauer, Marieke; Laan, Ellen

2011-11-01

According to incentive motivation models, sexual stimuli play a crucial role in eliciting sexual arousal, desire, and behavior. Therefore, it seems highly valuable to investigate the process through which stimuli acquire motivational value. Although many theories of human sexual behavior assume that sexual stimuli obtain arousing properties through classical conditioning, systematic research on classical conditioning of sexual responses in humans is scarce. Recently, however, our research group observed conditioned genital responses in women using a differential conditioning procedure and genital vibrostimulation as unconditional stimulus (US). The aim of the present experiment was to perform an extended replication of this previous study to test the efficacy of our conditioning paradigm. A differential conditioning experiment was conducted in 32 sexually functional women. Neutral pictures served as conditional stimuli (CSs) and genital vibrostimulation as US. Only one CS (the CS+) was followed by the US during the acquisition phase. Conditioned responses were assessed during the extinction phase. Vaginal pulse amplitude (VPA) and skin conductance level were assessed, and ratings of affective value and sexual arousal were obtained. As expected, during the extinction phase, VPA was higher in response to the CS+ than to the CS-. Also, the CS+ tended to be evaluated as more positive and as more sexually arousing than the CS-. In addition, the magnitude of conditioned subjective affect was related to scores on the Sexual Inhibition\\Sexual Excitation Scales. Skin conductance levels showed no conditioning effect. Genital and subjective sexual responses were successfully modulated by the differential conditioning paradigm. This replication of our previous study confirms the effectiveness of our conditioning procedure and indicates that it may provide a fruitful paradigm for further research on associative sexual reward learning in humans. © 2011 International Society for Sexual Medicine.

CHK1-targeted therapy to deplete DNA replication-stressed, p53-deficient, hyperdiploid colorectal cancer stem cells

PubMed Central

Russo, Giorgio; Corradi, Francesca; Siteni, Silvia; Musella, Martina; Vitale, Sara; De Angelis, Maria Laura; Pallocca, Matteo; Amoreo, Carla Azzurra; Sperati, Francesca; Di Franco, Simone; Barresi, Sabina; Policicchio, Eleonora; De Luca, Gabriele; De Nicola, Francesca; Mottolese, Marcella; Zeuner, Ann; Fanciulli, Maurizio; Stassi, Giorgio; Maugeri-Saccà, Marcello; Baiocchi, Marta; Tartaglia, Marco

2018-01-01

Objective Cancer stem cells (CSCs) are responsible for tumour formation and spreading, and their targeting is required for tumour eradication. There are limited therapeutic options for advanced colorectal cancer (CRC), particularly for tumours carrying RAS-activating mutations. The aim of this study was to identify novel CSC-targeting strategies. Design To discover potential therapeutics to be clinically investigated as single agent, we performed a screening with a panel of FDA-approved or investigational drugs on primary CRC cells enriched for CSCs (CRC-SCs) isolated from 27 patients. Candidate predictive biomarkers of efficacy were identified by integrating genomic, reverse-phase protein microarray (RPPA) and cytogenetic analyses, and validated by immunostainings. DNA replication stress (RS) was increased by employing DNA replication-perturbing or polyploidising agents. Results The drug-library screening led to the identification of LY2606368 as a potent anti-CSC agent acting in vitro and in vivo in tumour cells from a considerable number of patients (∼36%). By inhibiting checkpoint kinase (CHK)1, LY2606368 affected DNA replication in most CRC-SCs, including RAS-mutated ones, forcing them into premature, lethal mitoses. Parallel genomic, RPPA and cytogenetic analyses indicated that CRC-SCs sensitive to LY2606368 displayed signs of ongoing RS response, including the phosphorylation of RPA32 and ataxia telangiectasia mutated serine/threonine kinase (ATM). This was associated with mutation(s) in TP53 and hyperdiploidy, and made these CRC-SCs exquisitely dependent on CHK1 function. Accordingly, experimental increase of RS sensitised resistant CRC-SCs to LY2606368. Conclusions LY2606368 selectively eliminates replication-stressed, p53-deficient and hyperdiploid CRC-SCs independently of RAS mutational status. These results provide a strong rationale for biomarker-driven clinical trials with LY2606368 in patients with CRC. PMID:28389531

Genome-wide mapping of nuclear mitochondrial DNA sequences links DNA replication origins to chromosomal double-strand break formation in Schizosaccharomyces pombe

PubMed Central

Lenglez, Sandrine; Hermand, Damien; Decottignies, Anabelle

2010-01-01

Chromosomal double-strand breaks (DSBs) threaten genome integrity and repair of these lesions is often mutagenic. How and where DSBs are formed is a major question conveniently addressed in simple model organisms like yeast. NUMTs, nuclear DNA sequences of mitochondrial origin, are present in most eukaryotic genomes and probably result from the capture of mitochondrial DNA (mtDNA) fragments into chromosomal breaks. NUMT formation is ongoing and was reported to cause de novo human genetic diseases. Study of NUMTs is likely to contribute to the understanding of naturally occurring chromosomal breaks. We show that Schizosaccharomyces pombe NUMTs are exclusively located in noncoding regions with no preference for gene promoters and, when located into promoters, do not affect gene transcription level. Strikingly, most noncoding regions comprising NUMTs are also associated with a DNA replication origin (ORI). Chromatin immunoprecipitation experiments revealed that chromosomal NUMTs are probably not acting as ORI on their own but that mtDNA insertions occurred directly next to ORIs, suggesting that these loci may be prone to DSB formation. Accordingly, induction of excessive DNA replication origin firing, a phenomenon often associated with human tumor formation, resulted in frequent nucleotide deletion events within ORI3001 subtelomeric chromosomal locus, illustrating a novel aspect of DNA replication-driven genomic instability. How mtDNA is fragmented is another important issue that we addressed by sequencing experimentally induced NUMTs. This highlighted regions of S. pombe mtDNA prone to breaking. Together with an analysis of human NUMTs, we propose that these fragile sites in mtDNA may correspond to replication pause sites. PMID:20688779

Explosively driven air blast in a conical shock tube

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stewart, Joel B., E-mail: joel.b.stewart2.civ@mail.mil; Pecora, Collin, E-mail: collin.r.pecora.civ@mail.mil

2015-03-15

Explosively driven shock tubes present challenges in terms of safety concerns and expensive upkeep of test facilities but provide more realistic approximations to the air blast resulting from free-field detonations than those provided by gas-driven shock tubes. Likewise, the geometry of conical shock tubes can naturally approximate a sector cut from a spherically symmetric blast, leading to a better agreement with the blast profiles of free-field detonations when compared to those provided by shock tubes employing constant cross sections. The work presented in this article documents the design, fabrication, and testing of an explosively driven conical shock tube whose goalmore » was to closely replicate the blast profile seen from a larger, free-field detonation. By constraining the blast through a finite area, large blasts (which can add significant damage and safety constraints) can be simulated using smaller explosive charges. The experimental data presented herein show that a close approximation to the free-field air blast profile due to a 1.5 lb charge of C4 at 76 in. can be achieved by using a 0.032 lb charge in a 76-in.-long conical shock tube (which translates to an amplification factor of nearly 50). Modeling and simulation tools were used extensively in designing this shock tube to minimize expensive fabrication costs.« less

Stable DNA replication: interplay between DNA replication, homologous recombination, and transcription.

PubMed

Kogoma, T

1997-06-01

Chromosome replication in Escherichia coli is normally initiated at oriC, the origin of chromosome replication. E. coli cells possess at least three additional initiation systems for chromosome replication that are normally repressed but can be activated under certain specific conditions. These are termed the stable DNA replication systems. Inducible stable DNA replication (iSDR), which is activated by SOS induction, is proposed to be initiated from a D-loop, an early intermediate in homologous recombination. Thus, iSDR is a form of recombination-dependent DNA replication (RDR). Analysis of iSDR and RDR has led to the proposal that homologous recombination and double-strand break repair involve extensive semiconservative DNA replication. RDR is proposed to play crucial roles in homologous recombination, double-strand break repair, restoration of collapsed replication forks, and adaptive mutation. Constitutive stable DNA replication (cSDR) is activated in mhA mutants deficient in RNase HI or in recG mutants deficient in RecG helicase. cSDR is proposed to be initiated from an R-loop that can be formed by the invasion of duplex DNA by an RNA transcript, which most probably is catalyzed by RecA protein. The third form of SDR is nSDR, which can be transiently activated in wild-type cells when rapidly growing cells enter the stationary phase. This article describes the characteristics of these alternative DNA replication forms and reviews evidence that has led to the formulation of the proposed models for SDR initiation mechanisms. The possible interplay between DNA replication, homologous recombination, DNA repair, and transcription is explored.

Phosphorylated STAT5 directly facilitates parvovirus B19 DNA replication in human erythroid progenitors through interaction with the MCM complex

PubMed Central

Ganaie, Safder S.; Zou, Wei; Xu, Peng; Deng, Xuefeng; Kleiboeker, Steve

2017-01-01

Productive infection of human parvovirus B19 (B19V) exhibits high tropism for burst forming unit erythroid (BFU-E) and colony forming unit erythroid (CFU-E) progenitor cells in human bone marrow and fetal liver. This exclusive restriction of the virus replication to human erythroid progenitor cells is partly due to the intracellular factors that are essential for viral DNA replication, including erythropoietin signaling. Efficient B19V replication also requires hypoxic conditions, which upregulate the signal transducer and activator of transcription 5 (STAT5) pathway, and phosphorylated STAT5 is essential for virus replication. In this study, our results revealed direct involvement of STAT5 in B19V DNA replication. Consensus STAT5-binding elements were identified adjacent to the NS1-binding element within the minimal origins of viral DNA replication in the B19V genome. Phosphorylated STAT5 specifically interacted with viral DNA replication origins both in vivo and in vitro, and was actively recruited within the viral DNA replication centers. Notably, STAT5 interacted with minichromosome maintenance (MCM) complex, suggesting that STAT5 directly facilitates viral DNA replication by recruiting the helicase complex of the cellular DNA replication machinery to viral DNA replication centers. The FDA-approved drug pimozide dephosphorylates STAT5, and it inhibited B19V replication in ex vivo expanded human erythroid progenitors. Our results demonstrated that pimozide could be a promising antiviral drug for treatment of B19V-related diseases. PMID:28459842

Reconciling NOx emissions reductions and ozone trends in the U.S., 2002–2006

EPA Science Inventory

Dynamic evaluation seeks to assess the ability of photochemical models to replicate changes in air quality as emissions and other conditions change. When a model fails to replicate an observed change, a key challenge is to discern whether the discrepancy is caused by errors in me...

Randomized Clinical Trial Replication of a Psychosocial Treatment for Children with High-Functioning Autism Spectrum Disorders

ERIC Educational Resources Information Center

Thomeer, Marcus L.; Lopata, Christopher; Volker, Martin A.; Toomey, Jennifer A.; Lee, Gloria K.; Smerbeck, Audrey M.; Rodgers, Jonathan D.; McDonald, Christin A.; Smith, Rachael A.

2012-01-01

This replication randomized clinical trial examined the efficacy of a comprehensive psychosocial intervention for children aged 7 to 12 years with high-functioning autism spectrum disorders (HFASDs). Participants were randomly assigned to treatment or wait-list conditions. Treatment included instruction and therapeutic activities targeting social…

C–C Chemokines Released by Lipopolysaccharide (LPS)-stimulated Human Macrophages Suppress HIV-1 Infection in Both Macrophages and T Cells

PubMed Central

Verani, Alessia; Scarlatti, Gabriella; Comar, Manola; Tresoldi, Eleonora; Polo, Simona; Giacca, Mauro; Lusso, Paolo; Siccardi, Antonio G.; Vercelli, Donata

1997-01-01

Human immunodeficiency virus-1 (HIV-1) expression in monocyte-derived macrophages (MDM) infected in vitro is known to be inhibited by lipopolysaccharide (LPS). However, the mechanisms are incompletely understood. We show here that HIV-1 suppression is mediated by soluble factors released by MDM stimulated with physiologically significant concentrations of LPS. LPS-conditioned supernatants from MDM inhibited HIV-1 replication in both MDM and T cells. Depletion of C–C chemokines (RANTES, MIP-1α, and MIP-1β) neutralized the ability of LPS-conditioned supernatants to inhibit HIV-1 replication in MDM. A combination of recombinant C–C chemokines blocked HIV-1 infection as effectively as LPS. Here, we report an inhibitory effect of C–C chemokines on HIV replication in primary macrophages. Our results raise the possibility that monocytes may play a dual role in HIV infection: while representing a reservoir for the virus, they may contribute to the containment of the infection by releasing factors that suppress HIV replication not only in monocytes but also in T lymphocytes. PMID:9120386

Metaresearch for Evaluating Reproducibility in Ecology and Evolution

PubMed Central

Fidler, Fiona; Chee, Yung En; Wintle, Bonnie C.; Burgman, Mark A.; McCarthy, Michael A.; Gordon, Ascelin

2017-01-01

Abstract Recent replication projects in other disciplines have uncovered disturbingly low levels of reproducibility, suggesting that those research literatures may contain unverifiable claims. The conditions contributing to irreproducibility in other disciplines are also present in ecology. These include a large discrepancy between the proportion of “positive” or “significant” results and the average statistical power of empirical research, incomplete reporting of sampling stopping rules and results, journal policies that discourage replication studies, and a prevailing publish-or-perish research culture that encourages questionable research practices. We argue that these conditions constitute sufficient reason to systematically evaluate the reproducibility of the evidence base in ecology and evolution. In some cases, the direct replication of ecological research is difficult because of strong temporal and spatial dependencies, so here, we propose metaresearch projects that will provide proxy measures of reproducibility. PMID:28596617

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

PubMed

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.

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

PubMed

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.

Epidermal regulation of dermal fibroblast activity.

PubMed

Garner, W L

1998-07-01

Although the association between delayed burn wound healing and subsequent hypertrophic scar formation is well-established, the mechanism for this relationship is unknown. Unhealed burn wounds lack an epidermis, suggesting a possible regulatory role for the epidermis in controlling dermal fibroblast matrix synthesis. Therefore, we examined the effect of epidermal cells and media conditioned by epidermal cells on fibroblast collagen synthesis and replication. Purified fibroblast and keratinocyte cell strains were developed from discarded normal adult human skin. Conditioned media were created by incubation of cytokine-free and serum-free medium with either confluent fibroblast or keratinocyte cultures for 18 hours (n = 3). Nearly confluent fibroblast cultures were exposed for 48 hours to graded concentrations of either unconditioned medium (control), conditioned medium, or varying numbers of keratinocytes. Replication was quantified by the incorporation of 3H-thymidine. Collagen synthesis was measured by the incorporation of 3H-proline into collagenase-sensitive protein. Data were compared using analysis of variance (ANOVA) and linear regression. Keratinocyte conditioned medium induced a significant increase in replication (n = 3) (p = 0.004) and a decrease in collagen synthesis (n = 6) (p < 0.001). In contrast, neither fibroblast conditioned medium nor control medium had an effect on fibroblast replication or collagen synthesis. Co-culture of fibroblast with a graded number of keratinocytes similarly decreased collagen synthesis (n = 6) (p < 0.001). Dermal fibroblast collagen synthesis appears to be regulated by a soluble keratinocyte product. This result suggests a mechanism for the clinical observation that unhealed burn wounds, which lack the epidermis, demonstrate excess collagen production and scar. Clinical strategies to decrease hypertrophic scar should include an attempt at early wound closure with skin grafting or the application of cultured epithelial autografts.

Replication Rate, Framing, and Format Affect Attitudes and Decisions about Science Claims.

PubMed

Barnes, Ralph M; Tobin, Stephanie J; Johnston, Heather M; MacKenzie, Noah; Taglang, Chelsea M

2016-01-01

A series of five experiments examined how the evaluation of a scientific finding was influenced by information about the number of studies that had successfully replicated the initial finding. The experiments also tested the impact of frame (negative, positive) and numeric format (percentage, natural frequency) on the evaluation of scientific findings. In Experiments 1 through 4, an attitude difference score served as the dependent measure, while a measure of choice served as the dependent measure in Experiment 5. Results from a diverse sample of 188 non-institutionalized U.S. adults (Experiment 2) and 730 undergraduate college students (Experiments 1, 3, and 4) indicated that attitudes became more positive as the replication rate increased and attitudes were more positive when the replication information was framed positively. The results also indicate that the manner in which replication rate was framed had a greater impact on attitude than the replication rate itself. The large effect for frame was attenuated somewhat when information about replication was presented in the form of natural frequencies rather than percentages. A fifth study employing 662 undergraduate college students in a task in which choice served as the dependent measure confirmed the framing effect and replicated the replication rate effect in the positive frame condition, but provided no evidence that the use of natural frequencies diminished the effect.

Structural rearrangements in the mitochondrial genome of Drosophila melanogaster induced by elevated levels of the replicative DNA helicase

PubMed Central

Ciesielski, Grzegorz L; Nadalutti, Cristina A; Oliveira, Marcos T; Griffith, Jack D; Kaguni, Laurie S

2018-01-01

Abstract Pathological conditions impairing functions of mitochondria often lead to compensatory upregulation of the mitochondrial DNA (mtDNA) replisome machinery, and the replicative DNA helicase appears to be a key factor in regulating mtDNA copy number. Moreover, mtDNA helicase mutations have been associated with structural rearrangements of the mitochondrial genome. To evaluate the effects of elevated levels of the mtDNA helicase on the integrity and replication of the mitochondrial genome, we overexpressed the helicase in Drosophila melanogaster Schneider cells and analyzed the mtDNA by two-dimensional neutral agarose gel electrophoresis and electron microscopy. We found that elevation of mtDNA helicase levels increases the quantity of replication intermediates and alleviates pausing at the replication slow zones. Though we did not observe a concomitant alteration in mtDNA copy number, we observed deletions specific to the segment of repeated elements in the immediate vicinity of the origin of replication, and an accumulation of species characteristic of replication fork stalling. We also found elevated levels of RNA that are retained in the replication intermediates. Together, our results suggest that upregulation of mtDNA helicase promotes the process of mtDNA replication but also results in genome destabilization. PMID:29432582

Pathways for maintenance of telomeres and common fragile sites during DNA replication stress

PubMed Central

Özer, Özgün

2018-01-01

Oncogene activation during tumour development leads to changes in the DNA replication programme that enhance DNA replication stress. Certain regions of the human genome, such as common fragile sites and telomeres, are particularly sensitive to DNA replication stress due to their inherently ‘difficult-to-replicate’ nature. Indeed, it appears that these regions sometimes fail to complete DNA replication within the period of interphase when cells are exposed to DNA replication stress. Under these conditions, cells use a salvage pathway, termed ‘mitotic DNA repair synthesis (MiDAS)’, to complete DNA synthesis in the early stages of mitosis. If MiDAS fails, the ensuing mitotic errors threaten genome integrity and cell viability. Recent studies have provided an insight into how MiDAS helps cells to counteract DNA replication stress. However, our understanding of the molecular mechanisms and regulation of MiDAS remain poorly defined. Here, we provide an overview of how DNA replication stress triggers MiDAS, with an emphasis on how common fragile sites and telomeres are maintained. Furthermore, we discuss how a better understanding of MiDAS might reveal novel strategies to target cancer cells that maintain viability in the face of chronic oncogene-induced DNA replication stress. PMID:29695617

Concerted activities of Mcm4, Sld3, and Dbf4 in control of origin activation and DNA replication fork progression

PubMed Central

Sheu, Yi-Jun; Kinney, Justin B.; Stillman, Bruce

2016-01-01

Eukaryotic chromosomes initiate DNA synthesis from multiple replication origins in a temporally specific manner during S phase. The replicative helicase Mcm2-7 functions in both initiation and fork progression and thus is an important target of regulation. Mcm4, a helicase subunit, possesses an unstructured regulatory domain that mediates control from multiple kinase signaling pathways, including the Dbf4-dependent Cdc7 kinase (DDK). Following replication stress in S phase, Dbf4 and Sld3, an initiation factor and essential target of Cyclin-Dependent Kinase (CDK), are targets of the checkpoint kinase Rad53 for inhibition of initiation from origins that have yet to be activated, so-called late origins. Here, whole-genome DNA replication profile analysis is used to access under various conditions the effect of mutations that alter the Mcm4 regulatory domain and the Rad53 targets, Sld3 and Dbf4. Late origin firing occurs under genotoxic stress when the controls on Mcm4, Sld3, and Dbf4 are simultaneously eliminated. The regulatory domain of Mcm4 plays an important role in the timing of late origin firing, both in an unperturbed S phase and in dNTP limitation. Furthermore, checkpoint control of Sld3 impacts fork progression under replication stress. This effect is parallel to the role of the Mcm4 regulatory domain in monitoring fork progression. Hypomorph mutations in sld3 are suppressed by a mcm4 regulatory domain mutation. Thus, in response to cellular conditions, the functions executed by Sld3, Dbf4, and the regulatory domain of Mcm4 intersect to control origin firing and replication fork progression, thereby ensuring genome stability. PMID:26733669

Replication of urban innovations - prioritization of strategies for the replication of Dhaka's community-based decentralized composting model.

PubMed

Yedla, Sudhakar

2012-01-01

Dhaka's community-based decentralized composting (DCDC) is a successful demonstration of solid waste management by adopting low-cost technology, local resources community participation and partnerships among the various actors involved. This paper attempts to understand the model, necessary conditions, strategies and their priorities to replicate DCDC in the other developing cities of Asia. Thirteen strategies required for its replication are identified and assessed based on various criteria, namely transferability, longevity, economic viability, adaptation and also overall replication. Priority setting by multi-criteria analysis by applying analytic hierarchy process revealed that immediate transferability without long-term and economic viability consideration is not advisable as this would result in unsustainable replication of DCDC. Based on the analysis, measures to ensure the product quality control; partnership among stakeholders (public-private-community); strategies to achieve better involvement of the private sector in solid waste management (entrepreneurship in approach); simple and low-cost technology; and strategies to provide an effective interface among the complementing sectors are identified as important strategies for its replication.

Role of replication protein A as sensor in activation of the S-phase checkpoint in Xenopus egg extracts

PubMed Central

Recolin, Bénédicte; Van Der Laan, Siem; Maiorano, Domenico

2012-01-01

Uncoupling between DNA polymerases and helicase activities at replication forks, induced by diverse DNA lesions or replication inhibitors, generate long stretches of primed single-stranded DNA that is implicated in activation of the S-phase checkpoint. It is currently unclear whether nucleation of the essential replication factor RPA onto this substrate stimulates the ATR-dependent checkpoint response independently of its role in DNA synthesis. Using Xenopus egg extracts to investigate the role of RPA recruitment at uncoupled forks in checkpoint activation we have surprisingly found that in conditions in which DNA synthesis occurs, RPA accumulation at forks stalled by either replication stress or UV irradiation is dispensable for Chk1 phosphorylation. In contrast, when both replication fork uncoupling and RPA hyperloading are suppressed, Chk1 phosphorylation is inhibited. Moreover, we show that extracts containing reduced levels of RPA accumulate ssDNA and induce spontaneous, caffeine-sensitive, Chk1 phosphorylation in S-phase. These results strongly suggest that disturbance of enzymatic activities of replication forks, rather than RPA hyperloading at stalled forks, is a critical determinant of ATR activation. PMID:22187152

Adeno-associated virus type 2 enhances goose parvovirus replication in embryonated goose eggs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Malkinson, Mertyn; Winocour, Ernest

The autonomous goose parvovirus (GPV) and the human helper-dependent adeno-associated virus type 2 (AAV2) share a high degree of homology. To determine if this evolutionary relationship has a biological impact, we studied viral replication in human 293 cells and in embryonated goose eggs coinfected with both viruses. Similar experiments were performed with the minute virus of mice (MVM), an autonomous murine parvovirus with less homology to AAV2. In human 293 cells, both GPV and MVM augmented AAV2 replication. In contrast, AAV2 markedly enhanced GPV replication in embryonated goose eggs under conditions where a similar effect was not observed with MVM.more » AAV2 did not replicate in embryonated goose eggs and AAV2 inactivated by UV-irradiation also enhanced GPV replication. To our knowledge, this is the first report that a human helper-dependent member of the Parvoviridae can provide helper activity for an autonomous parvovirus in a natural host.« less

RFWD3-Dependent Ubiquitination of RPA Regulates Repair at Stalled Replication Forks.

PubMed

Elia, Andrew E H; Wang, David C; Willis, Nicholas A; Boardman, Alexander P; Hajdu, Ildiko; Adeyemi, Richard O; Lowry, Elizabeth; Gygi, Steven P; Scully, Ralph; Elledge, Stephen J

2015-10-15

We have used quantitative proteomics to profile ubiquitination in the DNA damage response (DDR). We demonstrate that RPA, which functions as a protein scaffold in the replication stress response, is multiply ubiquitinated upon replication fork stalling. Ubiquitination of RPA occurs on chromatin, involves sites outside its DNA binding channel, does not cause proteasomal degradation, and increases under conditions of fork collapse, suggesting a role in repair at stalled forks. We demonstrate that the E3 ligase RFWD3 mediates RPA ubiquitination. RFWD3 is necessary for replication fork restart, normal repair kinetics during replication stress, and homologous recombination (HR) at stalled replication forks. Mutational analysis suggests that multisite ubiquitination of the entire RPA complex is responsible for repair at stalled forks. Multisite protein group sumoylation is known to promote HR in yeast. Our findings reveal a similar requirement for multisite protein group ubiquitination during HR at stalled forks in mammalian cells. Copyright © 2015 Elsevier Inc. All rights reserved.

Information-Theoretic Considerations Concerning the Origin of Life

NASA Astrophysics Data System (ADS)

Adami, Christoph

2015-09-01

Research investigating the origins of life usually either focuses on exploring possible life-bearing chemistries in the pre-biotic Earth, or else on synthetic approaches. Comparatively little work has explored fundamental issues concerning the spontaneous emergence of life using only concepts (such as information and evolution) that are divorced from any particular chemistry. Here, I advocate studying the probability of spontaneous molecular self-replication as a function of the information contained in the replicator, and the environmental conditions that might enable this emergence. I show (under certain simplifying assumptions) that the probability to discover a self-replicator by chance depends exponentially on the relative rate of formation of the monomers. If the rate at which monomers are formed is somewhat similar to the rate at which they would occur in a self-replicating polymer, the likelihood to discover such a replicator by chance is increased by many orders of magnitude. I document such an increase in searches for a self-replicator within the digital life system avida.

DNA Damage Reduces the Quality, but Not the Quantity of Human Papillomavirus 16 E1 and E2 DNA Replication.

PubMed

Bristol, Molly L; Wang, Xu; Smith, Nathan W; Son, Minkyeong P; Evans, Michael R; Morgan, Iain M

2016-06-22

Human papillomaviruses (HPVs) are causative agents in almost all cervical carcinomas. HPVs are also causative agents in head and neck cancer, the cases of which are increasing rapidly. Viral replication activates the DNA damage response (DDR) pathway; associated proteins are recruited to replication foci, and this pathway may serve to allow for viral genome amplification. Likewise, HPV genome double-strand breaks (DSBs) could be produced during replication and could lead to linearization and viral integration. Many studies have shown that viral integration into the host genome results in unregulated expression of the viral oncogenes, E6 and E7, promoting HPV-induced carcinogenesis. Previously, we have demonstrated that DNA-damaging agents, such as etoposide, or knocking down viral replication partner proteins, such as topoisomerase II β binding protein I (TopBP1), does not reduce the level of DNA replication. Here, we investigated whether these treatments alter the quality of DNA replication by HPV16 E1 and E2. We confirm that knockdown of TopBP1 or treatment with etoposide does not reduce total levels of E1/E2-mediated DNA replication; however, the quality of replication is significantly reduced. The results demonstrate that E1 and E2 continue to replicate under genomically-stressed conditions and that this replication is mutagenic. This mutagenesis would promote the formation of substrates for integration of the viral genome into that of the host, a hallmark of cervical cancer.

Recent Carbon Cycle Dynamics in an Ombrotrophic Peatland: Implications From Warming and eCO2 Treatments and the Role of Vegetation Layers in the Flux of CO2 and CH4

NASA Astrophysics Data System (ADS)

Hanson, P. J.; Phillips, J. R.; Nettles, W. R., IV; Heiderman, R.

2017-12-01

Following 2 years of sustained whole-ecosystem warming treatments spanning a range from 0 to +9 °C (SPRUCE experiment), the net fluxes of CO2 and CH4 from a raised-bog peatland in northern Minnesota show increased emissions of both gases from the community of woody ericaceous shrubs, forbs and Sphagnum moss. Increased emissions for CO2 and CH4 are primarily driven by sustaining temperature conditions for metabolic activity throughout the growing season. Seasonal temperature relationships for each gas suggest that warming affected growth and metabolic processes in a consistent manner across a wide range of temperature treatments. Elevated CO2 treatments (eCO2) have not yet shown anticipated increases in the input and processing of recent carbon. Quantitative annual estimates of the amount of net C and greenhouse gas flux increases will be calculated and presented for all treatments. A mid-season deconstruction of the contribution of vegetation layers to net ecosystem exchange of C and community respiration processes was also completed for replicate ambient shrub communities. The deconstruction data demonstrate the fractional contribution of wood shrubs, forbs/sedges and moss to the community to the flux of C and provide further evidence that the current C cycle of the bog is driven primarily by surface phenomenon fed be recently fixed C. These results should be considered early results from the SPRUCE experiment anticipated to operate through 2025. Affiliated studies will add mechanisms to these observations and long-term cumulative effects may differ.

Characterizing observed circulation patterns within a bay using HF radar and numerical model simulations

NASA Astrophysics Data System (ADS)

O'Donncha, Fearghal; Hartnett, Michael; Nash, Stephen; Ren, Lei; Ragnoli, Emanuele

2015-02-01

In this study, High Frequency Radar (HFR), observations in conjunction with numerical model simulations investigate surface flow dynamics in a tidally-active, wind-driven bay; Galway Bay situated on the West coast of Ireland. Comparisons against ADCP sensor data permit an independent assessment of HFR and model performance, respectively. Results show root-mean-square (rms) differences in the range 10 - 12cm/s while model rms equalled 12 - 14cm/s. Subsequent analysis focus on a detailed comparison of HFR and model output. Harmonic analysis decompose both sets of surface currents based on distinct flow process, enabling a correlation analysis between the resultant output and dominant forcing parameters. Comparisons of barotropic model simulations and HFR tidal signal demonstrate consistently high agreement, particularly of the dominant M2 tidal signal. Analysis of residual flows demonstrate considerably poorer agreement, with the model failing to replicate complex flows. A number of hypotheses explaining this discrepancy are discussed, namely: discrepancies between regional-scale, coastal-ocean models and globally-influenced bay-scale dynamics; model uncertainties arising from highly-variable wind-driven flows across alarge body of water forced by point measurements of wind vectors; and the high dependence of model simulations on empirical wind-stress coefficients. The research demonstrates that an advanced, widely-used hydro-environmental model does not accurately reproduce aspects of surface flow processes, particularly with regards wind forcing. Considering the significance of surface boundary conditions in both coastal and open ocean dynamics, the viability of using a systematic analysis of results to improve model predictions is discussed.

Analyses of a whole-genome inter-clade recombination map of hepatitis delta virus suggest a host polymerase-driven and viral RNA structure-promoted template-switching mechanism for viral RNA recombination

PubMed Central

Chao, Mei; Wang, Tzu-Chi; Lin, Chia-Chi; Yung-Liang Wang, Robert; Lin, Wen-Bin; Lee, Shang-En; Cheng, Ying-Yu; Yeh, Chau-Ting; Iang, Shan-Bei

2017-01-01

The genome of hepatitis delta virus (HDV) is a 1.7-kb single-stranded circular RNA that folds into an unbranched rod-like structure and has ribozyme activity. HDV redirects host RNA polymerase(s) (RNAP) to perform viral RNA-directed RNA transcription. RNA recombination is known to contribute to the genetic heterogeneity of HDV, but its molecular mechanism is poorly understood. Here, we established a whole-genome HDV-1/HDV-4 recombination map using two cloned sequences coexisting in cultured cells. Our functional analyses of the resulting chimeric delta antigens (the only viral-encoded protein) and recombinant genomes provide insights into how recombination promotes the genotypic and phenotypic diversity of HDV. Our examination of crossover distribution and subsequent mutagenesis analyses demonstrated that ribozyme activity on HDV genome, which is required for viral replication, also contributes to the generation of an inter-clade junction. These data provide circumstantial evidence supporting our contention that HDV RNA recombination occurs via a replication-dependent mechanism. Furthermore, we identify an intrinsic asymmetric bulge on the HDV genome, which appears to promote recombination events in the vicinity. We therefore propose a mammalian RNAP-driven and viral-RNA-structure-promoted template-switching mechanism for HDV genetic recombination. The present findings improve our understanding of the capacities of the host RNAP beyond typical DNA-directed transcription. PMID:28977829

Effects of cetyltriethylammonium bromide on the replication of Bombyx mori nucleopolyhedrovirus.

PubMed

Zhou, Yajing; Zhang, Zhifang; He, Jialu; Zhang, Yuanxing

2002-05-01

An experimental study was undertaken to quantify the effects of cetyltriethylammonium bromide (CTAB) on the replication of Bombyx mori nucleopolyhedrovirus (BmNPV) and the transcriptionalactivity of BmNPV ie-1 promoter. The results demonstrated that the budded virus (BV) titer rose about 3.7-fold by adding CTAB to the culture media up to 0.1 mu g ml(-1) in infected Bm-N cells with a wild-type BmNPV. The transient expression level of luciferase driven by BmNPV ie-1 promoter was enhanced by more than 3-fold in the presence of 0.1 mu g ml(-1) of CTAB in uninfected insect cells via a transient expression system. Contrary to the rise in BV titer, the polyhedra inside the nucleus of infected cells dropped linearly from 4.0 x 10(6) ml(-1) down to 2.1 x 10(6) ml(-1) with in a range of CTAB concentrations from 0 to 0.25 mu g ml(-1). The same trend in expression level of beta -galactosidase or phytase was given when the Bm-N cells or fifth-instar silkworm larvae infected with a recombinant BmNPV containing the beta -galactosidase or phytase reporter gene driven by the polyhedrin promoter. We deduced that CTAB appeared to affect the virus bi-phasic life cycle stages and production pathways, resulting in an enhancement in BV production and a suppression of occluded virus (OV) production and expression of foreign genes controlled by the polyhedrin promoter.

Maximum Principle for General Controlled Systems Driven by Fractional Brownian Motions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han Yuecai; Hu Yaozhong; Song Jian, E-mail: jsong2@math.rutgers.edu

2013-04-15

We obtain a maximum principle for stochastic control problem of general controlled stochastic differential systems driven by fractional Brownian motions (of Hurst parameter H>1/2). This maximum principle specifies a system of equations that the optimal control must satisfy (necessary condition for the optimal control). This system of equations consists of a backward stochastic differential equation driven by both fractional Brownian motions and the corresponding underlying standard Brownian motions. In addition to this backward equation, the maximum principle also involves the Malliavin derivatives. Our approach is to use conditioning and Malliavin calculus. To arrive at our maximum principle we need tomore » develop some new results of stochastic analysis of the controlled systems driven by fractional Brownian motions via fractional calculus. Our approach of conditioning and Malliavin calculus is also applied to classical system driven by standard Brownian motions while the controller has only partial information. As a straightforward consequence, the classical maximum principle is also deduced in this more natural and simpler way.« less

Strand displacement amplification as an in vitro model for rolling-circle replication: deletion formation and evolution during serial transfer.

PubMed Central

Walter, N G; Strunk, G

1994-01-01

Strand displacement amplification is an isothermal DNA amplification reaction based on a restriction endonuclease nicking its recognition site and a polymerase extending the nick at its 3' end, displacing the downstream strand. The reaction resembles rolling-circle replication of single-stranded phages and small plasmids. The displaced sense strand serves as target for an antisense reaction and vice versa, resulting in exponential growth and the autocatalytic nature of this in vitro reaction as long as the template is the limiting agent. We describe the optimization of strand displacement amplification for in vitro evolution experiments under serial transfer conditions. The reaction was followed and controlled by use of the fluorescent dye thiazole orange binding to the amplified DNA. We were able to maintain exponential growth conditions with a doubling time of 3.0 min throughout 100 transfers or approximately 350 molecular generations by using an automatic handling device. Homology of in vitro amplification with rolling-circle replication was mirrored by the occurring evolutionary processes. Deletion events most likely caused by a slipped mispairing mechanism as postulated for in vivo replication took place. Under our conditions, the mutation rate was high and a molecular quasi-species formed with a mutant lacking internal hairpin formation ability and thus outgrowing all other species under dGTP/dCTP deficiency. Images PMID:8058737

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

ERIC Educational Resources Information Center

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…

From facilitation to competition: temperature-driven shift in dominant plant interactions affects population dynamics in seminatural grasslands.

PubMed

Olsen, Siri L; Töpper, Joachim P; Skarpaas, Olav; Vandvik, Vigdis; Klanderud, Kari

2016-05-01

Biotic interactions are often ignored in assessments of climate change impacts. However, climate-related changes in species interactions, often mediated through increased dominance of certain species or functional groups, may have important implications for how species respond to climate warming and altered precipitation patterns. We examined how a dominant plant functional group affected the population dynamics of four co-occurring forb species by experimentally removing graminoids in seminatural grasslands. Specifically, we explored how the interaction between dominants and subordinates varied with climate by replicating the removal experiment across a climate grid consisting of 12 field sites spanning broad-scale temperature and precipitation gradients in southern Norway. Biotic interactions affected population growth rates of all study species, and the net outcome of interactions between dominants and subordinates switched from facilitation to competition with increasing temperature along the temperature gradient. The impacts of competitive interactions on subordinates in the warmer sites could primarily be attributed to reduced plant survival. Whereas the response to dominant removal varied with temperature, there was no overall effect of precipitation on the balance between competition and facilitation. Our findings suggest that global warming may increase the relative importance of competitive interactions in seminatural grasslands across a wide range of precipitation levels, thereby favouring highly competitive dominant species over subordinate species. As a result, seminatural grasslands may become increasingly dependent on disturbance (i.e. traditional management such as grazing and mowing) to maintain viable populations of subordinate species and thereby biodiversity under future climates. Our study highlights the importance of population-level studies replicated under different climatic conditions for understanding the underlying mechanisms of climate change impacts on plants. © 2016 John Wiley & Sons Ltd.

Mammalian DNA enriched for replication origins is enriched for snap-back sequences.

PubMed

Zannis-Hadjopoulos, M; Kaufmann, G; Martin, R G

1984-11-15

Using the instability of replication loops as a method for the isolation of double-stranded nascent DNA, extruded DNA enriched for replication origins was obtained and denatured. Snap-back DNA, single-stranded DNA with inverted repeats (palindromic sequences), reassociates rapidly into stem-loop structures with zero-order kinetics when conditions are changed from denaturing to renaturing, and can be assayed by chromatography on hydroxyapatite. Origin-enriched nascent DNA strands from mouse, rat and monkey cells growing either synchronously or asynchronously were purified and assayed for the presence of snap-back sequences. The results show that origin-enriched DNA is also enriched for snap-back sequences, implying that some origins for mammalian DNA replication contain or lie near palindromic sequences.

Recombination at DNA replication fork barriers is not universal and is differentially regulated by Swi1.

PubMed

Pryce, David W; Ramayah, Soshila; Jaendling, Alessa; McFarlane, Ramsay J

2009-03-24

DNA replication stress has been implicated in the etiology of genetic diseases, including cancers. It has been proposed that genomic sites that inhibit or slow DNA replication fork progression possess recombination hotspot activity and can form potential fragile sites. Here we used the fission yeast, Schizosaccharomyces pombe, to demonstrate that hotspot activity is not a universal feature of replication fork barriers (RFBs), and we propose that most sites within the genome that form RFBs do not have recombination hotspot activity under nonstressed conditions. We further demonstrate that Swi1, the TIMELESS homologue, differentially controls the recombination potential of RFBs, switching between being a suppressor and an activator of recombination in a site-specific fashion.

Recombination at DNA replication fork barriers is not universal and is differentially regulated by Swi1

PubMed Central

Pryce, David W.; Ramayah, Soshila; Jaendling, Alessa; McFarlane, Ramsay J.

2009-01-01

DNA replication stress has been implicated in the etiology of genetic diseases, including cancers. It has been proposed that genomic sites that inhibit or slow DNA replication fork progression possess recombination hotspot activity and can form potential fragile sites. Here we used the fission yeast, Schizosaccharomyces pombe, to demonstrate that hotspot activity is not a universal feature of replication fork barriers (RFBs), and we propose that most sites within the genome that form RFBs do not have recombination hotspot activity under nonstressed conditions. We further demonstrate that Swi1, the TIMELESS homologue, differentially controls the recombination potential of RFBs, switching between being a suppressor and an activator of recombination in a site-specific fashion. PMID:19273851

Development of novel drugs from marine surface associated microorganisms.

PubMed

Penesyan, Anahit; Kjelleberg, Staffan; Egan, Suhelen

2010-03-01

While the oceans cover more than 70% of the Earth's surface, marine derived microbial natural products have been largely unexplored. The marine environment is a habitat for many unique microorganisms, which produce biologically active compounds ("bioactives") to adapt to particular environmental conditions. For example, marine surface associated microorganisms have proven to be a rich source for novel bioactives because of the necessity to evolve allelochemicals capable of protecting the producer from the fierce competition that exists between microorganisms on the surfaces of marine eukaryotes. Chemically driven interactions are also important for the establishment of cross-relationships between microbes and their eukaryotic hosts, in which organisms producing antimicrobial compounds ("antimicrobials"), may protect the host surface against over colonisation in return for a nutrient rich environment. As is the case for bioactive discovery in general, progress in the detection and characterization of marine microbial bioactives has been limited by a number of obstacles, such as unsuitable culture conditions, laborious purification processes, and a lack of de-replication. However many of these limitations are now being overcome due to improved microbial cultivation techniques, microbial (meta-) genomic analysis and novel sensitive analytical tools for structural elucidation. Here we discuss how these technical advances, together with a better understanding of microbial and chemical ecology, will inevitably translate into an increase in the discovery and development of novel drugs from marine microbial sources in the future.

Exploring Techniques of Developing Writing Skill in IELTS Preparatory Courses: A Data-Driven Study

ERIC Educational Resources Information Center

Ostovar-Namaghi, Seyyed Ali; Safaee, Seyyed Esmail

2017-01-01

Being driven by the hypothetico-deductive mode of inquiry, previous studies have tested the effectiveness of theory-driven interventions under controlled experimental conditions to come up with universally applicable generalizations. To make a case in the opposite direction, this data-driven study aims at uncovering techniques and strategies…

Monitoring method and apparatus using high-frequency carrier

DOEpatents

Haynes, Howard D.

1996-01-01

A method and apparatus for monitoring an electrical-motor-driven device by injecting a high frequency carrier signal onto the power line current. The method is accomplished by injecting a high frequency carrier signal onto an AC power line current. The AC power line current supplies the electrical-motor-driven device with electrical energy. As a result, electrical and mechanical characteristics of the electrical-motor-driven device modulate the high frequency carrier signal and the AC power line current. The high frequency carrier signal is then monitored, conditioned and demodulated. Finally, the modulated high frequency carrier signal is analyzed to ascertain the operating condition of the electrical-motor-driven device.

Novel infectivity-enhanced oncolytic adenovirus with a capsid-incorporated dual-imaging moiety for monitoring virotherapy in ovarian cancer.

PubMed

Kimball, Kristopher J; Rivera, Angel A; Zinn, Kurt R; Icyuz, Mert; Saini, Vaibhav; Li, Jing; Zhu, Zeng B; Siegal, Gene P; Douglas, Joanne T; Curiel, David T; Alvarez, Ronald D; Borovjagin, Anton V

2009-01-01

We sought to develop a cancer-targeted, infectivity-enhanced oncolytic adenovirus that embodies a capsid-labeling fusion for noninvasive dual-modality imaging of ovarian cancer virotherapy. A functional fusion protein composed of fluorescent and nuclear imaging tags was genetically incorporated into the capsid of an infectivity-enhanced conditionally replicative adenovirus. Incorporation of herpes simplex virus thymidine kinase (HSV-tk) and monomeric red fluorescent protein 1 (mRFP1) into the viral capsid and its genomic stability were verified by molecular analyses. Replication and oncolysis were evaluated in ovarian cancer cells. Fusion functionality was confirmed by in vitro gamma camera and fluorescent microscopy imaging. Comparison of tk-mRFP virus to single-modality controls revealed similar replication efficiency and oncolytic potency. Molecular fusion did not abolish enzymatic activity of HSV-tk as the virus effectively phosphorylated thymidine both ex vivo and in vitro. In vitro fluorescence imaging demonstrated a strong correlation between the intensity of fluorescent signal and cytopathic effect in infected ovarian cancer cells, suggesting that fluorescence can be used to monitor viral replication. We have in vitro validated a new infectivity-enhanced oncolytic adenovirus with a dual-imaging modality-labeled capsid, optimized for ovarian cancer virotherapy. The new agent could provide incremental gains toward climbing the barriers for achieving conditionally replicated adenovirus efficacy in human trials.

Replication Rate, Framing, and Format Affect Attitudes and Decisions about Science Claims

PubMed Central

Barnes, Ralph M.; Tobin, Stephanie J.; Johnston, Heather M.; MacKenzie, Noah; Taglang, Chelsea M.

2016-01-01

A series of five experiments examined how the evaluation of a scientific finding was influenced by information about the number of studies that had successfully replicated the initial finding. The experiments also tested the impact of frame (negative, positive) and numeric format (percentage, natural frequency) on the evaluation of scientific findings. In Experiments 1 through 4, an attitude difference score served as the dependent measure, while a measure of choice served as the dependent measure in Experiment 5. Results from a diverse sample of 188 non-institutionalized U.S. adults (Experiment 2) and 730 undergraduate college students (Experiments 1, 3, and 4) indicated that attitudes became more positive as the replication rate increased and attitudes were more positive when the replication information was framed positively. The results also indicate that the manner in which replication rate was framed had a greater impact on attitude than the replication rate itself. The large effect for frame was attenuated somewhat when information about replication was presented in the form of natural frequencies rather than percentages. A fifth study employing 662 undergraduate college students in a task in which choice served as the dependent measure confirmed the framing effect and replicated the replication rate effect in the positive frame condition, but provided no evidence that the use of natural frequencies diminished the effect. PMID:27920743

Rad53 regulates replication fork restart after DNA damage in Saccharomyces cerevisiae

PubMed Central

Szyjka, Shawn J.; Aparicio, Jennifer G.; Viggiani, Christopher J.; Knott, Simon; Xu, Weihong; Tavaré, Simon; Aparicio, Oscar M.

2008-01-01

Replication fork stalling at a DNA lesion generates a damage signal that activates the Rad53 kinase, which plays a vital role in survival by stabilizing stalled replication forks. However, evidence that Rad53 directly modulates the activity of replication forks has been lacking, and the nature of fork stabilization has remained unclear. Recently, cells lacking the Psy2–Pph3 phosphatase were shown to be defective in dephosphorylation of Rad53 as well as replication fork restart after DNA damage, suggesting a mechanistic link between Rad53 deactivation and fork restart. To test this possibility we examined the progression of replication forks in methyl-methanesulfonate (MMS)-damaged cells, under different conditions of Rad53 activity. Hyperactivity of Rad53 in pph3Δ cells slows fork progression in MMS, whereas deactivation of Rad53, through expression of dominant-negative Rad53-KD, is sufficient to allow fork restart during recovery. Furthermore, combined deletion of PPH3 and PTC2, a second, unrelated Rad53 phosphatase, results in complete replication fork arrest and lethality in MMS, demonstrating that Rad53 deactivation is a key mechanism controlling fork restart. We propose a model for regulation of replication fork progression through damaged DNA involving a cycle of Rad53 activation and deactivation that coordinates replication restart with DNA repair. PMID:18628397

Top2 and Sgs1-Top3 Act Redundantly to Ensure rDNA Replication Termination

PubMed Central

Fredsøe, Jacob; Nielsen, Ida; Pedersen, Jakob Madsen; Bentsen, Iben Bach; Lisby, Michael; Bjergbaek, Lotte; Andersen, Anni H

2015-01-01

Faithful DNA replication with correct termination is essential for genome stability and transmission of genetic information. Here we have investigated the potential roles of Topoisomerase II (Top2) and the RecQ helicase Sgs1 during late stages of replication. We find that cells lacking Top2 and Sgs1 (or Top3) display two different characteristics during late S/G2 phase, checkpoint activation and accumulation of asymmetric X-structures, which are both independent of homologous recombination. Our data demonstrate that checkpoint activation is caused by a DNA structure formed at the strongest rDNA replication fork barrier (RFB) during replication termination, and consistently, checkpoint activation is dependent on the RFB binding protein, Fob1. In contrast, asymmetric X-structures are formed independent of Fob1 at less strong rDNA replication fork barriers. However, both checkpoint activation and formation of asymmetric X-structures are sensitive to conditions, which facilitate fork merging and progression of replication forks through replication fork barriers. Our data are consistent with a redundant role of Top2 and Sgs1 together with Top3 (Sgs1-Top3) in replication fork merging at rDNA barriers. At RFB either Top2 or Sgs1-Top3 is essential to prevent formation of a checkpoint activating DNA structure during termination, but at less strong rDNA barriers absence of the enzymes merely delays replication fork merging, causing an accumulation of asymmetric termination structures, which are solved over time. PMID:26630413

p21 differentially regulates DNA replication and DNA-repair-associated processes after UV irradiation.

PubMed

Soria, Gaston; Speroni, Juliana; Podhajcer, Osvaldo L; Prives, Carol; Gottifredi, Vanesa

2008-10-01

Although p21 upregulation is required to block cell-cycle progression following many types of genotoxic insult, UV irradiation triggers p21 proteolysis. The significance of the increased p21 turnover is unclear and might be associated with DNA repair. While the role of p21 in nucleotide excision repair (NER) remains controversial, recent reports have explored its effect on translesion DNA synthesis (TLS), a process that avoids replication blockage during S phase. Herein, we analyze the effect of p21 on different PCNA-driven processes including DNA replication, NER and TLS. Whereas only the CDK-binding domain of p21 is required for cell-cycle arrest in unstressed cells, neither the CDK-binding nor the PCNA-binding domain of p21 is able to block early and late steps of NER. Intriguingly, through its PCNA-binding domain, p21 inhibits the interaction of the TLS polymerase, pol eta (pol eta), with PCNA and impairs the assembly of pol eta foci after UV. Moreover, this obstruction correlates with accumulation of phosphorylated H2AX and increased apoptosis. By showing that p21 is a negative regulator of PCNA-pol eta interaction, our data unveil a link between efficient TLS and UV-induced degradation of p21.

Alfalfa mosaic virus replicase proteins, P1 and P2, localize to the tonoplast in the presence of virus RNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ibrahim, Amr; Present address: Genomics Facility, Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza 12619; Hutchens, Heather M.

2012-11-25

To identify the virus components important for assembly of the Alfalfa mosaic virus replicase complex, we used live cell imaging of Arabidopsis thaliana protoplasts that expressed various virus cDNAs encoding native and GFP-fusion proteins of P1 and P2 replicase proteins and full-length virus RNAs. Expression of P1-GFP alone resulted in fluorescent vesicle-like bodies in the cytoplasm that colocalized with FM4-64, an endocytic marker, and RFP-AtVSR2, RabF2a/Rha1-mCherry, and RabF2b/Ara7-mCherry, all of which localize to multivesicular bodies (MVBs), which are also called prevacuolar compartments, that mediate traffic to the lytic vacuole. GFP-P2 was driven from the cytosol to MVBs when expressed withmore » P1 indicating that P1 recruited GFP-P2. P1-GFP localized on the tonoplast, which surrounds the vacuole, in the presence of infectious virus RNA, replication competent RNA2, or P2 and replication competent RNA1 or RNA3. This suggests that a functional replication complex containing P1, P2, and a full-length AMV RNA assembles on MVBs to traffic to the tonoplast.« less

Identification of a short sequence in the HCMV terminase pUL56 essential for interaction with pUL89 subunit.

PubMed

Ligat, G; Jacquet, C; Chou, S; Couvreux, A; Alain, S; Hantz, S

2017-08-18

The human cytomegalovirus (HCMV) terminase complex consists of several components acting together to cleave viral DNA into unit length genomes and translocate them into capsids, a critical process in the production of infectious virions subsequent to DNA replication. Previous studies suggest that the carboxyl-terminal portion of the pUL56 subunit interacts with the pUL89 subunit. However, the specific interacting residues of pUL56 remain unknown. We identified a conserved sequence in the C-terminal moiety of pUL56 ( 671 WMVVKYMGFF 680 ). Overrepresentation of conserved aromatic amino acids through 20 herpesviruses homologues of pUL56 suggests an involvement of this short peptide into the interaction between the larger pUL56 terminase subunit and the smaller pUL89 subunit. Use of Alpha technology highlighted an interaction between pUL56 and pUL89 driven through the peptide 671 WMVVKYMGFF 680 . A deletion of these residues blocks viral replication. We hypothesize that it is the consequence of the disruption of the pUL56-pUL89 interaction. These results show that this motif is essential for HCMV replication and could be a target for development of new small antiviral drugs or peptidomimetics.

Replication Origins and Timing of Temporal Replication in Budding Yeast: How to Solve the Conundrum?

PubMed Central

Barberis, Matteo; Spiesser, Thomas W.; Klipp, Edda

2010-01-01

Similarly to metazoans, the budding yeast Saccharomyces cereviasiae replicates its genome with a defined timing. In this organism, well-defined, site-specific origins, are efficient and fire in almost every round of DNA replication. However, this strategy is neither conserved in the fission yeast Saccharomyces pombe, nor in Xenopus or Drosophila embryos, nor in higher eukaryotes, in which DNA replication initiates asynchronously throughout S phase at random sites. Temporal and spatial controls can contribute to the timing of replication such as Cdk activity, origin localization, epigenetic status or gene expression. However, a debate is going on to answer the question how individual origins are selected to fire in budding yeast. Two opposing theories were proposed: the “replicon paradigm” or “temporal program” vs. the “stochastic firing”. Recent data support the temporal regulation of origin activation, clustering origins into temporal blocks of early and late replication. Contrarily, strong evidences suggest that stochastic processes acting on origins can generate the observed kinetics of replication without requiring a temporal order. In mammalian cells, a spatiotemporal model that accounts for a partially deterministic and partially stochastic order of DNA replication has been proposed. Is this strategy the solution to reconcile the conundrum of having both organized replication timing and stochastic origin firing also for budding yeast? In this review we discuss this possibility in the light of our recent study on the origin activation, suggesting that there might be a stochastic component in the temporal activation of the replication origins, especially under perturbed conditions. PMID:21037857

Non-daily pre-exposure prophylaxis for HIV prevention

PubMed Central

Anderson, Peter L.; García-Lerma, J. Gerardo; Heneine, Walid

2015-01-01

Purpose of review To discuss non-daily pre-exposure prophylaxis (PrEP) modalities that may provide advantages compared with daily PrEP in cost and cumulative toxicity, but may have lower adherence forgiveness. Recent Findings Animal models have informed our understanding of early viral transmission events, which help guide event-driven PrEP dosing strategies. These models indicate early establishment of viral replication in rectal or cervicovaginal tissues, so event-driven PrEP should rapidly deliver high mucosal drug concentrations within hours of the potential exposure event. Macaque models have demonstrated the high biological efficacy for event-driven dosing of oral tenofovir disoproxil fumarate (TDF) and emtricitabine (FTC) against both vaginal and rectal virus transmission. In humans, the IPERGAY study demonstrated 86% efficacy for event-driven oral TDF/FTC dosing among men who have sex with men (MSM), while no similar efficacy data are available on women or heterosexual men. The HPTN 067 study showed that certain MSM populations adhere well to non-daily PrEP while other populations of women adhere more poorly to non-daily versus daily regimens. Pharmacokinetic studies following oral TDF/FTC dosing in humans, indicate that TFV-diphosphate (the active form of TFV) accumulates to higher concentrations in rectal versus cervicovaginal tissue but non-adherence in trials complicates the interpretation of differential mucosal drug concentrations. Summary Event-driven dosing for TFV-based PrEP has promise for HIV prevention in MSM. Future research of event-driven PrEP in women and heterosexual men should be guided by a better understanding of the importance of mucosal drug concentrations for PrEP efficacy and its sensitivity to adherence. PMID:26633641

The scenario on the origin of translation in the RNA world: in principle of replication parsimony

PubMed Central

2010-01-01

Background It is now believed that in the origin of life, proteins should have been "invented" in an RNA world. However, due to the complexity of a possible RNA-based proto-translation system, this evolving process seems quite complicated and the associated scenario remains very blurry. Considering that RNA can bind amino acids with specificity, it has been reasonably supposed that initial peptides might have been synthesized on "RNA templates" containing multiple amino acid binding sites. This "Direct RNA Template (DRT)" mechanism is attractive because it should be the simplest mechanism for RNA to synthesize peptides, thus very likely to have been adopted initially in the RNA world. Then, how this mechanism could develop into a proto-translation system mechanism is an interesting problem. Presentation of the hypothesis Here an explanation to this problem is shown considering the principle of "replication parsimony" --- genetic information tends to be utilized in a parsimonious way under selection pressure, due to its replication cost (e.g., in the RNA world, nucleotides and ribozymes for RNA replication). Because a DRT would be quite long even for a short peptide, its replication cost would be great. Thus the diversity and the length of functional peptides synthesized by the DRT mechanism would be seriously limited. Adaptors (proto-tRNAs) would arise to allow a DRT's complementary strand (called "C-DRT" here) to direct the synthesis of the same peptide synthesized by the DRT itself. Because the C-DRT is a necessary part in the DRT's replication, fewer turns of the DRT's replication would be needed to synthesize definite copies of the functional peptide, thus saving the replication cost. Acting through adaptors, C-DRTs could transform into much shorter templates (called "proto-mRNAs" here) and substitute the role of DRTs, thus significantly saving the replication cost. A proto-rRNA corresponding to the small subunit rRNA would then emerge to aid the binding of proto-tRNAs and proto-mRNAs, allowing the reduction of base pairs between them (ultimately resulting in the triplet anticodon/codon pair), thus further saving the replication cost. In this context, the replication cost saved would allow the appearance of more and longer functional peptides and, finally, proteins. The hypothesis could be called "DRT-RP" ("RP" for "replication parsimony"). Testing the hypothesis The scenario described here is open for experimental work at some key scenes, including the compact DRT mechanism, the development of adaptors from aa-aptamers, the synthesis of peptides by proto-tRNAs and proto-mRNAs without the participation of proto-rRNAs, etc. Interestingly, a recent computer simulation study has demonstrated the plausibility of one of the evolving processes driven by replication parsimony in the scenario. Implication of the hypothesis An RNA-based proto-translation system could arise gradually from the DRT mechanism according to the principle of "replication parsimony" --- to save the replication cost of RNA templates for functional peptides. A surprising side deduction along the logic of the hypothesis is that complex, biosynthetic amino acids might have entered the genetic code earlier than simple, prebiotic amino acids, which is opposite to the common sense. Overall, the present discussion clarifies the blurry scenario concerning the origin of translation with a major clue, which shows vividly how life could "manage" to exploit potential chemical resources in nature, eventually in an efficient way over evolution. Reviewers This article was reviewed by Eugene V. Koonin, Juergen Brosius, and Arcady Mushegian. PMID:21110883

Optimism and education buffer the effects of syndemic conditions on HIV status among African American men who have sex with men.

PubMed

O'Leary, Ann; Jemmott, John B; Stevens, Robin; Rutledge, Scott Edward; Icard, Larry D

2014-11-01

The present study sought to replicate effects of the number of syndemic psychosocial health conditions on sexual risk behavior and HIV infection among a sample of high-risk African American men who have sex with men (MSM) and to identify resilience factors that may buffer these effects. We used baseline data from an HIV risk-reduction trial to examine whether a higher number of syndemic conditions was associated with higher rates of self-reported sexual risk behavior and HIV infection. Using logistic regression models, we tested for interactions between number of syndemic conditions and several potential resilience factors to identify buffering effects. Replicating previous studies, we found significant associations between numbers of syndemic conditions and higher rates of sexual risk behavior and HIV infection. Surprisingly, we also replicated a previous finding (Stall et al., Am J Public Health, 93(6):939-942, 2003) that the effects of syndemic burden on HIV status fell off at the highest levels of syndemic conditions. Among a variety of potential resilience factors, two-optimism and education-buffered the syndemic effect on HIV prevalence. This is, to our knowledge, the first paper to identify resilience factors buffering against syndemic effects among MSM. It also constitutes a significant contribution to the literature regarding prevention among black MSM. These results point to the need to identify HIV-positive black MSM and provide effective treatment for them and to develop interventions addressing both syndemic and resilience factors.

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

NASA Astrophysics Data System (ADS)

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 pressurization rates and permeability conditions.

Murine Gammaherpesvirus 68 LANA and SOX Homologs Counteract ATM-Driven p53 Activity during Lytic Viral Replication

PubMed Central

Sifford, Jeffrey M.; Stahl, James A.; Salinas, Eduardo

2015-01-01

ABSTRACT Tumor suppressor p53 is activated in response to numerous cellular stresses, including viral infection. However, whether murine gammaherpesvirus 68 (MHV68) provokes p53 during the lytic replication cycle has not been extensively evaluated. Here, we demonstrate that MHV68 lytic infection induces p53 phosphorylation and stabilization in a manner that is dependent on the DNA damage response (DDR) kinase ataxia telangiectasia mutated (ATM). The induction of p53 during MHV68 infection occurred in multiple cell types, including splenocytes of infected mice. ATM and p53 activation required early viral gene expression but occurred independently of viral DNA replication. At early time points during infection, p53-responsive cellular genes were induced, coinciding with p53 stabilization and phosphorylation. However, p53-related gene expression subsided as infection progressed, even though p53 remained stable and phosphorylated. Infected cells also failed to initiate p53-dependent gene expression and undergo apoptosis in response to treatment with exogenous p53 agonists. The inhibition of p53 responses during infection required the expression of the MHV68 homologs of the shutoff and exonuclease protein (muSOX) and latency-associated nuclear antigen (mLANA). Interestingly, mLANA, but not muSOX, was necessary to prevent p53-mediated death in MHV68-infected cells under the conditions tested. This suggests that muSOX and mLANA are differentially required for inhibiting p53 in specific settings. These data reveal that DDR responses triggered by MHV68 infection promote p53 activation. However, MHV68 encodes at least two proteins capable of limiting the potential consequences of p53 function. IMPORTANCE Gammaherpesviruses are oncogenic herpesviruses that establish lifelong chronic infections. Defining how gammaherpesviruses overcome host responses to infection is important for understanding how these viruses infect and cause disease. Here, we establish that murine gammaherpesvirus 68 induces the activation of tumor suppressor p53. p53 activation was dependent on the DNA damage response kinase ataxia telangiectasia mutated. Although active early after infection, p53 became dominantly inhibited as the infection cycle progressed. Viral inhibition of p53 was mediated by the murine gammaherpesvirus 68 homologs of muSOX and mLANA. The inhibition of the p53 pathway enabled infected cells to evade p53-mediated cell death responses. These data demonstrate that a gammaherpesvirus encodes multiple proteins to limit p53-mediated responses to productive viral infection, which likely benefits acute viral replication and the establishment of chronic infection. PMID:26676792

Impact of non-ionic surfactant on the long-term development of lab-scale-activated sludge bacterial communities.

PubMed

Lozada, Mariana; Basile, Laura; Erijman, Leonardo

2007-01-01

The development of bacterial communities in replicate lab-scale-activated sludge reactors degrading a non-ionic surfactant was evaluated by statistical analysis of denaturing gradient gel electrophoresis (DGGE) fingerprints. Four sequential batch reactors were fed with synthetic sewage, two of which received, in addition, 0.01% of nonylphenol ethoxylates (NPE). The dynamic character of bacterial community structure was confirmed by the differences in species composition among replicate reactors. Measurement of similarities between reactors was obtained by pairwise similarity analysis using the Bray Curtis coefficient. The group of NPE-amended reactors exhibited the highest similarity values (Sjk=0.53+/-0.03), indicating that the bacterial community structure of NPE-amended reactors was better replicated than control reactors (Sjk=0.36+/-0.04). Replicate NPE-amended reactors taken at different times of operation clustered together, whereas analogous relations within the control reactor cluster were not observed. The DGGE pattern of isolates grown in conditioned media prepared with media taken at the end of the aeration cycle grouped separately from other conditioned and synthetic media regardless of the carbon source amendment, suggesting that NPE degradation residuals could have a role in the shaping of the community structure.

Characteristics of polyomavirus BK (BKPyV) infection in primary human urothelial cells.

PubMed

Li, Ruomei; Sharma, Biswa Nath; Linder, Stig; Gutteberg, Tore Jarl; Hirsch, Hans H; Rinaldo, Christine Hanssen

2013-05-25

High-level polyomavirus BK (BKPyV) replication in urothelial cells is a hallmark of polyomavirus-associated hemorrhagic cystitis (PyVHC), a painful condition affecting bone marrow transplant recipients. In kidney transplant recipients, replication in tubular epithelial cells is associated with overt disease whereas high-level urothelial replication is clinically silent. We characterized BKPyV replication in primary human urothelial cells (HUCs) and compared it to replication in renal tubular epithelial cells (RPTECs). HUCs were easily infected, as shown by expression of T-antigens, VP1-3, and agnoprotein, and intranuclear virion production. Compared to RPTECs, progeny release was delayed by ≥24h and reduced. BKPyV-infected HUCs rounded up like "decoy cells" and detached without necrosis as shown by delayed cytokeratin-18 release, real-time viability monitoring and imaging. The data show that BKV infection of HUCs and RPTECs is significantly different and support the notion that PyVHC pathogenesis is not solely due to BKPyV replication, but likely requires urotoxic and immunological cofactors. Copyright © 2013 Elsevier Inc. All rights reserved.

Immunity to Salmonella typhi: considerations relevant to measurement of cellular immunity in typhoid-endemic regions.

PubMed Central

Murphy, J R; Wasserman, S S; Baqar, S; Schlesinger, L; Ferreccio, C; Lindberg, A A; Levine, M M

1989-01-01

Experiments were performed in Baltimore, Maryland and in Santiago, Chile, to determine the level of Salmonella typhi antigen-driven in vitro lymphocyte replication response which signifies specific acquired immunity to this bacterium and to determine the best method of data analysis and form of data presentation. Lymphocyte replication was measured as incorporation of 3H-thymidine into desoxyribonucleic acid. Data (ct/min/culture) were analyzed in raw form and following log transformation, by non-parametric and parametric statistical procedures. A preference was developed for log-transformed data and discriminant analysis. Discriminant analysis of log-transformed data revealed 3H-thymidine incorporation rates greater than 3,433 for particulate S. typhi, Ty2 antigen stimulated cultures signified acquired immunity at a sensitivity and specificity of 82.7; for soluble S. typhi O polysaccharide antigen-stimulated cultures, ct/min/culture values of greater than 1,237 signified immunity (sensitivity and specificity 70.5%). PMID:2702777

Mission possible? The performance of prosocially motivated employees depends on manager trustworthiness.

PubMed

Grant, Adam M; Sumanth, John J

2009-07-01

The authors propose that in mission-driven organizations, prosocially motivated employees are more likely to perform effectively when trust cues enhance their perceptions of task significance. The authors develop and test a model linking prosocial motivation, trust cues, task significance, and performance across 3 studies of fundraisers using 3 different objective performance measures. In Study 1, perceiving managers as trustworthy strengthened the relationship between employees' prosocial motivation and performance, measured in terms of calls made. This moderated relationship was mediated by employees' perceptions of task significance. Study 2 replicated the interaction of manager trustworthiness and prosocial motivation in predicting a new measure of performance: dollars raised. It also revealed 3-way interactions between prosocial motivation, manager trustworthiness, and dispositional trust propensity, such that high trust propensity compensated for low manager trustworthiness to strengthen the association between employees' prosocial motivation and performance. Study 3 replicated all of the previous mediation and moderation findings in predicting initiative taken by professional fundraisers. Implications for work motivation, work design, and trust in organizations are discussed.

High body mass index is associated with impaired cognitive control.

PubMed

Sellaro, Roberta; Colzato, Lorenza S

2017-06-01

The prevalence of weight problems is increasing worldwide. There is growing evidence that high body mass index (BMI) is associated with frontal lobe dysfunction and cognitive deficits concerning mental flexibility and inhibitory control efficiency. The present study aims at replicating and extending these observations. We compared cognitive control performance of normal weight (BMI < 25) and overweight (BMI ≥ 25) university students on a task tapping either inhibitory control (Experiment 1) or interference control (Experiment 2). Experiment 1 replicated previous findings that found less efficient inhibitory control in overweight individuals. Experiment 2 complemented these findings by showing that cognitive control impairments associated with high BMI also extend to the ability to resolve stimulus-induced response conflict and to engage in conflict-driven control adaptation. The present results are consistent with and extend previous literature showing that high BMI in young, otherwise healthy individuals is associated with less efficient cognitive control functioning. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structural Basis of Mitochondrial Transcription Initiation.

PubMed

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

2017-11-16

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

Identification of a small molecule inhibitor of Ebola virus genome replication and transcription using in silico screening.

PubMed

Easton, Victoria; McPhillie, Martin; Garcia-Dorival, Isabel; Barr, John N; Edwards, Thomas A; Foster, Richard; Fishwick, Colin; Harris, Mark

2018-06-02

Ebola virus (EBOV) causes a severe haemorrhagic fever in humans and has a mortality rate over 50%. With no licensed drug treatments available, EBOV poses a significant threat. Investigations into possible therapeutics have been severely hampered by the classification of EBOV as a BSL4 pathogen. Here, we describe a drug discovery pathway combining in silico screening of compounds predicted to bind to a hydrophobic pocket on the nucleoprotein (NP); with a robust and rapid EBOV minigenome assay for inhibitor validation at BSL2. One compound (MCCB4) was efficacious (EC 50 4.8 μM), exhibited low cytotoxicity (CC 50  > 100 μM) and was specific, with no effect on either a T7 RNA polymerase driven firefly luciferase or a Bunyamwera virus minigenome. Further investigations revealed that this small molecule inhibitor was able to outcompete established replication complexes, an essential aspect for a potential EBOV treatment. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Registered Replication Report: Rand, Greene, and Nowak (2012).

PubMed

Bouwmeester, S; Verkoeijen, P P J L; Aczel, B; Barbosa, F; Bègue, L; Brañas-Garza, P; Chmura, T G H; Cornelissen, G; Døssing, F S; Espín, A M; Evans, A M; Ferreira-Santos, F; Fiedler, S; Flegr, J; Ghaffari, M; Glöckner, A; Goeschl, T; Guo, L; Hauser, O P; Hernan-Gonzalez, R; Herrero, A; Horne, Z; Houdek, P; Johannesson, M; Koppel, L; Kujal, P; Laine, T; Lohse, J; Martins, E C; Mauro, C; Mischkowski, D; Mukherjee, S; Myrseth, K O R; Navarro-Martínez, D; Neal, T M S; Novakova, J; Pagà, R; Paiva, T O; Palfi, B; Piovesan, M; Rahal, R-M; Salomon, E; Srinivasan, N; Srivastava, A; Szaszi, B; Szollosi, A; Thor, K Ø; Tinghög, G; Trueblood, J S; Van Bavel, J J; van 't Veer, A E; Västfjäll, D; Warner, M; Wengström, E; Wills, J; Wollbrant, C E

2017-05-01

In an anonymous 4-person economic game, participants contributed more money to a common project (i.e., cooperated) when required to decide quickly than when forced to delay their decision (Rand, Greene & Nowak, 2012), a pattern consistent with the social heuristics hypothesis proposed by Rand 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 to conditions and who met the protocol inclusion criteria (an intent-to-treat approach that included the 65.9% of participants in the time-pressure condition and 7.5% in the forced-delay condition who did not adhere to the time constraints), and we observed a difference in contributions of -0.37 percentage points compared with an 8.6 percentage point difference calculated from the original data. Analyzing the data as the original article did, including data only for participants who complied with the time constraints, the RRR observed a 10.37 percentage point difference in contributions compared with a 15.31 percentage point difference in the original study. In combination, the results of the intent-to-treat analysis and the compliant-only analysis are consistent with the presence of selection biases and the absence of a causal effect of time pressure on cooperation.

Bovine lactoferrin digested with human gastrointestinal enzymes inhibits replication of human echovirus 5 in cell culture.

PubMed

Furlund, Camilla B; Kristoffersen, Anja B; Devold, Tove G; Vegarud, Gerd E; Jonassen, Christine M

2012-07-01

Many infant formulas are enriched with lactoferrin (Lf) because of its claimed beneficial effects on health. Native bovine Lf (bLf) is known to inhibit in vitro replication of human enteroviruses, a group of pathogenic viruses that replicate in the gut as their primary infection site. On the basis of a model digestion and human gastrointestinal enzymes, we hypothesized that bLf could retain its antiviral properties against enterovirus in the gastrointestinal tract, either as an intact protein or through bioactive peptide fragments released by digestive enzymes. To test our hypothesis, bLf was digested with human gastric juice and duodenal juice in a 2-step in vitro digestion model. Two gastric pH levels and reduction conditions were used to simulate physiological conditions in adults and infants. The antiviral activity of native bLf and of the digested fractions was studied on echovirus 5 in vitro, using various assay conditions, addressing several mechanisms for replication inhibition. Both native and digested bLf fractions revealed a significant inhibitory effect, when added before or simultaneously with the virus onto the cells. Furthermore, a significant stronger sustained antiviral effect was observed when bLf was fully digested in the gastric phase with fast pH reduction to 2.5, compared with native bLf, suggesting the release of antiviral peptides from bLf during the human digestion process. In conclusion, this study demonstrates that bLf may have a role in the prevention of human gastrointestinal virus infection under physiological conditions and that food containing bLf may protect against infection in vivo. Copyright © 2012 Elsevier Inc. All rights reserved.

Registered Replication Report: Rand, Greene, and Nowak (2012)

PubMed Central

Bouwmeester, S.; Verkoeijen, P. P. J. L.; Aczel, B.; Barbosa, F.; Bègue, L.; Brañas-Garza, P.; Chmura, T. G. H.; Cornelissen, G.; Døssing, F. S.; Espín, A. M.; Evans, A. M.; Ferreira-Santos, F.; Fiedler, S.; Flegr, J.; Ghaffari, M.; Glöckner, A.; Goeschl, T.; Guo, L.; Hauser, O. P.; Hernan-Gonzalez, R.; Herrero, A.; Horne, Z.; Houdek, P.; Johannesson, M.; Koppel, L.; Kujal, P.; Laine, T.; Lohse, J.; Martins, E. C.; Mauro, C.; Mischkowski, D.; Mukherjee, S.; Myrseth, K. O. R.; Navarro-Martínez, D.; Neal, T. M. S.; Novakova, J.; Pagà, R.; Paiva, T. O.; Palfi, B.; Piovesan, M.; Rahal, R.-M.; Salomon, E.; Srinivasan, N.; Srivastava, A.; Szaszi, B.; Szollosi, A.; Thor, K. Ø.; Tinghög, G.; Trueblood, J. S.; Van Bavel, J. J.; van ‘t Veer, A. E.; Västfjäll, D.; Warner, M.; Wengström, E.; Wills, J.; Wollbrant, C. E.

2017-01-01

In an anonymous 4-person economic game, participants contributed more money to a common project (i.e., cooperated) when required to decide quickly than when forced to delay their decision (Rand, Greene & Nowak, 2012), a pattern consistent with the social heuristics hypothesis proposed by Rand 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 to conditions and who met the protocol inclusion criteria (an intent-to-treat approach that included the 65.9% of participants in the time-pressure condition and 7.5% in the forced-delay condition who did not adhere to the time constraints), and we observed a difference in contributions of −0.37 percentage points compared with an 8.6 percentage point difference calculated from the original data. Analyzing the data as the original article did, including data only for participants who complied with the time constraints, the RRR observed a 10.37 percentage point difference in contributions compared with a 15.31 percentage point difference in the original study. In combination, the results of the intent-to-treat analysis and the compliant-only analysis are consistent with the presence of selection biases and the absence of a causal effect of time pressure on cooperation. PMID:28475467

Monitoring method and apparatus using high-frequency carrier

DOEpatents

Haynes, H.D.

1996-04-30

A method and apparatus for monitoring an electrical-motor-driven device by injecting a high frequency carrier signal onto the power line current. The method is accomplished by injecting a high frequency carrier signal onto an AC power line current. The AC power line current supplies the electrical-motor-driven device with electrical energy. As a result, electrical and mechanical characteristics of the electrical-motor-driven device modulate the high frequency carrier signal and the AC power line current. The high frequency carrier signal is then monitored, conditioned and demodulated. Finally, the modulated high frequency carrier signal is analyzed to ascertain the operating condition of the electrical-motor-driven device. 6 figs.

Construction of Nef-positive doxycycline-dependent HIV-1 variants using bicistronic expression elements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Velden, Yme U. van der; Kleibeuker, Wendy; Harwig, Alex

Conditionally replicating HIV-1 variants that can be switched on and off at will are attractive tools for HIV research. We previously developed a genetically modified HIV-1 variant that replicates exclusively when doxycycline (dox) is administered. The nef gene in this HIV-rtTA variant was replaced with the gene encoding the dox-dependent rtTA transcriptional activator. Because loss of Nef expression compromises virus replication in primary cells and precludes studies on Nef function, we tested different approaches to restore Nef production in HIV-rtTA. Strategies that involved translation via an EMCV or synthetic internal ribosome entry site (IRES) failed because these elements were incompatiblemore » with efficient virus replication. Fusion protein approaches with the FMDV 2A peptide and human ubiquitin were successful and resulted in genetically-stable Nef-expressing HIV-rtTA strains that replicate more efficiently in primary T-cells and human immune system (HIS) mice than Nef-deficient variants, thus confirming the positive effect of Nef on in vivo virus replication. - Highlights: • Different approaches to encode additional proteins in the HIV-1 genome were tested. • IRES translation elements are incompatible with efficient HIV-1 replication. • Ubiquitin and 2A fusion protein approaches allow efficient HIV-1 replication. • Doxycycline-controlled HIV-1 variants that encode all viral proteins were developed. • Nef stimulates HIV-rtTA replication in primary cells and human immune system mice.« less

Effects of Concept Mapping Instruction on the Vocabulary Acquisition Skills of Seventh-Graders with Mild Disabilities: A Replication Study

ERIC Educational Resources Information Center

Palmer, Jessica; Boon, Richard T.; Spencer, Vicky G.

2014-01-01

The present investigation replicates and extends an earlier study comparing 2 conditions, a dictionary approach versus a concept mapping model, on the learning of vocabulary words among 4 students with mild disabilities (i.e., emotional and/or behavioral disorders and other health impairments) attending a middle school. An A-B-A-B design was used…

The value of repeating studies and multiple controls: replicated 28-day growth studies of rainbow trout exposed to clofibric acid.

PubMed

Owen, Stewart F; Huggett, Duane B; Hutchinson, Thomas H; Hetheridge, Malcolm J; McCormack, Paul; Kinter, Lewis B; Ericson, Jon F; Constantine, Lisa A; Sumpter, John P

2010-12-01

Two studies to examine the effect of waterborne clofibric acid (CA) on growth-rate and condition of rainbow trout were conducted using accepted regulatory tests (Organisation for Economic Co-operation and Development [OECD] 215). The first study (in 2005) showed significant reductions after 21 d of exposure (21-d growth lowest-observed-effect concentration [LOEC] = 0.1 µg/L, 21-d condition LOEC = 0.1 µg/L) that continued to 28 d. Growth rate was reduced by approximately 50% (from 5.27 to 2.67% per day), while the condition of the fish reduced in a concentration-dependant manner. Additionally, in a concentration-dependent manner, significant changes in relative liver size were observed, such that increasing concentrations of CA resulted in smaller livers after 28-d exposure. A no-observed-effect concentration (NOEC) was not achieved in the 2005 study. An expanded second study (in 2006) that included a robust bridge to the 2005 study, with four replicate tanks of eight individual fish per concentration, did not repeat the 2005 findings. In the 2006 study, no significant effect on growth rate, condition, or liver biometry was observed after 21 or 28 d (28-d growth NOEC = 10 µg/L, 28-d condition NOEC = 10 µg/L), contrary to the 2005 findings. We do not dismiss either of these findings and suggest both are relevant and stand for comparison. However, the larger 2006 study carries more statistical power and multiple-tank replication, so probably produced the more robust findings. Despite sufficient statistical power in each study, interpretation of these and similar studies should be conducted with caution, because much significance is placed on the role of limited numbers of individual and tank replicates and the influence of control animals. Copyright © 2010 SETAC.

Quantile regression of microgeographic variation in population characteristics of an invasive vertebrate predator

USGS Publications Warehouse

Siers, Shane R.; Savidge, Julie A.; Reed, Robert

2017-01-01

Localized ecological conditions have the potential to induce variation in population characteristics such as size distributions and body conditions. The ability to generalize the influence of ecological characteristics on such population traits may be particularly meaningful when those traits influence prospects for successful management interventions. To characterize variability in invasive Brown Treesnake population attributes within and among habitat types, we conducted systematic and seasonally-balanced surveys, collecting 100 snakes from each of 18 sites: three replicates within each of six major habitat types comprising 95% of Guam’s geographic expanse. Our study constitutes one of the most comprehensive and controlled samplings of any published snake study. Quantile regression on snake size and body condition indicated significant ecological heterogeneity, with a general trend of relative consistency of size classes and body conditions within and among scrub and Leucaena forest habitat types and more heterogeneity among ravine forest, savanna, and urban residential sites. Larger and more robust snakes were found within some savanna and urban habitat replicates, likely due to relative availability of larger prey. Compared to more homogeneous samples in the wet season, variability in size distributions and body conditions was greater during the dry season. Although there is evidence of habitat influencing Brown Treesnake populations at localized scales (e.g., the higher prevalence of larger snakes—particularly males—in savanna and urban sites), the level of variability among sites within habitat types indicates little ability to make meaningful predictions about these traits at unsampled locations. Seasonal variability within sites and habitats indicates that localized population characterization should include sampling in both wet and dry seasons. Extreme values at single replicates occasionally influenced overall habitat patterns, while pooling replicates masked variability among sites. A full understanding of population characteristics should include an assessment of variability both at the site and habitat level.

Quantile regression of microgeographic variation in population characteristics of an invasive vertebrate predator

PubMed Central

Siers, Shane R.; Savidge, Julie A.; Reed, Robert N.

2017-01-01

Localized ecological conditions have the potential to induce variation in population characteristics such as size distributions and body conditions. The ability to generalize the influence of ecological characteristics on such population traits may be particularly meaningful when those traits influence prospects for successful management interventions. To characterize variability in invasive Brown Treesnake population attributes within and among habitat types, we conducted systematic and seasonally-balanced surveys, collecting 100 snakes from each of 18 sites: three replicates within each of six major habitat types comprising 95% of Guam’s geographic expanse. Our study constitutes one of the most comprehensive and controlled samplings of any published snake study. Quantile regression on snake size and body condition indicated significant ecological heterogeneity, with a general trend of relative consistency of size classes and body conditions within and among scrub and Leucaena forest habitat types and more heterogeneity among ravine forest, savanna, and urban residential sites. Larger and more robust snakes were found within some savanna and urban habitat replicates, likely due to relative availability of larger prey. Compared to more homogeneous samples in the wet season, variability in size distributions and body conditions was greater during the dry season. Although there is evidence of habitat influencing Brown Treesnake populations at localized scales (e.g., the higher prevalence of larger snakes—particularly males—in savanna and urban sites), the level of variability among sites within habitat types indicates little ability to make meaningful predictions about these traits at unsampled locations. Seasonal variability within sites and habitats indicates that localized population characterization should include sampling in both wet and dry seasons. Extreme values at single replicates occasionally influenced overall habitat patterns, while pooling replicates masked variability among sites. A full understanding of population characteristics should include an assessment of variability both at the site and habitat level. PMID:28570632

Quantile regression of microgeographic variation in population characteristics of an invasive vertebrate predator.

PubMed

Siers, Shane R; Savidge, Julie A; Reed, Robert N

2017-01-01

Localized ecological conditions have the potential to induce variation in population characteristics such as size distributions and body conditions. The ability to generalize the influence of ecological characteristics on such population traits may be particularly meaningful when those traits influence prospects for successful management interventions. To characterize variability in invasive Brown Treesnake population attributes within and among habitat types, we conducted systematic and seasonally-balanced surveys, collecting 100 snakes from each of 18 sites: three replicates within each of six major habitat types comprising 95% of Guam's geographic expanse. Our study constitutes one of the most comprehensive and controlled samplings of any published snake study. Quantile regression on snake size and body condition indicated significant ecological heterogeneity, with a general trend of relative consistency of size classes and body conditions within and among scrub and Leucaena forest habitat types and more heterogeneity among ravine forest, savanna, and urban residential sites. Larger and more robust snakes were found within some savanna and urban habitat replicates, likely due to relative availability of larger prey. Compared to more homogeneous samples in the wet season, variability in size distributions and body conditions was greater during the dry season. Although there is evidence of habitat influencing Brown Treesnake populations at localized scales (e.g., the higher prevalence of larger snakes-particularly males-in savanna and urban sites), the level of variability among sites within habitat types indicates little ability to make meaningful predictions about these traits at unsampled locations. Seasonal variability within sites and habitats indicates that localized population characterization should include sampling in both wet and dry seasons. Extreme values at single replicates occasionally influenced overall habitat patterns, while pooling replicates masked variability among sites. A full understanding of population characteristics should include an assessment of variability both at the site and habitat level.

MCM5: a new actor in the link between DNA replication and Meier-Gorlin syndrome.

PubMed

Vetro, Annalisa; Savasta, Salvatore; Russo Raucci, Annalisa; Cerqua, Cristina; Sartori, Geppo; Limongelli, Ivan; Forlino, Antonella; Maruelli, Silvia; Perucca, Paola; Vergani, Debora; Mazzini, Giuliano; Mattevi, Andrea; Stivala, Lucia Anna; Salviati, Leonardo; Zuffardi, Orsetta

2017-05-01

Meier-Gorlin syndrome (MGORS) is a rare disorder characterized by primordial dwarfism, microtia, and patellar aplasia/hypoplasia. Recessive mutations in ORC1, ORC4, ORC6, CDT1, CDC6, and CDC45, encoding members of the pre-replication (pre-RC) and pre-initiation (pre-IC) complexes, and heterozygous mutations in GMNN, a regulator of cell-cycle progression and DNA replication, have already been associated with this condition. We performed whole-exome sequencing (WES) in a patient with a clinical diagnosis of MGORS and identified biallelic variants in MCM5. This gene encodes a subunit of the replicative helicase complex, which represents a component of the pre-RC. Both variants, a missense substitution within a conserved domain critical for the helicase activity, and a single base deletion causing a frameshift and a premature stop codon, were predicted to be detrimental for the MCM5 function. Although variants of MCM5 have never been reported in specific human diseases, defect of this gene in zebrafish causes a phenotype of growth restriction overlapping the one associated with orc1 depletion. Complementation experiments in yeast showed that the plasmid carrying the missense variant was unable to rescue the lethal phenotype caused by mcm5 deletion. Moreover cell-cycle progression was delayed in patient's cells, as already shown for mutations in the ORC1 gene. Altogether our findings support the role of MCM5 as a novel gene involved in MGORS, further emphasizing that this condition is caused by impaired DNA replication.

Safety mechanism assisted by the repressor of tetracycline (SMART) vaccinia virus vectors for vaccines and therapeutics.

PubMed

Grigg, Patricia; Titong, Allison; Jones, Leslie A; Yilma, Tilahun D; Verardi, Paulo H

2013-09-17

Replication-competent viruses, such as Vaccinia virus (VACV), are powerful tools for the development of oncolytic viral therapies and elicit superior immune responses when used as vaccine and immunotherapeutic vectors. However, severe complications from uncontrolled viral replication can occur, particularly in immunocompromised individuals or in those with other predisposing conditions. VACVs constitutively expressing interferon-γ (IFN-γ) replicate in cell culture indistinguishably from control viruses; however, they replicate in vivo to low or undetectable levels, and are rapidly cleared even in immunodeficient animals. In an effort to develop safe and highly effective replication-competent VACV vectors, we established a system to inducibly express IFN-γ. Our SMART (safety mechanism assisted by the repressor of tetracycline) vectors are designed to express the tetracycline repressor under a constitutive VACV promoter and IFN-γ under engineered tetracycline-inducible promoters. Immunodeficient SCID mice inoculated with VACVs not expressing IFN-γ demonstrated severe weight loss, whereas those given VACVs expressing IFN-γ under constitutive VACV promoters showed no signs of infection. Most importantly, mice inoculated with a VACV expressing the IFN-γ gene under an inducible promoter remained healthy in the presence of doxycycline, but exhibited severe weight loss in the absence of doxycycline. In this study, we developed a safety mechanism for VACV based on the conditional expression of IFN-γ under a tightly controlled tetracycline-inducible VACV promoter for use in vaccines and oncolytic cancer therapies.

Ecology and Evolution in the RNA World Dynamics and Stability of Prebiotic Replicator Systems.

PubMed

Szilágyi, András; Zachar, István; Scheuring, István; Kun, Ádám; Könnyű, Balázs; Czárán, Tamás

2017-11-27

As of today, the most credible scientific paradigm pertaining to the origin of life on Earth is undoubtedly the RNA World scenario. It is built on the assumption that catalytically active replicators (most probably RNA-like macromolecules) may have been responsible for booting up life almost four billion years ago. The many different incarnations of nucleotide sequence (string) replicator models proposed recently are all attempts to explain on this basis how the genetic information transfer and the functional diversity of prebiotic replicator systems may have emerged, persisted and evolved into the first living cell. We have postulated three necessary conditions for an RNA World model system to be a dynamically feasible representation of prebiotic chemical evolution: (1) it must maintain and transfer a sufficient diversity of information reliably and indefinitely, (2) it must be ecologically stable and (3) it must be evolutionarily stable. In this review, we discuss the best-known prebiotic scenarios and the corresponding models of string-replicator dynamics and assess them against these criteria. We suggest that the most popular of prebiotic replicator systems, the hypercycle, is probably the worst performer in almost all of these respects, whereas a few other model concepts (parabolic replicator, open chaotic flows, stochastic corrector, metabolically coupled replicator system) are promising candidates for development into coherent models that may become experimentally accessible in the future.

Replication of the Escherichia coli chromosome in RNase HI-deficient cells: multiple initiation regions and fork dynamics.

PubMed

Maduike, Nkabuije Z; Tehranchi, Ashley K; Wang, Jue D; Kreuzer, Kenneth N

2014-01-01

DNA replication in Escherichia coli is normally initiated at a single origin, oriC, dependent on initiation protein DnaA. However, replication can be initiated elsewhere on the chromosome at multiple ectopic oriK sites. Genetic evidence indicates that initiation from oriK depends on RNA-DNA hybrids (R-loops), which are normally removed by enzymes such as RNase HI to prevent oriK from misfiring during normal growth. Initiation from oriK sites occurs in RNase HI-deficient mutants, and possibly in wild-type cells under certain unusual conditions. Despite previous work, the locations of oriK and their impact on genome stability remain unclear. We combined 2D gel electrophoresis and whole genome approaches to map genome-wide oriK locations. The DNA copy number profiles of various RNase HI-deficient strains contained multiple peaks, often in consistent locations, identifying candidate oriK sites. Removal of RNase HI protein also leads to global alterations of replication fork migration patterns, often opposite to normal replication directions, and presumably eukaryote-like replication fork merging. Our results have implications for genome stability, offering a new understanding of how RNase HI deficiency results in R-loop-mediated transcription-replication conflict, as well as inappropriate replication stalling or blockage at Ter sites outside of the terminus trap region and at ribosomal operons. © 2013 John Wiley & Sons Ltd.

Ecology and Evolution in the RNA World Dynamics and Stability of Prebiotic Replicator Systems

PubMed Central

Szilágyi, András; Kun, Ádám; Könnyű, Balázs; Czárán, Tamás

2017-01-01

As of today, the most credible scientific paradigm pertaining to the origin of life on Earth is undoubtedly the RNA World scenario. It is built on the assumption that catalytically active replicators (most probably RNA-like macromolecules) may have been responsible for booting up life almost four billion years ago. The many different incarnations of nucleotide sequence (string) replicator models proposed recently are all attempts to explain on this basis how the genetic information transfer and the functional diversity of prebiotic replicator systems may have emerged, persisted and evolved into the first living cell. We have postulated three necessary conditions for an RNA World model system to be a dynamically feasible representation of prebiotic chemical evolution: (1) it must maintain and transfer a sufficient diversity of information reliably and indefinitely, (2) it must be ecologically stable and (3) it must be evolutionarily stable. In this review, we discuss the best-known prebiotic scenarios and the corresponding models of string-replicator dynamics and assess them against these criteria. We suggest that the most popular of prebiotic replicator systems, the hypercycle, is probably the worst performer in almost all of these respects, whereas a few other model concepts (parabolic replicator, open chaotic flows, stochastic corrector, metabolically coupled replicator system) are promising candidates for development into coherent models that may become experimentally accessible in the future. PMID:29186916

Motor monitoring method and apparatus using high frequency current components

DOEpatents

Casada, D.A.

1996-05-21

A motor current analysis method and apparatus for monitoring electrical-motor-driven devices are disclosed. The method and apparatus utilize high frequency portions of the motor current spectra to evaluate the condition of the electric motor and the device driven by the electric motor. The motor current signal produced as a result of an electric motor is monitored and the low frequency components of the signal are removed by a high-pass filter. The signal is then analyzed to determine the condition of the electrical motor and the driven device. 16 figs.

Motor monitoring method and apparatus using high frequency current components

DOEpatents

Casada, Donald A.

1996-01-01

A motor current analysis method and apparatus for monitoring electrical-motor-driven devices. The method and apparatus utilize high frequency portions of the motor current spectra to evaluate the condition of the electric motor and the device driven by the electric motor. The motor current signal produced as a result of an electric motor is monitored and the low frequency components of the signal are removed by a high-pass filter. The signal is then analyzed to determine the condition of the electrical motor and the driven device.

A microengineered collagen scaffold for generating a polarized crypt-villus architecture of human small intestinal epithelium.

PubMed

Wang, Yuli; Gunasekara, Dulan B; Reed, Mark I; DiSalvo, Matthew; Bultman, Scott J; Sims, Christopher E; Magness, Scott T; Allbritton, Nancy L

2017-06-01

The human small intestinal epithelium possesses a distinct crypt-villus architecture and tissue polarity in which proliferative cells reside inside crypts while differentiated cells are localized to the villi. Indirect evidence has shown that the processes of differentiation and migration are driven in part by biochemical gradients of factors that specify the polarity of these cellular compartments; however, direct evidence for gradient-driven patterning of this in vivo architecture has been hampered by limitations of the in vitro systems available. Enteroid cultures are a powerful in vitro system; nevertheless, these spheroidal structures fail to replicate the architecture and lineage compartmentalization found in vivo, and are not easily subjected to gradients of growth factors. In the current work, we report the development of a micropatterned collagen scaffold with suitable extracellular matrix and stiffness to generate an in vitro self-renewing human small intestinal epithelium that replicates key features of the in vivo small intestine: a crypt-villus architecture with appropriate cell-lineage compartmentalization and an open and accessible luminal surface. Chemical gradients applied to the crypt-villus axis promoted the creation of a stem/progenitor-cell zone and supported cell migration along the crypt-villus axis. This new approach combining microengineered scaffolds, biophysical cues and chemical gradients to control the intestinal epithelium ex vivo can serve as a physiologically relevant mimic of the human small intestinal epithelium, and is broadly applicable to model other tissues that rely on gradients for physiological function. Copyright © 2017 Elsevier Ltd. All rights reserved.

Thermal force approach to molecular evolution.

PubMed

Braun, Dieter; Libchaber, Albert

2004-06-01

Recent experiments are discussed where temperature gradients across mesoscopic pores are shown to provide essential mechanisms for autonomous molecular evolution. On the one hand, laminar thermal convection can drive DNA replication as the molecules are continuously cycled between hot and cold regions of a chamber. On the other hand, thermophoresis can accumulate charged biopolymers in similar convection settings. The experiments show that temperature differences analogous to those across porous rocks present a robust nonequilibrium boundary condition to feed the replication and accumulation of evolving molecules. It is speculated that similar nonequilibrium conditions near porous submarine hydrothermal mounds could have triggered the origin of life. In such a scenario, the encapsulation of cells with membranes would be a later development. It is expected that detailed studies of mesoscopic boundary conditions under nonequilibrium conditions will reveal new connecting pieces in the fascinating puzzle of the origins of life.

Psychophysiological whole-brain network clustering based on connectivity dynamics analysis in naturalistic conditions.

PubMed

Raz, Gal; Shpigelman, Lavi; Jacob, Yael; Gonen, Tal; Benjamini, Yoav; Hendler, Talma

2016-12-01

We introduce a novel method for delineating context-dependent functional brain networks whose connectivity dynamics are synchronized with the occurrence of a specific psychophysiological process of interest. In this method of context-related network dynamics analysis (CRNDA), a continuous psychophysiological index serves as a reference for clustering the whole-brain into functional networks. We applied CRNDA to fMRI data recorded during the viewing of a sadness-inducing film clip. The method reliably demarcated networks in which temporal patterns of connectivity related to the time series of reported emotional intensity. Our work successfully replicated the link between network connectivity and emotion rating in an independent sample group for seven of the networks. The demarcated networks have clear common functional denominators. Three of these networks overlap with distinct empathy-related networks, previously identified in distinct sets of studies. The other networks are related to sensorimotor processing, language, attention, and working memory. The results indicate that CRNDA, a data-driven method for network clustering that is sensitive to transient connectivity patterns, can productively and reliably demarcate networks that follow psychologically meaningful processes. Hum Brain Mapp 37:4654-4672, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

The ‘male escape hypothesis’: sex-biased metamorphosis in response to climatic drivers in a facultatively paedomorphic amphibian

PubMed Central

Mathiron, Anthony G. E.; Lena, Jean-Paul; Baouch, Sarah

2017-01-01

Paedomorphosis is a major evolutionary process that bypasses metamorphosis and allows reproduction in larvae. In newts and salamanders, it can be facultative with paedomorphs retaining gills and metamorphs dispersing. The evolution of these developmental processes is thought to have been driven by the costs and benefits of inhabiting aquatic versus terrestrial habitats. In this context, we aimed at testing the hypothesis that climatic drivers affect phenotypic transition and the difference across sexes because sex-ratio is biased in natural populations. Through a replicated laboratory experiment, we showed that paedomorphic palmate newts (Lissotriton helveticus) metamorphosed at a higher frequency when water availability decreased and metamorphosed earlier when temperature increased in these conditions. All responses were sex-biased, and males were more prone to change phenotype than females. Our work shows how climatic variables can affect facultative paedomorphosis and support theoretical models predicting life on land instead of in water. Moreover, because males metamorphose and leave water more often and earlier than females, these results, for the first time, give an experimental explanation for the rarity of male paedomorphosis (the ‘male escape hypothesis’) and suggest the importance of sex in the evolution of paedomorphosis versus metamorphosis. PMID:28424346

Eco-evolutionary Red Queen dynamics regulate biodiversity in a metabolite-driven microbial system.

PubMed

Bonachela, Juan A; Wortel, Meike T; Stenseth, Nils Chr

2017-12-15

The Red Queen Hypothesis proposes that perpetual co-evolution among organisms can result from purely biotic drivers. After more than four decades, there is no satisfactory understanding as to which mechanisms trigger Red Queen dynamics or their implications for ecosystem features such as biodiversity. One reason for such a knowledge gap is that typical models are complicated theories where limit cycles represent an idealized Red Queen, and therefore cannot be used to devise experimental setups. Here, we bridge this gap by introducing a simple model for microbial systems able to show Red Queen dynamics. We explore diverse biotic sources that can drive the emergence of the Red Queen and that have the potential to be found in nature or to be replicated in the laboratory. Our model enables an analytical understanding of how Red Queen dynamics emerge in our setup, and the translation of model terms and phenomenology into general underlying mechanisms. We observe, for example, that in our system the Red Queen offers opportunities for the increase of biodiversity by facilitating challenging conditions for intraspecific dominance, whereas stasis tends to homogenize the system. Our results can be used to design and engineer experimental microbial systems showing Red Queen dynamics.

A Combined Solar and Geomagnetic Index for Thermospheric Climate

NASA Technical Reports Server (NTRS)

Hunt, Linda; Mlynczak, Marty

2015-01-01

Infrared radiation from nitric oxide (NO) at 5.3 Â is a primary mechanism by which the thermosphere cools to space. The SABER instrument on the NASA TIMED satellite has been measuring thermospheric cooling by NO for over 13 years. Physically, changes in NO emission are due to changes in temperature, atomic oxygen, and the NO density. These physical changes however are driven by changes in solar irradiance and changes in geomagnetic conditions. We show that the SABER time series of globally integrated infrared power (Watts) radiated by NO can be replicated accurately by a multiple linear regression fit using the F10.7, Ap, and Dst indices. This fit enables several fundamental properties of NO cooling to be determined as well as their variability with time, permitting reconstruction of the NO power time series back nearly 70 years with extant databases of these indices. The relative roles of solar ultraviolet and geomagnetic processes in determining the NO cooling are derived and shown to be solar cycle dependent. This reconstruction provides a long-term time series of an integral radiative constraint on thermospheric climate that can be used to test climate models.

The importance of replication in wildlife research

USGS Publications Warehouse

Johnson, D.H.

2002-01-01

Wildlife ecology and management studies have been widely criticized for deficiencies in design or analysis. Manipulative experiments--with controls, randomization, and replication in space and time--provide powerful ways of learning about natural systems and establishing causal relationships, but such studies are rare in our field. Observational studies and sample surveys are more common; they also require appropriate design and analysis. More important than the design and analysis of individual studies is metareplication: replication of entire studies. Similar conclusions obtained from studies of the same phenomenon conducted under widely differing conditions will give us greater confidence in the generality of those findings than would any single study, however well designed and executed.

Warning times for species extinctions due to climate change.

PubMed

Stanton, Jessica C; Shoemaker, Kevin T; Pearson, Richard G; Akçakaya, H Resit

2015-03-01

Climate change is likely to become an increasingly major obstacle to slowing the rate of species extinctions. Several new assessment approaches have been proposed for identifying climate-vulnerable species, based on the assumption that established systems such as the IUCN Red List need revising or replacing because they were not developed to explicitly consider climate change. However, no assessment approach has been tested to determine its ability to provide advanced warning time for conservation action for species that might go extinct due to climate change. To test the performance of the Red List system in this capacity, we used linked niche-demographic models with habitat dynamics driven by a 'business-as-usual' climate change scenario. We generated replicate 100-year trajectories for range-restricted reptiles and amphibians endemic to the United States. For each replicate, we categorized the simulated species according to IUCN Red List criteria at annual, 5-year, and 10-year intervals (the latter representing current practice). For replicates that went extinct, we calculated warning time as the number of years the simulated species was continuously listed in a threatened category prior to extinction. To simulate data limitations, we repeated the analysis using a single criterion at a time (disregarding other listing criteria). Results show that when all criteria can be used, the Red List system would provide several decades of warning time (median = 62 years; >20 years for 99% of replicates), but suggest that conservation actions should begin as soon as a species is listed as Vulnerable, because 50% of replicates went extinct within 20 years of becoming uplisted to Critically Endangered. When only one criterion was used, warning times were substantially shorter, but more frequent assessments increased the warning time by about a decade. Overall, we found that the Red List criteria reliably provide a sensitive and precautionary way to assess extinction risk under climate change. © 2014 John Wiley & Sons Ltd.

Replication of transformation-defective mutants of the Prague strain of Rous sarcoma virus and isolation of a td mutant from duck-adapted PR-RSV-C.

PubMed

Geryk, J; Mazo, A; Svoboda, J; Hlozánek, I

1980-01-01

The replication of transformation-defective mutants of the Prague strain of Rous sarcoma virus subgroup C was studied using roller cultures. Under such conditions, 10(5)--10(6) infectous units of virus per 0.2 ml were produced, as revealed in both the reverse transcriptase and 16Q complementation tests. A new td daPR-RSV-C mutant was isolated from duck-adapted PR-RSV-C. This mutant replicated in roller cultures with equal efficiency as the original td PR-RSV-C. It was verified that td daPR-RSV-C does not transform chicken fibroblasts, is not oncogenic for 3-week-old chickens and has subgroup C host-range specificity. Both td mutants replicate in duck cells and reach the same titres.

Copying of holograms by spot scanning approach.

PubMed

Okui, Makoto; Wakunami, Koki; Oi, Ryutaro; Ichihashi, Yasuyuki; Jackin, Boaz Jessie; Yamamoto, Kenji

2018-05-20

To replicate holograms, contact copying has conventionally been used. In this approach, a photosensitive material is fixed together with a master hologram and illuminated with a coherent beam. This method is simple and enables high-quality copies; however, it requires a large optical setup for large-area holograms. In this paper, we present a new method of replicating holograms that uses a relatively compact optical system even for the replication of large holograms. A small laser spot that irradiates only part of the hologram is used to reproduce the hologram by scanning the spot over the whole area of the hologram. We report on the results of experiments carried out to confirm the copy quality, along with a guide to design scanning conditions. The results show the potential effectiveness of the large-area hologram replication technology using a relatively compact apparatus.

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.

PubMed

Robinson, Mark D; McCarthy, Davis J; Smyth, Gordon K

2010-01-01

It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data. The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org).

A defect-driven diagnostic method for machine tool spindles

PubMed Central

Vogl, Gregory W.; Donmez, M. Alkan

2016-01-01

Simple vibration-based metrics are, in many cases, insufficient to diagnose machine tool spindle condition. These metrics couple defect-based motion with spindle dynamics; diagnostics should be defect-driven. A new method and spindle condition estimation device (SCED) were developed to acquire data and to separate system dynamics from defect geometry. Based on this method, a spindle condition metric relying only on defect geometry is proposed. Application of the SCED on various milling and turning spindles shows that the new approach is robust for diagnosing the machine tool spindle condition. PMID:28065985

Developing Inhibitors of Translesion DNA Synthesis as Therapeutic Agents against Lung Cancer

DTIC Science & Technology

2015-12-01

normal DNA synthesis. In contrast, pol eta shows a combination of high efficiency and low fidelity when replicating 8-oxo-G. These combined properties...are consistent with a pro- mutagenic role for pol eta when replicating this DNA lesion under cellular conditions. Studies with modified nucleotide...analogs indicate that pol eta relies heavily on hydrogen-bonding interactions during normal and translesion synthesis. However, some nucleobase

Characterization of Explosives Processing Waste Decomposition Due to Composting. Phase 2

DTIC Science & Technology

1992-11-01

with Ceriodaphnia (10 replicates, each containing 15 mL of test solution and one neonate ). In each temporal block of tests, Ceriodsnhnia survival and... neonate per replicate). This reference validated the biological quality of the dilution water, the Ceriodaphnia food, the test conditions (e.g...incubation temperature and photoperiod), and the health of the neonates used to initiate the tests. Information about the leachates, including the

Cytokines Elevated in HIV Elite Controllers Reduce HIV Replication In Vitro and Modulate HIV Restriction Factor Expression

PubMed Central

Jacobs, Evan S.; Abdel-Mohsen, Mohamed; Gibb, Stuart L.; Heitman, John W.; Inglis, Heather C.; Martin, Jeffrey N.; Zhang, Jinbing; Kaidarova, Zhanna; Deng, Xutao; Wu, Shiquan; Anastos, Kathryn; Crystal, Howard; Villacres, Maria C.; Young, Mary; Greenblatt, Ruth M.; Landay, Alan L.; Gange, Stephen J.; Deeks, Steven G.; Golub, Elizabeth T.; Pillai, Satish K.

2017-01-01

ABSTRACT A subset of HIV-infected individuals termed elite controllers (ECs) maintain CD4+ T cell counts and control viral replication in the absence of antiretroviral therapy (ART). Systemic cytokine responses may differentiate ECs from subjects with uncontrolled viral replication or from those who require ART to suppress viral replication. We measured 87 cytokines in four groups of women: 73 ECs, 42 with pharmacologically suppressed viremia (ART), 42 with uncontrolled viral replication (noncontrollers [NCs]), and 48 HIV-uninfected (NEG) subjects. Four cytokines were elevated in ECs but not NCs or ART subjects: CCL14, CCL21, CCL27, and XCL1. In addition, median stromal cell-derived factor-1 (SDF-1) levels were 43% higher in ECs than in NCs. The combination of the five cytokines suppressed R5 and X4 virus replication in resting CD4+ T cells, and individually SDF-1β, CCL14, and CCL27 suppressed R5 virus replication, while SDF-1β, CCL21, and CCL14 suppressed X4 virus replication. Functional studies revealed that the combination of the five cytokines upregulated CD69 and CCR5 and downregulated CXCR4 and CCR7 on CD4+ T cells. The CD69 and CXCR4 effects were driven by SDF-1, while CCL21 downregulated CCR7. The combination of the EC-associated cytokines induced expression of the anti-HIV host restriction factors IFITM1 and IFITM2 and suppressed expression of RNase L and SAMHD1. These results identify a set of cytokines that are elevated in ECs and define their effects on cellular activation, HIV coreceptor expression, and innate restriction factor expression. This cytokine pattern may be a signature characteristic of HIV-1 elite control, potentially important for HIV therapeutic and curative strategies. IMPORTANCE Approximately 1% of people infected with HIV control virus replication without taking antiviral medications. These subjects, termed elite controllers (ECs), are known to have stronger immune responses targeting HIV than the typical HIV-infected subject, but the exact mechanisms of how their immune responses control infection are not known. In this study, we identified five soluble immune signaling molecules (cytokines) in the blood that were higher in ECs than in subjects with typical chronic HIV infection. We demonstrated that these cytokines can activate CD4+ T cells, the target cells for HIV infection. Furthermore, these five EC-associated cytokines could change expression levels of intrinsic resistance factors, or molecules inside the target cell that fight HIV infection. This study is significant in that it identified cytokines elevated in subjects with a good immune response against HIV and defined potential mechanisms as to how these cytokines could induce resistance to the virus in target cells. PMID:28053103

Quantifying Limits on Replication, Death, and Quiescence of Mycobacterium tuberculosis in Mice

PubMed Central

McDaniel, Margaret M.; Krishna, Nitin; Handagama, Winode G.; Eda, Shigetoshi; Ganusov, Vitaly V.

2016-01-01

When an individual is exposed to Mycobacterium tuberculosis (Mtb) three outcomes are possible: bacterial clearance, active disease, or latent infection. It is generally believed that most individuals exposed to Mtb become latently infected and carry the mycobacteria for life. How Mtb is maintained during this latent infection remains largely unknown. During an Mtb infection in mice, there is a phase of rapid increase in bacterial numbers in the murine lungs within the first 3 weeks, and then bacterial numbers either stabilize or increase slowly over the period of many months. It has been debated whether the relatively constant numbers of bacteria in the chronic infection result from latent (dormant, quiescent), non-replicating bacteria, or whether the observed Mtb cell numbers are due to balance between rapid replication and death. A recent study of mice, infected with a Mtb strain carrying an unstable plasmid, showed that during the chronic phase, Mtb was replicating at significant rates. Using experimental data from this study and mathematical modeling we investigated the limits of the rates of bacterial replication, death, and quiescence during Mtb infection of mice. First, we found that to explain the data the rates of bacterial replication and death could not be constant and had to decrease with time since infection unless there were large changes in plasmid segregation probability over time. While a decrease in the rate of Mtb replication with time since infection was expected due to depletion of host's resources, a decrease in the Mtb death rate was counterintuitive since Mtb-specific immune response, appearing in the lungs 3–4 weeks after infection, should increase removal of bacteria. Interestingly, we found no significant correlation between estimated rates of Mtb replication and death suggesting the decline in these rates was driven by independent mechanisms. Second, we found that the data could not be explained by assuming that bacteria do not die, suggesting that some removal of bacteria from lungs of these mice had to occur even though the total bacterial counts in these mice always increased over time. Third and finally, we showed that to explain the data the majority of bacterial cells (at least ~60%) must be replicating in the chronic phase of infection further challenging widespread belief of nonreplicating Mtb in latency. Our predictions were robust to some changes in the structure of the model, for example, when the loss of plasmid-bearing cells was mainly due to high fitness cost of the plasmid. Further studies should determine if more mechanistic models for Mtb dynamics are also able to accurately explain these data. PMID:27379030

Cytokines Elevated in HIV Elite Controllers Reduce HIV Replication In Vitro and Modulate HIV Restriction Factor Expression.

PubMed

Jacobs, Evan S; Keating, Sheila M; Abdel-Mohsen, Mohamed; Gibb, Stuart L; Heitman, John W; Inglis, Heather C; Martin, Jeffrey N; Zhang, Jinbing; Kaidarova, Zhanna; Deng, Xutao; Wu, Shiquan; Anastos, Kathryn; Crystal, Howard; Villacres, Maria C; Young, Mary; Greenblatt, Ruth M; Landay, Alan L; Gange, Stephen J; Deeks, Steven G; Golub, Elizabeth T; Pillai, Satish K; Norris, Philip J

2017-03-15

A subset of HIV-infected individuals termed elite controllers (ECs) maintain CD4 + T cell counts and control viral replication in the absence of antiretroviral therapy (ART). Systemic cytokine responses may differentiate ECs from subjects with uncontrolled viral replication or from those who require ART to suppress viral replication. We measured 87 cytokines in four groups of women: 73 ECs, 42 with pharmacologically suppressed viremia (ART), 42 with uncontrolled viral replication (noncontrollers [NCs]), and 48 HIV-uninfected (NEG) subjects. Four cytokines were elevated in ECs but not NCs or ART subjects: CCL14, CCL21, CCL27, and XCL1. In addition, median stromal cell-derived factor-1 (SDF-1) levels were 43% higher in ECs than in NCs. The combination of the five cytokines suppressed R5 and X4 virus replication in resting CD4 + T cells, and individually SDF-1β, CCL14, and CCL27 suppressed R5 virus replication, while SDF-1β, CCL21, and CCL14 suppressed X4 virus replication. Functional studies revealed that the combination of the five cytokines upregulated CD69 and CCR5 and downregulated CXCR4 and CCR7 on CD4 + T cells. The CD69 and CXCR4 effects were driven by SDF-1, while CCL21 downregulated CCR7. The combination of the EC-associated cytokines induced expression of the anti-HIV host restriction factors IFITM1 and IFITM2 and suppressed expression of RNase L and SAMHD1. These results identify a set of cytokines that are elevated in ECs and define their effects on cellular activation, HIV coreceptor expression, and innate restriction factor expression. This cytokine pattern may be a signature characteristic of HIV-1 elite control, potentially important for HIV therapeutic and curative strategies. IMPORTANCE Approximately 1% of people infected with HIV control virus replication without taking antiviral medications. These subjects, termed elite controllers (ECs), are known to have stronger immune responses targeting HIV than the typical HIV-infected subject, but the exact mechanisms of how their immune responses control infection are not known. In this study, we identified five soluble immune signaling molecules (cytokines) in the blood that were higher in ECs than in subjects with typical chronic HIV infection. We demonstrated that these cytokines can activate CD4 + T cells, the target cells for HIV infection. Furthermore, these five EC-associated cytokines could change expression levels of intrinsic resistance factors, or molecules inside the target cell that fight HIV infection. This study is significant in that it identified cytokines elevated in subjects with a good immune response against HIV and defined potential mechanisms as to how these cytokines could induce resistance to the virus in target cells. Copyright © 2017 American Society for Microbiology.

Analysis of replication factories in human cells by super-resolution light microscopy

PubMed Central

2009-01-01

Background DNA replication in human cells is performed in discrete sub-nuclear locations known as replication foci or factories. These factories form in the nucleus during S phase and are sites of DNA synthesis and high local concentrations of enzymes required for chromatin replication. Why these structures are required, and how they are organised internally has yet to be identified. It has been difficult to analyse the structure of these factories as they are small in size and thus below the resolution limit of the standard confocal microscope. We have used stimulated emission depletion (STED) microscopy, which improves on the resolving power of the confocal microscope, to probe the structure of these factories at sub-diffraction limit resolution. Results Using immunofluorescent imaging of PCNA (proliferating cell nuclear antigen) and RPA (replication protein A) we show that factories are smaller in size (approximately 150 nm diameter), and greater in number (up to 1400 in an early S- phase nucleus), than is determined by confocal imaging. The replication inhibitor hydroxyurea caused an approximately 40% reduction in number and a 30% increase in diameter of replication factories, changes that were not clearly identified by standard confocal imaging. Conclusions These measurements for replication factory size now approach the dimensions suggested by electron microscopy. This agreement between these two methods, that use very different sample preparation and imaging conditions, suggests that we have arrived at a true measurement for the size of these structures. The number of individual factories present in a single nucleus that we measure using this system is greater than has been previously reported. This analysis therefore suggests that each replication factory contains fewer active replication forks than previously envisaged. PMID:20015367

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

PubMed Central

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

The right half of the Escherichia coli replication origin is not essential for viability, but facilitates multi-forked replication

PubMed Central

Stepankiw, Nicholas; Kaidow, Akihiro; Boye, Erik; Bates, David

2010-01-01

Summary Replication initiation is a key event in the cell cycle of all organisms and oriC, the replication origin in Escherichia coli, serves as the prototypical model for this process. The minimal sequence required for oriC function was originally determined entirely from plasmid studies using cloned origin fragments, which have previously been shown to differ dramatically in sequence requirement from the chromosome. Using an in vivo recombineering strategy to exchange wt oriCs for mutated ones regardless of whether they are functional origins or not, we have determined the minimal origin sequence that will support chromosome replication. Nearly the entire right half of oriC could be deleted without loss of origin function, demanding a reassessment of existing models for initiation. Cells carrying the new DnaA box-depleted 163 bp minimal oriC exhibited little or no loss of fitness under slow-growth conditions, but were sensitive to rich medium, suggesting that the dense packing of initiator binding sites that is a hallmark of prokaryotic origins, has likely evolved to support the increased demands of multi-forked replication. PMID:19737351

Control of Initiation of DNA Replication in Bacillus subtilis and Escherichia coli

PubMed Central

Jameson, Katie H.; Wilkinson, Anthony J.

2017-01-01

Initiation of DNA Replication is tightly regulated in all cells since imbalances in chromosomal copy number are deleterious and often lethal. In bacteria such as Bacillus subtilis and Escherichia coli, at the point of cytokinesis, there must be two complete copies of the chromosome to partition into the daughter cells following division at mid-cell during vegetative growth. Under conditions of rapid growth, when the time taken to replicate the chromosome exceeds the doubling time of the cells, there will be multiple initiations per cell cycle and daughter cells will inherit chromosomes that are already undergoing replication. In contrast, cells entering the sporulation pathway in B. subtilis can do so only during a short interval in the cell cycle when there are two, and only two, chromosomes per cell, one destined for the spore and one for the mother cell. Here, we briefly describe the overall process of DNA replication in bacteria before reviewing initiation of DNA replication in detail. The review covers DnaA-directed assembly of the replisome at oriC and the multitude of mechanisms of regulation of initiation, with a focus on the similarities and differences between E. coli and B. subtilis. PMID:28075389

Replication of poliovirus RNA and subgenomic RNA transcripts in transfected cells.

PubMed Central

Collis, P S; O'Donnell, B J; Barton, D J; Rogers, J A; Flanegan, J B

1992-01-01

Full-length and subgenomic poliovirus RNAs were transcribed in vitro and transfected into HeLa cells to study viral RNA replication in vivo. RNAs with deletion mutations were analyzed for the ability to replicate in either the absence or the presence of helper RNA by using a cotransfection procedure and Northern (RNA) blot analysis. An advantage of this approach was that viral RNA replication and genetic complementation could be characterized without first isolating conditional-lethal mutants. A subgenomic RNA with a large in-frame deletion in the capsid coding region (P1) replicated more efficiently than full-length viral RNA transcripts. In cotransfection experiments, both the full-length and subgenomic RNAs replicated at slightly reduced levels and appeared to interfere with each other's replication. In contrast, a subgenomic RNA with a similarly sized out-of-frame deletion in P1 did not replicate in transfected cells, either alone or in the presence of helper RNA. Similar results were observed with an RNA transcript containing a large in-frame deletion spanning the P1, P2, and P3 coding regions. A mutant RNA with an in-frame deletion in the P1-2A coding sequence was self-replicating but at a significantly reduced level. The replication of this RNA was fully complemented after cotransfection with a helper RNA that provided 2A in trans. A P1-2A-2B in-frame deletion, however, totally blocked RNA replication and was not complemented. Control experiments showed that all of the expected viral proteins were both synthesized and processed when the RNA transcripts were translated in vitro. Thus, our results indicated that 2A was a trans-acting protein and that 2B and perhaps other viral proteins were cis acting during poliovirus RNA replication in vivo. Our data support a model for poliovirus RNA replication which directly links the translation of a molecule of plus-strand RNA with the formation of a replication complex for minus-strand RNA synthesis. Images PMID:1328676

A comparison between electromechanical and pneumatic-controlled knee simulators for the investigation of wear of total knee replacements.

PubMed

Abdelgaied, Abdellatif; Fisher, John; Jennings, Louise M

2017-07-01

More robust preclinical experimental wear simulation methods are required in order to simulate a wider range of activities, observed in different patient populations such as younger more active patients, as well as to fully meet and be capable of going well beyond the existing requirements of the relevant international standards. A new six-station electromechanically driven simulator (Simulation Solutions, UK) with five fully independently controlled axes of articulation for each station, capable of replicating deep knee bending as well as other adverse conditions, which can be operated in either force or displacement control with improved input kinematic following, has been developed to meet these requirements. This study investigated the wear of a fixed-bearing total knee replacement using this electromechanically driven fully independent knee simulator and compared it to previous data from a predominantly pneumatically controlled simulator in which each station was not fully independently controlled. In addition, the kinematic performance and the repeatability of the simulators have been investigated and compared to the international standard requirements. The wear rates from the electromechanical and pneumatic knee simulators were not significantly different, with wear rates of 2.6 ± 0.9 and 2.7 ± 0.9 mm 3 /million cycles (MC; mean ± 95% confidence interval, p = 0.99) and 5.4 ± 1.4 and 6.7 ± 1.5 mm 3 /MC (mean ± 95 confidence interval, p = 0.54) from the electromechanical and pneumatic simulators under intermediate levels (maximum 5 mm) and high levels (maximum 10 mm) of anterior-posterior displacements, respectively. However, the output kinematic profiles of the control system, which drive the motion of the simulator, followed the input kinematic profiles more closely on the electromechanical simulator than the pneumatic simulator. In addition, the electromechanical simulator was capable of following kinematic and loading input cycles within the tolerances of the international standard requirements (ISO 14243-3). The new-generation electromechanical knee simulator with fully independent control has the potential to be used for a much wider range of kinematic conditions, including high-flexion and other severe conditions, due to its improved capability and performance in comparison to the previously used pneumatic-controlled simulators.

A comparison between electromechanical and pneumatic-controlled knee simulators for the investigation of wear of total knee replacements

PubMed Central

Abdelgaied, Abdellatif; Fisher, John; Jennings, Louise M

2017-01-01

More robust preclinical experimental wear simulation methods are required in order to simulate a wider range of activities, observed in different patient populations such as younger more active patients, as well as to fully meet and be capable of going well beyond the existing requirements of the relevant international standards. A new six-station electromechanically driven simulator (Simulation Solutions, UK) with five fully independently controlled axes of articulation for each station, capable of replicating deep knee bending as well as other adverse conditions, which can be operated in either force or displacement control with improved input kinematic following, has been developed to meet these requirements. This study investigated the wear of a fixed-bearing total knee replacement using this electromechanically driven fully independent knee simulator and compared it to previous data from a predominantly pneumatically controlled simulator in which each station was not fully independently controlled. In addition, the kinematic performance and the repeatability of the simulators have been investigated and compared to the international standard requirements. The wear rates from the electromechanical and pneumatic knee simulators were not significantly different, with wear rates of 2.6 ± 0.9 and 2.7 ± 0.9 mm3/million cycles (MC; mean ± 95% confidence interval, p = 0.99) and 5.4 ± 1.4 and 6.7 ± 1.5 mm3/MC (mean ± 95 confidence interval, p = 0.54) from the electromechanical and pneumatic simulators under intermediate levels (maximum 5 mm) and high levels (maximum 10 mm) of anterior–posterior displacements, respectively. However, the output kinematic profiles of the control system, which drive the motion of the simulator, followed the input kinematic profiles more closely on the electromechanical simulator than the pneumatic simulator. In addition, the electromechanical simulator was capable of following kinematic and loading input cycles within the tolerances of the international standard requirements (ISO 14243-3). The new-generation electromechanical knee simulator with fully independent control has the potential to be used for a much wider range of kinematic conditions, including high-flexion and other severe conditions, due to its improved capability and performance in comparison to the previously used pneumatic-controlled simulators. PMID:28661228

Chinese and American Employers’ Perspectives Regarding Hiring People with Behaviorally Driven Health Conditions: The Role of Stigma

PubMed Central

Corrigan, Patrick W.; Tsang, Hector W. H.; Shi, Kan; Lam, Chow S.; Larson, Jon

2010-01-01

Work opportunities for people with behaviorally driven health conditions such as HIV/AIDS, drug abuse, alcohol abuse, and psychosis are directly impacted by employer perspectives. To investigate this issue, we report findings from a mixed method design involving qualitative interviews followed by a quantitative survey of employers from Chicago (U.S.), Beijing (China), and Hong Kong (China). Findings from qualitative interviews of 100 employers were used to create 27 items measuring employer perspectives (the Employer Perspective Scale: EPS) about hiring people with health conditions. These perspectives reflect reasons for or against discrimination. In the quantitative phase of the study, representative samples of approximately 300 employers per city were administered the EPS in addition to measures of stigma, including attributions about disease onset and offset. The EPS and stigma scales were completed in the context of one of five randomly assigned health conditions. We weighted data with ratios of key demographics between the sample and the corresponding employer population data. Analyses showed that both onset and offset responsibility varied by behaviorally driven condition. Analyses also showed that employer perspectives were more negative for health conditions that are seen as more behaviorally driven, e.g., drug and alcohol abuse. Chicago employers endorsed onset and offset attributions less strongly compared to those in Hong Kong and Beijing. Chicago employers also recognized more benefits of hiring people with various health conditions. The implications of these findings for better understanding stigma and stigma change among employers are considered. PMID:21036445

Host phylogeny determines viral persistence and replication in novel hosts.

PubMed

Longdon, Ben; Hadfield, Jarrod D; Webster, Claire L; Obbard, Darren J; Jiggins, Francis M

2011-09-01

Pathogens switching to new hosts can result in the emergence of new infectious diseases, and determining which species are likely to be sources of such host shifts is essential to understanding disease threats to both humans and wildlife. However, the factors that determine whether a pathogen can infect a novel host are poorly understood. We have examined the ability of three host-specific RNA-viruses (Drosophila sigma viruses from the family Rhabdoviridae) to persist and replicate in 51 different species of Drosophilidae. Using a novel analytical approach we found that the host phylogeny could explain most of the variation in viral replication and persistence between different host species. This effect is partly driven by viruses reaching a higher titre in those novel hosts most closely related to the original host. However, there is also a strong effect of host phylogeny that is independent of the distance from the original host, with viral titres being similar in groups of related hosts. Most of this effect could be explained by variation in general susceptibility to all three sigma viruses, as there is a strong phylogenetic correlation in the titres of the three viruses. These results suggest that the source of new emerging diseases may often be predictable from the host phylogeny, but that the effect may be more complex than simply causing most host shifts to occur between closely related hosts.

Host Phylogeny Determines Viral Persistence and Replication in Novel Hosts

PubMed Central

Longdon, Ben; Hadfield, Jarrod D.; Webster, Claire L.

2011-01-01

Pathogens switching to new hosts can result in the emergence of new infectious diseases, and determining which species are likely to be sources of such host shifts is essential to understanding disease threats to both humans and wildlife. However, the factors that determine whether a pathogen can infect a novel host are poorly understood. We have examined the ability of three host-specific RNA-viruses (Drosophila sigma viruses from the family Rhabdoviridae) to persist and replicate in 51 different species of Drosophilidae. Using a novel analytical approach we found that the host phylogeny could explain most of the variation in viral replication and persistence between different host species. This effect is partly driven by viruses reaching a higher titre in those novel hosts most closely related to the original host. However, there is also a strong effect of host phylogeny that is independent of the distance from the original host, with viral titres being similar in groups of related hosts. Most of this effect could be explained by variation in general susceptibility to all three sigma viruses, as there is a strong phylogenetic correlation in the titres of the three viruses. These results suggest that the source of new emerging diseases may often be predictable from the host phylogeny, but that the effect may be more complex than simply causing most host shifts to occur between closely related hosts. PMID:21966271

Increase of stagnation pressure and enthalpy in shock tunnels

NASA Technical Reports Server (NTRS)

Bogdanoff, David W.; Cambier, Jean-Luc

1992-01-01

High stagnation pressures and enthalpies are required for the testing of aerospace vehicles such as aerospace planes, aeroassist vehicles, and reentry vehicles. Among the most useful ground test facilities for performing such tests are shock tunnels. With a given driver gas condition, the enthalpy and pressure in the driven tube nozzle reservoir condition can be varied by changing the driven tube geometry and initial gas fill pressure. Reducing the driven tube diameter yields only very modest increases in reservoir pressure and enthalpy. Reducing the driven tube initial gas fill pressure can increase the reservoir enthalpy significantly, but at the cost of reduced reservoir pressure and useful test time. A new technique, the insertion of a converging section in the driven tube is found to produce substantial increases in both reservoir pressure and enthalpy. Using a one-dimensional inviscid full kinetics code, a number of different locations and shapes for the converging driven tube section were studied and the best cases found. For these best cases, for driven tube diameter reductions of factors of 2 and 3, the reservoir pressure can be increased by factors of 2.1 and 3.2, respectively and the enthalpy can be increased by factors of 1.5 and 2.1, respectively.

Microscopic Observation of Self-Propagation of Calcifying Nanoparticles (Nanobacteria)

NASA Technical Reports Server (NTRS)

Mathew, Grace; McKay, David S.; Ciftcioglu, Neva

2007-01-01

Biologists typically define living organisms as carbon and water-based cellular forms with :self-replication" as the fundamental trait of the life process. However, this standard dictionary definition of life does not help scientists to categorize self-replicators like viruses, prions, proteons and artificial life. CNP also named nanobacteria were discovered in early 1990s as about 100 nanometer-sized bacteria-like particles with unique apatite mineral-shells around them, and found to be associated with pathological-calcification related diseases. Although CNP have been isolated and cultured from mammalian blood and diseased calcified tissues, and their biomineralizing properties well established, their biological nature and self-replicating capability have always been severely challenged. The terms "self-replication", "self-assembly" or "self-propagation" have been widely used for all systems including nanomachines, crystals, computer viruses and memes. In a simple taxonomy, all biological and non-biological "self replicators", have been classified into "living" or "nonliving" based on the properties of the systems and the amount of support they require to self-replicate. To enhance our understanding about self-replicating nature of CNP, we have investigated their growth in specific culture conditions using conventional inverted light microscope and BioStation IM, Nikon s latest time-lapse imaging system. Their morphological structure was examined using scanning (SEM) and transmission (TEM) electron microscopy. This present study, in conjunction with previous findings of metabolic activity, antibiotic sensitivity, antibody specificity, morphological aspects and infectivity, all concomitantly validate CNP as living self-replicators.

Collaboration can improve individual recognition memory: evidence from immediate and delayed tests.

PubMed

Rajaram, Suparna; Pereira-Pasarin, Luciane P

2007-02-01

In two experiments, we tested the effects of collaboration on individual recognition memory. In Experiment 1, participants studied pictures and words either for meaning or for surface properties and made recognition memory judgments individually either following group discussion among 3 members (collaborative condition) or in the absence of discussion (noncollaborative condition). Levels of processing and picture superiority effects were replicated, and collaboration significantly increased individual recognition memory. Experiment 2 replicated this positive effect and showed that even though memory sensitivity declined at longer delays (48 h and 1 week), collaboration continued to exert a positive influence. These findings show that (1) consensus is not necessary for producing benefits of collaboration on individual recognition, (2) collaborative facilitation on individual memory is robust, and (3) collaboration enhances individual memory further if conditions predispose individual accuracy in the absence of collaboration.

Decisional strategy determines whether frame influences treatment preferences for medical decisions.

PubMed

Woodhead, Erin L; Lynch, Elizabeth B; Edelstein, Barry A

2011-06-01

Decision makers are influenced by the frame of information such that preferences vary depending on whether survival or mortality data are presented. Research is inconsistent as to whether and how age impacts framing effects. This paper presents two studies that used qualitative analyses of think-aloud protocols to understand how the type of information used in the decision making process varies by frame and age. In Study 1, 40 older adults, age 65 to 89, and 40 younger adults, age 18 to 24, responded to a hypothetical lung cancer scenario in a within-subject design. Participants received both a survival and mortality frame. Qualitative analyses revealed that two main decisional strategies were used by all participants: one strategy reflected a data-driven decisional process, whereas the other reflected an experience-driven process. Age predicted decisional strategy, with older adults less likely to use a data-driven strategy. Frame interacted with strategy to predict treatment choice; only those using a data-driven strategy demonstrated framing effects. In Study 2, 61 older adults, age 65 to 98, and 63 younger adults, age 18 to 30, responded to the same scenarios as in Study 1 in a between-subject design. The results of Study 1 were replicated, with age significantly predicting decisional strategy and frame interacting with strategy to predict treatment choice. Findings suggest that framing effects may be more related to decisional strategy than to age. (c) 2011 APA, all rights reserved.

Practice-driven evaluation of a multi-layered psychosocial care package for children in areas of armed conflict.

PubMed

Jordans, M J D; Komproe, I H; Tol, W A; Susanty, D; Vallipuram, A; Ntamatumba, P; Lasuba, A C; De Jong, J T V M

2011-06-01

Psychosocial and mental health service delivery frameworks for children in low-income countries are scarce. This paper presents a practice-driven evaluation of a multi-layered community-based care package in Burundi, Indonesia, Sri Lanka and Sudan, through a set of indicators; (a) perceived treatment gains; (b) treatment satisfaction; (c) therapist burden; (d) access to care; (e) care package costs. Across four settings (n = 29,292 children), beneficiaries reported high levels of client satisfaction and moderate post-treatment problem reductions. Service providers reported significant levels of distress related to service delivery. Cost analyses demonstrated mean cost per service user to vary from 3.46 to 17.32 depending on country and specification of costs. The results suggest a multi-layered psychosocial care package appears feasible and satisfactory in reaching out to substantial populations of distressed children through different levels of care. Future replication should address therapist burden, cost reductions to increase sustainability and increase evidence for treatment efficacy.

Development of siRNA expression vector utilizing rock bream beta-actin promoter: a potential therapeutic tool against viral infection in fish.

PubMed

Zenke, Kosuke; Nam, Yoon Kwon; Kim, Ki Hong

2010-01-01

In the present study, we have developed short interfering RNA (siRNA) expression vector utilizing rock bream beta-actin promoter and examined the possible use for the inhibition of highly pathogenic fish virus, rock bream iridovirus (RBIV), replication in vitro. Initially, in order to express siRNA effectively, we added several modifications to wild-type rock bream beta-actin promoter. Next, we succeeded in knocking down the expression of enhanced green fluorescent protein reporter gene expression in fish cells using newly developed vector more effectively than the fugu U6 promoter-driven vector we described previously. Finally, we could observe that cells transfected with modified rock bream beta-actin promoter-driven siRNA expression vector targeting major capsid protein (MCP) gene of RBIV exhibited more resistance to RBIV challenge than other control cells. Our results indicate that this novel siRNA expression vector can be used as a new tool for therapeutics in virus infection in fish species.

Adaptive changes in HIV-1 subtype C proteins during early infection are driven by changes in HLA-associated immune pressure

PubMed Central

Treurnicht, F.K.; Seoighe, C.; Martin, D.P.; Wood, N.; Abrahams, M-R.; de Assis Rosa, D.; Bredell, H.; Woodman, Z.; Hide, W.; Mlisana, K.; Karim, S Abdool; Gray, C.M.; Williamson, C.

2009-01-01

It is unresolved whether recently transmitted human immunodeficiency viruses (HIV) have genetic features that specifically favour their transmissibility. To identify potential “transmission signatures”, we compared 20 full-length HIV-1 subtype C genomes from primary infections, with 66 sampled from ethnically and geographically matched individuals with chronic infections. Controlling for recombination and phylogenetic relatedness, we identified 39 sites at which amino acid frequency spectra differed significantly between groups. These sites were predominantly located within Env, Pol and Gag (14/39, 9/39 and 6/39 respectively) and were significantly clustered (33/39) within known immunoreactive peptides. Within 6 months of infection we detected reversion-to-consensus mutations at 14 sites and potential CTL escape mutations at seven. Here we provide evidence that frequent reversion mutations probably allows the virus to recover replicative fitness which, together with immune escape driven by the HLA alleles of the new hosts, differentiate sequences from chronic infections from those sampled shortly after transmission. PMID:19913270

Emotion in the Neutral Face: A Mechanism for Impression Formation?

PubMed Central

Adams, Reginald B.; Nelson, Anthony J.; Soto, José A.; Hess, Ursula; Kleck, Robert E.

2012-01-01

The current work examined contributions of emotion-resembling facial cues to impression formation. There exist common facial cues that make people look male or female, emotional, and from which we derive personality inferences. We first conducted a Pilot study to assess these effects. We found that neutral female versus neutral male faces were rated as more submissive, affiliative, naïve, honest, cooperative, babyish, fearful, happy, and less angry than neutral male faces. In our Primary Study, we then “warped” these same neutral faces over their corresponding anger and fear displays so the resultant facial appearance cues now structurally resembled emotion while retaining a neutral visage (e.g., no wrinkles, furrows, creases etc.). The gender effects found in the Pilot Study were replicated in the Primary Study, suggesting clear stereotype driven impressions. Critically, ratings of the neutral-over-fear warps versus neutral-over-anger warps also revealed a profile similar to the gender-based ratings, revealing perceptually driven impressions directly attributable to emotion overgeneralization. PMID:22471850

The Large Marseillevirus Explores Different Entry Pathways by Forming Giant Infectious Vesicles.

PubMed

Arantes, Thalita Souza; Rodrigues, Rodrigo Araújo Lima; Dos Santos Silva, Ludmila Karen; Oliveira, Graziele Pereira; de Souza, Helton Luís; Khalil, Jacques Y B; de Oliveira, Danilo Bretas; Torres, Alice Abreu; da Silva, Luis Lamberti; Colson, Philippe; Kroon, Erna Geessien; da Fonseca, Flávio Guimarães; Bonjardim, Cláudio Antônio; La Scola, Bernard; Abrahão, Jônatas Santos

2016-06-01

Triggering the amoebal phagocytosis process is a sine qua non condition for most giant viruses to initiate their replication cycle and consequently to promote their progeny formation. It is well known that the amoebal phagocytosis process requires the recognition of particles of >500 nm, and most amoebal giant viruses meet this requirement, such as mimivirus, pandoravirus, pithovirus, and mollivirus. However, in the context of the discovery of amoebal giant viruses in the last decade, Marseillevirus marseillevirus (MsV) has drawn our attention, because despite its ability to successfully replicate in Acanthamoeba, remarkably it does not fulfill the >500-nm condition, since it presents an ∼250-nm icosahedrally shaped capsid. We deeply investigated the MsV cycle by using a set of methods, including virological, molecular, and microscopic (immunofluorescence, scanning electron microscopy, and transmission electron microscopy) assays. Our results revealed that MsV is able to form giant vesicles containing dozens to thousands of viral particles wrapped by membranes derived from amoebal endoplasmic reticulum. Remarkably, our results strongly suggested that these giant vesicles are able to stimulate amoebal phagocytosis and to trigger the MsV replication cycle by an acidification-independent process. Also, we observed that MsV entry may occur by the phagocytosis of grouped particles (without surrounding membranes) and by an endosome-stimulated pathway triggered by single particles. Taken together, not only do our data deeply describe the main features of MsV replication cycle, but this is the first time, to our knowledge, that the formation of giant infective vesicles related to a DNA virus has been described. Triggering the amoebal phagocytosis process is a sine qua non condition required by most giant viruses to initiate their replication cycle. This process requires the recognition of particles of >500 nm, and many giant viruses meet this requirement. However, MsV is unusual, as despite having particles of ∼250 nm it is able to replicate in Acanthamoeba Our results revealed that MsV is able to form giant vesicles, containing dozens to thousands of viral particles, wrapped in membranes derived from amoebal endoplasmic reticulum. Remarkably, our results strongly suggest that these giant vesicles are able to stimulate phagocytosis using an acidification-independent process. Our work not only describes the main features of the MsV replication cycle but also describes, for the first time to our knowledge, the formation of huge infective vesicles in a large DNA viruses. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Aneuploidy and asynchronous replication in non-alcholic fatty liver disease and cryptogenic cirrhosis.

PubMed

Laish, Ido; Mannasse-Green, Batya; Hadary, Ruth; Konikoff, Fred M; Amiel, Aliza; Kitay-Cohen, Yona

2016-11-15

Non-alcoholic fatty liver disease (NAFLD) and cryptogenic cirrhosis (CC), which is largely a late sequela of NAFLD, are considered pre-neoplastic conditions that might progress to hepatocellular carcinoma. Aneuploidy, telomere aggregates and synchronization of replication were evaluated as markers of genetic instability in these patients. Peripheral blood lymphocytes from 22 patients with NAFLD, 20 patients with CC and 20 age-matched healthy controls were analyzed. To determine random aneuploidy, we used the fluorescence in situ hybridization (FISH) with probes for chromosomes 9 and 18. The rate of aneuploidy was inferred from the fraction of cells revealing one, three or more hybridization signals per cell. Aggregate size was divided into three fusion groups of 2-5, 6-10 and 11-15 telomeres, relative to the size of a single telomere. The replication pattern was determined by FISH in two pairs of alleles, 15qter and 13qter. Asynchrony was determined by the presence of one single and one set of double dots in the same cell. Significantly higher random aneuploidy rate was found in the CC patients than in the control group, and to a lesser degree in NAFLD patients. Telomere aggregates were insignificantly higher in both groups. Only patients with CC showed significantly higher rate of asynchronous replication with proportionately more cells with two single dots among the normal cells (p<0.001). These results likely reflect changes in gene replication and cell cycle progression in these conditions, possibly correlating with their malignant potential. Copyright © 2016 Elsevier B.V. All rights reserved.

Cancer Terminator Viruses and Approaches for Enhancing Therapeutic Outcomes

PubMed Central

Das, Swadesh K.; Sarkar, Siddik; Dash, Rupesh; Dent, Paul; Wang, Xiang-Yang; Sarkar, Devanand; Fisher, Paul B.

2015-01-01

No single or combinatorial therapeutic approach has proven effective in decreasing morbidity or engendering a cure of metastatic cancer. In principle, conditionally replication-competent adenoviruses that induce tumor oncolysis through cancer-specific replication hold promise for cancer therapy. However, a single-agent approach may not be adequate to completely eradicate cancer in a patient because most cancers arise from abnormalities in multiple genetic and signal transduction pathways and targeting disseminated metastases is difficult to achieve. Based on these considerations, a novel class of cancer destroying adenoviruses have been produced, cancer terminator viruses (CTVs), in which cancer-specific replication is controlled by the progression-elevated gene-3 promoter and replicating viruses produce a second transgene encoding an apoptosis-inducing and immunomodulatory cytokine, either melanoma differentiation-associated gene-7/interleukin-24 (mda-7/IL-24) or interferon-γ. This review focuses on these viruses and ways to improve their delivery systemically and enhance their therapeutic efficacy. PMID:23021240

Viral Interference and Persistence in Mosquito-Borne Flaviviruses.

PubMed

Salas-Benito, Juan Santiago; De Nova-Ocampo, Mónica

2015-01-01

Mosquito-borne flaviviruses are important pathogens for humans, and the detection of two or more flaviviruses cocirculating in the same geographic area has often been reported. However, the epidemiological impact remains to be determined. Mosquito-borne flaviviruses are primarily transmitted through Aedes and Culex mosquitoes; these viruses establish a life-long or persistent infection without apparent pathological effects. This establishment requires a balance between virus replication and the antiviral host response. Viral interference is a phenomenon whereby one virus inhibits the replication of other viruses, and this condition is frequently associated with persistent infections. Viral interference and persistent infection are determined by several factors, such as defective interfering particles, competition for cellular factors required for translation/replication, and the host antiviral response. The interaction between two flaviviruses typically results in viral interference, indicating that these viruses share common features during the replicative cycle in the vector. The potential mechanisms involved in these processes are reviewed here.

Observation and modeling of mixing-layer development in HED blast-wave-driven shear flow

NASA Astrophysics Data System (ADS)

di Stefano, Carlos

2013-10-01

This talk describes work exploring the sensitivity to initial conditions of hydrodynamic mixing-layer growth due to shear flow in the high-energy-density regime. This work features an approach in two parts, experimental and theoretical. First, an experiment, conducted at the OMEGA-60 laser facility, seeks to measure the development of such a mixing layer. This is accomplished by placing a layer of low-density (initially of either 0.05 or 0.1 g/cm3, to vary the system's Atwood number) carbon foam against a layer of higher-density (initially 1.4 g/cm3) polyamide-imide that has been machined to a nominally-flat surface at its interface with the foam. Inherent roughness of this surface's finish is precisely measured and varied from piece to piece. Ten simultaneous OMEGA beams, comprising a 4.5 kJ, 1-ns pulse focused to a roughly 1-mm-diameter spot, irradiate a thin polycarbonate ablator, driving a blast wave into the foam, parallel to its interface with the polyamide-imide. The ablator is framed by a gold washer, such that the blast wave is driven only into the foam, and not into the polyamide-imide. The subsequent forward motion of the shocked foam creates the desired shear effect, and the system is imaged by X-ray radiography 35 ns after the beginning of the driving laser pulse. Second, a simulation is performed, intending to replicate the flow observed in the experiment as closely as possible. Using the resulting simulated flow parameters, an analytical model can be used to predict the evolution of the mixing layer, as well as track the motion of the fluid in the experiment prior to the snapshot seen in the radiograph. The ability of the model to predict growth of the mixing layer under the various conditions observed in the experiment is then examined. This work is funded by the Predictive Sciences Academic Alliances Program in NNSA-ASC via grant DEFC52- 08NA28616, by the NNSA-DS and SC-OFES Joint Program in High-Energy-Density Laboratory Plasmas, grant number DE-NA0001840, and by the National Laser Use.

Towards Self-Replicating Chemical Systems Based on Cytidylic and Guanylic Acids

NASA Technical Reports Server (NTRS)

Kanavarioti, Anastassia

1999-01-01

This project was aimed towards a better understanding of template-directed reactions and, based on this, towards the development of efficient non-enzymatic RNA replicating systems. These systems could serve as models for the prebiotic synthesis of an RNA world. The major objectives of this project are: (a) To elucidate the mechanistic aspects of template-directed (TD) chemistry and (b) to identify active boundary regions, or conditions, environmental and other, that favor "organized chemistry" and stereo-selective polymerization of nucleotides. "Organized chemistry" may lead to enhanced polymerization efficiency which in turn is expected to facilitate the road towards a self-replicating chemical system based on all four nucleic acid bases.

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

PubMed

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.

Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment.

PubMed

Gierliński, Marek; Cole, Christian; Schofield, Pietà; Schurch, Nicholas J; Sherstnev, Alexander; Singh, Vijender; Wrobel, Nicola; Gharbi, Karim; Simpson, Gordon; Owen-Hughes, Tom; Blaxter, Mark; Barton, Geoffrey J

2015-11-15

High-throughput RNA sequencing (RNA-seq) is now the standard method to determine differential gene expression. Identifying differentially expressed genes crucially depends on estimates of read-count variability. These estimates are typically based on statistical models such as the negative binomial distribution, which is employed by the tools edgeR, DESeq and cuffdiff. Until now, the validity of these models has usually been tested on either low-replicate RNA-seq data or simulations. A 48-replicate RNA-seq experiment in yeast was performed and data tested against theoretical models. The observed gene read counts were consistent with both log-normal and negative binomial distributions, while the mean-variance relation followed the line of constant dispersion parameter of ∼0.01. The high-replicate data also allowed for strict quality control and screening of 'bad' replicates, which can drastically affect the gene read-count distribution. RNA-seq data have been submitted to ENA archive with project ID PRJEB5348. g.j.barton@dundee.ac.uk. © The Author 2015. Published by Oxford University Press.

Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment

PubMed Central

Cole, Christian; Schofield, Pietà; Schurch, Nicholas J.; Sherstnev, Alexander; Singh, Vijender; Wrobel, Nicola; Gharbi, Karim; Simpson, Gordon; Owen-Hughes, Tom; Blaxter, Mark; Barton, Geoffrey J.

2015-01-01

Motivation: High-throughput RNA sequencing (RNA-seq) is now the standard method to determine differential gene expression. Identifying differentially expressed genes crucially depends on estimates of read-count variability. These estimates are typically based on statistical models such as the negative binomial distribution, which is employed by the tools edgeR, DESeq and cuffdiff. Until now, the validity of these models has usually been tested on either low-replicate RNA-seq data or simulations. Results: A 48-replicate RNA-seq experiment in yeast was performed and data tested against theoretical models. The observed gene read counts were consistent with both log-normal and negative binomial distributions, while the mean-variance relation followed the line of constant dispersion parameter of ∼0.01. The high-replicate data also allowed for strict quality control and screening of ‘bad’ replicates, which can drastically affect the gene read-count distribution. Availability and implementation: RNA-seq data have been submitted to ENA archive with project ID PRJEB5348. Contact: g.j.barton@dundee.ac.uk PMID:26206307

Intestinal colonization by enteroaggregative Escherichia coli supports long-term bacteriophage replication in mice.

PubMed

Maura, Damien; Morello, Eric; du Merle, Laurence; Bomme, Perrine; Le Bouguénec, Chantal; Debarbieux, Laurent

2012-08-01

Bacteriophages have been known to be present in the gut for many years, but studies of relationships between these viruses and their hosts in the intestine are still in their infancy. We isolated three bacteriophages specific for an enteroaggregative O104:H4 Escherichia coli (EAEC) strain responsible for diarrhoeal diseases in humans. We studied the replication of these bacteriophages in vitro and in vivo in a mouse model of gut colonization. Each bacteriophage was able to replicate in vitro in both aerobic and anaerobic conditions. Each bacteriophage individually reduced biofilms formed on plastic pegs and a cocktail of the three bacteriophages was found to be more efficient. The cocktail was also able to infect bacterial aggregates formed on the surface of epithelial cells. In the mouse intestine, bacteriophages replicated for at least 3 weeks, provided the host was present, with no change in host levels in the faeces. This model of stable and continuous viral replication provides opportunities for studying the long-term coevolution of virulent bacteriophages with their hosts within a mammalian polymicrobial ecosystem. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Youth Climate Summits: Empowering & Engaging Youth to Lead on Climate Change

NASA Astrophysics Data System (ADS)

Kretser, J.

2017-12-01

The Wild Center's Youth Climate Summits is a program that engages youth in climate literacy from knowledge and understanding to developing action in their schools and communities. Each Youth Climate Summit is a one to three day event that brings students and teachers together to learn about climate change science, impacts and solutions at a global and local level. Through speakers, workshops and activities, the Summit culminates in a student-driven Climate Action Plan that can be brought back to schools and communities. The summits have been found to be powerful vehicles for inspiration, learning, community engagement and youth leadership development. Climate literacy with a focus on local climate impacts and solutions is a key component of the Youth Climate Summit. The project-based learning surrounding the creation of a unique, student driven, sustainability and Climate Action Plan promotes leadership skills applicable and the tools necessary for a 21st Century workforce. Student driven projects range from school gardens and school energy audits to working with NYS officials to commit to going 100% renewable electricty at the three state-owned downhill ski facilities. The summit model has been scaled and replicated in other communities in New York State, Vermont, Ohio, Michigan and Washington states as well as internationally in Finland, Germany and Sri Lanka.

Startle modulation and explicit valence evaluations dissociate during backward fear conditioning.

PubMed

Luck, Camilla C; Lipp, Ottmar V

2017-05-01

Blink startle magnitude is linearly modulated by affect such that, relative to neutral stimuli, startle magnitude is inhibited during pleasant stimuli and potentiated during unpleasant stimuli. Andreatta, Mühlberger, Yarali, Gerber, and Pauli (2010), however, report a dissociation between startle modulation and explicit valence evaluations during backward conditioning, a procedure in which the unconditional stimulus precedes the conditional stimulus (CS). Relative to controls, startles elicited during the CS were inhibited, suggesting that the CS had acquired positive valence, but participants still evaluated the CS as unpleasant after the experiment. In Experiment 1, we aimed to replicate this dissociation using a trial-by-trial measure of CS valence to measure startle modulation and CS valence simultaneously during forward and backward differential fear conditioning. In Experiment 2, we examined whether early and late portions of the CS could acquire differential valence by presenting startle probes at early and late probe positions during the CS. In both experiments, the dissociation between startle modulation and explicit valence evaluations in backward conditioning replicated, with CS+ evaluated as less pleasant than CS-, but startles elicited during CS+ inhibited relative to CS-. In Experiment 2, we provide preliminary evidence that this inhibition was present early, but not late, during the CS+. The results replicate the dissociation between implicit and explicit CS valence reported by Andreatta et al. (2010) using a trial-by-trial measure of valence. We also provide preliminary evidence that this dissociation may occur because the implicit and explicit measures are recorded at different times during the CS presentation. © 2017 Society for Psychophysiological Research.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sagan, C.; Salpeter, E.E.

The eddy diffusion coefficient is estimated as a function of altitude, separately for the Jovian troposphere and mesosphere. The growth-rate and motion of particles is estimated for various substances: the water clouds are probably nucleated by NH/sub 4/Cl and sodium compunds are likely to be absent at and above the levels of the water clouds. Complex organic molecules produced by the L..cap alpha.. photolysis of methane may possibly be the absorbers in the lower mesosphere which account for the low reflectivity of Jupiter in the near-ultraviolet. The optical frequency chromophores are localized at or just below the Jovian tropopause. Candidatemore » chromophore molecules must satisfy the condition that they are produced sufficiently rapidly that convective pyrolysis maintains the observed chromophore optical depth. Organic molecules and polymeric sulfur produced through H/sub 2/S photolysis at lambda>2300 A probably fail this test, even if a slow, deep circulation pattern, driven by latent heat, is present. The condition may be satisfied if complex organic chromophores are produced with high quantum yield by NH/sub 3/ photolysis at lambda<2300 A. However, Jovian photoautotrophs in the upper troposphere satisfy this condition well, even with fast circulation, only biochemical properties of comparable terrestrial organisms are assured. Unless buoyancy can be achieved, a hypothetical organism drifts downward and is pyralyzed. An organism in the form of a thin, gas-filled balloon can grow fast enough to replicate if (i) it can survive at the low mesospheric temperatures, or if (ii) photosynthesis occurs in the troposphere. If hypothetical organisms are capable of slow, powered locomotion and coalescence, they can grow large enough to achieve buoyancy. Ecological niches for sinkers, floaters, and hunters appear to exist in the Jovian atmosphere.« less

The neural systems for perceptual updating.

PubMed

Stöttinger, Elisabeth; Aichhorn, Markus; Anderson, Britt; Danckert, James

2018-04-01

In a constantly changing environment we must adapt to both abrupt and gradual changes to incoming information. Previously, we demonstrated that a distributed network (including the anterior insula and anterior cingulate cortex) was active when participants updated their initial representations (e.g., it's a cat) in a gradually morphing picture task (e.g., now it's a rabbit; Stöttinger et al., 2015). To shed light on whether these activations reflect the proactive decisions to update or perceptual uncertainty, we introduced two additional conditions. By presenting picture morphs twice we controlled for uncertainty in perceptual decision making. Inducing an abrupt shift in a third condition allowed us to differentiate between a proactive decision in uncertainty-driven updating and a reactive decision in surprise-based updating. We replicated our earlier result, showing the robustness of the effect. In addition, we found activation in the anterior insula (bilaterally) and the mid frontal area/ACC in all three conditions, indicative of the importance of these areas in updating of all kinds. When participants were naïve as to the identity of the second object, we found higher activations in the mid-cingulate cortex and cuneus - areas typically associated with task difficulty, in addition to higher activations in the right TPJ most likely reflecting the shift to a new perspective. Activations associated with the proactive decision to update to a new interpretation were found in a network including the dorsal ACC known to be involved in exploration and the endogenous decision to switch to a new interpretation. These findings suggest a general network commonly engaged in all types of perceptual decision making supported by additional networks associated with perceptual uncertainty or updating provoked by either proactive or reactive decision making. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Competitive fitness in coronaviruses is not correlated with size or number of double-membrane vesicles under reduced-temperature growth conditions.

PubMed

Al-Mulla, Hawaa M N; Turrell, Lauren; Smith, Nicola M; Payne, Luke; Baliji, Surendranath; Züst, Roland; Thiel, Volker; Baker, Susan C; Siddell, Stuart G; Neuman, Benjamin W

2014-04-01

Positive-stranded viruses synthesize their RNA in membrane-bound organelles, but it is not clear how this benefits the virus or the host. For coronaviruses, these organelles take the form of double-membrane vesicles (DMVs) interconnected by a convoluted membrane network. We used electron microscopy to identify murine coronaviruses with mutations in nsp3 and nsp14 that replicated normally while producing only half the normal amount of DMVs under low-temperature growth conditions. Viruses with mutations in nsp5 and nsp16 produced small DMVs but also replicated normally. Quantitative reverse transcriptase PCR (RT-PCR) confirmed that the most strongly affected of these, the nsp3 mutant, produced more viral RNA than wild-type virus. Competitive growth assays were carried out in both continuous and primary cells to better understand the contribution of DMVs to viral fitness. Surprisingly, several viruses that produced fewer or smaller DMVs showed a higher fitness than wild-type virus at the reduced temperature, suggesting that larger and more numerous DMVs do not necessarily confer a competitive advantage in primary or continuous cell culture. For the first time, this directly demonstrates that replication and organelle formation may be, at least in part, studied separately during infection with positive-stranded RNA virus. IMPORTANCE The viruses that cause severe acute respiratory syndrome (SARS), poliomyelitis, and hepatitis C all replicate in double-membrane vesicles (DMVs). The big question about DMVs is why they exist in the first place. In this study, we looked at thousands of infected cells and identified two coronavirus mutants that made half as many organelles as normal and two others that made typical numbers but smaller organelles. Despite differences in DMV size and number, all four mutants replicated as efficiently as wild-type virus. To better understand the relative importance of replicative organelles, we carried out competitive fitness experiments. None of these viruses was found to be significantly less fit than wild-type, and two were actually fitter in tests in two kinds of cells. This suggests that viruses have evolved to have tremendous plasticity in the ability to form membrane-associated replication complexes and that large and numerous DMVs are not exclusively associated with efficient coronavirus replication.

Insulated hsp70B' promoter: stringent heat-inducible activity in replication-deficient, but not replication-competent adenoviruses.

PubMed

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.

Leveraging Genomic Annotations and Pleiotropic Enrichment for Improved Replication Rates in Schizophrenia GWAS

PubMed Central

Wang, Yunpeng; Thompson, Wesley K.; Schork, Andrew J.; Holland, Dominic; Chen, Chi-Hua; Bettella, Francesco; Desikan, Rahul S.; Li, Wen; Witoelar, Aree; Zuber, Verena; Devor, Anna; Nöthen, Markus M.; Rietschel, Marcella; Chen, Qiang; Werge, Thomas; Cichon, Sven; Weinberger, Daniel R.; Djurovic, Srdjan; O’Donovan, Michael; Visscher, Peter M.; Andreassen, Ole A.; Dale, Anders M.

2016-01-01

Most of the genetic architecture of schizophrenia (SCZ) has not yet been identified. Here, we apply a novel statistical algorithm called Covariate-Modulated Mixture Modeling (CM3), which incorporates auxiliary information (heterozygosity, total linkage disequilibrium, genomic annotations, pleiotropy) for each single nucleotide polymorphism (SNP) to enable more accurate estimation of replication probabilities, conditional on the observed test statistic (“z-score”) of the SNP. We use a multiple logistic regression on z-scores to combine information from auxiliary information to derive a “relative enrichment score” for each SNP. For each stratum of these relative enrichment scores, we obtain nonparametric estimates of posterior expected test statistics and replication probabilities as a function of discovery z-scores, using a resampling-based approach that repeatedly and randomly partitions meta-analysis sub-studies into training and replication samples. We fit a scale mixture of two Gaussians model to each stratum, obtaining parameter estimates that minimize the sum of squared differences of the scale-mixture model with the stratified nonparametric estimates. We apply this approach to the recent genome-wide association study (GWAS) of SCZ (n = 82,315), obtaining a good fit between the model-based and observed effect sizes and replication probabilities. We observed that SNPs with low enrichment scores replicate with a lower probability than SNPs with high enrichment scores even when both they are genome-wide significant (p < 5x10-8). There were 693 and 219 independent loci with model-based replication rates ≥80% and ≥90%, respectively. Compared to analyses not incorporating relative enrichment scores, CM3 increased out-of-sample yield for SNPs that replicate at a given rate. This demonstrates that replication probabilities can be more accurately estimated using prior enrichment information with CM3. PMID:26808560

Selective Modification of Adenovirus Replication Can Be Achieved through Rational Mutagenesis of the Adenovirus Type 5 DNA Polymerase

PubMed Central

Capella, Cristina; Beltejar, Michael-John; Brown, Caitlin; Fong, Vincent; Daddacha, Waaqo; Kim, Baek

2012-01-01

Mutations that reduce the efficiency of deoxynucleoside (dN) triphosphate (dNTP) substrate utilization by the HIV-1 DNA polymerase prevent viral replication in resting cells, which contain low dNTP concentrations, but not in rapidly dividing cells such as cancer cells, which contain high levels of dNTPs. We therefore tested whether mutations in regions of the adenovirus type 5 (Ad5) DNA polymerase that interact with the dNTP substrate or DNA template could alter virus replication. The majority of the mutations created, including conservative substitutions, were incompatible with virus replication. Five replication-competent mutants were recovered from 293 cells, but four of these mutants failed to replicate in A549 lung carcinoma cells and Wi38 normal lung cells. Purified polymerase proteins from these viruses exhibited only a 2- to 4-fold reduction in their dNTP utilization efficiency but nonetheless could not be rescued, even when intracellular dNTP concentrations were artificially raised by the addition of exogenous dNs to virus-infected A549 cells. The fifth mutation (I664V) reduced biochemical dNTP utilization by the viral polymerase by 2.5-fold. The corresponding virus replicated to wild-type levels in three different cancer cell lines but was significantly impaired in all normal cell lines in which it was tested. Efficient replication and virus-mediated cell killing were rescued by the addition of exogenous dNs to normal lung fibroblasts (MRC5 cells), confirming the dNTP-dependent nature of the polymerase defect. Collectively, these data provide proof-of-concept support for the notion that conditionally replicating, tumor-selective adenovirus vectors can be created by modifying the efficiency with which the viral DNA polymerase utilizes dNTP substrates. PMID:22811532

Improved Quantitative Plant Proteomics via the Combination of Targeted and Untargeted Data Acquisition

PubMed Central

Hart-Smith, Gene; Reis, Rodrigo S.; Waterhouse, Peter M.; Wilkins, Marc R.

2017-01-01

Quantitative proteomics strategies – which are playing important roles in the expanding field of plant molecular systems biology – are traditionally designated as either hypothesis driven or non-hypothesis driven. Many of these strategies aim to select individual peptide ions for tandem mass spectrometry (MS/MS), and to do this mixed hypothesis driven and non-hypothesis driven approaches are theoretically simple to implement. In-depth investigations into the efficacies of such approaches have, however, yet to be described. In this study, using combined samples of unlabeled and metabolically 15N-labeled Arabidopsis thaliana proteins, we investigate the mixed use of targeted data acquisition (TDA) and data dependent acquisition (DDA) – referred to as TDA/DDA – to facilitate both hypothesis driven and non-hypothesis driven quantitative data collection in individual LC-MS/MS experiments. To investigate TDA/DDA for hypothesis driven data collection, 7 miRNA target proteins of differing size and abundance were targeted using inclusion lists comprised of 1558 m/z values, using 3 different TDA/DDA experimental designs. In samples in which targeted peptide ions were of particularly low abundance (i.e., predominantly only marginally above mass analyser detection limits), TDA/DDA produced statistically significant increases in the number of targeted peptides identified (230 ± 8 versus 80 ± 3 for DDA; p = 1.1 × 10-3) and quantified (35 ± 3 versus 21 ± 2 for DDA; p = 0.038) per experiment relative to the use of DDA only. These expected improvements in hypothesis driven data collection were observed alongside unexpected improvements in non-hypothesis driven data collection. Untargeted peptide ions with m/z values matching those in inclusion lists were repeatedly identified and quantified across technical replicate TDA/DDA experiments, resulting in significant increases in the percentages of proteins repeatedly quantified in TDA/DDA experiments only relative to DDA experiments only (33.0 ± 2.6% versus 8.0 ± 2.7%, respectively; p = 0.011). These results were observed together with uncompromised broad-scale MS/MS data collection in TDA/DDA experiments relative to DDA experiments. Using our observations we provide guidelines for TDA/DDA method design for quantitative plant proteomics studies, and suggest that TDA/DDA is a broadly underutilized proteomics data acquisition strategy. PMID:29021799

Chinese and American employers' perspectives regarding hiring people with behaviorally driven health conditions: the role of stigma.

PubMed

Corrigan, Patrick W; Tsang, Hector W H; Shi, Kan; Lam, Chow S; Larson, Jon

2010-12-01

Work opportunities for people with behaviorally driven health conditions such as HIV/AIDS, drug abuse, alcohol abuse, and psychosis are directly impacted by employer perspectives. To investigate this issue, we report findings from a mixed method design involving qualitative interviews followed by a quantitative survey of employers from Chicago (U.S.), Beijing (China), and Hong Kong (China). Findings from qualitative interviews of 100 employers were used to create 27 items measuring employer perspectives (the Employer Perspective Scale: EPS) about hiring people with health conditions. These perspectives reflect reasons for or against discrimination. In the quantitative phase of the study, representative samples of approximately 300 employers per city were administered the EPS in addition to measures of stigma, including attributions about disease onset and offset. The EPS and stigma scales were completed in the context of one of five randomly assigned health conditions. We weighted data with ratios of key demographics between the sample and the corresponding employer population data. Analyses showed that both onset and offset responsibility varied by behaviorally driven condition. Analyses also showed that employer perspectives were more negative for health conditions that are seen as more behaviorally driven, e.g., drug and alcohol abuse. Chicago employers endorsed onset and offset attributions less strongly compared to those in Hong Kong and Beijing. Chicago employers also recognized more benefits of hiring people with various health conditions. The implications of these findings for better understanding stigma and stigma change among employers are considered. Copyright © 2010 Elsevier Ltd. All rights reserved.

MTOR-Driven Metabolic Reprogramming Regulates Legionella pneumophila Intracellular Niche Homeostasis

PubMed Central

Abshire, Camille F.; Roy, Craig R.

2016-01-01

Vacuolar bacterial pathogens are sheltered within unique membrane-bound organelles that expand over time to support bacterial replication. These compartments sequester bacterial molecules away from host cytosolic immunosurveillance pathways that induce antimicrobial responses. The mechanisms by which the human pulmonary pathogen Legionella pneumophila maintains niche homeostasis are poorly understood. We uncovered that the Legionella-containing vacuole (LCV) required a sustained supply of host lipids during expansion. Lipids shortage resulted in LCV rupture and initiation of a host cell death response, whereas excess of host lipids increased LCVs size and housing capacity. We found that lipids uptake from serum and de novo lipogenesis are distinct redundant supply mechanisms for membrane biogenesis in Legionella-infected macrophages. During infection, the metabolic checkpoint kinase Mechanistic Target of Rapamycin (MTOR) controlled lipogenesis through the Serum Response Element Binding Protein 1 and 2 (SREBP1/2) transcription factors. In Legionella-infected macrophages a host-driven response that required the Toll-like receptors (TLRs) adaptor protein Myeloid differentiation primary response gene 88 (Myd88) dampened MTOR signaling which in turn destabilized LCVs under serum starvation. Inactivation of the host MTOR-suppression pathway revealed that L. pneumophila sustained MTOR signaling throughout its intracellular infection cycle by a process that required the upstream regulator Phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K) and one or more Dot/Icm effector proteins. Legionella-sustained MTOR signaling facilitated LCV expansion and inhibition of the PI3K-MTOR-SREPB1/2 axis through pharmacological or genetic interference or by activation of the host MTOR-suppression response destabilized expanding LCVs, which in turn triggered cell death of infected macrophages. Our work identified a host metabolic requirement for LCV homeostasis and demonstrated that L. pneumophila has evolved to manipulate MTOR-dependent lipogenesis for optimal intracellular replication. PMID:27942021

PCNA-coupled p21 degradation after DNA damage: The exception that confirms the rule?

PubMed

Soria, Gastón; Gottifredi, Vanesa

2010-04-04

While many are the examples of DNA damaging treatments that induce p21 accumulation, the conception of p21 upregulation as the universal response to genotoxic stress has come to an end. Compelling evidences have demonstrated the existence of converging signals that negatively regulate p21 bellow basal levels when replication forks are blocked. Moreover, conclusive reports identified the E3-ligase CRL4(CDT2) (CUL4-DDB1-CDT2) as the enzymatic complex that promotes p21 proteolysis when treatments such as UV irradiation trigger replication fork stress. A pre-requisite for CRL4(CDT2)-driven proteolysis is the interaction of p21 with PCNA. Interestingly as well, CRL4(CDT2)-dependent proteolysis is not limited to p21 and affects other PCNA partners, including the specialized DNA polymerase eta (pol eta). These recent discoveries are particularly intriguing since the UV-induced degradation of p21 has been shown to be required for efficient pol eta recruitment to DNA lesions. Herein we review the findings that lead to the identification of the molecular mechanism that triggers damage-induced PCNA-coupled protein proteolysis. We propose a novel model in which CRL4(CDT2)-dependent protein degradation facilitates a sequential and dynamic exchange between PIP box bearing proteins at stall forks during Translesion DNA synthesis (TLS). Moreover, given the tight spatiotemporal control that CRL4(CDT2)-driven proteolysis is able to confer to PCNA-regulated processes, we discuss the impact that this degradation mechanism might have in other molecular switches associated with the repair of damaged DNA. 2010 Elsevier B.V. All rights reserved.

Uncommon Pathways of Immune Escape Attenuate HIV-1 Integrase Replication Capacity

PubMed Central

Chopera, Denis R.; Olvera, Alex; Brumme, Chanson J.; Sela, Jennifer; Markle, Tristan J.; Martin, Eric; Carlson, Jonathan M.; Le, Anh Q.; McGovern, Rachel; Cheung, Peter K.; Kelleher, Anthony D.; Jessen, Heiko; Markowitz, Martin; Rosenberg, Eric; Frahm, Nicole; Sanchez, Jorge; Mallal, Simon; John, Mina; Harrigan, P. Richard; Heckerman, David; Brander, Christian; Walker, Bruce D.; Brumme, Zabrina L.

2012-01-01

An attenuation of the HIV-1 replication capacity (RC) has been observed for immune-mediated escape mutations in Gag restricted by protective HLA alleles. However, the extent to which escape mutations affect other viral proteins during natural infection is not well understood. We generated recombinant viruses encoding plasma HIV-1 RNA integrase sequences from antiretroviral-naïve individuals with early (n = 88) and chronic (n = 304) infections and measured the in vitro RC of each. In contrast to data from previous studies of Gag, we observed little evidence that host HLA allele expression was associated with integrase RC. A modest negative correlation was observed between the number of HLA-B-associated integrase polymorphisms and RC in chronic infection (R = −0.2; P = 0.003); however, this effect was not driven by mutations restricted by protective HLA alleles. Notably, the integrase variants S119R, G163E, and I220L, which represent uncommon polymorphisms associated with HLA-C*05, -A*33, and -B*52, respectively, correlated with lower RC (all q < 0.2). We identified a novel C*05-restricted epitope (HTDNGSNF114–121) that likely contributes to the selection of the S119R variant, the polymorphism most significantly associated with lower RC in patient sequences. An NL4-3 mutant encoding the S119R polymorphism displayed a ∼35%-reduced function that was rescued by a single compensatory mutation of A91E. Together, these data indicate that substantial HLA-driven attenuation of integrase is not a general phenomenon during HIV-1 adaptation to host immunity. However, uncommon polymorphisms selected by HLA alleles that are not conventionally regarded to be protective may be associated with impaired protein function. Vulnerable epitopes in integrase might therefore be considered for future vaccine strategies. PMID:22496233

Uncommon pathways of immune escape attenuate HIV-1 integrase replication capacity.

PubMed

Brockman, Mark A; Chopera, Denis R; Olvera, Alex; Brumme, Chanson J; Sela, Jennifer; Markle, Tristan J; Martin, Eric; Carlson, Jonathan M; Le, Anh Q; McGovern, Rachel; Cheung, Peter K; Kelleher, Anthony D; Jessen, Heiko; Markowitz, Martin; Rosenberg, Eric; Frahm, Nicole; Sanchez, Jorge; Mallal, Simon; John, Mina; Harrigan, P Richard; Heckerman, David; Brander, Christian; Walker, Bruce D; Brumme, Zabrina L

2012-06-01

An attenuation of the HIV-1 replication capacity (RC) has been observed for immune-mediated escape mutations in Gag restricted by protective HLA alleles. However, the extent to which escape mutations affect other viral proteins during natural infection is not well understood. We generated recombinant viruses encoding plasma HIV-1 RNA integrase sequences from antiretroviral-naïve individuals with early (n = 88) and chronic (n = 304) infections and measured the in vitro RC of each. In contrast to data from previous studies of Gag, we observed little evidence that host HLA allele expression was associated with integrase RC. A modest negative correlation was observed between the number of HLA-B-associated integrase polymorphisms and RC in chronic infection (R = -0.2; P = 0.003); however, this effect was not driven by mutations restricted by protective HLA alleles. Notably, the integrase variants S119R, G163E, and I220L, which represent uncommon polymorphisms associated with HLA-C*05, -A*33, and -B*52, respectively, correlated with lower RC (all q < 0.2). We identified a novel C*05-restricted epitope (HTDNGSNF(114-121)) that likely contributes to the selection of the S119R variant, the polymorphism most significantly associated with lower RC in patient sequences. An NL4-3 mutant encoding the S119R polymorphism displayed a ~35%-reduced function that was rescued by a single compensatory mutation of A91E. Together, these data indicate that substantial HLA-driven attenuation of integrase is not a general phenomenon during HIV-1 adaptation to host immunity. However, uncommon polymorphisms selected by HLA alleles that are not conventionally regarded to be protective may be associated with impaired protein function. Vulnerable epitopes in integrase might therefore be considered for future vaccine strategies.

Systematic procedures to promote U.S. HIV medication adherence via Photovoice.

PubMed

Teti, Michelle; Shaffer, Victoria; Majee, Wilson; Farnan, Rose; Gerkovich, Mary

2017-06-21

Medication adherence is essential to promote the health of people living with HIV (PL-HIV) and prevent HIV transmission in the U.S. Novel medication health promotion interventions are needed that address patient-centeredness, understandability, and communication with providers. The aims of this article are to define the systematic stages we used to develop an effective health promotion intervention via the products (e.g. images and stories) of Photovoice. We designed an intervention to improve HIV adherence knowledge, attitudes, and communication with providers through Photovoice. 16 PL-HIV used Photovoice strategies to describe their experiences with medication via images and captions and create an intervention (10 adherence promotion posters) that integrated photo-stories of their adherence motivators, journeys from sickness to health, and how they manage and counter HIV stigma. We outline the systematic process we used to adapt Photovoice to create the effective intervention for replication. The process included six stages: (i) identify scope of the project; (ii) create collaborative project team; (iii) design project materials; (iv) review and revise materials with team members; (v) disseminate materials; and (vi) evaluate materials. Photovoice is used traditionally as a social action research method. In this project, it was adapted to create patient-driven images and stories for health promotion posters. Poster viewers experienced improved self-efficacy for HIV medication adherence. Describing the adaptation of the Photovoice process in a deliberate and transparent way can support fidelity to the essence of the participant-driven method, while also allowing researchers and practitioners to replicate Photovoice as a successful health promotion intervention. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

In vivo biomechanical measurement and haptic simulation of portal placement procedure in shoulder arthroscopic surgery

PubMed Central

Chae, Sanghoon; Jung, Sung-Weon

2018-01-01

A survey of 67 experienced orthopedic surgeons indicated that precise portal placement was the most important skill in arthroscopic surgery. However, none of the currently available virtual reality simulators include simulation / training in portal placement, including haptic feedback of the necessary puncture force. This study aimed to: (1) measure the in vivo force and stiffness during a portal placement procedure in an actual operating room and (2) implement active haptic simulation of a portal placement procedure using the measured in vivo data. We measured the force required for port placement and the stiffness of the joint capsule during portal placement procedures performed by an experienced arthroscopic surgeon. Based on the acquired mechanical property values, we developed a cable-driven active haptic simulator designed to train the portal placement skill and evaluated the validity of the simulated haptics. Ten patients diagnosed with rotator cuff tears were enrolled in this experiment. The maximum peak force and joint capsule stiffness during posterior portal placement procedures were 66.46 (±10.76N) and 2560.82(±252.92) N/m, respectively. We then designed an active haptic simulator using the acquired data. Our cable-driven mechanism structure had a friction force of 3.763 ± 0.341 N, less than 6% of the mean puncture force. Simulator performance was evaluated by comparing the target stiffness and force with the stiffness and force reproduced by the device. R-squared values were 0.998 for puncture force replication and 0.902 for stiffness replication, indicating that the in vivo data can be used to implement a realistic haptic simulator. PMID:29494691

A Cross-disciplinary Framework for the Description of Contextually Mediated Change

NASA Astrophysics Data System (ADS)

Gabora, Liane; Aerts, Diederik

We present a mathematical framework (referred to as Context-driven Actualization of Potential, or CAP) for describing how entities change over time under the influence of a context. The approach facilitates comparison of change of state of entities studied in different disciplines. Processes are seen to differ according to the degree of nondeterminism, and the degree to which they are sensitive to, internalize, and depend upon a particular context. Our analysis suggests that the dynamical evolution of a quantum entity described by the Schrödinger equation is not fundamentally different from change provoked by a measurement often referred to as collapse but a limiting case, with only one way to collapse. The biological transition to coded replication is seen as a means of preserving structure in the face of context, and sexual replication as a means of increasing potentiality thus enhancing diversity through interaction with context. The framework sheds light on concepts like selection and fitness, reveals how exceptional Darwinian evolution is as a means of 'change of state', and clarifies in what sense culture (and the creative process underlying it) are Darwinian.

Associating LIPS and SWOLLEN: delayed attentional disengagement following words in sex contexts.

PubMed

Oosterwijk, Suzanne; van der Leij, Andries R; Rotteveel, Mark

2017-09-01

With a series of three studies, using an adapted dot-probe paradigm, we investigated the elicitation of spontaneous affective meaning. Although it is well established that humans show delays in disengaging their attention from conventional affective stimuli, it is unknown whether contextually acquired affective meaning similarly impacts attention. We examined attentional disengagement following pairs of neutral or slightly ambiguous words that in combination could evoke sex, violence or neutral associations. Study 1 demonstrated slower disengagement following words that conveyed sex or violence associations compared to words that conveyed neutral associations. This pattern was only present for participants who were aware of sex or violence associations. Study 2 replicated these results in a large sample, but only for sex associations. Study 3 replicated the effect while instructing participants explicitly to expect sex and violence associations. Finally, two control studies countered reasonable alternative explanations for our findings. Together, these studies show that contextually driven affective associations can arise quickly with the potential to influence attentional processes. These findings are consistent with theoretical models of emotion and language that highlight the importance of context in the generation of affective meaning.

The nuclear DEK interactome supports multi-functionality.

PubMed

Smith, Eric A; Krumpelbeck, Eric F; Jegga, Anil G; Prell, Malte; Matrka, Marie M; Kappes, Ferdinand; Greis, Kenneth D; Ali, Abdullah M; Meetei, Amom R; Wells, Susanne I

2018-01-01

DEK is an oncoprotein that is overexpressed in many forms of cancer and participates in numerous cellular pathways. Of these different pathways, relevant interacting partners and functions of DEK are well described in regard to the regulation of chromatin structure, epigenetic marks, and transcription. Most of this understanding was derived by investigating DNA-binding and chromatin processing capabilities of the oncoprotein. To facilitate the generation of mechanism-driven hypotheses regarding DEK activities in underexplored areas, we have developed the first DEK interactome model using tandem-affinity purification and mass spectrometry. With this approach, we identify IMPDH2, DDX21, and RPL7a as novel DEK binding partners, hinting at new roles for the oncogene in de novo nucleotide biosynthesis and ribosome formation. Additionally, a hydroxyurea-specific interaction with replication protein A (RPA) was observed, suggesting that a DEK-RPA complex may form in response to DNA replication fork stalling. Taken together, these findings highlight diverse activities for DEK across cellular pathways and support a model wherein this molecule performs a plethora of functions. © 2017 Wiley Periodicals, Inc.

Testing a Theory-Based Health Communication Program: A Replication of Go Sun Smart in Outdoor Winter Recreation

PubMed Central

ANDERSEN, PETER A.; BULLER, DAVID B.; WALKOSZ, BARBARA J.; MALOY, JULIE; SCOTT, MICHAEL D.; CUTTER, GARY R.; DIGNAN, MARK B.

2010-01-01

The epidemic of preventable skin cancer in the United States creates an urgent need for health communication campaigns to improve sun protection. Go Sun Smart (GSS), a theory-driven multichannel health communication campaign showed positive effects on sun safety behaviors of employees and guests in a randomized trial at high-altitude ski areas. In this article we report findings from the North American GSS campaign for guests at ski areas that comprosed the original control-group resorts, replicating the results of the original guest intervention. Results showed that after GSS was deployed, guests at the original control group ski areas increased sun protection and reported greater recall of sun safety messages. Conversely, GSS had no effect on sunburning attitudes or self-efficacy beliefs. Like the original GSS guest intervention, the present study found that greater exposure to GSS messages was associated with greater use of sunscreen, sunscreen lip balm, and face covering, but not gloves or overall sun protection. There was no evidence that GSS decreased sunburning or attitudes and self-efficacy beliefs regarding sun safety. PMID:19466647

Effects of artificial settlement plate materials and methods of deployment on the sessile epibenthic community development in a tropical environment

NASA Astrophysics Data System (ADS)

Field, S. N.; Glassom, D.; Bythell, J.

2007-06-01

The choice of substrata and the methods of deployment in analyses of settlement in benthic communities are often driven by the cost of materials and their local availability, and comparisons are often made between studies using different methodologies. The effects of varying artificial substratum, size of replicates and method of deployment were determined on a shallow reef in Eilat, Israel, while the effect of size of replicates was also investigated on a shallow reef in Sharm El Sheikh, Egypt. When statistical power was high enough, that is, when sufficient numbers of settlers were recorded, significant differences were found between materials used, tile size and methods of deployment. Significant differences were detected in total coral settlement rates and for the two dominant taxonomic groups, acroporids and pocilloporids. Standardisation of tile materials, dimensions, and method of deployment is needed for comparison between coral and other epibiont settlement studies. However, a greater understanding of the effects of these experimental variables on settlement processes may enable retrospective comparisons between studies utilising a range of materials and methods.

A Distinct Class of Genome Rearrangements Driven by Heterologous Recombination.

PubMed

León-Ortiz, Ana María; Panier, Stephanie; Sarek, Grzegorz; Vannier, Jean-Baptiste; Patel, Harshil; Campbell, Peter J; Boulton, Simon J

2018-01-18

Erroneous DNA repair by heterologous recombination (Ht-REC) is a potential threat to genome stability, but evidence supporting its prevalence is lacking. Here we demonstrate that recombination is possible between heterologous sequences and that it is a source of chromosomal alterations in mitotic and meiotic cells. Mechanistically, we find that the RTEL1 and HIM-6/BLM helicases and the BRCA1 homolog BRC-1 counteract Ht-REC in Caenorhabditis elegans, whereas mismatch repair does not. Instead, MSH-2/6 drives Ht-REC events in rtel-1 and brc-1 mutants and excessive crossovers in rtel-1 mutant meioses. Loss of vertebrate Rtel1 also causes a variety of unusually large and complex structural variations, including chromothripsis, breakage-fusion-bridge events, and tandem duplications with distant intra-chromosomal insertions, whose structure are consistent with a role for RTEL1 in preventing Ht-REC during break-induced replication. Our data establish Ht-REC as an unappreciated source of genome instability that underpins a novel class of complex genome rearrangements that likely arise during replication stress. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Improving the compression dewatering of sewage sludge through bioacidification conditioning driven by Acidithiobacillus ferrooxidans: dewatering rate vs. dewatering extent.

PubMed

Lu, Yi; Zhang, Chunmei; Zheng, Guanyu; Zhou, Lixiang

2018-04-22

Prior to mechanical dewatering, sludge conditioning is indispensable to reduce the difficulty of sludge treatment and disposal. The effect of bioacidification conditioning driven by Acidithiobacillus ferrooxidans LX5 on the dewatering rate and extent of sewage sludge during compression dewatering process was investigated in this study. The results showed that the bioacidification of sludge driven by A. ferrooxidans LX5 simultaneously improved both the sludge dewatering rate and extent, which was not attained by physical/chemical conditioning approaches, including ultrasonication, microwave, freezing/thawing, or by adding the chemical conditioner cationic polyacrylamide (CPAM). During the bioacidification of sludge, the decrease in sludge pH induced the damage of sludge microbial cell structures, which enhanced the dewatering extent of sludge, and the added Fe 2+ and the subsequent bio-oxidized Fe 3+ effectively flocculated the damaged sludge flocs to improve the sludge dewatering rate. In the compression dewatering process consisting of filtration and expression stages, high removal of moisture and a short dewatering time were achieved during the filtration stage and the expression kinetics were also improved because of the high elasticity of sludge cake and the rapid creeping of the aggregates within the sludge cake. In addition, the usefulness of bioacidification driven by A. ferrooxidans LX5 in improving the compression dewatering of sewage sludge could not be attained by the chemical treatment of sludge through pH modification and Fe 3+ addition. Therefore, the bioacidification of sludge driven by A. ferrooxidans LX5 is an effective conditioning method to simultaneously improve the rate and extent of compression dewatering of sewage sludge.

Realistic Vascular Replicator for TAVR Procedures.

PubMed

Rotman, Oren M; Kovarovic, Brandon; Sadasivan, Chander; Gruberg, Luis; Lieber, Baruch B; Bluestein, Danny

2018-04-13

Transcatheter aortic valve replacement (TAVR) is an over-the-wire procedure for treatment of severe aortic stenosis (AS). TAVR valves are conventionally tested using simplified left heart simulators (LHS). While those provide baseline performance reliably, their aortic root geometries are far from the anatomical in situ configuration, often overestimating the valves' performance. We report on a novel benchtop patient-specific arterial replicator designed for testing TAVR and training interventional cardiologists in the procedure. The Replicator is an accurate model of the human upper body vasculature for training physicians in percutaneous interventions. It comprises of fully-automated Windkessel mechanism to recreate physiological flow conditions. Calcified aortic valve models were fabricated and incorporated into the Replicator, then tested for performing TAVR procedure by an experienced cardiologist using the Inovare valve. EOA, pressures, and angiograms were monitored pre- and post-TAVR. A St. Jude mechanical valve was tested as a reference that is less affected by the AS anatomy. Results in the Replicator of both valves were compared to the performance in a commercial ISO-compliant LHS. The AS anatomy in the Replicator resulted in a significant decrease of the TAVR valve performance relative to the simplified LHS, with EOA and transvalvular pressures comparable to clinical data. Minor change was seen in the mechanical valve performance. The Replicator showed to be an effective platform for TAVR testing. Unlike a simplified geometric anatomy LHS, it conservatively provides clinically-relevant outcomes and complement it. The Replicator can be most valuable for testing new valves under challenging patient anatomies, physicians training, and procedural planning.

High-fidelity in vivo replication of DNA base shape mimics without Watson–Crick hydrogen bonds

PubMed Central

Delaney, James C.; Henderson, Paul T.; Helquist, Sandra A.; Morales, Juan C.; Essigmann, John M.; Kool, Eric T.

2003-01-01

We report studies testing the importance of Watson–Crick hydrogen bonding, base-pair geometry, and steric effects during DNA replication in living bacterial cells. Nonpolar DNA base shape mimics of thymine and adenine (abbreviated F and Q, respectively) were introduced into Escherichia coli by insertion into a phage genome followed by transfection of the vector into bacteria. Genetic assays showed that these two base mimics were bypassed with moderate to high efficiency in the cells and with very high efficiency under damage-response (SOS induction) conditions. Under both sets of conditions, the T-shape mimic (F) encoded genetic information in the bacteria as if it were thymine, directing incorporation of adenine opposite it with high fidelity. Similarly, the A mimic (Q) directed incorporation of thymine opposite itself with high fidelity. The data establish that Watson–Crick hydrogen bonding is not necessary for high-fidelity replication of a base pair in vivo. The results suggest that recognition of DNA base shape alone serves as the most powerful determinant of fidelity during transfer of genetic information in a living organism. PMID:12676985

Time-varying Entry Heating Profile Replication with a Rotating Arc Jet Test Article

NASA Technical Reports Server (NTRS)

Grinstead, Jay Henderson; Venkatapathy, Ethiraj; Noyes, Eric A.; Mach, Jeffrey J.; Empey, Daniel M.; White, Todd R.

2014-01-01

A new approach for arc jet testing of thermal protection materials at conditions approximating the time-varying conditions of atmospheric entry was developed and demonstrated. The approach relies upon the spatial variation of heat flux and pressure over a cylindrical test model. By slowly rotating a cylindrical arc jet test model during exposure to an arc jet stream, each point on the test model will experience constantly changing applied heat flux. The predicted temporal profile of heat flux at a point on a vehicle can be replicated by rotating the cylinder at a prescribed speed and direction. An electromechanical test model mechanism was designed, built, and operated during an arc jet test to demonstrate the technique.

Synaptic Plasticity and NO-cGMP-PKG Signaling Coordinately Regulate ERK-Driven Gene Expression in the Lateral Amygdala and in the Auditory Thalamus Following Pavlovian Fear Conditioning

ERIC Educational Resources Information Center

Ota, Kristie T.; Monsey, Melissa S.; Wu, Melissa S.; Young, Grace J.; Schafe, Glenn E.

2010-01-01

We have recently hypothesized that NO-cGMP-PKG signaling in the lateral nucleus of the amygdala (LA) during auditory fear conditioning coordinately regulates ERK-driven transcriptional changes in both auditory thalamic (MGm/PIN) and LA neurons that serve to promote pre- and postsynaptic alterations at thalamo-LA synapses, respectively. In the…

Why Engaging in Mathematical Practices May Explain Stronger Outcomes in Affect and Engagement: Comparing Student-Driven with Highly Guided Inquiry

ERIC Educational Resources Information Center

Sengupta-Irving, Tesha; Enyedy, Noel

2015-01-01

This article investigates why students reported liking a student-driven learning design better than a highly guided design despite equivalent gains in knowledge assessments in both conditions. We created two learning designs based on the distinction in the literature between student-driven and teacher-led approaches. One teacher assigned each of…

EcoHIV infection of mice establishes latent viral reservoirs in T cells and active viral reservoirs in macrophages that are sufficient for induction of neurocognitive impairment

PubMed Central

Gu, Chao-Jiang; Kelschenbach, Jennifer; Kim, Boe-Hyun; Arancio, Ottavio; Suh, Jin; Polsky, Bruce; Edagwa, Benson; Gendelman, Howard E.

2018-01-01

Suppression of HIV replication by antiretroviral therapy (ART) or host immunity can prevent AIDS but not other HIV-associated conditions including neurocognitive impairment (HIV-NCI). Pathogenesis in HIV-suppressed individuals has been attributed to reservoirs of latent-inducible virus in resting CD4+ T cells. Macrophages are persistently infected with HIV but their role as HIV reservoirs in vivo has not been fully explored. Here we show that infection of conventional mice with chimeric HIV, EcoHIV, reproduces physiological conditions for development of disease in people on ART including immunocompetence, stable suppression of HIV replication, persistence of integrated, replication-competent HIV in T cells and macrophages, and manifestation of learning and memory deficits in behavioral tests, termed here murine HIV-NCI. EcoHIV established latent reservoirs in CD4+ T lymphocytes in chronically-infected mice but could be induced by epigenetic modulators ex vivo and in mice. In contrast, macrophages expressed EcoHIV constitutively in mice for up to 16 months; murine leukemia virus (MLV), the donor of gp80 envelope in EcoHIV, did not infect macrophages. Both EcoHIV and MLV were found in brain tissue of infected mice but only EcoHIV induced NCI. Murine HIV-NCI was prevented by antiretroviral prophylaxis but once established neither persistent EcoHIV infection in mice nor NCI could be reversed by long-acting antiretroviral therapy. EcoHIV-infected, athymic mice were more permissive to virus replication in macrophages than were wild-type mice, suffered cognitive dysfunction, as well as increased numbers of monocytes and macrophages infiltrating the brain. Our results suggest an important role of HIV expressing macrophages in HIV neuropathogenesis in hosts with suppressed HIV replication. PMID:29879225

EcoHIV infection of mice establishes latent viral reservoirs in T cells and active viral reservoirs in macrophages that are sufficient for induction of neurocognitive impairment.

PubMed

Gu, Chao-Jiang; Borjabad, Alejandra; Hadas, Eran; Kelschenbach, Jennifer; Kim, Boe-Hyun; Chao, Wei; Arancio, Ottavio; Suh, Jin; Polsky, Bruce; McMillan, JoEllyn; Edagwa, Benson; Gendelman, Howard E; Potash, Mary Jane; Volsky, David J

2018-06-01

Suppression of HIV replication by antiretroviral therapy (ART) or host immunity can prevent AIDS but not other HIV-associated conditions including neurocognitive impairment (HIV-NCI). Pathogenesis in HIV-suppressed individuals has been attributed to reservoirs of latent-inducible virus in resting CD4+ T cells. Macrophages are persistently infected with HIV but their role as HIV reservoirs in vivo has not been fully explored. Here we show that infection of conventional mice with chimeric HIV, EcoHIV, reproduces physiological conditions for development of disease in people on ART including immunocompetence, stable suppression of HIV replication, persistence of integrated, replication-competent HIV in T cells and macrophages, and manifestation of learning and memory deficits in behavioral tests, termed here murine HIV-NCI. EcoHIV established latent reservoirs in CD4+ T lymphocytes in chronically-infected mice but could be induced by epigenetic modulators ex vivo and in mice. In contrast, macrophages expressed EcoHIV constitutively in mice for up to 16 months; murine leukemia virus (MLV), the donor of gp80 envelope in EcoHIV, did not infect macrophages. Both EcoHIV and MLV were found in brain tissue of infected mice but only EcoHIV induced NCI. Murine HIV-NCI was prevented by antiretroviral prophylaxis but once established neither persistent EcoHIV infection in mice nor NCI could be reversed by long-acting antiretroviral therapy. EcoHIV-infected, athymic mice were more permissive to virus replication in macrophages than were wild-type mice, suffered cognitive dysfunction, as well as increased numbers of monocytes and macrophages infiltrating the brain. Our results suggest an important role of HIV expressing macrophages in HIV neuropathogenesis in hosts with suppressed HIV replication.

Identification of significant features by the Global Mean Rank test.

PubMed

Klammer, Martin; Dybowski, J Nikolaj; Hoffmann, Daniel; Schaab, Christoph

2014-01-01

With the introduction of omics-technologies such as transcriptomics and proteomics, numerous methods for the reliable identification of significantly regulated features (genes, proteins, etc.) have been developed. Experimental practice requires these tests to successfully deal with conditions such as small numbers of replicates, missing values, non-normally distributed expression levels, and non-identical distributions of features. With the MeanRank test we aimed at developing a test that performs robustly under these conditions, while favorably scaling with the number of replicates. The test proposed here is a global one-sample location test, which is based on the mean ranks across replicates, and internally estimates and controls the false discovery rate. Furthermore, missing data is accounted for without the need of imputation. In extensive simulations comparing MeanRank to other frequently used methods, we found that it performs well with small and large numbers of replicates, feature dependent variance between replicates, and variable regulation across features on simulation data and a recent two-color microarray spike-in dataset. The tests were then used to identify significant changes in the phosphoproteomes of cancer cells induced by the kinase inhibitors erlotinib and 3-MB-PP1 in two independently published mass spectrometry-based studies. MeanRank outperformed the other global rank-based methods applied in this study. Compared to the popular Significance Analysis of Microarrays and Linear Models for Microarray methods, MeanRank performed similar or better. Furthermore, MeanRank exhibits more consistent behavior regarding the degree of regulation and is robust against the choice of preprocessing methods. MeanRank does not require any imputation of missing values, is easy to understand, and yields results that are easy to interpret. The software implementing the algorithm is freely available for academic and commercial use.

Social comparison modulates reward-driven attentional capture.

PubMed

Jiao, Jun; Du, Feng; He, Xiaosong; Zhang, Kan

2015-10-01

It is well established that attention can be captured by task irrelevant and non-salient objects associated with value through reward learning. However, it is unknown whether social comparison influences reward-driven attentional capture. The present study created four social contexts to examine whether different social comparisons modulate the reward-driven capture of attention. The results showed that reward-driven attentional capture varied with different social comparison conditions. Most prominently, reward-driven attentional capture is dramatically reduced in the disadvantageous social comparison context, in which an individual is informed that the other participant is earning more monetary reward for performing the same task. These findings suggest that social comparison can affect the reward-driven capture of attention.

System-wide Analysis of SUMOylation Dynamics in Response to Replication Stress Reveals Novel Small Ubiquitin-like Modified Target Proteins and Acceptor Lysines Relevant for Genome Stability*

PubMed Central

Xiao, Zhenyu; Chang, Jer-Gung; Hendriks, Ivo A.; Sigurðsson, Jón Otti; Olsen, Jesper V.; Vertegaal, Alfred C.O.

2015-01-01

Genotoxic agents can cause replication fork stalling in dividing cells because of DNA lesions, eventually leading to replication fork collapse when the damage is not repaired. Small Ubiquitin-like Modifiers (SUMOs) are known to counteract replication stress, nevertheless, only a small number of relevant SUMO target proteins are known. To address this, we have purified and identified SUMO-2 target proteins regulated by replication stress in human cells. The developed methodology enabled single step purification of His10-SUMO-2 conjugates under denaturing conditions with high yield and high purity. Following statistical analysis on five biological replicates, a total of 566 SUMO-2 targets were identified. After 2 h of hydroxyurea treatment, 10 proteins were up-regulated for SUMOylation and two proteins were down-regulated for SUMOylation, whereas after 24 h, 35 proteins were up-regulated for SUMOylation, and 13 proteins were down-regulated for SUMOylation. A site-specific approach was used to map over 1000 SUMO-2 acceptor lysines in target proteins. The methodology is generic and is widely applicable in the ubiquitin field. A large subset of these identified proteins function in one network that consists of interacting replication factors, transcriptional regulators, DNA damage response factors including MDC1, ATR-interacting protein ATRIP, the Bloom syndrome protein and the BLM-binding partner RMI1, the crossover junction endonuclease EME1, BRCA1, and CHAF1A. Furthermore, centromeric proteins and signal transducers were dynamically regulated by SUMOylation upon replication stress. Our results uncover a comprehensive network of SUMO target proteins dealing with replication damage and provide a framework for detailed understanding of the role of SUMOylation to counteract replication stress. Ultimately, our study reveals how a post-translational modification is able to orchestrate a large variety of different proteins to integrate different nuclear processes with the aim of dealing with the induced DNA damage. PMID:25755297

Intrinsic Innate Immunity Fails To Control Herpes Simplex Virus and Vesicular Stomatitis Virus Replication in Sensory Neurons and Fibroblasts

PubMed Central

Rosato, Pamela C.

2014-01-01

ABSTRACT Herpes simplex virus 1 (HSV-1) establishes lifelong latent infections in the sensory neurons of the trigeminal ganglia (TG), wherein it retains the capacity to reactivate. The interferon (IFN)-driven antiviral response is critical for the control of HSV-1 acute replication. We therefore sought to further investigate this response in TG neurons cultured from adult mice deficient in a variety of IFN signaling components. Parallel experiments were also performed in fibroblasts isolated concurrently. We showed that HSV-1 replication was comparable in wild-type (WT) and IFN signaling-deficient neurons and fibroblasts. Unexpectedly, a similar pattern was observed for the IFN-sensitive vesicular stomatitis virus (VSV). Despite these findings, TG neurons responded to IFN-β pretreatment with STAT1 nuclear localization and restricted replication of both VSV and an HSV-1 strain deficient in γ34.5, while wild-type HSV-1 replication was unaffected. This was in contrast to fibroblasts in which all viruses were restricted by the addition of IFN-β. Taken together, these data show that adult TG neurons can mount an effective antiviral response only if provided with an exogenous source of IFN-β, and HSV-1 combats this response through γ34.5. These results further our understanding of the antiviral response of neurons and highlight the importance of paracrine IFN-β signaling in establishing an antiviral state. IMPORTANCE Herpes simplex virus 1 (HSV-1) is a ubiquitous virus that establishes a lifelong latent infection in neurons. Reactivation from latency can cause cold sores, blindness, and death from encephalitis. Humans with deficiencies in innate immunity have significant problems controlling HSV infections. In this study, we therefore sought to elucidate the role of neuronal innate immunity in the control of viral infection. Using neurons isolated from mice, we found that the intrinsic capacity of neurons to restrict virus replication was unaffected by the presence or absence of innate immunity. In contrast, neurons were able to mount a robust antiviral response when provided with beta interferon, a molecule that strongly stimulates innate immunity, and that HSV-1 can combat this response through the γ34.5 viral gene. Our results have important implications for understanding how the nervous system defends itself against virus infections. PMID:24942587

Development of a Glycoprotein D-Expressing Dominant-Negative and Replication-Defective Herpes Simplex Virus 2 (HSV-2) Recombinant Viral Vaccine against HSV-2 Infection in Mice ▿

PubMed Central

Akhrameyeva, Natalie V.; Zhang, Pengwei; Sugiyama, Nao; Behar, Samuel M.; Yao, Feng

2011-01-01

Using the T-REx (Invitrogen, California) gene switch technology and a dominant-negative mutant polypeptide of herpes simplex virus 1 (HSV-1)-origin binding protein UL9, we previously constructed a glycoprotein D-expressing replication-defective and dominant-negative HSV-1 recombinant viral vaccine, CJ9-gD, for protection against HSV infection and disease. It was demonstrated that CJ9-gD is avirulent following intracerebral inoculation in mice, cannot establish detectable latent infection following different routes of infection, and offers highly effective protective immunity against primary HSV-1 and HSV-2 infection and disease in mouse and guinea pig models of HSV infections. Given these favorable safety and immunological profiles of CJ9-gD, aiming to maximize levels of HSV-2 glycoprotein D (gD2) expression, we have constructed an ICP0 null mutant-based dominant-negative and replication-defective HSV-2 recombinant, CJ2-gD2, that contains 2 copies of the gD2 gene driven by the tetracycline operator (tetO)-bearing HSV-1 major immediate-early ICP4 promoter. CJ2-gD2 expresses gD2 as efficiently as wild-type HSV-2 infection and can lead to a 150-fold reduction in wild-type HSV-2 viral replication in cells coinfected with CJ2-gD2 and wild-type HSV-2 at the same multiplicity of infection. CJ2-gD2 is avirulent following intracerebral injection and cannot establish a detectable latent infection following subcutaneous (s.c.) immunization. CJ2-gD2 is a more effective vaccine than HSV-1 CJ9-gD and a non-gD2-expressing dominant-negative and replication-defective HSV-2 recombinant in protection against wild-type HSV-2 genital disease. Using recall response, we showed that immunization with CJ2-gD2 elicited strong HSV-2-specific memory CD4+ and CD8+ T-cell responses. Collectively, given the demonstrated preclinical immunogenicity and its unique safety profiles, CJ2-gD2 represents a new class of HSV-2 replication-defective recombinant viral vaccines in protection against HSV-2 genital infection and disease. PMID:21389121

A Tumor-stroma Targeted Oncolytic Adenovirus Replicated in Human Ovary Cancer Samples and Inhibited Growth of Disseminated Solid Tumors in Mice

PubMed Central

Lopez, M Veronica; Rivera, Angel A; Viale, Diego L; Benedetti, Lorena; Cuneo, Nicasio; Kimball, Kristopher J; Wang, Minghui; Douglas, Joanne T; Zhu, Zeng B; Bravo, Alicia I; Gidekel, Manuel; Alvarez, Ronald D; Curiel, David T; Podhajcer, Osvaldo L

2012-01-01

Targeting the tumor stroma in addition to the malignant cell compartment is of paramount importance to achieve complete tumor regression. In this work, we modified a previously designed tumor stroma-targeted conditionally replicative adenovirus (CRAd) based on the SPARC promoter by introducing a mutated E1A unable to bind pRB and pseudotyped with a chimeric Ad5/3 fiber (Ad F512v1), and assessed its replication/lytic capacity in ovary cancer in vitro and in vivo. AdF512v1 was able to replicate in fresh samples obtained from patients: (i) with primary human ovary cancer; (ii) that underwent neoadjuvant treatment; (iii) with metastatic disease. In addition, we show that four intraperitoneal (i.p.) injections of 5 × 1010 v.p. eliminated 50% of xenografted human ovary tumors disseminated in nude mice. Moreover, AdF512v1 replication in tumor models was enhanced 15–40-fold when the tumor contained a mix of malignant and SPARC-expressing stromal cells (fibroblasts and endothelial cells). Contrary to the wild-type virus, AdF512v1 was unable to replicate in normal human ovary samples while the wild-type virus can replicate. This study provides evidence on the lytic capacity of this CRAd and highlights the importance of targeting the stromal tissue in addition to the malignant cell compartment to achieve tumor regression. PMID:22948673

Mycobacterium tuberculosis Ser/Thr protein kinase B mediates an oxygen-dependent replication switch

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ortega, Corrie; Liao, Reiling; Anderson, Lindsey N.

In the majority of cases, Mycobacterium tuberculosis (Mtb) infections are clinically latent, characterized by little or no bacterial replication and drug tolerance. Low oxygen tension is a major host factor inducing bacteriostasis, but the molecular mechanisms driving oxygen-dependent replication are poorly understood. Mtb encodes eleven serine/threonine protein kinases, a family of signaling molecules known to regulate similar replicative adaptations in other bacteria. Here, we tested the role of serine/threonine phosphorylation in the Mtb response to altered oxygen status, using an in vitro model of latency (hypoxia) and reactivation (reaeration). Broad kinase inhibition compromised survival of Mtb in hypoxia. Activity-based proteinmore » profiling and genetic mutation identified PknB as the kinase critical for surviving hypoxia. Mtb replication was highly sensitive to changes in PknB levels in aerated culture, and even more so in hypoxia. A mutant overexpressing PknB specifically in hypoxia showed a 10-fold loss in viability in low oxygen conditions. In contrast, chemically reducing PknB activity during hypoxia specifically compromised resumption of growth during reaeration. These data support a model in which PknB activity is reduced to achieve bacteriostasis, and elevated when replication resumes. Together, these data show that phosphosignaling controls replicative transitions associated with latency and reactivation, that PknB is a major regulator of these transitions, and that PknB could provide a highly vulnerable therapeutic target at every step of the Mtb life cycle - active disease, latency, and reactivation.« less

Herpes Simplex Virus Type 2 Triggers Reactivation of Kaposi's Sarcoma-Associated Herpesvirus from Latency and Collaborates with HIV-1 Tat

PubMed Central

Zhu, Xiaolei; Ma, Xinting; Yan, Qin; Zeng, Yi; Guo, Yuanyuan; Feng, Ninghan; Lu, Chun

2012-01-01

Kaposi's sarcoma-associated herpesvirus (KSHV) infection was necessary but not sufficient for Kaposi's sarcoma (KS) development without other cofactors. Previously, we identified that both human immunodeficiency type 1 (HIV-1) Tat and herpes simplex virus 1 (HSV-1) were important cofactors reactivating KSHV from latency. Here, we further investigated the potential of herpes simplex virus 2 (HSV-2) to influence KSHV replication and examined the role of Tat in this procedure. We demonstrated that HSV-2 was a potentially important factor in the pathogenesis of KS, as determined by production of lytic phase mRNA transcripts, viral proteins and infectious viral particles in BCBL-1 cells. These results were further confirmed by an RNA interference experiment using small interfering RNA targeting KSHV Rta and a luciferase reporter assay testing Rta promoter-driven luciferase activity. Mechanistic studies showed that HSV-2 infection activated nuclear factor-kappa B (NF-κB) signaling pathway. Inhibition of NF-κB pathway enhanced HSV-2-mediated KSHV activation, whereas activation of NF-κB pathway suppressed KSHV replication in HSV-2-infected BCBL-1 cells. Additionally, ectopic expression of Tat enhanced HSV-2-induced KSHV replication. These novel findings suggest a role of HSV-2 in the pathogenesis of KS and provide the first laboratory evidence that Tat may participate HSV-2-mediated KSHV activation, implying the complicated pathogenesis of acquired immunodeficiency syndrome (AIDS)-related KS (AIDS-KS) patients. PMID:22347501

Stability analysis of hybrid-driven underwater glider

NASA Astrophysics Data System (ADS)

Niu, Wen-dong; Wang, Shu-xin; Wang, Yan-hui; Song, Yang; Zhu, Ya-qiang

2017-10-01

Hybrid-driven underwater glider is a new type of unmanned underwater vehicle, which combines the advantages of autonomous underwater vehicles and traditional underwater gliders. The autonomous underwater vehicles have good maneuverability and can travel with a high speed, while the traditional underwater gliders are highlighted by low power consumption, long voyage, long endurance and good stealth characteristics. The hybrid-driven underwater gliders can realize variable motion profiles by their own buoyancy-driven and propeller propulsion systems. Stability of the mechanical system determines the performance of the system. In this paper, the Petrel-II hybrid-driven underwater glider developed by Tianjin University is selected as the research object and the stability of hybrid-driven underwater glider unitedly controlled by buoyancy and propeller has been targeted and evidenced. The dimensionless equations of the hybrid-driven underwater glider are obtained when the propeller is working. Then, the steady speed and steady glide path angle under steady-state motion have also been achieved. The steady-state operating conditions can be calculated when the hybrid-driven underwater glider reaches the desired steady-state motion. And the steadystate operating conditions are relatively conservative at the lower bound of the velocity range compared with the range of the velocity derived from the method of the composite Lyapunov function. By calculating the hydrodynamic coefficients of the Petrel-II hybrid-driven underwater glider, the simulation analysis has been conducted. In addition, the results of the field trials conducted in the South China Sea and the Danjiangkou Reservoir of China have been presented to illustrate the validity of the analysis and simulation, and to show the feasibility of the method of the composite Lyapunov function which verifies the stability of the Petrel-II hybrid-driven underwater glider.

Changing contributions of stochastic and deterministic processes in community assembly over a successional gradient.

PubMed

Måren, Inger Elisabeth; Kapfer, Jutta; Aarrestad, Per Arild; Grytnes, John-Arvid; Vandvik, Vigdis

2018-01-01

Successional dynamics in plant community assembly may result from both deterministic and stochastic ecological processes. The relative importance of different ecological processes is expected to vary over the successional sequence, between different plant functional groups, and with the disturbance levels and land-use management regimes of the successional systems. We evaluate the relative importance of stochastic and deterministic processes in bryophyte and vascular plant community assembly after fire in grazed and ungrazed anthropogenic coastal heathlands in Northern Europe. A replicated series of post-fire successions (n = 12) were initiated under grazed and ungrazed conditions, and vegetation data were recorded in permanent plots over 13 years. We used redundancy analysis (RDA) to test for deterministic successional patterns in species composition repeated across the replicate successional series and analyses of co-occurrence to evaluate to what extent species respond synchronously along the successional gradient. Change in species co-occurrences over succession indicates stochastic successional dynamics at the species level (i.e., species equivalence), whereas constancy in co-occurrence indicates deterministic dynamics (successional niche differentiation). The RDA shows high and deterministic vascular plant community compositional change, especially early in succession. Co-occurrence analyses indicate stochastic species-level dynamics the first two years, which then give way to more deterministic replacements. Grazed and ungrazed successions are similar, but the early stage stochasticity is higher in ungrazed areas. Bryophyte communities in ungrazed successions resemble vascular plant communities. In contrast, bryophytes in grazed successions showed consistently high stochasticity and low determinism in both community composition and species co-occurrence. In conclusion, stochastic and individualistic species responses early in succession give way to more niche-driven dynamics in later successional stages. Grazing reduces predictability in both successional trends and species-level dynamics, especially in plant functional groups that are not well adapted to disturbance. © 2017 The Authors. Ecology, published by Wiley Periodicals, Inc., on behalf of the Ecological Society of America.

Synchronization of heteroclinic circuits through learning in coupled neural networks

NASA Astrophysics Data System (ADS)

Selskii, Anton; Makarov, Valeri A.

2016-01-01

The synchronization of oscillatory activity in neural networks is usually implemented by coupling the state variables describing neuronal dynamics. Here we study another, but complementary mechanism based on a learning process with memory. A driver network, acting as a teacher, exhibits winner-less competition (WLC) dynamics, while a driven network, a learner, tunes its internal couplings according to the oscillations observed in the teacher. We show that under appropriate training the learner can "copy" the coupling structure and thus synchronize oscillations with the teacher. The replication of the WLC dynamics occurs for intermediate memory lengths only, consequently, the learner network exhibits a phenomenon of learning resonance.

Long-range correlations and asymmetry in the Bitcoin market

NASA Astrophysics Data System (ADS)

Alvarez-Ramirez, J.; Rodriguez, E.; Ibarra-Valdez, C.

2018-02-01

This work studies long-range correlations and informational efficiency of the Bitcoin market for the period from June 30, 2013 to June 3rd, 2017. To this end, the detrended fluctuation analysis (DFA) was implemented over sliding windows to estimate long-range correlations for price returns. It was found that the Bitcoin market exhibits periods of efficiency alternating with periods where the price dynamics are driven by anti-persistence. The pattern is replicated by prices samples at day, hour and second frequencies. The Bitcoin market also presents asymmetric correlations with respect to increasing and decreasing price trending, with the former trend linked to anti-persistence of returns dynamics.

On the classification of buoyancy-driven chemo-hydrodynamic instabilities of chemical fronts.

PubMed

D'Hernoncourt, J; Zebib, A; De Wit, A

2007-03-01

Exothermic autocatalytic fronts traveling in the gravity field can be deformed by buoyancy-driven convection due to solutal and thermal contributions to changes in the density of the product versus the reactant solutions. We classify the possible instability mechanisms, such as Rayleigh-Benard, Rayleigh-Taylor, and double-diffusive mechanisms known to operate in such conditions in a parameter space spanned by the corresponding solutal and thermal Rayleigh numbers. We also discuss a counterintuitive instability leading to buoyancy-driven deformation of statically stable fronts across which a solute-light and hot solution lies on top of a solute-heavy and colder one. The mechanism of this chemically driven instability lies in the coupling of a localized reaction zone and of differential diffusion of heat and mass. Dispersion curves of the various cases are analyzed. A discussion of the possible candidates of autocatalytic reactions and experimental conditions necessary to observe the various instability scenarios is presented.

Recurrence measure of conditional dependence and applications.

PubMed

Ramos, Antônio M T; Builes-Jaramillo, Alejandro; Poveda, Germán; Goswami, Bedartha; Macau, Elbert E N; Kurths, Jürgen; Marwan, Norbert

2017-05-01

Identifying causal relations from observational data sets has posed great challenges in data-driven causality inference studies. One of the successful approaches to detect direct coupling in the information theory framework is transfer entropy. However, the core of entropy-based tools lies on the probability estimation of the underlying variables. Here we propose a data-driven approach for causality inference that incorporates recurrence plot features into the framework of information theory. We define it as the recurrence measure of conditional dependence (RMCD), and we present some applications. The RMCD quantifies the causal dependence between two processes based on joint recurrence patterns between the past of the possible driver and present of the potentially driven, excepting the contribution of the contemporaneous past of the driven variable. Finally, it can unveil the time scale of the influence of the sea-surface temperature of the Pacific Ocean on the precipitation in the Amazonia during recent major droughts.

Recurrence measure of conditional dependence and applications

NASA Astrophysics Data System (ADS)

Ramos, Antônio M. T.; Builes-Jaramillo, Alejandro; Poveda, Germán; Goswami, Bedartha; Macau, Elbert E. N.; Kurths, Jürgen; Marwan, Norbert

2017-05-01

Identifying causal relations from observational data sets has posed great challenges in data-driven causality inference studies. One of the successful approaches to detect direct coupling in the information theory framework is transfer entropy. However, the core of entropy-based tools lies on the probability estimation of the underlying variables. Here we propose a data-driven approach for causality inference that incorporates recurrence plot features into the framework of information theory. We define it as the recurrence measure of conditional dependence (RMCD), and we present some applications. The RMCD quantifies the causal dependence between two processes based on joint recurrence patterns between the past of the possible driver and present of the potentially driven, excepting the contribution of the contemporaneous past of the driven variable. Finally, it can unveil the time scale of the influence of the sea-surface temperature of the Pacific Ocean on the precipitation in the Amazonia during recent major droughts.

The steady state solutions of radiatively driven stellar winds for a non-Sobolev, pure absorption model

NASA Technical Reports Server (NTRS)

Poe, C. H.; Owocki, S. P.; Castor, J. I.

1990-01-01

The steady state solution topology for absorption line-driven flows is investigated for the condition that the Sobolev approximation is not used to compute the line force. The solution topology near the sonic point is of the nodal type with two positive slope solutions. The shallower of these slopes applies to reasonable lower boundary conditions and realistic ion thermal speed v(th) and to the Sobolev limit of zero of the usual Castor, Abbott, and Klein model. At finite v(th), this solution consists of a family of very similar solutions converging on the sonic point. It is concluded that a non-Sobolev, absorption line-driven flow with a realistic values of v(th) has no uniquely defined steady state. To the extent that a pure absorption model of the outflow of stellar winds is applicable, radiatively driven winds should be intrinsically variable.

Skin Cooling and Force Replication at the Ankle in Healthy Individuals: A Crossover Randomized Controlled Trial

PubMed Central

Haupenthal, Daniela Pacheco dos Santos; de Noronha, Marcos; Haupenthal, Alessandro; Ruschel, Caroline; Nunes, Guilherme S.

2015-01-01

Context Proprioception of the ankle is determined by the ability to perceive the sense of position of the ankle structures, as well as the speed and direction of movement. Few researchers have investigated proprioception by force-replication ability and particularly after skin cooling. Objective To analyze the ability of the ankle-dorsiflexor muscles to replicate isometric force after a period of skin cooling. Design Randomized controlled clinical trial. Setting Laboratory. Patients or Other Participants Twenty healthy individuals (10 men, 10 women; age = 26.8 ± 5.2 years, height = 171 ± 7 cm, mass = 66.8 ± 10.5 kg). Intervention(s) Skin cooling was carried out using 2 ice applications: (1) after maximal voluntary isometric contraction (MVIC) performance and before data collection for the first target force, maintained for 20 minutes; and (2) before data collection for the second target force, maintained for 10 minutes. We measured skin temperature before and after ice applications to ensure skin cooling. Main Outcome Measure(s) A load cell was placed under an inclined board for data collection, and 10 attempts of force replication were carried out for 2 values of MVIC (20%, 50%) in each condition (ice, no ice). We assessed force sense with absolute and root mean square errors (the difference between the force developed by the dorsiflexors and the target force measured with the raw data and after root mean square analysis, respectively) and variable error (the variance around the mean absolute error score). A repeated-measures multivariate analysis of variance was used for statistical analysis. Results The absolute error was greater for the ice than for the no-ice condition (F1,19 = 9.05, P = .007) and for the target force at 50% of MVIC than at 20% of MVIC (F1,19 = 26.01, P < .001). Conclusions The error was greater in the ice condition and at 50% of MVIC. Skin cooling reduced the proprioceptive ability of the ankle-dorsiflexor muscles to replicate isometric force. PMID:25761136

Temporal patterns of inputs to cerebellum necessary and sufficient for trace eyelid conditioning.

PubMed

Kalmbach, Brian E; Ohyama, Tatsuya; Mauk, Michael D

2010-08-01

Trace eyelid conditioning is a form of associative learning that requires several forebrain structures and cerebellum. Previous work suggests that at least two conditioned stimulus (CS)-driven signals are available to the cerebellum via mossy fiber inputs during trace conditioning: one driven by and terminating with the tone and a second driven by medial prefrontal cortex (mPFC) that persists through the stimulus-free trace interval to overlap in time with the unconditioned stimulus (US). We used electric stimulation of mossy fibers to determine whether this pattern of dual inputs is necessary and sufficient for cerebellar learning to express normal trace eyelid responses. We find that presenting the cerebellum with one input that mimics persistent activity observed in mPFC and the lateral pontine nuclei during trace eyelid conditioning and another that mimics tone-elicited mossy fiber activity is sufficient to produce responses whose properties quantitatively match trace eyelid responses using a tone. Probe trials with each input delivered separately provide evidence that the cerebellum learns to respond to the mPFC-like input (that overlaps with the US) and learns to suppress responding to the tone-like input (that does not). This contributes to precisely timed responses and the well-documented influence of tone offset on the timing of trace responses. Computer simulations suggest that the underlying cerebellar mechanisms involve activation of different subsets of granule cells during the tone and during the stimulus-free trace interval. These results indicate that tone-driven and mPFC-like inputs are necessary and sufficient for the cerebellum to learn well-timed trace conditioned responses.

Interindividual Responses of Appetite to Acute Exercise: A Replicated Crossover Study.

PubMed

Goltz, Fernanda R; Thackray, Alice E; King, James A; Dorling, James L; Atkinson, Greg; Stensel, David J

2018-04-01

Acute exercise transiently suppresses appetite, which coincides with alterations in appetite-regulatory hormone concentrations. Individual variability in these responses is suspected, but replicated trials are needed to quantify them robustly. We examined the reproducibility of appetite and appetite-regulatory hormone responses to acute exercise and quantified the individual differences in responses. Fifteen healthy, recreationally active men completed two control (60-min resting) and two exercise (60-min fasted treadmill running at 70% peak oxygen uptake) conditions in randomized sequences. Perceived appetite and circulating concentrations of acylated ghrelin and total peptide YY (PYY) were measured immediately before and after the interventions. Interindividual differences were explored by correlating the two sets of response differences between exercise and control conditions. Within-participant covariate-adjusted linear mixed models were used to quantify participant-condition interactions. Compared with control, exercise suppressed mean acylated ghrelin concentrations and appetite perceptions (all ES = 0.62-1.47, P < 0.001) and elevated total PYY concentrations (ES = 1.49, P < 0.001). For all variables, the standard deviation of the change scores was substantially greater in the exercise versus control conditions. Moderate-to-large positive correlations were observed between the two sets of control-adjusted exercise responses for all variables (r = 0.54-0.82, P ≤ 0.036). After adjusting for baseline measurements, participant-condition interactions were present for all variables (P ≤ 0.053). Our replicated crossover study allowed, for the first time, the interaction between participant and acute exercise response in appetite parameters to be quantified. Even after adjustment for individual baseline measurements, participants demonstrated individual differences in perceived appetite and hormone responses to acute exercise bouts beyond any random within-subject variability over time.

Turning the gene tap off; implications of regulating gene expression for cancer therapeutics

PubMed Central

Curtin, James F.; Candolfi, Marianela; Xiong, Weidong; Lowenstein, Pedro R.; Castro, Maria G.

2008-01-01

Cancer poses a tremendous therapeutic challenge worldwide, highlighting the critical need for developing novel therapeutics. A promising cancer treatment modality is gene therapy, which is a form of molecular medicine designed to introduce into target cells genetic material with therapeutic intent. Anticancer gene therapy strategies currently used in preclinical models, and in some cases in the clinic, include proapoptotic genes, oncolytic/replicative vectors, conditional cytotoxic approaches, inhibition of angiogenesis, inhibition of growth factor signaling, inactivation of oncogenes, inhibition of tumor invasion and stimulation of the immune system. The translation of these novel therapeutic modalities from the preclinical setting to the clinic has been driven by encouraging preclinical efficacy data and advances in gene delivery technologies. One area of intense research involves the ability to accurately regulate the levels of therapeutic gene expression to achieve enhanced efficacy and provide the capability to switch gene expression off completely if adverse side effects should arise. This feature could also be implemented to switch gene expression off when a successful therapeutic outcome ensues. Here, we will review recent developments related to the engineering of transcriptional switches within gene delivery systems, which could be implemented in clinical gene therapy applications directed at the treatment of cancer. PMID:18347132

The 'male escape hypothesis': sex-biased metamorphosis in response to climatic drivers in a facultatively paedomorphic amphibian.

PubMed

Mathiron, Anthony G E; Lena, Jean-Paul; Baouch, Sarah; Denoël, Mathieu

2017-04-26

Paedomorphosis is a major evolutionary process that bypasses metamorphosis and allows reproduction in larvae. In newts and salamanders, it can be facultative with paedomorphs retaining gills and metamorphs dispersing. The evolution of these developmental processes is thought to have been driven by the costs and benefits of inhabiting aquatic versus terrestrial habitats. In this context, we aimed at testing the hypothesis that climatic drivers affect phenotypic transition and the difference across sexes because sex-ratio is biased in natural populations. Through a replicated laboratory experiment, we showed that paedomorphic palmate newts ( Lissotriton helveticus ) metamorphosed at a higher frequency when water availability decreased and metamorphosed earlier when temperature increased in these conditions. All responses were sex-biased, and males were more prone to change phenotype than females. Our work shows how climatic variables can affect facultative paedomorphosis and support theoretical models predicting life on land instead of in water. Moreover, because males metamorphose and leave water more often and earlier than females, these results, for the first time, give an experimental explanation for the rarity of male paedomorphosis (the 'male escape hypothesis') and suggest the importance of sex in the evolution of paedomorphosis versus metamorphosis. © 2017 The Author(s).

Experimental evolution of an emerging plant virus in host genotypes that differ in their susceptibility to infection.

PubMed

Hillung, Julia; Cuevas, José M; Valverde, Sergi; Elena, Santiago F

2014-09-01

This study evaluates the extent to which genetic differences among host individuals from the same species condition the evolution of a plant RNA virus. We performed a threefold replicated evolution experiment in which Tobacco etch potyvirus isolate At17b (TEV-At17b), adapted to Arabidopsis thaliana ecotype Ler-0, was serially passaged in five genetically heterogeneous ecotypes of A. thaliana. After 15 passages we found that evolved viruses improved their fitness, showed higher infectivity and stronger virulence in their local host ecotypes. The genome of evolved lineages was sequenced and putative adaptive mutations identified. Host-driven convergent mutations have been identified. Evidences supported selection for increased translational efficiency. Next, we sought for the specificity of virus adaptation by infecting all five ecotypes with all 15 evolved virus populations. We found that some ecotypes were more permissive to infection than others, and that some evolved virus isolates were more specialist/generalist than others. The bipartite network linking ecotypes with evolved viruses was significantly nested but not modular, suggesting that hard-to-infect ecotypes were infected by generalist viruses whereas easy-to-infect ecotypes were infected by all viruses, as predicted by a gene-for-gene model of infection. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Redox Energy and Sulfur Chemistry in Prebiotic Polymer Synthesis and Replication

NASA Technical Reports Server (NTRS)

Weber, Arthur L.

1997-01-01

In the past year we have made significant progress in three research areas: (1) Most importantly, we discovered a new pathway of prebiotic amino acid synthesis in which formaldehyde and glycolaldehyde (substrates of the formose reaction) react with ammonia yielding alanine and homoserine in the presence of thiol catalysts. This thiol-dependent synthesis of amino acids undoubtedly occurs via amino acid thioester intermediates capable of forming peptides. This 'one-pot' reaction system operates under mild aqueous conditions, and like modern amino acid biosynthesis, uses sugar intermediates which are converted to amino acids by energy-yielding redox disproportionation. (2) Finally, in preparation for the analysis of Martian meteorite samples, we upgraded our HPLC system and developed an improved method capable of detecting a I femtomole of amino acid enantiomers. (3) We completed our analysis of the energetics of metabolism that revealed that life depends on biosynthetic processes driven by chemical energy made available by the redox disproportionation of carbon groups of sugars. We established that the favorable energy of redox disproportionation is based on the universal reduction potentials of carbon groups. We concluded that it is hard to imagine any other organic molecule besides sugars (formaldehyde oligomers) having the energy and reactivity needed to drive either modem biosynthesis or the chemical processes behind its origin.

The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota

PubMed Central

Lagier, Jean-Christophe; Hugon, Perrine; Khelaifia, Saber; Fournier, Pierre-Edouard; La Scola, Bernard

2015-01-01

SUMMARY Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a “dark matter” of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the “great plate count anomaly,” which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire. PMID:25567229

Active machine learning-driven experimentation to determine compound effects on protein patterns.

PubMed

Naik, Armaghan W; Kangas, Joshua D; Sullivan, Devin P; Murphy, Robert F

2016-02-03

High throughput screening determines the effects of many conditions on a given biological target. Currently, to estimate the effects of those conditions on other targets requires either strong modeling assumptions (e.g. similarities among targets) or separate screens. Ideally, data-driven experimentation could be used to learn accurate models for many conditions and targets without doing all possible experiments. We have previously described an active machine learning algorithm that can iteratively choose small sets of experiments to learn models of multiple effects. We now show that, with no prior knowledge and with liquid handling robotics and automated microscopy under its control, this learner accurately learned the effects of 48 chemical compounds on the subcellular localization of 48 proteins while performing only 29% of all possible experiments. The results represent the first practical demonstration of the utility of active learning-driven biological experimentation in which the set of possible phenotypes is unknown in advance.

Vlasov dynamics of periodically driven systems

NASA Astrophysics Data System (ADS)

Banerjee, Soumyadip; Shah, Kushal

2018-04-01

Analytical solutions of the Vlasov equation for periodically driven systems are of importance in several areas of plasma physics and dynamical systems and are usually approximated using ponderomotive theory. In this paper, we derive the plasma distribution function predicted by ponderomotive theory using Hamiltonian averaging theory and compare it with solutions obtained by the method of characteristics. Our results show that though ponderomotive theory is relatively much easier to use, its predictions are very restrictive and are likely to be very different from the actual distribution function of the system. We also analyse all possible initial conditions which lead to periodic solutions of the Vlasov equation for periodically driven systems and conjecture that the irreducible polynomial corresponding to the initial condition must only have squares of the spatial and momentum coordinate. The resulting distribution function for other initial conditions is aperiodic and can lead to complex relaxation processes within the plasma.

Chapter One---Cancer terminator viruses and approaches for enhancing therapeutic outcomes.

PubMed

Das, Swadesh K; Sarkar, Siddik; Dash, Rupesh; Dent, Paul; Wang, Xiang-Yang; Sarkar, Devanand; Fisher, Paul B

2012-01-01

No single or combinatorial therapeutic approach has proven effective in decreasing morbidity or engendering a cure of metastatic cancer. In principle, conditionally replication-competent adenoviruses that induce tumor oncolysis through cancer-specific replication hold promise for cancer therapy. However, a single-agent approach may not be adequate to completely eradicate cancer in a patient because most cancers arise from abnormalities in multiple genetic and signal transduction pathways and targeting disseminated metastases is difficult to achieve. Based on these considerations, a novel class of cancer destroying adenoviruses have been produced, cancer terminator viruses (CTVs), in which cancer-specific replication is controlled by the progression-elevated gene-3 promoter and replicating viruses produce a second transgene encoding an apoptosis-inducing and immunomodulatory cytokine, either melanoma differentiation-associated gene-7/interleukin-24 (mda-7/IL-24) or interferon-γ. This review focuses on these viruses and ways to improve their delivery systemically and enhance their therapeutic efficacy. Copyright © 2012 Elsevier Inc. All rights reserved.

A ribonucleotide Origin for Life - Fluctuation and Near-ideal Reactions

NASA Astrophysics Data System (ADS)

Yarus, Michael

2013-02-01

Oligoribonucleotides are potentially capable of Darwinian evolution - they may replicate and can express an independent chemical phenotype, as embodied in modern enzymatic cofactors. Using quantitative chemical kinetics on a sporadically fed ribonucleotide pool, unreliable supplies of unstable activated ribonucleotides A and B at low concentrations recurrently yield a replicating AB polymer with a potential chemical phenotype. Self-complementary replication in the pool occurs during a minority (here ≈ 35 %) of synthetic episodes that exploit coincidental overlaps between 4, 5 or 6 spikes of arbitrarily arriving substrates. Such uniquely productive synthetic episodes, in which near-ideal reaction sequences recur at random, account for most AB oligonucleotide synthesis, and therefore underlie the emergence of net replication under realistic primordial conditions. Because overlapping substrate spikes are unexpectedly frequent, and in addition, complex spike sequences appear disproportionately, a sporadically fed pool can host unexpectedly complex syntheses. Thus, primordial substrate fluctuations are not necessarily a barrier to Darwinism, but instead can facilitate early evolution.

A ribonucleotide Origin for Life--fluctuation and near-ideal reactions.

PubMed

Yarus, Michael

2013-02-01

Oligoribonucleotides are potentially capable of Darwinian evolution - they may replicate and can express an independent chemical phenotype, as embodied in modern enzymatic cofactors. Using quantitative chemical kinetics on a sporadically fed ribonucleotide pool, unreliable supplies of unstable activated ribonucleotides A and B at low concentrations recurrently yield a replicating AB polymer with a potential chemical phenotype. Self-complementary replication in the pool occurs during a minority (here ≈ 35 %) of synthetic episodes that exploit coincidental overlaps between 4, 5 or 6 spikes of arbitrarily arriving substrates. Such uniquely productive synthetic episodes, in which near-ideal reaction sequences recur at random, account for most AB oligonucleotide synthesis, and therefore underlie the emergence of net replication under realistic primordial conditions. Because overlapping substrate spikes are unexpectedly frequent, and in addition, complex spike sequences appear disproportionately, a sporadically fed pool can host unexpectedly complex syntheses. Thus, primordial substrate fluctuations are not necessarily a barrier to Darwinism, but instead can facilitate early evolution.

Hydrogen silsesquioxane mold coatings for improved replication of nanopatterns by injection molding

NASA Astrophysics Data System (ADS)

Hobæk, Thor Christian; Matschuk, Maria; Kafka, Jan; Pranov, Henrik J.; Larsen, Niels B.

2015-03-01

We demonstrate the replication of nanosized pillars in polymer (cyclic olefin copolymer) by injection molding using nanostructured thermally cured hydrogen silsesquioxane (HSQ) ceramic coatings on stainless steel mold inserts with mold nanostructures produced by a simple embossing process. At isothermal mold conditions, the average pillar height increases by up to 100% and a more uniform height distribution is observed compared to a traditional metal mold insert. Thermal heat transfer simulations predict that the HSQ film retards the cooling of the polymer melt during the initial stages of replication, thus allowing more time to fill the nanoscale cavities compared to standard metal molds. A monolayer of a fluorinated silane (heptadecafluorotrichlorosilane) deposited on the mold surface reduces the mold/polymer interfacial energy to support demolding of the polymer replica. The mechanical stability of thermally cured HSQ makes it a promising material for nanopattern replication on an industrial scale without the need for slow and energy intensive variotherm processes.

Does a single session of reading literary fiction prime enhanced mentalising performance? Four replication experiments of Kidd and Castano (2013).

PubMed

Samur, Dalya; Tops, Mattie; Koole, Sander L

2018-02-01

Prior experiments indicated that reading literary fiction improves mentalising performance relative to reading popular fiction, non-fiction, or not reading. However, the experiments had relatively small sample sizes and hence low statistical power. To address this limitation, the present authors conducted four high-powered replication experiments (combined N = 1006) testing the causal impact of reading literary fiction on mentalising. Relative to the original research, the present experiments used the same literary texts in the reading manipulation; the same mentalising task; and the same kind of participant samples. Moreover, one experiment was pre-registered as a direct replication. In none of the experiments did reading literary fiction have any effect on mentalising relative to control conditions. The results replicate earlier findings that familiarity with fiction is positively correlated with mentalising. Taken together, the present findings call into question whether a single session of reading fiction leads to immediate improvements in mentalising.

Short- and long-term immunogenicity and protection induced by non-replicating smallpox vaccine candidates in mice and comparison with the traditional 1st generation vaccine.

PubMed

Ferrier-Rembert, Audrey; Drillien, Robert; Tournier, Jean-Nicolas; Garin, Daniel; Crance, Jean-Marc

2008-03-25

This study assessed three non-replicating smallpox vaccine candidates (modified vaccinia Ankara (MVA), NYVAC and HR) for their immunogenicity and ability to protect mice against an intranasal cowpox virus challenge and compared them with the traditional replicating vaccine. A single immunisation with the non-replicating vaccines induced a complete protection from death at short-term, but was not fully protective when mice were challenged 150 days post-vaccination with protection correlated with the specific neutralizing antibodies and CD4(+) T-cells responses. Prime-boost vaccination enabled effective long-term protection from death for mice vaccinated with MVA, but protection from disease and CD4(+) T-cell level were lower than the ones induced by the traditional vaccine over the long-term period. Further investigations are necessary with MVA to determine the optimal conditions of immunisation to induce at long-term immunogenicity and protection observed with the 1st generation smallpox vaccine.

In vivo intratumoral Epstein-Barr virus replication is associated with XBP1 activation and early-onset post-transplant lymphoproliferative disorders with prognostic implications.

PubMed

Gonzalez-Farre, Blanca; Rovira, Jordina; Martinez, Daniel; Valera, Alexandra; Garcia-Herrera, Adriana; Marcos, Maria Angeles; Sole, Carla; Roue, Gael; Colomer, Dolors; Gonzalvo, Elena; Ribera-Cortada, Imma; Araya, Monica; Lloreta, Josep; Colomo, Luis; Campo, Elias; Lopez-Guillermo, Armando; Martinez, Antonio

2014-12-01

Post-transplant lymphoproliferative disorders are life-threatening complications following hematopoietic or solid organ transplantation. They represent a spectrum of mostly EBV-driven lymphoplasmacytic proliferations. While the oncogenic effect of EBV is related to latent infection, lytic infection also has a role in lymphomagenesis. In vitro, EBV replication is linked to plasma cell differentiation and XBP1 activation, although this phenomenon has never been addressed in vivo. We analyzed for the first time latent and lytic intratumoral EBV infection in a series of 35 adult patients with a diagnosis of post-transplant lymphoproliferative disorder (26M/9F, median age 54 years). A complete EBV study was performed including the analysis of the latent EBER, latent membrane protein-11, and EBV nuclear antigens as well as the immediate-early BZLF1/ZEBRA and early BMRF1/EADE31 lytic genes. XBP1 activation was assessed by nuclear protein expression. EBV infection was observed in 28 (80%) cases being latency II and III the most frequently observed 22 (79%). Intratumoral EBV replication was detected in 17 (60%) cases. Among these, XBP1 activation was observed in 11/12 evaluable cases associated with strong cytoplasmic immunoglobulin expression consistent with plasma cell differentiation. Intriguingly, the combination of latency III infection and EBV replication identified a high-risk subgroup of patients with significantly shorter survival (overall survival at 1 year 18% vs 48%) and early-onset (median of 7 vs 26 months) post-transplant lymphoproliferative disorder. Moreover, these patients appear to be more heavily immunosuppressed, so they exhibit lower rates of rejection and graft vs host disease but higher rates of cytomegalovirus reactivation. In conclusion, EBV replication is associated with plasma cell differentiation and XBP1 activation with prognostic implications. Both latency III and lytic EBV infection are related to aggressive and early-onset post-transplant lymphoproliferative disorder. These results suggest that immunohistochemical study of latent and lytic EBV genes in the clinical practice may help to select higher-risk patients to new therapies including antiviral treatments.

Tidal flushing and wind driven circulation of Ahe atoll lagoon (Tuamotu Archipelago, French Polynesia) from in situ observations and numerical modelling.

PubMed

Dumas, F; Le Gendre, R; Thomas, Y; Andréfouët, S

2012-01-01

Hydrodynamic functioning and water circulation of the semi-closed deep lagoon of Ahe atoll (Tuamotu Archipelago, French Polynesia) were investigated using 1 year of field data and a 3D hydrodynamical model. Tidal amplitude averaged less than 30 cm, but tide generated very strong currents (2 ms(-1)) in the pass, creating a jet-like circulation that partitioned the lagoon into three residual circulation cells. The pass entirely flushed excess water brought by waves-induced radiation stress. Circulation patterns were computed for climatological meteorological conditions and summarized with stream function and flushing time. Lagoon hydrodynamics and general overturning circulation was driven by wind. Renewal time was 250 days, whereas the e-flushing time yielded a lagoon-wide 80-days average. Tide-driven flush through the pass and wind-driven overturning circulation designate Ahe as a wind-driven, tidally and weakly wave-flushed deep lagoon. The 3D model allows studying pearl oyster larvae dispersal in both realistic and climatological conditions for aquaculture applications. Copyright © 2012 Elsevier Ltd. All rights reserved.

Physical modeling of transverse drainage mechanisms

NASA Astrophysics Data System (ADS)

Douglass, J. C.; Schmeeckle, M. W.

2005-12-01

Streams that incise across bedrock highlands such as anticlines, upwarps, cuestas, or horsts are termed transverse drainages. Their relevance today involves such diverse matters as highway and dam construction decisions, location of wildlife corridors, better-informed sediment budgets, and detailed studies into developmental histories of late Cenozoic landscapes. The transient conditions responsible for transverse drainage incision have been extensively studied on a case-by-case basis, and the dominate mechanisms proposed include: antecedence, superimposition, overflow, and piracy. Modeling efforts have been limited to antecedence, and such the specific erosional conditions required for transverse drainage incision, with respect to the individual mechanisms, remains poorly understood. In this study, fifteen experiments attempted to simulate the four mechanisms and constructed on a 9.15 m long, 2.1 m wide, and 0.45 m deep stream table. Experiments lasted between 50 and 220 minutes. The stream table was filled with seven tons of sediment consisting of a silt and clay (30%) and a fine to coarse sand (70%) mixture. The physical models highlighted the importance of downstream aggradation with regard to antecedent incision versus possible defeat and diversion. The overflow experiments indicate that retreating knickpoints across a basin outlet produce a high probability of downstream flooding when associated with a deep lake. Misters used in a couple of experiments illustrate a potential complication with regard to headward erosion driven piracy. Relatively level asymmetrically sloped ridges allow for the drainage divide across the ridge to retreat from headward erosion, but hindered when the ridge's apex undulates or when symmetrically sloped. Although these physical models cannot strictly simulate natural transverse drainages, the observed processes, their development over time, and resultant landforms roughly emulate their natural counterparts. Proposed originally from an extensive literature search, most of the criteria that indicate the expected evidence associated with each mechanism following transverse drainage incision were replicated for antecedence, overflow, and piracy. Two superimposition experiments failed to replicate the mechanism and test the associated criteria. Following experimentation, the criteria were applied in a cursory fashion to twenty randomly selected sites in the southwestern USA. Development of first order hypotheses were ranked on a confidence scale tied to individual criterion noted in the field, literature, and DEMs for each site. The results indicate a possible link between the dominant tectonic regime and the proposed mechanisms; and highlight the importance of short-lived fluvial instabilities in relation to understanding long-term drainage development.

Replication stress affects the fidelity of nucleosome-mediated epigenetic inheritance

PubMed Central

Li, Wenzhu; Yi, Jia; Agbu, Pamela; Zhou, Zheng; Kelley, Richard L.; Jia, Songtao

2017-01-01

The fidelity of epigenetic inheritance or, the precision by which epigenetic information is passed along, is an essential parameter for measuring the effectiveness of the process. How the precision of the process is achieved or modulated, however, remains largely elusive. We have performed quantitative measurement of epigenetic fidelity, using position effect variegation (PEV) in Schizosaccharomyces pombe as readout, to explore whether replication perturbation affects nucleosome-mediated epigenetic inheritance. We show that replication stresses, due to either hydroxyurea treatment or various forms of genetic lesions of the replication machinery, reduce the inheritance accuracy of CENP-A/Cnp1 nucleosome positioning within centromere. Mechanistically, we demonstrate that excessive formation of single-stranded DNA, a common molecular abnormality under these conditions, might have correlation with the reduction in fidelity of centromeric chromatin duplication. Furthermore, we show that replication stress broadly changes chromatin structure at various loci in the genome, such as telomere heterochromatin expanding and mating type locus heterochromatin spreading out of the boundaries. Interestingly, the levels of inheritable expanding at sub-telomeric heterochromatin regions are highly variable among independent cell populations. Finally, we show that HU treatment of the multi-cellular organisms C. elegans and D. melanogaster affects epigenetically programmed development and PEV, illustrating the evolutionary conservation of the phenomenon. Replication stress, in addition to its demonstrated role in genetic instability, promotes variable epigenetic instability throughout the epigenome. PMID:28749973

A doxycycline-dependent human immunodeficiency virus type 1 replicates in vivo without inducing CD4+ T-cell depletion

PubMed Central

Legrand, Nicolas; van der Velden, Gisela J.; Fang, Raphaël Ho Tsong; Douaisi, Marc; Weijer, Kees; Das, Atze T.; Blom, Bianca; Uittenbogaart, Christel H.; Berkhout, Ben

2012-01-01

A novel genetic approach for the control of virus replication was used for the design of a conditionally replicating human immunodeficiency virus (HIV) variant, HIV-rtTA. HIV-rtTA gene expression and virus replication are strictly dependent on the presence of a non-toxic effector molecule, doxycycline (dox), and thus can be turned on and off at will in a graded and reversible manner. The in vivo replication capacity, pathogenicity and genetic stability of this HIV-rtTA variant were evaluated in a humanized mouse model of haematopoiesis that harbours lymphoid and myeloid components of the human immune system (HIS). Infection of dox-fed BALB Rag/γc HIS (BRG-HIS) mice with HIV-rtTA led to the establishment of a productive infection without CD4+ T-cell depletion. The virus did not show any sign of escape from dox control for up to 10 weeks after the onset of infection. No reversion towards a functional Tat–transactivating responsive (TAR) RNA element axis was observed, confirming the genetic stability of the HIV-rtTA variant in vivo. These results demonstrate the proof of concept that HIV-rtTA replicates efficiently in vivo. HIV-rtTA is a promising tool for fundamental research to study virus–host interactions in vivo in a controlled fashion. PMID:22647372

Normal Distribution of CD8+ T-Cell-Derived ELISPOT Counts within Replicates Justifies the Reliance on Parametric Statistics for Identifying Positive Responses.

PubMed

Karulin, Alexey Y; Caspell, Richard; Dittrich, Marcus; Lehmann, Paul V

2015-03-02

Accurate assessment of positive ELISPOT responses for low frequencies of antigen-specific T-cells is controversial. In particular, it is still unknown whether ELISPOT counts within replicate wells follow a theoretical distribution function, and thus whether high power parametric statistics can be used to discriminate between positive and negative wells. We studied experimental distributions of spot counts for up to 120 replicate wells of IFN-γ production by CD8+ T-cell responding to EBV LMP2A (426 - 434) peptide in human PBMC. The cells were tested in serial dilutions covering a wide range of average spot counts per condition, from just a few to hundreds of spots per well. Statistical analysis of the data using diagnostic Q-Q plots and the Shapiro-Wilk normality test showed that in the entire dynamic range of ELISPOT spot counts within replicate wells followed a normal distribution. This result implies that the Student t-Test and ANOVA are suited to identify positive responses. We also show experimentally that borderline responses can be reliably detected by involving more replicate wells, plating higher numbers of PBMC, addition of IL-7, or a combination of these. Furthermore, we have experimentally verified that the number of replicates needed for detection of weak responses can be calculated using parametric statistics.

A data driven method for estimation of B(avail) and appK(D) using a single injection protocol with [¹¹C]raclopride in the mouse.

PubMed

Wimberley, Catriona J; Fischer, Kristina; Reilhac, Anthonin; Pichler, Bernd J; Gregoire, Marie Claude

2014-10-01

The partial saturation approach (PSA) is a simple, single injection experimental protocol that will estimate both B(avail) and appK(D) without the use of blood sampling. This makes it ideal for use in longitudinal studies of neurodegenerative diseases in the rodent. The aim of this study was to increase the range and applicability of the PSA by developing a data driven strategy for determining reliable regional estimates of receptor density (B(avail)) and in vivo affinity (1/appK(D)), and validate the strategy using a simulation model. The data driven method uses a time window guided by the dynamic equilibrium state of the system as opposed to using a static time window. To test the method, simulations of partial saturation experiments were generated and validated against experimental data. The experimental conditions simulated included a range of receptor occupancy levels and three different B(avail) and appK(D) values to mimic diseases states. Also the effect of using a reference region and typical PET noise on the stability and accuracy of the estimates was investigated. The investigations showed that the parameter estimates in a simulated healthy mouse, using the data driven method were within 10±30% of the simulated input for the range of occupancy levels simulated. Throughout all experimental conditions simulated, the accuracy and robustness of the estimates using the data driven method were much improved upon the typical method of using a static time window, especially at low receptor occupancy levels. Introducing a reference region caused a bias of approximately 10% over the range of occupancy levels. Based on extensive simulated experimental conditions, it was shown the data driven method provides accurate and precise estimates of B(avail) and appK(D) for a broader range of conditions compared to the original method. Copyright © 2014 Elsevier Inc. All rights reserved.

The wavelength of supercritical surface tension driven Benard convection

NASA Technical Reports Server (NTRS)

Koschmieder, E. L.

1991-01-01

The size or the wavelength of moderately supercritical surface tension driven Benard convection has been investigated experimentally in a thin fluid layer of large aspect ratio. It has been found that the number of the hexagonal convection cells increases with increased temperature differences, up to 1.3 times the critical temperature difference. That means that the wavelength of surface tension driven convection decreases after onset of the instability for moderately nonlinear conditions. This result is in striking contrast to the well-known increase of the wavelength of buoyancy driven Rayleigh-Benard convection.

Replicating the Conditions on Mars: the Possibility of Sustaining Life

NASA Astrophysics Data System (ADS)

Abdul-Masih, Michael; Guinan, E. F.

2013-01-01

We describe a laboratory experiment that replicates environmental conditions on Mars’s surface to determine the viability of Earth-based life under conditions on Mars. Of all the organisms currently known, the ones that are best suited for the harsh environments found throughout our solar system are the extremophiles found on Earth that tolerate extreme environmental conditions. The environmental conditions on Mars are the least extreme of all the planets in our solar system excluding Earth. The average temperature near the equator varies from +10 C to -20 C and the surface pressure is P ~ 0.01 Atm. The thin atmosphere means that the UV radiation from the Sun is relatively unshielded. Carbon Dioxide (CO2) makes up approximately 95% of Mars’ atmosphere and the soil is composed primarily of iron oxides. This being said, water can exist in liquid form under the surface and because of this, so can life. To test this, we constructed an air-tight chamber out of Plexiglas that replicates the environmental conditions on Mars. As a first step, two different organisms were tested for survival: E-coli, which was the control, and Hypsibius (Tardigrades), a member of the Tardigradas phylum. We hypothesized that the E-coli would perish while the more hardy Tardigrades would survive. The trials were two days each and the chosen temperature was ~4°C. Many trials were conducted. After the first compilation of the results, the hypothesis did not hold. The E-coli surprisingly survived while the Tardigrades did not survive. The E-coli did not grow while in the chamber, but after being removed they grew showing that they were still viable and that the conditions were not harsh enough to kill them. After these initial results, the experiment was altered slightly to ensure that the Tardigrades were able to successfully enter their hibernation like state that allows them to survive extreme conditions. These experiments are continuing and we will discuss the results under controlled differing environmental conditions. This research is supported by a grant from Villanova University Center for Undergraduate Research and Fellowships & also supported by NSF/RUI Grant AST-1009903.

Surface-Acoustic-Wave (SAW)-Driven Device for Dynamic Cell Cultures.

PubMed

Greco, Gina; Agostini, Matteo; Tonazzini, Ilaria; Sallemi, Damiano; Barone, Stefano; Cecchini, Marco

2018-06-19

In the last few decades, new types of cell cultures have been introduced to provide better cell survival and development, with micro- and nanoenvironmental physicochemical conditions aimed at mimicking those present in vivo. However, despite the efforts made, the systems available to date are often difficult to replicate and use. Here, an easy-to-use surface-acoustic-wave (SAW)-based platform is presented for realizing dynamic cell cultures that is compatible with standard optical microscopes, incubators, and cell-culture dishes. The SAW chip is coupled to a standard Petri dish via a polydimethylsiloxane (PDMS) disc and consists of a lithium niobate (LN) substrate on which gold interdigital transducers (IDTs) are patterned to generate the SAWs and induce acoustic streaming in the dish. SAW excitation is verified and characterized by laser Doppler vibrometry, and the fluid dynamics is studied by microparticle image velocimetry (μPIV). Heating is measured by an infrared (IR) thermal camera. We finally tested this device with the U-937 monocyte cell line for viability and proliferation and cell-morphological analysis. The data demonstrate that it is possible to induce significant fluid recirculation within the Petri dish while maintaining negligible heating. Remarkably, cell proliferation in this condition was enhanced by 36 ± 12% with respect to those of standard static cultures. Finally, we show that cell death does not increase and that cell morphology is not altered in the presence of SAWs. This device is the first demonstration that SAW-induced streaming can mechanically improve cell proliferation and further supports the great versatility and biocompatibility of the SAW technology for cell manipulation.

Different levels of learning interact to shape the congruency sequence effect.

PubMed

Weissman, Daniel H; Hawks, Zoë W; Egner, Tobias

2016-04-01

The congruency effect in distracter interference tasks is often reduced after incongruent relative to congruent trials. Moreover, this congruency sequence effect (CSE) is influenced by learning related to concrete stimulus and response features as well as by learning related to abstract cognitive control processes. There is an ongoing debate, however, over whether interactions between these learning processes are best explained by an episodic retrieval account, an adaptation by binding account, or a cognitive efficiency account of the CSE. To make this distinction, we orthogonally manipulated the expression of these learning processes in a novel factorial design involving the prime-probe arrow task. In Experiment 1, these processes interacted in an over-additive fashion to influence CSE magnitude. In Experiment 2, we replicated this interaction while showing it was not driven by conditional differences in the size of the congruency effect. In Experiment 3, we ruled out an alternative account of this interaction as reflecting conditional differences in learning related to concrete stimulus and response features. These findings support an episodic retrieval account of the CSE, in which repeating a stimulus feature from the previous trial facilitates the retrieval and use of previous-trial control parameters, thereby boosting control in the current trial. In contrast, they do not fit with (a) an adaptation by binding account, in which CSE magnitude is directly related to the size of the congruency effect, or (b) a cognitive efficiency account, in which costly control processes are recruited only when behavioral adjustments cannot be mediated by low-level associative mechanisms. (c) 2016 APA, all rights reserved).

How do patch quality and spatial context affect invertebrate communities in a natural moss microlandscape?

NASA Astrophysics Data System (ADS)

Trekels, Hendrik; Driesen, Mario; Vanschoenwinkel, Bram

2017-11-01

Globally, moss associated invertebrates remain poorly studied and it is largely unknown to what extent their diversity is driven by local environmental conditions or the landscape context. Here, we investigated small scale drivers of invertebrate communities in a moss landscape in a temperate forest in Western Europe. By comparing replicate quadrats of 5 different moss species in a continuous moss landscape, we found that mosses differed in invertebrate density and community composition. Although, in general, richness was similar among moss species, some invertebrate taxa were significantly linked to certain moss species. Only moss biomass and not relative moisture content could explain differences in invertebrate densities among moss species. Second, we focused on invertebrate communities associated with the locally common moss species Kindbergia praelonga in isolated moss patches on dead tree trunks to look at effects of patch size, quality, heterogeneity and connectivity on invertebrate communities. Invertebrate richness was higher in patches under closed canopies than under more open canopies, presumably due to the higher input of leaf litter and/or lower evaporation. In addition, increased numbers of other moss species in the same patch seemed to promote invertebrate richness in K. praelonga, possibly due to mass effects. Since invertebrate richness was unaffected by patch size and isolation, dispersal was probably not limiting in this system with patches separated by tens of meters, or stochastic extinctions may be uncommon. Overall, we conclude that invertebrate composition in moss patches may not only depend on local patch conditions, in a particular moss species, but also on the presence of other moss species in the direct vicinity.

Evaluation of the river die-away biodegradation test

USGS Publications Warehouse

Wylie, Glenn D.; Jones, John R.; Johnson, B. Thomas

1982-01-01

The reliability of the river die-away (RDA) test for establishing the biodegradability of chemicals was assessed. Reproducibility of biodegradation in the RDA test was analyzed under conditions in which the test is commonly done. Biodegradation results were not reproducible for di-2-ethylexyl phthalate (DEHP) and phthalic acid in replicated RDA tests using Missouri River water. Chemical and biological changes during the RDA tests probably reflected relative laboratory conditions. Initial suspended solids and subsequent DEHP biodegradation were directly related. Interpretation of RDA test results is enhanced by replicating experiments and comparing biodegradation of the test compound with a compound whose degradation properties are known. However, biodegradation measured with the RDA test is too variable and too dependent on laboratory treatment of samples to apply results directly to the aquatic environment.

Analysis of branched DNA replication and recombination intermediates from prokaryotic cells by two-dimensional (2D) native-native agarose gel electrophoresis.

PubMed

Robinson, Nicholas P

2013-01-01

Branched DNA molecules are generated by the essential processes of replication and recombination. Owing to their distinctive extended shapes, these intermediates migrate differently from linear double-stranded DNA under certain electrophoretic conditions. However, these branched species exist in the cell at much low abundance than the bulk linear DNA. Consequently, branched molecules cannot be visualized by conventional electrophoresis and ethidium bromide staining. Two-dimensional native-native agarose electrophoresis has therefore been developed as a method to facilitate the separation and visualization of branched replication and recombination intermediates. A wide variety of studies have employed this technique to examine branched molecules in eukaryotic, archaeal, and bacterial cells, providing valuable insights into how DNA is duplicated and repaired in all three domains of life.

Wind effect on diurnal thermally driven flow in vegetated nearshore of a lake

NASA Astrophysics Data System (ADS)

Lin, Y. T.

2014-12-01

In this study, a highly idealized model is developed to discuss the interplay of diurnal heating/cooling induced buoyancy and wind stress on thermally driven flow over a vegetated slope. Since the model is linear, the horizontal velocity components can be broken into buoyancy-driven and surface wind-driven parts. Due to the presence of rooted emergent vegetation, the circulation strength even under the surface wind condition is still significantly reduced, and the transient (adjustment) stage for the initial conditions is shorter than that without vegetation. The flow in shallows is dominated by a viscosity/buoyancy balance as the case without wind, while the effect of wind stress is limited to the upper layer in deep water. In the lower layer of deep regions, vegetative drag is prevailing except the near bottom regions, where viscosity dominates. Under the unidirectional wind condition, a critical dimensionless shear stress to stop the induced flow can be found and is a function of horizontal location . For the periodic wind condition, if the two forcing mechanisms work in concert, the circulation magnitude can be increased. For the case where buoyancy and wind shear stress act against each other, the circulation strength is reduced and its structure becomes more complex. However, the flow magnitudes near the bottom for and are comparable because surface wind almost has no influence.

Spatiotemporal Patterns of Noise-Driven Confined Actin Waves in Living Cells.

PubMed

Bernitt, Erik; Döbereiner, Hans-Günther

2017-01-27

Cells utilize waves of polymerizing actin to reshape their morphologies, which is central to physiological and pathological processes alike. Here, we force dorsal actin waves to propagate on one-dimensional domains with periodic boundary conditions, which results in striking spatiotemporal patterns with a clear signature of noise-driven dynamics. We show that these patterns can be very closely reproduced with a noise-driven active medium at coherence resonance.

Executive control of stimulus-driven and goal-directed attention in visual working memory.

PubMed

Hu, Yanmei; Allen, Richard J; Baddeley, Alan D; Hitch, Graham J

2016-10-01

We examined the role of executive control in stimulus-driven and goal-directed attention in visual working memory using probed recall of a series of objects, a task that allows study of the dynamics of storage through analysis of serial position data. Experiment 1 examined whether executive control underlies goal-directed prioritization of certain items within the sequence. Instructing participants to prioritize either the first or final item resulted in improved recall for these items, and an increase in concurrent task difficulty reduced or abolished these gains, consistent with their dependence on executive control. Experiment 2 examined whether executive control is also involved in the disruption caused by a post-series visual distractor (suffix). A demanding concurrent task disrupted memory for all items except the most recent, whereas a suffix disrupted only the most recent items. There was no interaction when concurrent load and suffix were combined, suggesting that deploying selective attention to ignore the distractor did not draw upon executive resources. A final experiment replicated the independent interfering effects of suffix and concurrent load while ruling out possible artifacts. We discuss the results in terms of a domain-general episodic buffer in which information is retained in a transient, limited capacity privileged state, influenced by both stimulus-driven and goal-directed processes. The privileged state contains the most recent environmental input together with goal-relevant representations being actively maintained using executive resources.

Can We Practically Bring Physics-based Modeling Into Operational Analytics Tools?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Granderson, Jessica; Bonvini, Marco; Piette, Mary Ann

We present that analytics software is increasingly used to improve and maintain operational efficiency in commercial buildings. Energy managers, owners, and operators are using a diversity of commercial offerings often referred to as Energy Information Systems, Fault Detection and Diagnostic (FDD) systems, or more broadly Energy Management and Information Systems, to cost-effectively enable savings on the order of ten to twenty percent. Most of these systems use data from meters and sensors, with rule-based and/or data-driven models to characterize system and building behavior. In contrast, physics-based modeling uses first-principles and engineering models (e.g., efficiency curves) to characterize system and buildingmore » behavior. Historically, these physics-based approaches have been used in the design phase of the building life cycle or in retrofit analyses. Researchers have begun exploring the benefits of integrating physics-based models with operational data analytics tools, bridging the gap between design and operations. In this paper, we detail the development and operator use of a software tool that uses hybrid data-driven and physics-based approaches to cooling plant FDD and optimization. Specifically, we describe the system architecture, models, and FDD and optimization algorithms; advantages and disadvantages with respect to purely data-driven approaches; and practical implications for scaling and replicating these techniques. Finally, we conclude with an evaluation of the future potential for such tools and future research opportunities.« less

Reference conditions for silvicultural field studies in Maine: limitations and opportunities

Treesearch

Laura S. Kenefic; Alan S. White; Shawn Fraver

2004-01-01

There are many types of controls or reference conditions for silvicultural experiments. The most basic are pretreatment records of composition and structure, but such data provide little information about response to treatment compared to natural developmental and disturbance patterns. Ideally, experiments should have untreated stand replicates in which development can...

A Rapid Assessment of Instructional Strategies to Teach Auditory-Visual Conditional Discriminations to Children with Autism

ERIC Educational Resources Information Center

Kodak, Tiffany; Clements, Andrea; LeBlanc, Brittany

2013-01-01

The purpose of the present investigation was to evaluate a rapid assessment procedure to identify effective instructional strategies to teach auditory-visual conditional discriminations to children diagnosed with autism. We replicated and extended previous rapid skills assessments (Lerman, Vorndran, Addison, & Kuhn, 2004) by evaluating the effects…

On the accuracy and reliability of predictions by control-system theory.

PubMed

Bourbon, W T; Copeland, K E; Dyer, V R; Harman, W K; Mosley, B L

1990-12-01

In three experiments we used control-system theory (CST) to predict the results of tracking tasks on which people held a handle to keep a cursor even with a target on a computer screen. 10 people completed a total of 104 replications of the task. In each experiment, there were two conditions: in one, only the handle affected the position of the cursor; in the other, a random disturbance also affected the cursor. From a person's performance during Condition 1, we derived constants used in the CST model to predict the results of Condition 2. In two experiments, predictions occurred a few minutes before Condition 2; in one experiment, the delay was 1 yr. During a 1-min. experimental run, the positions of handle and cursor, produced by the person, were each sampled 1800 times, once every 1/30 sec. During a modeling run, the model predicted the positions of the handle and target for each of the 1800 intervals sampled in the experimental run. In 104 replications, the mean correlation between predicted and actual positions of the handle was .996; SD = .002.

PELS (Planetary Environmental Liquid Simulator): a new type of simulation facility to study extraterrestrial aqueous environments.

PubMed

Martin, Derek; Cockell, Charles S

2015-02-01

Investigations of other planetary bodies, including Mars and icy moons such as Enceladus and Europa, show that they may have hosted aqueous environments in the past and may do so even today. Therefore, a major challenge in astrobiology is to build facilities that will allow us to study the geochemistry and habitability of these extraterrestrial environments. Here, we describe a simulation facility (PELS: Planetary Environmental Liquid Simulator) with the capability for liquid input and output that allows for the study of such environments. The facility, containing six separate sample vessels, allows for statistical replication of samples. Control of pressure, gas composition, UV irradiation conditions, and temperature allows for the precise replication of aqueous conditions, including subzero brines under martian atmospheric conditions. A sample acquisition system allows for the collection of both liquid and solid samples from within the chamber without breaking the atmospheric conditions, enabling detailed studies of the geochemical evolution and habitability of past and present extraterrestrial environments. The facility we describe represents a new frontier in planetary simulation-continuous flow-through simulation of extraterrestrial aqueous environments.

Analysis of slow- and fast-α band asymmetry during performance of a saccadic eye movement task: dissociation between memory- and attention-driven systems.

PubMed

Sanfim, Antonio; Velasques, Bruna; Machado, Sergio; Arias-Carrión, Oscar; Paes, Flávia; Teixeira, Silmar; Santos, Joana Luz; Bittencourt, Juliana; Basile, Luis F; Cagy, Mauricio; Piedade, Roberto; Sack, Alexander T; Nardi, Antonio Egídio; Ribeiro, Pedro

2012-01-15

This study aimed at analyzing the relationship between slow- and fast-alpha asymmetry within frontal cortex and the planning, execution and voluntary control of saccadic eye movements (SEM), and quantitative electroencephalography (qEEG) was recorded using a 20-channel EEG system in 12 healthy participants performing a fixed (i.e., memory-driven) and a random SEM (i.e., stimulus-driven) condition. We find main effects for SEM condition in slow- and fast-alpha asymmetry at electrodes F3-F4, which are located over premotor cortex, specifically a negative asymmetry between conditions. When analyzing electrodes F7-F8, which are located over prefrontal cortex, we found a main effect for condition in slow-alpha asymmetry, particularly a positive asymmetry between conditions. In conclusion, the present approach supports the association of slow- and fast-alpha bands with the planning and preparation of SEM, and the specific role of these sub-bands for both, the attention network and the coordination and integration of sensory information with a (oculo)-motor response. Copyright © 2011 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vaezi, P.; Holland, C.; Thakur, S. C.

The Controlled Shear Decorrelation Experiment (CSDX) linear plasma device provides a unique platform for investigating the underlying physics of self-regulating drift-wave turbulence/zonal flow dynamics. A minimal model of 3D drift-reduced nonlocal cold ion fluid equations which evolves density, vorticity, and electron temperature fluctuations, with proper sheath boundary conditions, is used to simulate dynamics of the turbulence in CSDX and its response to changes in parallel boundary conditions. These simulations are then carried out using the BOUndary Turbulence (BOUT++) framework and use equilibrium electron density and temperature profiles taken from experimental measurements. The results show that density gradient-driven drift-waves are themore » dominant instability in CSDX. However, the choice of insulating or conducting endplate boundary conditions affects the linear growth rates and energy balance of the system due to the absence or addition of Kelvin-Helmholtz modes generated by the sheath-driven equilibrium E × B shear and sheath-driven temperature gradient instability. Moreover, nonlinear simulation results show that the boundary conditions impact the turbulence structure and zonal flow formation, resulting in less broadband (more quasi-coherent) turbulence and weaker zonal flow in conducting boundary condition case. These results are qualitatively consistent with earlier experimental observations.« less

The Proximity of Ribosomal Protein Genes to oriC Enhances Vibrio cholerae Fitness in the Absence of Multifork Replication.

PubMed

Soler-Bistué, Alfonso; Timmermans, Michaël; Mazel, Didier

2017-02-28

Recent works suggest that bacterial gene order links chromosome structure to cell homeostasis. Comparative genomics showed that, in fast-growing bacteria, ribosomal protein genes (RP) locate near the replication origin ( oriC ). We recently showed that Vibrio cholerae employs this positional bias as a growth optimization strategy: under fast-growth conditions, multifork replication increases RP dosage and expression. However, RP location may provide advantages in a dosage-independent manner: for example, the physical proximity of the many ribosomal components, in the context of a crowded cytoplasm, may favor ribosome biogenesis. To uncover putative dosage-independent effects, we studied isogenic V. cholerae derivatives in which the major RP locus, S10-spc-α (S10), was relocated to alternative genomic positions. When bacteria grew fast, bacterial fitness was reduced according to the S10 relative distance to oriC The growth of wild-type V. cholerae could not be improved by additional copies of the locus, suggesting a physiologically optimized genomic location. Slow growth is expected to uncouple RP position from dosage, since multifork replication does not occur. Under these conditions, we detected a fitness impairment when S10 was far from oriC Deep sequencing followed by marker frequency analysis in the absence of multifork replication revealed an up to 30% S10 dosage reduction associated with its relocation that closely correlated with fitness alterations. Hence, the impact of S10 location goes beyond a growth optimization strategy during feast periods. RP location may be important during the whole life cycle of this pathogen. IMPORTANCE The role of gene order within the bacterial chromosome is poorly understood. In fast growers, the location of genes linked with the expression of genetic information (i.e., transcription and translation) is biased toward oriC It was proposed that the location of these genes helps to maximize their expression by recruiting multifork replication during fast growth. Our results show that such genomic positioning impacts cell fitness beyond fast-growth conditions, probably across the whole life cycle of fast growers. Thus, the genomic position of key highly expressed genes, such as RP, was finely tuned during the evolution of fast-growing bacteria and may also be important in slow growers. In the near future, many more genes whose genomic position impacts bacterial phenotype will be described. These studies will contribute to discovery the rules of genome organization and application of them for the design of synthetic chromosomes and the creation of artificial life forms. Copyright © 2017 Soler-Bistué et al.

Human Papillomavirus E6E7-Mediated Adenovirus Cell Killing: Selectivity of Mutant Adenovirus Replication in Organotypic Cultures of Human Keratinocytes

PubMed Central

Balagué, Cristina; Noya, Francisco; Alemany, Ramon; Chow, Louise T.; Curiel, David T.

2001-01-01

Replication-competent adenoviruses are being investigated as potential anticancer agents. Exclusive virus replication in cancer cells has been proposed as a safety trait to be considered in the design of oncolytic adenoviruses. From this perspective, we have investigated several adenovirus mutants for their potential to conditionally replicate and promote the killing of cells expressing human papillomavirus (HPV) E6 and E7 oncoproteins, which are present in a high percentage of anogenital cancers. For this purpose, we have employed an organotypic model of human stratified squamous epithelium derived from primary keratinocytes that have been engineered to express HPV-18 oncoproteins stably. We show that, whereas wild-type adenovirus promotes a widespread cytopathic effect in all infected cells, E1A- and E1A/E1B-deleted adenoviruses cause no deleterious effect regardless of the coexpression of HPV18 E6E7. An adenovirus deleted in the CR2 domain of E1A, necessary for binding to the pRB family of pocket proteins, shows no selectivity of replication as it efficiently kills all normal and E6E7-expressing keratinocytes. Finally, an adenovirus mutant deleted in the CR1 and CR2 domains of E1A exhibits preferential replication and cell killing in HPV E6E7-expressing cultures. We conclude that the organotypic keratinocyte culture represents a distinct model to evaluate adenovirus selectivity and that, based on this model, further modifications of the adenovirus genome are required to restrict adenovirus replication to tumor cells. PMID:11462032

RIPK3 activates parallel pathways of MLKL-driven necroptosis and FADD-mediated apoptosis to protect against influenza A virus

PubMed Central

Nogusa, Shoko; Thapa, Roshan J.; Dillon, Christopher P.; Liedmann, Swantje; Oguin, Thomas H.; Ingram, Justin P.; Rodriguez, Diego A.; Kosoff, Rachelle; Sharma, Shalini; Sturm, Oliver; Verbist, Katherine; Gough, Peter J.; Bertin, John; Hartmann, Boris M.; Sealfon, Stuart C.; Kaiser, William J.; Mocarski, Edward S.; López, Carolina B.; Thomas, Paul G.; Oberst, Andrew; Green, Douglas R.; Balachandran, Siddharth

2016-01-01

Summary Influenza A virus (IAV) is a lytic virus in primary cultures of many cell types and in vivo. We report that the kinase RIPK3 is essential for IAV-induced lysis of mammalian fibroblasts and lung epithelial cells. Replicating IAV drives assembly of a RIPK3-containing complex that includes the kinase RIPK1, the pseudokinase MLKL, and the adaptor protein FADD, and forms independently of signaling by RNA-sensing innate immune receptors (RLRs, TLRs, PKR), or the cytokines type I interferons and TNF-α. Downstream of RIPK3, IAV activates parallel pathways of MLKL-driven necroptosis and FADD-mediated apoptosis, with the former reliant on RIPK3 kinase activity and neither on RIPK1 activity. Mice deficient in RIPK3 or doubly-deficient in MLKL and FADD, but not MLKL alone, are more susceptible to IAV than their wild-type counterparts, revealing an important role for RIPK3-mediated apoptosis in antiviral immunity. Collectively, these results outline RIPK3-activated cytolytic mechanisms essential for controlling respiratory IAV infection. PMID:27321907

Evaporation effects in a shock-driven multiphase instability with a spherical interface

NASA Astrophysics Data System (ADS)

Paudel, Manoj; Dahal, Jeevan; McFarland, Jacob

2017-11-01

This talk presents results from 3D numerical simulations of a shock driven instability of a gas-particle system with a spherical interface. Two cases, one with an evaporating particle cloud and another with a gas only approximation of this particle cloud, were run in the hydrodynamics code FLASH, developed at University of Chicago. It is shown that the gas only approximation, a classical Richtmyer Meshkov instability, cannot replicate effects from particles like, lag, clustering, and evaporation. Instead, both gas hydrodynamics and particle properties influence one another and are coupled. Results are presented to highlight the coupling of interface evolution and particle evaporation. Qualitative and quantitative differences in the RMI and SDMI are presented by studying the change in gas properties like density and vorticity within the interface. Similarly, the effect of gas hydrodynamics on particles distribution and evaporation is studied. Particle evaporation rates are compared with 1D models and show poor agreement. The variation in evaporation rates for similar sized particles and the role of gas hydrodynamics in these variation is explored.

Epithelial reticulon 4B (Nogo-B) is an endogenous regulator of Th2-driven lung inflammation

PubMed Central

Wright, Paulette L.; Yu, Jun; Di, Y.P. Peter; Homer, Robert J.; Chupp, Geoffrey; Elias, Jack A.; Cohn, Lauren

2010-01-01

Nogo-B is a member of the reticulon family of proteins (RTN-4B) that is highly expressed in lung tissue; however, its function remains unknown. We show that mice with Th2-driven lung inflammation results in a loss of Nogo expression in airway epithelium and smooth muscle compared with nonallergic mice, a finding which is replicated in severe human asthma. Mice lacking Nogo-A/B (Nogo-KO) display an exaggerated asthma-like phenotype, and epithelial reconstitution of Nogo-B in transgenic mice blunts Th2-mediated lung inflammation. Microarray analysis of lungs from Nogo-KO mice reveals a marked reduction in palate lung and nasal clone (PLUNC) gene expression, and the levels of PLUNC are enhanced in epithelial Nogo-B transgenic mice. Finally, transgenic expression of PLUNC into Nogo-KO mice rescues the enhanced asthmatic-like responsiveness in these KO mice. These data identify Nogo-B as a novel protective gene expressed in lung epithelia, and its expression regulates the levels of the antibacterial antiinflammatory protein PLUNC. PMID:20975041

Don't fear 'fear conditioning': Methodological considerations for the design and analysis of studies on human fear acquisition, extinction, and return of fear.

PubMed

Lonsdorf, Tina B; Menz, Mareike M; Andreatta, Marta; Fullana, Miguel A; Golkar, Armita; Haaker, Jan; Heitland, Ivo; Hermann, Andrea; Kuhn, Manuel; Kruse, Onno; Meir Drexler, Shira; Meulders, Ann; Nees, Frauke; Pittig, Andre; Richter, Jan; Römer, Sonja; Shiban, Youssef; Schmitz, Anja; Straube, Benjamin; Vervliet, Bram; Wendt, Julia; Baas, Johanna M P; Merz, Christian J

2017-06-01

The so-called 'replicability crisis' has sparked methodological discussions in many areas of science in general, and in psychology in particular. This has led to recent endeavours to promote the transparency, rigour, and ultimately, replicability of research. Originating from this zeitgeist, the challenge to discuss critical issues on terminology, design, methods, and analysis considerations in fear conditioning research is taken up by this work, which involved representatives from fourteen of the major human fear conditioning laboratories in Europe. This compendium is intended to provide a basis for the development of a common procedural and terminology framework for the field of human fear conditioning. Whenever possible, we give general recommendations. When this is not feasible, we provide evidence-based guidance for methodological decisions on study design, outcome measures, and analyses. Importantly, this work is also intended to raise awareness and initiate discussions on crucial questions with respect to data collection, processing, statistical analyses, the impact of subtle procedural changes, and data reporting specifically tailored to the research on fear conditioning. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Understanding the impact of insulating and conducting endplate boundary conditions on turbulence in CSDX through nonlocal simulations

DOE PAGES

Vaezi, P.; Holland, C.; Thakur, S. C.; ...

2017-04-01

The Controlled Shear Decorrelation Experiment (CSDX) linear plasma device provides a unique platform for investigating the underlying physics of self-regulating drift-wave turbulence/zonal flow dynamics. A minimal model of 3D drift-reduced nonlocal cold ion fluid equations which evolves density, vorticity, and electron temperature fluctuations, with proper sheath boundary conditions, is used to simulate dynamics of the turbulence in CSDX and its response to changes in parallel boundary conditions. These simulations are then carried out using the BOUndary Turbulence (BOUT++) framework and use equilibrium electron density and temperature profiles taken from experimental measurements. The results show that density gradient-driven drift-waves are themore » dominant instability in CSDX. However, the choice of insulating or conducting endplate boundary conditions affects the linear growth rates and energy balance of the system due to the absence or addition of Kelvin-Helmholtz modes generated by the sheath-driven equilibrium E × B shear and sheath-driven temperature gradient instability. Moreover, nonlinear simulation results show that the boundary conditions impact the turbulence structure and zonal flow formation, resulting in less broadband (more quasi-coherent) turbulence and weaker zonal flow in conducting boundary condition case. These results are qualitatively consistent with earlier experimental observations.« less

Chaos control and synchronization in Bragg acousto-optic bistable systems driven by a separate chaotic system.

PubMed

Wang, Rong; Gao, Jin-Yue

2005-09-01

In this paper we propose a new scheme to achieve chaos control and synchronization in Bragg acousto-optic bistable systems. In the scheme, we use the output of one system to drive two identical chaotic systems. Using the maximal conditional Lyapunov exponent (MCLE) as the criterion, we analyze the conditions for realizing chaos synchronization. Numerical calculation shows that the two identical systems in chaos with negative MCLEs and driven by a chaotic system can go into chaotic synchronization whether or not they were in chaos initially. The two systems can go into different periodic states from chaos following an inverse period-doubling bifurcation route as well when driven by a periodic system.

Replication of an Experimental Study Investigating the Efficacy of a Multisyllabic Word Reading Intervention With and Without Motivational Beliefs Training for Struggling Readers.

PubMed

Toste, Jessica R; Capin, Philip; Williams, Kelly J; Cho, Eunsoo; Vaughn, Sharon

2018-05-01

This randomized control trial examined the efficacy of an intervention aimed at improving multisyllabic word reading (MWR) skills among fourth- and fifth-grade struggling readers ( n = 109, 48.6% male), as well as the relative effects of an embedded motivational beliefs training component. This study was a closely aligned replication of our earlier work. The intervention was replicated with a three-condition design: MWR only, MWR with a motivational beliefs component, and business-as-usual control. Students were tutored in small groups for 40 lessons (four 40-min lessons each week). When we combined performance of students in both MWR conditions, intervention students significantly outperformed controls on proximal measures of affix reading and MWR, as well as standardized measures of decoding, spelling, and text comprehension. Furthermore, there was a noted interaction between English learner status and treatment on spelling performance. There were no statistically significant main effects between the MWR groups on proximal or standardized measures of interest. Findings are discussed in terms of their relevance to MWR instruction for students with persistent reading difficulties and considerations for future research related to the malleability of motivation.

Field of Vision Influences Sensory-Motor Control of Skilled and Less-Skilled Dart Players

PubMed Central

Rienhoff, Rebecca; Baker, Joseph; Fischer, Lennart; Strauss, Bernd; Schorer, Jörg

2012-01-01

One characteristic of perceptual expertise in sport and other domains is known as ’the quiet eye', which assumes that fixated information is processed during gaze stability and insufficient spatial information leads to a decrease in performance. The aims of this study were a) replicating inter- and intra-group variability and b) investigating the extent to which quiet eye supports information pick-up of varying fields of vision (i.e., central versus peripheral) using a specific eye-tracking paradigm to compare different skill levels in a dart throwing task. Differences between skill levels were replicated at baseline, but no significant differences in throwing performance were revealed among the visual occlusion conditions. Findings are generally in line with the association between quiet eye duration and aiming performance, but raise questions regarding the relevance of central vision information pick-up for the quiet eye. Key pointsInvestigation of throwing performance and quiet eye duration in dart throwing under several vision conditionsFirst investigation using a dynamic occlusion paradigm, manipulating field of vision in situReplication of previous findings concerning throwing performance and quiet eye durationNew insights about the role of central (and peripheral) vision concerning the quiet eye phenomena PMID:24149366

Electrophoretic interactions and aggregation of colloidal biological particles

NASA Technical Reports Server (NTRS)

Davis, Robert H.; Nichols, Scott C.; Loewenberg, Michael; Todd, Paul

1994-01-01

The separation of cells or particles from solution has traditionally been accomplished with centrifuges or by sedimentation; however, many particles have specific densities close to unity, making buoyancy-driven motion slow or negligible, but most cells and particles carry surface charges, making them ideal for electrophoretic separation. Both buoyancy-driven and electrophoretic separation may be influenced by hydrodynamic interactions and aggregation of neighboring particles. Aggregation by electrophoresis was analyzed for two non-Brownian particles with different zeta potentials and thin double layers migrating through a viscous fluid. The results indicate that the initial rate of electrophoretically-driven aggregation may exceed that of buoyancy-driven aggregation, even under conditions in which buoyancy-driven relative motion of noninteracting particles is dominant.

The development of the conditionally replication-competent adenovirus: replacement of E4 orf1-4 region by exogenous gene.

PubMed

Nam, Jae-Kook; Lee, Mi-Hyang; Seo, Hae-Hyun; Kim, Seok-Ki; Lee, Kang-Huyn; Kim, In-Hoo; Lee, Sang-Jin

2010-05-01

Tumor or tissue specific replicative adenovirus armed with a therapeutic gene has shown a promising anti-cancer therapeutic modality. However, because the genomic packaging capacity is constrained, only a few places inside it are available for transgene insertion. In the present study, we introduce a novel strategy utilizing the early E4 region for the insertion of therapeutic gene(s). We constructed the conditionally replication-competent adenovirus (CRAd), Ad5E4(mRFP) by: (i) replacing the E4/E1a promoter by the prostate-specific enhancer element; (ii) inserting mRFP inside the E4orf1-4 deletion region; and (iii) sub-cloning enhanced green fluorescent protein controlled by cytomegalovirus promoter in the left end of the viral genome. Subsequently, we evaluated its replication abilities and killing activities in vitro, as well as its in vivo anti-tumor efficacy in CWR22rv xenografts. When infected with Ad5E4(mRFP), the number and intensity of the mRFP gene products increased in a prostate cancer cell-specific manner as designed, suggesting that the mRFP gene and E4orfs other than E4orf1-4 were well synthesized from one transcript via alternative splicing as the recombinant adenovirus replicated. As expected from the confirmed virus replication capability, Ad5E4(mRFP) induced cell lysis as potent as the wild-type adenovirus and effectively suppressed tumor growth when tested in the CWR22rv xenografts in nude mice. Furthermore, Ad5E4(endo/angio) harboring an endostatin-angiostatin gene in E4orf1-4 was able to enhance CRAd by replacing mRFP with a therapeutic gene. The approach employed in the present study for the insertion of a therapeutic transgene in CRAd should facilitate the construction of CRAd containing multiple therapeutic genes in the viral genome that may have the potential to serve as highly potent cancer therapeutic reagents. Copyright (c) 2010 John Wiley & Sons, Ltd.

Task-Driven Activity Reduces the Cortical Activity Space of the Brain: Experiment and Whole-Brain Modeling

PubMed Central

Hagmann, Patric; Deco, Gustavo

2015-01-01

How a stimulus or a task alters the spontaneous dynamics of the brain remains a fundamental open question in neuroscience. One of the most robust hallmarks of task/stimulus-driven brain dynamics is the decrease of variability with respect to the spontaneous level, an effect seen across multiple experimental conditions and in brain signals observed at different spatiotemporal scales. Recently, it was observed that the trial-to-trial variability and temporal variance of functional magnetic resonance imaging (fMRI) signals decrease in the task-driven activity. Here we examined the dynamics of a large-scale model of the human cortex to provide a mechanistic understanding of these observations. The model allows computing the statistics of synaptic activity in the spontaneous condition and in putative tasks determined by external inputs to a given subset of brain regions. We demonstrated that external inputs decrease the variance, increase the covariances, and decrease the autocovariance of synaptic activity as a consequence of single node and large-scale network dynamics. Altogether, these changes in network statistics imply a reduction of entropy, meaning that the spontaneous synaptic activity outlines a larger multidimensional activity space than does the task-driven activity. We tested this model’s prediction on fMRI signals from healthy humans acquired during rest and task conditions and found a significant decrease of entropy in the stimulus-driven activity. Altogether, our study proposes a mechanism for increasing the information capacity of brain networks by enlarging the volume of possible activity configurations at rest and reliably settling into a confined stimulus-driven state to allow better transmission of stimulus-related information. PMID:26317432

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

PubMed

Lin, Chieh-Hua; Lian, Chun-Yi; Hsiung, Chao Agnes; Chen, Feng-Chi

2011-10-05

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

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

PubMed

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.

Replication of Simulated Prebiotic Amphiphilic Vesicles in a Finite Environment Exhibits Complex Behavior That Includes High Progeny Variability and Competition

PubMed Central

Armstrong, Don L.; Lancet, Doron

2018-01-01

Abstract We studied the simulated replication and growth of prebiotic vesicles composed of 140 phospholipids and cholesterol using our R-GARD (Real Graded Autocatalysis Replication Domain) formalism that utilizes currently extant lipids that have known rate constants of lipid-vesicle interactions from published experimental data. R-GARD normally modifies kinetic parameters of lipid-vesicle interactions based on vesicle composition and properties. Our original R-GARD model tracked the growth and division of one vesicle at a time in an environment with unlimited lipids at a constant concentration. We explore here a modified model where vesicles compete for a finite supply of lipids. We observed that vesicles exhibit complex behavior including initial fast unrestricted growth, followed by intervesicle competition for diminishing resources, then a second growth burst driven by better-adapted vesicles, and ending with a final steady state. Furthermore, in simulations without kinetic parameter modifications (“invariant kinetics”), the initial replication was an order of magnitude slower, and vesicles' composition variability at the final steady state was much lower. The complex kinetic behavior was not observed either in the previously published R-GARD simulations or in additional simulations presented here with only one lipid component. This demonstrates that both a finite environment (inducing selection) and multiple components (providing variation for selection to act upon) are crucial for portraying evolution-like behavior. Such properties can improve survival in a changing environment by increasing the ability of early protocellular entities to respond to rapid environmental fluctuations likely present during abiogenesis both on Earth and possibly on other planets. This in silico simulation predicts that a relatively simple in vitro chemical system containing only lipid molecules might exhibit properties that are relevant to prebiotic processes. Key Words: Phospholipid vesicles—Prebiotic compartments—Prebiotic vesicle competition—Prebiotic vesicle variability. Astrobiology 18, 419–430. PMID:29634319

Performance analysis of replication ALOHA for fading mobile communications channels

NASA Technical Reports Server (NTRS)

Yan, Tsun-Yee; Clare, Loren P.

1986-01-01

This paper describes an ALOHA random access protocol for fading communications channels. A two-state Markov model is used for the channel error process to account for the channel fading memory. The ALOHA protocol is modified to send multiple contiguous copies of a message at each transmission attempt. Both pure and slotted ALOHA channels are considered. The analysis is applicable to fading environments where the channel memory is short compared to the propagation delay. It is shown that smaller delay may be achieved using replications and, in noisy conditions, can also improve throughput.

HSV-2-Driven Increase in the Expression of α4β7 Correlates with Increased Susceptibility to Vaginal SHIVSF162P3 Infection

PubMed Central

Goode, Diana; Truong, Rosaline; Villegas, Guillermo; Calenda, Giulia; Guerra-Perez, Natalia; Piatak, Michael; Lifson, Jeffrey D.; Blanchard, James; Gettie, Agegnehu; Robbiani, Melissa; Martinelli, Elena

2014-01-01

The availability of highly susceptible HIV target cells that can rapidly reach the mucosal lymphoid tissues may increase the chances of an otherwise rare transmission event to occur. Expression of α4β7 is required for trafficking of immune cells to gut inductive sites where HIV can expand and it is expressed at high level on cells particularly susceptible to HIV infection. We hypothesized that HSV-2 modulates the expression of α4β7 and other homing receptors in the vaginal tissue and that this correlates with the increased risk of HIV acquisition in HSV-2 positive individuals. To test this hypothesis we used an in vivo rhesus macaque (RM) model of HSV-2 vaginal infection and a new ex vivo model of macaque vaginal explants. In vivo we found that HSV-2 latently infected RMs appeared to be more susceptible to vaginal SHIVSF162P3 infection, had higher frequency of α4β7 high CD4+ T cells in the vaginal tissue and higher expression of α4β7 and CD11c on vaginal DCs. Similarly, ex vivo HSV-2 infection increased the susceptibility of the vaginal tissue to SHIVSF162P3. HSV-2 infection increased the frequencies of α4β7 high CD4+ T cells and this directly correlated with HSV-2 replication. A higher amount of inflammatory cytokines in vaginal fluids of the HSV-2 infected animals was similar to those found in the supernatants of the infected explants. Remarkably, the HSV-2-driven increase in the frequency of α4β7 high CD4+ T cells directly correlated with SHIV replication in the HSV-2 infected tissues. Our results suggest that the HSV-2-driven increase in availability of CD4+ T cells and DCs that express high levels of α4β7 is associated with the increase in susceptibility to SHIV due to HSV-2. This may persists in absence of HSV-2 shedding. Hence, higher availability of α4β7 positive HIV target cells in the vaginal tissue may constitute a risk factor for HIV transmission. PMID:25521298

HSV-2-driven increase in the expression of α4β7 correlates with increased susceptibility to vaginal SHIV(SF162P3) infection.

PubMed

Goode, Diana; Truong, Rosaline; Villegas, Guillermo; Calenda, Giulia; Guerra-Perez, Natalia; Piatak, Michael; Lifson, Jeffrey D; Blanchard, James; Gettie, Agegnehu; Robbiani, Melissa; Martinelli, Elena

2014-12-01

The availability of highly susceptible HIV target cells that can rapidly reach the mucosal lymphoid tissues may increase the chances of an otherwise rare transmission event to occur. Expression of α4β7 is required for trafficking of immune cells to gut inductive sites where HIV can expand and it is expressed at high level on cells particularly susceptible to HIV infection. We hypothesized that HSV-2 modulates the expression of α4β7 and other homing receptors in the vaginal tissue and that this correlates with the increased risk of HIV acquisition in HSV-2 positive individuals. To test this hypothesis we used an in vivo rhesus macaque (RM) model of HSV-2 vaginal infection and a new ex vivo model of macaque vaginal explants. In vivo we found that HSV-2 latently infected RMs appeared to be more susceptible to vaginal SHIVSF162P3 infection, had higher frequency of α4β7high CD4+ T cells in the vaginal tissue and higher expression of α4β7 and CD11c on vaginal DCs. Similarly, ex vivo HSV-2 infection increased the susceptibility of the vaginal tissue to SHIVSF162P3. HSV-2 infection increased the frequencies of α4β7high CD4+ T cells and this directly correlated with HSV-2 replication. A higher amount of inflammatory cytokines in vaginal fluids of the HSV-2 infected animals was similar to those found in the supernatants of the infected explants. Remarkably, the HSV-2-driven increase in the frequency of α4β7high CD4+ T cells directly correlated with SHIV replication in the HSV-2 infected tissues. Our results suggest that the HSV-2-driven increase in availability of CD4+ T cells and DCs that express high levels of α4β7 is associated with the increase in susceptibility to SHIV due to HSV-2. This may persists in absence of HSV-2 shedding. Hence, higher availability of α4β7 positive HIV target cells in the vaginal tissue may constitute a risk factor for HIV transmission.

Insensitivity of chromosome I and the cell cycle to blockage of replication and segregation of Vibrio cholerae chromosome II.

PubMed

Kadoya, Ryosuke; Chattoraj, Dhruba K

2012-01-01

Vibrio cholerae has two chromosomes (chrI and chrII) whose replication and segregation are under different genetic controls. The region covering the replication origin of chrI resembles that of the Escherichia coli chromosome, and both origins are under control of the highly conserved initiator, DnaA. The origin region of chrII resembles that of plasmids that have iterated initiator-binding sites (iterons) and is under control of the chrII-specific initiator, RctB. Both chrI and chrII encode chromosome-specific orthologs of plasmid partitioning proteins, ParA and ParB. Here, we have interfered with chrII replication, segregation, or both, using extra copies of sites that titrate RctB or ParB. Under these conditions, replication and segregation of chrI remain unaffected for at least 1 cell cycle. In this respect, chrI behaves similarly to the E. coli chromosome when plasmid maintenance is disturbed in the same cell. Apparently, no checkpoint exists to block cell division before the crippled chromosome is lost by a failure to replicate or to segregate. Whether blocking chrI replication can affect chrII replication remains to be tested. Chromosome replication, chromosome segregation, and cell division are the three main events of the cell cycle. They occur in an orderly fashion once per cell cycle. How the sequence of events is controlled is only beginning to be answered in bacteria. The finding of bacteria that possess more than one chromosome raises the important question: how are different chromosomes coordinated in their replication and segregation? It appears that in the evolution of the two-chromosome genome of V. cholerae, either the secondary chromosome adapted to the main chromosome to ensure its maintenance or it is maintained independently, as are bacterial plasmids. An understanding of chromosome coordination is expected to bear on the evolutionary process of chromosome acquisition and on the efficacy of possible strategies for selective elimination of a pathogen by targeting a specific chromosome.

Meta-analyses are no substitute for registered replications: a skeptical perspective on religious priming

PubMed Central

van Elk, Michiel; Matzke, Dora; Gronau, Quentin F.; Guan, Maime; Vandekerckhove, Joachim; Wagenmakers, Eric-Jan

2015-01-01

According to a recent meta-analysis, religious priming has a positive effect on prosocial behavior (Shariff et al., 2015). We first argue that this meta-analysis suffers from a number of methodological shortcomings that limit the conclusions that can be drawn about the potential benefits of religious priming. Next we present a re-analysis of the religious priming data using two different meta-analytic techniques. A Precision-Effect Testing–Precision-Effect-Estimate with Standard Error (PET-PEESE) meta-analysis suggests that the effect of religious priming is driven solely by publication bias. In contrast, an analysis using Bayesian bias correction suggests the presence of a religious priming effect, even after controlling for publication bias. These contradictory statistical results demonstrate that meta-analytic techniques alone may not be sufficiently robust to firmly establish the presence or absence of an effect. We argue that a conclusive resolution of the debate about the effect of religious priming on prosocial behavior – and about theoretically disputed effects more generally – requires a large-scale, preregistered replication project, which we consider to be the sole remedy for the adverse effects of experimenter bias and publication bias. PMID:26441741

The late endocytic Rab39a GTPase regulates the interaction between multivesicular bodies and chlamydial inclusions.

PubMed

Gambarte Tudela, Julian; Capmany, Anahi; Romao, Maryse; Quintero, Cristian; Miserey-Lenkei, Stephanie; Raposo, Graca; Goud, Bruno; Damiani, Maria Teresa

2015-08-15

Given their obligate intracellular lifestyle, Chlamydia trachomatis ensure that they have access to multiple host sources of essential lipids by interfering with vesicular transport. These bacteria hijack Rab6-, Rab11- and Rab14-controlled trafficking pathways to acquire sphingomyelin from the Golgi complex. Another important source of sphingolipids, phospholipids and cholesterol are multivesicular bodies (MVBs). Despite their participation in chlamydial inclusion development and bacterial replication, the molecular mechanisms mediating the interaction between MVBs and chlamydial inclusions remain unknown. In the present study, we demonstrate that Rab39a labels a subset of late endocytic vesicles - mainly MVBs - that move along microtubules. Moreover, Rab39a is actively recruited to chlamydial inclusions throughout the pathogen life cycle by a bacterial-driven process that depends on the Rab39a GTP- or GDP-binding state. Interestingly, Rab39a participates in the delivery of MVBs and host sphingolipids to maturing chlamydial inclusions, thereby promoting inclusion growth and bacterial development. Taken together, our findings indicate that Rab39a favours chlamydial replication and infectivity. This is the first report showing that a late endocytic Rab GTPase is involved in chlamydial infection development. © 2015. Published by The Company of Biologists Ltd.

Cocaine promotes both initiation and elongation phase of HIV-1 transcription by activating NF-κB and MSK1 and inducing selective epigenetic modifications at HIV-1 LTR.

PubMed

Sahu, Geetaram; Farley, Kalamo; El-Hage, Nazira; Aiamkitsumrit, Benjamas; Fassnacht, Ryan; Kashanchi, Fatah; Ochem, Alex; Simon, Gary L; Karn, Jonathan; Hauser, Kurt F; Tyagi, Mudit

2015-09-01

Cocaine accelerates human immunodeficiency virus (HIV-1) replication by altering specific cell-signaling and epigenetic pathways. We have elucidated the underlying molecular mechanisms through which cocaine exerts its effect in myeloid cells, a major target of HIV-1 in central nervous system (CNS). We demonstrate that cocaine treatment promotes HIV-1 gene expression by activating both nuclear factor-kappa B (NF-ĸB) and mitogen- and stress-activated kinase 1 (MSK1). MSK1 subsequently catalyzes the phosphorylation of histone H3 at serine 10, and p65 subunit of NF-ĸB at 276th serine residue. These modifications enhance the interaction of NF-ĸB with P300 and promote the recruitment of the positive transcription elongation factor b (P-TEFb) to the HIV-1 LTR, supporting the development of an open/relaxed chromatin configuration, and facilitating the initiation and elongation phases of HIV-1 transcription. Results are also confirmed in primary monocyte derived macrophages (MDM). Overall, our study provides detailed insights into cocaine-driven HIV-1 transcription and replication. Copyright © 2015 Elsevier Inc. All rights reserved.

Cocaine promotes both initiation and elongation phase of HIV-1 transcription by activating NF-κB and MSK1 and inducing selective epigenetic modifications at HIV-1 LTR

PubMed Central

Sahu, Geetaram; Farley, Kalamo; El-Hage, Nazira; Aiamkitsumrit, Benjamas; Fassnacht, Ryan; Kashanchi, Fatah; Ochem, Alex; Simon, Gary L.; Karn, Jonathan; Hauser, Kurt F.; Tyagi, Mudit

2015-01-01

Cocaine accelerates human immunodeficiency virus (HIV-1) replication by altering specific cell-signaling and epigenetic pathways. We have elucidated the underlying molecular mechanisms through which cocaine exerts its effect in myeloid cells, a major target of HIV-1 in central nervous system (CNS). We demonstrate that cocaine treatment promotes HIV-1 gene expression by activating both nuclear factor-kappa B (NF-κB) and mitogen- and stress-activated kinase 1 (MSK1). MSK1 subsequently catalyzes the phosphorylation of histone H3 at serine 10, and p65 subunit of NF-κB at 276th serine residue. These modifications enhance the interaction of NF-κB with P300 and promote the recruitment of the positive transcription elongation factor b (P-TEFb) to the HIV-1 LTR, supporting the development of an open/relaxed chromatin configuration, and facilitating the initiation and elongation phases of HIV-1 transcription. Results are also confirmed in primary monocyte derived macrophages (MDM). Overall, our study provides detailed insights into cocaine-driven HIV-1 transcription and replication. PMID:25980739

The Narrow Road to the Deep Past: In Search of the Chemistry of the Origin of Life.

PubMed

Szostak, Jack W

2017-09-04

The sequence of events that gave rise to the first life on our planet took place in the Earth's deep past, seemingly forever beyond our reach. Perhaps for that very reason the idea of reconstructing our ancient story is tantalizing, almost irresistible. Understanding the processes that led to synthesis of the chemical building blocks of biology and the ways in which these molecules self-assembled into cells that could grow, divide and evolve, nurtured by a rich and complex environment, seems at times insurmountably difficult. And yet, to my own surprise, simple experiments have revealed robust processes that could have driven the growth and division of primitive cell membranes. The nonenzymatic replication of RNA is more complicated and less well understood, but here too significant progress has come from surprising developments. Even our efforts to combine replicating compartments and genetic materials into a full protocell model have moved forward in unexpected ways. Fortunately, many challenges remain before we will be close to a full understanding of the origin of life, so the future of research in this field is brighter than ever! © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Decoding the attended speech stream with multi-channel EEG: implications for online, daily-life applications

NASA Astrophysics Data System (ADS)

Mirkovic, Bojana; Debener, Stefan; Jaeger, Manuela; De Vos, Maarten

2015-08-01

Objective. Recent studies have provided evidence that temporal envelope driven speech decoding from high-density electroencephalography (EEG) and magnetoencephalography recordings can identify the attended speech stream in a multi-speaker scenario. The present work replicated the previous high density EEG study and investigated the necessary technical requirements for practical attended speech decoding with EEG. Approach. Twelve normal hearing participants attended to one out of two simultaneously presented audiobook stories, while high density EEG was recorded. An offline iterative procedure eliminating those channels contributing the least to decoding provided insight into the necessary channel number and optimal cross-subject channel configuration. Aiming towards the future goal of near real-time classification with an individually trained decoder, the minimum duration of training data necessary for successful classification was determined by using a chronological cross-validation approach. Main results. Close replication of the previously reported results confirmed the method robustness. Decoder performance remained stable from 96 channels down to 25. Furthermore, for less than 15 min of training data, the subject-independent (pre-trained) decoder performed better than an individually trained decoder did. Significance. Our study complements previous research and provides information suggesting that efficient low-density EEG online decoding is within reach.

Innovations in oral health: A toolkit for interprofessional education.

PubMed

Dolce, Maria C; Parker, Jessica L; Werrlein, Debra T

2017-05-01

The integration of oral health competencies into non-dental health professions curricula can serve as an effective driver for interprofessional education (IPE). The purpose of this report is to describe a replicable oral-health-driven IPE model and corresponding online toolkit, both of which were developed as part of the Innovations in Oral Health (IOH): Technology, Instruction, Practice, and Service programme at Bouvé College of Health Sciences, Northeastern University, USA. Tooth decay is a largely preventable disease that is connected to overall health and wellness, and it affects the majority of adults and a fifth of children in the United States. To prepare all health professionals to address this problem, the IOH model couples programming from the online resource Smiles for Life: A National Oral Health Curriculum with experiential learning opportunities designed for undergraduate and graduate students that include simulation-learning (technology), hands-on workshops and didactic sessions (instruction), and opportunities for both cooperative education (practice) and community-based learning (service). The IOH Toolkit provides the means for others to replicate portions of the IOH model or to establish a large-scale IPE initiative that will support the creation of an interprofessional workforce-one equipped with oral health competencies and ready for collaborative practice.

Topographic design and application of hierarchical polymer surfaces replicated by microinjection compression molding

NASA Astrophysics Data System (ADS)

Guan, Wei-Sheng; Huang, Han-Xiong; Wang, Bin

2013-10-01

In recent years, the fast growing demand for biomimetic surfaces featuring unique wettability and functionality in various fields highlights the necessity of developing a reliable technique for mass production. In this work, hierarchical topography designs of templates were applied to prepare superhydrophobic surfaces via microinjection compression molding, comprehensively considering the feasibility of mechanical demolding and the superhydrophobicity and mechanical robustness of the molded polypropylene parts. Mimicking the wettability of a lotus leaf or rose petal, superhydrophobic surfaces were replicated. An unstable wetting state formed on the surface exhibiting the petal effect. On such a surface, the increased water pressure could cause water penetration into the micro gaps between the hierarchical asperities featuring low-roughness sidewalls and bottom surface; the resultant water membrane led to drastically increased water adhesion of the surface. Moreover, the low-adhesion superhydrophobicity of the molded surface was changed into superhydrophilicity, by means of introducing carbonyl groups via ultraviolet/ozone treatment and the subsequent water membrane preserved in microstructures via the pre-wetting process. Patterning the superhydrophilic micro channel on the superhydrophobic surface developed the surface microfluidic devices for micro-liter fluid pumping and mixing processes driven by surface tension.

Scan-layered reconstructions: A pilot study of a nondestructive dental histoanatomical analysis method and digital workflow to create restorations driven by natural dentin and enamel morphology.

PubMed

Malta Barbosa, João; Tovar, Nick; A Tuesta, Pablo; Hirata, Ronaldo; Guimarães, Nuno; Romanini, José C; Moghadam, Marjan; Coelho, Paulo G; Jahangiri, Leila

2017-07-08

This work aims to present a pilot study of a non-destructive dental histo-anatomical analysis technique as well as to push the boundaries of the presently available restorative workflows for the fabrication of highly customized ceramic restorations. An extracted human maxillary central incisor was subject to a micro computed tomography scan and the acquired data was transferred into a workstation, reconstructed, segmented, evaluated and later imported into a Computer-Aided Design/Computer-Aided Manufacturing software for the fabrication of a ceramic resin-bonded prosthesis. The obtained prosthesis presented an encouraging optical behavior and was used clinically as final restoration. The digitally layered restorative replication of natural tooth morphology presents today as a clear possibility. New clinical and laboratory-fabricated, biologically inspired digital restorative protocols are to be expected in the near future. The digitally layered restorative replication of natural tooth morphology presents today as a clear possibility. This pilot study may represent a stimulus for future research and applications of digital imaging as well as digital restorative workflows in service of esthetic dentistry. © 2017 Wiley Periodicals, Inc.

Stress-Driven Melt Segregation and Organization in Partially Molten Rocks III: Annealing Experiments and Surface Tension-Driven Redistribution of Melt

NASA Astrophysics Data System (ADS)

Parsons, R.; Hustoft, J. W.; Holtzman, B. K.; Kohlstedt, D. L.; Phipps Morgan, J.

2004-12-01

As discussed in the two previous abstracts in this series, simple shear experiments on synthetic upper mantle-type rock samples reveal the segregation of melt into melt-rich bands separated by melt-depleted lenses. Here, we present new results from experiments designed to understand the driving forces working for and against melt segregation. To better understand the kinetics of surface tension-driven melt redistribution, we first deform samples at similar conditions (starting material, sample size, stress and strain) to produce melt-rich band networks that are statistically similar. Then the load is removed and the samples are statically annealed to allow surface tension to redistribute the melt-rich networks. Three samples of olivine + 20 vol% chromite + 4 vol% MORB were deformed at a confining pressure of 300 MPa and a temperature of 1523 K in simple shear at shear stresses of 20 - 55 MPa to shear strains of 3.5 and then statically annealed for 0, 10, or 100 h at the same P-T conditions. Melt-rich bands are fewer in number and appear more diffuse when compared to the deformed but not annealed samples. Bands with less melt tend to disappear more rapidly than more melt-rich ones. The melt fraction in the melt-rich bands decreased from 0.2 in the quenched sample to 0.1 in the sample annealed for 100 h. After deformation, the melt fraction in the melt-depleted regions are ~0.006; after static annealing for 100 h, this value increases to 0.02. These experiments provide new quantitative constraints on the kinetics of melt migration driven by surface tension. By quantifying this driving force in the same samples in which stress-driven distribution occurred, we learn about the relative kinetics of stress-driven melt segregation. The kinetics of both of these processes must be scaled together to mantle conditions to understand the importance of stress-driven melt segregation in the Earth, and to understand the interaction of this process with melt-rock reaction-driven processes.

Making sense of the noise: Replication difficulties of Correll's (2008) modulation of 1/f noise in a racial bias task.

PubMed

Madurski, Christine; LeBel, Etienne P

2015-08-01

Correll (Journal of Personality and Social Psychology, 94, 48-59, 2008; Study 2) found that instructions to use or avoid race information decreased the emission of 1/f noise in a weapon identification task (WIT). These results suggested that 1/f noise in racial bias tasks reflected an effortful deliberative process, providing new insights regarding the mechanisms underlying implicit racial biases. Given the potential theoretical and applied importance of understanding the psychological processes underlying implicit racial biases - and in light of the growing demand for independent direct replications of findings to ensure the cumulative nature of our science - we attempted to replicate Correll's finding in two high-powered studies. Despite considerable effort to closely duplicate all procedural and methodological details of the original study (i.e., same cover story, experimental manipulation, implicit measure task, original stimuli, task instructions, sampling frame, population, and statistical analyses), both replication attempts were unsuccessful in replicating the original finding challenging the theoretical account that 1/f noise in racial bias tasks reflects a deliberative process. However, the emission of 1/f noise did consistently emerge across samples in each of our conditions. Hence, future research is needed to clarify the psychological significance of 1/f noise in racial bias tasks.

The role of MatP, ZapA and ZapB in chromosomal organization and dynamics in Escherichia coli

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mannik, Jaana; Castillo, Daniel E.; Yang, Da

Despite extensive research over several decades, a comprehensive view of how the Escherichia coli chromosome is organized within the nucleoid, and how two daughter chromosomes segregate has yet to emerge. Here we investigate the role of the MatP, ZapA and ZapB proteins in organizing the replication terminus (Ter) region and in the chromosomal segregation process. Quantitative image analysis of the fluorescently labeled Ter region shows that the replication terminus attaches to the divisome in a single segment along the perimeter of the cell in a MatP, ZapA and ZapB-dependent manner. The attachment does not significantly affect the bulk chromosome segregationmore » in slow growth conditions. With or without the attachment, two chromosomal masses separate from each other at a speed comparable to the cell growth. The separation starts even before the replication terminus region positions itself at the center of the nucleoid. Modeling of the segregation based on conformational entropy correctly predicts the positioning of the replication terminus region within the nucleoid. Furthermore, the model produces a distinctly different chromosomal density distribution than the experiment, indicating that the conformational entropy plays a limited role in segregating the chromosomes in the late stages of replication.« less

Replication Protein A-1 Has a Preference for the Telomeric G-rich Sequence in Trypanosoma cruzi.

PubMed

Pavani, Raphael Souza; Vitarelli, Marcela O; Fernandes, Carlos A H; Mattioli, Fabio F; Morone, Mariana; Menezes, Milene C; Fontes, Marcos R M; Cano, Maria Isabel N; Elias, Maria Carolina

2018-05-01

Replication protein A (RPA), the major eukaryotic single-stranded binding protein, is a heterotrimeric complex formed by RPA-1, RPA-2, and RPA-3. RPA is a fundamental player in replication, repair, recombination, and checkpoint signaling. In addition, increasing evidences have been adding functions to RPA in telomere maintenance, such as interaction with telomerase to facilitate its activity and also involvement in telomere capping in some conditions. Trypanosoma cruzi, the etiological agent of Chagas disease is a protozoa parasite that appears early in the evolution of eukaryotes. Recently, we have showed that T. cruziRPA presents canonical functions being involved with DNA replication and DNA damage response. Here, we found by FISH/IF assays that T. cruziRPA localizes at telomeres even outside replication (S) phase. In vitro analysis showed that one telomeric repeat is sufficient to bind RPA-1. Telomeric DNA induces different secondary structural modifications on RPA-1 in comparison with other types of DNA. In addition, RPA-1 presents a higher affinity for telomeric sequence compared to randomic sequence, suggesting that RPA may play specific roles in T. cruzi telomeric region. © 2017 The Author(s) Journal of Eukaryotic Microbiology © 2017 International Society of Protistologists.

Preparation of ordered mesoporous and macroporous thermoplastic polyurethane surfaces for potential medical applications.

PubMed

Chennell, Philip; Feschet-Chassot, Emmanuelle; Sautou, Valérie; Mailhot-Jensen, Bénédicte

2018-05-01

Thermoplastic polyurethanes are widely used in medical devices. In order to limit some of their shortfalls, like microbial attachment, surfaces modifications can be required. In this work, a two-step replication method was used to create ordered macroporous and mesoporous thermoplastic polyurethane surfaces using anodic aluminum oxide as master template. The intermediate mould materials that were tested were polystyrene and a polyacrylate resin with inorganic filler. All obtained surfaces were characterized by scanning electron microscopy. The initial anodic aluminum oxide surfaces possessed macro or mesopores, function of anodization conditions. The intermediate mould structure correctly replicated the pattern, but the polystyrene surface structures (pillars) were less resistant than the polyacrylate resin ones. The thermoplastic polyurethane pattern possessed macropores or mesopores of about 130 nm or 46 nm diameter and of about 300 nm or 99 nm interpore distances, respectively, in accordance with the initial pattern. Thermoplastic polyurethanes pore depth was however less than initial anodic aluminum oxide pore depth, linked to an incomplete replication during intermediate mould preparation (60 to 90% depth replication). The correct replication of the original pattern confirms that this novel fabrication method is a promising route for surface patterning of thermoplastic polyurethanes that could be used for medical applications.

The role of MatP, ZapA and ZapB in chromosomal organization and dynamics in Escherichia coli

DOE PAGES

Mannik, Jaana; Castillo, Daniel E.; Yang, Da; ...

2016-01-13

Despite extensive research over several decades, a comprehensive view of how the Escherichia coli chromosome is organized within the nucleoid, and how two daughter chromosomes segregate has yet to emerge. Here we investigate the role of the MatP, ZapA and ZapB proteins in organizing the replication terminus (Ter) region and in the chromosomal segregation process. Quantitative image analysis of the fluorescently labeled Ter region shows that the replication terminus attaches to the divisome in a single segment along the perimeter of the cell in a MatP, ZapA and ZapB-dependent manner. The attachment does not significantly affect the bulk chromosome segregationmore » in slow growth conditions. With or without the attachment, two chromosomal masses separate from each other at a speed comparable to the cell growth. The separation starts even before the replication terminus region positions itself at the center of the nucleoid. Modeling of the segregation based on conformational entropy correctly predicts the positioning of the replication terminus region within the nucleoid. Furthermore, the model produces a distinctly different chromosomal density distribution than the experiment, indicating that the conformational entropy plays a limited role in segregating the chromosomes in the late stages of replication.« less

Identification and functional evaluation of cellular and viral factors involved in the alteration of nuclear architecture during herpes simplex virus 1 infection.

PubMed

Simpson-Holley, Martha; Colgrove, Robert C; Nalepa, Grzegorz; Harper, J Wade; Knipe, David M

2005-10-01

Herpes simplex virus 1 (HSV-1) replicates in the nucleus of host cells and radically alters nuclear architecture as part of its replication process. Replication compartments (RCs) form, and host chromatin is marginalized. Chromatin is later dispersed, and RCs spread past it to reach the nuclear edge. Using a lamin A-green fluorescent protein fusion, we provide direct evidence that the nuclear lamina is disrupted during HSV-1 infection and that the UL31 and UL34 proteins are required for this. We show nuclear expansion from 8 h to 24 h postinfection and place chromatin rearrangement and disruption of the lamina in the context of this global change in nuclear architecture. We show HSV-1-induced disruption of the localization of Cdc14B, a cellular protein and component of a putative nucleoskeleton. We also show that UL31 and UL34 are required for nuclear expansion. Studies with inhibitors of globular actin (G-actin) indicate that G-actin plays an essential role in nuclear expansion and chromatin dispersal but not in lamina alterations induced by HSV-1 infection. From analyses of HSV infections under various conditions, we conclude that nuclear expansion and chromatin dispersal are dispensable for optimal replication, while lamina rearrangement is associated with efficient replication.

Retail food environments research: Promising future with more work to be done.

PubMed

Fuller, Daniel; Engler-Stringer, Rachel; Muhajarine, Nazeem

2016-06-09

As members of the scientific committee for the Food Environments in Canada conference, we reflect on the current state of food environments research in Canada. We are very encouraged that the field is growing and there have been many collaborative efforts to link researchers in Canada, including the 2015 Food Environments in Canada Symposium and Workshop. We believe there are 5 key challenges the field will need to collectively address: theory and causality; replication and extension; consideration of rural, northern and vulnerable populations; policy analysis; and intervention research. In addressing the challenges, we look forward to working together to conduct more sophisticated, complex and community-driven food environments research in the future.

Adventures in hepatocarcinogenesis.

PubMed

Pitot, Henry C

2007-01-01

Neoplasia is a heritably altered, relatively autonomous growth of tissue. Hepatocarcinogenesis, the pathogenesis of neoplasia in liver, as modeled in the rat exhibits three distinct, quantifiable stages: initiation, promotion, and progression. Simple mutations and/or epigenetic alterations may result in the irreversible stage of initiation. The stage of promotion results from selective enhancement of cell replication and selective inhibition of cellular apoptosis of initiated cells dependent on the genetic and/or epigenetic alterations of the latter. The irreversible stage of progression results from initial karyotypic alterations that evolve into greater degrees of genomic instability. The initial genomic alteration in the transition from promotion to progression may involve primarily epigenetic mechanisms driven by epigenetic and genetic alterations fixed during the stage of promotion.

Patterns of Learning in Verbal Discrimination as an Interaction of Social Reinforcement and Sex Combinations

ERIC Educational Resources Information Center

Ratliff, Richard G.; And Others

1976-01-01

A total of 540 college students were run in two verbal discrimination learning studies (the second, a replication of the first) with one of three verbal reward conditions. In both studies, equal numbers of male and female subjects were run in each reward condition by each male and female experimenter. (MS)

A Further Evaluation of Picture Prompts during Auditory-Visual Conditional Discrimination Training

ERIC Educational Resources Information Center

Carp, Charlotte L.; Peterson, Sean P.; Arkel, Amber J.; Petursdottir, Anna I.; Ingvarsson, Einar T.

2012-01-01

This study was a systematic replication and extension of Fisher, Kodak, and Moore (2007), in which a picture prompt embedded into a least-to-most prompting sequence facilitated acquisition of auditory-visual conditional discriminations. Participants were 4 children who had been diagnosed with autism; 2 had limited prior receptive skills, and 2 had…

A Comparison of Methods for Teaching Receptive Labeling to Children with Autism Spectrum Disorders: A Systematic Replication

ERIC Educational Resources Information Center

Grow, Laura L.; Kodak, Tiffany; Carr, James E.

2014-01-01

Previous research has demonstrated that the conditional-only method (starting with a multiple-stimulus array) is more efficient than the simple-conditional method (progressive incorporation of more stimuli into the array) for teaching receptive labeling to children with autism spectrum disorders (Grow, Carr, Kodak, Jostad, & Kisamore, 2011).…

Multi-Fluid Interpenetration Mixing in X-ray and Directly Laser driven ICF Capsule Implosions

NASA Astrophysics Data System (ADS)

Wilson, Douglas

2003-10-01

Mix between a surrounding shell and the fuel leads to degradation in ICF capsule performance. Both indirectly (X-ray) and directly laser driven implosions provide a wealth of data to test mix models. One model, the multi-fluid interpenetration mix model of Scannapieco and Cheng (Phys. Lett. A., 299, 49, 2002), was implemented in an ICF code and applied to a wide variety of experiments (e.g. J. D. Kilkenny et al., Proc. Conf Plasm. Phys. Contr. Nuc. Fus. Res. 3, 29(1988), P. Amendt, R. E. Turner, O. L. Landen, Phy. Rev. Lett., 89, 165001 (2002), or Li et al., Phy. Rev. Lett, 89, 165002 (2002)). With its single adjustable parameter fixed, it replicates well the yield degradation with increasing convergence ratio for both directly and indirectly driven capsules. Often, but not always the ion temperatures with mixing are calculated to be higher than in an unmixed implosion, agreeing with observations. Comparison with measured directly driven implosion yield rates ( from the neutron temporal diagnostic or NTD) shows mixing increases rapidly during the burn. The model also reproduces the decrease of the fuel "rho-r" with fill gas pressure, measured by observing escaping deuterons or secondary neutrons. The mix model assumes fully atomically mixed constituents, but when experiments with deuterated plastic layers and 3He fuel are modeled, less that full atomic mix is appropriate. Applying the mix model to the ablator - solid DT interface in indirectly driven ignition capsules for the NIF or LMJ suggests that the capsules will ignite, but that burn after ignition may be somewhat degraded. Situations in which the Scannapieco and Cheng model fails to agree with experiments can guide us to improvements or the development of other models. Some directly driven symmetric implosions suggest that in highly mixed situations, a higher value of the mix parameter may needed. Others show the model underestimating the fuel burn temperature. This work was performed by the Los Alamos National Laboratory under DOE contract number W-7405-Eng-36.

Swell-generated Set-up and Infragravity Wave Propagation Over a Fringing Coral Reef: Implications for Wave-driven Inundation of Atoll Islands

NASA Astrophysics Data System (ADS)

Cheriton, O. M.; Storlazzi, C. D.; Rosenberger, K. J.; Quataert, E.; van Dongeren, A.

2014-12-01

The Republic of the Marshall Islands is comprised of 1156 islands on 29 low-lying atolls with a mean elevation of 2 m that are susceptible to sea-level rise and often subjected to overwash during large wave events. A 6-month deployment of wave and tide gauges across two shore-normal sections of north-facing coral reef on the Roi-Namur Island on Kwajalein Atoll was conducted during 2013-2014 to quantify wave dynamics and wave-driven water levels on the fringing coral reef. Wave heights and periods on the reef flat were strongly correlated to the water levels. On the fore reef, the majority of wave energy was concentrated in the incident band (5-25 s); due to breaking at the reef crest, however, the wave energy over the reef flat was dominated by infragravity-band (25-250 s) motions. Two large wave events with heights of 6-8 m at 15 s over the fore reef were observed. During these events, infragravity-band wave heights exceeded the incident band wave heights and approximately 1.0 m of set-up was established over the innermost reef flat. This set-up enabled the propagation of large waves across the reef flat, reaching maximum heights of nearly 2 m on the innermost reef flat adjacent to the toe of the beach. XBEACH models of the instrument transects were able to replicate the incident waves, infragravity waves, and wave-driven set-up across the reef when the hydrodynamic roughness of the reef was correctly parameterized. These events led to more than 3 m of wave-driven run-up and inundation of the island that drove substantial morphological change to the beach face.

Toward laboratory torsional spine magnetic reconnection

NASA Astrophysics Data System (ADS)

Chesny, David L.; Orange, N. Brice; Oluseyi, Hakeem M.; Valletta, David R.

2017-12-01

Magnetic reconnection is a fundamental energy conversion mechanism in nature. Major attempts to study this process in controlled settings on Earth have largely been limited to reproducing approximately two-dimensional (2-D) reconnection dynamics. Other experiments describing reconnection near three-dimensional null points are non-driven, and do not induce any of the 3-D modes of spine fan, torsional fan or torsional spine reconnection. In order to study these important 3-D modes observed in astrophysical plasmas (e.g. the solar atmosphere), laboratory set-ups must be designed to induce driven reconnection about an isolated magnetic null point. As such, we consider the limited range of fundamental resistive magnetohydrodynamic (MHD) and kinetic parameters of dynamic laboratory plasmas that are necessary to induce the torsional spine reconnection (TSR) mode characterized by a driven rotational slippage of field lines - a feature that has yet to be achieved in operational laboratory magnetic reconnection experiments. Leveraging existing reconnection models, we show that within a 3$ apparatus, TSR can be achieved in dense plasma regimes ( 24~\\text{m}-3$ ) in magnetic fields of -1~\\text{T}$ . We find that MHD and kinetic parameters predict reconnection in thin current sheets on time scales of . While these plasma regimes may not explicitly replicate the plasma parameters of observed astrophysical phenomena, studying the dynamics of the TSR mode within achievable set-ups signifies an important step in understanding the fundamentals of driven 3-D magnetic reconnection and the self-organization of current sheets. Explicit control of this reconnection mode may have implications for understanding particle acceleration in astrophysical environments, and may even have practical applications to fields such as spacecraft propulsion.

Heterogeneity of spontaneous DNA replication errors in single isogenic Escherichia coli cells

PubMed Central

2018-01-01

Despite extensive knowledge of the molecular mechanisms that control mutagenesis, it is not known how spontaneous mutations are produced in cells with fully operative mutation-prevention systems. By using a mutation assay that allows visualization of DNA replication errors and stress response transcriptional reporters, we examined populations of isogenic Escherichia coli cells growing under optimal conditions without exogenous stress. We found that spontaneous DNA replication errors in proliferating cells arose more frequently in subpopulations experiencing endogenous stresses, such as problems with proteostasis, genome maintenance, and reactive oxidative species production. The presence of these subpopulations of phenotypic mutators is not expected to affect the average mutation frequency or to reduce the mean population fitness in a stable environment. However, these subpopulations can contribute to overall population adaptability in fluctuating environments by serving as a reservoir of increased genetic variability.

Behaviour and physiology shape the growth accelerations associated with predation risk, high temperatures and southern latitudes in Ischnura damselfly larvae.

PubMed

Stoks, Robby; Swillen, Ine; De Block, Marjan

2012-09-01

1. To better predict effects of climate change and predation risk on prey animals and ecosystems, we need studies documenting not only latitudinal patterns in growth rate but also growth plasticity to temperature and predation risk and the underlying proximate mechanisms: behaviour (food intake) and digestive physiology (growth efficiency). The mechanistic underpinnings of predator-induced growth increases remain especially poorly understood. 2. We reared larvae from replicated northern and southern populations of the damselfly Ischnura elegans in a common garden experiment manipulating temperature and predation risk and quantified growth rate, food intake and growth efficiency. 3. The predator-induced and temperature-induced growth accelerations were the same at both latitudes, despite considerably faster growth rates in the southern populations. While the higher growth rates in the southern populations and the high rearing temperature were driven by both an increased food intake and a higher growth efficiency, the higher growth rates under predation risk were completely driven by a higher growth efficiency, despite a lowered food intake. 4. The emerging pattern that higher growth rates associated with latitude, temperature and predation risk were all (partly or completely) mediated by a higher growth efficiency has two major implications. First, it indicates that energy allocation trade-offs and the associated physiological costs play a major role both in shaping large-scale geographic variation in growth rates and in shaping the extent and direction of growth rate plasticity. Secondly, it suggests that the efficiency of energy transfer in aquatic food chains, where damselfly larvae are important intermediate predators, will be higher in southern populations, at higher temperatures and under predation risk. This may eventually contribute to the lengthening of food chains under these conditions and highlights that the prey identity may determine the influence of predation risk on food chain length. © 2012 The Authors. Journal of Animal Ecology © 2012 British Ecological Society.

Simulation of Wind-Driven Circulation in the Salton Sea: Implications for Indigenous Ecosystems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cook, Chris B.; Orlob, Gerald T.; Huston, David W.

The Salton Sea Authority is seeking methods for reducing water levels and controlling salinity within ranges that will protect beneficial uses of the Sea, its adjacent lands, and its indigenous ecosystems. Proposed solutions include various physical changes in the bathymetry and configuration of the Sea. Because circulation in the Sea is driven primarily by wind stresses imposed on the water surface, and circulation changes are likely to affect the Sea?s quality and ecology, a methodology for quantifying the effects of specific alternatives is required. For this purpose a mathematical model for simulation of the hydrodynamic behavior of the Sea hasmore » been developed, calibrated to data gathered by a field investigation conducted in 1997, and applied to alternative schemes that will isolate sections of the southern basin. The Salton Sea Hydrodynamic/Water Quality Model is constructed using the finite element method to represent the bathymetry of the Sea in a three-dimensional grid. Given certain boundary conditions, for example wind stresses imposed on the surface, the model solves the three-dimensional equations of motion and continuity, the advection-dispersion equation, and an equation of state dependent upon temperature and salinity, to obtain temporal and spatial descriptions of velocities and temperatures over a specified period of time. The model successfully replicated principal features of the Sea's behavior, especially the persistence of a counterclockwise gyre in the southern basin and seasonal stratification. Once calibrated, the model was applied to evaluate the possible effects of changing water surface elevations in the Sea and altering its configuration to isolate sections for evaporative concentration of salts. These effects, evident in changes in velocity, were quantified with regard to their possible impacts on the aquatic habitat and the health of the Salton Sea ecology. A comparative evaluation of alternatives is presented.« less

Three-Dimensional Smoothed Particle Hydrodynamics Modeling of Preferential Flow Dynamics at Fracture Intersections on a High-Performance Computing Platform

NASA Astrophysics Data System (ADS)

Kordilla, J.; Bresinsky, L. T.

2017-12-01

The physical mechanisms that govern preferential flow dynamics in unsaturated fractured rock formations are complex and not well understood. Fracture intersections may act as an integrator of unsaturated flow, leading to temporal delay, intermittent flow and partitioning dynamics. In this work, a three-dimensional Pairwise-Force Smoothed Particle Hydrodynamics (PF-SPH) model is being applied in order to simulate gravity-driven multiphase flow at synthetic fracture intersections. SPH, as a meshless Lagrangian method, is particularly suitable for modeling deformable interfaces, such as three-phase contact dynamics of droplets, rivulets and free-surface films. The static and dynamic contact angle can be recognized as the most important parameter of gravity-driven free-surface flow. In SPH, surface tension and adhesion naturally emerges from the implemented pairwise fluid-fluid (sff) and solid-fluid (ssf) interaction force. The model was calibrated to a contact angle of 65°, which corresponds to the wetting properties of water on Poly(methyl methacrylate). The accuracy of the SPH simulations were validated against an analytical solution of Poiseuille flow between two parallel plates and against laboratory experiments. Using the SPH model, the complex flow mode transitions from droplet to rivulet flow of an experimental study were reproduced. Additionally, laboratory dimensionless scaling experiments of water droplets were successfully replicated in SPH. Finally, SPH simulations were used to investigate the partitioning dynamics of single droplets into synthetic horizontal fractures with various apertures (Δdf = 0, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0 mm) and offsets (Δdoff = -1.5, -1.0, -0.5, 0, 1.0, 2.0, 3.0 mm). Fluid masses were measured in the domains R1, R2 and R3. The perfect conditions of ideally smooth surfaces and the SPH inherent advantage of particle tracking allow the recognition of small scale partitioning mechanisms and its importance for bulk flow behavior.

A Fluorescent G-quadruplex Sensor for Chemical RNA Copying.

PubMed

Giurgiu, Constantin; Wright, Tom; O'Flaherty, Derek; Szostak, Jack

2018-06-25

Non-enzymatic RNA replication may have been one of the processes involved in the appearance of life on Earth. Attempts to recreate this process in a laboratory setting have not been successful thus far, highlighting a critical need for finding prebiotic conditions that increase the rate and the yield. Here, we present a highly parallel assay for template directed RNA synthesis that relies on the intrinsic fluorescence of a 2-aminopurine modified G-quadruplex. We demonstrate the application of the assay to examine the combined influence of multiple variables including pH, divalent metal concentrations and ribonucleotide concentrations on the copying of RNA sequences. The assay enables a direct survey of physical and chemical conditions, potentially prebiotic, which could enable the chemical replication of RNA. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficient Replication of over 180 Genetic Associations with Self-Reported Medical Data

PubMed Central

Tung, Joyce Y.; Do, Chuong B.; Hinds, David A.; Kiefer, Amy K.; Macpherson, J. Michael; Chowdry, Arnab B.; Francke, Uta; Naughton, Brian T.; Mountain, Joanna L.; Wojcicki, Anne; Eriksson, Nicholas

2011-01-01

While the cost and speed of generating genomic data have come down dramatically in recent years, the slow pace of collecting medical data for large cohorts continues to hamper genetic research. Here we evaluate a novel online framework for obtaining large amounts of medical information from a recontactable cohort by assessing our ability to replicate genetic associations using these data. Using web-based questionnaires, we gathered self-reported data on 50 medical phenotypes from a generally unselected cohort of over 20,000 genotyped individuals. Of a list of genetic associations curated by NHGRI, we successfully replicated about 75% of the associations that we expected to (based on the number of cases in our cohort and reported odds ratios, and excluding a set of associations with contradictory published evidence). Altogether we replicated over 180 previously reported associations, including many for type 2 diabetes, prostate cancer, cholesterol levels, and multiple sclerosis. We found significant variation across categories of conditions in the percentage of expected associations that we were able to replicate, which may reflect systematic inflation of the effects in some initial reports, or differences across diseases in the likelihood of misdiagnosis or misreport. We also demonstrated that we could improve replication success by taking advantage of our recontactable cohort, offering more in-depth questions to refine self-reported diagnoses. Our data suggest that online collection of self-reported data from a recontactable cohort may be a viable method for both broad and deep phenotyping in large populations. PMID:21858135

Efficient replication of over 180 genetic associations with self-reported medical data.

PubMed

Tung, Joyce Y; Do, Chuong B; Hinds, David A; Kiefer, Amy K; Macpherson, J Michael; Chowdry, Arnab B; Francke, Uta; Naughton, Brian T; Mountain, Joanna L; Wojcicki, Anne; Eriksson, Nicholas

2011-01-01

While the cost and speed of generating genomic data have come down dramatically in recent years, the slow pace of collecting medical data for large cohorts continues to hamper genetic research. Here we evaluate a novel online framework for obtaining large amounts of medical information from a recontactable cohort by assessing our ability to replicate genetic associations using these data. Using web-based questionnaires, we gathered self-reported data on 50 medical phenotypes from a generally unselected cohort of over 20,000 genotyped individuals. Of a list of genetic associations curated by NHGRI, we successfully replicated about 75% of the associations that we expected to (based on the number of cases in our cohort and reported odds ratios, and excluding a set of associations with contradictory published evidence). Altogether we replicated over 180 previously reported associations, including many for type 2 diabetes, prostate cancer, cholesterol levels, and multiple sclerosis. We found significant variation across categories of conditions in the percentage of expected associations that we were able to replicate, which may reflect systematic inflation of the effects in some initial reports, or differences across diseases in the likelihood of misdiagnosis or misreport. We also demonstrated that we could improve replication success by taking advantage of our recontactable cohort, offering more in-depth questions to refine self-reported diagnoses. Our data suggest that online collection of self-reported data from a recontactable cohort may be a viable method for both broad and deep phenotyping in large populations.

Enhanced inhibition of parvovirus B19 replication by cidofovir in extendedly exposed erythroid progenitor cells.

PubMed

Bonvicini, Francesca; Bua, Gloria; Manaresi, Elisabetta; Gallinella, Giorgio

2016-07-15

Human parvovirus B19 (B19V) commonly induces self-limiting infections but can also cause severe clinical manifestations in patients with underlying haematological disorders or with immune system deficits. Currently, therapeutic options for B19V entirely rely on symptomatic and supportive treatments since a specific antiviral therapy is not yet available. Recently a first step in the research for active compounds inhibiting B19V replication has allowed identifying the acyclic nucleoside phosphonate cidofovir (CDV). Herein, the effect of CDV against B19V replication was characterized in human erythroid progenitor cells (EPCs) cultured and infected following different experimental approaches to replicate in vitro the infection of an expanding erythroid cell population in the bone marrow. B19V replication was selectively inhibited both in infected EPCs extendedly exposed to CDV 500μM (viral inhibition 82%) and in serially infected EPCs cultures with passage of the virus progeny, constantly under drug exposure (viral inhibition 99%). In addition, a potent inhibitory effect against B19V (viral inhibition 92%) was assessed in a short-term infection of EPCs treated with CDV 500μM 1day before viral infection. In the evaluated experimental conditions, the enhanced effect of CDV against B19V might be ascribed both to the increased intracellular drug concentration achieved by extended exposure, and to a progressive reduction in efficiency of the replicative process within treated EPCs population. Copyright © 2016 Elsevier B.V. All rights reserved.

Evidence for an unorthodox firing sequence employed by the Berlin Painter. Deciphering ancient ceramic firing conditions through high-resolution material characterization and replication

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cianchetta, I.; Trentelman, K.; Maish, J.

XANES spectroscopy was used to complement the results previously obtained with Raman spectroscopy by the same group to determine the firing conditions used in the production of a single vessel painted by the Berlin Painter in the 5th century B.C. The vessel, part of the collection of the J. Paul Getty Museum, presents a complicated layered architecture of black and red gloss, with different stratigraphies present on the interior and exterior surfaces. The study of two samples, one each from the interior and exterior surface of the vessel, was performed with the complementary analytical techniques of X-ray nano- and micro-spectroscopymore » (X-ray fluorescence spectroscopy (XRF) and full-field transmission X-ray micro-spectroscopy (FF-XANES) across the Fe K edge), and supported by a replication study. The replicates, made in a laboratory furnace providing complete control over the firing temperature and oxygen partial pressure, provided a paradigm for the comparison of the mineralogical phases observed in the ancient samples, which led to a deeper understanding of the firing conditions necessary for the production of the Berlin Painter's vessel. Our results confirm the necessity of multiple firings and painting applications to obtain the Berlin Painter's architecture and provide a further example of the multiplicity of techniques and practices employed by the potters of the Kerameikos in ancient Athens.« less

Evidence for an unorthodox firing sequence employed by the Berlin Painter. Deciphering ancient ceramic firing conditions through high-resolution material characterization and replication

DOE PAGES

Cianchetta, I.; Trentelman, K.; Maish, J.; ...

2014-12-10

XANES spectroscopy was used to complement the results previously obtained with Raman spectroscopy by the same group to determine the firing conditions used in the production of a single vessel painted by the Berlin Painter in the 5th century B.C. The vessel, part of the collection of the J. Paul Getty Museum, presents a complicated layered architecture of black and red gloss, with different stratigraphies present on the interior and exterior surfaces. The study of two samples, one each from the interior and exterior surface of the vessel, was performed with the complementary analytical techniques of X-ray nano- and micro-spectroscopymore » (X-ray fluorescence spectroscopy (XRF) and full-field transmission X-ray micro-spectroscopy (FF-XANES) across the Fe K edge), and supported by a replication study. The replicates, made in a laboratory furnace providing complete control over the firing temperature and oxygen partial pressure, provided a paradigm for the comparison of the mineralogical phases observed in the ancient samples, which led to a deeper understanding of the firing conditions necessary for the production of the Berlin Painter's vessel. Our results confirm the necessity of multiple firings and painting applications to obtain the Berlin Painter's architecture and provide a further example of the multiplicity of techniques and practices employed by the potters of the Kerameikos in ancient Athens.« less

No Evidence That Gratitude Enhances Neural Performance Monitoring or Conflict-Driven Control

PubMed Central

Saunders, Blair; He, Frank F. H.; Inzlicht, Michael

2015-01-01

It has recently been suggested that gratitude can benefit self-regulation by reducing impulsivity during economic decision making. We tested if comparable benefits of gratitude are observed for neural performance monitoring and conflict-driven self-control. In a pre-post design, 61 participants were randomly assigned to either a gratitude or happiness condition, and then performed a pre-induction flanker task. Subsequently, participants recalled an autobiographical event where they had felt grateful or happy, followed by a post-induction flanker task. Despite closely following existing protocols, participants in the gratitude condition did not report elevated gratefulness compared to the happy group. In regard to self-control, we found no association between gratitude—operationalized by experimental condition or as a continuous predictor—and any control metric, including flanker interference, post-error adjustments, or neural monitoring (the error-related negativity, ERN). Thus, while gratitude might increase economic patience, such benefits may not generalize to conflict-driven control processes. PMID:26633830

No Evidence That Gratitude Enhances Neural Performance Monitoring or Conflict-Driven Control.

PubMed

Saunders, Blair; He, Frank F H; Inzlicht, Michael

2015-01-01

It has recently been suggested that gratitude can benefit self-regulation by reducing impulsivity during economic decision making. We tested if comparable benefits of gratitude are observed for neural performance monitoring and conflict-driven self-control. In a pre-post design, 61 participants were randomly assigned to either a gratitude or happiness condition, and then performed a pre-induction flanker task. Subsequently, participants recalled an autobiographical event where they had felt grateful or happy, followed by a post-induction flanker task. Despite closely following existing protocols, participants in the gratitude condition did not report elevated gratefulness compared to the happy group. In regard to self-control, we found no association between gratitude--operationalized by experimental condition or as a continuous predictor--and any control metric, including flanker interference, post-error adjustments, or neural monitoring (the error-related negativity, ERN). Thus, while gratitude might increase economic patience, such benefits may not generalize to conflict-driven control processes.

Role of magnetic fluctuations in mode selection of magnetically driven instabilities

NASA Astrophysics Data System (ADS)

Dan, Jia-Kun; Ren, Xiao-Dong; Huang, Xian-Bin; Ouyang, Kai; Chen, Guang-Hua

2014-12-01

The influences of magnetic fluctuations on quasiperiodic structure formation and fundamental wavelength selection of the instability have been studied using two 25-μm-diameter tungsten wires on a 100 ns rise time, 220 kA pulsed power facility. Two different load configurations were adopted to make end surfaces of electrodes approximately satisfy reflecting and absorbing boundary conditions, respectively. The experimental results that the fundamental wavelength in the case of absorbing boundary condition is about one half of that in the case of reflecting boundary condition have demonstrated that magnetic fluctuations appear to play a key role in mode selection of magnetically driven instabilities. The dominant wavelength should be proportional to magnetic field and inversely proportional to square root of mass density, provided that the magnetosonic wave propagating perpendicular to magnetic fields provides a leading candidate for magnetic fluctuations. Therefore, magnetic fluctuation is one of the three key perturbations, along with surface contaminants and surface roughness, that seeds magnetically driven instabilities.

Data-driven mono-component feature identification via modified nonlocal means and MEWT for mechanical drivetrain fault diagnosis

NASA Astrophysics Data System (ADS)

Pan, Jun; Chen, Jinglong; Zi, Yanyang; Yuan, Jing; Chen, Binqiang; He, Zhengjia

2016-12-01

It is significant to perform condition monitoring and fault diagnosis on rolling mills in steel-making plant to ensure economic benefit. However, timely fault identification of key parts in a complicated industrial system under operating condition is still a challenging task since acquired condition signals are usually multi-modulated and inevitably mixed with strong noise. Therefore, a new data-driven mono-component identification method is proposed in this paper for diagnostic purpose. First, the modified nonlocal means algorithm (NLmeans) is proposed to reduce noise in vibration signals without destroying its original Fourier spectrum structure. During the modified NLmeans, two modifications are investigated and performed to improve denoising effect. Then, the modified empirical wavelet transform (MEWT) is applied on the de-noised signal to adaptively extract empirical mono-component modes. Finally, the modes are analyzed for mechanical fault identification based on Hilbert transform. The results show that the proposed data-driven method owns superior performance during system operation compared with the MEWT method.

Active machine learning-driven experimentation to determine compound effects on protein patterns

PubMed Central

Naik, Armaghan W; Kangas, Joshua D; Sullivan, Devin P; Murphy, Robert F

2016-01-01

High throughput screening determines the effects of many conditions on a given biological target. Currently, to estimate the effects of those conditions on other targets requires either strong modeling assumptions (e.g. similarities among targets) or separate screens. Ideally, data-driven experimentation could be used to learn accurate models for many conditions and targets without doing all possible experiments. We have previously described an active machine learning algorithm that can iteratively choose small sets of experiments to learn models of multiple effects. We now show that, with no prior knowledge and with liquid handling robotics and automated microscopy under its control, this learner accurately learned the effects of 48 chemical compounds on the subcellular localization of 48 proteins while performing only 29% of all possible experiments. The results represent the first practical demonstration of the utility of active learning-driven biological experimentation in which the set of possible phenotypes is unknown in advance. DOI: http://dx.doi.org/10.7554/eLife.10047.001 PMID:26840049

The control of paramyxovirus genome hexamer length and mRNA editing.

PubMed

Matsumoto, Yusuke; Ohta, Keisuke; Kolakofsky, Daniel; Nishio, Machiko

2018-04-01

The unusual ability of a human parainfluenza virus type 2 (hPIV2) nucleoprotein point mutation (NP Q202A ) to strongly enhance minigenome replication was found to depend on the absence of a functional, internal element of the bipartite replication promoter (CRII). This point mutation allows relatively robust CRII-minus minigenome replication in a CRII-independent manner, under conditions in which NP wt is essentially inactive. The nature of the amino acid at position 202 apparently controls whether viral RNA-dependent RNA polymerase (vRdRp) can, or cannot, initiate RNA synthesis in a CRII-independent manner. By repressing genome synthesis when vRdRp cannot correctly interact with CRII, gln 202 of N, the only residue of the RNA-binding groove that contacts a nucleotide base in the N-RNA, acts as a gatekeeper for wild-type (CRII-dependent) RNA synthesis. This ensures that only hexamer-length genomes are replicated, and that the critical hexamer phase of the cis -acting mRNA editing sequence is maintained. © 2018 Matsumoto et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

TRANSFER OF AVERSIVE RESPONDENT ELICITATION IN ACCORDANCE WITH EQUIVALENCE RELATIONS

PubMed Central

Valverde, Miguel RodrÍguez; Luciano, Carmen; Barnes-Holmes, Dermot

2009-01-01

The present study investigates the transfer of aversively conditioned respondent elicitation through equivalence classes, using skin conductance as the measure of conditioning. The first experiment is an attempt to replicate Experiment 1 in Dougher, Augustson, Markham, Greenway, and Wulfert (1994), with different temporal parameters in the aversive conditioning procedure employed. Match-to-sample procedures were used to teach 17 participants two 4-member equivalence classes. Then, one member of one class was paired with electric shock and one member of the other class was presented without shock. The remaining stimuli from each class were presented in transfer tests. Unlike the findings in the original study, transfer of conditioning was not achieved. In Experiment 2, similar procedures were used with 30 participants, although several modifications were introduced (formation of five-member classes, direct conditioning with several elements of each class, random sequences of stimulus presentation in transfer tests, reversal in aversive conditioning contingencies). More than 80% of participants who had shown differential conditioning also showed the transfer of function effect. Moreover, this effect was replicated within subjects for 3 participants. This is the first demonstration of the transfer of aversive respondent elicitation through stimulus equivalence classes with the presentation of transfer test trials in random order. The latter prevents the possibility that transfer effects are an artefact of transfer test presentation order. PMID:20119523

Phonation interval modification and speech performance quality during fluency-inducing conditions by adults who stutter

PubMed Central

Ingham, Roger J.; Bothe, Anne K.; Wang, Yuedong; Purkhiser, Krystal; New, Anneliese

2012-01-01

Purpose To relate changes in four variables previously defined as characteristic of normally fluent speech to changes in phonatory behavior during oral reading by persons who stutter (PWS) and normally fluent controls under multiple fluency-inducing (FI) conditions. Method Twelve PWS and 12 controls each completed 4 ABA experiments. During A phases, participants read normally. B phases were 4 different FI conditions: auditory masking, chorus reading, whispering, and rhythmic stimulation. Dependent variables were the durations of accelerometer-recorded phonated intervals; self-judged speech effort; and observer-judged stuttering frequency, speech rate, and speech naturalness. The method enabled a systematic replication of Ingham et al. (2009). Results All FI conditions resulted in decreased stuttering and decreases in the number of short phonated intervals, as compared with baseline conditions, but the only FI condition that satisfied all four characteristics of normally fluent speech was chorus reading. Increases in longer phonated intervals were associated with decreased stuttering but also with poorer naturalness and/or increased speech effort. Previous findings concerning the effects of FI conditions on speech naturalness and effort were replicated. Conclusions Measuring all relevant characteristics of normally fluent speech, in the context of treatments that aim to reduce the occurrence of short-duration PIs, may aid the search for an explanation of the nature of stuttering and may also maximize treatment outcomes for adults who stutter. PMID:22365886

Initial conditions and modeling for simulations of shock driven turbulent material mixing

DOE PAGES

Grinstein, Fernando F.

2016-11-17

Here, we focus on the simulation of shock-driven material mixing driven by flow instabilities and initial conditions (IC). Beyond complex multi-scale resolution issues of shocks and variable density turbulence, me must address the equally difficult problem of predicting flow transition promoted by energy deposited at the material interfacial layer during the shock interface interactions. Transition involves unsteady large-scale coherent-structure dynamics capturable by a large eddy simulation (LES) strategy, but not by an unsteady Reynolds-Averaged Navier–Stokes (URANS) approach based on developed equilibrium turbulence assumptions and single-point-closure modeling. On the engineering end of computations, such URANS with reduced 1D/2D dimensionality and coarsermore » grids, tend to be preferred for faster turnaround in full-scale configurations.« less

Stimulus-driven attentional capture by subliminal onset cues.

PubMed

Schoeberl, Tobias; Fuchs, Isabella; Theeuwes, Jan; Ansorge, Ulrich

2015-04-01

In two experiments, we tested whether subliminal abrupt onset cues capture attention in a stimulus-driven way. An onset cue was presented 16 ms prior to the stimulus display that consisted of clearly visible color targets. The onset cue was presented either at the same side as the target (the valid cue condition) or on the opposite side of the target (the invalid cue condition). Because the onset cue was presented 16 ms before other placeholders were presented, the cue was subliminal to the participant. To ensure that this subliminal cue captured attention in a stimulus-driven way, the cue's features did not match the top-down attentional control settings of the participants: (1) The color of the cue was always different than the color of the non-singleton targets ensuring that a top-down set for a specific color or for a singleton would not match the cue, and (2) colored targets and distractors had the same objective luminance (measured by the colorimeter) and subjective lightness (measured by flicker photometry), preventing a match between the top-down set for target and cue contrast. Even though a match between the cues and top-down settings was prevented, in both experiments, the cues captured attention, with faster response times in valid than invalid cue conditions (Experiments 1 and 2) and faster response times in valid than the neutral conditions (Experiment 2). The results support the conclusion that subliminal cues capture attention in a stimulus-driven way.

Class I Histone Deacetylase HDAC1 and WRN RECQ Helicase Contribute Additively to Protect Replication Forks upon Hydroxyurea-induced Arrest.

PubMed

Kehrli, Keffy; Phelps, Michael; Lazarchuk, Pavlo; Chen, Eleanor; Monnat, Ray; Sidorova, Julia M

2016-11-18

The WRN helicase/exonuclease is mutated in Werner syndrome of genomic instability and premature aging. WRN-depleted fibroblasts, although remaining largely viable, have a reduced capacity to maintain replication forks active during a transient hydroxyurea-induced arrest. A strand exchange protein, RAD51, is also required for replication fork maintenance, and here we show that recruitment of RAD51 to stalled forks is reduced in the absence of WRN. We performed a siRNA screen for genes that are required for viability of WRN-depleted cells after hydroxyurea treatment, and identified HDAC1, a member of the class I histone deacetylase family. One of the functions of HDAC1, which it performs together with a close homolog HDAC2, is deacetylation of new histone H4 deposited at replication forks. We show that HDAC1 depletion exacerbates defects in fork reactivation and progression after hydroxyurea treatment observed in WRN- or RAD51-deficient cells. The additive WRN, HDAC1 loss-of-function phenotype is also observed with a catalytic mutant of HDAC1; however, it does not correlate with changes in histone H4 deacetylation at replication forks. On the other hand, inhibition of histone deacetylation by an inhibitor specific to HDACs 1-3, CI-994, correlates with increased processing of newly synthesized DNA strands in hydroxyurea-stalled forks. WRN co-precipitates with HDAC1 and HDAC2. Taken together, our findings indicate that WRN interacts with HDACs 1 and 2 to facilitate activity of stalled replication forks under conditions of replication stress. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Dense CO in Mrk 71-A: Superwind Suppressed in a Young Super Star Cluster

NASA Astrophysics Data System (ADS)

Oey, M. S.; Herrera, C. N.; Silich, Sergiy; Reiter, Megan; James, Bethan L.; Jaskot, A. E.; Micheva, Genoveva

2017-11-01

We report the detection of CO(J=2-1) coincident with the super star cluster (SSC) Mrk 71-A in the nearby Green Pea analog galaxy, NGC 2366. Our observations with the Northern Extended Millimeter Array reveal a compact, ˜7 pc, molecular cloud whose mass ({10}5 {M}⊙ ) is similar to that of the SSC, consistent with a high star formation efficiency, on the order of 0.5. There are two spatially distinct components separated by 11 {km} {{{s}}}-1. If expanding, these could be due to momentum-driven stellar wind feedback. Alternatively, we may be seeing remnants of the infalling, colliding clouds responsible for triggering the SSC formation. The kinematics are also consistent with a virialized system. These extreme, high-density, star-forming conditions inhibit energy-driven feedback; the co-spatial existence of a massive, molecular cloud with the SSC supports this scenario, and we quantitatively confirm that any wind-driven feedback in Mrk 71-A is momentum-driven, rather than energy-driven. Since Mrk 71-A is a candidate Lyman continuum emitter, this implies that energy-driven superwinds may not be a necessary condition for the escape of ionizing radiation. In addition, the detection of nebular continuum emission yields an accurate astrometric position for the Mrk 71-A. We also detect four other massive molecular clouds in this giant star-forming complex.

Plasmon-driven sequential chemical reactions in an aqueous environment.

PubMed

Zhang, Xin; Wang, Peijie; Zhang, Zhenglong; Fang, Yurui; Sun, Mengtao

2014-06-24

Plasmon-driven sequential chemical reactions were successfully realized in an aqueous environment. In an electrochemical environment, sequential chemical reactions were driven by an applied potential and laser irradiation. Furthermore, the rate of the chemical reaction was controlled via pH, which provides indirect evidence that the hot electrons generated from plasmon decay play an important role in plasmon-driven chemical reactions. In acidic conditions, the hot electrons were captured by the abundant H(+) in the aqueous environment, which prevented the chemical reaction. The developed plasmon-driven chemical reactions in an aqueous environment will significantly expand the applications of plasmon chemistry and may provide a promising avenue for green chemistry using plasmon catalysis in aqueous environments under irradiation by sunlight.

Plasmon-driven sequential chemical reactions in an aqueous environment

PubMed Central

Zhang, Xin; Wang, Peijie; Zhang, Zhenglong; Fang, Yurui; Sun, Mengtao

2014-01-01

Plasmon-driven sequential chemical reactions were successfully realized in an aqueous environment. In an electrochemical environment, sequential chemical reactions were driven by an applied potential and laser irradiation. Furthermore, the rate of the chemical reaction was controlled via pH, which provides indirect evidence that the hot electrons generated from plasmon decay play an important role in plasmon-driven chemical reactions. In acidic conditions, the hot electrons were captured by the abundant H+ in the aqueous environment, which prevented the chemical reaction. The developed plasmon-driven chemical reactions in an aqueous environment will significantly expand the applications of plasmon chemistry and may provide a promising avenue for green chemistry using plasmon catalysis in aqueous environments under irradiation by sunlight. PMID:24958029

Genetic variants associated with warfarin dose in African-American individuals: a genome-wide association study.

PubMed

Perera, Minoli A; Cavallari, Larisa H; Limdi, Nita A; Gamazon, Eric R; Konkashbaev, Anuar; Daneshjou, Roxana; Pluzhnikov, Anna; Crawford, Dana C; Wang, Jelai; Liu, Nianjun; Tatonetti, Nicholas; Bourgeois, Stephane; Takahashi, Harumi; Bradford, Yukiko; Burkley, Benjamin M; Desnick, Robert J; Halperin, Jonathan L; Khalifa, Sherief I; Langaee, Taimour Y; Lubitz, Steven A; Nutescu, Edith A; Oetjens, Matthew; Shahin, Mohamed H; Patel, Shitalben R; Sagreiya, Hersh; Tector, Matthew; Weck, Karen E; Rieder, Mark J; Scott, Stuart A; Wu, Alan H B; Burmester, James K; Wadelius, Mia; Deloukas, Panos; Wagner, Michael J; Mushiroda, Taisei; Kubo, Michiaki; Roden, Dan M; Cox, Nancy J; Altman, Russ B; Klein, Teri E; Nakamura, Yusuke; Johnson, Julie A

2013-08-31

VKORC1 and CYP2C9 are important contributors to warfarin dose variability, but explain less variability for individuals of African descent than for those of European or Asian descent. We aimed to identify additional variants contributing to warfarin dose requirements in African Americans. We did a genome-wide association study of discovery and replication cohorts. Samples from African-American adults (aged ≥18 years) who were taking a stable maintenance dose of warfarin were obtained at International Warfarin Pharmacogenetics Consortium (IWPC) sites and the University of Alabama at Birmingham (Birmingham, AL, USA). Patients enrolled at IWPC sites but who were not used for discovery made up the independent replication cohort. All participants were genotyped. We did a stepwise conditional analysis, conditioning first for VKORC1 -1639G→A, followed by the composite genotype of CYP2C9*2 and CYP2C9*3. We prespecified a genome-wide significance threshold of p<5×10(-8) in the discovery cohort and p<0·0038 in the replication cohort. The discovery cohort contained 533 participants and the replication cohort 432 participants. After the prespecified conditioning in the discovery cohort, we identified an association between a novel single nucleotide polymorphism in the CYP2C cluster on chromosome 10 (rs12777823) and warfarin dose requirement that reached genome-wide significance (p=1·51×10(-8)). This association was confirmed in the replication cohort (p=5·04×10(-5)); analysis of the two cohorts together produced a p value of 4·5×10(-12). Individuals heterozygous for the rs12777823 A allele need a dose reduction of 6·92 mg/week and those homozygous 9·34 mg/week. Regression analysis showed that the inclusion of rs12777823 significantly improves warfarin dose variability explained by the IWPC dosing algorithm (21% relative improvement). A novel CYP2C single nucleotide polymorphism exerts a clinically relevant effect on warfarin dose in African Americans, independent of CYP2C9*2 and CYP2C9*3. Incorporation of this variant into pharmacogenetic dosing algorithms could improve warfarin dose prediction in this population. National Institutes of Health, American Heart Association, Howard Hughes Medical Institute, Wisconsin Network for Health Research, and the Wellcome Trust. Copyright © 2013 Elsevier Ltd. All rights reserved.

Genetics Home Reference: 5q31.3 microdeletion syndrome

MedlinePlus

... of the characteristic features of the condition. The protein produced from the PURA gene, called Pur-alpha ( ... aiding in the copying (replication) of DNA. This protein is especially important for normal brain development; it ...

Replicative Functions of Minute Virus of Mice NS1 Protein Are Regulated In Vitro by Phosphorylation through Protein Kinase C

PubMed Central

Nüesch, Jürg P. F.; Dettwiler, Sabine; Corbau, Romuald; Rommelaere, Jean

1998-01-01

NS1, the major nonstructural protein of the parvovirus minute virus of mice, is a multifunctional phosphoprotein which is involved in cytotoxicity, transcriptional regulation, and initiation of viral DNA replication. For coordination of these various functions during virus propagation, NS1 has been proposed to be regulated by posttranslational modifications, in particular phosphorylation. Recent in vitro studies (J. P. F. Nüesch, R. Corbau, P. Tattersall, and J. Rommelaere, J. Virol. 72:8002–8012, 1998) provided evidence that distinct NS1 activities, notably the intrinsic helicase function, are modulated by the phosphorylation state of the protein. In order to study the dependence of the initiation of viral DNA replication on NS1 phosphorylation and to identify the protein kinases involved, we established an in vitro replication system that is devoid of endogenous protein kinases and is based on plasmid substrates containing the minimal left-end origins of replication. Cellular components necessary to drive NS1-dependent rolling-circle replication (RCR) were freed from endogenous serine/threonine protein kinases by affinity chromatography, and the eukaryotic DNA polymerases were replaced by the bacteriophage T4 DNA polymerase. While native NS1 (NS1P) supported RCR under these conditions, dephosphorylated NS1 (NS1O) was impaired. Using fractionated HeLa cell extracts, we identified two essential protein components which are able to phosphorylate NS1O, are enriched in protein kinase C (PKC), and, when present together, reactivate NS1O for replication. One of these components, containing atypical PKC, was sufficient to restore NS1O helicase activity. The requirement of NS1O reactivation for characteristic PKC cofactors such as Ca2+/phosphatidylserine or phorbol esters strongly suggests the involvement of this protein kinase family in regulation of NS1 replicative functions in vitro. PMID:9811734

Rod- versus cone-driven ERGs at different stimulus sizes in normal subjects and retinitis pigmentosa patients.

PubMed

Aher, Avinash J; McKeefry, Declan J; Parry, Neil R A; Maguire, John; Murray, I J; Tsai, Tina I; Huchzermeyer, Cord; Kremers, Jan

2018-02-01

To study how rod- and cone-driven responses depend on stimulus size in normal subjects and patients with retinitis pigmentosa (RP), and to show that comparisons between responses to full-field (FF) and smaller stimuli can be useful in diagnosing and monitoring disorders of the peripheral retina without the need for lengthy dark adaptation periods. The triple silent substitution technique was used to isolate L-cone-, M-cone- and rod-driven ERGs with 19, 18 and 33% photoreceptor contrasts, respectively, under identical mean luminance conditions. Experiments were conducted on five normal subjects and three RP patients. ERGs on control subjects were recorded at nine different temporal frequencies (between 2 and 60 Hz) for five different stimulus sizes: FF, 70°, 60°, 50° and 40° diameter circular stimuli. Experiments on RP patients involved rod- and L-cone-driven ERG measurements with FF and 40° stimuli at 8 and 48 Hz. Response amplitudes were defined as those of the first harmonic component after Fourier analysis. In normal subjects, rod-driven responses displayed a fundamentally different behavior than cone-driven responses, particularly at low temporal frequencies. At low and intermediate temporal frequencies (≤ 12 Hz), rod-driven signals increased by a factor of about four when measured with smaller stimuli. In contrast, L- and M-cone-driven responses in this frequency region did not change substantially with stimulus size. At high temporal frequencies (≥ 24 Hz), both rod- and cone-driven response amplitudes decreased with decreasing stimulus size. Signals obtained from rod-isolating stimuli under these conditions are likely artefactual. Interestingly, in RP patients, both rod-driven and L-cone-driven ERGs were similar using 40° and FF stimuli. The increased responses with smaller stimuli in normal subjects to rod-isolating stimuli indicate that a fundamentally different mechanism drives the ERGs in comparison with the cone-driven responses. We propose that the increased responses are caused by stray light stimulating the peripheral retina, thereby allowing peripheral rod-driven function to be studied using the triple silent substitution technique at photopic luminances. The method is effective in studying impaired peripheral rod- and cone- function in RP patients.

Accurate position estimation methods based on electrical impedance tomography measurements

NASA Astrophysics Data System (ADS)

Vergara, Samuel; Sbarbaro, Daniel; Johansen, T. A.

2017-08-01

Electrical impedance tomography (EIT) is a technology that estimates the electrical properties of a body or a cross section. Its main advantages are its non-invasiveness, low cost and operation free of radiation. The estimation of the conductivity field leads to low resolution images compared with other technologies, and high computational cost. However, in many applications the target information lies in a low intrinsic dimensionality of the conductivity field. The estimation of this low-dimensional information is addressed in this work. It proposes optimization-based and data-driven approaches for estimating this low-dimensional information. The accuracy of the results obtained with these approaches depends on modelling and experimental conditions. Optimization approaches are sensitive to model discretization, type of cost function and searching algorithms. Data-driven methods are sensitive to the assumed model structure and the data set used for parameter estimation. The system configuration and experimental conditions, such as number of electrodes and signal-to-noise ratio (SNR), also have an impact on the results. In order to illustrate the effects of all these factors, the position estimation of a circular anomaly is addressed. Optimization methods based on weighted error cost functions and derivate-free optimization algorithms provided the best results. Data-driven approaches based on linear models provided, in this case, good estimates, but the use of nonlinear models enhanced the estimation accuracy. The results obtained by optimization-based algorithms were less sensitive to experimental conditions, such as number of electrodes and SNR, than data-driven approaches. Position estimation mean squared errors for simulation and experimental conditions were more than twice for the optimization-based approaches compared with the data-driven ones. The experimental position estimation mean squared error of the data-driven models using a 16-electrode setup was less than 0.05% of the tomograph radius value. These results demonstrate that the proposed approaches can estimate an object’s position accurately based on EIT measurements if enough process information is available for training or modelling. Since they do not require complex calculations it is possible to use them in real-time applications without requiring high-performance computers.

Open-ocean boundary conditions from interior data: Local and remote forcing of Massachusetts Bay

USGS Publications Warehouse

Bogden, P.S.; Malanotte-Rizzoli, P.; Signell, R.

1996-01-01

Massachusetts and Cape Cod Bays form a semienclosed coastal basin that opens onto the much larger Gulf of Maine. Subtidal circulation in the bay is driven by local winds and remotely driven flows from the gulf. The local-wind forced flow is estimated with a regional shallow water model driven by wind measurements. The model uses a gravity wave radiation condition along the open-ocean boundary. Results compare reasonably well with observed currents near the coast. In some offshore regions however, modeled flows are an order of magnitude less energetic than the data. Strong flows are observed even during periods of weak local wind forcing. Poor model-data comparisons are attributable, at least in part, to open-ocean boundary conditions that neglect the effects of remote forcing. Velocity measurements from within Massachusetts Bay are used to estimate the remotely forced component of the flow. The data are combined with shallow water dynamics in an inverse-model formulation that follows the theory of Bennett and McIntosh [1982], who considered tides. We extend their analysis to consider the subtidal response to transient forcing. The inverse model adjusts the a priori open-ocean boundary condition, thereby minimizing a combined measure of model-data misfit and boundary condition adjustment. A "consistency criterion" determines the optimal trade-off between the two. The criterion is based on a measure of plausibility for the inverse solution. The "consistent" inverse solution reproduces 56% of the average squared variation in the data. The local-wind-driven flow alone accounts for half of the model skill. The other half is attributable to remotely forced flows from the Gulf of Maine. The unexplained 44% comes from measurement errors and model errors that are not accounted for in the analysis. 

Bottom-up driven involuntary auditory evoked field change: constant sound sequencing amplifies but does not sharpen neural activity.

PubMed

Okamoto, Hidehiko; Stracke, Henning; Lagemann, Lothar; Pantev, Christo

2010-01-01

The capability of involuntarily tracking certain sound signals during the simultaneous presence of noise is essential in human daily life. Previous studies have demonstrated that top-down auditory focused attention can enhance excitatory and inhibitory neural activity, resulting in sharpening of frequency tuning of auditory neurons. In the present study, we investigated bottom-up driven involuntary neural processing of sound signals in noisy environments by means of magnetoencephalography. We contrasted two sound signal sequencing conditions: "constant sequencing" versus "random sequencing." Based on a pool of 16 different frequencies, either identical (constant sequencing) or pseudorandomly chosen (random sequencing) test frequencies were presented blockwise together with band-eliminated noises to nonattending subjects. The results demonstrated that the auditory evoked fields elicited in the constant sequencing condition were significantly enhanced compared with the random sequencing condition. However, the enhancement was not significantly different between different band-eliminated noise conditions. Thus the present study confirms that by constant sound signal sequencing under nonattentive listening the neural activity in human auditory cortex can be enhanced, but not sharpened. Our results indicate that bottom-up driven involuntary neural processing may mainly amplify excitatory neural networks, but may not effectively enhance inhibitory neural circuits.

Variation of Magnetic Field (By , Bz) Polarity and Statistical Analysis of Solar Wind Parameters during the Magnetic Storm Period

NASA Astrophysics Data System (ADS)

Moon, Ga-Hee

2011-06-01

It is generally believed that the occurrence of a magnetic storm depends upon the solar wind conditions, particularly the southward interplanetary magnetic field (IMF) component. To understand the relationship between solar wind parameters and magnetic storms, variations in magnetic field polarity and solar wind parameters during magnetic storms are examined. A total of 156 storms during the period of 1997~2003 are used. According to the interplanetary driver, magnetic storms are divided into three types, which are coronal mass ejection (CME)-driven storms, co-rotating interaction region (CIR)-driven storms, and complicated type storms. Complicated types were not included in this study. For this purpose, the manner in which the direction change of IMF By and Bz components (in geocentric solar magnetospheric coordinate system coordinate) during the main phase is related with the development of the storm is examined. The time-integrated solar wind parameters are compared with the time-integrated disturbance storm time (Dst) index during the main phase of each magnetic storm. The time lag with the storm size is also investigated. Some results are worth noting: CME-driven storms, under steady conditions of Bz < 0, represent more than half of the storms in number. That is, it is found that the average number of storms for negative sign of IMF Bz (T1~T4) is high, at 56.4%, 53.0%, and 63.7% in each storm category, respectively. However, for the CIR-driven storms, the percentage of moderate storms is only 29.2%, while the number of intense storms is more than half (60.0%) under the Bz < 0 condition. It is found that the correlation is highest between the time-integrated IMF Bz and the time-integrated Dst index for the CME-driven storms. On the other hand, for the CIR-driven storms, a high correlation is found, with the correlation coefficient being 0.93, between time-integrated Dst index and time-integrated solar wind speed, while a low correlation, 0.51, is found between timeintegrated Bz and time-integrated Dst index. The relationship between storm size and time lag in terms of hours from Bz minimum to Dst minimum values is investigated. For the CME-driven storms, time lag of 26% of moderate storms is one hour, whereas time lag of 33% of moderate storms is two hours for the CIR-driven storms. The average values of solar wind parameters for the CME and CIR-driven storms are also examined. The average values of |Dstmin| and |Bzmin| for the CME-driven storms are higher than those of CIR-driven storms, while the average value of temperature is lower.

Boundary Conditions for the Maintenance of Memory by PKM[zeta] in Neocortex

ERIC Educational Resources Information Center

Shema, Reul; Hazvi, Shoshi; Sacktor, Todd C.; Dudai, Yadin

2009-01-01

We report here that ZIP, a selective inhibitor of the atypical protein kinase C isoform PKM[zeta], abolishes very long-term conditioned taste aversion (CTA) associations in the insular cortex of the behaving rat, at least 3 mo after encoding. The effect of ZIP is not replicated by a general serine/threonine protein kinase inhibitor that is…

Temperature and nutrient effects on periphyton associated ...

EPA Pesticide Factsheets

Nutrient pollution is a leading cause of water quality impairments and degraded aquatic ecosystem condition. Reliable and reproducible indicators of ecosystem condition are needed to help manage nutrient pollution. The diatom component of periphyton has been used as a water quality indicator due to identifiable cell morphology and existence of relationships between nutrient concentration and diatom community composition. However, morphological identification of diatoms requires highly specialized personnel, is very time consuming, and can produce variable results, suggesting the need for alternative methods that are less expensive and more reproducible. DNA sequencing of the bacterial 16S rRNA gene is well documented and provides genus-level resolution of the community structure. The goal of this study was to evaluate the effects of nutrient loading and temperature on periphyton-associated bacterial communities using standard periphytometer techniques and next generation sequencing technologies. Continuous flow mesocosms were established in an eight tank system consisting of two temperature conditions (10°C and 20°C) and four nutrient conditions (1x to 6x ambient concentrations). Experimental conditions were replicated in July/August 2013 and September 2013. Replicate DNA samples were extracted and the 16S rRNA gene was sequenced using universal Bacterial primers. Initial analyses revealed strong differences in community structure based on temperature (p <

Replicating and extending Bourdon's (1902) experiment on motion parallax.

PubMed

Ono, Hiroshi; Lillakas, Linda; Kapoor, Anjani; Wong, Irene

2013-01-01

Bourdon conducted the first laboratory experiment on observer-produced motion parallax as a cue to depth. In three experiments, we replicated and extended Bourdon's experiment. In experiment 1, we reproduced his finding: when the two cues, motion parallax and relative height, were combined, accuracy of depth perception was high, and when the two cues were in conflict, accuracy was lower. In experiment 2, the relative height cue was replaced with relative retinal image size. As in experiment 1, when the two cues (motion parallax and relative retinal image size) were combined, accuracy was high, but when they were in conflict, it was lower. In experiment 3, the stimuli from experiments 1 and 2 were viewed monocularly with head movement and binocularly without head movement. In the binocular conditions, accuracy, certainty, and the extent of perceived depth were higher than in the monocular condition. In the conflict conditions, accuracy, certainty, and the extent of perceived depth were lower than in the no-conflict condition, but the extent of perceived motion was larger. These results are discussed in terms of recent findings about the effectiveness of motion parallax as a cue for depth.

Tag mechanism as a strategy for the RNA replicase to resist parasites in the RNA world

PubMed Central

Yu, Chunwu; Zhang, Wentao; Yin, Shaolin; Chen, Yong; Feng, Yu; Ma, Wentao

2017-01-01

The idea that life may have started with an “RNA world” is attractive. Wherein, a crucial event (perhaps at the very beginning of the scenario) should have been the emergence of a ribozyme that catalyzes its own replication, i.e., an RNA replicase. Although now there is experimental evidence supporting the chemical feasibility of such a ribozyme, the evolutionary dynamics of how the replicase could overcome the “parasite” problem (because other RNAs may also exploit this ribozyme) and thrive, as described in the scenario, remains unclear. It has been suggested that spatial limitation may have been important for the replicase to confront parasites. However, more studies showed that such a mechanism is not sufficient when this ribozyme’s altruistic trait is taken into full consideration. “Tag mechanism”, which means labeling the replicase with a short subsequence for recognition in replication, may be a further mechanism supporting the thriving of the replicase. However, because parasites may also “equip” themselves with the tag, it is far from clear whether the tag mechanism could take effect. Here, we conducted a computer simulation using a Monte-Carlo model to study the evolutionary dynamics surrounding the development of a tag-driven (polymerase-type) RNA replicase in the RNA world. We concluded that (1) with the tag mechanism the replicase could resist the parasites and become prosperous, (2) the main underlying reason should be that the parasitic molecules, especially those strong parasites, are more difficult to appear in the tag-driven system, and (3) the tag mechanism has a synergic effect with the spatial limitation mechanism–while the former provides “time” for the replicase to escape from parasites, the latter provides “space” for the replicase to escape. Notably, tags may readily serve as “control handles”, and once the tag mechanism was exploited, the evolution towards complex life may have been much easier. PMID:28253281

[Is it possible to "cancel" aging process of cell cultures under optimal conditions for cultivation?].

PubMed

Bozhkov, A I; Kovaleva, M K; Menzianova, N G

2011-01-01

The characteristics of the cells epigenotypes Dunaliella viridis Teod. in the process of chronological and replicative aging were investigated. By 40th day of accumulative cultivation (which coincided with the stationary growth phase) DNA content in the cells of Dunaliella viridis increased 2 times, triacylglycerides 3 times, beta-carotene and carbonyl proteins 2 times, RNA content decreased in comparison with cells in exponential growth phase, i. e., the 40th day of growth of culture forms the age-related epigenotype. 4 received subcultures were being transplanted during 2 years in mid-logarithmic growth phase (subculture-10), early stationary phase of growth (subculture-20), in the mid-stationary growth phase (subculture-30), and late stationary growth phase (subculture-40). It is shown that epigenotype of subculture-10 remained unchanged over 2 years of cultivation, i. e., it does not manifest replicative aging. At the same time, the subculture-20, although long enough (at least 40 passages), maintained epigenotype characteristic of young cultures, and showed age-related changes. Pronounced age-dependent changes of epigenotype in the course of cultivation were identified for subculture-30, and subculture-40 was characterized by unstable epigenotype. Thus, cultivation conditions determine the intensity of replicative aging in Dunaliella viridis.

Attention Training to Reduce Attention Bias and Social Stressor Reactivity: An Attempt to Replicate and Extend Previous Findings

PubMed Central

Julian, Kristin; Beard, Courtney; Schmidt, Norman B.; Powers, Mark B.; Smits, Jasper A. J.

2012-01-01

Cognitive theories suggest that social anxiety is maintained, in part, by an attentional bias toward threat. Recent research shows that a single session of attention modification training (AMP) reduces attention bias and vulnerability to a social stressor (Amir, Weber, Beard, Bomyea, & Taylor, 2008). In addition, exercise may augment the effects of attention training by its direct effects on attentional control and inhibition, thereby allowing participants receiving the AMP to more effectively disengage attention from the threatening cues and shift attention to the neutral cues. We attempted to replicate and extend previous findings by randomizing participants (N = 112) to a single session of: a) Exercise + attention training (EX + AMP); b) Rest + attention training (REST + AMP); c) Exercise + attention control condition (EX + ACC); or d) Rest + attention control condition (REST + ACC) prior to completing a public speaking challenge. We used identical assessment and training procedures to those employed by Amir et al. (2008). Results showed there was no effect of attention training on attention bias or anxiety reactivity to the speech challenge and no interactive effects of attention training and exercise on attention bias or anxiety reactivity to the speech challenge. The failure to replicate previous findings is discussed. PMID:22466022

Evolutionary adaptation of an RNA bacteriophage to the simultaneous increase in the within-host and extracellular temperatures.

PubMed

Lázaro, Ester; Arribas, María; Cabanillas, Laura; Román, Ismael; Acosta, Esther

2018-05-24

Bacteriophages are the most numerous biological entities on Earth. They are on the basis of most ecosystems, regulating the diversity and abundance of bacterial populations and contributing to the nutrient and energy cycles. Bacteriophages have two well differentiated phases in their life cycle, one extracellular, in which they behave as inert particles, and other one inside their hosts, where they replicate to give rise to a progeny. In both phases they are exposed to environmental conditions that often act as selective pressures that limit both their survival in the environment and their ability to replicate, two fitness traits that frequently cannot be optimised simultaneously. In this study we have analysed the evolutionary ability of an RNA bacteriophage, the bacteriophage Qβ, when it is confronted with a temperature increase that affects both the extracellular and the intracellular media. Our results show that Qβ can optimise its survivability when exposed to short-term high temperature extracellular heat shocks, as well as its replicative ability at higher-than-optimal temperature. Mutations responsible for simultaneous adaptation were the same as those selected when adaptation to each condition proceeded separately, showing the absence of important trade-offs between survival and reproduction in this virus.

Novel Real-Time Temperature Diagnosis of Conventional Hot-Embossing Process Using an Ultrasonic Transducer

PubMed Central

Cheng, Chin-Chi; Yang, Sen-Yeu; Lee, Dasheng

2014-01-01

This paper presents an integrated high temperature ultrasonic transducer (HTUT) on a sensor insert and its application for real-time diagnostics of the conventional hot embossing process to fabricate V-cut patterns. The sensor was directly deposited onto the sensor insert of the hot embossing mold by using a sol-gel spray technique. It could operate at temperatures higher than 400 °C and uses an ultrasonic pulse-echo technique. The ultrasonic velocity could indicate the three statuses of the hot embossing process and also evaluate the replication of V-cut patterns on a plastic plate under various processing conditions. The progression of the process, including mold closure, plastic plate softening, cooling and plate detachment inside the mold, was clearly observed using ultrasound. For an ultrasonic velocity range from 2197.4 to 2435.9 m/s, the height of the V-cut pattern decreased from 23.0 to 3.2 μm linearly, with a ratio of −0.078 μm/(m/s). The incompleteness of the replication of the V-cut patterns could be indirectly observed by the ultrasonic signals. This study demonstrates the effectiveness of the ultrasonic sensors and technology for diagnosing the replicating condition of microstructures during the conventional hot embossing process. PMID:25330051

Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bendall, Matthew L.; Luong, Khai; Wetmore, Kelly M.

2013-08-30

We performed whole genome analyses of DNA methylation in Shewanella 17 oneidensis MR-1 to examine its possible role in regulating gene expression and 18 other cellular processes. Single-Molecule Real Time (SMRT) sequencing 19 revealed extensive methylation of adenine (N6mA) throughout the 20 genome. These methylated bases were located in five sequence motifs, 21 including three novel targets for Type I restriction/modification enzymes. The 22 sequence motifs targeted by putative methyltranferases were determined via 23 SMRT sequencing of gene knockout mutants. In addition, we found S. 24 oneidensis MR-1 cultures grown under various culture conditions displayed 25 different DNA methylation patterns.more » However, the small number of differentially 26 methylated sites could not be directly linked to the much larger number of 27 differentially expressed genes in these conditions, suggesting DNA methylation is 28 not a major regulator of gene expression in S. oneidensis MR-1. The enrichment 29 of methylated GATC motifs in the origin of replication indicate DNA methylation 30 may regulate genome replication in a manner similar to that seen in Escherichia 31 coli. Furthermore, comparative analyses suggest that many 32 Gammaproteobacteria, including all members of the Shewanellaceae family, may 33 also utilize DNA methylation to regulate genome replication.« less

ATR suppresses endogenous DNA damage and allows completion of homologous recombination repair.

PubMed

Brown, Adam D; Sager, Brian W; Gorthi, Aparna; Tonapi, Sonal S; Brown, Eric J; Bishop, Alexander J R

2014-01-01

DNA replication fork stalling or collapse that arises from endogenous damage poses a serious threat to genome stability, but cells invoke an intricate signaling cascade referred to as the DNA damage response (DDR) to prevent such damage. The gene product ataxia telangiectasia and Rad3-related (ATR) responds primarily to replication stress by regulating cell cycle checkpoint control, yet it's role in DNA repair, particularly homologous recombination (HR), remains unclear. This is of particular interest since HR is one way in which replication restart can occur in the presence of a stalled or collapsed fork. Hypomorphic mutations in human ATR cause the rare autosomal-recessive disease Seckel syndrome, and complete loss of Atr in mice leads to embryonic lethality. We recently adapted the in vivo murine pink-eyed unstable (pun) assay for measuring HR frequency to be able to investigate the role of essential genes on HR using a conditional Cre/loxP system. Our system allows for the unique opportunity to test the effect of ATR loss on HR in somatic cells under physiological conditions. Using this system, we provide evidence that retinal pigment epithelium (RPE) cells lacking ATR have decreased density with abnormal morphology, a decreased frequency of HR and an increased level of chromosomal damage.

Supersoft lithography: Candy-based fabrication of soft silicone microstructures

PubMed Central

Moraes, Christopher; Labuz, Joseph M.; Shao, Yue; Fu, Jianping; Takayama, Shuichi

2015-01-01

We designed a fabrication technique able to replicate microstructures in soft silicone materials (E < 1 kPa). Sugar-based ‘hard candy’ recipes from the confectionery industry were modified to be compatible with silicone processing conditions, and used as templates for replica molding. Microstructures fabricated in soft silicones can then be easily released by dissolving the template in water. We anticipate that this technique will be of particular importance in replicating physiologically soft, microstructured environments for cell culture, and demonstrate a first application in which intrinsically soft microstructures are used to measure forces generated by fibroblast-laden contractile tissues. PMID:26245893