The Inherent Asymmetry of DNA Replication.

PubMed

Snedeker, Jonathan; Wooten, Matthew; Chen, Xin

2017-10-06

Semiconservative DNA replication has provided an elegant solution to the fundamental problem of how life is able to proliferate in a way that allows cells, organisms, and populations to survive and replicate many times over. Somewhat lost, however, in our admiration for this mechanism is an appreciation for the asymmetries that occur in the process of DNA replication. As we discuss in this review, these asymmetries arise as a consequence of the structure of the DNA molecule and the enzymatic mechanism of DNA synthesis. Increasing evidence suggests that asymmetries in DNA replication are able to play a central role in the processes of adaptation and evolution by shaping the mutagenic landscape of cells. Additionally, in eukaryotes, recent work has demonstrated that the inherent asymmetries in DNA replication may play an important role in the process of chromatin replication. As chromatin plays an essential role in defining cell identity, asymmetries generated during the process of DNA replication may play critical roles in cell fate decisions related to patterning and development.

Support, shape and number of replicate samples for tree foliage analysis.

PubMed

Luyssaert, Sebastiaan; Mertens, Jan; Raitio, Hannu

2003-06-01

Many fundamental features of a sampling program are determined by the heterogeneity of the object under study and the settings for the error (alpha), the power (beta), the effect size (ES), the number of replicate samples, and sample support, which is a feature that is often overlooked. The number of replicates, alpha, beta, ES, and sample support are interconnected. The effect of the sample support and its shape on the required number of replicate samples was investigated by means of a resampling method. The method was applied to a simulated distribution of Cd in the crown of a Salix fragilis L. tree. Increasing the dimensions of the sample support results in a decrease in the variance of the element concentration under study. Analysis of the variance is often the foundation of statistical tests, therefore, valid statistical testing requires the use of a fixed sample support during the experiment. This requirement might be difficult to meet in time-series analyses and long-term monitoring programs. Sample supports have their largest dimension in the direction with the largest heterogeneity, i.e. the direction representing the crown height, and this will give more accurate results than supports with other shapes. Taking the relationships between the sample support and the variance of the element concentrations in tree crowns into account provides guidelines for sampling efficiency in terms of precision and costs. In terms of time, the optimal support to test whether the average Cd concentration of the crown exceeds a threshold value is 0.405 m3 (alpha = 0.05, beta = 0.20, ES = 1.0 mg kg(-1) dry mass). The average weight of this support is 23 g dry mass, and 11 replicate samples need to be taken. It should be noted that in this case the optimal support applies to Cd under conditions similar to those of the simulation, but not necessarily all the examinations for this tree species, element, and hypothesis test.

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

PubMed

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

2016-09-26

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

Advanced Plasma Shape Control to Enable High-Performance Divertor Operation on NSTX-U

NASA Astrophysics Data System (ADS)

Vail, Patrick; Kolemen, Egemen; Boyer, Mark; Welander, Anders

2017-10-01

This work presents the development of an advanced framework for control of the global plasma shape and its application to a variety of shape control challenges on NSTX-U. Operations in high-performance plasma scenarios will require highly-accurate and robust control of the plasma poloidal shape to accomplish such tasks as obtaining the strong-shaping required for the avoidance of MHD instabilities and mitigating heat flux through regulation of the divertor magnetic geometry. The new control system employs a high-fidelity model of the toroidal current dynamics in NSTX-U poloidal field coils and conducting structures as well as a first-principles driven calculation of the axisymmetric plasma response. The model-based nature of the control system enables real-time optimization of controller parameters in response to time-varying plasma conditions and control objectives. The new control scheme is shown to enable stable and on-demand plasma operations in complicated magnetic geometries such as the snowflake divertor. A recently-developed code that simulates the nonlinear evolution of the plasma equilibrium is used to demonstrate the capabilities of the designed shape controllers. Plans for future real-time implementations on NSTX-U and elsewhere are also presented. Supported by the US DOE under DE-AC02-09CH11466.

Impact of radiation therapy on the oncolytic adenovirus dl520: implications on the treatment of glioblastoma.

PubMed

Bieler, Alexa; Mantwill, Klaus; Holzmüller, Regina; Jürchott, Karsten; Kaszubiak, Alexander; Stärk, Sybille; Glockzin, Gabriel; Lage, Hermann; Grosu, Anca-Ligia; Gansbacher, Bernd; Holm, Per Sonne

2008-03-01

Viral oncolytic therapy is emerging as a new form of anticancer therapy and has shown promising preclinical results, especially in combination with radio- and chemotherapy. We recently reported that nuclear localization of the human transcription factor YB-1 in multidrug-resistant cells facilitates E1-independent adenoviral replication. The aim of this study was to evaluate the combined treatment of the conditionally-replicating adenovirus dl520 and radiotherapy in glioma cell lines in vitro and in human tumor xenografts. Furthermore, the dependency of YB-1 on dl520 replication was verified by shRNA directed down regulation of YB-1. Localization of YB-1 was determined by immunostaining. Glioma cell lines LN-18, U373 and U87 were infected with dl520. Induction of cytopathic effect (CPE), viral replication, viral yield and viral release were determined after viral infection, radiation therapy and the combination of both treatment modalities. The capacity of treatments alone or combined to induce tumor growth inhibition of subcutaneous U373 tumors was tested also in nude mice. Quantitative real-time PCR demonstrated that the shRNA-mediated down regulation of YB-1 is leading to a dramatic decrease in adenoviral replication of dl520. Immunostaining analysis showed that the YB-1 protein was predominantly located in the cytoplasm in the perinuclear space and less abundant in the nucleus. After irradiation we found an increase of nuclear YB-1. The addition of radiotherapy increased the oncolytic effect of dl520 with enhanced viral replication, viral yield and viral release. The oncolytic activity of dl520 plus radiation inhibited the growth of subcutaneous U373 tumors in a xenograft mouse model. Radiation mediated increase of nuclear YB-1 in glioma cells enhanced the oncolytic potential of adenovirus dl520.

Shaping the Flavivirus Replication Complex: It's Curvaceous!

PubMed

Aktepe, Turgut E; Mackenzie, Jason M

2018-06-22

Flavivirus replication is intimately involved with remodelled membrane organelles that are compartmentalised for different functions during their life cycle. Recent advances in lipid analyses and gene depletion have identified a number of host components that enable efficient virus replication in infected cells. Here we describe the current understanding on the role and contribution of host lipids and membrane bending proteins to flavivirus replication, with a particular focus on the components that bend and shape the membrane bilayer to induce the flavivirus-induced organelles characteristic of infection. This article is protected by copyright. All rights reserved.

A maize root tip system to study DNA replication programmes in somatic and endocycling nuclei during plant development.

PubMed

Bass, Hank W; Wear, Emily E; Lee, Tae-Jin; Hoffman, Gregg G; Gumber, Hardeep K; Allen, George C; Thompson, William F; Hanley-Bowdoin, Linda

2014-06-01

The progress of nuclear DNA replication is complex in both time and space, and may reflect several levels of chromatin structure and 3-dimensional organization within the nucleus. To understand the relationship between DNA replication and developmental programmes, it is important to examine replication and nuclear substructure in different developmental contexts including natural cell-cycle progressions in situ. Plant meristems offer an ideal opportunity to analyse such processes in the context of normal growth of an organism. Our current understanding of large-scale chromosomal DNA replication has been limited by the lack of appropriate tools to visualize DNA replication with high resolution at defined points within S phase. In this perspective, we discuss a promising new system that can be used to visualize DNA replication in isolated maize (Zea mays L.) root tip nuclei after in planta pulse labelling with the thymidine analogue, 5-ethynyl-2'-deoxyuridine (EdU). Mixed populations of EdU-labelled nuclei are then separated by flow cytometry into sequential stages of S phase and examined directly using 3-dimensional deconvolution microscopy to characterize spatial patterns of plant DNA replication. Combining spatiotemporal analyses with studies of replication and epigenetic inheritance at the molecular level enables an integrated experimental approach to problems of mitotic inheritance and cellular differentiation. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

A cluster merging method for time series microarray with production values.

PubMed

Chira, Camelia; Sedano, Javier; Camara, Monica; Prieto, Carlos; Villar, Jose R; Corchado, Emilio

2014-09-01

A challenging task in time-course microarray data analysis is to cluster genes meaningfully combining the information provided by multiple replicates covering the same key time points. This paper proposes a novel cluster merging method to accomplish this goal obtaining groups with highly correlated genes. The main idea behind the proposed method is to generate a clustering starting from groups created based on individual temporal series (representing different biological replicates measured in the same time points) and merging them by taking into account the frequency by which two genes are assembled together in each clustering. The gene groups at the level of individual time series are generated using several shape-based clustering methods. This study is focused on a real-world time series microarray task with the aim to find co-expressed genes related to the production and growth of a certain bacteria. The shape-based clustering methods used at the level of individual time series rely on identifying similar gene expression patterns over time which, in some models, are further matched to the pattern of production/growth. The proposed cluster merging method is able to produce meaningful gene groups which can be naturally ranked by the level of agreement on the clustering among individual time series. The list of clusters and genes is further sorted based on the information correlation coefficient and new problem-specific relevant measures. Computational experiments and results of the cluster merging method are analyzed from a biological perspective and further compared with the clustering generated based on the mean value of time series and the same shape-based algorithm.

Replication-associated mutational asymmetry in the human genome.

PubMed

Chen, Chun-Long; Duquenne, Lauranne; Audit, Benjamin; Guilbaud, Guillaume; Rappailles, Aurélien; Baker, Antoine; Huvet, Maxime; d'Aubenton-Carafa, Yves; Hyrien, Olivier; Arneodo, Alain; Thermes, Claude

2011-08-01

During evolution, mutations occur at rates that can differ between the two DNA strands. In the human genome, nucleotide substitutions occur at different rates on the transcribed and non-transcribed strands that may result from transcription-coupled repair. These mutational asymmetries generate transcription-associated compositional skews. To date, the existence of such asymmetries associated with replication has not yet been established. Here, we compute the nucleotide substitution matrices around replication initiation zones identified as sharp peaks in replication timing profiles and associated with abrupt jumps in the compositional skew profile. We show that the substitution matrices computed in these regions fully explain the jumps in the compositional skew profile when crossing initiation zones. In intergenic regions, we observe mutational asymmetries measured as differences between complementary substitution rates; their sign changes when crossing initiation zones. These mutational asymmetries are unlikely to result from cryptic transcription but can be explained by a model based on replication errors and strand-biased repair. In transcribed regions, mutational asymmetries associated with replication superimpose on the previously described mutational asymmetries associated with transcription. We separate the substitution asymmetries associated with both mechanisms, which allows us to determine for the first time in eukaryotes, the mutational asymmetries associated with replication and to reevaluate those associated with transcription. Replication-associated mutational asymmetry may result from unequal rates of complementary base misincorporation by the DNA polymerases coupled with DNA mismatch repair (MMR) acting with different efficiencies on the leading and lagging strands. Replication, acting in germ line cells during long evolutionary times, contributed equally with transcription to produce the present abrupt jumps in the compositional skew. These results demonstrate that DNA replication is one of the major processes that shape human genome composition.

Rapid and repeatable fabrication of high A/R silk fibroin microneedles using thermally-drawn micromolds.

PubMed

Lee, JiYong; Park, Seung Hyun; Seo, Il Ho; Lee, Kang Ju; Ryu, WonHyoung

2015-08-01

Thermal drawing is a versatile rapid prototyping method that can freely form microneedle (MN) structures with ultra-high aspect ratio without relying on any complex and expensive process. However, it is still challenging to repeatedly produce MNs with identical shapes using this thermal drawing due to small fluctuations in processing conditions such as temperatures, drawing speeds, drawing heights, or parallelism in the drawing setup. In addition, thermal drawing is only applicable to thermoplastic materials and most natural biomaterials are incompatible with this method. Thus, we propose use of thermal drawing to fabricate master molds with high aspect ratios and replicate the shape by micromolding. In this work, high A/R MNs with various body profiles were fabricated by thermal drawing and replicated to silk fibroin (SF) MNs multiple times using micromolding. The original MN shape was precisely copied to the SF MNs. Methanol treatment enhanced the mechanical strength of SF MNs up to about 113% more depending on the treatment duration. We also demonstrated that methanol exposure time could effectively control drug release rates from SF MNs. Copyright © 2015 Elsevier B.V. All rights reserved.

Single-stranded DNA and RNA origami.

PubMed

Han, Dongran; Qi, Xiaodong; Myhrvold, Cameron; Wang, Bei; Dai, Mingjie; Jiang, Shuoxing; Bates, Maxwell; Liu, Yan; An, Byoungkwon; Zhang, Fei; Yan, Hao; Yin, Peng

2017-12-15

Self-folding of an information-carrying polymer into a defined structure is foundational to biology and offers attractive potential as a synthetic strategy. Although multicomponent self-assembly has produced complex synthetic nanostructures, unimolecular folding has seen limited progress. We describe a framework to design and synthesize a single DNA or RNA strand to self-fold into a complex yet unknotted structure that approximates an arbitrary user-prescribed shape. We experimentally construct diverse multikilobase single-stranded structures, including a ~10,000-nucleotide (nt) DNA structure and a ~6000-nt RNA structure. We demonstrate facile replication of the strand in vitro and in living cells. The work here thus establishes unimolecular folding as a general strategy for constructing complex and replicable nucleic acid nanostructures, and expands the design space and material scalability for bottom-up nanotechnology. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Life satisfaction and age: Dealing with underidentification in age-period-cohort models.

PubMed

de Ree, Joppe; Alessie, Rob

2011-07-01

Recent literature typically finds a U shaped relationship between life satisfaction and age. Age profiles, however, are not identified without forcing arbitrary restrictions on the cohort and/or time profiles. In this paper we report what can be identified about the relationship between life satisfaction and age without applying such restrictions. Also, we identify the restrictions needed to conclude that life satisfaction is U shaped in age. For the case of Germany, we find that the relationship between life satisfaction and age is indeed U shaped, but only under the untestable condition that the linear time trend is negative and that the linear trend across birth cohorts is practically flat. Copyright © 2011 Elsevier Ltd. All rights reserved.

Growth trajectories in the cave bear and its extant relatives: an examination of ontogenetic patterns in phylogeny.

PubMed

Fuchs, Manuela; Geiger, Madeleine; Stange, Madlen; Sánchez-Villagra, Marcelo R

2015-11-02

The study of postnatal ontogeny can provide insights into evolution by offering an understanding of how growth trajectories have evolved resulting in adult morphological disparity. The Ursus lineage is a good subject for studying cranial and mandibular shape and size variation in relation to postnatal ontogeny and phylogeny because it is at the same time not diverse but the species exhibit different feeding ecologies. Cranial and mandibular shapes of Ursus arctos (brown bear), U. maritimus (polar bear), U. americanus (American black bear), and the extinct U. spelaeus (cave bear) were examined, using a three-dimensional geometric morphometric approach. Additionally, ontogenetic series of crania and mandibles of U. arctos and U. spelaeus ranging from newborns to senile age were sampled. The distribution of specimens in morphospace allowed to distinguish species and age classes and the ontogenetic trajectories U. arctos and U. spelaeus were found to be more similar than expected by chance. Cranial shape changes during ontogeny are largely size related whereas the evolution of cranial shape disparity in this clade appears to be more influenced by dietary adaptation than by size and phylogeny. The different feeding ecologies are reflected in different cranial and mandibular shapes among species. The cranial and mandibular shape disparity in the Ursus lineage appears to be more influenced by adaptation to diet than by size or phylogeny. In contrast, the cranial and mandibular shape changes during postnatal ontogeny in U. arctos and U. spelaeus are probably largely size related. The patterns of morphospace occupation of the cranium and the mandible in adults and through ontogeny are different.

Radial chromatin positioning is shaped by local gene density, not by gene expression

PubMed Central

2009-01-01

G- and R-bands of metaphase chromosomes are characterized by profound differences in gene density, CG content, replication timing, and chromatin compaction. The preferential localization of gene-dense, transcriptionally active, and early replicating chromatin in the nuclear interior and of gene-poor, later replicating chromatin at the nuclear envelope has been demonstrated to be evolutionary-conserved in various cell types. Yet, the impact of different local chromatin features on the radial nuclear arrangement of chromatin is still not well understood. In particular, it is not known whether radial chromatin positioning is preferentially shaped by local gene density per se or by other related parameters such as replication timing or transcriptional activity. The interdependence of these distinct chromatin features on the linear deoxyribonucleic acid (DNA) sequence precludes a simple dissection of these parameters with respect to their importance for the reorganization of the linear DNA organization into the distinct radial chromatin arrangements observed in the nuclear space. To analyze this problem, we generated probe sets of pooled bacterial artificial chromosome (BAC) clones from HSA 11, 12, 18, and 19 representing R/G-band-assigned chromatin, segments with different gene density and gene loci with different expression levels. Using multicolor 3D flourescent in situ hybridization (FISH) and 3D image analysis, we determined their localization in the nucleus and their positions within or outside the corresponding chromosome territory (CT). For each BAC data on local gene density within 2- and 10-Mb windows, as well as GC (guanine and cytosine) content, replication timing and expression levels were determined. A correlation analysis of these parameters with nuclear positioning revealed regional gene density as the decisive parameter determining the radial positioning of chromatin in the nucleus in contrast to band assignment, replication timing, and transcriptional activity. We demonstrate a polarized distribution of gene-dense vs gene-poor chromatin within CTs with respect to the nuclear border. Whereas we confirm previous reports that a particular gene-dense and transcriptionally highly active region of about 2 Mb on 11p15.5 often loops out from the territory surface, gene-dense and highly expressed sequences were not generally found preferentially at the CT surface as previously suggested. PMID:17333233

[Comparison of two shaping methods for double-lumen endotracheal tube intubation by Shikani optical stylet laryngoscope].

PubMed

Xu, T; Li, M; Xu, M; Guo, X Y

2016-12-18

To compare the efficacy and safety of two different shaping methods for double-lumen endotracheal tube (DLT).DLT was shaped with the rod of a Shikani optical stylet (SOS) with the tracheal orifice aligned with the convex aspect of the distal curvature or the concave aspect of the distal curvature. Patients scheduled for elective thoracic surgery and required intubation with a left-sided DLT were enrolled in this study. They were randomized into two groups. They were intubated with a DLT, which was shaped with the rod of a SOS with its tracheal orifice aligned with the convex aspect of the distal curvature (group T) or the concave aspect of the distal curvature (group U). Time for SOS manipulation, intubation attempts, intubation resistance score, malposition of bronchial intubation, time for fiberoptic bronchoscope (FOB) identification of bronchial placement, total intubation time and oral mucosal or dental injury were recorded. Hoarseness and throat sore of the patients were evaluated 1 hour and 24 hours after surgery. A total of 136 patients completed the study, with 68 in each group. Time for SOS manipulation was significantly shorter in group U [(35.1±6.1) s vs. 39.6±11.8) s, P=0.007]. First attempt success rate did not differ between the groups (92.6% vs.88.2%, P=0.561). Intubation resistance score was significantly lower in group U. Group T had fewer patients who suffered malposition of bronchial intubation than group U (4 vs.13, P=0.020) and cost less time for FOB identification of bronchial placement [(44.1±20.9) s vs.(53.6±29.2) s, P=0.032]. Total intubation time and the incidence of oral mucosal or dental injury did not differ between the groups. The severity and incidence of hoarseness were lower in group U than in group T 1 hour after surgery. The severity and incidence of sore throat were lower in group U than in group T 1 hour and 24 hours postoperatively. When lacing a left-sided DLT using a SOS, shaping the DLT with the tracheal orifice aligned with the concave aspect of the distal curvature saves SOS manipulation time, decreases the severity and incidence of postoperative hoarseness and sore throat. However, this modified shaping method increases the incidence of malposition of bronchial intubation and time for FOB identification of bronchial placement.

Role of Bunyamwera Orthobunyavirus NSs protein in infection of mosquito cells.

PubMed

Szemiel, Agnieszka M; Failloux, Anna-Bella; Elliott, Richard M

2012-01-01

Bunyamwera orthobunyavirus is both the prototype and study model of the Bunyaviridae family. The viral NSs protein seems to contribute to the different outcomes of infection in mammalian and mosquito cell lines. However, only limited information is available on the growth of Bunyamwera virus in cultured mosquito cells other than the Aedes albopictus C6/36 line. To determine potential functions of the NSs protein in mosquito cells, replication of wild-type virus and a recombinant NSs deletion mutant was compared in Ae. albopictus C6/36, C7-10 and U4.4 cells, and in Ae. aegypti Ae cells by monitoring N protein production and virus yields at various times post infection. Both viruses established persistent infections, with the exception of NSs deletion mutant in U4.4 cells. The NSs protein was nonessential for growth in C6/36 and C7-10 cells, but was important for productive replication in U4.4 and Ae cells. Fluorescence microscopy studies using recombinant viruses expressing green fluorescent protein allowed observation of three stages of infection, early, acute and late, during which infected cells underwent morphological changes. In the absence of NSs, these changes were less pronounced. An RNAi response efficiently reduced virus replication in U4.4 cells transfected with virus specific dsRNA, but not in C6/36 or C7/10 cells. Lastly, Ae. aegypti mosquitoes were exposed to blood-meal containing either wild-type or NSs deletion virus, and at various times post-feeding, infection and disseminated infection rates were measured. Compared to wild-type virus, infection rates by the mutant virus were lower and more variable. If the NSs deletion virus was able to establish infection, it was detected in salivary glands at 6 days post-infection, 3 days later than wild-type virus. Bunyamwera virus NSs is required for efficient replication in certain mosquito cell lines and in Ae. aegypti mosquitoes.

Electron microscopic analysis of rotavirus assembly-replication intermediates

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

Boudreaux, Crystal E.; Kelly, Deborah F.; McDonald, Sarah M., E-mail: mcdonaldsa@vtc.vt.edu

2015-03-15

Rotaviruses (RVs) replicate their segmented, double-stranded RNA genomes in tandem with early virion assembly. In this study, we sought to gain insight into the ultrastructure of RV assembly-replication intermediates (RIs) using transmission electron microscopy (EM). Specifically, we examined a replicase-competent, subcellular fraction that contains all known RV RIs. Three never-before-seen complexes were visualized in this fraction. Using in vitro reconstitution, we showed that ~15-nm doughnut-shaped proteins in strings were nonstructural protein 2 (NSP2) bound to viral RNA transcripts. Moreover, using immunoaffinity-capture EM, we revealed that ~20-nm pebble-shaped complexes contain the viral RNA polymerase (VP1) and RNA capping enzyme (VP3). Finally,more » using a gel purification method, we demonstrated that ~30–70-nm electron-dense, particle-shaped complexes represent replicase-competent core RIs, containing VP1, VP3, and NSP2 as well as capsid proteins VP2 and VP6. The results of this study raise new questions about the interactions among viral proteins and RNA during the concerted assembly–replicase process. - Highlights: • Rotaviruses replicate their genomes in tandem with early virion assembly. • Little is known about rotavirus assembly-replication intermediates. • Assembly-replication intermediates were imaged using electron microscopy.« less

Expressed emotion and sociocultural moderation in the course of schizophrenia.

PubMed

Aguilera, Adrian; López, Steven R; Breitborde, Nicholas J K; Kopelowicz, Alex; Zarate, Roberto

2010-11-01

This study examined whether the sociocultural context moderates the relationship between families' expressed emotion (EE) and clinical outcomes in schizophrenia. In a sample of 60 Mexican American caregivers and their ill relatives, we first assessed whether EE and its indices (criticism, emotional overinvolvement [EOI], and warmth) related to relapse. Second, we extended the analysis of EE and its indices to a longitudinal assessment of symptomatology. Last, we tested whether bidimensional acculturation moderated the relationship between EE (and its indices) and both relapse and symptom trajectory over time. Results indicated that EOI was associated with increased relapse and that criticism was associated with increased symptomatology. Additionally, as patients' Mexican enculturation (Spanish language and media involvement) decreased, EE was increasingly related to relapse. For symptomatology, as patients' U.S. acculturation (English language and media involvement) increased, EE was associated with increased symptoms longitudinally. Our results replicate and extend past research on how culture might shape the way family factors relate to the course of schizophrenia. PsycINFO Database Record (c) 2010 APA, all rights reserved

Is a High Tone Pointy? Speakers of Different Languages Match Mandarin Chinese Tones to Visual Shapes Differently

PubMed Central

Shang, Nan; Styles, Suzy J.

2017-01-01

Studies investigating cross-modal correspondences between auditory pitch and visual shapes have shown children and adults consistently match high pitch to pointy shapes and low pitch to curvy shapes, yet no studies have investigated linguistic-uses of pitch. In the present study, we used a bouba/kiki style task to investigate the sound/shape mappings for Tones of Mandarin Chinese, for three groups of participants with different language backgrounds. We recorded the vowels [i] and [u] articulated in each of the four tones of Mandarin Chinese. In Study 1 a single auditory stimulus was presented with two images (one curvy, one spiky). In Study 2 a single image was presented with two auditory stimuli differing only in tone. Participants were asked to select the best match in an online ‘Quiz.’ Across both studies, we replicated the previously observed ‘u-curvy, i-pointy’ sound/shape cross-modal correspondence in all groups. However, Tones were mapped differently by people with different language backgrounds: speakers of Mandarin Chinese classified as Chinese-dominant systematically matched Tone 1 (high, steady) to the curvy shape and Tone 4 (falling) to the pointy shape, while English speakers with no knowledge of Chinese preferred to match Tone 1 (high, steady) to the pointy shape and Tone 3 (low, dipping) to the curvy shape. These effects were observed most clearly in Study 2 where tone-pairs were contrasted explicitly. These findings are in line with the dominant patterns of linguistic pitch perception for speakers of these languages (pitch-change, and pitch height, respectively). Chinese English balanced bilinguals showed a bivalent pattern, swapping between the Chinese pitch-change pattern and the English pitch-height pattern depending on the task. These findings show for that the supposedly universal pattern of mapping linguistic sounds to shape is modulated by the sensory properties of a speaker’s language system, and that people with high functioning in more than one language can dynamically shift between patterns. PMID:29270147

Plasma boundary shape control and real-time equilibrium reconstruction on NSTX-U

DOE PAGES

Boyer, M. D.; Battaglia, D. J.; Mueller, D.; ...

2018-01-25

Here, the upgrade to the National Spherical Torus eXperiment (NSTX-U) included two main improvements: a larger center-stack, enabling higher toroidal field and longer pulse duration, and the addition of three new tangentially aimed neutral beam sources, which increase available heating and current drive, and allow for flexibility in shaping power, torque, current, and particle deposition profiles. To best use these new capabilities and meet the high-performance operational goals of NSTX-U, major upgrades to the NSTX-U control system (NCS) hardware and software have been made. Several control algorithms, including those used for real-time equilibrium reconstruction and shape control, have been upgradedmore » to improve and extend plasma control capabilities. As part of the commissioning phase of first plasma operations, the shape control system was tuned to control the boundary in both inner-wall limited and diverted discharges. It has been used to accurately track the requested evolution of the boundary (including the size of the inner gap between the plasma and central solenoid, which is a challenge for the ST configuration), X-point locations, and strike point locations, enabling repeatable discharge evolutions for scenario development and diagnostic commissioning.« less

Plasma boundary shape control and real-time equilibrium reconstruction on NSTX-U

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

Boyer, M. D.; Battaglia, D. J.; Mueller, D.

Here, the upgrade to the National Spherical Torus eXperiment (NSTX-U) included two main improvements: a larger center-stack, enabling higher toroidal field and longer pulse duration, and the addition of three new tangentially aimed neutral beam sources, which increase available heating and current drive, and allow for flexibility in shaping power, torque, current, and particle deposition profiles. To best use these new capabilities and meet the high-performance operational goals of NSTX-U, major upgrades to the NSTX-U control system (NCS) hardware and software have been made. Several control algorithms, including those used for real-time equilibrium reconstruction and shape control, have been upgradedmore » to improve and extend plasma control capabilities. As part of the commissioning phase of first plasma operations, the shape control system was tuned to control the boundary in both inner-wall limited and diverted discharges. It has been used to accurately track the requested evolution of the boundary (including the size of the inner gap between the plasma and central solenoid, which is a challenge for the ST configuration), X-point locations, and strike point locations, enabling repeatable discharge evolutions for scenario development and diagnostic commissioning.« less

Plasma boundary shape control and real-time equilibrium reconstruction on NSTX-U

NASA Astrophysics Data System (ADS)

Boyer, M. D.; Battaglia, D. J.; Mueller, D.; Eidietis, N.; Erickson, K.; Ferron, J.; Gates, D. A.; Gerhardt, S.; Johnson, R.; Kolemen, E.; Menard, J.; Myers, C. E.; Sabbagh, S. A.; Scotti, F.; Vail, P.

2018-03-01

The upgrade to the National Spherical Torus eXperiment (NSTX-U) included two main improvements: a larger center-stack, enabling higher toroidal field and longer pulse duration, and the addition of three new tangentially aimed neutral beam sources, which increase available heating and current drive, and allow for flexibility in shaping power, torque, current, and particle deposition profiles. To best use these new capabilities and meet the high-performance operational goals of NSTX-U, major upgrades to the NSTX-U control system (NCS) hardware and software have been made. Several control algorithms, including those used for real-time equilibrium reconstruction and shape control, have been upgraded to improve and extend plasma control capabilities. As part of the commissioning phase of first plasma operations, the shape control system was tuned to control the boundary in both inner-wall limited and diverted discharges. It has been used to accurately track the requested evolution of the boundary (including the size of the inner gap between the plasma and central solenoid, which is a challenge for the ST configuration), X-point locations, and strike point locations, enabling repeatable discharge evolutions for scenario development and diagnostic commissioning.

Comparison of exendin-4 on beta-cell replication in mouse and human islet grafts.

PubMed

Tian, Lei; Gao, Jie; Weng, Guangbin; Yi, Huimin; Tian, Bole; O'Brien, Timothy D; Guo, Zhiguang

2011-08-01

Exendin-4 can stimulate β-cell replication in mice. Whether it can stimulate β-cell replication in human islet grafts remains unknown. Therefore, we compared the effects of exendin-4 on β-cell replication in mouse and human islet grafts. Islets, isolated from mouse and human donors at different ages, were transplanted into diabetic mice and/or diabetic nude mice that were given bromodeoxyuridine (BrdU) with or without exendin-4. At 4 weeks post-transplantation, islet grafts were removed for insulin and BrdU staining and quantification of insulin(+)/BrdU(+) cells. Although diabetes was reversed in all mice transplanting syngeneic mouse islets from young or old donors, normoglycemia was achieved significantly faster in exendin-4 treated mice. Mouse islet grafts in exendin-4 treated mice had significantly more insulin(+)/BrdU(+) β cells than in untreated mice (P < 0.01). Human islet grafts from ≤22-year-old donors had more insulin(+)/BrdU(+) β cells in exendin-4 treated mice than that in untreated mice (P < 0.01). However, human islet grafts from ≥35-year-old donors contained few insulin(+)/BrdU(+) β cells in exendin-4 treated or untreated mice. Our data demonstrated that the capacity for β-cell replication in mouse and human islet grafts is different with and without exendin-4 treatment and indicated that GLP-1 agonists can stimulate β-cell replication in human islets from young donors. © 2011 The Authors. Transplant International © 2011 European Society for Organ Transplantation.

Early intranuclear replication of African swine fever virus genome modifies the landscape of the host cell nucleus.

PubMed

Simões, Margarida; Martins, Carlos; Ferreira, Fernando

2015-12-02

Although African swine fever virus (ASFV) replicates in viral cytoplasmic factories, the presence of viral DNA within the host cell nucleus has been previously reported to be essential for productive infection. Herein, we described, for the first time, the intranuclear distribution patterns of viral DNA replication events, preceding those that occur in the cytoplasmic compartment. Using BrdU pulse-labelling experiments, newly synthesized ASFV genomes were exclusively detected inside the host cell nucleus at the early phase of infection, both in swine monocyte-derived macrophages (MDMs) and Vero cells. From 8hpi onwards, BrdU labelling was only observed in ASFV cytoplasmic factories. Our results also show that ASFV specifically activates the Ataxia Telangiectasia Mutated Rad-3 related (ATR) pathway in ASFV-infected swine MDMs from the early phase of infection, most probably because ASFV genome is recognized as foreign DNA. Morphological changes of promyelocytic leukaemia nuclear bodies (PML-NBs), nuclear speckles and Cajal bodies were also found in ASFV-infected swine MDMs, strongly suggesting the viral modulation of cellular antiviral responses and cellular transcription, respectively. As described for other viral infections, the nuclear reorganization that takes place during ASFV infection may also provide an environment that favours its intranuclear replication events. Altogether, our results contribute for a better understanding of ASFV replication strategies, starting with an essential intranuclear DNA replication phase which induces host nucleus changes towards a successful viral infection. Copyright © 2015 Elsevier B.V. All rights reserved.

A Domain of Herpes Simplex Virus pUL33 Required To Release Monomeric Viral Genomes from Cleaved Concatemeric DNA.

PubMed

Yang, Kui; Dang, Xiaoqun; Baines, Joel D

2017-10-15

Monomeric herpesvirus DNA is cleaved from concatemers and inserted into preformed capsids through the actions of the viral terminase. The terminase of herpes simplex virus (HSV) is composed of three subunits encoded by U L 15, U L 28, and U L 33. The U L 33-encoded protein (pU L 33) interacts with pU L 28, but its precise role in the DNA cleavage and packaging reaction is unclear. To investigate the function of pU L 33, we generated a panel of recombinant viruses with either deletions or substitutions in the most conserved regions of U L 33 using a bacterial artificial chromosome system. Deletion of 11 amino acids (residues 50 to 60 or residues 110 to 120) precluded viral replication, whereas the truncation of the last 10 amino acids from the pU L 33 C terminus did not affect viral replication or the interaction of pU L 33 with pU L 28. Mutations that replaced the lysine at codon 110 and the arginine at codon 111 with alanine codons failed to replicate, and the pU L 33 mutant interacted with pU L 28 less efficiently. Interestingly, genomic termini of the large (L) and small (S) components were detected readily in cells infected with these mutants, indicating that concatemeric DNA was cleaved efficiently. However, the release of monomeric genomes as assessed by pulsed-field gel electrophoresis was greatly diminished, and DNA-containing capsids were not observed. These results suggest that pU L 33 is necessary for one of the two viral DNA cleavage events required to release individual genomes from concatemeric viral DNA. IMPORTANCE This paper shows a role for pU L 33 in one of the two DNA cleavage events required to release monomeric genomes from concatemeric viral DNA. This is the first time that such a phenotype has been observed and is the first identification of a function of this protein relevant to DNA packaging other than its interaction with other terminase components. Copyright © 2017 Yang et al.

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.

DNA hypomethylation induces a DNA replication-associated cell cycle arrest to block hepatic outgrowth in uhrf1 mutant zebrafish embryos

PubMed Central

Jacob, Vinitha; Chernyavskaya, Yelena; Chen, Xintong; Tan, Poh Seng; Kent, Brandon; Hoshida, Yujin; Sadler, Kirsten C.

2015-01-01

UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) recruits DNMT1 to hemimethylated DNA during replication and is essential for maintaining DNA methylation. uhrf1 mutant zebrafish have global DNA hypomethylation and display embryonic defects, including a small liver, and they die as larvae. We make the surprising finding that, despite their reduced organ size, uhrf1 mutants express high levels of genes controlling S-phase and have many more cells undergoing DNA replication, as measured by BrdU incorporation. In contrast to wild-type hepatocytes, which are continually dividing during hepatic outgrowth and thus dilute the BrdU label, uhrf1 mutant hepatocytes retain BrdU throughout outgrowth, reflecting cell cycle arrest. Pulse-chase-pulse experiments with BrdU and EdU, and DNA content analysis indicate that uhrf1 mutant cells undergo DNA re-replication and that apoptosis is the fate of many of the re-replicating and arrested hepatocytes. Importantly, the DNA re-replication phenotype and hepatic outgrowth failure are preceded by global loss of DNA methylation. Moreover, uhrf1 mutants are phenocopied by mutation of dnmt1, and Dnmt1 knockdown in uhrf1 mutants enhances their small liver phenotype. Together, these data indicate that unscheduled DNA replication and failed cell cycle progression leading to apoptosis are the mechanisms by which DNA hypomethylation prevents organ expansion in uhrf1 mutants. We propose that cell cycle arrest leading to apoptosis is a strategy that restricts propagation of epigenetically damaged cells during embryogenesis. PMID:25564650

DNA hypomethylation induces a DNA replication-associated cell cycle arrest to block hepatic outgrowth in uhrf1 mutant zebrafish embryos.

PubMed

Jacob, Vinitha; Chernyavskaya, Yelena; Chen, Xintong; Tan, Poh Seng; Kent, Brandon; Hoshida, Yujin; Sadler, Kirsten C

2015-02-01

UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) recruits DNMT1 to hemimethylated DNA during replication and is essential for maintaining DNA methylation. uhrf1 mutant zebrafish have global DNA hypomethylation and display embryonic defects, including a small liver, and they die as larvae. We make the surprising finding that, despite their reduced organ size, uhrf1 mutants express high levels of genes controlling S-phase and have many more cells undergoing DNA replication, as measured by BrdU incorporation. In contrast to wild-type hepatocytes, which are continually dividing during hepatic outgrowth and thus dilute the BrdU label, uhrf1 mutant hepatocytes retain BrdU throughout outgrowth, reflecting cell cycle arrest. Pulse-chase-pulse experiments with BrdU and EdU, and DNA content analysis indicate that uhrf1 mutant cells undergo DNA re-replication and that apoptosis is the fate of many of the re-replicating and arrested hepatocytes. Importantly, the DNA re-replication phenotype and hepatic outgrowth failure are preceded by global loss of DNA methylation. Moreover, uhrf1 mutants are phenocopied by mutation of dnmt1, and Dnmt1 knockdown in uhrf1 mutants enhances their small liver phenotype. Together, these data indicate that unscheduled DNA replication and failed cell cycle progression leading to apoptosis are the mechanisms by which DNA hypomethylation prevents organ expansion in uhrf1 mutants. We propose that cell cycle arrest leading to apoptosis is a strategy that restricts propagation of epigenetically damaged cells during embryogenesis. © 2015. Published by The Company of Biologists Ltd.

Theoretical foundations for environmental Kuznets curve analysis

NASA Astrophysics Data System (ADS)

Lantz, Van

This thesis provides a dynamic theory for analyzing the paths of aggregate output and pollution in a country over time. An infinite horizon, competitive growth-pollution model is explored in order to determine the role that economic scale, production techniques, and pollution regulations play in explaining the inverted U-shaped relationship between output and some forms of pollution (otherwise known as the Environmental Kuznets Curve, or EKC). Results indicate that the output-pollution relationship may follow a strictly increasing, strictly decreasing (but bounded), inverted U-shaped, or some combination of curves. While the 'scale' effect may cause output and pollution to exhibit a monotonic relationship, 'technique' and 'regulation' effects may ultimately cause a de-linking of these two variables. Pollution-minimizing energy regulation policies are also investigated within this framework. It is found that the EKC may be 'flattened' or even eliminated moving from a poorly-regulated economy to one that minimizes pollution. The model is calibrated to the US economy for output (gross national product, GNP) and two pollutants (sulfur dioxide, SO2, and carbon dioxide, CO2) over the period 1900 to 1990. Results indicate that the model replicates the observations quite well. The predominance of 'scale' effects cause aggregate SO2 and CO2 levels to increase with GNP in the early stages of development. Then, in the case of SO 2, 'technique' and 'regulation' effects may be the cause of falling SO2 levels with continued economic growth (establishing the EKC). CO2 continues to monotonically increase as output levels increase over time. The positive relationship may be due to the lack of regulations on this pollutant. If stricter regulation policies were instituted in the two case studies, an improved allocation of resources may result. While GNP may be 2.596 to 20% lower than what has been realized in the US economy (depending on the pollution variable analyzed), individual welfare may increase from lower pollution levels.

Urokinase–urokinase receptor interaction mediates an inhibitory signal for HIV-1 replication

PubMed Central

Alfano, Massimo; Sidenius, Nicolai; Panzeri, Barbara; Blasi, Francesco; Poli, Guido

2002-01-01

Elevated levels of soluble urokinase-type plasminogen activator (uPA) receptor, CD87/u-PAR, predict survival in individuals infected with HIV-1. Here, we report that pro-uPA (or uPA) inhibits HIV-1 expression in U937-derived chronically infected promonocytic U1 cells stimulated with phorbol 12-myristate 13-acetate (PMA) or tumor necrosis factor-α (TNF-α). However, pro-uPA did not inhibit PMA or TNF-α-dependent activation of nuclear factor-kB or activation protein-1 in U1 cells. Cell-associated HIV protein synthesis also was not decreased by pro-uPA, although the release of virion-associated reverse transcriptase activity was substantially inhibited, suggesting a functional analogy between pro-uPA and the antiviral effects of IFNs. Indeed, cell disruption reversed the inhibitory effect of pro-uPA on activated U1 cells, and ultrastructural analysis confirmed that virions were preferentially retained within cell vacuoles in pro-uPA treated cells. Neither expression of endogenous IFNs nor activation of the IFN-inducible Janus kinase/signal transducer and activator of transcription pathway were induced by pro-uPA. Pro-uPA also inhibited acute HIV replication in monocyte-derived macrophages and activated peripheral blood mononuclear cells, although with great inter-donor variability. However, pro-uPA inhibited HIV replication in acutely infected promonocytic U937 cells and in ex vivo cultures of lymphoid tissue infected in vitro. Because these effects occurred at concentrations substantially lower than those affecting thrombolysis, pro-uPA may represent a previously uncharacterized class of antiviral agents mimicking IFNs in their inhibitory effects on HIV expression and replication. PMID:12084931

Constant Flux of Spatial Niche Partitioning through High-Resolution Sampling of Magnetotactic Bacteria.

PubMed

He, Kuang; Gilder, Stuart A; Orsi, William D; Zhao, Xiangyu; Petersen, Nikolai

2017-10-15

Magnetotactic bacteria (MTB) swim along magnetic field lines in water. They are found in aquatic habitats throughout the world, yet knowledge of their spatial and temporal distribution remains limited. To help remedy this, we took MTB-bearing sediment from a natural pond, mixed the thoroughly homogenized sediment into two replicate aquaria, and then counted three dominant MTB morphotypes (coccus, spirillum, and rod-shaped MTB cells) at a high spatiotemporal sampling resolution: 36 discrete points in replicate aquaria were sampled every ∼30 days over 198 days. Population centers of the MTB coccus and MTB spirillum morphotypes moved in continual flux, yet they consistently inhabited separate locations, displaying significant anticorrelation. Rod-shaped MTB were initially concentrated toward the northern end of the aquaria, but at the end of the experiment, they were most densely populated toward the south. The finding that the total number of MTB cells increased over time during the experiment argues that population reorganization arose from relative changes in cell division and death and not from migration. The maximum net growth rates were 10, 3, and 1 doublings day -1 and average net growth rates were 0.24, 0.11, and 0.02 doublings day -1 for MTB cocci, MTB spirilla, and rod-shaped MTB, respectively; minimum growth rates for all three morphotypes were -0.03 doublings day -1 Our results suggest that MTB cocci and MTB spirilla occupy distinctly different niches: their horizontal positioning in sediment is anticorrelated and under constant flux. IMPORTANCE Little is known about the horizontal distribution of magnetotactic bacteria in sediment or how the distribution changes over time. We therefore measured three dominant magnetotactic bacterium morphotypes at 36 places in two replicate aquaria each month for 7 months. We found that the spatial positioning of population centers changed over time and that the two most abundant morphotypes (MTB cocci and MTB spirilla) occupied distinctly different niches in the aquaria. Maximum and average growth and death rates were quantified for each of the three morphotypes based on 72 sites that were measured six times. The findings provided novel insight into the differential behavior of noncultured magnetotactic bacteria. Copyright © 2017 American Society for Microbiology.

U-shaped associations between time in bed and the physical and mental functioning of Japanese civil servants: the roles of work, family, behavioral and sleep quality characteristics.

PubMed

Sekine, M; Tatsuse, T; Cable, N; Chandola, T; Marmot, M

2014-09-01

This study aimed to evaluate (i) whether work, family, behavioral and sleep quality characteristics differ among individuals with different time in bed (TIB), and (ii) whether and how much the U-shaped associations between TIB and health can be explained by these characteristics. Participants were 3510 employees (2371 males and 1139 females) aged 20-65 years working in local government in Japan. They completed a questionnaire regarding work, family, and behavioral characteristics. Sleep quality and physical and mental functioning were evaluated using the Pittsburgh Sleep Quality Index and the Short Form 36. High job demands, long work hours, and high work-family conflict were more prevalent among those with short TIB. Those with long TIB had daily drinking habits. Whereas those with short TIB had poor sleep, mainly due to poor subjective sleep quality and daytime dysfunction, those with long TIB had poor sleep, mainly due to long sleep latency, poor sleep efficiency and sleep disturbances. The U-shaped associations between TIB and poor physical and mental health, with the best health observed in those spending ~8 h in bed, weakened considerably after adjustment for sleep quality, followed by work and family characteristics. After adjusting for behavioral characteristics and long-standing illnesses, the associations hardly changed. The U-shaped associations between TIB and health may be explained by U-shaped associations between TIB and poor sleep and psychosocial stress in work and family life. Copyright © 2014 Elsevier B.V. All rights reserved.

High-speed pulse-shape generator, pulse multiplexer

DOEpatents

Burkhart, Scott C.

2002-01-01

The invention combines arbitrary amplitude high-speed pulses for precision pulse shaping for the National Ignition Facility (NIF). The circuitry combines arbitrary height pulses which are generated by replicating scaled versions of a trigger pulse and summing them delayed in time on a pulse line. The combined electrical pulses are connected to an electro-optic modulator which modulates a laser beam. The circuit can also be adapted to combine multiple channels of high speed data into a single train of electrical pulses which generates the optical pulses for very high speed optical communication. The invention has application in laser pulse shaping for inertial confinement fusion, in optical data links for computers, telecommunications, and in laser pulse shaping for atomic excitation studies. The invention can be used to effect at least a 10.times. increase in all fiber communication lines. It allows a greatly increased data transfer rate between high-performance computers. The invention is inexpensive enough to bring high-speed video and data services to homes through a super modem.

Growth shapes and turbulent spots in unstable systems

NASA Astrophysics Data System (ADS)

Conrado, Claudine V.; Bohr, Tomas

1995-05-01

We study the growth shapes of localized turbulent patches (turbulent spots) in a class of partial differential equations (PDEs) in two spatial dimensions, of first order in time and in one scalar field u. The PDE's are chosen such that the ``laminar'' state u=0 is unstable, at least convectively (i.e., in a moving frame). We show which symmetry breaking terms are required to generate the characteristic nonconvex growth shapes found in turbulent spots in boundary layers, and how the shapes transform when we vary the coefficients of these terms. Finally, we show how it is possible, in certain cases, to find exact solutions for the nonliear growth shapes and how to measure Lyapunov exponents of growing turbulent spots.

Hematopoietic Cancer Cell Lines Can Support Replication of Sabin Poliovirus Type 1

PubMed Central

van Eikenhorst, Gerco; de Gruijl, Tanja D.; van der Pol, Leo A.; Bakker, Wilfried A. M.

2015-01-01

Viral vaccines can be produced in adherent or in suspension cells. The objective of this work was to screen human suspension cell lines for the capacity to support viral replication. As the first step, it was investigated whether poliovirus can replicate in such cell lines. Sabin poliovirus type 1 was serially passaged on five human cell lines, HL60, K562, KG1, THP-1, and U937. Sabin type 1 was capable of efficiently replicating in three cell lines (K562, KG1, and U937), yielding high viral titers after replication. Expression of CD155, the poliovirus receptor, did not explain susceptibility to replication, since all cell lines expressed CD155. Furthermore, we showed that passaged virus replicated more efficiently than parental virus in KG1 cells, yielding higher virus titers in the supernatant early after infection. Infection of cell lines at an MOI of 0.01 resulted in high viral titers in the supernatant at day 4. Infection of K562 with passaged Sabin type 1 in a bioreactor system yielded high viral titers in the supernatant. Altogether, these data suggest that K562, KG1, and U937 cell lines are useful for propagation of poliovirus. PMID:25815312

Combination process of diamond machining and roll-to-roll UV-replication for thin film micro- and nanostructures

NASA Astrophysics Data System (ADS)

Väyrynen, J.; Mönkkönen, K.; Siitonen, S.

2016-09-01

Roll-to-roll (R2R) ultraviolet (UV) curable embossing replication process is a highly accurate and cost effective way to replicate large quantities of thin film polymer parts. These structures can be used for microfluidics, LED-optics, light guides, displays, cameras, diffusers, decorative, laser sensing and measuring devices. In the R2R UV-process, plastic thin film coated with UV-curable lacquer, passes through an imprinting embossing drum and is then hardened by an UV-lamp. One key element for mastering this process is the ability to manufacture a rotating drum containing micro- and nanostructures. Depending on the pattern shapes, the drum can be directly machined by diamond machining or it can be done through wafer level lithographical process. Due to the shrinkage of UV-curable lacquer, the R2R drum pattern process needs to be prototyped few times, in order to get the desired performance and shape from the R2R produced part. To speed up the prototyping and overall process we have developed a combination process where planar diamond machining patterns are being turned into a drum roller. Initially diamond machined patterns from a planar surface are replicated on a polymer sheet using UV-replication. Secondly, a nickel stamper shim is grown form the polymer sheet and at the end the stamper is turned into a roller and used in the R2R process. This process allows various micro milled, turned, grooved and ruled structures to be made at thin film products through the R2R process. In this paper, the process flow and examples of fabricating R2R embossed UVcurable thin film micro- and nanostructures from planar diamond machined patterns, is reported.

Experimentally Guided Models Reveal Replication Principles that Shape the Mutation Distribution of RNA Viruses

DTIC Science & Technology

2015-01-30

intracel- lular replication. Two classic replication modes have been described for single-stranded RNA viruses: the ‘stamping machine’ mode ( Stent ...Journal of Theoretical Biology 218:309–321. doi: 10.1006/jtbi.2002.3078. Stent GS. 1963. Molecular Biology of Bacterial Viruses. San Francisco, Calif: W H

3D chromatin conformation correlates with replication timing and is conserved in resting cells

PubMed Central

Moindrot, Benoit; Audit, Benjamin; Klous, Petra; Baker, Antoine; Thermes, Claude; de Laat, Wouter; Bouvet, Philippe; Mongelard, Fabien; Arneodo, Alain

2012-01-01

Although chromatin folding is known to be of functional importance to control the gene expression program, less is known regarding its interplay with DNA replication. Here, using Circular Chromatin Conformation Capture combined with high-throughput sequencing, we identified megabase-sized self-interacting domains in the nucleus of a human lymphoblastoid cell line, as well as in cycling and resting peripheral blood mononuclear cells (PBMC). Strikingly, the boundaries of those domains coincide with early-initiation zones in every cell types. Preferential interactions have been observed between the consecutive early-initiation zones, but also between those separated by several tens of megabases. Thus, the 3D conformation of chromatin is strongly correlated with the replication timing along the whole chromosome. We furthermore provide direct clues that, in addition to the timing value per se, the shape of the timing profile at a given locus defines its set of genomic contacts. As this timing-related scheme of chromatin organization exists in lymphoblastoid cells, resting and cycling PBMC, this indicates that it is maintained several weeks or months after the previous S-phase. Lastly, our work highlights that the major chromatin changes accompanying PBMC entry into cell cycle occur while keeping largely unchanged the long-range chromatin contacts. PMID:22879376

Augmentation of DHCR24 expression by hepatitis C virus infection facilitates viral replication in hepatocytes.

PubMed

Takano, Takashi; Tsukiyama-Kohara, Kyoko; Hayashi, Masahiro; Hirata, Yuichi; Satoh, Masaaki; Tokunaga, Yuko; Tateno, Chise; Hayashi, Yukiko; Hishima, Tsunekazu; Funata, Nobuaki; Sudoh, Masayuki; Kohara, Michinori

2011-09-01

We characterized the role of 24-dehydrocholesterol reductase (DHCR24) in hepatitis C virus infection (HCV). DHCR24 is a cholesterol biosynthetic enzyme and cholesterol is a major component of lipid rafts, which is reported to play an important role in HCV replication. Therefore, we examined the potential of DHCR24 as a target for novel HCV therapeutic agents. We examined DHCR24 expression in human hepatocytes in both the livers of HCV-infected patients and those of chimeric mice with human hepatocytes. We targeted DHCR24 with siRNA and U18666A which is an inhibitor of both DHCR24 and cholesterol synthesis. We measured the level of HCV replication in these HCV replicon cell lines and HCV infected cells. U18666A was administrated into chimeric mice with humanized liver, and anti-viral effects were assessed. Expression of DHCR24 was induced by HCV infection in human hepatocytes in vitro, and in human hepatocytes of chimeric mouse liver. Silencing of DHCR24 by siRNA decreased HCV replication in replicon cell lines and HCV JFH-1 strain-infected cells. Treatment with U18666A suppressed HCV replication in the replicon cell lines. Moreover, to evaluate the anti-viral effect of U18666A in vivo, we administrated U18666A with or without pegylated interferon to chimeric mice and observed an inhibitory effect of U18666A on HCV infection and a synergistic effect with interferon. DHCR24 is an essential host factor which augmented its expression by HCV infection, and plays a significant role in HCV replication. DHCR24 may serve as a novel anti-HCV drug target. Copyright © 2010 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

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

Biofidelic Human Activity Modeling and Simulation with Large Variability

DTIC Science & Technology

2014-11-25

A systematic approach was developed for biofidelic human activity modeling and simulation by using body scan data and motion capture data to...replicate a human activity in 3D space. Since technologies for simultaneously capturing human motion and dynamic shapes are not yet ready for practical use, a...that can replicate a human activity in 3D space with the true shape and true motion of a human. Using this approach, a model library was built to

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.

The impact of sampling, PCR, and sequencing replication on discerning changes in drinking water bacterial community over diurnal time-scales.

PubMed

Bautista-de Los Santos, Quyen Melina; Schroeder, Joanna L; Blakemore, Oliver; Moses, Jonathan; Haffey, Mark; Sloan, William; Pinto, Ameet J

2016-03-01

High-throughput and deep DNA sequencing, particularly amplicon sequencing, is being increasingly utilized to reveal spatial and temporal dynamics of bacterial communities in drinking water systems. Whilst the sampling and methodological biases associated with PCR and sequencing have been studied in other environments, they have not been quantified for drinking water. These biases are likely to have the greatest effect on the ability to characterize subtle spatio-temporal patterns influenced by process/environmental conditions. In such cases, intra-sample variability may swamp any underlying small, systematic variation. To evaluate this, we undertook a study with replication at multiple levels including sampling sites, sample collection, PCR amplification, and high throughput sequencing of 16S rRNA amplicons. The variability inherent to the PCR amplification and sequencing steps is significant enough to mask differences between bacterial communities from replicate samples. This was largely driven by greater variability in detection of rare bacteria (relative abundance <0.01%) across PCR/sequencing replicates as compared to replicate samples. Despite this, we captured significant changes in bacterial community over diurnal time-scales and find that the extent and pattern of diurnal changes is specific to each sampling location. Further, we find diurnal changes in bacterial community arise due to differences in the presence/absence of the low abundance bacteria and changes in the relative abundance of dominant bacteria. Finally, we show that bacterial community composition is significantly different across sampling sites for time-periods during which there are typically rapid changes in water use. This suggests hydraulic changes (driven by changes in water demand) contribute to shaping the bacterial community in bulk drinking water over diurnal time-scales. Copyright © 2015 Elsevier Ltd. All rights reserved.

A dynamic processes study of PM retention by trees under different wind conditions.

PubMed

Xie, Changkun; Kan, Liyan; Guo, Jiankang; Jin, Sijia; Li, Zhigang; Chen, Dan; Li, Xin; Che, Shengquan

2018-02-01

Particulate matter (PM) is one of the most serious environmental problems, exacerbating respiratory and vascular illnesses. Plants have the ability to reduce non-point source PM pollution through retention on leaves and branches. Studies of the dynamic processes of PM retention by plants and the mechanisms influencing this process will help to improve the efficiency of urban greening for PM reduction. We examined dynamic processes of PM retention and the major factors influencing PM retention by six trees with different branch structure characteristics in wind tunnel experiments at three different wind speeds. The results showed that the changes of PM numbers retained by plant leaves over time were complex dynamic processes for which maximum values could exceed minimum values by over 10 times. The average value of PM measured in multiple periods and situations can be considered a reliable indicator of the ability of the plant to retain PM. The dynamic processes were similar for PM 10 and PM 2.5 . They could be clustered into three groups simulated by continually-rising, inverse U-shaped, and U-shaped polynomial functions, respectively. The processes were the synthetic effect of characteristics such as species, wind speed, period of exposure and their interactions. Continually-rising functions always explained PM retention in species with extremely complex branch structure. Inverse U-shaped processes explained PM retention in species with relatively simple branch structure and gentle wind. The U-shaped processes mainly explained PM retention at high wind speeds and in species with a relatively simple crown. These results indicate that using plants with complex crowns in urban greening and decreasing wind speed in plant communities increases the chance of continually-rising or inverse U-shaped relationships, which have a positive effect in reducing PM pollution. Copyright © 2017 Elsevier Ltd. All rights reserved.

Sister acts: coordinating DNA replication and cohesion establishment

PubMed Central

Sherwood, Rebecca; Takahashi, Tatsuro S.; Jallepalli, Prasad V.

2010-01-01

The ring-shaped cohesin complex links sister chromatids and plays crucial roles in homologous recombination and mitotic chromosome segregation. In cycling cells, cohesin's ability to generate cohesive linkages is restricted to S phase and depends on loading and establishment factors that are intimately connected to DNA replication. Here we review how cohesin is regulated by the replication machinery, as well as recent evidence that cohesin itself influences how chromosomes are replicated. PMID:21159813

Phasic alertness cues modulate visual processing speed in healthy aging.

PubMed

Haupt, Marleen; Sorg, Christian; Napiórkowski, Natan; Finke, Kathrin

2018-05-31

Warning signals temporarily increase the rate of visual information in younger participants and thus optimize perception in critical situations. It is unclear whether such important preparatory processes are preserved in healthy aging. We parametrically assessed the effects of auditory alertness cues on visual processing speed and their time course using a whole report paradigm based on the computational Theory of Visual Attention. We replicated prior findings of significant alerting benefits in younger adults. In conditions with short cue-target onset asynchronies, this effect was baseline-dependent. As younger participants with high baseline speed did not show a profit, an inverted U-shaped function of phasic alerting and visual processing speed was implied. Older adults also showed a significant cue-induced benefit. Bayesian analyses indicated that the cueing benefit on visual processing speed was comparably strong across age groups. Our results indicate that in aging individuals, comparable to younger ones, perception is active and increased expectancy of the appearance of a relevant stimulus can increase the rate of visual information uptake. Copyright © 2018 Elsevier Inc. All rights reserved.

Infectious haematopoietic necrosis virus genogroup-specific virulence mechanisms in sockeye salmon, Oncorhynchus nerka (Walbaum), from Redfish Lake, Idaho

USGS Publications Warehouse

Purcell, M.K.; Garver, K.A.; Conway, C.; Elliott, D.G.; Kurath, G.

2009-01-01

Characterization of infectious haematopoietic necrosis virus (IHNV) field isolates from North America has established three main genogroups (U, M and L) that differ in host-specific virulence. In sockeye salmon, Oncorhynchus nerka, the U genogroup is highly virulent, whereas the M genogroup is nearly non-pathogenic. In this study, we sought to characterize the virus-host dynamics that contribute to genogroup-specific virulence in a captive stock of sockeye salmon from Redfish Lake in Idaho. Juvenile sockeye salmon were challenged by immersion and injection with either a representative U or M viral strain and sampled periodically until 14 days post-infection (p.i.). Fish challenged with each strain had positive viral titre by day 3, regardless of challenge route, but the fish exposed to the M genogroup virus had significantly lower virus titres than fish exposed to the U genogroup virus. Gene expression analysis by quantitative reverse transcriptase PCR was used to simultaneously assess viral load and host interferon (IFN) response in the anterior kidney. Viral load was significantly higher in the U-challenged fish relative to M-challenged fish. Both viruses induced expression of the IFN-stimulated genes (ISGs), but expression was usually significantly lower in the M-challenged group, particularly at later time points (7 and 14 days p.i.). However, ISG expression was comparable with 3 days post-immersion challenge despite a significant difference in viral load. Our data indicated that the M genogroup virus entered the host, replicated and spread in the sockeye salmon tissues, but to a lesser extent than the U genogroup. Both virus types induced a host IFN response, but the high virulence strain (U) continued to replicate in the presence of this response, whereas the low virulence strain (M) was cleared below detectable levels. We hypothesize that high virulence is associated with early in vivo replication allowing the virus to achieve a threshold level, which the host innate immune system cannot control. ?? 2009 Blackwell Publishing Ltd.

Infectious haematopoietic necrosis virus genogroup-specific virulence mechanisms in sockeye salmon, Oncorhynchus nerka (Walbaum), from Redfish Lake, Idaho.

PubMed

Purcell, M K; Garver, K A; Conway, C; Elliott, D G; Kurath, G

2009-07-01

Characterization of infectious haematopoietic necrosis virus (IHNV) field isolates from North America has established three main genogroups (U, M and L) that differ in host-specific virulence. In sockeye salmon, Oncorhynchus nerka, the U genogroup is highly virulent, whereas the M genogroup is nearly non-pathogenic. In this study, we sought to characterize the virus-host dynamics that contribute to genogroup-specific virulence in a captive stock of sockeye salmon from Redfish Lake in Idaho. Juvenile sockeye salmon were challenged by immersion and injection with either a representative U or M viral strain and sampled periodically until 14 days post-infection (p.i.). Fish challenged with each strain had positive viral titre by day 3, regardless of challenge route, but the fish exposed to the M genogroup virus had significantly lower virus titres than fish exposed to the U genogroup virus. Gene expression analysis by quantitative reverse transcriptase PCR was used to simultaneously assess viral load and host interferon (IFN) response in the anterior kidney. Viral load was significantly higher in the U-challenged fish relative to M-challenged fish. Both viruses induced expression of the IFN-stimulated genes (ISGs), but expression was usually significantly lower in the M-challenged group, particularly at later time points (7 and 14 days p.i.). However, ISG expression was comparable with 3 days post-immersion challenge despite a significant difference in viral load. Our data indicated that the M genogroup virus entered the host, replicated and spread in the sockeye salmon tissues, but to a lesser extent than the U genogroup. Both virus types induced a host IFN response, but the high virulence strain (U) continued to replicate in the presence of this response, whereas the low virulence strain (M) was cleared below detectable levels. We hypothesize that high virulence is associated with early in vivo replication allowing the virus to achieve a threshold level, which the host innate immune system cannot control.

Systematic Determination of Replication Activity Type Highlights Interconnections between Replication, Chromatin Structure and Nuclear Localization

PubMed Central

Polten, Andreas; Hezroni, Hadas; Eldar, Yonina C.; Meshorer, Eran; Yakhini, Zohar; Simon, Itamar

2012-01-01

DNA replication is a highly regulated process, with each genomic locus replicating at a distinct time of replication (ToR). Advances in ToR measurement technology enabled several genome-wide profiling studies that revealed tight associations between ToR and general genomic features and a remarkable ToR conservation in mammals. Genome wide studies further showed that at the hundreds kb-to-megabase scale the genome can be divided into constant ToR regions (CTRs) in which the replication process propagates at a faster pace due to the activation of multiple origins and temporal transition regions (TTRs) in which the replication process propagates at a slower pace. We developed a computational tool that assigns a ToR to every measured locus and determines its replication activity type (CTR versus TTR). Our algorithm, ARTO (Analysis of Replication Timing and Organization), uses signal processing methods to fit a constant piece-wise linear curve to the measured raw data. We tested our algorithm and provide performance and usability results. A Matlab implementation of ARTO is available at http://bioinfo.cs.technion.ac.il/people/zohar/ARTO/. Applying our algorithm to ToR data measured in multiple mouse and human samples allowed precise genome-wide ToR determination and replication activity type characterization. Analysis of the results highlighted the plasticity of the replication program. For example, we observed significant ToR differences in 10–25% of the genome when comparing different tissue types. Our analyses also provide evidence for activity type differences in up to 30% of the probes. Integration of the ToR data with multiple aspects of chromosome organization characteristics suggests that ToR plays a role in shaping the regional chromatin structure. Namely, repressive chromatin marks, are associated with late ToR both in TTRs and CTRs. Finally, characterization of the differences between TTRs and CTRs, with matching ToR, revealed that TTRs are associated with compact chromatin and are located significantly closer to the nuclear envelope. Supplementary material is available. Raw and processed data were deposited in Geo (GSE17236). PMID:23145042

The Analysis of Leaf Shape Using Fractal Geometry.

ERIC Educational Resources Information Center

Hartvigsen, Gregg

2000-01-01

Describes ways to examine leaf structure and shape using fractal geometry. Students can test hypotheses using the leaves of replicated plants to look for non-linear trends in leaf shape along the stems of plants, across species, and under different environmental growth conditions. (SAH)

Fertility and Childlessness in the United States.

PubMed

Baudin, Thomas; de la Croix, David

2015-06-01

We develop a theory of fertility, distinguishing its intensive margin from its extensive margin. The deep parameters are identified using facts from the 1990 US Census: (i) fertility of mothers decreases with education; (ii) childlessness exhibits a U-shaped relationship with education; (iii) the relationship between marriage rates and education is hump-shaped for women and increasing for men. We estimate that 2.5 percent of women were childless because of poverty and 8.1 percent because of high opportunity cost of childrearing. Over time, historical trends in total factor productivity and in education led to a U-shaped response in childlessness rates while fertility of mothers decreased.

Large-Area Fabrication of Droplet Pancake Bouncing Surface and Control of Bouncing State.

PubMed

Song, Jinlong; Gao, Mingqian; Zhao, Changlin; Lu, Yao; Huang, Liu; Liu, Xin; Carmalt, Claire J; Deng, Xu; Parkin, Ivan P

2017-09-26

Superhydrophobic pillar arrays, which can generate the droplet pancake bouncing phenomenon with reduced liquid-solid contact time, have huge application prospects in anti-icing of aircraft wings from freezing rain. However, the previously reported pillar arrays, suitable for obtaining pancake bouncing, have a diameter ≤100 μm and height-diameter ratio >10, which are difficult to fabricate over a large area. Here, we have systematically studied the influence of the dimension of the superhydrophobic pillar arrays on the bouncing dynamics of water droplets. We show that the typical pancake bouncing with 57.8% reduction in contact time with the surface was observed on the superhydrophobic pillar arrays with 1.05 mm diameter, 0.8 mm height, and 0.25 mm space. Such pillar arrays with millimeter diameter and <1 height-diameter ratio can be easily fabricated over large areas. Further, a simple replication-spraying method was developed for the large-area fabrication of the superhydrophobic pillar arrays to induce pancake bouncing. No sacrificial layer was needed to reduce the adhesion in the replication processes. Since the bouncing dynamics were rather sensitive to the space between the pillars, a method to control the contact time, bouncing shape, horizontal bouncing direction, and reversible switch between pancake bouncing and conventional bouncing was realized by adjusting the inclination angle of the shape memory polymer pillars.

Strand-Specific Analysis of DNA Synthesis and Proteins Association with DNA Replication Forks in Budding Yeast.

PubMed

Yu, Chuanhe; Gan, Haiyun; Zhang, Zhiguo

2018-01-01

DNA replication initiates at DNA replication origins after unwinding of double-strand DNA(dsDNA) by replicative helicase to generate single-stranded DNA (ssDNA) templates for the continuous synthesis of leading-strand and the discontinuous synthesis of lagging-strand. Therefore, methods capable of detecting strand-specific information will likely yield insight into the association of proteins at leading and lagging strand of DNA replication forks and the regulation of leading and lagging strand synthesis during DNA replication. The enrichment and Sequencing of Protein-Associated Nascent DNA (eSPAN), which measure the relative amounts of proteins at nascent leading and lagging strands of DNA replication forks, is a step-wise procedure involving the chromatin immunoprecipitation (ChIP) of a protein of interest followed by the enrichment of protein-associated nascent DNA through BrdU immunoprecipitation. The isolated ssDNA is then subjected to strand-specific sequencing. This method can detect whether a protein is enriched at leading or lagging strand of DNA replication forks. In addition to eSPAN, two other strand-specific methods, (ChIP-ssSeq), which detects potential protein-ssDNA binding and BrdU-IP-ssSeq, which can measure synthesis of both leading and lagging strand, were developed along the way. These methods can provide strand-specific and complementary information about the association of the target protein with DNA replication forks as well as synthesis of leading and lagging strands genome wide. Below, we describe the detailed eSPAN, ChIP-ssSeq, and BrdU-IP-ssSeq protocols.

Differential regulation of hepatitis B virus core protein expression and genome replication by a small upstream open reading frame and naturally occurring mutations in the precore region.

PubMed

Zong, Li; Qin, Yanli; Jia, Haodi; Ye, Lei; Wang, Yongxiang; Zhang, Jiming; Wands, Jack R; Tong, Shuping; Li, Jisu

2017-05-01

Hepatitis B virus (HBV) transcribes two subsets of 3.5-kb RNAs: precore RNA for hepatitis B e antigen (HBeAg) expression, and pregenomic RNA for core and P protein translation as well as genome replication. HBeAg expression could be prevented by mutations in the precore region, while an upstream open reading frame (uORF) has been proposed as a negative regulator of core protein translation. We employed replication competent HBV DNA constructs and transient transfection experiments in Huh7 cells to verify the uORF effect and to explore the alternative function of precore RNA. Optimized Kozak sequence for the uORF or extra ATG codons as present in some HBV genotypes reduced core protein expression. G1896A nonsense mutation promoted more efficient core protein expression than mutated precore ATG, while a +1 frameshift mutation was ineffective. In conclusion, various HBeAg-negative precore mutations and mutations affecting uORF differentially regulate core protein expression and genome replication. Copyright © 2017 Elsevier Inc. All rights reserved.

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

PubMed

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

2014-02-01

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

Ecological mechanisms favouring behavioural diversification in the absence of morphological diversification: a theoretical examination using brook charr (Salvelinus fontinalis).

PubMed

De Kerckhove, Derrick; McLaughlin, Robert L; Noakes, David L G

2006-03-01

1. Behavioural diversification is thought to be an important initial step in the origin of resource polymorphisms. We developed a model for young brook charr (Salvelinus fontinalis Mitchill) to examine four mechanisms that could generate a U-shaped relationship between growth rate (fitness) and the proportion of time spent moving that would favour alternative foraging tactics in the absence of obvious differences in body size and shape. 2. Recently emerged brook charr of similar size and shape inhabit still-water pools along the sides of streams. Some individuals tend to sit and wait for crustacean prey at the pool substrate near the bank, while others tend to search actively for insect prey at the pool surface away from the bank. 3. The ecological mechanisms modelled were (i) the relationship between the rate of prey capture and the proportion of time spent moving is curvilinear, such that net rate of energy gain is maximized at two different levels of activity; (ii) switching between foraging locations and, hence, tactics involves lost opportunity and travel costs; (iii) switching between prey types and, hence, tactics involves a learning cost; and (iv) foraging success is status-dependent with individuals switching between tactics having a lower status than those specializing at a tactic. 4. Singly, no mechanism predicted the U-shaped relationship between growth rate and the proportion of time spent moving. Together, a U-shaped relationship was obtained, indicating that the behavioural diversification and diversifying selection observed in the field may be a consequence of multiple, subtle mechanisms.

Bacillus subtilis actin-like protein MreB influences the positioning of the replication machinery and requires membrane proteins MreC/D and other actin-like proteins for proper localization.

PubMed

Defeu Soufo, Hervé Joël; Graumann, Peter L

2005-03-03

Bacterial actin-like proteins have been shown to perform essential functions in several aspects of cellular physiology. They affect cell growth, cell shape, chromosome segregation and polar localization of proteins, and localize as helical filaments underneath the cell membrane. Bacillus subtilis MreB and Mbl have been shown to perform dynamic motor like movements within cells, extending along helical tracks in a time scale of few seconds. In this work, we show that Bacillus subtilis MreB has a dual role, both in the formation of rod cell shape, and in chromosome segregation, however, its function in cell shape is distinct from that of MreC. Additionally, MreB is important for the localization of the replication machinery to the cell centre, which becomes aberrant soon after depletion of MreB. 3D image reconstructions suggest that frequently, MreB filaments consist of several discontinuous helical filaments with varying length. The localization of MreB was abnormal in cells with decondensed chromosomes, as well as during depletion of Mbl, MreBH and of the MreC/MreD proteins, which we show localize to the cell membrane. Thus, proper positioning of MreB filaments depends on and is affected by a variety of factors in the cell. Our data provide genetic and cytological links between MreB and the membrane, as well as with other actin like proteins, and further supports the connection of MreB with the chromosome. The functional dependence on MreB of the localization of the replication machinery suggests that the replisome is not anchored at the cell centre, but is positioned in a dynamic manner.

Ethidium bromide as a marker of mtDNA replication in living cells

NASA Astrophysics Data System (ADS)

Villa, Anna Maria; Fusi, Paola; Pastori, Valentina; Amicarelli, Giulia; Pozzi, Chiara; Adlerstein, Daniel; Doglia, Silvia Maria

2012-04-01

Mitochondrial DNA (mtDNA) in tumor cells was found to play an important role in maintaining the malignant phenotype. Using laser scanning confocal fluorescence microscopy (LSCFM) in a recent work, we reported a variable fluorescence intensity of ethidium bromide (EB) in mitochondria nucleoids of living carcinoma cells. Since when EB is bound to nucleic acids its fluorescence is intensified; a higher EB fluorescence intensity could reflect a higher DNA accessibility to EB, suggesting a higher mtDNA replication activity. To prove this hypothesis, in the present work we studied, by LSCFM, the EB fluorescence in mitochondria nucleoids of living neuroblastoma cells, a model system in which differentiation affects the level of mtDNA replication. A drastic decrease of fluorescence was observed after differentiation. To correlate EB fluorescence intensity to the mtDNA replication state, we evaluated the mtDNA nascent strands content by ligation-mediated real-time PCR, and we found a halved amount of replicating mtDNA molecules in differentiating cells. A similar result was obtained by BrdU incorporation. These results indicate that the low EB fluorescence of nucleoids in differentiated cells is correlated to a low content of replicating mtDNA, suggesting that EB may be used as a marker of mtDNA replication in living cells.

Dropping the Other U: An Alternative Approach to U-Shaped Developmental Functions

ERIC Educational Resources Information Center

Brainerd, C. J.

2004-01-01

The aim of this article is to introduce readers to an alternative way of applying U-shaped functions to understand development, especially cognitive development. In classical developmental applications, age is the abscissa; that is, in the fundamental equation B = f(A), some behavioral variable (B) plots as a U-shaped or inverted U-shaped function…

Remote Acculturation of Early Adolescents in Jamaica towards European American Culture: A Replication and Extension.

PubMed

Ferguson, Gail M; Bornstein, Marc H

2015-03-01

Remote acculturation is a modern form of non-immigrant acculturation identified among early adolescents in Jamaica as "Americanization". This study aimed to replicate the original remote acculturation findings in a new cohort of early adolescents in Jamaica ( n = 222; M = 12.08 years) and to extend our understanding of remote acculturation by investigating potential vehicles of indirect and intermittent intercultural contact. Cluster analyses replicated prior findings: Relative to Traditional Jamaican adolescents (62%), Americanized Jamaican adolescents (38%) reported stronger European American cultural orientation, lower Jamaican orientation, lower family obligations, and greater conflict with parents. More U.S. media (girls) and less local media and local sports (all) were the primary vehicles of intercultural contact predicting higher odds of Americanization. U.S. food, U.S. tourism, and transnational communication were also linked to U.S. orientation. Findings have implications for acculturation research and for practice and policy targeting Caribbean youth and families.

Mechanism of Origin DNA Recognition and Assembly of an Initiator-Helicase Complex by SV40 Large Tumor Antigen

PubMed Central

Chang, Y. Paul; Xu, Meng; Machado, Ana Carolina Dantas; Yu, Xian Jessica; Rohs, Remo; Chen, Xiaojiang S.

2013-01-01

SUMMARY The DNA tumor virus Simian virus 40 (SV40) is a model system for studying eukaryotic replication. SV40 large tumor antigen (LTag) is the initiator/helicase that is essential for genome replication. LTag recognizes and assembles at the viral replication origin. We determined the structure of two multidomain LTag subunits bound to origin DNA. The structure reveals that the origin binding domains (OBDs) and Zn and AAA+ domains are involved in origin recognition and assembly. Notably, the OBDs recognize the origin in an unexpected manner. The histidine residues of the AAA+ domains insert into a narrow minor groove region with enhanced negative electrostatic potential. Computational analysis indicates that this region is intrinsically narrow, demonstrating the role of DNA shape readout in origin recognition. Our results provide important insights into the assembly of the LTag initiator/ helicase at the replication origin and suggest that histidine contacts with the minor groove serve as a mechanism of DNA shape readout. PMID:23545501

MSH6- or PMS2-deficiency causes re-replication in DT40 B cells, but it has little effect on immunoglobulin gene conversion or on repair of AID-generated uracils

PubMed Central

Campo, Vanina A.; Patenaude, Anne-Marie; Kaden, Svenja; Horb, Lori; Firka, Daniel; Jiricny, Josef; Di Noia, Javier M.

2013-01-01

The mammalian antibody repertoire is shaped by somatic hypermutation (SHM) and class switch recombination (CSR) of the immunoglobulin (Ig) loci of B lymphocytes. SHM and CSR are triggered by non-canonical, error-prone processing of G/U mismatches generated by activation-induced deaminase (AID). In birds, AID does not trigger SHM, but it triggers Ig gene conversion (GC), a ‘homeologous’ recombination process involving the Ig variable region and proximal pseudogenes. Because recombination fidelity is controlled by the mismatch repair (MMR) system, we investigated whether MMR affects GC in the chicken B cell line DT40. We show here that Msh6−/− and Pms2−/− DT40 cells display cell cycle defects, including genomic re-replication. However, although IgVλ GC tracts in MMR-deficient cells were slightly longer than in normal cells, Ig GC frequency, donor choice or the number of mutations per sequence remained unaltered. The finding that the avian MMR system, unlike that of mammals, does not seem to contribute towards the processing of G/U mismatches in vitro could explain why MMR is unable to initiate Ig GC in this species, despite initiating SHM and CSR in mammalian cells. Moreover, as MMR does not counteract or govern Ig GC, we report a rare example of ‘homeologous’ recombination insensitive to MMR. PMID:23314153

Hand-operated and rotary ProTaper instruments: a comparison of working time and number of rotations in simulated root canals.

PubMed

Pasqualini, Damiano; Scotti, Nicola; Tamagnone, Lorenzo; Ellena, Federica; Berutti, Elio

2008-03-01

The aim of this study was to compare the effective shaping time and number of rotations required by an endodontist working with hand and rotary ProTaper instruments to completely shape simulated root canals. Eighty Endo Training Blocks (curved canal shape) were used. Manual preflaring was performed with K-Flexofiles #08-10-12-15-17 and #20 Nitiflex at a working length of 18 mm. Specimens were then randomly assigned to 2 different groups (n = 40); group 1 was shaped by using hand ProTaper and group 2 with ProTaper rotary. The number of rotations made in the canal and the effective time required to achieve complete canal shaping were recorded for each instrument. Differences between groups were analyzed with the nonparametric Mann-Whitney U test (P < .05). Hand ProTaper required significantly fewer rotations (P < .001) than rotary ProTaper, whereas the effective working time to fully shape the simulated canal was significantly higher (P < .001) with hand ProTaper.

A four-component model of the action potential in mouse detrusor smooth muscle cell

PubMed Central

Brain, Keith L.; Young, John S.; Manchanda, Rohit

2018-01-01

Background and hypothesis Detrusor smooth muscle cells (DSMCs) of the urinary bladder are electrically connected to one another via gap junctions and form a three dimensional syncytium. DSMCs exhibit spontaneous electrical activity, including passive depolarizations and action potentials. The shapes of spontaneous action potentials (sAPs) observed from a single DSM cell can vary widely. The biophysical origins of this variability, and the precise components which contribute to the complex shapes observed are not known. To address these questions, the basic components which constitute the sAPs were investigated. We hypothesized that linear combinations of scaled versions of these basic components can produce sAP shapes observed in the syncytium. Methods and results The basic components were identified as spontaneous evoked junction potentials (sEJP), native AP (nAP), slow after hyperpolarization (sAHP) and very slow after hyperpolarization (vsAHP). The experimental recordings were grouped into two sets: a training data set and a testing data set. A training set was used to estimate the components, and a test set to evaluate the efficiency of the estimated components. We found that a linear combination of the identified components when appropriately amplified and time shifted replicated various AP shapes to a high degree of similarity, as quantified by the root mean square error (RMSE) measure. Conclusions We conclude that the four basic components—sEJP, nAP, sAHP, and vsAHP—identified and isolated in this work are necessary and sufficient to replicate all varieties of the sAPs recorded experimentally in DSMCs. This model has the potential to generate testable hypotheses that can help identify the physiological processes underlying various features of the sAPs. Further, this model also provides a means to classify the sAPs into various shape classes. PMID:29351282

A four-component model of the action potential in mouse detrusor smooth muscle cell.

PubMed

Padmakumar, Mithun; Brain, Keith L; Young, John S; Manchanda, Rohit

2018-01-01

Detrusor smooth muscle cells (DSMCs) of the urinary bladder are electrically connected to one another via gap junctions and form a three dimensional syncytium. DSMCs exhibit spontaneous electrical activity, including passive depolarizations and action potentials. The shapes of spontaneous action potentials (sAPs) observed from a single DSM cell can vary widely. The biophysical origins of this variability, and the precise components which contribute to the complex shapes observed are not known. To address these questions, the basic components which constitute the sAPs were investigated. We hypothesized that linear combinations of scaled versions of these basic components can produce sAP shapes observed in the syncytium. The basic components were identified as spontaneous evoked junction potentials (sEJP), native AP (nAP), slow after hyperpolarization (sAHP) and very slow after hyperpolarization (vsAHP). The experimental recordings were grouped into two sets: a training data set and a testing data set. A training set was used to estimate the components, and a test set to evaluate the efficiency of the estimated components. We found that a linear combination of the identified components when appropriately amplified and time shifted replicated various AP shapes to a high degree of similarity, as quantified by the root mean square error (RMSE) measure. We conclude that the four basic components-sEJP, nAP, sAHP, and vsAHP-identified and isolated in this work are necessary and sufficient to replicate all varieties of the sAPs recorded experimentally in DSMCs. This model has the potential to generate testable hypotheses that can help identify the physiological processes underlying various features of the sAPs. Further, this model also provides a means to classify the sAPs into various shape classes.

Expression of the p12 subunit of human DNA polymerase δ (Pol δ), CDK inhibitor p21(WAF1), Cdt1, cyclin A, PCNA and Ki-67 in relation to DNA replication in individual cells.

PubMed

Zhao, Hong; Zhang, Sufang; Xu, Dazhong; Lee, Marietta Ywt; Zhang, Zhongtao; Lee, Ernest Yc; Darzynkiewicz, Zbigniew

2014-01-01

We recently reported that the p12 subunit of human DNA polymerase δ (Pol δ4) is degraded by CRL4(Cdt2) which regulates the licensing factor Cdt1 and p21(WAF1) during the G1 to S transition. Presently, we performed multiparameter laser scanning cytometric analyses of changes in levels of p12, Cdt1 and p21(WAF1), detected immunocytochemically in individual cells, vis-à-vis the initiation and completion of DNA replication. The latter was assessed by pulse-labeling A549 cells with the DNA precursor ethynyl-2'-deoxyribose (EdU). The loss of p12 preceded the initiation of DNA replication and essentially all cells incorporating EdU were p12 negative. Completion of DNA replication and transition to G2 phase coincided with the re-appearance and rapid rise of p12 levels. Similar to p12 a decline of p21(WAF1) and Cdt1 was seen at the end of G1 phase and all DNA replicating cells were p21(WAF1) and Cdt1 negative. The loss of p21(WAF1) preceded that of Cdt1 and p12 and the disappearance of the latter coincided with the onset of DNA replication. Loss of p12 leads to conversion of Pol δ4 to its trimeric form, Pol δ3, so that the results provide strong support to the notion that Pol δ3 is engaged in DNA replication during unperturbed progression through the S phase of cell cycle. Also assessed was a correlation between EdU incorporation, likely reflecting the rate of DNA replication in individual cells, and the level of expression of positive biomarkers of replication cyclin A, PCNA and Ki-67 in these cells. Of interest was the observation of stronger correlation between EdU incorporation and expression of PCNA (r = 0.73) than expression of cyclin A (r = 0.47) or Ki-67 (r = 0.47).

Design and fabrication of nano-imprint templates using unique pattern transforms and primitives

NASA Astrophysics Data System (ADS)

MacDonald, Susan; Mellenthin, David; Rentzsch, Kevin; Kramer, Kenneth; Ellenson, James; Hostetler, Tim; Enck, Ron

2005-11-01

Increasing numbers of MEMS, photonic, and integrated circuit manufacturers are investigating the use of Nano-imprint Lithography or Step and Flash Imprint Lithography (SFIL) as a lithography choice for making various devices and products. Their main interests in using these technologies are the lack of aberrations inherent in traditional optical reduction lithography, and the relative low cost of imprint tools. Since imprint templates are at 1X scale, the small sizes of these structures have necessitated the use of high-resolution 50KeV, and 100KeV e-beam lithography tools to build these templates. For MEMS and photonic applications, the structures desired are often circles, arches, and other non-orthogonal shapes. It has long been known that both 50keV, and especially 100keV e-beam lithography tools are extremely accurate, and can produce very high resolution structures, but the trade off is long write times. The main drivers in write time are shot count and stage travel. This work will show how circles and other non-orthogonal shapes can be produced with a 50KeV Variable Shaped Beam (VSB) e-beam lithography system using unique pattern transforms and primitive shapes, while keeping the shot count and write times under control. The quality of shapes replicated into the resist on wafer using an SFIL tool will also be presented.

BPM analysis of all-optical fiber interferometric sensor based on a U-shape microcavity

NASA Astrophysics Data System (ADS)

Wu, Hongbin; Yuan, Lei; Wang, Sumei; Zhao, Longjiang; Cao, Zhitao

2014-02-01

Reflectivity spectrum of beam propagation method (BPM), for the first time to the best of our knowledge, is realized and utilized to model all-optical fiber interferometric sensor formed by a U-shape microcavity embedded in a single mode optical fiber and illustrate the principle of sensor structures varied by the length and the depth of U-shape microcavity. BPM analysis gives a constructive guideline to get a high interferometric fringe visibility which is most important for sensing application. The simulated results are completely in agreement with the interferometric sensor principle of Fabry-Perot interferometer (FPI) theory. With the conclusion of FPI sensor, refractive index (RI) sensitivity and temperature sensitivity are then simulated and obtained as 1049+/-5.2nm/RIU (refractive index unit) within RI range of solutions and 1.04+/-0.03pm/°C respectively.

78 FR 48214 - Self-Regulatory Organizations; The Options Clearing Corporation; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-07

... and Rules to Certain U.S. Dollar-Settled Gold Futures Designed to Replicate Positions in the Spot... Futures That Were Based on the Value of Gold in the Spot Market With an Additional Daily Cost of Carry... Rules to certain U.S. dollar-settled gold futures designed to replicate positions in the spot market...

Electron microscopic analysis of rotavirus assembly-replication intermediates

PubMed Central

Boudreaux, Crystal E.; Kelly, Deborah F.; McDonald, Sarah M.

2015-01-01

Rotaviruses (RVs) replicate their segmented, double-stranded RNA genomes in tandem with early virion assembly. In this study, we sought to gain insight into the ultrastructure of RV assembly-replication intermediates (RIs) using transmission electron microscopy (EM). Specifically, we examined a replicase-competent, subcellular fraction that contains all known RV RIs. Three never-before-seen complexes were visualized in this fraction. Using in vitro reconstitution, we showed that ~15-nm doughnut-shaped proteins in strings were nonstructural protein 2 (NSP2) bound to viral RNA transcripts. Moreover, using immunoaffinity-capture EM, we revealed that ~20-nm pebble-shaped complexes contain the viral RNA polymerase (VP1) and RNA capping enzyme (VP3). Finally, using a gel purification method, we demonstrated that ~30–70-nm electron-dense, particle-shaped complexes represent replicase-competent core RIs, containing VP1, VP3, and NSP2 as well as capsid proteins VP2 and VP6. The results of this study raise new questions about the interactions among viral proteins and RNA during the concerted assembly-replicase process. PMID:25635339

Effects of interferon-tau on cattle persistently infected with bovine viral diarrhea virus.

PubMed

Kohara, Junko; Nishikura, Yumiko; Konnai, Satoru; Tajima, Motoshi; Onuma, Misao

2012-08-01

In this study, the antiviral effects of bovine interferon-tau (boIFN-tau) on bovine viral diarrhea virus (BVDV) were examined in vitro and in vivo. In the in vitro experiments, the replication of cytopathic and non-cytopathic BVDV was inhibited in the bovine cells treated with boIFN-tau. The replication of BVDV was completely suppressed by boIFN-tau at a concentration higher than 10(2) U/ml. In order to examine the effect of boIFN-tau on virus propagation in cattle persistently infected (PI) with non-cytopathic BVDV, boIFN-tau was subcutaneously administered to PI cattle at 10(5) U/kg or 10(6) U/kg body weight 5 times per week for 2 weeks. No physical abnormality such as depression was observed in the cattle during the experiment. The mean BVDV titers in the serum of the PI cattle decreased slightly during the boIFN-tau administration period with the dose of 10(6) U/kg. However, the BVDV titers in the serum returned to the pre-administration level after the final boIFN-tau administration. These results suggest that boIFN-tau demonstrates an anti-BVDV effect, reducing the BVDV level in serum transiently when injected into PI cattle.

Defect reduction in GaN on dome-shaped patterned-sapphire substrates

NASA Astrophysics Data System (ADS)

Chen, Po-Hsun; Su, Vin-Cent; Wu, Shang-Hsuan; Lin, Ray-Ming; Kuan, Chieh-Hsiung

2018-02-01

This paper demonstrates the behavior of defect reduction in un-doped GaN (u-GaN) grown on a commercial dome-shaped patterned-sapphire substrate (CDPSS). Residual strain inside the u-GaN grown on the CDPSS have been investigated as well. As verified by the experimentally measured data, the limited growth rate of the u-GaN on the sidewall of the CDPSS enhances the lateral growth of the GaN on the trench region while increasing the growth time. This subsequently contributes to improve the crystalline quality of the GaN on the CDPSS. The more prominent dislocations occur in the u-GaN epilayers on the CDPSS after reaching the summit of the accumulated strain inside the epilayers. Such prominent bent dislocations improve their blocking abilities, followed by the achievement of the better crystalline quality for the growth of the u-GaN on the CDPSS.

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.

Workplace social capital and the onset of major depressive episode among workers in Japan: a 3-year prospective cohort study.

PubMed

Sakuraya, Asuka; Imamura, Kotaro; Inoue, Akiomi; Tsutsumi, Akizumi; Shimazu, Akihito; Takahashi, Masaya; Totsuzaki, Takafumi; Kawakami, Norito

2017-06-01

This study examined the prospective association of workplace social capital (WSC) with major depressive episode (MDE) among Japanese employees. A 3-year prospective cohort study was conducted among 1058 employees from a private think-tank company who participated in a baseline survey; after excluding those with MDE in the past 12 months, 929 were followed up. WSC at baseline was measured using a 3-item scale. MDE was assessed at baseline and at follow-up every year, by using a web-based, self-administered version of the WHO Composite International Diagnostic Interview (WHO-CIDI) 3.0 depression section, based on the Diagnostic and Statistical Manual of Mental Disorders Fourth Edition: Text Revision (DSM-IV-TR)/DSM-5 criteria. Cox discrete-time hazards analyses were used to estimate HRs and 95% CIs, adjusting for covariates. A group with middle-level WSC scores had the lowest risk of MDE after being fully adjusted (HR 0.34, 95% CI 0.14 to 0.84, p=0.02). The relationship between WSC and MDE was U-shaped, although a non-linear model fit better than a linear model, with only marginally statistical significance (p=0.06). Dichotomised and continuous variables of WSC scores were significantly and negatively associated with MDE (p=0.03 and p<0.01, respectively). The current study replicated a previous finding from Finland that WSC was a protective factor of the onset of MDE in Japan. The slightly U-shaped relationship, that is, the group with high WSC having a small elevated risk of MDE, may reflect a dark side of WSC in a country with collectivity-oriented and hierarchy-oriented culture, such as Japan. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Exploring the Convergence of the Liberal Arts Model and the Ecuadorian Culture in a Latin American University

ERIC Educational Resources Information Center

Santana Paredes, Matias

2013-01-01

The replication of the U.S. cultural models in business and social organizations is a common practice in Latin America. In Ecuador, a university operates under the liberal arts model, understanding it as a replication of an U.S. cultural model, in an environment where the Ecuadorian cultural beliefs and values constitute the national cultural…

Deletion of the S component inverted repeat sequence c' and the nonessential genes U(S)1 through U(S)5 from the herpes simplex virus type 1 genome substantially impairs productive viral infection in cell culture and pathogenesis in the rat central nervous system.

PubMed

Rasty, S; Poliani, P L; Fink, D J; Glorioso, J C

1997-08-01

A distinctive feature of the genetic make-up of herpes simplex virus type 1 (HSV-1), a human neurotropic virus, is that approximately half of the 81 known viral genes are not absolutely required for productive infection in Vero cells, and most can be individually deleted without substantially impairing viral replication in cell culture. If large blocks of contiguous viral genes could be replaced with foreign DNA sequences, it would be possible to engineer highly attenuated recombinant HSV-1 gene transfer vectors capable of carrying large cellular genes or multiple genes having related functions. We report the isolation and characterization of an HSV-1 mutant, designated d311, containing a 12 kb deletion of viral DNA located between the L-S Junction a sequence and the U(S)6 gene, spanning the S component inverted repeat sequence c' and the nonessential genes U(S)1 through U(S)5. Replication of d311 was totally inhibited in rat B103 and mouse Neuro-2A neuroblastoma cell lines, and was reduced by over three orders of magnitude in human SK-N-SH neuroblastoma cells compared to wild-type (wt) HSV-1 KOS. This suggested that the deleted genes, while nonessential for replication in Vero cells, play an important role in HSV replication in neuronal cells, particularly those of rodent origin. Unlike wt KOS which replicated locally and spread to other regions of brain following stereotactic inoculation into rat hippocampus, d311 was unable to replicate and spread within the brain, and did not cause any apparent local neuronal cell damage. These results demonstrate that d311 is highly attenuated for the rat central nervous system. d311 and other mutants of HSV containing major deletions of the nonessential genes within U(S) have the potential to serve as useful tools for gene transfer applications to brain.

Two subunits of human ORC are dispensable for DNA replication and proliferation.

PubMed

Shibata, Etsuko; Kiran, Manjari; Shibata, Yoshiyuki; Singh, Samarendra; Kiran, Shashi; Dutta, Anindya

2016-12-01

The six-subunit Origin Recognition Complex (ORC) is believed to be an essential eukaryotic ATPase that binds to origins of replication as a ring-shaped heterohexamer to load MCM2-7 and initiate DNA replication. We have discovered that human cell lines in culture proliferate with intact chromosomal origins of replication after disruption of both alleles of ORC2 or of the ATPase subunit, ORC1 . The ORC1 or ORC2 -depleted cells replicate with decreased chromatin loading of MCM2-7 and become critically dependent on another ATPase, CDC6, for survival and DNA replication. Thus, either the ORC ring lacking a subunit, even its ATPase subunit, can load enough MCM2-7 in partnership with CDC6 to initiate DNA replication, or cells have an ORC-independent, CDC6-dependent mechanism to load MCM2-7 on origins of replication.

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

PubMed

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

1998-06-01

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

In-vitro replication of Chelonid herpesvirus 5 in organotypic skin cultures from Hawaiian green turtles (Chelonia mydas)

USGS Publications Warehouse

Work, Thierry M.; Dagenais, Julie; Weatherby, Tina; Ackermann, Mathias; Balazs, George H.

2017-01-01

Fibropapillomatosis (FP) is a tumor disease of marine turtles associated with Chelonid herpesvirus 5 (ChHV5) that has historically been refractory to growth in tissue culture. Here, we show for the first time de novo formation of ChHV5-positive intranuclear inclusions in cultured green turtle cells, which is indicative for active lytic replication of the virus. The minimal requirements to achieve lytic replication in cultured cells included 1) either in-vitro culturing of ChHV5-positive tumor biopsies (plugs) or organotypic cultures (rafts) consisting of ChHV5-positive turtle fibroblasts in collagen rafts seeded with turtle keratinocytes and 2) keratinocyte maturation induced by raising raft or biopsy cultures to the air-liquid interface. Virus growth was confirmed by detailed electron microscopic studies revealing intranuclear sun-shaped capsid factories, tubules, various stages of capsid formation, nuclear export by budding into the perinuclear space, tegumentation, and envelopment to complete de novo virus production. Membrane synthesis was also observed as a sign for active viral replication. Interestingly, cytoplasmic particles became associated with keratin filaments, a feature not seen in conventional monolayer cell cultures where most studies of herpesvirus replication have been performed. Our findings draw a rich and realistic picture of ChHV5 replication in cells derived from its natural host and may be crucial not only to better understand ChHV5 circulation but also to eventually complete Koch's postulates for FP. Moreover, the principles described here may serve as model to culture other viruses that are resistant to replication in conventional cell culture.

Genetic Bio-Ancestry and Social Construction of Racial Classification in Social Surveys in the Contemporary United States

PubMed Central

Guo, Guang; Fu, Yilan; Lee, Hedwig; Cai, Tianji; Harris, Kathleen Mullan; Li, Yi

2013-01-01

Self-reported race is generally considered the basis for racial classification in social surveys, including the U.S. census. Drawing on recent advances in human molecular genetics and social science perspectives of socially constructed race, our study takes into account both genetic bio-ancestry and social context in understanding racial classification. This article accomplishes two objectives. First, our research establishes geographic genetic bio-ancestry as a component of racial classification. Second, it shows how social forces trump biology in racial classification and/or how social context interacts with bio-ancestry in shaping racial classification. The findings were replicated in two racially and ethnically diverse data sets: the College Roommate Study (N = 2,065) and the National Longitudinal Study of Adolescent Health (N = 2,281). PMID:24019100

The auditory dynamic attending theory revisited: A closer look at the pitch comparison task.

PubMed

Bauer, Anna-Katharina R; Jaeger, Manuela; Thorne, Jeremy D; Bendixen, Alexandra; Debener, Stefan

2015-11-11

The dynamic attending theory as originally proposed by Jones, 1976. Psychol. Rev. 83(5), 323-355 posits that tone sequences presented at a regular rhythm entrain attentional oscillations and thereby facilitate the processing of sounds presented in phase with this rhythm. The increased interest in neural correlates of dynamic attending requires robust behavioral indicators of the phenomenon. Here we aimed to replicate and complement the most prominent experimental implementation of dynamic attending (Jones et al., 2002. Psychol. Sci. 13(4), 313-319). The paradigm uses a pitch comparison task in which two tones, the initial and the last of a longer series, have to be compared. In-between the two, distractor tones with variable pitch are presented, at a regular pace. A comparison tone presented in phase with the entrained rhythm is hypothesized to lead to better behavioral performance. Aiming for a conceptual replication, four different variations of the original paradigm were created which were followed by an exact replication attempt. Across all five experiments, only 40 of the 140 tested participants showed the hypothesized pattern of an inverted U-shaped profile in task accuracy, and the group average effects did not replicate the pattern reported by Jones et al., 2002. Psychol. Sci. 13(4), 313-319 in any of the five experiments. However, clear evidence for a relationship between musicality and overall behavioral performance was found. This study casts doubt on the suitability of the pitch comparison task for demonstrating auditory dynamic attending. We discuss alternative tasks that have been shown to support dynamic attending theory, thus lending themselves more readily to studying its neural correlates. This article is part of a Special Issue entitled SI: Prediction and Attention. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Remote Acculturation of Early Adolescents in Jamaica towards European American Culture: A Replication and Extension

PubMed Central

Ferguson, Gail M.; Bornstein, Marc H.

2015-01-01

Remote acculturation is a modern form of non-immigrant acculturation identified among early adolescents in Jamaica as “Americanization”. This study aimed to replicate the original remote acculturation findings in a new cohort of early adolescents in Jamaica (n = 222; M = 12.08 years) and to extend our understanding of remote acculturation by investigating potential vehicles of indirect and intermittent intercultural contact. Cluster analyses replicated prior findings: Relative to Traditional Jamaican adolescents (62%), Americanized Jamaican adolescents (38%) reported stronger European American cultural orientation, lower Jamaican orientation, lower family obligations, and greater conflict with parents. More U.S. media (girls) and less local media and local sports (all) were the primary vehicles of intercultural contact predicting higher odds of Americanization. U.S. food, U.S. tourism, and transnational communication were also linked to U.S. orientation. Findings have implications for acculturation research and for practice and policy targeting Caribbean youth and families. PMID:25709142

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

PubMed

Hamperl, Stephan; Cimprich, Karlene A

2016-12-01

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

Controlling Energy Performance on the Big Stage - The New York Times Company

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

Settlemyre, Kevin; Regnier, Cindy

2015-08-01

The Times partnered with the U.S. Department of Energy (DOE) as part of DOE’s Commercial Building Partnerships (CBP) Program to develop a post-occupancy evaluation (POE) of three EEMs that were implemented during the construction of The Times building between 2004-2006. With aggressive goals to reduce energy use and carbon emissions at a national level, one strategy of the US Department of Energy is looking to exemplary buildings that have already invested in new approaches to achieving the energy performance goals that are now needed at scale. The Times building incorporated a number of innovative technologies, systems and processes that makemore » their project a model for widespread replication in new and existing buildings. The measured results from the post occupancy evaluation study, the tools and processes developed, and continuous improvements in the performance and cost of the systems studied suggest that these savings are scalable and replicable in a wide range of commercial buildings nationwide.« less

U.S.-MEXICO BORDER PROGRAM ARIZONA BORDER STUDY--QA ANALYTICAL RESULTS FOR METALS IN REPLICATE SAMPLES

EPA Science Inventory

The Metals in Replicate Samples data set contains the analytical results of measurements of up to 2 metals in 172 replicate (duplicate) samples from 86 households. Measurements were made in samples of blood. Duplicate samples for a small percentage of the total number of sample...

Expanding Health Care Access Through Education: Dissemination and Implementation of the ECHO Model.

PubMed

Katzman, Joanna G; Galloway, Kevin; Olivas, Cynthia; McCoy-Stafford, Kimberly; Duhigg, Daniel; Comerci, George; Kalishman, Summers; Buckenmaier, Chester C; McGhee, Laura; Joltes, Kristin; Bradford, Andrea; Shelley, Brian; Hernandez, Jessica; Arora, Sanjeev

2016-03-01

Project ECHO (Extension for Community Healthcare Outcomes) is an evidence-based model that provides high-quality medical education for common and complex diseases through telementoring and comanagement of patients with primary care clinicians. In a one to many knowledge network, the ECHO model helps to bridge the gap between primary care clinicians and specialists by enhancing the knowledge, skills, confidence, and practice of primary care clinicians in their local communities. As a result, patients in rural and urban underserved areas are able to receive best practice care without long waits or having to travel long distances. The ECHO model has been replicated in 43 university hubs in the United States and five other countries. A new replication tool was developed by the Project ECHO Pain team and U.S. Army Medical Command to ensure a high-fidelity replication of the model. The adoption of the tool led to successful replication of ECHO in the Army Pain initiative. This replication tool has the potential to improve the fidelity of ECHO replication efforts around the world. Reprint & Copyright © 2016 Association of Military Surgeons of the U.S.

HLA-B27 Modulates Intracellular Growth of Salmonella Pathogenicity Island 2 Mutants and Production of Cytokines in Infected Monocytic U937 Cells

PubMed Central

Ge, Shichao; He, Qiushui; Granfors, Kaisa

2012-01-01

Background Salmonella enterica serovar Enteritidis PT4 KS8822/88 replicates rapidly in HLA-B27-transfected human monocytic U937 cells. In this process, Salmonella pathogenicity island 2 (SPI-2) genes play a crucial role. Our previous study indicated that 118 Salmonella genes, including 8 SPI-2 genes were affected by HLA-B27 antigen during Salmonella infection of U937 cells. Methods/Principal Findings To further investigate Salmonella replication in HLA-B27-positive U937 monocytic cells, two SPI-2 genes, ssaS and sscA up-regulated most during Salmonella infection of HLA-B27-transfected U937 cells, were mutated by using one-step gene disruption method. Intracellular survival and replication of the mutants in the U937 cells was compared to that of the wild type strain. Surprisingly, the two mutated strains replicated significantly more than the wild type bacteria in HLA-B27-transfected cells. Secretion of tumor necrosis factor alpha (TNF-α) and interleukin 10 (IL-10) was significantly induced during the infection of HLA-B27-transfected U937 cells with the mutants. The results indicated that the certain SPI-2 genes in wild type bacteria suppress Salmonella intracellular growth and production of cytokines in infected HLA-B27-transfected cells. HLA-B27-associated modulation of Salmonella SPI-2 genes and cytokine production may have importance in the persistent infection of the bacteria and the pathogenesis of reactive arthritis. Conclusions The study provides evidence that certain virulence factors of pathogens can reduce the intracellular growth in the host cells. We suggest that the limiting intracellular growth might be a strategy for persistence of bacteria in host cells, keeping a balance between pathogenic growth and pathogenesis. PMID:22470519

Pragmatic replication trial of health promotion coaching for obesity in serious mental illness and maintenance of outcomes.

PubMed

Bartels, Stephen J; Pratt, Sarah I; Aschbrenner, Kelly A; Barre, Laura K; Naslund, John A; Wolfe, Rosemarie; Xie, Haiyi; McHugo, Gregory J; Jimenez, Daniel E; Jue, Ken; Feldman, James; Bird, Bruce L

2015-04-01

Few studies targeting obesity in serious mental illness have reported clinically significant risk reduction, and none have been replicated in community settings or demonstrated sustained outcomes after intervention withdrawal. The authors sought to replicate positive health outcomes demonstrated in a previous randomized effectiveness study of the In SHAPE program across urban community mental health organizations serving an ethnically diverse population. Persons with serious mental illness and a body mass index (BMI) >25 receiving services in three community mental health organizations were recruited and randomly assigned either to the 12-month In SHAPE program, which included membership in a public fitness club and weekly meetings with a health promotion coach, or to fitness club membership alone. The primary outcome measures were weight and cardiorespiratory fitness (as measured with the 6-minute walk test), assessed at baseline and at 3, 6, 9, 12, and 18 months. Participants (N=210) were ethnically diverse (46% were nonwhite), with a mean baseline BMI of 36.8 (SD=8.2). At 12 months, the In SHAPE group (N=104) had greater reduction in weight and improved fitness compared with the fitness club membership only group (N=106). Primary outcomes were maintained at 18 months. Approximately half of the In SHAPE group (51% at 12 months and 46% at 18 months) achieved clinically significant cardiovascular risk reduction (a weight loss ≥5% or an increase of >50 meters on the 6-minute walk test). This is the first replication study confirming the effectiveness of a health coaching intervention in achieving and sustaining clinically significant reductions in cardiovascular risk for overweight and obese persons with serious mental illness.

Tube support for moisture separator reheater

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

Sabatino, R.A.

1987-08-11

In combination with a moisture separator reheater for a nuclear steam generating power plant, a reheater is described comprising: a sealed elongated substantially horizontal tubular shell member, a cycle fluid inlet passing through the shell member in predetermined position, mositure separator means positioned within the shell member proximate the bottom portion thereof, heat exchanger means comprising a plurality of elongated metallic U-shaped members disposed substantially within the shell member, a tube sheet member supporing the U-shaped tube members at one end thereof. The improvement consists of: the tube support member means proximate the U-bend portion of the U-shaped tube membersmore » each comprising an upper movable tube support member and a lower immovable tube support member, the remainder of the tube support means being immovable, the upper movable tube support member spacing and supporting the top leg portions of the U-shaped tube members, the lower immovable tube support member spacing and supporting the bottom leg portions of the U-shaped tube members, whereby the top leg portions of the U-shaped tube members proximate the U-bend are permitted to move to compensate for any increase in radius in the U-bend portion of the U-shaped tube member due to thermal expansion.« less

76 FR 71535 - Taking of Marine Mammals Incidental to Specified Activities; U.S. Marine Corps Training Exercises...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-18

... small arms, large arms, bombs, rockets, missiles, and pyrotechnics. All munitions used at BT-11 are... shapes each time. Mine simulation shapes include MK76, MK80 series, and BDU practice bombs ranging from... disabling enemy ships or boats. During training, fixed wing or rotary wing aircraft deliver bombs against...

On the necessity of U-shaped learning.

PubMed

Carlucci, Lorenzo; Case, John

2013-01-01

A U-shaped curve in a cognitive-developmental trajectory refers to a three-step process: good performance followed by bad performance followed by good performance once again. U-shaped curves have been observed in a wide variety of cognitive-developmental and learning contexts. U-shaped learning seems to contradict the idea that learning is a monotonic, cumulative process and thus constitutes a challenge for competing theories of cognitive development and learning. U-shaped behavior in language learning (in particular in learning English past tense) has become a central topic in the Cognitive Science debate about learning models. Antagonist models (e.g., connectionism versus nativism) are often judged on their ability of modeling or accounting for U-shaped behavior. The prior literature is mostly occupied with explaining how U-shaped behavior occurs. Instead, we are interested in the necessity of this kind of apparently inefficient strategy. We present and discuss a body of results in the abstract mathematical setting of (extensions of) Gold-style computational learning theory addressing a mathematically precise version of the following question: Are there learning tasks that require U-shaped behavior? All notions considered are learning in the limit from positive data. We present results about the necessity of U-shaped learning in classical models of learning as well as in models with bounds on the memory of the learner. The pattern emerges that, for parameterized, cognitively relevant learning criteria, beyond very few initial parameter values, U-shapes are necessary for full learning power! We discuss the possible relevance of the above results for the Cognitive Science debate about learning models as well as directions for future research. Copyright © 2013 Cognitive Science Society, Inc.

Eukaryotic Replicative Helicase Subunit Interaction with DNA and Its Role in DNA Replication

PubMed Central

Martinez, Matthew P.; Wacker, Amanda L.; Bruck, Irina; Kaplan, Daniel L.

2017-01-01

The replicative helicase unwinds parental double-stranded DNA at a replication fork to provide single-stranded DNA templates for the replicative polymerases. In eukaryotes, the replicative helicase is composed of the Cdc45 protein, the heterohexameric ring-shaped Mcm2-7 complex, and the tetrameric GINS complex (CMG). The CMG proteins bind directly to DNA, as demonstrated by experiments with purified proteins. The mechanism and function of these DNA-protein interactions are presently being investigated, and a number of important discoveries relating to how the helicase proteins interact with DNA have been reported recently. While some of the protein-DNA interactions directly relate to the unwinding function of the enzyme complex, other protein-DNA interactions may be important for minichromosome maintenance (MCM) loading, origin melting or replication stress. This review describes our current understanding of how the eukaryotic replicative helicase subunits interact with DNA structures in vitro, and proposed models for the in vivo functions of replicative helicase-DNA interactions are also described. PMID:28383499

Amiloride inhibits the initiation of Coxsackievirus and poliovirus RNA replication by inhibiting VPg uridylylation.

PubMed

Ogram, Sushma A; Boone, Christopher D; McKenna, Robert; Flanegan, James B

2014-09-01

The mechanism of amiloride inhibition of Coxsackievirus B3 (CVB3) and poliovirus type 1 (PV1) RNA replication was investigated using membrane-associated RNA replication complexes. Amiloride was shown to inhibit viral RNA replication and VPgpUpU synthesis. However, the drug had no effect on polymerase elongation activity during either (-) strand or (+) strand synthesis. These findings indicated that amiloride inhibited the initiation of RNA synthesis by inhibiting VPg uridylylation. In addition, in silico binding studies showed that amiloride docks in the VPg binding site on the back of the viral RNA polymerase, 3D(pol). Since VPg binding at this site on PV1 3D(pol) was previously shown to be required for VPg uridylylation, our results suggest that amiloride inhibits VPg binding to 3D(pol). In summary, our findings are consistent with a model in which amiloride inhibits VPgpUpU synthesis and viral RNA replication by competing with VPg for binding to 3D(pol). Copyright © 2014 Elsevier Inc. All rights reserved.

Polymer deformation and filling modes during microembossing

NASA Astrophysics Data System (ADS)

Rowland, Harry D.; King, William P.

2004-12-01

This work investigates the initial stages of polymer deformation during hot embossing micro-manufacturing at processing temperatures near the glass transition temperature (Tg) of polymer films having sufficient thickness such that polymer flow is not supply limited. Several stages of polymer flow can be observed by employing stamp geometries of various widths and varying imprint conditions of time and temperature to modulate polymer viscosity. Experiments investigate conditions affecting cavity filling phenomena, including apparent polymer viscosity. Stamps with periodic ridges of height and width 4 µm and periodicity 30, 50 and 100 µm emboss trenches into polymethyl methacrylate films at Tg - 10 °C < Temboss < Tg + 20 °C. Imprint parameters of time, temperature and load are correlated with replicated polymer shape, height and imprinted area. Polymer replicates are measured by atomic force microscopy and inspected by scanning electron microscopy. Cavity size and the temperature dependence of polymer viscosity significantly influence the nature of polymer deformation in hot embossing micro-manufacturing and must be accounted for in rational process design.

Entropy of space-time outcome in a movement speed-accuracy task.

PubMed

Hsieh, Tsung-Yu; Pacheco, Matheus Maia; Newell, Karl M

2015-12-01

The experiment reported was set-up to investigate the space-time entropy of movement outcome as a function of a range of spatial (10, 20 and 30 cm) and temporal (250-2500 ms) criteria in a discrete aiming task. The variability and information entropy of the movement spatial and temporal errors considered separately increased and decreased on the respective dimension as a function of an increment of movement velocity. However, the joint space-time entropy was lowest when the relative contribution of spatial and temporal task criteria was comparable (i.e., mid-range of space-time constraints), and it increased with a greater trade-off between spatial or temporal task demands, revealing a U-shaped function across space-time task criteria. The traditional speed-accuracy functions of spatial error and temporal error considered independently mapped to this joint space-time U-shaped entropy function. The trade-off in movement tasks with joint space-time criteria is between spatial error and timing error, rather than movement speed and accuracy. Copyright © 2015 Elsevier B.V. All rights reserved.

Development of a New Punch Head Shape to Replicate Scale-Up Issues on a Laboratory Tablet Press III: Replicating sticking phenomenon using the SAS punch and evaluation by checking the tablet surface using 3D laser scanning microscope.

PubMed

Ito, Manabu; Aoki, Shigeru; Uchiyama, Jumpei; Yamato, Keisuke

2018-04-20

Sticking is a common observation in the scale-up stage on the punch tip using a commercial tableting machine. The difference in the total compression time between a laboratory and a commercial tableting machine is considered one of the main root causes of scale up issues in the tableting processes. The proposed Size Adjusted for Scale-up (SAS) punch can be used to adjust the consolidation and dwell times for commercial tableting machine. As a result, the sticking phenomenon is able to be replicated at the pilot scale stage. As reported in this paper, the quantification of sticking was measured using a 3D laser scanning microscope to check the tablet surface. It was shown that the sticking area decreased with the addition of magnesium stearate in the formulation, but the sticking depth was not affected by the additional amount of magnesium stearate. It is proposed that use of a 3D laser scanning microscope can be applied to evaluate sticking as a process analytical technology (PAT) tool and so sticking can be monitored continuously without stopping the machine. Copyright © 2018. Published by Elsevier Inc.

Fast neutron-gamma discrimination on neutron emission profile measurement on JT-60U.

PubMed

Ishii, K; Shinohara, K; Ishikawa, M; Baba, M; Isobe, M; Okamoto, A; Kitajima, S; Sasao, M

2010-10-01

A digital signal processing (DSP) system is applied to stilbene scintillation detectors of the multichannel neutron emission profile monitor in JT-60U. Automatic analysis of the neutron-γ pulse shape discrimination is a key issue to diminish the processing time in the DSP system, and it has been applied using the two-dimensional (2D) map. Linear discriminant function is used to determine the dividing line between neutron events and γ-ray events on a 2D map. In order to verify the validity of the dividing line determination, the pulse shape discrimination quality is evaluated. As a result, the γ-ray contamination in most of the beam heating phase was negligible compared with the statistical error with 10 ms time resolution.

Fast neutron-gamma discrimination on neutron emission profile measurement on JT-60U

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

Ishii, K.; Okamoto, A.; Kitajima, S.

2010-10-15

A digital signal processing (DSP) system is applied to stilbene scintillation detectors of the multichannel neutron emission profile monitor in JT-60U. Automatic analysis of the neutron-{gamma} pulse shape discrimination is a key issue to diminish the processing time in the DSP system, and it has been applied using the two-dimensional (2D) map. Linear discriminant function is used to determine the dividing line between neutron events and {gamma}-ray events on a 2D map. In order to verify the validity of the dividing line determination, the pulse shape discrimination quality is evaluated. As a result, the {gamma}-ray contamination in most of themore » beam heating phase was negligible compared with the statistical error with 10 ms time resolution.« less

Effects of aging on the relationship between cognitive demand and step variability during dual-task walking.

PubMed

Decker, Leslie M; Cignetti, Fabien; Hunt, Nathaniel; Potter, Jane F; Stergiou, Nicholas; Studenski, Stephanie A

2016-08-01

A U-shaped relationship between cognitive demand and gait control may exist in dual-task situations, reflecting opposing effects of external focus of attention and attentional resource competition. The purpose of the study was twofold: to examine whether gait control, as evaluated from step-to-step variability, is related to cognitive task difficulty in a U-shaped manner and to determine whether age modifies this relationship. Young and older adults walked on a treadmill without attentional requirement and while performing a dichotic listening task under three attention conditions: non-forced (NF), forced-right (FR), and forced-left (FL). The conditions increased in their attentional demand and requirement for inhibitory control. Gait control was evaluated by the variability of step parameters related to balance control (step width) and rhythmic stepping pattern (step length and step time). A U-shaped relationship was found for step width variability in both young and older adults and for step time variability in older adults only. Cognitive performance during dual tasking was maintained in both young and older adults. The U-shaped relationship, which presumably results from a trade-off between an external focus of attention and competition for attentional resources, implies that higher-level cognitive processes are involved in walking in young and older adults. Specifically, while these processes are initially involved only in the control of (lateral) balance during gait, they become necessary for the control of (fore-aft) rhythmic stepping pattern in older adults, suggesting that attentional resources turn out to be needed in all facets of walking with aging. Finally, despite the cognitive resources required by walking, both young and older adults spontaneously adopted a "posture second" strategy, prioritizing the cognitive task over the gait task.

Polymer deformation in Brownian ratchets: theory and molecular dynamics simulations.

PubMed

Kenward, Martin; Slater, Gary W

2008-11-01

We examine polymers in the presence of an applied asymmetric sawtooth (ratchet) potential which is periodically switched on and off, using molecular dynamics (MD) simulations with an explicit Lennard-Jones solvent. We show that the distribution of the center of mass for a polymer in a ratchet is relatively wide for potential well depths U0 on the order of several kBT. The application of the ratchet potential also deforms the polymer chains. With increasing U0 the Flory exponent varies from that for a free three-dimensional (3D) chain, nu=35 (U0=0), to that corresponding to a 2D compressed (pancake-shaped) polymer with a value of nu=34 for moderate U0. This has the added effect of decreasing a polymer's diffusion coefficient from its 3D value D3D to that of a pancaked-shaped polymer moving parallel to its minor axis D2D. The result is that a polymer then has a time-dependent diffusion coefficient D(t) during the ratchet off time. We further show that this suggests a different method to operate a ratchet, where the off time of the ratchet, toff, is defined in terms of the relaxation time of the polymer, tauR. We also derive a modified version of the Bader ratchet model [Bader, Proc. Natl. Acad. Sci. U.S.A. 96, 13165 (1999)] which accounts for this deformation and we present a simple expression to describe the time dependent diffusion coefficient D(t). Using this model we then illustrate that polymer deformation can be used to modulate polymer migration in a ratchet potential.

78 FR 19224 - Taking of Marine Mammals Incidental to Specified Activities; U.S. Marine Corps Training Exercises...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-29

... arms, large arms, bombs, rockets, missiles, and pyrotechnics. All munitions used at BT-11 are inert... shapes each time. Mine simulation shapes include MK76, MK80 series, and BDU practice bombs ranging from... bombs against surface maritime targets at BT-9 or BT-11,day or night, using either unguided or precision...

Space Optic Manufacturing - X-ray Mirror

NASA Technical Reports Server (NTRS)

1998-01-01

NASA's Space Optics Manufacturing Center has been working to expand our view of the universe via sophisticated new telescopes. The Optics Center's goal is to develop low-cost, advanced space optics technologies for the NASA program in the 21st century - including the long-term goal of imaging Earth-like planets in distant solar systems. To reduce the cost of mirror fabrication, Marshall Space Flight Center (MSFC) has developed replication techniques, the machinery and materials to replicate electro-formed nickel mirrors. The process allows fabricating precisely shaped mandrels to be used and reused as masters for replicating high-quality mirrors. This image shows a lightweight replicated x-ray mirror with gold coatings applied.

Space Science

NASA Image and Video Library

1998-08-31

NASA's Space Optics Manufacturing Center has been working to expand our view of the universe via sophisticated new telescopes. The Optics Center's goal is to develop low-cost, advanced space optics technologies for the NASA program in the 21st century - including the long-term goal of imaging Earth-like planets in distant solar systems. To reduce the cost of mirror fabrication, Marshall Space Flight Center (MSFC) has developed replication techniques, the machinery and materials to replicate electro-formed nickel mirrors. The process allows fabricating precisely shaped mandrels to be used and reused as masters for replicating high-quality mirrors. This image shows a lightweight replicated x-ray mirror with gold coatings applied.

Space Science

NASA Image and Video Library

1999-04-01

NASA's Space Optics Manufacturing Center has been working to expand our view of the universe via sophisticated new telescopes. The Optics Center's goal is to develop low-cost, advanced space optics technologies to the NASA program in the 21st century - including the long-term goal of imaging Earth-like planets in distant solar systems. To reduce the cost of mirror fabrication, Marshall Space Flight Center (MSFC) has developed replication techniques, the machinery, and materials to replicate electro-formed nickel mirrors. The process allows fabricating precisely shaped mandrels to be used and reused as masters for replicating high-quality mirrors. Photograph shows J.R. Griffith inspecting a replicated x-ray mirror mandrel.

Life Cycle Characterization of Sulfolobus Monocaudavirus 1, an Extremophilic Spindle-Shaped Virus with Extracellular Tail Development

PubMed Central

Uldahl, Kristine B.; Jensen, Signe B.; Bhoobalan-Chitty, Yuvaraj; Martínez-Álvarez, Laura; Papathanasiou, Pavlos

2016-01-01

ABSTRACT We provide here, for the first time, insights into the initial infection stages of a large spindle-shaped archaeal virus and explore the following life cycle events. Our observations suggest that Sulfolobus monocaudavirus 1 (SMV1) exhibits a high adsorption rate and that virions adsorb to the host cells via three distinct attachment modes: nosecone association, body association, and body/tail association. In the body/tail association mode, the entire virion, including the tail(s), aligns to the host cell surface and the main body is greatly flattened, suggesting a possible fusion entry mechanism. Upon infection, the intracellular replication cycle lasts about 8 h, at which point the virions are released as spindle-shaped tailless particles. Replication of the virus retarded host growth but did not cause lysis of the host cells. Once released from the host and at temperatures resembling that of its natural habitat, SMV1 starts developing one or two tails. This exceptional property of undergoing a major morphological development outside, and independently of, the host cell has been reported only once before for the related Acidianus two-tailed virus. Here, we show that SMV1 can develop tails of more than 900 nm in length, more than quadrupling the total virion length. IMPORTANCE Very little is known about the initial life cycle stages of viruses infecting hosts of the third domain of life, Archaea. This work describes the first example of an archaeal virus employing three distinct association modes. The virus under study, Sulfolobus monocaudavirus 1, is a representative of the large spindle-shaped viruses that are frequently found in acidic hot springs. The results described here will add valuable knowledge about Archaea, the least studied domain in the virology field. PMID:27053548

Life Cycle Characterization of Sulfolobus Monocaudavirus 1, an Extremophilic Spindle-Shaped Virus with Extracellular Tail Development.

PubMed

Uldahl, Kristine B; Jensen, Signe B; Bhoobalan-Chitty, Yuvaraj; Martínez-Álvarez, Laura; Papathanasiou, Pavlos; Peng, Xu

2016-06-15

We provide here, for the first time, insights into the initial infection stages of a large spindle-shaped archaeal virus and explore the following life cycle events. Our observations suggest that Sulfolobus monocaudavirus 1 (SMV1) exhibits a high adsorption rate and that virions adsorb to the host cells via three distinct attachment modes: nosecone association, body association, and body/tail association. In the body/tail association mode, the entire virion, including the tail(s), aligns to the host cell surface and the main body is greatly flattened, suggesting a possible fusion entry mechanism. Upon infection, the intracellular replication cycle lasts about 8 h, at which point the virions are released as spindle-shaped tailless particles. Replication of the virus retarded host growth but did not cause lysis of the host cells. Once released from the host and at temperatures resembling that of its natural habitat, SMV1 starts developing one or two tails. This exceptional property of undergoing a major morphological development outside, and independently of, the host cell has been reported only once before for the related Acidianus two-tailed virus. Here, we show that SMV1 can develop tails of more than 900 nm in length, more than quadrupling the total virion length. Very little is known about the initial life cycle stages of viruses infecting hosts of the third domain of life, Archaea This work describes the first example of an archaeal virus employing three distinct association modes. The virus under study, Sulfolobus monocaudavirus 1, is a representative of the large spindle-shaped viruses that are frequently found in acidic hot springs. The results described here will add valuable knowledge about Archaea, the least studied domain in the virology field. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

The postoperative course of gamma-glutamyl transpeptidase--a marker of cytomegalovirus (CMV) replication risk?

PubMed

Schenk, M; Zipfel, A; Kratt, T; Petersen, P; Becker, H D; Viebahn, R

2000-11-01

Cytomegalovirus (CMV) infection is a common complication in the postoperative course of liver transplantation. In order to start early prophylactic therapy, but to avoid unnecessary treatment, or expensive screening, a desirable goal in post-transplant monitoring is to find appropriate markers in standard laboratory diagnostics. In the present study, the results of a 6-week CMV replication monitoring schedule by the pp65 antigenemia assay in 100 liver graft recipients were included. The activities of transaminases, glutamate dehydrogenase and gamma-glutamyl transpeptidase (gamma-GT) were measured by routine laboratory methods. In contrast to the transaminases, the serum activity of gamma-GT increased during the first postoperative week. The maximum levels were 246 +/- 211 U/l in patients without (n = 46) and 140 +/- 89 U/l in patients with early CMV replication (n = 54; p = 0.02). Patients with gamma-GT levels below 200 U/l on the 5th postoperative day (n = 72) had a CMV replication risk of 65%, whereas those patients with gamma-GT levels above this threshold had a risk of 30% (n = 28; p = 0.0007; relative risk = 2.9). These findings provide a routinely usable marker for the identification of patients at an increased risk of CMV replication. It can be considered that these phenomena may be caused by an additional immunosuppressive effect of the CMV virus.

EdU induces DNA damage response and cell death in mESC in culture.

PubMed

Kohlmeier, Fanni; Maya-Mendoza, Apolinar; Jackson, Dean A

2013-03-01

Recently, a novel DNA replication precursor analogue called 5-ethynyl-2'-deoxyuridine (EdU) has been widely used to monitor DNA synthesis as an alternative to bromodeoxyuridine. Use of EdU benefits from simplicity and reproducibility and the simple chemical detection systems allows excellent preservation of nuclear structure. However, the alkyne moiety is highly reactive, raising the possibility that incorporation might compromise genome stability. To assess the extent of possible DNA damage, we have analysed the effect of EdU incorporation into DNA during short- and long-term cell culture using a variety of cell lines. We show that EdU incorporation has no measurable impact on the rate of elongation of replication forks during synthesis. However, using different cell lines we find that during long-term cell culture variable responses to EdU incorporation are seen, which range from delayed cell cycle progression to complete cell cycle arrest. The most profound phenotypes were seen in mouse embryonic stem cells, which following incorporation of EdU accumulated in the G2/M-phase of the cell cycle before undergoing apoptosis. In long-term cell culture, EdU incorporation also triggered a DNA damage response in all cell types analysed. Our study shows that while EdU is extremely useful to tag sites of on-going replication, for long-term studies (i.e. beyond the cell cycle in which labelling is performed), a careful analysis of cell cycle perturbations must be performed in order to ensure that any conclusions made after EdU treatment are not a direct consequence of EdU-dependent activation of cell stress responses.

Lineage diversification of fringe-toed lizards (Phrynosomatidae: Uma notata complex) in the Colorado Desert: Delimiting species in the presence of gene flow

USGS Publications Warehouse

Gottscho, Andrew D.; Wood, Dustin A.; Vandergast, Amy; Lemos Espinal, Julio A.; Gatesy, John; Reeder, Tod

2017-01-01

Multi-locus nuclear DNA data were used to delimit species of fringe-toed lizards of theUma notata complex, which are specialized for living in wind-blown sand habitats in the deserts of southwestern North America, and to infer whether Quaternary glacial cycles or Tertiary geological events were important in shaping the historical biogeography of this group. We analyzed ten nuclear loci collected using Sanger sequencing and genome-wide sequence and single-nucleotide polymorphism (SNP) data collected using restriction-associated DNA (RAD) sequencing. A combination of species discovery methods (concatenated phylogenies, parametric and non-parametric clustering algorithms) and species validation approaches (coalescent-based species tree/isolation-with-migration models) were used to delimit species, infer phylogenetic relationships, and to estimate effective population sizes, migration rates, and speciation times. Uma notata, U. inornata, U. cowlesi, and an undescribed species from Mohawk Dunes, Arizona (U. sp.) were supported as distinct in the concatenated analyses and by clustering algorithms, and all operational taxonomic units were decisively supported as distinct species by ranking hierarchical nested speciation models with Bayes factors based on coalescent-based species tree methods. However, significant unidirectional gene flow (2NM >1) from U. cowlesi and U. notata into U. rufopunctata was detected under the isolation-with-migration model. Therefore, we conservatively delimit four species-level lineages within this complex (U. inornata, U. notata, U. cowlesi, and U. sp.), treating U. rufopunctata as a hybrid population (U. notata x cowlesi). Both concatenated and coalescent-based estimates of speciation times support the hypotheses that speciation within the complex occurred during the late Pleistocene, and that the geological evolution of the Colorado River delta during this period was an important process shaping the observed phylogeographic patterns.

Various plus unique: Viral protein U as a plurifunctional protein for HIV-1 replication.

PubMed

Soper, Andrew; Juarez-Fernandez, Guillermo; Aso, Hirofumi; Moriwaki, Miyu; Yamada, Eri; Nakano, Yusuke; Koyanagi, Yoshio; Sato, Kei

2017-04-01

Human immunodeficiency virus type 1 (HIV-1), the causative agent of acquired immunodeficiency syndrome, encodes four accessory genes, one of which is viral protein U (Vpu). Recently, the study of Vpu has been of great interest. For instance, various cellular proteins are degraded (e.g. CD4) and down-modulated (e.g. tetherin) by Vpu. Vpu also antagonizes the function of tetherin and inhibits NF-κB. Moreover, Vpu is a viroporin forming ion channels and may represent a promising target for anti-HIV-1 drugs. In this review, we summarize the domains/residues that are responsible for Vpu's functions, describe the current understanding of the role of Vpu in HIV-1-infected cells, and review the effect of Vpu on HIV-1 in replication and pathogenesis. Future investigations that simultaneously assess a combination of Vpu functions are required to clearly delineate the most important functions for viral replication. Impact statement Viral protein U (Vpu) is a unique protein encoded by human immunodeficiency virus type 1 (HIV-1) and related lentiviruses, playing multiple roles in viral replication and pathogenesis. In this review, we briefly summarize the most up-to-date knowledge of HIV-1 Vpu.

Computer simulation of the classical entanglement of U-shaped particles in three dimensions

NASA Astrophysics Data System (ADS)

Maddock, Brian; Lindner, John

2014-03-01

Classical entanglement is important in a wide range of phenomena, such as velcro hook-and-loop-fasteners, seed dispersal by animal fur, and bent liquid crystal molecules. We present a computer simulation of the entanglement of U-shaped particles in three dimensions. We represent the particles by phenomenological potentials and evolve them by integrating Newton's laws of motion. We drop them into a virtual cylinder, shake them, and ultimately release the cylinder. As the particle piles relax, we quantify their entanglement by the exponential decay times of their heights, which we correlate to the particles' height-to-length ratios.

Cell lines that support replication of a novel herpes simplex virus 1 U{sub L}31 deletion mutant can properly target U{sub L}34 protein to the nuclear rim in the absence of U{sub L}31

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

Liang Li; Tanaka, Michiko; Kawaguchi, Yasushi

2004-11-10

Previous results indicated that the herpes simplex virus 1 (HSV-1) U{sub L}31 gene is necessary and sufficient for localization of the U{sub L}34 protein exclusively to the nuclear membrane of infected Hep2 cells. In the current studies, a bacterial artificial chromosome containing the entire HSV-1 strain F genome was used to construct a recombinant viral genome in which a gene encoding kanamycin resistance was inserted in place of 262 codons of the 306 codon U{sub L}31 open reading frame. The deletion virus produced virus titers approximately 10- to 50-fold lower in rabbit skin cells, more than 2000-fold lower in Veromore » cells, and more than 1500-fold lower in CV1 cells, compared to a virus bearing a restored U{sub L}31 gene. The replication of the U{sub L}31 deletion virus was restored on U{sub L}31-complementing cell lines derived either from rabbit skin cells or CV1 cells. Confocal microscopy indicated that the majority of U{sub L}34 protein localized aberrantly in the cytoplasm and nucleoplasm of Vero cells and CV1 cells, whereas U{sub L}34 protein localized at the nuclear membrane in rabbit skin cells, and U{sub L}31 complementing CV1 cells infected with the U{sub L}31 deletion virus. We conclude that rabbit skin cells encode a function that allows proper localization of U{sub L}34 protein to the nuclear membrane. We speculate that this function partially complements that of U{sub L}31 and may explain why U{sub L}31 is less critical for replication in rabbit skin cells as opposed to Vero and CV1 cells.« less

A randomized prospective comparison of the needleless mini-sling "hammock" and "U-shape" configurations for management of stress urinary incontinence: 18 month follow-up results.

PubMed

Dogan, Ozan; Basbug, Alper; Kaya, Aski Ellibes; Pulatoglu, Cigdem; Yassa, Murat

2018-06-01

To compare the efficacy of needleless mini-sling placed either retropubic (U-shape) or trans-obturator (hammock-shape) to treat stress urinary incontinence. One hundred and twenty six women were randomized in a 2:1 ratio to receive hammock-shaped or U-shaped of Contasure-NDL. All surgical procedures were performed by one senior surgeon experienced in anti-incontinence surgery with mesh. Cough-stress test was considered for objective outcome. Subjective outcomes consisted of International Consultation on Incontinence Questionnaire Short Form (ICIQ-SF), Patient Global Impression of Improvement (PGI-I) and three-item Likert scale to measure satisfaction. Assessments were performed preoperatively and at postoperative 6th, 12th and 18th month. The objective cure rates at postoperative 6th and 12th month were significantly lower in U-shape group compared to hammock-shape group (85.4 vs. 96.4%; p = 0.034) and was comparable with hammock-shape group at 18 th month postoperative (90.2 vs. 96.4%, respectively; p = 0.216). The subjective cure rates at postoperative 6th, 12th and 18th month were similar between groups (90.2/90.2/100% vs. 96.4/96.4/96.4%, respectively; p > 0.05). Median of total ICIQ-SF scores was significantly lower in hammock-shaped group (1.62 ± 2.92) compared to U-shape (3.80 ± 2.64) at 18th month (p < 0.001). The rate of patients reported as very satisfied or satisfied to the Likert scale was 90.2% in U-shape group and 96.4% in hammock group. Patients' responses to PGI-I were majorly distributed to "much better" and "very much better" with a mean score of 1.93 ± 2 in U-shape and 1.33 ± 1 in hammock group at 18th month of follow-up (p < 0.001). U-shape placement of needleless single-incision mini-sling mimicking the retropubic route did not satisfy in achieving the patient's goal when compared to hammock-shape placement.

Topologically associating domains are stable units of replication-timing regulation.

PubMed

Pope, Benjamin D; Ryba, Tyrone; Dileep, Vishnu; Yue, Feng; Wu, Weisheng; Denas, Olgert; Vera, Daniel L; Wang, Yanli; Hansen, R Scott; Canfield, Theresa K; Thurman, Robert E; Cheng, Yong; Gülsoy, Günhan; Dennis, Jonathan H; Snyder, Michael P; Stamatoyannopoulos, John A; Taylor, James; Hardison, Ross C; Kahveci, Tamer; Ren, Bing; Gilbert, David M

2014-11-20

Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell-type-specific with at least half the genome switching replication timing during development, primarily in units of 400-800 kilobases ('replication domains'), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements. Early and late replication correlate, respectively, with open and closed three-dimensional chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, late replication correlates with lamina-associated domains (LADs). Recent Hi-C mapping has unveiled substructure within chromatin compartments called topologically associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to replication domains. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale. Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure. Here we localize boundaries of replication domains to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, replication domain boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure replication domain boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type-specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell-type-specific sub-nuclear compartmentalization and replication timing with developmentally stable structural domains and offer a unified model for large-scale chromosome structure and function.

Biosonar, diving and movements of two tagged white-beaked dolphin in Icelandic waters

NASA Astrophysics Data System (ADS)

Rasmussen, M. H.; Akamatsu, T.; Teilmann, J.; Vikingsson, G.; Miller, L. A.

2013-04-01

For the first time bio-logging tags were attached to free-ranging white-beaked dolphins, Lagenorhynchus albirostris. A satellite tag was attached to one animal while an acoustic A-tag, a time-depth recorder and a VHF transmitter complex was attached to a second dolphin with a suction cup. The satellite tag transmitted for 201 day, during which time the dolphin stayed in the coastal waters of western Iceland. The acoustic tag complex was on the second animal for 13 h and 40 min and provided the first insight into the echolocation behaviour of a free-ranging white-beaked dolphin. The tag registered 162 dives. The dolphin dove to a maximum depth of 45 m, which is about the depth of the bay in which the dolphin was swimming. Two basic types of dives were identified; U-shaped and V-shaped dives. The dolphin used more time in U-shaped dives, more clicks and sonar signals with shorter click intervals compared to those it used in V-shaped dives. The dolphin was in acoustic contact with other dolphins about five hours after it was released and stayed with these for the rest of the tagging time. Possible foraging attempts were found based on the reduction of click intervals from about 100 ms to 2-3 ms, which suggests a prey capture attempt. We found 19 punitive prey capture attempts and of these 53% occurred at the maximum dive depth. This suggests that more than half of the possible prey capture events occurred at or near the sea bed.

Developing a novel catalytic approach for imine formation by using self-replicating catalyst

NASA Astrophysics Data System (ADS)

Nasir, Fatin Ilyani; Philp, Douglas; Hasbullah, Siti Aishah; Hassan, Nurul Izzaty

2015-09-01

Synthesis of imine compounds usually results in moderate yield due its reversibility characteristic and prone to hydrolysis. Hence, to increase the formation of imine compound, self-replicating catalyst was introduced. The self-replicating catalyst is the imine product itself. The first imine compound, 4-{[4-(3,5-Dimethyl-phenylcarbamoyl)-benzylidene]-amino}-phenyl)-acetic acid has been synthesized from 4-Amino-N-(3,5-dimethyl-phenyl)-benzamide and (4-formyl-phenyl)-acetic acid. Simultaneously, 4-formylbenzoic acid was reacted with thionyl chloride to produce 4-formylbenzoyl chloride, which was then reacted with 2-amino-4,6-dimethylpyridine in the presence of triethylamine to afford N-(4,6-dimethyl-pyridin-2-yl)-4-formyl-benzamide. N-(4,6-dimethyl-pyridin-2-yl)-4-formyl-benzamide formed then reacted with 4-amino-2-methylbenzoic acid to form the second imine derivative, 4-{[4-(4,6-dimethyl-pyridin-2-ylcarbamoyl)-benzylidene]-amino}-2-methyl-benzoic acid. The concentration time profile for the synthesis of self-replicating imine 1 reveals the classic sigmoidal shape characteristics of an autocatalytic process and the rate of the reaction are higher than that observed in the absence of recognition. In order to demonstrate the nature of self-replicating catalyst, a preformed imine 1 was doped into the reaction mixture of amine 1 and the corresponding aldehyde, 4-formylbenzoic acid. The insertion of substoichiometric amounts (15 mol%) of imine 1 at the start of the reaction has accelerated the rate formation of imine 1.

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

The contribution of lot-to-lot variation to the measurement uncertainty of an LC-MS-based multi-mycotoxin assay.

PubMed

Stadler, David; Sulyok, Michael; Schuhmacher, Rainer; Berthiller, Franz; Krska, Rudolf

2018-05-01

Multi-mycotoxin determination by LC-MS is commonly based on external solvent-based or matrix-matched calibration and, if necessary, the correction for the method bias. In everyday practice, the method bias (expressed as apparent recovery RA), which may be caused by losses during the recovery process and/or signal/suppression enhancement, is evaluated by replicate analysis of a single spiked lot of a matrix. However, RA may vary for different lots of the same matrix, i.e., lot-to-lot variation, which can result in a higher relative expanded measurement uncertainty (U r ). We applied a straightforward procedure for the calculation of U r from the within-laboratory reproducibility, which is also called intermediate precision, and the uncertainty of RA (u r,RA ). To estimate the contribution of the lot-to-lot variation to U r , the measurement results of one replicate of seven different lots of figs and maize and seven replicates of a single lot of these matrices, respectively, were used to calculate U r . The lot-to-lot variation was contributing to u r,RA and thus to U r for the majority of the 66 evaluated analytes in both figs and maize. The major contributions of the lot-to-lot variation to u r,RA were differences in analyte recovery in figs and relative matrix effects in maize. U r was estimated from long-term participation in proficiency test schemes with 58%. Provided proper validation, a fit-for-purpose U r of 50% was proposed for measurement results obtained by an LC-MS-based multi-mycotoxin assay, independent of the concentration of the analytes.

Male Mutation Bias Is the Main Force Shaping Chromosomal Substitution Rates in Monotreme Mammals

PubMed Central

Link, Vivian; Aguilar-Gómez, Diana; Ramírez-Suástegui, Ciro; Hurst, Laurence D.

2017-01-01

Abstract In many species, spermatogenesis involves more cell divisions than oogenesis, and the male germline, therefore, accumulates more DNA replication errors, a phenomenon known as male mutation bias. The extent of male mutation bias (α) is estimated by comparing substitution rates of the X, Y, and autosomal chromosomes, as these chromosomes spend different proportions of their time in the germlines of the two sexes. Male mutation bias has been characterized in placental and marsupial mammals as well as birds, but analyses in monotremes failed to detect any such bias. Monotremes are an ancient lineage of egg-laying mammals with distinct biological properties, which include unique germline features. Here, we sought to assess the presence and potential characteristics of male mutation bias in platypus and the short-beaked echidna based on substitution rate analyses of X, Y, and autosomes. We established the presence of moderate male mutation bias in monotremes, corresponding to an α value of 2.12–3.69. Given that it has been unclear what proportion of the variation in substitution rates on the different chromosomal classes is really due to differential number of replications, we analyzed the influence of other confounding forces (selection, replication-timing, etc.) and found that male mutation bias is the main force explaining the between-chromosome classes differences in substitution rates. Finally, we estimated the proportion of variation at the gene level in substitution rates that is owing to replication effects and found that this phenomenon can explain >68% of these variations in monotremes, and in control species, rodents, and primates. PMID:28922870

Differential virulence mechanisms of infectious hematopoietic necrosis virus in rainbow trout (Oncorhynchus mykiss) include host entry and virus replication kinetics

USGS Publications Warehouse

Penaranda, M.M.D.; Purcell, M.K.; Kurath, G.

2009-01-01

Host specificity is a phenomenon exhibited by all viruses. For the fish rhabdovirus infectious hematopoietic necrosis virus (IHNV), differential specificity of virus strains from the U and M genogroups has been established both in the field and in experimental challenges. In rainbow trout (Oncorhynchus mykiss), M IHNV strains are consistently more prevalent and more virulent than U IHNV. The basis of the differential ability of these two IHNV genogroups to cause disease in rainbow trout was investigated in live infection challenges with representative U and M IHNV strains. When IHNV was delivered by intraperitoneal injection, the mortality caused by U IHNV increased, indicating that the low virulence of U IHNV is partly due to inefficiency in entering the trout host. Analyses of in vivo replication showed that U IHNV consistently had lower prevalence and lower viral load than M IHNV during the course of infection. In analyses of the host immune response, M IHNV-infected fish consistently had higher and longer expression of innate immune-related genes such as Mx-1. This suggests that the higher virulence of M IHNV is not due to suppression of the immune response in rainbow trout. Taken together, the results support a kinetics hypothesis wherein faster replication enables M IHNV to rapidly achieve a threshold level of virus necessary to override the strong host innate immune response. ?? 2009 SGM.

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

Fulkerson, Edward; Lanning, Rodney K.; Telford, Steven

A device includes a u-channel shaped member and a printed circuit board including a plurality of capacitors. Each of the plurality of capacitors has a mounting surface mounted to the printed circuit board and an opposing heat transfer surface thermally coupled to the u-channel shaped member. The device also includes an output cable coupled to the printed circuit board and a return cable coupled to the printed circuit board. The device further includes a control transistor disposed inside the u-channel shaped member and a current sensing resistor disposed inside the u-channel shaped member.

A Parametric Approach to Shape Field-Relevant Blast Wave Profiles in Compressed-Gas-Driven Shock Tube

PubMed Central

Sundaramurthy, Aravind; Chandra, Namas

2014-01-01

Detonation of a high-explosive produces shock-blast wave, shrapnel, and gaseous products. While direct exposure to blast is a concern near the epicenter, shock-blast can affect subjects, even at farther distances. When a pure shock-blast wave encounters the subject, in the absence of shrapnels, fall, or gaseous products the loading is termed as primary blast loading and is the subject of this paper. The wave profile is characterized by blast overpressure, positive time duration, and impulse and called herein as shock-blast wave parameters (SWPs). These parameters in turn are uniquely determined by the strength of high explosive and the distance of the human subjects from the epicenter. The shape and magnitude of the profile determine the severity of injury to the subjects. As shown in some of our recent works (1–3), the profile not only determines the survival of the subjects (e.g., animals) but also the acute and chronic biomechanical injuries along with the following bio-chemical sequelae. It is extremely important to carefully design and operate the shock tube to produce field-relevant SWPs. Furthermore, it is vital to identify and eliminate the artifacts that are inadvertently introduced in the shock-blast profile that may affect the results. In this work, we examine the relationship between shock tube adjustable parameters (SAPs) and SWPs that can be used to control the blast profile; the results can be easily applied to many of the laboratory shock tubes. Further, replication of shock profile (magnitude and shape) can be related to field explosions and can be a standard in comparing results across different laboratories. Forty experiments are carried out by judiciously varying SAPs such as membrane thickness, breech length (66.68–1209.68 mm), measurement location, and type of driver gas (nitrogen, helium). The effects SAPs have on the resulting shock-blast profiles are shown. Also, the shock-blast profiles of a TNT explosion from ConWep software is compared with the profiles obtained from the shock tube. To conclude, our experimental results demonstrate that a compressed-gas shock tube when designed and operated carefully can replicate the blast time profiles of field explosions accurately. Such a faithful replication is an essential first step when studying the effects of blast induced neurotrauma using animal models. PMID:25520701

Roles of polypyrimidine tract binding proteins in major immediate-early gene expression and viral replication of human cytomegalovirus.

PubMed

Cosme, Ruth S Cruz; Yamamura, Yasuhiro; Tang, Qiyi

2009-04-01

Human cytomegalovirus (HCMV), a member of the beta subgroup of the family Herpesviridae, causes serious health problems worldwide. HCMV gene expression in host cells is a well-defined sequential process: immediate-early (IE) gene expression, early-gene expression, DNA replication, and late-gene expression. The most abundant IE gene, major IE (MIE) gene pre-mRNA, needs to be spliced before being exported to the cytoplasm for translation. In this study, the regulation of MIE gene splicing was investigated; in so doing, we found that polypyrimidine tract binding proteins (PTBs) strongly repressed MIE gene production in cotransfection assays. In addition, we discovered that the repressive effects of PTB could be rescued by splicing factor U2AF. Taken together, the results suggest that PTBs inhibit MIE gene splicing by competing with U2AF65 for binding to the polypyrimidine tract in pre-mRNA. In intron deletion mutation assays and RNA detection experiments (reverse transcription [RT]-PCR and real-time RT-PCR), we further observed that PTBs target all the introns of the MIE gene, especially intron 2, and affect gene splicing, which was reflected in the variation in the ratio of pre-mRNA to mRNA. Using transfection assays, we demonstrated that PTB knockdown cells induce a higher degree of MIE gene splicing/expression. Consistently, HCMV can produce more viral proteins and viral particles in PTB knockdown cells after infection. We conclude that PTB inhibits HCMV replication by interfering with MIE gene splicing through competition with U2AF for binding to the polypyrimidine tract in MIE gene introns.

Roles of Polypyrimidine Tract Binding Proteins in Major Immediate-Early Gene Expression and Viral Replication of Human Cytomegalovirus▿

PubMed Central

Cosme, Ruth S. Cruz; Yamamura, Yasuhiro; Tang, Qiyi

2009-01-01

Human cytomegalovirus (HCMV), a member of the β subgroup of the family Herpesviridae, causes serious health problems worldwide. HCMV gene expression in host cells is a well-defined sequential process: immediate-early (IE) gene expression, early-gene expression, DNA replication, and late-gene expression. The most abundant IE gene, major IE (MIE) gene pre-mRNA, needs to be spliced before being exported to the cytoplasm for translation. In this study, the regulation of MIE gene splicing was investigated; in so doing, we found that polypyrimidine tract binding proteins (PTBs) strongly repressed MIE gene production in cotransfection assays. In addition, we discovered that the repressive effects of PTB could be rescued by splicing factor U2AF. Taken together, the results suggest that PTBs inhibit MIE gene splicing by competing with U2AF65 for binding to the polypyrimidine tract in pre-mRNA. In intron deletion mutation assays and RNA detection experiments (reverse transcription [RT]-PCR and real-time RT-PCR), we further observed that PTBs target all the introns of the MIE gene, especially intron 2, and affect gene splicing, which was reflected in the variation in the ratio of pre-mRNA to mRNA. Using transfection assays, we demonstrated that PTB knockdown cells induce a higher degree of MIE gene splicing/expression. Consistently, HCMV can produce more viral proteins and viral particles in PTB knockdown cells after infection. We conclude that PTB inhibits HCMV replication by interfering with MIE gene splicing through competition with U2AF for binding to the polypyrimidine tract in MIE gene introns. PMID:19144709

DNA replication stress induces deregulation of the cell cycle events in root meristems of Allium cepa

PubMed Central

Żabka, Aneta; Polit, Justyna Teresa; Maszewski, Janusz

2012-01-01

Background and Aims Prolonged treatment of Allium cepa root meristems with changing concentrations of hydroxyurea (HU) results in either premature chromosome condensation or cell nuclei with an uncommon form of biphasic chromatin organization. The aim of the current study was to assess conditions that compromise cell cycle checkpoints and convert DNA replication stress into an abnormal course of mitosis. Methods Interphase-mitotic (IM) cells showing gradual changes of chromatin condensation were obtained following continuous 72 h treatment of seedlings with 0·75 mm HU (without renewal of the medium). HU-treated root meristems were analysed using histochemical stainings (DNA-DAPI/Feulgen; starch-iodide and DAB staining for H2O2 production), Western blotting [cyclin B-like (CBL) proteins] and immunochemistry (BrdU incorporation, detection of γ-H2AX and H3S10 phosphorylation). Key Results Continuous treatment of onion seedlings with a low concentration of HU results in shorter root meristems, enhanced production of H2O2, γ-phosphorylation of H2AX histones and accumulation of CBL proteins. HU-induced replication stress gives rise to axially elongated cells with half interphase/half mitotic structures (IM-cells) having both decondensed and condensed domains of chromatin. Long-term HU treatment results in cell nuclei resuming S phase with gradients of BrdU labelling. This suggests a polarized distribution of factors needed to re-initiate stalled replication forks. Furthermore, prolonged HU treatment extends both the relative time span and the spatial scale of H3S10 phosphorylation known in plants. Conclusions The minimum cell length and a threshold level of accumulated CBL proteins are both determining factors by which the nucleus attains commitment to induce an asynchronous course of chromosome condensation. Replication stress-induced alterations in an orderly route of the cell cycle events probably reflect a considerable reprogramming of metabolic functions of chromatin combined with gradients of morphological changes spread along the nucleus. PMID:23087128

Commercial Building Partnerships Replication and Diffusion

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

Antonopoulos, Chrissi A.; Dillon, Heather E.; Baechler, Michael C.

2013-09-16

This study presents findings from survey and interview data investigating replication efforts of Commercial Building Partnership (CBP) partners that worked directly with the Pacific Northwest National Laboratory (PNNL). PNNL partnered directly with 12 organizations on new and retrofit construction projects, which represented approximately 28 percent of the entire U.S. Department of Energy (DOE) CBP program. Through a feedback survey mechanism, along with personal interviews, PNNL gathered quantitative and qualitative data relating to replication efforts by each organization. These data were analyzed to provide insight into two primary research areas: 1) CBP partners’ replication efforts of technologies and approaches used inmore » the CBP project to the rest of the organization’s building portfolio (including replication verification), and, 2) the market potential for technology diffusion into the total U.S. commercial building stock, as a direct result of the CBP program. The first area of this research focused specifically on replication efforts underway or planned by each CBP program participant. Factors that impact replication include motivation, organizational structure and objectives firms have for implementation of energy efficient technologies. Comparing these factors between different CBP partners revealed patterns in motivation for constructing energy efficient buildings, along with better insight into market trends for green building practices. The second area of this research develops a diffusion of innovations model to analyze potential broad market impacts of the CBP program on the commercial building industry in the United States.« less

Transcriptome analysis of rainbow trout infected with high and low virulence strains of Infectious hematopoietic necrosis virus

USGS Publications Warehouse

Purcell, Maureen K.; Marjara, Inderjit Singh; Batts, William; Kurath, Gael; Hansen, John D.

2010-01-01

There are three main genetic lineages or genogroups of Infectious hematopoietic necrosis virus (IHNV) in N. America. Strains representing the M genogroup are more virulent in rainbow trout relative to the U genogroup. In this study, we used microarray analysis to evaluate potential mechanisms responsible for host-specific virulence in rainbow trout that were given intraperitoneal injections of buffer or a representative M or U type virus strain. Reverse transcriptase quantitative PCR (RT-qPCR) was used to assess viral load and gene expression of select immune genes. Viral load was significantly higher in trout infected with the M virus starting at 24 h post-infection (p.i.) and continuing until 72 h p.i. Microarray analysis of the 48 h time point revealed 153 up-regulated and 248 down-regulated features in response to M virus infection but only 62 up-regulated and 49 down-regulated features following U virus infection. Translation and transcription features were among the most frequent down-regulated features in response to M virus infection and may be associated with the host cell shutoff phenomenon. A greater host cell shutoff response by the M virus may facilitate subversion of the host cell transcriptional machinery and enhance viral replication, suggesting the M virus may be better optimized to manipulate the rainbow trout transcriptional and translational machinery. Anti-viral associated features were the most commonly up-regulated features. A common set of features were up-regulated in both the M and U infection groups, but were induced to a higher magnitude in the M infection group. Gene expression of the anti-viral genes Mx-1 and Vig-1 was correlated but not entirely dependent on viral load in the anterior kidney. Slower replication of the U virus may allow the host more time to induce protective anti-viral immune mechanisms.

Initiation and Reinitiation of DNA Synthesis during Replication of Bacteriophage T7*

PubMed Central

Dressler, David; Wolfson, John; Magazin, Marilyn

1972-01-01

In its first round of replication, the T7 chromosome follows a simple pattern, as viewed in the electron microscope. The iniation of DNA synthesis occurs about 17% from the genetic left end of the viral DNA rod. Bidirectional DNA synthesis from this origin then generates a replicating intermediate that we call an “eye form.” In the eye form, when synthesis in the leftward direction reaches the left end of the viral chromosome, the molecule is converted into a Y-shaped replicating rod. The remaining growing point continues synthesis rightward, until presumably it runs off the right end of the DNA rod, thus terminating replication. Numerous T7 chromosomes were found in which a second round of replication had begun before the first round had finished. Analysis of these reinitiated DNA molecules showed that the second round of replication, like the first, began 17% from the end of the chromosome and involved bidirectional DNA synthesis. Images PMID:4554539

Shape-memory NiTi foams produced by replication of NaCl space-holders.

PubMed

Bansiddhi, A; Dunand, D C

2008-11-01

NiTi foams were created with a structure (32-36% open pores 70-400 microm in size) and mechanical properties (4-25 GPa stiffness, >1000 MPa compressive strength, >42% compressive ductility, and shape-memory strains up to 4%) useful for bone implant applications. A mixture of NiTi and NaCl powders was hot-isostatically pressed at 950 and 1065 degrees C and the NaCl phase was then dissolved in water. The resulting NiTi foams show interconnected pores that replicate the shape and size of the NaCl powders, indicating that NiTi powders densified significantly before NaCl melted at 801 degrees C. Densifying NiTi or other metal powders above the melting point of the space-holder permits the use of NaCl, with the following advantages compared with higher-melting, solid space-holders such as oxides and fluorides used to date: (i) no temperature limit for densification; (ii) lower cost; (iii) greater flexibility in powder (and thus pore) shape; (iv) faster dissolution; (v) reduced metal corrosion during dissolution; (vi) lower toxicity if space-holder residues remain in the foam.

Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program

PubMed Central

Foti, Rossana; Gnan, Stefano; Cornacchia, Daniela; Dileep, Vishnu; Bulut-Karslioglu, Aydan; Diehl, Sarah; Buness, Andreas; Klein, Felix A.; Huber, Wolfgang; Johnstone, Ewan; Loos, Remco; Bertone, Paul; Gilbert, David M.; Manke, Thomas; Jenuwein, Thomas; Buonomo, Sara C.B.

2016-01-01

Summary DNA replication is temporally and spatially organized in all eukaryotes, yet the molecular control and biological function of the replication-timing program are unclear. Rif1 is required for normal genome-wide regulation of replication timing, but its molecular function is poorly understood. Here we show that in mouse embryonic stem cells, Rif1 coats late-replicating domains and, with Lamin B1, identifies most of the late-replicating genome. Rif1 is an essential determinant of replication timing of non-Lamin B1-bound late domains. We further demonstrate that Rif1 defines and restricts the interactions between replication-timing domains during the G1 phase, thereby revealing a function of Rif1 as organizer of nuclear architecture. Rif1 loss affects both number and replication-timing specificity of the interactions between replication-timing domains. In addition, during the S phase, Rif1 ensures that replication of interacting domains is temporally coordinated. In summary, our study identifies Rif1 as the molecular link between nuclear architecture and replication-timing establishment in mammals. PMID:26725008

Short-term visual deprivation, tactile acuity, and haptic solid shape discrimination.

PubMed

Crabtree, Charles E; Norman, J Farley

2014-01-01

Previous psychophysical studies have reported conflicting results concerning the effects of short-term visual deprivation upon tactile acuity. Some studies have found that 45 to 90 minutes of total light deprivation produce significant improvements in participants' tactile acuity as measured with a grating orientation discrimination task. In contrast, a single 2011 study found no such improvement while attempting to replicate these earlier findings. A primary goal of the current experiment was to resolve this discrepancy in the literature by evaluating the effects of a 90-minute period of total light deprivation upon tactile grating orientation discrimination. We also evaluated the potential effect of short-term deprivation upon haptic 3-D shape discrimination using a set of naturally-shaped solid objects. According to previous research, short-term deprivation enhances performance in a tactile 2-D shape discrimination task - perhaps a similar improvement also occurs for haptic 3-D shape discrimination. The results of the current investigation demonstrate that not only does short-term visual deprivation not enhance tactile acuity, it additionally has no effect upon haptic 3-D shape discrimination. While visual deprivation had no effect in our study, there was a significant effect of experience and learning for the grating orientation task - the participants' tactile acuity improved over time, independent of whether they had, or had not, experienced visual deprivation.

The effect of Ku on telomere replication time is mediated by telomere length but is independent of histone tail acetylation.

PubMed

Lian, Hui-Yong; Robertson, E Douglas; Hiraga, Shin-ichiro; Alvino, Gina M; Collingwood, David; McCune, Heather J; Sridhar, Akila; Brewer, Bonita J; Raghuraman, M K; Donaldson, Anne D

2011-05-15

DNA replication in Saccharomyces cerevisiae proceeds according to a temporal program. We have investigated the role of the telomere-binding Ku complex in specifying late replication of telomere-proximal sequences. Genome-wide analysis shows that regions extending up to 80 kb from telomeres replicate abnormally early in a yku70 mutant. We find that Ku does not appear to regulate replication time by binding replication origins directly, nor is its effect on telomere replication timing mediated by histone tail acetylation. We show that Ku instead regulates replication timing through its effect on telomere length, because deletion of the telomerase regulator Pif1 largely reverses the short telomere defect of a yku70 mutant and simultaneously rescues its replication timing defect. Consistent with this conclusion, deleting the genome integrity component Elg1 partially rescued both length and replication timing of yku70 telomeres. Telomere length-mediated control of replication timing requires the TG(1-3) repeat-counting component Rif1, because a rif1 mutant replicates telomeric regions early, despite having extended TG(1-3) tracts. Overall, our results suggest that the effect of Ku on telomere replication timing results from its impact on TG(1-3) repeat length and support a model in which Rif1 measures telomere repeat length to ensure that telomere replication timing is correctly programmed.

Numerical investigation of shape domain effect to its elasticity and surface energy using adaptive finite element method

NASA Astrophysics Data System (ADS)

Alfat, Sayahdin; Kimura, Masato; Firihu, Muhammad Zamrun; Rahmat

2018-05-01

In engineering area, investigation of shape effect in elastic materials was very important. It can lead changing elasticity and surface energy, and also increase of crack propagation in the material. A two-dimensional mathematical model was developed to investigation of elasticity and surface energy in elastic material by Adaptive Finite Element Method. Besides that, behavior of crack propagation has observed for every those materials. The government equations were based on a phase field approach in crack propagation model that developed by Takaishi-Kimura. This research has varied four shape domains where physical properties of materials were same (Young's modulus E = 70 GPa and Poisson's ratio ν = 0.334). Investigation assumptions were; (1) homogeneous and isotropic material, (2) there was not initial cracking at t = 0, (3) initial displacement was zero [u1, u2] = 0) at initial condition (t = 0), and (4) length of time simulation t = 5 with interval Δt = 0.005. Mode I/II or mixed mode crack propagation has been used for the numerical investigation. Results of this studies were very good and accurate to show changing energy and behavior of crack propagation. In the future time, this research can be developed to complex phenomena and domain. Furthermore, shape optimization can be investigation by the model.

U-shaped development: an old but unsolved problem.

PubMed

Pauls, Franz; Macha, Thorsten; Petermann, Franz

2013-01-01

Even today the investigation of U-shaped functions in human development is of considerable importance for different domains of Developmental Psychology. More and more scientific researchers focus their efforts on the challenge to describe and explain the phenomenon by identifying those skills and abilities being affected. The impact of U-shaped functions on diagnostic decision-making and on therapeutic treatment programs highlights the importance of understanding the nature of non-monotonic development. The present article therefore addresses the relevant questions of how U-shaped functions are defined in theory, in which developmental domains such non-monotonic growth curves are suggested to occur, and which implications there are for future methodology and diagnostic practice. Finally, it is recommended to clearly identify those interactions between proximal and distal subcomponents which are expected to contribute to a U-shaped development.

U-Shaped Development: An Old but Unsolved Problem

PubMed Central

Pauls, Franz; Macha, Thorsten; Petermann, Franz

2013-01-01

Even today the investigation of U-shaped functions in human development is of considerable importance for different domains of Developmental Psychology. More and more scientific researchers focus their efforts on the challenge to describe and explain the phenomenon by identifying those skills and abilities being affected. The impact of U-shaped functions on diagnostic decision-making and on therapeutic treatment programs highlights the importance of understanding the nature of non-monotonic development. The present article therefore addresses the relevant questions of how U-shaped functions are defined in theory, in which developmental domains such non-monotonic growth curves are suggested to occur, and which implications there are for future methodology and diagnostic practice. Finally, it is recommended to clearly identify those interactions between proximal and distal subcomponents which are expected to contribute to a U-shaped development. PMID:23750146

Dynamic transport study of the plasmas with transport improvement in LHD and JT-60U

NASA Astrophysics Data System (ADS)

Ida, K.; Sakamoto, Y.; Inagaki, S.; Takenaga, H.; Isayama, A.; Matsunaga, G.; Sakamoto, R.; Tanaka, K.; Ide, S.; Fujita, T.; Funaba, H.; Kubo, S.; Yoshinuma, M.; Shimozuma, T.; Takeiri, Y.; Ikeda, K.; Michael, C.; Tokuzawa, T.; LHD experimental Group; JT-60 Team

2009-01-01

Transport analysis during the transient phase of heating (a dynamic transport study) applied to the plasma with internal transport barriers (ITBs) in the Large Helical Device (LHD) heliotron and the JT-60U tokamak is described. In the dynamic transport study the time of transition from the L-mode plasma to the ITB plasma is clearly determined by the onset of flattening of the temperature profile in the core region and a spontaneous phase transition from a zero curvature ITB (hyperbolic tangent shaped ITB) or a positive curvature ITB (concaved shaped ITB) to a negative curvature ITB (convex shaped ITB) and its back-transition are observed. The flattening of the core region of the ITB transition and the back-transition between a zero curvature ITB and a convex ITB suggest the strong interaction of turbulent transport in space.

Top-down deactivation of interference from irrelevant spatial or verbal stimulus features.

PubMed

Frings, Christian; Wühr, Peter

2014-11-01

The selective-attention model of Houghton and Tipper (1994) assumes top-down deactivation of (conflicting) distractor representations as a mechanism of visual attention. Deactivation should produce an inverted-U-shaped activation function for distractor representations. In a recent study, Frings, Wentura, and Wühr (2012) tested this prediction in a variant of the flanker task in which a cue sometimes required participants to respond to the distractors rather than to the target. When reaction times and error rates were plotted as a function of the target-cue stimulus onset asynchrony, a quadratic trend emerged, consistent with the notion of distractor deactivation. However, in the flanker task, an alternative explanation for the quadratic trend in terms of attentional zooming is possible. The present experiments tested the deactivation account against the attentional-zooming account with the Stroop and the Simon task, in which attentional zooming should have minimal effects on distractor processing, because the target and distractor are presented at the same spatial location. Both experiments replicated the quadratic trend in the performance functions for responses to incongruent distractors, and additionally showed linear trends in the performance functions for responses to congruent distractors. These results provide additional support for the notion of top-down deactivation of distractor representations as a mechanism of visual selective attention.

Characteristics of a Pulse-Periodic Corona Discharge in Atmospheric Air

NASA Astrophysics Data System (ADS)

Tarasenko, V. F.; Baksht, E. Kh.; Sosnin, E. A.; Burachenko, A. G.; Panarin, V. A.; Skakun, V. S.

2018-05-01

Pulse-periodic corona discharge in atmospheric air excited by applying a voltage pulse with a subnanosecond or microsecond rise time to a point electrode is studied experimentally. It is shown that, at a voltage rise rate of dU/ dt 1014 V/s, positive and negative ball-shaped streamers with a front velocity of ≥2 mm/ns form near the point electrode. As dU/ dt is reduced to 1010-1011 V/s, the streamer shape changes and becomes close to cylindrical. The propagation velocity of cylindrical streamers is found to be 0.1 mm/ns at dU/ dt 2 × 1010 V/s. It is shown that the propagation direction of a cylindrical streamer can be changed by tilting the point electrode, on the axis of which the electric field strength reaches its maximum value. It is established that, for the negative polarity of the point electrode and a microsecond rise time of the voltage pulse, a higher voltage is required to form a cylindrical streamer than for the positive polarity of the point electrode.

Design and synthesis of diverse functional kinked nanowire structures for nanoelectronic bioprobes.

PubMed

Xu, Lin; Jiang, Zhe; Qing, Quan; Mai, Liqiang; Zhang, Qingjie; Lieber, Charles M

2013-02-13

Functional kinked nanowires (KNWs) represent a new class of nanowire building blocks, in which functional devices, for example, nanoscale field-effect transistors (nanoFETs), are encoded in geometrically controlled nanowire superstructures during synthesis. The bottom-up control of both structure and function of KNWs enables construction of spatially isolated point-like nanoelectronic probes that are especially useful for monitoring biological systems where finely tuned feature size and structure are highly desired. Here we present three new types of functional KNWs including (1) the zero-degree KNW structures with two parallel heavily doped arms of U-shaped structures with a nanoFET at the tip of the "U", (2) series multiplexed functional KNW integrating multi-nanoFETs along the arm and at the tips of V-shaped structures, and (3) parallel multiplexed KNWs integrating nanoFETs at the two tips of W-shaped structures. First, U-shaped KNWs were synthesized with separations as small as 650 nm between the parallel arms and used to fabricate three-dimensional nanoFET probes at least 3 times smaller than previous V-shaped designs. In addition, multiple nanoFETs were encoded during synthesis in one of the arms/tip of V-shaped and distinct arms/tips of W-shaped KNWs. These new multiplexed KNW structures were structurally verified by optical and electron microscopy of dopant-selective etched samples and electrically characterized using scanning gate microscopy and transport measurements. The facile design and bottom-up synthesis of these diverse functional KNWs provides a growing toolbox of building blocks for fabricating highly compact and multiplexed three-dimensional nanoprobes for applications in life sciences, including intracellular and deep tissue/cell recordings.

France: Factors Shaping Foreign Policy, and Issues in U.S.-French Relations

DTIC Science & Technology

2009-05-20

TYPE 3. DATES COVERED 00-00-2009 to 00-00-2009 4. TITLE AND SUBTITLE France : Factors Shaping Foreign Policy, and Issues in U.S.- French ...Z39-18 France : Factors Shaping Foreign Policy, and Issues in U.S.- French Relations Congressional Research Service Summary The factors that shape... French foreign policy have changed since the end of the Cold War. The perspectives of France and the United States have diverged in some cases. More

Wishful thinking in the 2008 U.S. presidential election.

PubMed

Krizan, Zlatan; Miller, Jeffrey C; Johar, Omesh

2010-01-01

In elections, political preferences are strongly linked to the expectations of the electoral winner-people usually expect their favorite candidate to win. This link could be driven by wishful thinking (a biasing influence of preferences), driven by a biasing influence of expectations on one's wishes, or produced spuriously. To examine these competing possibilities in the 2008 U.S. presidential election, a longitudinal study assessed uncommitted young voters' electoral expectations and preferences over four time points during the month before the election. The findings indicated clear support for wishful thinking: Over time, people's preferences shaped their expectations, but the reverse was not the case. Moreover, these relations were larger among those more strongly identified with their political party and held even when perceptions of general candidate popularity were taken into account. Finally, changes in electoral expectations were consequential, as they shaped disappointment in the electoral results even after taking candidate preferences into account.

Replication timing and nuclear structure.

PubMed

Fu, Haiqing; Baris, Adrian; Aladjem, Mirit I

2018-06-01

DNA replication proceeds along spatially and temporally coordinated patterns within the nucleus, thus protecting the genome during the synthesis of new genetic material. While we have been able to visualize replication patterns on DNA fibers for 50 years, recent developments and discoveries have provided a greater insight into how DNA replication is controlled. In this review, we highlight many of these discoveries. Of great interest are the physiological role of the replication timing program, cis and trans-acting factors that modulate replication timing and the effects of chromatin structure on the replication timing program. We also discuss future directions in the study of replication timing. Published by Elsevier Ltd.

Object Manipulation Facilitates Kind-Based Object Individuation of Shape-Similar Objects

ERIC Educational Resources Information Center

Kingo, Osman S.; Krojgaard, Peter

2011-01-01

Five experiments investigated the importance of shape and object manipulation when 12-month-olds were given the task of individuating objects representing exemplars of kinds in an event-mapping design. In Experiments 1 and 2, results of the study from Xu, Carey, and Quint (2004, Experiment 4) were partially replicated, showing that infants were…

Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication

PubMed Central

Kindler, Eveline; Gil-Cruz, Cristina; Spanier, Julia; Li, Yize; Wilhelm, Jochen; Rabouw, Huib H.; Züst, Roland; Marti, Sabrina; Habjan, Matthias; Cervantes-Barragan, Luisa; Elliot, Ruth; Karl, Nadja; Gaughan, Christina; Silverman, Robert H.; Keller, Markus; Ludewig, Burkhard; Bergmann, Cornelia C.; Ziebuhr, John; Kalinke, Ulrich

2017-01-01

Coronaviruses are of veterinary and medical importance and include highly pathogenic zoonotic viruses, such as SARS-CoV and MERS-CoV. They are known to efficiently evade early innate immune responses, manifesting in almost negligible expression of type-I interferons (IFN-I). This evasion strategy suggests an evolutionary conserved viral function that has evolved to prevent RNA-based sensing of infection in vertebrate hosts. Here we show that the coronavirus endonuclease (EndoU) activity is key to prevent early induction of double-stranded RNA (dsRNA) host cell responses. Replication of EndoU-deficient coronaviruses is greatly attenuated in vivo and severely restricted in primary cells even during the early phase of the infection. In macrophages we found immediate induction of IFN-I expression and RNase L-mediated breakdown of ribosomal RNA. Accordingly, EndoU-deficient viruses can retain replication only in cells that are deficient in IFN-I expression or sensing, and in cells lacking both RNase L and PKR. Collectively our results demonstrate that the coronavirus EndoU efficiently prevents simultaneous activation of host cell dsRNA sensors, such as Mda5, OAS and PKR. The localization of the EndoU activity at the site of viral RNA synthesis–within the replicase complex—suggests that coronaviruses have evolved a viral RNA decay pathway to evade early innate and intrinsic antiviral host cell responses. PMID:28158275

HSV-1-induced activation of NF-κB protects U937 monocytic cells against both virus replication and apoptosis

PubMed Central

Marino-Merlo, Francesca; Papaianni, Emanuela; Medici, Maria Antonietta; Macchi, Beatrice; Grelli, Sandro; Mosca, Claudia; Borner, Christoph; Mastino, Antonio

2016-01-01

The transcription factor nuclear factor-kappa B (NF-κB) is a crucial player of the antiviral innate response. Intriguingly, however, NF-κB activation is assumed to favour herpes simplex virus (HSV) infection rather than restrict it. Apoptosis, a form of innate response to viruses, is completely inhibited by HSV in fully permissive cells, but not in cells incapable to fully sustain HSV replication, such as immunocompetent cells. To resolve the intricate interplay among NF-κB signalling, apoptosis and permissiveness to HSV-1 in monocytic cells, we utilized U937 monocytic cells in which NF-κB activation was inhibited by expressing a dominant-negative IκBα. Surprisingly, viral production was increased in monocytic cells in which NF-κB was inhibited. Moreover, inhibition of NF-κB led to increased apoptosis following HSV-1 infection, associated with lysosomal membrane permeabilization. High expression of late viral proteins and induction of apoptosis occurred in distinct cells. Transcriptional analysis of known innate response genes by real-time quantitative reverse transcription-PCR excluded a contribution of the assayed genes to the observed phenomena. Thus, in monocytic cells NF-κB activation simultaneously serves as an innate process to restrict viral replication as well as a mechanism to limit the damage of an excessive apoptotic response to HSV-1 infection. This finding may clarify mechanisms controlling HSV-1 infection in monocytic cells. PMID:27584793

Breast MRI radiomics: comparison of computer- and human-extracted imaging phenotypes.

PubMed

Sutton, Elizabeth J; Huang, Erich P; Drukker, Karen; Burnside, Elizabeth S; Li, Hui; Net, Jose M; Rao, Arvind; Whitman, Gary J; Zuley, Margarita; Ganott, Marie; Bonaccio, Ermelinda; Giger, Maryellen L; Morris, Elizabeth A

2017-01-01

In this study, we sought to investigate if computer-extracted magnetic resonance imaging (MRI) phenotypes of breast cancer could replicate human-extracted size and Breast Imaging-Reporting and Data System (BI-RADS) imaging phenotypes using MRI data from The Cancer Genome Atlas (TCGA) project of the National Cancer Institute. Our retrospective interpretation study involved analysis of Health Insurance Portability and Accountability Act-compliant breast MRI data from The Cancer Imaging Archive, an open-source database from the TCGA project. This study was exempt from institutional review board approval at Memorial Sloan Kettering Cancer Center and the need for informed consent was waived. Ninety-one pre-operative breast MRIs with verified invasive breast cancers were analysed. Three fellowship-trained breast radiologists evaluated the index cancer in each case according to size and the BI-RADS lexicon for shape, margin, and enhancement (human-extracted image phenotypes [HEIP]). Human inter-observer agreement was analysed by the intra-class correlation coefficient (ICC) for size and Krippendorff's α for other measurements. Quantitative MRI radiomics of computerised three-dimensional segmentations of each cancer generated computer-extracted image phenotypes (CEIP). Spearman's rank correlation coefficients were used to compare HEIP and CEIP. Inter-observer agreement for HEIP varied, with the highest agreement seen for size (ICC 0.679) and shape (ICC 0.527). The computer-extracted maximum linear size replicated the human measurement with p  < 10 -12 . CEIP of shape, specifically sphericity and irregularity, replicated HEIP with both p values < 0.001. CEIP did not demonstrate agreement with HEIP of tumour margin or internal enhancement. Quantitative radiomics of breast cancer may replicate human-extracted tumour size and BI-RADS imaging phenotypes, thus enabling precision medicine.

[Study of fusion of bacteriophage f2 double-stranded RNA, poly(A).poly(U), and poly(G).poly(C) in the presence of tetraethylammonium bromide].

PubMed

Permogorov, V I; Tiaglov, B V; Minaev, V E

1980-01-01

The data on the dependence of the melting curve parameters of double-stranded RNA (replicative form of RNA of f2 bacteriophage) poly(A) times poly(U) and poly(G) times poly(C) on the concentration of (C2H5)4NBr were obtained. The RNA melting range width is shown to pass through the minimum value T =2.1+/-0.1degrees at the point of inversion of relative stability of GC and AU pairs that corresponds to 4.0+/-0.1 M concentration of (C2H5)4NBr. Using the melting temperatures of poly(A) times poly(U) and poly(G) times poly(C) the rependence of Tgc-Tau parameter on (C2H5)4NBr concentration was shown. It was concluded from these data that the effect of the double-stranded RNA stacking heterogeneity was negligible in the 0-3 M range of (C2H5)4NBr concentration. Melting curves of RNA were obtained at various values of Tgc-Tau parameter. It was shown that the profile of fine structure of melting curves depends on the value of Tgc-Tau parameter.

Identification of the Essential Role of Viral Bcl-2 for Kaposi's Sarcoma-Associated Herpesvirus Lytic Replication

PubMed Central

Liang, Qiming; Chang, Brian; Lee, Patrick; Brulois, Kevin F.; Ge, Jianning; Shi, Mude; Rodgers, Mary A.; Feng, Pinghui; Oh, Byung-Ha; Liang, Chengyu

2015-01-01

ABSTRACT Kaposi's sarcoma-associated herpesvirus (KSHV) evades host defenses through tight suppression of autophagy by targeting each step of its signal transduction: by viral Bcl-2 (vBcl-2) in vesicle nucleation, by viral FLIP (vFLIP) in vesicle elongation, and by K7 in vesicle maturation. By exploring the roles of KSHV autophagy-modulating genes, we found, surprisingly, that vBcl-2 is essential for KSHV lytic replication, whereas vFLIP and K7 are dispensable. Knocking out vBcl-2 from the KSHV genome resulted in decreased lytic gene expression at the mRNA and protein levels, a lower viral DNA copy number, and, consequently, a dramatic reduction in the amount of progeny infectious viruses, as also described in the accompanying article (A. Gelgor, I. Kalt, S. Bergson, K. F. Brulois, J. U. Jung, and R. Sarid, J Virol 89:5298–5307, 2015). More importantly, the antiapoptotic and antiautophagic functions of vBcl-2 were not required for KSHV lytic replication. Using a comprehensive mutagenesis analysis, we identified that glutamic acid 14 (E14) of vBcl-2 is critical for KSHV lytic replication. Mutating E14 to alanine totally blocked KSHV lytic replication but showed little or no effect on the antiapoptotic and antiautophagic functions of vBcl-2. Our study indicates that vBcl-2 harbors at least three important and genetically separable functions to modulate both cellular signaling and the virus life cycle. IMPORTANCE The present study shows for the first time that vBcl-2 is essential for KSHV lytic replication. Removal of the vBcl-2 gene results in a lower level of KSHV lytic gene expression, impaired viral DNA replication, and consequently, a dramatic reduction in the level of progeny production. More importantly, the role of vBcl-2 in KSHV lytic replication is genetically separated from its antiapoptotic and antiautophagic functions, suggesting that the KSHV Bcl-2 carries a novel function in viral lytic replication. PMID:25740994

Male Mutation Bias Is the Main Force Shaping Chromosomal Substitution Rates in Monotreme Mammals.

PubMed

Link, Vivian; Aguilar-Gómez, Diana; Ramírez-Suástegui, Ciro; Hurst, Laurence D; Cortez, Diego

2017-09-01

In many species, spermatogenesis involves more cell divisions than oogenesis, and the male germline, therefore, accumulates more DNA replication errors, a phenomenon known as male mutation bias. The extent of male mutation bias (α) is estimated by comparing substitution rates of the X, Y, and autosomal chromosomes, as these chromosomes spend different proportions of their time in the germlines of the two sexes. Male mutation bias has been characterized in placental and marsupial mammals as well as birds, but analyses in monotremes failed to detect any such bias. Monotremes are an ancient lineage of egg-laying mammals with distinct biological properties, which include unique germline features. Here, we sought to assess the presence and potential characteristics of male mutation bias in platypus and the short-beaked echidna based on substitution rate analyses of X, Y, and autosomes. We established the presence of moderate male mutation bias in monotremes, corresponding to an α value of 2.12-3.69. Given that it has been unclear what proportion of the variation in substitution rates on the different chromosomal classes is really due to differential number of replications, we analyzed the influence of other confounding forces (selection, replication-timing, etc.) and found that male mutation bias is the main force explaining the between-chromosome classes differences in substitution rates. Finally, we estimated the proportion of variation at the gene level in substitution rates that is owing to replication effects and found that this phenomenon can explain >68% of these variations in monotremes, and in control species, rodents, and primates. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Oligomer formation and G-quadruplex binding by purified murine Rif1 protein, a key organizer of higher-order chromatin architecture.

PubMed

Moriyama, Kenji; Yoshizawa-Sugata, Naoko; Masai, Hisao

2018-03-09

Rap1-interacting protein 1 (Rif1) regulates telomere length in budding yeast. We previously reported that, in metazoans and fission yeast, Rif1 also plays pivotal roles in controlling genome-wide DNA replication timing. We proposed that Rif1 may assemble chromatin compartments that contain specific replication-timing domains by promoting chromatin loop formation. Rif1 also is involved in DNA lesion repair, restart after replication fork collapse, anti-apoptosis activities, replicative senescence, and transcriptional regulation. Although multiple physiological functions of Rif1 have been characterized, biochemical and structural information on mammalian Rif1 is limited, mainly because of difficulties in purifying the full-length protein. Here, we expressed and purified the 2418-amino-acid-long, full-length murine Rif1 as well as its partially truncated variants in human 293T cells. Hydrodynamic analyses indicated that Rif1 forms elongated or extended homo-oligomers in solution, consistent with the presence of a HEAT-type helical repeat segment known to adopt an elongated shape. We also observed that the purified murine Rif1 bound G-quadruplex (G4) DNA with high specificity and affinity, as was previously shown for Rif1 from fission yeast. Both the N-terminal (HEAT-repeat) and C-terminal segments were involved in oligomer formation and specifically bound G4 DNA, and the central intrinsically disordered polypeptide segment increased the affinity for G4. Of note, pulldown assays revealed that Rif1 simultaneously binds multiple G4 molecules. Our findings support a model in which Rif1 modulates chromatin loop structures through binding to multiple G4 assemblies and by holding chromatin fibers together. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Q & A: Alexander Varshavsky.

PubMed

Varshavsky, Alexander

2003-07-01

Alexander Varshavsky is Smits Professor of Cell Biology at the California Institute of Technology. He moved to Caltech in 1992, after 15 years at the MIT's Department of Biology. He was born and educated in Russia, and was 30 at the time of his emigration to the U.S. in 1977. In Russia, and for a while at MIT, he studied the structure and replication of chromosomes. Over the last 24 years, the work of his laboratory focused on the ubiquitin system and closely related fields. He is a member of the U.S. National Academy of Sciences, and has received the Gairdner Award, the Lasker Award, the General Motors Sloan Prize, the Wolf Prize, the Horwitz Prize, and the Wilson Medal.

An Overview of the U.S. Better Buildings Initiative as a Model for Other Countries

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

Liu, Xu; Ge, Jing; Feng, Wei

This report offers a comprehensive overview of the U.S. Better Building Initiative, including the program structure, management and implementation. The report also summarizes lessons learned for a U.S. audience and offers approaches that might be replicated in China and elsewhere.

Chromosome Banding in Amphibia. XXXII. The Genus Xenopus (Anura, Pipidae).

PubMed

Schmid, Michael; Steinlein, Claus

2015-01-01

Mitotic chromosomes of 16 species of the frog genus Xenopus were prepared from kidney and lung cell cultures. In the chromosomes of 7 species, high-resolution replication banding patterns could be induced by treating the cultures with 5-bromodeoxyuridine (BrdU) and deoxythymidine (dT) in succession, and in 6 of these species the BrdU/dT-banded chromosomes could be arranged into karyotypes. In the 3 species of the clade with 2n = 20 and 4n = 40 chromosomes (X. tropicalis, X. epitropicalis, X. new tetraploid 1), as well as in the 3 species with 4n = 36 chromosomes (X. laevis, X. borealis, X. muelleri), the BrdU/dT-banded karyotypes show a high degree of homoeology, though differences were detected between these groups. Translocations, inversions, insertions or sex-specific replication bands were not observed. Minor replication asynchronies found between chromosomes probably involve heterochromatic regions. BrdU/dT replication banding of Xenopus chromosomes provides the landmarks necessary for the exact physical mapping of genes and repetitive sequences. FISH with an X. laevis 5S rDNA probe detected multiple hybridization sites at or near the long-arm telomeric regions in most chromosomes of X. laevis and X. borealis, whereas in X. muelleri, the 5S rDNA sequences are located exclusively at the long-arm telomeres of a single chromosome pair. Staining with the AT base pair-specific fluorochrome quinacrine mustard revealed brightly fluorescing heterochromatic regions in the majority of X. borealis chromosomes which are absent in other Xenopus species.

Relationship between air quality and economic development in the provincial capital cities of China.

PubMed

Chen, Nengcheng; Xu, Lei

2017-01-01

Air pollution in China has become increasingly severe with rapid economic growth in recent years. We analyzed the relationship between the gross regional product (GRP) per capita and the Integrated Air Pollution Index (IAPI) in all the provincial capital cities in China from 2003 to 2014 and clustered them into six urban development patterns. These patterns are as follows: inverse U-shaped, N-1-shaped, N-2-shaped, U-shaped, linear decline, and stable. The majority of the provincial capitals are N-1, N-2, and U types, suggesting that the air quality is deteriorating currently or will deteriorate in the future. Meteorological conditions and industrial structure are taken into consideration when testing the environmental Kuznets curve (EKC) hypothesis between the economy and air pollutant concentration. Results show that there exists no direct relationship between three main pollutants and GRP per capita, while an inverse U-shaped relationship with the secondary industry and a U-shaped relationship with the tertiary industry. These results will be a meaningful reference for policy makers to develop policies that coordinate the environmental protection and economic development.

Electroactive polymer and shape memory alloy actuators in biomimetics and humanoids

NASA Astrophysics Data System (ADS)

Tadesse, Yonas

2013-04-01

There is a strong need to replicate natural muscles with artificial materials as the structure and function of natural muscle is optimum for articulation. Particularly, the cylindrical shape of natural muscle fiber and its interconnected structure promote the critical investigation of artificial muscles geometry and implementation in the design phase of certain platforms. Biomimetic robots and Humanoid Robot heads with Facial Expressions (HRwFE) are some of the typical platforms that can be used to study the geometrical effects of artificial muscles. It has been shown that electroactive polymer and shape memory alloy artificial muscles and their composites are some of the candidate materials that may replicate natural muscles and showed great promise for biomimetics and humanoid robots. The application of these materials to these systems reveals the challenges and associated technologies that need to be developed in parallel. This paper will focus on the computer aided design (CAD) models of conductive polymer and shape memory alloys in various biomimetic systems and Humanoid Robot with Facial Expressions (HRwFE). The design of these systems will be presented in a comparative manner primarily focusing on three critical parameters: the stress, the strain and the geometry of the artificial muscle.

Electroform replication of grazing incidence X-ray optics. [spaceborne telescopes

NASA Technical Reports Server (NTRS)

Ulmer, M. P.; Purcell, W. R.; Bedford, D.; Simnett, G. R.

1985-01-01

Work to produce mirrors via electroform replication is reported. Work on small (6 cm by 9 cm) cylindrical pieces and on 40 cm long by 12 cm wide Wolter shaped mirrors is summarized. It is shown that electroforming is a viable technique for producing relatively inexpensive grazing incidence X-ray optics, as long as modest resolution (1 min of arc) and size (12 cm diameter by 40 cm long) are specified.

Genome-Wide Analysis of the Arabidopsis Replication Timing Program1[OPEN

PubMed Central

Brooks, Ashley M.; Wheeler, Emily; LeBlanc, Chantal; Lee, Tae-Jin; Martienssen, Robert A.; Thompson, William F.

2018-01-01

Eukaryotes use a temporally regulated process, known as the replication timing program, to ensure that their genomes are fully and accurately duplicated during S phase. Replication timing programs are predictive of genomic features and activity and are considered to be functional readouts of chromatin organization. Although replication timing programs have been described for yeast and animal systems, much less is known about the temporal regulation of plant DNA replication or its relationship to genome sequence and chromatin structure. We used the thymidine analog, 5-ethynyl-2′-deoxyuridine, in combination with flow sorting and Repli-Seq to describe, at high-resolution, the genome-wide replication timing program for Arabidopsis (Arabidopsis thaliana) Col-0 suspension cells. We identified genomic regions that replicate predominantly during early, mid, and late S phase, and correlated these regions with genomic features and with data for chromatin state, accessibility, and long-distance interaction. Arabidopsis chromosome arms tend to replicate early while pericentromeric regions replicate late. Early and mid-replicating regions are gene-rich and predominantly euchromatic, while late regions are rich in transposable elements and primarily heterochromatic. However, the distribution of chromatin states across the different times is complex, with each replication time corresponding to a mixture of states. Early and mid-replicating sequences interact with each other and not with late sequences, but early regions are more accessible than mid regions. The replication timing program in Arabidopsis reflects a bipartite genomic organization with early/mid-replicating regions and late regions forming separate, noninteracting compartments. The temporal order of DNA replication within the early/mid compartment may be modulated largely by chromatin accessibility. PMID:29301956

Acousto-optic replication of ultrashort laser pulses

NASA Astrophysics Data System (ADS)

Yushkov, Konstantin B.; Molchanov, Vladimir Ya.; Ovchinnikov, Andrey V.; Chefonov, Oleg V.

2017-10-01

Precisely controlled sequences of ultrashort laser pulses are required in various scientific and engineering applications. We developed a phase-only acousto-optic pulse shaping method for replication of ultrashort laser pulses in a TW laser system. A sequence of several Fourier-transform-limited pulses is generated from a single femtosecond laser pulse by means of applying a piecewise linear phase modulation over the whole emission spectrum. Analysis demonstrates that the main factor which limits maximum delay between the pulse replicas is spectral resolution of the acousto-optic dispersive delay line used for pulse shaping. In experiments with a Cr:forsterite laser system, we obtained delays from 0.3 to 3.5 ps between two replicas of 190 fs transform-limited pulses at the central wavelength of laser emission, 1230 nm.

Laser Embossing of Micro-and Submicrometer Surface Structures in Copper

NASA Astrophysics Data System (ADS)

Ehrhardt, Martin; Lorenz, Pierre; Frost, Frank; Zimmer, Klaus

Micro- and submicrometer structures have been transferred from nickel foils into solid copper surfaces by laser microembossing. The developed arrangement for laser microembossing allows a large-area replication using multi- pulse laser scanning scheme, guaranties a low contamination of the embossed surface and enables the utilization of thick workpieces. In the micrometer range the replicated patterns feature a high accuracy regarding the shape. A significant difference between the master and the replication pattern could be observed for the laser embossing of submicrometer patterns. In conclusion, the results show that the proposed laser embossing process is a promising method with a number of applications in microengineering.

Familiar shapes attract attention in figure-ground displays.

PubMed

Nelson, Rolf A; Palmer, Stephen E

2007-04-01

We report five experiments that explore the effect of figure-ground factors on attention. We hypothesized that figural cues, such as familiar shape, would draw attention to the figural side in an attentional cuing task using bipartite figure-ground displays. The first two experiments used faces in profile as the familiar shape and found a perceptual advantage for targets presented on the meaningful side of the central contour in detection speed (Experiment 1) and discrimination accuracy (Experiment 2). The third experiment demonstrated the figural advantage in response time (RT) with nine other familiar shapes (including a sea horse, a guitar, a fir tree, etc.), but only when targets appeared in close proximity to the contour. A fourth experiment obtained a figural advantage in a discrimination task with the larger set of familiar shapes. The final experiment ruled out eye movements as a possible confounding factor by replicating the RT advantage for targets on the figural side of face displays when all trials containing eye movements were eliminated. The results are discussed in terms of ecological influences on attention, and are cast within the framework of Yantis and Jonides's hypothesis that attention is exogenously drawn to the onset of new perceptual objects. We argue that the figural side constitutes an "object" whereas the ground side does not, and that figural cues such as shape familiarity are effective in determining which areas represent objects.

The Organization of Shape and Color in Vision and Art

PubMed Central

Pinna, Baingio

2011-01-01

The aim of this work is to study the phenomenal organization of shape and color in vision and art in terms of microgenesis of the object perception and creation. The idea of “microgenesis” is that the object perception and creation takes time to develop. Our hypothesis is that the roles of shape and color are extracted in sequential order and in the same order these roles are also used by artists to paint objects. Boundary contours are coded before color contours. The microgenesis of the object formation was demonstrated (i) by introducing new conditions derived from the watercolor illusion, where the juxtaposed contours are displaced horizontally or vertically, and based on variations of Matisse’s Woman, (ii) by studying descriptions and replications of visual objects in adults and children of different ages, and (iii) by analyzing the linguistic sequence and organization in a free naming task of the attributes related to shape and color. The results supported the idea of the microgenesis of the object perception, namely the temporal order in the formation of the roles of the object properties (shape before color). Some general principles were extracted from the experimental results. They can be a starting point to explore a new domain focused on the microgenesis of shape and color within the more general problem of object organization, where integrated and multidisciplinary studies based on art and vision science can be very useful. PMID:22065954

Short-Term Visual Deprivation, Tactile Acuity, and Haptic Solid Shape Discrimination

PubMed Central

Crabtree, Charles E.; Norman, J. Farley

2014-01-01

Previous psychophysical studies have reported conflicting results concerning the effects of short-term visual deprivation upon tactile acuity. Some studies have found that 45 to 90 minutes of total light deprivation produce significant improvements in participants' tactile acuity as measured with a grating orientation discrimination task. In contrast, a single 2011 study found no such improvement while attempting to replicate these earlier findings. A primary goal of the current experiment was to resolve this discrepancy in the literature by evaluating the effects of a 90-minute period of total light deprivation upon tactile grating orientation discrimination. We also evaluated the potential effect of short-term deprivation upon haptic 3-D shape discrimination using a set of naturally-shaped solid objects. According to previous research, short-term deprivation enhances performance in a tactile 2-D shape discrimination task – perhaps a similar improvement also occurs for haptic 3-D shape discrimination. The results of the current investigation demonstrate that not only does short-term visual deprivation not enhance tactile acuity, it additionally has no effect upon haptic 3-D shape discrimination. While visual deprivation had no effect in our study, there was a significant effect of experience and learning for the grating orientation task – the participants' tactile acuity improved over time, independent of whether they had, or had not, experienced visual deprivation. PMID:25397327

KIC 8462852 Brightness Pattern Repeating Every 1600 days

NASA Astrophysics Data System (ADS)

Gary, Bruce; Bourne, Rafik

2017-12-01

Observations of KIC 8462852 (aka Boyajian's Star) reveal a yearlong fade pattern that is remarkably similar to the fade pattern derived from Kepler mission observations. The ground-based observations reported here can be described as a gradual fade that ended in late 2016 with the beginning of a yearlong U-shaped fade of 1.1 percent. Near the end of this U-shaped fade a series of very brief dips occurred. The Kepler data exhibit a similar pattern 1600 days earlier, except with an abrupt end of observations before the U-shape recovery. Observations lasting many years are needed, especially during our predicted repeat of the U-shape and short dip pattern in 2021.

Electrical receptacle

DOEpatents

Leong, R.

1993-06-22

The invention is a receptacle for a three prong electrical plug which has either a tubular or U-shaped grounding prong. The inventive receptacle has a grounding prong socket which is sufficiently spacious to prevent the socket from significantly stretching when a larger, U-shaped grounding prong is inserted into the socket, and having two ridges to allow a snug fit when a smaller tubular shape grounding prong is inserted into the socket. The two ridges are made to prevent the socket from expanding when either the U-shaped grounding prong or the tubular grounding prong is inserted.

Electrical receptacle

DOEpatents

Leong, Robert

1993-01-01

The invention is a receptacle for a three prong electrical plug which has either a tubular or U-shaped grounding prong. The inventive receptacle has a grounding prong socket which is sufficiently spacious to prevent the socket from significantly stretching when a larger, U-shaped grounding prong is inserted into the socket, and having two ridges to allow a snug fit when a smaller tubular shape grounding prong is inserted into the socket. The two ridges are made to prevent the socket from expanding when either the U-shaped grounding prong or the tubular grounding prong is inserted.

Effect of incubation time of sago (metroxylon sago) waste by local microorganism ″ginta″ on ph, crude protein, and crude fiber content

NASA Astrophysics Data System (ADS)

Ginting, Nurzainah; Pase, E.

2018-03-01

This study aims to examine the effect of incubation times of sago waste by local microorganism (MOL) “Ginta” to the crude protein and crude fiber content in relation to finding a cheap and good quality ruminants feed alternative. Incubation times were 0 hours to 144 hours. The data obtained were analyzed using Completely Randomize Design consisting of seven treatments and three replications. The result showed that the duration of incubation of sago waste by local microorganism (MOL) “Ginta” caused pH reduction, improved crude protein and crude fiber content. pH reduction was from 7.03 at 0 hour to 4.05 at 144 hours incubation. The highest increased in crude protein was H6U3 (5.58%) : 144 hours incubation and the lowest was H0U2 (3.22%) : 0 hour incubation while the highest crude fiber was H0U1 (19.99%) : 0 hour incubation and the lowest was H6U3 (18.23%) : 144 hours incubation. It can be concluded that incubation of sago waste triggered lower pH, higher crude protein and lower crude fiber than uninoculated. A recommendation could be given on using MOL ‘Ginta” in order to produce a cheap and good quality ruminans feed alternative.

Behavioral Priming 2.0: Enter a Dynamical Systems Perspective

PubMed Central

Krpan, Dario

2017-01-01

On a daily basis, people are exposed to numerous stimuli, ranging from colors and smells to sounds and words, that could potentially activate different cognitive constructs and influence their actions. This type of influence on human behavior is referred to as priming. Roughly two decades ago, behavioral priming was hailed as one of the core forces that shape automatic behavior. However, failures to replicate some of the representative findings in this domain soon followed, which posed the following question: “How robust are behavioral priming effects, and to what extent are they actually important in shaping people's actions?” To shed a new light on this question, I revisit behavioral priming through the prism of a dynamical systems perspective (DSP). The DSP is a scientific paradigm that has been developed through a combined effort of many different academic disciplines, ranging from mathematics and physics to biology, economics, psychology, etc., and it deals with behavior of simple and complex systems over time. In the present paper, I use conceptual and methodological tools stemming from the DSP to propose circumstances under which behavioral priming effects are likely to occur. More precisely, I outline three possible types of the influence of priming on human behavior, to which I refer as emergence, readjustment, and attractor switch, and propose experimental designs to examine them. Finally, I discuss relevant implications for behavioral priming effects and their replications. PMID:28769846

Improved understanding of protein complex offers insight into DNA

Science.gov Websites

replication - through its crystal structure offers new insight into fundamental mechanisms of DNA replication Advanced Photon Source (APS), a U.S. Department of Energy User Facility based at Argonne National Laboratory, to obtain the first atomic-level resolution picture of this complex. The structure shows that

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...

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

PubMed Central

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

2015-01-01

Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCV DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. PMID:25155200

78 FR 22899 - Certain Electronic Devices Having Placeshifting or Display Replication Functionality and Products...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-17

... INTERNATIONAL TRADE COMMISSION [Investigation No. 337-TA-878] Certain Electronic Devices Having... pursuant to 19 U.S.C. 1337 AGENCY: U.S. International Trade Commission. ACTION: Notice. SUMMARY: Notice is hereby given that a complaint was filed with the U.S. International Trade Commission on March 12, 2013...

DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states.

PubMed

White, Eric J; Emanuelsson, Olof; Scalzo, David; Royce, Thomas; Kosak, Steven; Oakeley, Edward J; Weissman, Sherman; Gerstein, Mark; Groudine, Mark; Snyder, Michael; Schübeler, Dirk

2004-12-21

Duplication of the genome during the S phase of the cell cycle does not occur simultaneously; rather, different sequences are replicated at different times. The replication timing of specific sequences can change during development; however, the determinants of this dynamic process are poorly understood. To gain insights into the contribution of developmental state, genomic sequence, and transcriptional activity to replication timing, we investigated the timing of DNA replication at high resolution along an entire human chromosome (chromosome 22) in two different cell types. The pattern of replication timing was correlated with respect to annotated genes, gene expression, novel transcribed regions of unknown function, sequence composition, and cytological features. We observed that chromosome 22 contains regions of early- and late-replicating domains of 100 kb to 2 Mb, many (but not all) of which are associated with previously described chromosomal bands. In both cell types, expressed sequences are replicated earlier than nontranscribed regions. However, several highly transcribed regions replicate late. Overall, the DNA replication-timing profiles of the two different cell types are remarkably similar, with only nine regions of difference observed. In one case, this difference reflects the differential expression of an annotated gene that resides in this region. Novel transcribed regions with low coding potential exhibit a strong propensity for early DNA replication. Although the cellular function of such transcripts is poorly understood, our results suggest that their activity is linked to the replication-timing program.

Patterned gallium surfaces as molecular mirrors.

PubMed

Bossi, Alessandra; Rivetti, Claudio; Mangiarotti, Laura; Whitcombe, Michael J; Turner, Anthony P F; Piletsky, Sergey A

2007-09-30

An entirely new means of printing molecular information on a planar film, involving casting nanoscale impressions of the template protein molecules in molten gallium, is presented here for the first time. The metallic imprints not only replicate the shape and size of the proteins used as template. They also show specific binding for the template species. Such a simple approach to the creation of antibody-like properties in metallic mirrors can lead to applications in separations, microfluidic devices, and the development of new optical and electronic sensors, and will be of interest to chemists, materials scientists, analytical specialists, and electronic engineers.

Increasing magnetoplasticity in polycrystalline Ni-Mn-Ga by reducing internal constraints through porosity.

PubMed

Boonyongmaneerat, Yuttanant; Chmielus, Markus; Dunand, David C; Müllner, Peter

2007-12-14

Foams with 55% and 76% open porosity were produced from a Ni-Mn-Ga magnetic shape-memory alloy by replication casting. These polycrystalline martensitic foams display a fully reversible magnetic-field-induced strain of up to 0.115% without bias stress, which is about 50 times larger than nonporous, fine-grained Ni-Mn-Ga. This very large improvement is attributed to the bamboolike structure of grains in the foam struts which, due to reduced internal constraints, deform by magnetic-field-induced twinning more easily than equiaxed grains in nonporous Ni-Mn-Ga.

Solid shape discrimination from vision and haptics: natural objects (Capsicum annuum) and Gibson's "feelies".

PubMed

Norman, J Farley; Phillips, Flip; Holmin, Jessica S; Norman, Hideko F; Beers, Amanda M; Boswell, Alexandria M; Cheeseman, Jacob R; Stethen, Angela G; Ronning, Cecilia

2012-10-01

A set of three experiments evaluated 96 participants' ability to visually and haptically discriminate solid object shape. In the past, some researchers have found haptic shape discrimination to be substantially inferior to visual shape discrimination, while other researchers have found haptics and vision to be essentially equivalent. A primary goal of the present study was to understand these discrepant past findings and to determine the true capabilities of the haptic system. All experiments used the same task (same vs. different shape discrimination) and stimulus objects (James Gibson's "feelies" and a set of naturally shaped objects--bell peppers). However, the methodology varied across experiments. Experiment 1 used random 3-dimensional (3-D) orientations of the stimulus objects, and the conditions were full-cue (active manipulation of objects and rotation of the visual objects in depth). Experiment 2 restricted the 3-D orientations of the stimulus objects and limited the haptic and visual information available to the participants. Experiment 3 compared restricted and full-cue conditions using random 3-D orientations. We replicated both previous findings in the current study. When we restricted visual and haptic information (and placed the stimulus objects in the same orientation on every trial), the participants' visual performance was superior to that obtained for haptics (replicating the earlier findings of Davidson et al. in Percept Psychophys 15(3):539-543, 1974). When the circumstances resembled those of ordinary life (e.g., participants able to actively manipulate objects and see them from a variety of perspectives), we found no significant difference between visual and haptic solid shape discrimination.

Core psychopathology in anorexia nervosa and bulimia nervosa: A network analysis.

PubMed

Forrest, Lauren N; Jones, Payton J; Ortiz, Shelby N; Smith, April R

2018-04-25

The cognitive-behavioral theory of eating disorders (EDs) proposes that shape and weight overvaluation are the core ED psychopathology. Core symptoms can be statistically identified using network analysis. Existing ED network studies support that shape and weight overvaluation are the core ED psychopathology, yet no studies have estimated AN core psychopathology and concerns exist about the replicability of network analysis findings. The current study estimated ED symptom networks among people with anorexia nervosa (AN) and bulimia nervosa (BN) and among a combined group of people with AN and BN. Participants were girls and women with AN (n = 604) and BN (n = 477) seeking residential ED treatment. ED symptoms were assessed with the Eating Disorder Examination-Questionnaire (EDE-Q); 27 of the EDE-Q items were included as nodes in symptom networks. Core symptoms were determined by expected influence and strength values. In all networks, desiring weight loss, restraint, shape and weight preoccupation, and shape overvaluation emerged as the most important symptoms. In addition, in the AN and combined networks, fearing weight gain emerged as an important symptom. In the BN network, weight overvaluation emerged as another important symptom. Findings support the cognitive-behavioral premise that shape and weight overvaluation are at the core of AN psychopathology. Our BN and combined network findings provide a high degree of replication of previous findings. Clinically, findings highlight the importance of considering shape and weight overvaluation as a severity specifier and primary treatment target for people with EDs. © 2018 Wiley Periodicals, Inc.

Regulation of DNA Replication Timing on Human Chromosome by a Cell-Type Specific DNA Binding Protein SATB1

PubMed Central

Oda, Masako; Kanoh, Yutaka; Watanabe, Yoshihisa; Masai, Hisao

2012-01-01

Background Replication timing of metazoan DNA during S-phase may be determined by many factors including chromosome structures, nuclear positioning, patterns of histone modifications, and transcriptional activity. It may be determined by Mb-domain structures, termed as “replication domains”, and recent findings indicate that replication timing is under developmental and cell type-specific regulation. Methodology/Principal Findings We examined replication timing on the human 5q23/31 3.5-Mb segment in T cells and non-T cells. We used two independent methods to determine replication timing. One is quantification of nascent replicating DNA in cell cycle-fractionated stage-specific S phase populations. The other is FISH analyses of replication foci. Although the locations of early- and late-replicating domains were common between the two cell lines, the timing transition region (TTR) between early and late domains were offset by 200-kb. We show that Special AT-rich sequence Binding protein 1 (SATB1), specifically expressed in T-cells, binds to the early domain immediately adjacent to TTR and delays the replication timing of the TTR. Measurement of the chromosome copy number along the TTR during synchronized S phase suggests that the fork movement may be slowed down by SATB1. Conclusions Our results reveal a novel role of SATB1 in cell type-specific regulation of replication timing along the chromosome. PMID:22879953

Regulation of DNA replication timing on human chromosome by a cell-type specific DNA binding protein SATB1.

PubMed

Oda, Masako; Kanoh, Yutaka; Watanabe, Yoshihisa; Masai, Hisao

2012-01-01

Replication timing of metazoan DNA during S-phase may be determined by many factors including chromosome structures, nuclear positioning, patterns of histone modifications, and transcriptional activity. It may be determined by Mb-domain structures, termed as "replication domains", and recent findings indicate that replication timing is under developmental and cell type-specific regulation. We examined replication timing on the human 5q23/31 3.5-Mb segment in T cells and non-T cells. We used two independent methods to determine replication timing. One is quantification of nascent replicating DNA in cell cycle-fractionated stage-specific S phase populations. The other is FISH analyses of replication foci. Although the locations of early- and late-replicating domains were common between the two cell lines, the timing transition region (TTR) between early and late domains were offset by 200-kb. We show that Special AT-rich sequence Binding protein 1 (SATB1), specifically expressed in T-cells, binds to the early domain immediately adjacent to TTR and delays the replication timing of the TTR. Measurement of the chromosome copy number along the TTR during synchronized S phase suggests that the fork movement may be slowed down by SATB1. Our results reveal a novel role of SATB1 in cell type-specific regulation of replication timing along the chromosome.

Reconstruing U-Shaped Functions

ERIC Educational Resources Information Center

Werker, Janet F.; Hall, D. Geoffrey; Fais, Laurel

2004-01-01

U-shaped developmental functions, and their N-shaped cousins, have intrigued developmental psychologists for decades because they provide a compelling demonstration that development does not always entail a monotonic increase across age in a single underlying ability. Instead, the causes of development are much more complex. Indeed,…

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

PubMed

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

2013-01-01

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

Development of a homogeneous pulse shape discriminating flow-cell radiation detection system

NASA Astrophysics Data System (ADS)

Hastie, K. H.; DeVol, T. A.; Fjeld, R. A.

1999-02-01

A homogeneous flow-cell radiation detection system which utilizes coincidence counting and pulse shape discrimination circuitry was assembled and tested with five commercially available liquid scintillation cocktails. Two of the cocktails, Ultima Flo (Packard) and Mono Flow 5 (National Diagnostics) have low viscosities and are intended for flow applications; and three of the cocktails, Optiphase HiSafe 3 (Wallac), Ultima Gold AB (Packard), and Ready Safe (Beckman), have higher viscosities and are intended for static applications. The low viscosity cocktails were modified with 1-methylnaphthalene to increase their capability for alpha/beta pulse shape discrimination. The sample loading and pulse shape discriminator setting were optimized to give the lowest minimum detectable concentration for alpha radiation in a 30 s count time. Of the higher viscosity cocktails, Optiphase HiSafe 3 had the lowest minimum detectable activities for alpha and beta radiation, 0.2 and 0.4 Bq/ml for 233U and 90Sr/ 90Y, respectively, for a 30 s count time. The sample loading was 70% and the corresponding alpha/beta spillover was 5.5%. Of the low viscosity cocktails, Mono Flow 5 modified with 2.5% (by volume) 1-methylnaphthalene resulted in the lowest minimum detectable activities for alpha and beta radiation; 0.3 and 0.5 Bq/ml for 233U and 90Sr/ 90Y, respectively, for a 30 s count time. The sample loading was 50%, and the corresponding alpha/beta spillover was 16.6%. HiSafe 3 at a 10% sample loading was used to evaluate the system under simulated flow conditions.

Patterns on serpentine shapes elicit visual attention in marmosets (Callithrix jacchus).

PubMed

Wombolt, Jessica R; Caine, Nancy G

2016-09-01

Given the prevalence of threatening snakes in the evolutionary history, and modern-day environments of human and nonhuman primates, sensory, and perceptual abilities that allow for quick detection of, and appropriate response to snakes are likely to have evolved. Many studies have demonstrated that primates recognize snakes faster than other stimuli, and it is suggested that the unique serpentine shape is responsible for its quick detection. However, there are many nonthreatening serpentine shapes in the environment (e.g., vines) that are not threatening; therefore, other cues must be used to distinguish threatening from benign serpentine objects. In two experiments, we systematically evaluated how common marmosets (Callithrix jacchus) visually attend to specific snake-like features. In the first experiment, we examined if skin pattern is a cue that elicits increased visual inspection of serpentine shapes by measuring the amount of time the marmosets looked into a blind before, during, and after presentation of clay models with and without patterns. The marmosets spent the most time looking at the objects, both serpentine and triangle, that were etched with scales, suggesting that something may be uniquely salient about scales in evoking attention. In contrast, they showed relatively little interest in the unpatterned serpentine and control (a triangle) stimuli. In experiment 2, we replicated and extended the results of experiment 1 by adding additional stimulus conditions. We found that patterns on a serpentine shape generated more inspection than those same patterns on a triangle shape. We were unable to confirm that a scaled pattern is unique in its ability to elicit visual interest; the scaled models elicited similar looking times as line and star patterns. Our data provide a foundation for future research to examine how snakes are detected and identified by primates. Am. J. Primatol. 78:928-936, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Amplified Self-replication of DNA Origami Nanostructures through Multi-cycle Fast-annealing Process

NASA Astrophysics Data System (ADS)

Zhou, Feng; Zhuo, Rebecca; He, Xiaojin; Sha, Ruojie; Seeman, Nadrian; Chaikin, Paul

We have developed a non-biological self-replication process using templated reversible association of components and irreversible linking with annealing and UV cycles. The current method requires a long annealing time, up to several days, to achieve the specific self-assembly of DNA nanostructures. In this work, we accomplished the self-replication with a shorter time and smaller replication rate per cycle. By decreasing the ramping time, we obtained the comparable replication yield within 90 min. Systematic studies show that the temperature and annealing time play essential roles in the self-replication process. In this manner, we can amplify the self-replication process to a factor of 20 by increasing the number of cycles within the same amount of time.

Ultraviolet irradiation of herpes simplex virus (type 1): delayed transcription and comparative sensitivites of virus functions.

PubMed

Eglin, R P; Gugerli, P; Wildy, P

1980-07-01

The delay in the replication of herpes simplex virus surviving u.v. irradiation occurs after the uncoating of virus, as judged by sensitivity to DNase. It occurs before translation, judged by the kinetics of appearance of various virus-specific proteins, and before transcription, judged by the detection of virus-specific RNA by in situ hybridization. Since the delays in both transcription and translation are reversed by photoreactivation, the simplest hypothesis is that pyrimidine dimers directly obstruct transcription;unless these are broken by photoreactivating enzymes, there will be transcriptional delay until reactivating processes have repaired the lesion. The u.v. sensitivities of the abilities to induce various enzymes (thymidine kinase, DNase and DNA polymerase) were only about four times less than that of infectivity. The The ability to induce the three enzymes was three times less sensitive than that of the structural antigen (Band II).

Topologically-associating domains are stable units of replication-timing regulation

PubMed Central

Pope, Benjamin D.; Ryba, Tyrone; Dileep, Vishnu; Yue, Feng; Wu, Weisheng; Denas, Olgert; Vera, Daniel L.; Wang, Yanli; Hansen, R. Scott; Canfield, Theresa K.; Thurman, Robert E.; Cheng, Yong; Gülsoy, Günhan; Dennis, Jonathan H.; Snyder, Michael P.; Stamatoyannopoulos, John A.; Taylor, James; Hardison, Ross C.; Kahveci, Tamer; Ren, Bing; Gilbert, David M.

2014-01-01

Summary Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program1. During mammalian development, at least half the genome changes replication timing, primarily in units of 400–800 kb (“replication domains”; RDs), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements2–7. Early and late replication correlate strongly with open and closed chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, lamina-associated domains (LADs)4,5,8,9. Recent Hi-C mapping has unveiled a substructure of topologically-associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to RDs8,10. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale11,12. Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure8,9,13. Here, we localize boundaries of RDs to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, RD boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure RD boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell type specific sub-nuclear compartmentalization with developmentally stable chromosome domains and offer a unified model for large-scale chromosome structure and function. PMID:25409831

Initiation and termination of DNA replication during S phase in relation to cyclins D1, E and A, p21WAF1, Cdt1 and the p12 subunit of DNA polymerase δ revealed in individual cells by cytometry

PubMed Central

Darzynkiewicz, Zbigniew; Zhao, Hong; Zhang, Sufang; Marietta, Y.W.T. Lee; Ernest, Y.C. Lee; Zhang, Zhongtao

2015-01-01

During our recent studies on mechanism of the regulation of human DNA polymerase δ in preparation for DNA replication or repair, multiparameter imaging cytometry as exemplified by laser scanning cytometry (LSC) has been used to assess changes in expression of the following nuclear proteins associated with initiation of DNA replication: cyclin A, PCNA, Ki-67, p21WAF1, DNA replication factor Cdt1 and the smallest subunit of DNA polymerase δ, p12. In the present review, rather than focusing on Pol δ, we emphasize the application of LSC in these studies and outline possibilities offered by the concurrent differential analysis of DNA replication in conjunction with expression of the nuclear proteins. A more extensive analysis of the data on a correlation between rates of EdU incorporation, likely reporting DNA replication, and expression of these proteins, is presently provided. New data, specifically on the expression of cyclin D1 and cyclin E with respect to EdU incorporation as well as on a relationship between expression of cyclin A vs. p21WAF1 and Ki-67 vs. Cdt1, are also reported. Of particular interest is the observation that this approach makes it possible to assess the temporal sequence of degradation of cyclin D1, p21WAF1, Cdt1 and p12, each with respect to initiation of DNA replication and with respect to each other. Also the sequence or reappearance of these proteins in G2 after termination of DNA replication is assessed. The reviewed data provide a more comprehensive presentation of potential markers, whose presence or absence marks the DNA replicating cells. Discussed is also usefulness of these markers as indicators of proliferative activity in cancer tissues that may bear information on tumor progression and have a prognostic value. PMID:26059433

Initiation and termination of DNA replication during S phase in relation to cyclins D1, E and A, p21WAF1, Cdt1 and the p12 subunit of DNA polymerase δ revealed in individual cells by cytometry.

PubMed

Darzynkiewicz, Zbigniew; Zhao, Hong; Zhang, Sufang; Lee, Marietta Y W T; Lee, Ernest Y C; Zhang, Zhongtao

2015-05-20

During our recent studies on mechanism of the regulation of human DNA polymerase δ in preparation for DNA replication or repair, multiparameter imaging cytometry as exemplified by laser scanning cytometry (LSC) has been used to assess changes in expression of the following nuclear proteins associated with initiation of DNA replication: cyclin A, PCNA, Ki-67, p21(WAF1), DNA replication factor Cdt1 and the smallest subunit of DNA polymerase δ, p12. In the present review, rather than focusing on Pol δ, we emphasize the application of LSC in these studies and outline possibilities offered by the concurrent differential analysis of DNA replication in conjunction with expression of the nuclear proteins. A more extensive analysis of the data on a correlation between rates of EdU incorporation, likely reporting DNA replication, and expression of these proteins, is presently provided. New data, specifically on the expression of cyclin D1 and cyclin E with respect to EdU incorporation as well as on a relationship between expression of cyclin A vs. p21(WAF1) and Ki-67 vs. Cdt1, are also reported. Of particular interest is the observation that this approach makes it possible to assess the temporal sequence of degradation of cyclin D1, p21(WAF1), Cdt1 and p12, each with respect to initiation of DNA replication and with respect to each other. Also the sequence or reappearance of these proteins in G2 after termination of DNA replication is assessed. The reviewed data provide a more comprehensive presentation of potential markers, whose presence or absence marks the DNA replicating cells. Discussed is also usefulness of these markers as indicators of proliferative activity in cancer tissues that may bear information on tumor progression and have a prognostic value.

Sharing and Shaping Usable Science through the Inter-Agency Climate Change Forum

DTIC Science & Technology

2011-10-31

pressure on participants time, this increase is a clear indicator that the forum serves a valuable role, with more persons connecting as they learn about...Science through the Inter-Agency Climate Change Forum William  D.  Goran,  U.S.  Army  Corps  of  Engineers   Sam  Higuchi...COVERED 00-00-2011 to 00-00-2011 4. TITLE AND SUBTITLE Sharing and Shaping Usable Science through the Inter-Agency Climate Change Forum 5a

Space Science

NASA Image and Video Library

1999-04-21

NASA's Space Optics Manufacturing Center has been working to expand our view of the universe via sophisticated new telescopes. The Optics Center's goal is to develop low-cost, advanced space optics technologies for the NASA program in the 21st century - including the long-term goal of imaging Earth-like planets in distant solar systems. To reduce the cost of mirror fabrication, Marshall Space Flight Center (MSFC) has developed replication techniques, the machinery, and materials to replicate electro-formed nickel mirrors. The process allows fabricating precisely shaped mandrels to be used and reused as masters for replicating high-quality mirrors. Dr. Joe Ritter examines a replicated electro-formed nickel-alloy mirror which exemplifies the improvements in mirror fabrication techniques, with benefits such as dramtic weight reduction that have been achieved at the Marshall Space Flight Center's Space Optics Manufacturing Technology Center (SOMTC).

Iran With Nuclear Weapons: Anticipating the Consequences for U.S. Policy

DTIC Science & Technology

2008-09-01

per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing...and, at the same time , develop and/ or acquire more sophisticated defensive technologies to protect high-value aim-points, including nuclear weapons...efforts to shape the political agendas of its Persian Gulf neighbors at a time when allies or coalition partners might not agree about the nature and

Growing What Works: Lessons Learned Replicating Promising Practices for Latino Student Success

ERIC Educational Resources Information Center

Santiago, Deborah A.; Lopez, Estela

2013-01-01

How does the country accelerate Latino student success in higher education? The U.S. has to find programs and strategies that improve the success of Latino students, and then replicate or scale up those programs and strategies to serve more students. Those are the basic principles behind "Excelencia" in Education's Growing What Works (GWW)…

Vocabulary Development in European Portuguese: A Replication Study Using the Language Development Survey

ERIC Educational Resources Information Center

Rescorla, Leslie; Nyame, Josephine; Dias, Pedro

2016-01-01

Purpose: Our objective was to replicate previous cross­linguistic findings by comparing Portuguese and U.S. children with respect to (a) effects of language, gender, and age on vocabulary size; (b) lexical composition; and (c) late talking. Method: We used the Language Development Survey (LDS; Rescorla, 1989) with children (18-35 months) learning…

Rapport, Motivation, Participation, and Perceptions of Learning in U.S. and Turkish Student Classrooms: A Replication and Cultural Comparison

ERIC Educational Resources Information Center

Frisby, Brandi N.; Slone, Amanda R.; Bengu, Elif

2017-01-01

Building on previous rapport research, Hofstede's dimensions of culture, and calls for culture-centered instructional research, this study examined instructor-student rapport in U.S. and Turkish college classrooms. U.S. participants (N = 143) and Turkish participants (N = 185) completed measures of rapport, state motivation, participation, and…

A Study of the quality of CsI detectors and pulse-shape discrimination of scintillators for ?[U+0251]-particles, ?[U+0263]-particles, and neutrons

NASA Astrophysics Data System (ADS)

Salyer, Kaitlin; Rogachev, Grigory; Hooker, Joshua

2016-09-01

This project studied the capabilities of two different scintillators, Cesium Iodide (CsI) and p-Terphenyl. First, the resolution of a CsI detector was investigated by exposing only very small areas of its surface at a time to an alpha source. Second, the abilities of p-Terphenyl to detect alpha particles, gamma particles, and neutrons were analyzed through pulse shape discrimination. p-Terphenyl is of particular interest because it will be used in the Mitchell Institute Neutrino Experiment at Reactor (MINER) at Texas A&M University for measuring background data. The information learned from conducting these tests will be useful in understanding and expanding the limits of the experiments in which these detectors will ultimately be used.

Real-time monitoring of disintegration activity of catalytic core domain of HIV-1 integrase using molecular beacon.

PubMed

Zhang, Da-wei; Zhao, Ming-ming; He, Hong-qiu; Guo, Shun-xing

2013-09-15

HIV-1 integrase, an essential enzyme for retroviral replication, is a validated target for anti-HIV therapy development. The catalytic core domain of integrase (IN-CCD) is capable of catalyzing disintegration reaction. In this work, a hairpin-shaped disintegration substrate was designed and validated by enzyme-linked immunosorbent assay; a molecular beacon-based assay was developed for disintegration reaction of IN-CCD. Results showed that the disintegration substrate could be recognized and catalyzed by IN-CCD, and the disintegration reaction can be monitored according to the increase of fluorescent signal. The assay can be applied to real-time detection of disintegration with advantages of simplicity, high sensitivity, and excellent specificity. Copyright © 2013 Elsevier Inc. All rights reserved.

France: Factors Shaping Foreign Policy, and Issues in U.S.-French Relations

DTIC Science & Technology

2008-05-21

view, France should seek a balance that embraces diversity yet preserves a degree of uniformity that sustains the French “identity.” He believes that...Order Code RL32464 France : Factors Shaping Foreign Policy, and Issues in U.S.- French Relations Updated May 21, 2008 Paul Gallis Specialist in... France : Factors Shaping Foreign Policy, and Issues in U.S.- French Relations 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6

Does the Rotator Cuff Tear Pattern Influence Clinical Outcomes After Surgical Repair?

PubMed Central

Watson, Scott; Allen, Benjamin; Robbins, Chris; Bedi, Asheesh; Gagnier, Joel J.; Miller, Bruce

2018-01-01

Background: Limited literature exists regarding the influence of rotator cuff tear morphology on patient outcomes. Purpose: To determine the effect of rotator cuff tear pattern (crescent, U-shape, L-shape) on patient-reported outcomes after rotator cuff repair. Study Design: Cohort study; Level of evidence, 3. Methods: Patients undergoing arthroscopic repair of known full-thickness rotator cuff tears were observed prospectively at regular intervals from baseline to 1 year. The tear pattern was classified at the time of surgery as crescent, U-shaped, or L-shaped. Primary outcome measures were the Western Ontario Rotator Cuff Index (WORC), the American Shoulder and Elbow Surgeons (ASES), and a visual analog scale (VAS) for pain. The tear pattern was evaluated as the primary predictor while controlling for variables known to affect rotator cuff outcomes. Mixed-methods regression and analysis of variance (ANOVA) were used to examine the effects of tear morphology on patient-reported outcomes after surgical repair from baseline to 1 year. Results: A total of 82 patients were included in the study (53 male, 29 female; mean age, 58 years [range, 41-75 years]). A crescent shape was the most common tear pattern (54%), followed by U-shaped (25%) and L-shaped tears (21%). There were no significant differences in outcome scores between the 3 groups at baseline. All 3 groups showed statistically significant improvement from baseline to 1 year, but analysis failed to show any predictive effect in the change in outcome scores from baseline to 1 year for the WORC, ASES, or VAS when tear pattern was the primary predictor. Further ANOVA also failed to show any significant difference in the change in outcome scores from baseline to 1 year for the WORC (P = .96), ASES (P = .71), or VAS (P = .86). Conclusion: Rotator cuff tear pattern is not a predictor of functional outcomes after arthroscopic rotator cuff repair. PMID:29623283

Does the Rotator Cuff Tear Pattern Influence Clinical Outcomes After Surgical Repair?

PubMed

Watson, Scott; Allen, Benjamin; Robbins, Chris; Bedi, Asheesh; Gagnier, Joel J; Miller, Bruce

2018-03-01

Limited literature exists regarding the influence of rotator cuff tear morphology on patient outcomes. To determine the effect of rotator cuff tear pattern (crescent, U-shape, L-shape) on patient-reported outcomes after rotator cuff repair. Cohort study; Level of evidence, 3. Patients undergoing arthroscopic repair of known full-thickness rotator cuff tears were observed prospectively at regular intervals from baseline to 1 year. The tear pattern was classified at the time of surgery as crescent, U-shaped, or L-shaped. Primary outcome measures were the Western Ontario Rotator Cuff Index (WORC), the American Shoulder and Elbow Surgeons (ASES), and a visual analog scale (VAS) for pain. The tear pattern was evaluated as the primary predictor while controlling for variables known to affect rotator cuff outcomes. Mixed-methods regression and analysis of variance (ANOVA) were used to examine the effects of tear morphology on patient-reported outcomes after surgical repair from baseline to 1 year. A total of 82 patients were included in the study (53 male, 29 female; mean age, 58 years [range, 41-75 years]). A crescent shape was the most common tear pattern (54%), followed by U-shaped (25%) and L-shaped tears (21%). There were no significant differences in outcome scores between the 3 groups at baseline. All 3 groups showed statistically significant improvement from baseline to 1 year, but analysis failed to show any predictive effect in the change in outcome scores from baseline to 1 year for the WORC, ASES, or VAS when tear pattern was the primary predictor. Further ANOVA also failed to show any significant difference in the change in outcome scores from baseline to 1 year for the WORC ( P = .96), ASES ( P = .71), or VAS ( P = .86). Rotator cuff tear pattern is not a predictor of functional outcomes after arthroscopic rotator cuff repair.

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips[OPEN

PubMed Central

LeBlanc, Chantal; Lee, Tae-Jin; Mulvaney, Patrick; Allen, George C.; Martienssen, Robert A.; Thompson, William F.

2017-01-01

All plants and animals must replicate their DNA, using a regulated process to ensure that their genomes are completely and accurately replicated. DNA replication timing programs have been extensively studied in yeast and animal systems, but much less is known about the replication programs of plants. We report a novel adaptation of the “Repli-seq” assay for use in intact root tips of maize (Zea mays) that includes several different cell lineages and present whole-genome replication timing profiles from cells in early, mid, and late S phase of the mitotic cell cycle. Maize root tips have a complex replication timing program, including regions of distinct early, mid, and late S replication that each constitute between 20 and 24% of the genome, as well as other loci corresponding to ∼32% of the genome that exhibit replication activity in two different time windows. Analyses of genomic, transcriptional, and chromatin features of the euchromatic portion of the maize genome provide evidence for a gradient of early replicating, open chromatin that transitions gradually to less open and less transcriptionally active chromatin replicating in mid S phase. Our genomic level analysis also demonstrated that the centromere core replicates in mid S, before heavily compacted classical heterochromatin, including pericentromeres and knobs, which replicate during late S phase. PMID:28842533

Developmental regulation of DNA replication timing at the human beta globin locus.

PubMed

Simon, I; Tenzen, T; Mostoslavsky, R; Fibach, E; Lande, L; Milot, E; Gribnau, J; Grosveld, F; Fraser, P; Cedar, H

2001-11-01

The human beta globin locus replicates late in most cell types, but becomes early replicating in erythroid cells. Using FISH to map DNA replication timing around the endogenous beta globin locus and by applying a genetic approach in transgenic mice, we have demonstrated that both the late and early replication states are controlled by regulatory elements within the locus control region. These results also show that the pattern of replication timing is set up by mechanisms that work independently of gene transcription.

Forging Ahead through Darkness: PCNA, Still the Principal Conductor at the Replication Fork.

PubMed

Choe, Katherine N; Moldovan, George-Lucian

2017-02-02

Proliferating cell nuclear antigen (PCNA) lies at the center of the faithful duplication of eukaryotic genomes. With its distinctive doughnut-shaped molecular structure, PCNA was originally studied for its role in stimulating DNA polymerases. However, we now know that PCNA does much more than promote processive DNA synthesis. Because of the complexity of the events involved, cellular DNA replication poses major threats to genomic integrity. Whatever predicament lies ahead for the replication fork, PCNA is there to orchestrate the events necessary to handle it. Through its many protein interactions and various post-translational modifications, PCNA has far-reaching impacts on a myriad of cellular functions. Copyright © 2017 Elsevier Inc. All rights reserved.

Shape-Controlled Synthesis of Colloidal Metal Nanocrystals by Replicating the Surface Atomic Structure on the Seed.

PubMed

Gilroy, Kyle D; Yang, Xuan; Xie, Shuifen; Zhao, Ming; Qin, Dong; Xia, Younan

2018-06-01

Controlling the surface structure of metal nanocrystals while maximizing the utilization efficiency of the atoms is a subject of great importance. An emerging strategy that has captured the attention of many research groups involves the conformal deposition of one metal as an ultrathin shell (typically 1-6 atomic layers) onto the surface of a seed made of another metal and covered by a set of well-defined facets. This approach forces the deposited metal to faithfully replicate the surface atomic structure of the seed while at the same time serving to minimize the usage of the deposited metal. Here, the recent progress in this area is discussed and analyzed by focusing on the synthetic and mechanistic requisites necessary for achieving surface atomic replication of precious metals. Other related methods are discussed, including the one-pot synthesis, electrochemical deposition, and skin-layer formation through thermal annealing. To close, some of the synergies that arise when the thickness of the deposited shell is decreased controllably down to a few atomic layers are highlighted, along with how the control of thickness can be used to uncover the optimal physicochemical properties necessary for boosting the performance toward a range of catalytic reactions. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Formation Process of Non-Neutral Plasmas by Multiple Electron Beams on BX-U

NASA Astrophysics Data System (ADS)

Sanpei, Akio; Himura, Haruhiko; Masamune, Sadao

An imaging diagnostic system, which is composed of a handmade phosphor screen and a high-speed camera, has been applied to identify the dynamics of multiple electron beams on BX-U. The relaxation process of those toward a non-neutral plasma is experimentally identified. Also, the radial density profile of the plasma is measured as a function of time. Assuming that the plasma is a spheroidal shape, the value of electron density ne is in the range between 2.2 × 106 and 4.4 × 108 cm-3 on BX-U.

Transport of Zinc Oxide Nanoparticles in a Simulated Gastric Environment

NASA Astrophysics Data System (ADS)

Mayfield, Ryan T.

Recent years have seen a growing interest in the use of many types of nano sized materials in the consumer sector. Potential uses include encapsulation of nutrients, providing antimicrobial activity, altering texture, or changing bioavailability of nutrients. Engineered nanoparticles (ENP) possess properties that are different than larger particles made of the same constituents. Properties such as solubility, aggregation state, and toxicity can all be changed as a function of size. The gastric environment is an important area for study of engineered nanoparticles because of the varied physical, chemical, and enzymatic processes that are prevalent there. These all have the potential to alter those properties of ENP that make them different from their bulk counterparts. The Human Gastric Simulator (HGS) is an advanced in vitro model that can be used to study many facets of digestion. The HGS consists of a plastic lining that acts as the stomach cavity with two sets of U-shaped arms on belts that provide the physical forces needed to replicate peristalsis. Altering the position of the arms or changing the speed of the motor which powers them allows one to tightly hone and replicate varied digestive conditions. Gastric juice, consisting of salts, enzymes, and acid levels which replicate physiological conditions, is introduced to the cavity at a controllable rate. The release of digested food from the lumen of simulated stomach is controlled by a peristaltic pump. The goal of the HGS is to accurately and repeatedly simulate human digestion. This study focused on introducing foods spiked with zinc oxide ENP and bulk zinc oxide into the HGS and then monitoring how the concentration of each changed at two locations in the HGS over a two hour period. The two locations chosen were the highest point in the lumen of the stomach, which represented the fundus, and a point just beyond the equivalent of the pylorus, which represented the antrum of the stomach. These points were chosen in order to elucidate if and how two different particle sizes of the same material are transported during digestion. Results showed that particles preferentially collected at Location A; time played a minor role in the separation to the two locations while particle size did not play any role.

Bisphenol-A exposures and behavioural aberrations: median and linear spline and meta-regression analyses of 12 toxicity studies in rodents.

PubMed

Peluso, Marco E M; Munnia, Armelle; Ceppi, Marcello

2014-11-05

Exposures to bisphenol-A, a weak estrogenic chemical, largely used for the production of plastic containers, can affect the rodent behaviour. Thus, we examined the relationships between bisphenol-A and the anxiety-like behaviour, spatial skills, and aggressiveness, in 12 toxicity studies of rodent offspring from females orally exposed to bisphenol-A, while pregnant and/or lactating, by median and linear splines analyses. Subsequently, the meta-regression analysis was applied to quantify the behavioural changes. U-shaped, inverted U-shaped and J-shaped dose-response curves were found to describe the relationships between bisphenol-A with the behavioural outcomes. The occurrence of anxiogenic-like effects and spatial skill changes displayed U-shaped and inverted U-shaped curves, respectively, providing examples of effects that are observed at low-doses. Conversely, a J-dose-response relationship was observed for aggressiveness. When the proportion of rodents expressing certain traits or the time that they employed to manifest an attitude was analysed, the meta-regression indicated that a borderline significant increment of anxiogenic-like effects was present at low-doses regardless of sexes (β)=-0.8%, 95% C.I. -1.7/0.1, P=0.076, at ≤120 μg bisphenol-A. Whereas, only bisphenol-A-males exhibited a significant inhibition of spatial skills (β)=0.7%, 95% C.I. 0.2/1.2, P=0.004, at ≤100 μg/day. A significant increment of aggressiveness was observed in both the sexes (β)=67.9,C.I. 3.4, 172.5, P=0.038, at >4.0 μg. Then, bisphenol-A treatments significantly abrogated spatial learning and ability in males (P<0.001 vs. females). Overall, our study showed that developmental exposures to low-doses of bisphenol-A, e.g. ≤120 μg/day, were associated to behavioural aberrations in offspring. Copyright © 2014. Published by Elsevier Ireland Ltd.

Sliding down the U-shape? A dynamic panel investigation of the age-well-being relationship, focusing on young adults.

PubMed

Piper, Alan T

2015-10-01

Much of the work within economics attempting to understand the relationship between age and well-being has focused on the U-shape, whether it exists and, more recently, potential reasons for its existence. This paper focuses on one part of the lifecycle rather than the whole: young people. This focus offers a better understanding of the age-well-being relationship for young people, and helps with increasing general understanding regarding the U-shape itself. The empirical estimations employ both static and dynamic panel estimations, with the latter preferred for several reasons. The empirical results are in line with the U-shape, and the results from the dynamic analysis indicate that this result is a lifecycle effect. Copyright © 2015 Elsevier Ltd. All rights reserved.

Improved accuracy in Wigner-Ville distribution-based sizing of rod-shaped particle using flip and replication technique

NASA Astrophysics Data System (ADS)

Chuamchaitrakool, Porntip; Widjaja, Joewono; Yoshimura, Hiroyuki

2018-01-01

A method for improving accuracy in Wigner-Ville distribution (WVD)-based particle size measurements from inline holograms using flip and replication technique (FRT) is proposed. The FRT extends the length of hologram signals being analyzed, yielding better spatial-frequency resolution of the WVD output. Experimental results verify reduction in measurement error as the length of the hologram signals increases. The proposed method is suitable for particle sizing from holograms recorded using small-sized image sensors.

Evidence for Sequential and Increasing Activation of Replication Origins along Replication Timing Gradients in the Human Genome

PubMed Central

Guilbaud, Guillaume; Rappailles, Aurélien; Baker, Antoine; Chen, Chun-Long; Arneodo, Alain; Goldar, Arach; d'Aubenton-Carafa, Yves; Thermes, Claude; Audit, Benjamin; Hyrien, Olivier

2011-01-01

Genome-wide replication timing studies have suggested that mammalian chromosomes consist of megabase-scale domains of coordinated origin firing separated by large originless transition regions. Here, we report a quantitative genome-wide analysis of DNA replication kinetics in several human cell types that contradicts this view. DNA combing in HeLa cells sorted into four temporal compartments of S phase shows that replication origins are spaced at 40 kb intervals and fire as small clusters whose synchrony increases during S phase and that replication fork velocity (mean 0.7 kb/min, maximum 2.0 kb/min) remains constant and narrowly distributed through S phase. However, multi-scale analysis of a genome-wide replication timing profile shows a broad distribution of replication timing gradients with practically no regions larger than 100 kb replicating at less than 2 kb/min. Therefore, HeLa cells lack large regions of unidirectional fork progression. Temporal transition regions are replicated by sequential activation of origins at a rate that increases during S phase and replication timing gradients are set by the delay and the spacing between successive origin firings rather than by the velocity of single forks. Activation of internal origins in a specific temporal transition region is directly demonstrated by DNA combing of the IGH locus in HeLa cells. Analysis of published origin maps in HeLa cells and published replication timing and DNA combing data in several other cell types corroborate these findings, with the interesting exception of embryonic stem cells where regions of unidirectional fork progression seem more abundant. These results can be explained if origins fire independently of each other but under the control of long-range chromatin structure, or if replication forks progressing from early origins stimulate initiation in nearby unreplicated DNA. These findings shed a new light on the replication timing program of mammalian genomes and provide a general model for their replication kinetics. PMID:22219720

Differences in the Detection of BrdU/EdU Incorporation Assays Alter the Calculation for G1, S, and G2 Phases of the Cell Cycle in Trypanosomatids.

PubMed

da Silva, Marcelo Santos; Muñoz, Paula Andrea Marin; Armelin, Hugo Aguirre; Elias, Maria Carolina

2017-11-01

Trypanosomatids are the etiologic agents of various infectious diseases in humans. They diverged early during eukaryotic evolution and have attracted attention as peculiar models for evolutionary and comparative studies. Here, we show a meticulous study comparing the incorporation and detection of the thymidine analogs BrdU and EdU in Leishmania amazonensis, Trypanosoma brucei, and Trypanosoma cruzi to monitor their DNA replication. We used BrdU- and EdU-incorporated parasites with the respective standard detection approaches: indirect immunofluorescence to detect BrdU after standard denaturation (2 M HCl) and "click" chemistry to detect EdU. We found a discrepancy between these two thymidine analogs due to the poor detection of BrdU, which is reflected on the estimative of the duration of the cell cycle phases G1, S, and G2. To solve this discrepancy, we increase the exposure of incorporated BrdU using different concentrations of HCl. Using a new value for HCl concentration, we re-estimated the phases G1, S, G2 + M, and cytokinesis durations, confirming the values found by this approach using EdU. In conclusion, we suggest that the studies using BrdU with standard detection approach, not only in trypanosomatids but also in others cell types, should be reviewed to ensure an accurate estimation of DNA replication monitoring. © 2017 The Author(s) Journal of Eukaryotic Microbiology © 2017 International Society of Protistologists.

First-Principles-Driven Model-Based Optimal Control of the Current Profile in NSTX-U

NASA Astrophysics Data System (ADS)

Ilhan, Zeki; Barton, Justin; Wehner, William; Schuster, Eugenio; Gates, David; Gerhardt, Stefan; Kolemen, Egemen; Menard, Jonathan

2014-10-01

Regulation in time of the toroidal current profile is one of the main challenges toward the realization of the next-step operational goals for NSTX-U. A nonlinear, control-oriented, physics-based model describing the temporal evolution of the current profile is obtained by combining the magnetic diffusion equation with empirical correlations obtained at NSTX-U for the electron density, electron temperature, and non-inductive current drives. In this work, the proposed model is embedded into the control design process to synthesize a time-variant, linear-quadratic-integral, optimal controller capable of regulating the safety factor profile around a desired target profile while rejecting disturbances. Neutral beam injectors and the total plasma current are used as actuators to shape the current profile. The effectiveness of the proposed controller in regulating the safety factor profile in NSTX-U is demonstrated via closed-loop predictive simulations carried out in PTRANSP. Supported by PPPL.

Comparison of roll-to-roll replication approaches for microfluidic and optical functions in lab-on-a-chip diagnostic devices

NASA Astrophysics Data System (ADS)

Brecher, Christian; Baum, Christoph; Bastuck, Thomas

2015-03-01

Economically advantageous microfabrication technologies for lab-on-a-chip diagnostic devices substituting commonly used glass etching or injection molding processes are one of the key enablers for the emerging market of microfluidic devices. On-site detection in fields of life sciences, point of care diagnostics and environmental analysis requires compact, disposable and highly functionalized systems. Roll-to-roll production as a high volume process has become the emerging fabrication technology for integrated, complex high technology products within recent years (e.g. fuel cells). Differently functionalized polymer films enable researchers to create a new generation of lab-on-a-chip devices by combining electronic, microfluidic and optical functions in multilayer architecture. For replication of microfluidic and optical functions via roll-to-roll production process competitive approaches are available. One of them is to imprint fluidic channels and optical structures of micro- or nanometer scale from embossing rollers into ultraviolet (UV) curable lacquers on polymer substrates. Depending on dimension, shape and quantity of those structures there are alternative manufacturing technologies for the embossing roller. Ultra-precise diamond turning, electroforming or casting polymer materials are used either for direct structuring or manufacturing of roller sleeves. Mastering methods are selected for application considering replication quality required and structure complexity. Criteria for the replication quality are surface roughness and contour accuracy. Structure complexity is evaluated by shapes producible (e.g. linear, circular) and aspect ratio. Costs for the mastering process and structure lifetime are major cost factors. The alternative replication approaches are introduced and analyzed corresponding to the criteria presented. Advantages and drawbacks of each technology are discussed and exemplary applications are presented.

A Drop in the Bucket or a Pebble in a Pond: Commercial Building Partners’ Replication of EEMs Across Their Portfolios

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

Antonopoulos, Chrissi A.; Baechler, Michael C.; Dillon, Heather E.

This study presents findings from questionnaire and interview data investigating replication efforts of Commercial Building Partnership (CBP) partners that worked directly with the Pacific Northwest National Laboratory (PNNL). PNNL partnered with 12 organizations on new and retrofit construction projects as part of the U.S. Department of Energy (DOE) CBP program. PNNL and other national laboratories collaborate with industry leaders that own large portfolios of buildings to develop high performance projects for new construction and renovation. This project accelerates market adoption of commercially available energy saving technologies into the design process for new and upgraded commercial buildings. The labs provide assistancemore » to the partners’ design teams and make a business case for energy investments. From the owner’s perspective, a sound investment results in energy savings based on corporate objectives and design. Through a feedback questionnaire, along with personal interviews, PNNL gathered qualitative and quantitative information relating to replication efforts by each organization. Data through this process were analyzed to provide insight into two primary research areas: 1) CBP partners’ replication efforts of technologies and approaches used in the CBP project to the rest of the organization’s building portfolio (including replication verification), and, 2) the market potential for technology diffusion into the total U.S. commercial building stock, as a direct result of the CBP entire program.« less

Multiplex CRISPR/Cas9 system impairs HCMV replication by excising an essential viral gene.

PubMed

Gergen, Janina; Coulon, Flora; Creneguy, Alison; Elain-Duret, Nathan; Gutierrez, Alejandra; Pinkenburg, Olaf; Verhoeyen, Els; Anegon, Ignacio; Nguyen, Tuan Huy; Halary, Franck Albert; Haspot, Fabienne

2018-01-01

Anti-HCMV treatments used in immunosuppressed patients reduce viral replication, but resistant viral strains can emerge. Moreover, these drugs do not target latently infected cells. We designed two anti-viral CRISPR/Cas9 strategies to target the UL122/123 gene, a key regulator of lytic replication and reactivation from latency. The singleplex strategy contains one gRNA to target the start codon. The multiplex strategy contains three gRNAs to excise the complete UL122/123 gene. Primary fibroblasts and U-251 MG cells were transduced with lentiviral vectors encoding Cas9 and one or three gRNAs. Both strategies induced mutations in the target gene and a concomitant reduction of immediate early (IE) protein expression in primary fibroblasts. Further detailed analysis in U-251 MG cells showed that the singleplex strategy induced 50% of indels in the viral genome, leading to a reduction in IE protein expression. The multiplex strategy excised the IE gene in 90% of all viral genomes and thus led to the inhibition of IE protein expression. Consequently, viral genome replication and late protein expression were reduced by 90%. Finally, the production of new viral particles was nearly abrogated. In conclusion, the multiplex anti-UL122/123 CRISPR/Cas9 system can target the viral genome efficiently enough to significantly prevent viral replication.

A System for Individualizing Instruction. Practical Answers to U-SAIL Implementation Questions. Monograph No. 4.

ERIC Educational Resources Information Center

Utah System Approach to Individualized Learning Project.

The U-SAIL system is a practical approach to individualization of instruction in which a problem-solving process is employed to install a program in logical sequential phases. U-SAIL is a nationally validated, successfully replicated, cost-feasible system for individualization of instruction which can be implemented in a variety of settings with…

MAP kinase dependent cyclinE/cdk2 activity promotes DNA replication in early sea urchin embryos

PubMed Central

Kisielewska, J.; Philipova, R.; Huang, J.-Y.; Whitaker, M.

2009-01-01

Sea urchins provide an excellent model for studying cell cycle control mechanisms governing DNA replication in vivo. Fertilization and cell cycle progression are tightly coordinated by Ca2+ signals, but the mechanisms underlying the onset of DNA replication after fertilization remain less clear. In this study we demonstrate that calcium-dependent activation of ERK1 promotes accumulation of cyclinE/cdk2 into the male and female pronucleus and entry into first S-phase. We show that cdk2 activity rises quickly after fertilization to a maximum at 4 min, corresponding in timing to the early ERK1 activity peak. Abolishing MAP kinase activity after fertilization with MEK inhibitor, U0126, substantially reduces the early peak of cdk2 activity and prevents cyclinE and cdk2 accumulation in both sperm pronucleus and zygote nucleus in vivo. Both p27kip1 and roscovitine, cdk2 inhibitors, prevented DNA replication suggesting cdk2 involvement in this process in sea urchin. Inhibition of cdk2 activity using p27kip1 had no effect on the phosphorylation of MBP by ERK, but completely abolished phosphorylation of retinoblastoma protein, a cdk2 substrate, indicating that cdk2 activity is downstream of ERK1 activation. This pattern of regulation of DNA synthesis conforms to the pattern observed in mammalian somatic cells. PMID:19665013

Features in visual search combine linearly

PubMed Central

Pramod, R. T.; Arun, S. P.

2014-01-01

Single features such as line orientation and length are known to guide visual search, but relatively little is known about how multiple features combine in search. To address this question, we investigated how search for targets differing in multiple features (intensity, length, orientation) from the distracters is related to searches for targets differing in each of the individual features. We tested race models (based on reaction times) and co-activation models (based on reciprocal of reaction times) for their ability to predict multiple feature searches. Multiple feature searches were best accounted for by a co-activation model in which feature information combined linearly (r = 0.95). This result agrees with the classic finding that these features are separable i.e., subjective dissimilarity ratings sum linearly. We then replicated the classical finding that the length and width of a rectangle are integral features—in other words, they combine nonlinearly in visual search. However, to our surprise, upon including aspect ratio as an additional feature, length and width combined linearly and this model outperformed all other models. Thus, length and width of a rectangle became separable when considered together with aspect ratio. This finding predicts that searches involving shapes with identical aspect ratio should be more difficult than searches where shapes differ in aspect ratio. We confirmed this prediction on a variety of shapes. We conclude that features in visual search co-activate linearly and demonstrate for the first time that aspect ratio is a novel feature that guides visual search. PMID:24715328

New Views on Strand Asymmetry in Insect Mitochondrial Genomes

PubMed Central

Wei, Shu-Jun; Shi, Min; Chen, Xue-Xin; Sharkey, Michael J.; van Achterberg, Cornelis; Ye, Gong-Yin; He, Jun-Hua

2010-01-01

Strand asymmetry in nucleotide composition is a remarkable feature of animal mitochondrial genomes. Understanding the mutation processes that shape strand asymmetry is essential for comprehensive knowledge of genome evolution, demographical population history and accurate phylogenetic inference. Previous studies found that the relative contributions of different substitution types to strand asymmetry are associated with replication alone or both replication and transcription. However, the relative contributions of replication and transcription to strand asymmetry remain unclear. Here we conducted a broad survey of strand asymmetry across 120 insect mitochondrial genomes, with special reference to the correlation between the signs of skew values and replication orientation/gene direction. The results show that the sign of GC skew on entire mitochondrial genomes is reversed in all species of three distantly related families of insects, Philopteridae (Phthiraptera), Aleyrodidae (Hemiptera) and Braconidae (Hymenoptera); the replication-related elements in the A+T-rich regions of these species are inverted, confirming that reversal of strand asymmetry (GC skew) was caused by inversion of replication origin; and finally, the sign of GC skew value is associated with replication orientation but not with gene direction, while that of AT skew value varies with gene direction, replication and codon positions used in analyses. These findings show that deaminations during replication and other mutations contribute more than selection on amino acid sequences to strand compositions of G and C, and that the replication process has a stronger affect on A and T content than does transcription. Our results may contribute to genome-wide studies of replication and transcription mechanisms. PMID:20856815

The Relation Between Valence and Arousal in Subjective Experience Varies With Personality and Culture.

PubMed

Kuppens, Peter; Tuerlinckx, Francis; Yik, Michelle; Koval, Peter; Coosemans, Joachim; Zeng, Kevin J; Russell, James A

2017-08-01

While in general arousal increases with positive or negative valence (a so-called V-shaped relation), there are large differences among individuals in how these two fundamental dimensions of affect are related in people's experience. In two studies, we examined two possible sources of this variation: personality and culture. In Study 1, participants (Belgian university students) recalled a recent event that was characterized by high or low valence or arousal and reported on their feelings and their personality in terms of the Five-Factor Model. In Study 2, participants from Canada, China/Hong Kong, Japan, Korea, and Spain reported on their feelings in a thin slice of time and on their personality. In Study 1, we replicated the V-shape as characterizing the relation between valence and arousal, and identified personality correlates of experiencing particular valence-arousal combinations. In Study 2, we documented how the V-shaped relation varied as a function of Western versus Eastern cultural background and personality. The results showed that the steepness of the V-shaped relation between valence and arousal increases with Extraversion within cultures, and with a West-East distinction between cultures. Implications for the personality-emotion link and research on cultural differences in affect are discussed. © 2016 Wiley Periodicals, Inc.

Functional centromeres determine the activation time of pericentric origins of DNA replication in Saccharomyces cerevisiae.

PubMed

Pohl, Thomas J; Brewer, Bonita J; Raghuraman, M K

2012-01-01

The centromeric regions of all Saccharomyces cerevisiae chromosomes are found in early replicating domains, a property conserved among centromeres in fungi and some higher eukaryotes. Surprisingly, little is known about the biological significance or the mechanism of early centromere replication; however, the extensive conservation suggests that it is important for chromosome maintenance. Do centromeres ensure their early replication by promoting early activation of nearby origins, or have they migrated over evolutionary time to reside in early replicating regions? In Candida albicans, a neocentromere contains an early firing origin, supporting the first hypothesis but not addressing whether the new origin is intrinsically early firing or whether the centromere influences replication time. Because the activation time of individual origins is not an intrinsic property of S. cerevisiae origins, but is influenced by surrounding sequences, we sought to test the hypothesis that centromeres influence replication time by moving a centromere to a late replication domain. We used a modified Meselson-Stahl density transfer assay to measure the kinetics of replication for regions of chromosome XIV in which either the functional centromere or a point-mutated version had been moved near origins that reside in a late replication region. We show that a functional centromere acts in cis over a distance as great as 19 kb to advance the initiation time of origins. Our results constitute a direct link between establishment of the kinetochore and the replication initiation machinery, and suggest that the proposed higher-order structure of the pericentric chromatin influences replication initiation.

Functional Centromeres Determine the Activation Time of Pericentric Origins of DNA Replication in Saccharomyces cerevisiae

PubMed Central

Pohl, Thomas J.; Brewer, Bonita J.; Raghuraman, M. K.

2012-01-01

The centromeric regions of all Saccharomyces cerevisiae chromosomes are found in early replicating domains, a property conserved among centromeres in fungi and some higher eukaryotes. Surprisingly, little is known about the biological significance or the mechanism of early centromere replication; however, the extensive conservation suggests that it is important for chromosome maintenance. Do centromeres ensure their early replication by promoting early activation of nearby origins, or have they migrated over evolutionary time to reside in early replicating regions? In Candida albicans, a neocentromere contains an early firing origin, supporting the first hypothesis but not addressing whether the new origin is intrinsically early firing or whether the centromere influences replication time. Because the activation time of individual origins is not an intrinsic property of S. cerevisiae origins, but is influenced by surrounding sequences, we sought to test the hypothesis that centromeres influence replication time by moving a centromere to a late replication domain. We used a modified Meselson-Stahl density transfer assay to measure the kinetics of replication for regions of chromosome XIV in which either the functional centromere or a point-mutated version had been moved near origins that reside in a late replication region. We show that a functional centromere acts in cis over a distance as great as 19 kb to advance the initiation time of origins. Our results constitute a direct link between establishment of the kinetochore and the replication initiation machinery, and suggest that the proposed higher-order structure of the pericentric chromatin influences replication initiation. PMID:22589733

Tipping points? Curvilinear associations between activity level and mental development in toddlers.

PubMed

Flom, Megan; Cohen, Madeleine; Saudino, Kimberly J

2017-05-01

The Theory of Optimal Stimulation (Zentall & Zentall, Psychological Bulletin, 94, 1983, 446) posits that the relation between activity level (AL) and cognitive performance follows an inverted U shape where midrange AL predicts better cognitive performance than AL at the extremes. We explored this by fitting linear and quadratic models predicting mental development from AL assessed via multiple methods (parent ratings, observations, and actigraphs) and across multiple situations (laboratory play, laboratory test, home) in over 600 twins (2- and 3-year olds). Only observed AL in the laboratory was curvilinearly related to mental development scores. Results replicated across situations, age, and twin samples, providing strong support for the optimal stimulation model for this measure of AL in early childhood. Different measures of AL provide different information. Observations of AL which include both qualitative and quantitative aspects of AL within structured situations are able to capture beneficial aspects of normative AL as well as detriments of both low and high AL. © 2016 Association for Child and Adolescent Mental Health.

In search of the elusive U-shaped performance-turnover relationship: are high performing Swiss bankers more liable to quit?

PubMed

Salamin, Alain; Hom, Peter W

2005-11-01

This project revisits the perennial debate over the relationship between job performance and turnover. Disputing traditional findings, C. Trevor, B. Gerhart, and J. Boudreau (1997) observed that high and low performers quit more than do average performers. They further challenged received wisdom by showing that promotions can induce turnover, especially among poor performers, by signaling ability. The authors sought to replicate and extend these unconventional findings by exploring curvilinear and moderating effects on the performance-exit relationship among 11,098 Swiss nationals employed in a bank. Survival regression revealed that performance is curvilinearly related to quits and that bonus pay deterred superior performers from leaving more than did pay increases. Further, the average number of job levels advanced per promotion rather than promotion rate increased quit risks. Cultural and organizational moderators of performance-termination associations and effective strategies for retaining top performers are discussed. ((c) 2005 APA, all rights reserved).

Twentieth century warming of the tropical Atlantic captured by Sr-U paleothermometry

NASA Astrophysics Data System (ADS)

Alpert, Alice E.; Cohen, Anne L.; Oppo, Delia W.; DeCarlo, Thomas M.; Gaetani, Glenn A.; Hernandez-Delgado, Edwin A.; Winter, Amos; Gonneea, Meagan E.

2017-02-01

Coral skeletons are valuable archives of past ocean conditions. However, interpretation of coral paleotemperature records is confounded by uncertainties associated with single-element ratio thermometers, including Sr/Ca. A new approach, Sr-U, uses U/Ca to constrain the influence of Rayleigh fractionation on Sr/Ca. Here we build on the initial Pacific Porites Sr-U calibration to include multiple Atlantic and Pacific coral genera from multiple coral reef locations spanning a temperature range of 23.15-30.12°C. Accounting for the wintertime growth cessation of one Bermuda coral, we show that Sr-U is strongly correlated with the average water temperature at each location (r2 = 0.91, P < 0.001, n = 19). We applied the multispecies spatial calibration between Sr-U and temperature to reconstruct a 96 year long temperature record at Mona Island, Puerto Rico, using a coral not included in the calibration. Average Sr-U derived temperature for the period 1900-1996 is within 0.12°C of the average instrumental temperature at this site and captures the twentieth century warming trend of 0.06°C per decade. Sr-U also captures the timing of multiyear variability but with higher amplitude than implied by the instrumental data. Mean Sr-U temperatures and patterns of multiyear variability were replicated in a second coral in the same grid box. Conversely, Sr/Ca records from the same two corals were inconsistent with each other and failed to capture absolute sea temperatures, timing of multiyear variability, or the twentieth century warming trend. Our results suggest that coral Sr-U paleothermometry is a promising new tool for reconstruction of past ocean temperatures.

Twentieth century warming of the tropical Atlantic captured by Sr-U paleothermometry

USGS Publications Warehouse

Alpert, Alice E.; Cohen, Anne L.; Oppo, Delia W.; DeCarlo, Thomas M.; Gaetani, Glenn A.; Hernandez-Delgado, Edwin A.; Winter, Amos; Gonneea, Meagan

2017-01-01

Coral skeletons are valuable archives of past ocean conditions. However, interpretation of coral paleotemperature records is confounded by uncertainties associated with single-element ratio thermometers, including Sr/Ca. A new approach, Sr-U, uses U/Ca to constrain the influence of Rayleigh fractionation on Sr/Ca. Here we build on the initial Pacific Porites Sr-U calibration to include multiple Atlantic and Pacific coral genera from multiple coral reef locations spanning a temperature range of 23.15–30.12°C. Accounting for the wintertime growth cessation of one Bermuda coral, we show that Sr-U is strongly correlated with the average water temperature at each location (r2 = 0.91, P < 0.001, n = 19). We applied the multispecies spatial calibration between Sr-U and temperature to reconstruct a 96 year long temperature record at Mona Island, Puerto Rico, using a coral not included in the calibration. Average Sr-U derived temperature for the period 1900–1996 is within 0.12°C of the average instrumental temperature at this site and captures the twentieth century warming trend of 0.06°C per decade. Sr-U also captures the timing of multiyear variability but with higher amplitude than implied by the instrumental data. Mean Sr-U temperatures and patterns of multiyear variability were replicated in a second coral in the same grid box. Conversely, Sr/Ca records from the same two corals were inconsistent with each other and failed to capture absolute sea temperatures, timing of multiyear variability, or the twentieth century warming trend. Our results suggest that coral Sr-U paleothermometry is a promising new tool for reconstruction of past ocean temperatures.

Remotely replaceable tokamak plasma limiter tiles

DOEpatents

Gallix, R.

1987-12-09

U-shaped tiles placed end-to-end over a pair of parallel runners have two rods which engage L-shaped slots. A sliding bar between the runners has grooves with clips to retain the rods pressed into receiving legs of the L-shaped slots in the runners. Sliding the bar in the direction of retaining legs of the L-shaped slots latches the tiles in place over the wall. Resilient contact strips under the parallel sides of the U-shaped tile assure thermal and electrical contact with the wall. 6 figs.

Short term memory for single surface features and bindings in ageing: A replication study.

PubMed

Isella, Valeria; Molteni, Federica; Mapelli, Cristina; Ferrarese, Carlo

2015-06-01

In the present study we replicated a previous experiment investigating visuo-spatial short term memory binding in young and older healthy individuals, in the attempt to verify the pattern of impairment that can be observed in normal elderly for short term memory for single items vs short term memory for bindings. Assessing a larger sample size (25 young and 25 older subjects), using a more appropriate measure of accuracy for a change detection task (A'), and adding the evaluation of speed of performance, we confirmed that old normals show a decline in short term memory for bindings of shape and colour that is of comparable extent, and not major, to the decline in memory for single shapes and single colours. The absence of a specific deficit of short term memory for conjunctions of surface features seems to distinguish cognitive ageing from Alzheimer's Disease. Copyright © 2015 Elsevier Inc. All rights reserved.

Going viral: a review of replication-selective oncolytic adenoviruses

PubMed Central

Larson, Christopher; Oronsky, Bryan; Scicinski, Jan; Fanger, Gary R.; Stirn, Meaghan; Oronsky, Arnold; Reid, Tony R.

2015-01-01

Oncolytic viruses have had a tumultuous course, from the initial anecdotal reports of patients having antineoplastic effects after natural viral infections a century ago to the development of current cutting-edge therapies in clinical trials. Adenoviruses have long been the workhorse of virotherapy, and we review both the scientific and the not-so-scientific forces that have shaped the development of these therapeutics from wild-type viral pathogens, turning an old foe into a new friend. After a brief review of the mechanics of viral replication and how it has been modified to engineer tumor selectivity, we give particular attention to ONYX-015, the forerunner of virotherapy with extensive clinical testing that pioneered the field. The findings from those as well as other oncolytic trials have shaped how we now view these viruses, which our immune system has evolved to vigorously attack, as promising immunotherapy agents. PMID:26280277

Continual renewal and replication of persistent Leishmania major parasites in concomitantly immune hosts

PubMed Central

Mandell, Michael A.

2017-01-01

In most natural infections or after recovery, small numbers of Leishmania parasites remain indefinitely in the host. Persistent parasites play a vital role in protective immunity against disease pathology upon reinfection through the process of concomitant immunity, as well as in transmission and reactivation, yet are poorly understood. A key question is whether persistent parasites undergo replication, and we devised several approaches to probe the small numbers in persistent infections. We find two populations of persistent Leishmania major: one rapidly replicating, similar to parasites in acute infections, and another showing little evidence of replication. Persistent Leishmania were not found in “safe” immunoprivileged cell types, instead residing in macrophages and DCs, ∼60% of which expressed inducible nitric oxide synthase (iNOS). Remarkably, parasites within iNOS+ cells showed normal morphology and genome integrity and labeled comparably with BrdU to parasites within iNOS− cells, suggesting that these parasites may be unexpectedly resistant to NO. Nonetheless, because persistent parasite numbers remain roughly constant over time, their replication implies that ongoing destruction likewise occurs. Similar results were obtained with the attenuated lpg2− mutant, a convenient model that rapidly enters a persistent state without inducing pathology due to loss of the Golgi GDP mannose transporter. These data shed light on Leishmania persistence and concomitant immunity, suggesting a model wherein a parasite reservoir repopulates itself indefinitely, whereas some progeny are terminated in antigen-presenting cells, thereby stimulating immunity. This model may be relevant to understanding immunity to other persistent pathogen infections. PMID:28096392

Development of the Miniature Pulse Tube Cryocooler

NASA Astrophysics Data System (ADS)

Matsumoto, N.; Yasukawa, Y.; Ohshima, K.; Toyama, K.; Tsukahara, Y.; Kamoshita, T.; Takeuchi, T.

2004-06-01

Fuji Electric has developed a pulse tube cryocooler (PTC) with in-line configuration with a cooling capacity of 3 W at 70 K and requiring 100 W of electrical input power. The emphasis has been on compactness, lightweight, high performance and low cost. In particular, the dimensions of the PTC have been reduced to a width of 190 mm and a height of 300 mm. Presently, we are developing a U-shaped PTC based on the technology of the in-line PTC. The advantage of the U-shaped PTC is that the cold head is located at the end for easy accessing. The key issue for developing the U-shaped PTC is the design of the flow straightener at the cold head. As a first step in the development we visualized the inside of the pulse tube by using particle image velocimetry (PIV). The design of the flow straightener is based on the visualization results. Preliminary tests indicated that the cooling performance of the U-shaped PTC is 2 W at 70 K while requiring 51 W PV power. We will present the test results on the U-shaped PTC as well as the in-line PTC.

Self-shaping composites with programmable bioinspired microstructures.

PubMed

Erb, Randall M; Sander, Jonathan S; Grisch, Roman; Studart, André R

2013-01-01

Shape change is a prevalent function apparent in a diverse set of natural structures, including seed dispersal units, climbing plants and carnivorous plants. Many of these natural materials change shape by using cellulose microfibrils at specific orientations to anisotropically restrict the swelling/shrinkage of their organic matrices upon external stimuli. This is in contrast to the material-specific mechanisms found in synthetic shape-memory systems. Here we propose a robust and universal method to replicate this unusual shape-changing mechanism of natural systems in artificial bioinspired composites. The technique is based upon the remote control of the orientation of reinforcing inorganic particles within the composite using a weak external magnetic field. Combining this reinforcement orientational control with swellable/shrinkable polymer matrices enables the creation of composites whose shape change can be programmed into the material's microstructure rather than externally imposed. Such bioinspired approach can generate composites with unusual reversibility, twisting effects and site-specific programmable shape changes.

Self-shaping composites with programmable bioinspired microstructures

NASA Astrophysics Data System (ADS)

Erb, Randall M.; Sander, Jonathan S.; Grisch, Roman; Studart, André R.

2013-04-01

Shape change is a prevalent function apparent in a diverse set of natural structures, including seed dispersal units, climbing plants and carnivorous plants. Many of these natural materials change shape by using cellulose microfibrils at specific orientations to anisotropically restrict the swelling/shrinkage of their organic matrices upon external stimuli. This is in contrast to the material-specific mechanisms found in synthetic shape-memory systems. Here we propose a robust and universal method to replicate this unusual shape-changing mechanism of natural systems in artificial bioinspired composites. The technique is based upon the remote control of the orientation of reinforcing inorganic particles within the composite using a weak external magnetic field. Combining this reinforcement orientational control with swellable/shrinkable polymer matrices enables the creation of composites whose shape change can be programmed into the material’s microstructure rather than externally imposed. Such bioinspired approach can generate composites with unusual reversibility, twisting effects and site-specific programmable shape changes.

Midlatitude Storm Potential in a Changing Climate

NASA Astrophysics Data System (ADS)

Seeley, J.; Romps, D. M.

2013-12-01

The effect of climate change on severe weather over the continental U.S. is calculated using CMIP5 output from ten GCMs. The potential for severe weather is evaluated in these models using an operational proxy of CAPE times shear; the calculation of CAPE is made possible by the presence of high-frequency data in the CMIP5 archive that was not available in CMIP3. First, the ability of each GCM to replicate modern-day distributions of CAPE and shear is assessed. It is found that the GCMs replicate the observed seasonal cycle of CAPE with reasonable fidelity, but a majority of the GCMs show an erroneous summertime CAPE maximum on the East Coast. The source of this persistent bias is explored. Second, the predicted changes in future severe-storm potential over the continental U.S. are evaluated using the RCP4.5 emissions scenario. The seasonal cycle of domain-averaged undilute CAPE over CONUS for 10 GCMs and radiosonde measurements. Data is averaged over the recent past ("RP") period of 1999-2008. Summertime (JJA) climatologies of CAPE over CONUS for 10 GCMs and radiosonde observations. Data is averaged over the recent past ("RP") period of 1999-2008. Six of the models show an erroneous CAPE maximum on the East Coast.

Computationally efficient optimization of radiation drives

NASA Astrophysics Data System (ADS)

Zimmerman, George; Swift, Damian

2017-06-01

For many applications of pulsed radiation, the temporal pulse shape is designed to induce a desired time-history of conditions. This optimization is normally performed using multi-physics simulations of the system, adjusting the shape until the desired response is induced. These simulations may be computationally intensive, and iterative forward optimization is then expensive and slow. In principle, a simulation program could be modified to adjust the radiation drive automatically until the desired instantaneous response is achieved, but this may be impracticable in a complicated multi-physics program. However, the computational time increment is typically much shorter than the time scale of changes in the desired response, so the radiation intensity can be adjusted so that the response tends toward the desired value. This relaxed in-situ optimization method can give an adequate design for a pulse shape in a single forward simulation, giving a typical gain in computational efficiency of tens to thousands. This approach was demonstrated for the design of laser pulse shapes to induce ramp loading to high pressure in target assemblies where different components had significantly different mechanical impedance, requiring careful pulse shaping. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

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.

Measurements of natural uranium concentration and isotopic composition with permil-level precision by inductively coupled plasma-quadrupole mass spectrometry

NASA Astrophysics Data System (ADS)

Shen, Chuan-Chou; Lin, Huei-Ting; Chu, Mei-Fei; Yu, Ein-Fen; Wang, Xianfeng; Dorale, Jeffrey A.

2006-09-01

A new analytical technique using inductively coupled plasma-quadrupole mass spectrometry (ICP-QMS) has been developed that produces permil-level precision in the measurement of uranium concentration ([U]) and isotopic composition (δ234U) in natural materials. A 233U-236U double spike method was used to correct for mass fractionation during analysis. To correct for ratio drifting, samples were bracketed by uranium standard measurements. A sensitivity of 6-7 × 108 cps/ppm was generated with a sample solution uptake rate of 30 μL/min. With a measurement time of 15-20 min, standards of 30-ng uranium produced a within-run precision better than 3‰ (±2 R.S.D.) for δ234U and better than 2‰ for [U]. Replicate measurements made on standards show that a between-run reproducibility of 3.5‰ for δ234U and 2‰ for [U] can be achieved. ICP-QMS data of δ234U and [U] in seawater, coral, and speleothem materials are consistent with the data measured by other ICP-MS and TIMS techniques. Advantages of the ICP-QMS method include low cost, easy maintenance, simple instrumental operation, and few sample preparation steps. Sample size requirements are small, such as 10-14 mg of coral material. The results demonstrate that this technique can be applied to natural samples with various matrices.

Space Science

NASA Image and Video Library

1999-04-01

NASA's Space Optics Manufacturing Center has been working to expand our view of the universe via sophisticated new telescopes. The Optics Center's goal is to develop low-cost, advanced space optics technologies for the NASA program in the 21st century - including the long-term goal of imaging Earth-like planets in distant solar systems. To reduce the cost of mirror fabrication, Marshall Space Flight Center (MSFC) has developed replication techniques, the machinery, and materials to replicate electro-formed nickel mirrors. The process allows fabricating precisely shaped mandrels to be used and reused as masters for replicating high-quality mirrors. Image shows Dr. Alan Shapiro cleaning mirror mandrel to be applied with highly reflective and high-density coating in the Large Aperture Coating Chamber, MFSC Space Optics Manufacturing Technology Center (SOMTC).

Replication dynamics of the yeast genome.

PubMed

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

2001-10-05

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

Large-volume flux closure during plasmoid-mediated reconnection in coaxial helicity injection

DOE Data Explorer

Ebrahimi, Fatima [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States)] (ORCID:0000000331095367); Raman, Roger [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States)] (ORCID:0000000220273271)

2016-01-01

A large-volume flux closure during transient coaxial helicity injection (CHI) in NSTX-U is demonstrated through resistive magnetohydrodynamics (MHD) simulations. Several major improvements, including the improved positioning of the divertor poloidal field coils, are projected to improve the CHI start-up phase in NSTX-U. Simulations in the NSTX-U configuration with constant in time coil currents show that with strong flux shaping the injected open field lines (injector flux) rapidly reconnect and form large volume of closed flux surfaces. This is achieved by driving parallel current in the injector flux coil and oppositely directed currents in the flux shaping coils to form a narrow injector flux footprint and push the injector flux into the vessel. As the helicity and plasma are injected into the device, the oppositely directed field lines in the injector region are forced to reconnect through a local Sweet–Parker type reconnection, or to spontaneously reconnect when the elongated current sheet becomes MHD unstable to form plasmoids. In these simulations for the first time, it is found that the closed flux is over 70% of the initial injector flux used to initiate the discharge. These results could work well for the application of transient CHI in devices that employ super conducting coils to generate and sustain the plasma equilibrium.

Large-volume flux closure during plasmoid-mediated reconnection in coaxial helicity injection

DOE Data Explorer

Ebrahimi, F. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Raman, R. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States)

2016-04-01

A large-volume flux closure during transient coaxial helicity injection (CHI) in NSTX-U is demonstrated through resistive magnetohydrodynamics (MHD) simulations. Several major improvements, including the improved positioning of the divertor poloidal field coils, are projected to improve the CHI start-up phase in NSTX-U. Simulations in the NSTX-U configuration with constant in time coil currents show that with strong flux shaping the injected open field lines (injector flux) rapidly reconnect and form large volume of closed flux surfaces. This is achieved by driving parallel current in the injector flux coil and oppositely directed currents in the flux shaping coils to form a narrow injector flux footprint and push the injector flux into the vessel. As the helicity and plasma are injected into the device, the oppositely directed field lines in the injector region are forced to reconnect through a local Sweet–Parker type reconnection, or to spontaneously reconnect when the elongated current sheet becomes MHD unstable to form plasmoids. In these simulations for the first time, it is found that the closed flux is over 70% of the initial injector flux used to initiate the discharge. These results could work well for the application of transient CHI in devices that employ super conducting coils to generate and sustain the plasma equilibrium.

France: Factors Shaping Foreign Policy, and Issues in U.S.-French Relations

DTIC Science & Technology

2005-01-10

Policy, and Issues in U.S.- French Relations 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK...298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 France : Factors Shaping Foreign Policy, and Issues in U.S.- French Relations Summary The factors that...shape French foreign policy have changed since the end of the Cold War. The perspectives of France and the United States have diverged in some cases

France: Factors Shaping Foreign Policy, and Issues in U.S.-French Relations

DTIC Science & Technology

2006-05-19

Policy, and Issues in U.S.- French Relations 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK...298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 France : Factors Shaping Foreign Policy, and Issues in U.S.- French Relations Summary The factors that...shape French foreign policy have changed since the end of the Cold War. The perspectives of France and the United States have diverged in some cases

What's in a U? The Shapes of Cognitive Development

ERIC Educational Resources Information Center

Marcus, Gary F.

2004-01-01

"Little by little, the child develops," wrote an undergraduate in a friend's cognitive development class, and so, for the most part, it is. But what explains the U's of cognitive development? Namy, Campbell, and Tomasello and Cashon and Cohen take a standard approach to understanding U-shaped curves: as the product of a mix of different cognitive…

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

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

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

1990-03-01

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

Cross-cultural generalizability of personality dimensions: relating indigenous and imported dimensions in two cultures.

PubMed

Katigbak, M S; Church, A T; Akamine, T X

1996-01-01

The cross-cultural generalizability of personality dimensions was investigated by (a) identifying indigenous Philippine dimensions, (b) testing the cross-cultural replicability of the NEO 5-factor model (P. T. Costa & R.R. McCrae, 1992), and (c) relating Philippine and Western dimensions in Philippine and U.S. samples of college students. Filipino self-ratings (N = 536) on indigenous items were factor analyzed, and 6 Philippine dimensions were obtained. Conclusions about the replicability of the 5-factor model in the Philippines (N = 432) depended on whether exploratory, Procrustes, or confirmatory factor methods were used. In regression and joint factor analyses, moderate to strong associations were found between the Philippine dimensions and (a) dimensions from the 5-factor model in both Philippine (N = 387) and U.S. (N = 610) samples, and (b) the Tellegen model (A. Tellegen, 1985; A. Tellegen & N.G. Waller, in press) in a U.S. sample (N = 603).

78 FR 73563 - Certain Electronic Devices Having Placeshifting or Display Replication Functionality and Products...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-06

... INTERNATIONAL TRADE COMMISSION [Investigation No. 337-TA-878] Certain Electronic Devices Having... AGENCY: U.S. International Trade Commission. ACTION: Notice. SUMMARY: Notice is hereby given that the U.S. International Trade Commission has issued (1) a limited exclusion order against infringing electronic devices...

Assessment of Diverse Biological Indicators in Gulf War Illness: Are They Replicable? Are They Related?

DTIC Science & Technology

2014-10-01

CONTRACTING ORGANIZATION: Baylor University Waco , TX 76706-1003 REPORT DATE: October 2014 TYPE OF REPORT: Annual PREPARED FOR: U.S. Army...University Waco , TX 76706 - 1003 9. SPONSORING / MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSOR/MONITOR’S ACRONYM(S) U.S

Impact of source height on the characteristic of U-shaped channel tunnel field-effect transistor

NASA Astrophysics Data System (ADS)

Yang, Zhaonian; Zhang, Yue; Yang, Yuan; Yu, Ningmei

2017-11-01

Tunnel field-effect transistor (TFET) is very attractive in replacing a MOSFET, particularly for low-power nanoelectronic circuits. The U-shaped channel TFET (U-TFET) was proposed to improve the drain-source current with a reduced footprint. In this work, the impact of the source height (HS) on the characteristic of the U-shaped channel tunnel field-effect transistor (U-TFET) is investigated by using TCAD simulation. It is found that with a fixed gate height (HG) the drain-source current has a negative correlation with HS. This is because when the gate region is deeper than the source region, the electric field near the corner of the tunneling junction can be enhanced and the tunneling rate is increased. When HS becomes very thin, the drain-source current is limited by the source region volume. The U-TFET with an n+ pocket is also studied and the same trend is observed.

An Analysis of Radiation Penetration through the U-Shaped Cast Concrete Joints of Concrete Shielding in the Multipurpose Gamma Irradiator of BATAN

NASA Astrophysics Data System (ADS)

Ardiyati, Tanti; Rozali, Bang; Kasmudin

2018-02-01

An analysis of radiation penetration through the U-shaped joints of cast concrete shielding in BATAN’s multipurpose gamma irradiator has been carried out. The analysis has been performed by calculating the radiation penetration through the U-shaped joints of the concrete shielding using MCNP computer code. The U-shaped joints were a new design in massive concrete construction in Indonesia and, in its actual application, it is joined by a bonding agent. In the MCNP simulation model, eight detectors were located close to the observed irradiation room walls of the concrete shielding. The simulation results indicated that the radiation levels outside the concrete shielding was less than the permissible limit of 2.5 μSv/h so that the workers could safely access electrical room, control room, water treatment facility and outside irradiation room. The radiation penetration decreased as the density of material increased.

Modulation of Medium pH by Caulobacter crescentus Facilitates Recovery from Uranium-Induced Growth Arrest

PubMed Central

Park, Dan M.

2014-01-01

The oxidized form of uranium [U(VI)] predominates in oxic environments and poses a major threat to ecosystems. Due to its ability to mineralize U(VI), the oligotroph Caulobacter crescentus is an attractive candidate for U(VI) bioremediation. However, the physiological basis for U(VI) tolerance is unclear. Here we demonstrated that U(VI) caused a temporary growth arrest in C. crescentus and three other bacterial species, although the duration of growth arrest was significantly shorter for C. crescentus. During the majority of the growth arrest period, cell morphology was unaltered and DNA replication initiation was inhibited. However, during the transition from growth arrest to exponential phase, cells with shorter stalks were observed, suggesting a decoupling between stalk development and the cell cycle. Upon recovery from growth arrest, C. crescentus proliferated with a growth rate comparable to that of a control without U(VI), although a fraction of these cells appeared filamentous with multiple replication start sites. Normal cell morphology was restored by the end of exponential phase. Cells did not accumulate U(VI) resistance mutations during the prolonged growth arrest, but rather, a reduction in U(VI) toxicity occurred concomitantly with an increase in medium pH. Together, these data suggest that C. crescentus recovers from U(VI)-induced growth arrest by reducing U(VI) toxicity through pH modulation. Our finding represents a unique U(VI) detoxification strategy and provides insight into how microbes cope with U(VI) under nongrowing conditions, a metabolic state that is prevalent in natural environments. PMID:25002429

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

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

Shin, Jong; Phelan, Paul J.; Chhum, Panharith

2014-11-15

Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCVmore » DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. - Highlights: • Development of a high-throughput screening assay for JCV DNA replication using C33A cells. • Evidence that T-ag fails to accumulate in the nuclei of established glioma cell lines. • Evidence that NF-1 directly promotes JCV DNA replication in C33A cells. • Proof-of-concept that the HTS assay can be used to identify pharmacological inhibitor of JCV DNA replication.« less

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

Meagher, Martin; Enemark, Eric J.

The crystal structure of the N-terminal domain of thePyrococcus furiosusminichromosome maintenance (MCM) protein as a double hexamer is described. The MCM complex is a ring-shaped helicase that unwinds DNA at the replication fork of eukaryotes and archaea. Prior to replication initiation, the MCM complex assembles as an inactive double hexamer at specific sites of DNA. The presented structure is highly consistent with previous MCM double-hexamer structures and shows two MCM hexamers with a head-to-head interaction mediated by the N-terminal domain. Minor differences include a diminished head-to-head interaction and a slightly reduced inter-hexamer rotation.

Variability in pesticide deposition and source contributions to snowpack in western U.S. National Parks

USGS Publications Warehouse

Hageman, Kimberly J.; Hafner, William D.; Campbell, Donald H.; Jaffe, Daniel A.; Landers, Dixon H.; Massey Simonich, Staci L.

2010-01-01

Fifty-six seasonal snowpack samples were collected at remote alpine, subarctic, and arctic sites in eight Western U.S. national parks during three consecutive years (2003−2005). Four current-use pesticides (CUPs) (dacthal (DCPA), chlorpyrifos, endosulfans, and γ-hexachlorocyclohexane (HCH)) and four historic-use pesticides (HUPs) (dieldrin, α-HCH, chlordanes, and hexachlorobenzene (HCB)) were commonly measured at all sites, during all years. The mean coefficient of variation for pesticide concentrations was 15% for site replicate samples, 41% for intrapark replicate samples, and 59% for interannual replicate samples. The relative pesticide concentration profiles were consistent from year to year but unique for individual parks, indicating a regional source effect. HUP concentrations were well-correlated with regional cropland intensity when the effect of temperature on snow-air partitioning was considered. The mass of individual CUPs used in regions located one-day upwind of the parks was calculated using air mass back trajectories, and this was used to explain the distribution of CUPs among the parks. The percent of the snowpack pesticide concentration due to regional transport was high (>75%) for the majority of pesticides in all parks. These results suggest that the majority of pesticide contamination in U.S. national parks is due to regional pesticide use in North America.

Radiochemical and Chemical Constituents in Water from Selected Wells and Springs from the Southern Boundary of the Idaho National Engineering and Environmental Laboratory to the Hagerman Area, Idaho, 2002

USGS Publications Warehouse

Rattray, Gordon W.; Campbell, Linford J.

2004-01-01

The U.S. Geological Survey, Idaho Department of Water Resources, and the State of Idaho INEEL Oversight Program, in cooperation with the U.S. Department of Energy, sampled water from 17 sites as part of the sixth round of a long-term project to monitor water quality of the eastern Snake River Plain aquifer from the southern boundary of the Idaho National Engineering and Environmental Laboratory to the Hagerman area. The samples were collected from eight irrigation wells, three domestic wells, one stock well, one dairy well, one commercial well, one observation well, and two springs and analyzed for selected radiochemical and chemical constituents. One quality-assurance sample, a sequential replicate, also was collected and analyzed. Many of the radionuclide and inorganic-constituent concentrations were greater than the reporting levels and most of the organic-constituent concentrations were less than the reporting levels. However, none of the reported radiochemical- or chemical-constituent concentrations exceeded the maximum contaminant levels for drinking water established by the U.S. Environmental Protection Agency. Statistical evaluation of the replicate sample pair indicated that, with 95 percent confidence, 132 of the 135 constituent concentrations of the replicate pair were equivalent.

Variability in pesticide deposition and source contributions to snowpack in Western U.S. national parks.

PubMed

Hageman, Kimberly J; Hafner, William D; Campbell, Donald H; Jaffe, Daniel A; Landers, Dixon H; Simonich, Staci L Massey

2010-06-15

Fifty-six seasonal snowpack samples were collected at remote alpine, subarctic, and arctic sites in eight Western U.S. national parks during three consecutive years (2003-2005). Four current-use pesticides (CUPs) (dacthal (DCPA), chlorpyrifos, endosulfans, and gamma-hexachlorocyclohexane (HCH)) and four historic-use pesticides (HUPs) (dieldrin, alpha-HCH, chlordanes, and hexachlorobenzene (HCB)) were commonly measured at all sites, during all years. The mean coefficient of variation for pesticide concentrations was 15% for site replicate samples, 41% for intrapark replicate samples, and 59% for interannual replicate samples. The relative pesticide concentration profiles were consistent from year to year but unique for individual parks, indicating a regional source effect. HUP concentrations were well-correlated with regional cropland intensity when the effect of temperature on snow-air partitioning was considered. The mass of individual CUPs used in regions located one-day upwind of the parks was calculated using air mass back trajectories, and this was used to explain the distribution of CUPs among the parks. The percent of the snowpack pesticide concentration due to regional transport was high (>75%) for the majority of pesticides in all parks. These results suggest that the majority of pesticide contamination in U.S. national parks is due to regional pesticide use in North America.

A U-shaped Association between Body Mass Index and Psychological Distress on the Multiphasic Personality Inventory: Retrospective Cross-sectional Analysis of 19-year-old Men in Korea.

PubMed

Kim, Taehyun; Kim, Jung Jun; Kim, Mi Yeon; Kim, Shin Kyoung; Roh, Sungwon; Seo, Jeong Seok

2015-06-01

Objective personality tests, such as the Minnesota Multiphasic Personality Inventory (MMPI), might be more sensitive to reflect subclinical personality and be more state-dependent in an individual's lifetime, so they are good scales to predict the psychological distress regarding certain states. The aim of this study was to identify the specific pattern between body mass index (BMI) and psychological distress using the objective personality test. For this study, we investigated BMI and the Korean Military Multiphasic Personality Inventory (MPI). A retrospective cross-sectional study was conducted with 19-yr-old examinees who were admitted to the Military Manpower Administration in Korea from February 2007 to January 2010. Of 1,088,107 examinees, we enrolled 771,408 subjects who were psychologically apparent healthy possible-military-service groups. Afterwards, we reviewed and analyzed directly measured BMI and MPI results. In terms of the validity scales, the faking-good subscale showed an inverted U-shaped association, and faking-bad and infrequency subscales showed a U-shaped association with BMI groups. In terms of the neurosis scales, all clinical subscales (anxiety, depression, somatization, and personality disorder) also showed a U-shaped association with BMI groups. For the psychopath scales, the schizophrenia subscale showed a U-shaped association, and the paranoia subscale showed a near-positive correlation with BMI. In conclusion, a specific U-shaped pattern was observed between BMI and the MPI in 19-yr-old men in Korea. Underweight and obesity are related to psychological distress, so supportive advice and education are needed to them.

Implementation Plan for Flexible Automation in U.S. Shipyards

DTIC Science & Technology

1985-01-01

process steps, cramped work sites, interrupted geometries , irregular or novel shapes, and other factors that affect automatability. We also try to...held by 2 hands in awkward places. Interrupt geometry of plates and beams. Cannot predict outcome. Creates need to measure and recut. Automation, if...of standard. enough over time I every job. I Rearrange work.Redefine work units. Too many interruptions Time, space, geometry only a little work gets

The Prevalence, Comorbidity, and Age of Onset of Social Anxiety Disorder among U.S. Latinos

PubMed Central

Polo, Antonio; Alegría, Margarita; Chen, Chih-Nan; Blanco, Carlos

2013-01-01

Objective Social Anxiety Disorder (SAD) is increasingly being recognized as a prevalent, unremitting, and highly comorbid disorder1 yet studies focusing on this disorder among U.S. Latinos and immigrant populations are not available. This article evaluates ethnic differences in the prevalence, comorbidity, and age of onset of SAD. Cultural and contextual factors associated with risk of SAD are also examined within the Latino population. Method Data are analyzed using the National Latino and Asian American Study (NLAAS) and the National Comorbidity Survey-Replication (NCS-R). Both studies utilized the World Mental Health – Composite International Diagnostic Interview, which estimates the prevalence of lifetime and 12-month psychiatric disorders according to DSM-IV criteria. Results Latinos (LAT) reported lower lifetime and 12-month SAD prevalence and a later age of onset than U.S.-born non-Latino Whites (NLW). On the other hand, LAT diagnosed with 12-month SAD reported higher impairment across home, work, and relationship domains than their NLW counterparts. Overall, high SAD comorbidity was found with depressive, anxiety, and substance-related disorders among both ethnic groups. However, relative to NLW, LAT who entered the U.S. after the age of 21 were less likely to have lifetime SAD comorbidity with drug abuse and dependence and more likely to report lifetime SAD comorbidity with agoraphobia. Conclusion Varied trajectories of SAD risk are present across ethnicity and nativity groups. Clinicians must consider how culture and ethnicity shape these different presentations and determine treatment options accordingly. Outreach efforts are needed to reach immigrant Latinos, and those with comorbid SAD and Agoraphobia in particular. PMID:21899817

The influence of stream bed geomorphology on chemical species within the hyporheic zone over time and space

NASA Astrophysics Data System (ADS)

Quick, A. M.; Reeder, W. J.; Farrell, T. B.; Benner, S. G.; Tonina, D.; Feris, K. P.

2017-12-01

The hyporheic zone is well established as an important zone of biogeochemical activity in streams and rivers. Multiple large scale flume experiments were carried out to mimic bedform-controlled hyporheic zones in small streams. The laboratory setting allowed for geochemical measurement resolution and replicates that would not be possible in a natural setting. Two flume experiments that consisted of three small streams with variable sizes of bedform dunes were carried out in which chemical species were measured in the surface water and along hyporheic flow lines in the subsurface. The species measured included dissolved oxygen, pH, alkalinity, major cations (Na+, Mg2+, Ca2+, K+, Si4+, Al3+), anions (NO3-, NO2-, SO42-, PO43-, Cl-), and many trace elements (As, Sr, Co, Ni, Cu, Zn, Pb, U, V). Observed spatial and temporal trends reflect microbiological processes, changing redox conditions, and chemical weathering. In general, microbial respiration causes DO to decrease with residence time, leading to aerobic and anaerobic zones that influence redox-sensitive species and pH gradients that influence mineral solubility. Most other species concentrations, including those of major cations and trace elements, increase with residence time and generally decrease over time elapsed during the experiment. The different dune morphologies dictate flow velocities in the hyporheic zone; for most species, steeper dunes with higher velocities had lower concentrations at the end of the experiment, indicating the role of dune shape in the weathering rates of minerals in hyporheic sediment and the concentrations of dissolved species entering the surface water over time. Many of the observed trends can be applied, at least qualitatively, to understanding how these species will behave in natural settings. This insight will contribute to the understanding of many of the applications of the hyporheic zone (e.g. bioremediation, habitat, greenhouse gas emissions, etc.).

Inhibitors of the tick-borne, hemorrhagic fever-associated flaviviruses.

PubMed

Flint, Mike; McMullan, Laura K; Dodd, Kimberly A; Bird, Brian H; Khristova, Marina L; Nichol, Stuart T; Spiropoulou, Christina F

2014-06-01

No antiviral therapies are available for the tick-borne flaviviruses associated with hemorrhagic fevers: Kyasanur Forest disease virus (KFDV), both classical and the Alkhurma hemorrhagic fever virus (AHFV) subtype, and Omsk hemorrhagic fever virus (OHFV). We tested compounds reported to have antiviral activity against members of the Flaviviridae family for their ability to inhibit AHFV replication. 6-Azauridine (6-azaU), 2'-C-methylcytidine (2'-CMC), and interferon alpha 2a (IFN-α2a) inhibited the replication of AHFV and also KFDV, OHFV, and Powassan virus. The combination of IFN-α2a and 2'-CMC exerted an additive antiviral effect on AHFV, and the combination of IFN-α2a and 6-azaU was moderately synergistic. The combination of 2'-CMC and 6-azaU was complex, being strongly synergistic but with a moderate level of antagonism. The antiviral activity of 6-azaU was reduced by the addition of cytidine but not guanosine, suggesting that it acted by inhibiting pyrimidine biosynthesis. To investigate the mechanism of action of 2'-CMC, AHFV variants with reduced susceptibility to 2'-CMC were selected. We used a replicon system to assess the substitutions present in the selected AHFV population. A double NS5 mutant, S603T/C666S, and a triple mutant, S603T/C666S/M644V, were more resistant to 2'-CMC than the wild-type replicon. The S603T/C666S mutant had a reduced level of replication which was increased when M644V was also present, although the replication of this triple mutant was still below that of the wild type. The S603 and C666 residues were predicted to lie in the active site of the AHFV NS5 polymerase, implicating the catalytic center of the enzyme as the binding site for 2'-CMC. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Taraxacum officinale and Urtica dioica extracts inhibit dengue virus serotype 2 replication in vitro.

PubMed

Flores-Ocelotl, María R; Rosas-Murrieta, Nora H; Moreno, Diego A; Vallejo-Ruiz, Verónica; Reyes-Leyva, Julio; Domínguez, Fabiola; Santos-López, Gerardo

2018-03-16

Urtica dioica, Taraxacum officinale, Calea integrifolia and Caesalpinia pulcherrima are widely used all over the world for treatment of different illnesses. In Mexico, these plants are traditionally used to alleviate or counteract rheumatism and inflammatory muscle diseases. In the present study we evaluated the activity of aqueous and methanolic extracts of these four plants, on the replication of dengue virus serotype 2 (DENV2). Extraction process was carried out in a Soxtherm® system at 60, 85 and 120 °C; a chemical fractionation in silica gel chromatography was performed and compounds present in the active fractions were identified by HPLC-DAD-ESI/MSn. The cytotoxic concentration and the inhibitory effect of extracts or fractions on the DENV2 replication were analyzed in the BHK-21 cell line (plaque forming assay). The half maximal inhibitory concentration (IC 50 ) and the selectivity index (SI) were calculated for the extracts and fractions. The methanolic extracts at 60 °C of T. officinale and U. dioica showed the higher inhibitory effects on DENV2 replication. After the chemical fractionation, the higher activity fraction was found for U. dioica and T. officinale, presenting IC 50 values of 165.7 ± 3.85 and 126.1 ± 2.80 μg/ml, respectively; SI values were 5.59 and 6.01 for each fraction. The compounds present in T. officinale, were luteolin and caffeoylquinic acids derivatives and quercertin diclycosides. The compounds in the active fraction of U. dioica, were, chlorogenic acid, quercertin derivatives and flavonol glycosides (quercetin and kaempferol). Two fractions from U. dioica and T. officinale methanolic extracts with anti-dengue activity were found. The compounds present in both fractions were identified, several recognized molecules have demonstrated activity against other viral species. Subsequent biological analysis of the molecules, alone or in combination, contained in the extracts will be carried out to develop therapeutics against DENV2.

Inhibitors of the Tick-Borne, Hemorrhagic Fever-Associated Flaviviruses

PubMed Central

Flint, Mike; McMullan, Laura K.; Dodd, Kimberly A.; Bird, Brian H.; Khristova, Marina L.; Nichol, Stuart T.

2014-01-01

No antiviral therapies are available for the tick-borne flaviviruses associated with hemorrhagic fevers: Kyasanur Forest disease virus (KFDV), both classical and the Alkhurma hemorrhagic fever virus (AHFV) subtype, and Omsk hemorrhagic fever virus (OHFV). We tested compounds reported to have antiviral activity against members of the Flaviviridae family for their ability to inhibit AHFV replication. 6-Azauridine (6-azaU), 2′-C-methylcytidine (2′-CMC), and interferon alpha 2a (IFN-α2a) inhibited the replication of AHFV and also KFDV, OHFV, and Powassan virus. The combination of IFN-α2a and 2′-CMC exerted an additive antiviral effect on AHFV, and the combination of IFN-α2a and 6-azaU was moderately synergistic. The combination of 2′-CMC and 6-azaU was complex, being strongly synergistic but with a moderate level of antagonism. The antiviral activity of 6-azaU was reduced by the addition of cytidine but not guanosine, suggesting that it acted by inhibiting pyrimidine biosynthesis. To investigate the mechanism of action of 2′-CMC, AHFV variants with reduced susceptibility to 2′-CMC were selected. We used a replicon system to assess the substitutions present in the selected AHFV population. A double NS5 mutant, S603T/C666S, and a triple mutant, S603T/C666S/M644V, were more resistant to 2′-CMC than the wild-type replicon. The S603T/C666S mutant had a reduced level of replication which was increased when M644V was also present, although the replication of this triple mutant was still below that of the wild type. The S603 and C666 residues were predicted to lie in the active site of the AHFV NS5 polymerase, implicating the catalytic center of the enzyme as the binding site for 2′-CMC. PMID:24663025

Finite element modeling of borehole heat exchanger systems. Part 1. Fundamentals

NASA Astrophysics Data System (ADS)

Diersch, H.-J. G.; Bauer, D.; Heidemann, W.; Rühaak, W.; Schätzl, P.

2011-08-01

Single borehole heat exchanger (BHE) and arrays of BHE are modeled by using the finite element method. The first part of the paper derives the fundamental equations for BHE systems and their finite element representations, where the thermal exchange between the borehole components is modeled via thermal transfer relations. For this purpose improved relationships for thermal resistances and capacities of BHE are introduced. Pipe-to-grout thermal transfer possesses multiple grout points for double U-shape and single U-shape BHE to attain a more accurate modeling. The numerical solution of the final 3D problems is performed via a widely non-sequential (essentially non-iterative) coupling strategy for the BHE and porous medium discretization. Four types of vertical BHE are supported: double U-shape (2U) pipe, single U-shape (1U) pipe, coaxial pipe with annular (CXA) and centred (CXC) inlet. Two computational strategies are used: (1) The analytical BHE method based on Eskilson and Claesson's (1988) solution, (2) numerical BHE method based on Al-Khoury et al.'s (2005) solution. The second part of the paper focusses on BHE meshing aspects, the validation of BHE solutions and practical applications for borehole thermal energy store systems.

How External Misfortunes Shaped Higher Education

ERIC Educational Resources Information Center

Orkodashvili, Mariam

2008-01-01

The essay makes an attempt to trace the influences that external political and socioeconomic factors like World Wars I, II and Great Depression had on higher education in the U.S. Higher education - autonomous and self - contained system - proved to be one of the center points of main societal developments, at the same time being significantly…

Qualitative Differences in the Representation of Spatial Relations for Different Object Classes

ERIC Educational Resources Information Center

Cooper, Eric E.; Brooks, Brian E.

2004-01-01

Two experiments investigated whether the representations used for animal, produce, and object recognition code spatial relations in a similar manner. Experiment 1 tested the effects of planar rotation on the recognition of animals and nonanimal objects. Response times for recognizing animals followed an inverted U-shaped function, whereas those…

19 CFR 10.26 - Articles assembled or processed in a beneficiary country in whole of U.S. components or...

Code of Federal Regulations, 2010 CFR

2010-04-01

... textile components cut to shape in the United States. 10.26 Section 10.26 Customs Duties U.S. CUSTOMS AND... ingredients; articles assembled in a beneficiary country from textile components cut to shape in the United... assembled in a beneficiary country in whole of textile components cut to shape (but not to length, width, or...

Determination of As in tree-rings of poplar (Populus alba L.) by U-shaped DC arc.

PubMed

Marković, D M; Novović, I; Vilotić, D; Ignjatović, Lj

2009-04-01

An argon-stabilized U-shaped DC arc with a system for aerosol introduction was used for determination of As in poplar (Populus alba L.) tree-rings. After optimization of the operating parameters and selection of the most appropriate signal integration time (30 s), the limit of detection for As was reduced to 15.0 ng/mL. This detection limit obtained with the optimal integration time was compared with those for other methods: inductively coupled plasma-atomic emission spectrometry (ICP-AES), direct coupled plasma-atomic emission spectrometry (DCP-AES), microwave induced plasma-atomic emission spectrometry (MIP-AES) and improved thermospray flame furnace atomic absorption spectrometry (TS-FF-AAS). Arsenic is toxic trace element which can adversely affect plant, animal and human health. As an indicator of environment pollution we collected poplar tree-rings from two locations. The first area was close to the "Nikola Tesla" (TENT-A) power plant, Obrenovac, while the other was in the urban area of Novi Sad. In all cases elevated average concentrations of As were registered in poplar tree-rings from the Obrenovac location.

Progress on the FIReTIP Diagnostic on NSTX-U

NASA Astrophysics Data System (ADS)

Scott, Evan; Barchfeld, Robert; Riemenschneider, Paul; Muscatello, Chris; Sohrabi, Mohammad; Domier, Calvin; Ren, Yang; Kaita, Robert; Luhmann, Neville, Jr.; NSTX-U Team

2016-10-01

The Far-infrared Tangential Interferometer/Polarimeter (FIReTIP) system on NSTX-U at the PPPL aims to provide robust, line-averaged electron density measurements. The system consists of three optically-pumped 119 µm methanol lasers, one of which can be tuned via Stark broadening, allowing for uniquely high intermediate frequencies and time resolutions. One of the major goals of FIReTIP is to incorporate it into the NSTX-U plasma control system (PCS) for real-time plasma density feedback control. The front-end optics mounted to Bay G, which shape and position the beam going into the plasma, and internal retroreflector located near Bay B, which facilitates double-pass measurements, are hard-mounted to the NSTX-U vacuum vessel. Because interferometric density measurements are sensitive to vibrational effects, FIReTIP has been upgraded to a two-color interferometer system with the inclusion of a 633 nm laser interferometer for the direct measurement of vibrations and a field programmable gate array (FPGA) for the subsequent subtraction of vibrational effects from the density measurement in real-time. This work is supported by the U.S. Department of Energy Grant DE-FG02-99ER54518.

High taxonomic variability despite stable functional structure across microbial communities.

PubMed

Louca, Stilianos; Jacques, Saulo M S; Pires, Aliny P F; Leal, Juliana S; Srivastava, Diane S; Parfrey, Laura Wegener; Farjalla, Vinicius F; Doebeli, Michael

2016-12-05

Understanding the processes that are driving variation of natural microbial communities across space or time is a major challenge for ecologists. Environmental conditions strongly shape the metabolic function of microbial communities; however, other processes such as biotic interactions, random demographic drift or dispersal limitation may also influence community dynamics. The relative importance of these processes and their effects on community function remain largely unknown. To address this uncertainty, here we examined bacterial and archaeal communities in replicate 'miniature' aquatic ecosystems contained within the foliage of wild bromeliads. We used marker gene sequencing to infer the taxonomic composition within nine metabolic functional groups, and shotgun environmental DNA sequencing to estimate the relative abundances of these groups. We found that all of the bromeliads exhibited remarkably similar functional community structures, but that the taxonomic composition within individual functional groups was highly variable. Furthermore, using statistical analyses, we found that non-neutral processes, including environmental filtering and potentially biotic interactions, at least partly shaped the composition within functional groups and were more important than spatial dispersal limitation and demographic drift. Hence both the functional structure and taxonomic composition within functional groups of natural microbial communities may be shaped by non-neutral and roughly separate processes.

Replication fork collapse is a major cause of the high mutation frequency at three-base lesion clusters

PubMed Central

Sedletska, Yuliya; Radicella, J. Pablo; Sage, Evelyne

2013-01-01

Unresolved repair of clustered DNA lesions can lead to the formation of deleterious double strand breaks (DSB) or to mutation induction. Here, we investigated the outcome of clusters composed of base lesions for which base excision repair enzymes have different kinetics of excision/incision. We designed multiply damaged sites (MDS) composed of a rapidly excised uracil (U) and two oxidized bases, 5-hydroxyuracil (hU) and 8-oxoguanine (oG), excised more slowly. Plasmids harboring these U-oG/hU MDS-carrying duplexes were introduced into Escherichia coli cells either wild type or deficient for DNA n-glycosylases. Induction of DSB was estimated from plasmid survival and mutagenesis determined by sequencing of surviving clones. We show that a large majority of MDS is converted to DSB, whereas almost all surviving clones are mutated at hU. We demonstrate that mutagenesis at hU is correlated with excision of the U placed on the opposite strand. We propose that excision of U by Ung initiates the loss of U-oG-carrying strand, resulting in enhanced mutagenesis at the lesion present on the opposite strand. Our results highlight the importance of the kinetics of excision by base excision repair DNA n-glycosylases in the processing and fate of MDS and provide evidence for the role of strand loss/replication fork collapse during the processing of MDS on their mutational consequences. PMID:23945941

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.

ICTV Virus Taxonomy Profile: Virgaviridae

USDA-ARS?s Scientific Manuscript database

The family Virgaviridae is comprised of plant-infecting viruses with rod-shaped particles, single stranded RNA genomes with 3' terminal tRNA-like structures, and replication proteins typical of alphalike viruses. Differences in the number of genome components, genome organization and transmission m...

PolyI.polyC12U-mediated inhibition of loss of alloantigen responsiveness viral replication in human CD4+ T cell clones exposed to human immunodeficiency virus in vitro.

PubMed Central

Laurence, J; Kulkosky, J; Friedman, S M; Posnett, D N; Ts'o, P O

1987-01-01

Two alloreactive human CD4+ T cell clones, recognizing HLA-DR2 and HLA-DR1 determinants, lost their specific proliferative capacity after infection with HIV. This system was used to explore the effect of polyI.polyC12U on HIV replication and immune suppression. The mismatched double-stranded RNA blocked HIV-associated particulate reverse transcriptase activity and viral-mediated cytopathic effects. Also, polyI.polyC12U preserved the alloreactivity of T cell clones after exposure to HIV.PolyI.polyC12U appeared to act at a level subsequent to host cell infection and reverse transcription. It had no effect on the enhancement of gene expression by the HIV transcription unit tatIII. These findings indicate that early in the course of infection of CD4+ T lymphocytes, HIV can directly abrogate proliferation to specific allodeterminants, and that this function is preserved in the presence of polyI.polyC12U. They also provide insight into the mechanism of antiviral action of a class of agent with potential clinical utility in AIDS. Images PMID:2960696

Replication-Dependent Radiosensitization of Human Glioma Cells by Inhibition of Poly(ADP-Ribose) Polymerase: Mechanisms and Therapeutic Potential

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

Dungey, Fiona A.; Loeser, Dana A.; Chalmers, Anthony J.

2008-11-15

Purpose: Current treatments for glioblastoma multiforme are inadequate and limited by the radiation sensitivity of normal brain. Because glioblastoma multiforme are rapidly proliferating tumors within nondividing normal tissue, the therapeutic ratio might be enhanced by combining radiotherapy with a replication-specific radiosensitizer. KU-0059436 (AZD2281) is a potent and nontoxic inhibitor of poly(ADP-ribose) polymerase-1 (PARP-1) undergoing a Phase II clinical trial as a single agent. Methods and Materials: Based on previous observations that the radiosensitizing effects of PARP inhibition are more pronounced in dividing cells, we investigated the mechanisms underlying radiosensitization of human glioma cells by KU-0059436, evaluating the replication dependence ofmore » this effect and its therapeutic potential. Results: KU-0059436 increased the radiosensitivity of four human glioma cell lines (T98G, U373-MG, UVW, and U87-MG). Radiosensitization was enhanced in populations synchronized in S phase and abrogated by concomitant exposure to aphidicolin. Sensitization was further enhanced when the inhibitor was combined with a fractionated radiation schedule. KU-0059436 delayed repair of radiation-induced DNA breaks and was associated with a replication-dependent increase in {gamma}H2AX and Rad51 foci. Conclusion: The results of our study have shown that KU-0059436 increases radiosensitivity in a replication-dependent manner that is enhanced by fractionation. A mechanism is proposed whereby PARP inhibition increases the incidence of collapsed replication forks after ionizing radiation, generating persistent DNA double-strand breaks. These observations indicate that KU-0059436 is likely to enhance the therapeutic ratio achieved by radiotherapy in the treatment of glioblastoma multiforme. A Phase I clinical trial is in development.« less

Destabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase

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

Prakash, Aishwarya; Moharana, Kedar; Wallace, Susan S.

The base excision repair (BER) pathway repairs oxidized lesions in the DNA that result from reactive oxygen species generated in cells. If left unrepaired, these damaged DNA bases can disrupt cellular processes such as replication. NEIL1 is one of the 11 human DNA glycosylases that catalyze the first step of the BER pathway, i.e. recognition and excision of DNA lesions. NEIL1 interacts with essential replication proteins such as the ring-shaped homotrimeric proliferating cellular nuclear antigen (PCNA). We isolated a complex formed between NEIL1 and PCNA (±DNA) using size exclusion chromatography (SEC). This interaction was confirmed using native gel electrophoresis andmore » mass spectrometry. Stokes radii measured by SEC hinted that PCNA in complex with NEIL1 (±DNA) was no longer a trimer. Height measurements and images obtained by atomic force microscopy also demonstrated the dissociation of the PCNA homotrimer in the presence of NEIL1 and DNA, while small-angle X-ray scattering analysis confirmed the NEIL1 mediated PCNA trimer dissociation and formation of a 1:1:1 NEIL1-DNA-PCNA(monomer) complex. Furthermore, ab initio shape reconstruction provides insights into the solution structure of this previously unreported complex. Together, these data point to a potential mechanistic switch between replication and BER.« less

Facile preparation of hierarchically porous carbon using diatomite as both template and catalyst and methylene blue adsorption of carbon products.

PubMed

Liu, Dong; Yuan, Peng; Tan, Daoyong; Liu, Hongmei; Wang, Tong; Fan, Mingde; Zhu, Jianxi; He, Hongping

2012-12-15

Hierarchically porous carbons were prepared using a facile preparation method in which diatomite was utilized as both template and catalyst. The porous structures of the carbon products and their formation mechanisms were investigated. The macroporosity and microporosity of the diatomite-templated carbons were derived from replication of diatom shell and structure-reconfiguration of the carbon film, respectively. The macroporosity of carbons was strongly dependent on the original morphology of the diatomite template. The macroporous structure composed of carbon plates connected by the pillar- and tube-like macropores resulted from the replication of the central and edge pores of the diatom shells with disk-shaped morphology, respectively. And another macroporous carbon tubes were also replicated from canoe-shaped diatom shells. The acidity of diatomite dramatically affected the porosity of the carbons, more acid sites of diatomite template resulted in higher surface area and pore volume of the carbon products. The diatomite-templated carbons exhibited higher adsorption capacity for methylene blue than the commercial activated carbon (CAC), although the specific surface area was much smaller than that of CAC, due to the hierarchical porosity of diatomite-templated carbons. And the carbons were readily reclaimed and regenerated. Copyright © 2012 Elsevier Inc. All rights reserved.

Critical disease windows shaped by stress exposure alter allocation trade-offs between development and immunity.

PubMed

Kirschman, Lucas J; Crespi, Erica J; Warne, Robin W

2018-01-01

Ubiquitous environmental stressors are often thought to alter animal susceptibility to pathogens and contribute to disease emergence. However, duration of exposure to a stressor is likely critical, because while chronic stress is often immunosuppressive, acute stress can temporarily enhance immune function. Furthermore, host susceptibility to stress and disease often varies with ontogeny; increasing during critical developmental windows. How the duration and timing of exposure to stressors interact to shape critical windows and influence disease processes is not well tested. We used ranavirus and larval amphibians as a model system to investigate how physiological stress and pathogenic infection shape development and disease dynamics in vertebrates. Based on a resource allocation model, we designed experiments to test how exposure to stressors may induce resource trade-offs that shape critical windows and disease processes because the neuroendocrine stress axis coordinates developmental remodelling, immune function and energy allocation in larval amphibians. We used wood frog larvae (Lithobates sylvaticus) to investigate how chronic and acute exposure to corticosterone, the dominant amphibian glucocorticoid hormone, mediates development and immune function via splenocyte immunohistochemistry analysis in association with ranavirus infection. Corticosterone treatments affected immune function, as both chronic and acute exposure suppressed splenocyte proliferation, although viral replication rate increased only in the chronic corticosterone treatment. Time to metamorphosis and survival depended on both corticosterone treatment and infection status. In the control and chronic corticosterone treatments, ranavirus infection decreased survival and delayed metamorphosis, although chronic corticosterone exposure accelerated rate of metamorphosis in uninfected larvae. Acute corticosterone exposure accelerated metamorphosis increased survival in infected larvae. Interactions between stress exposure (via glucocorticoid actions) and infection impose resource trade-offs that shape optimal allocation between development and somatic function. As a result, critical disease windows are likely shaped by stress exposure because any conditions that induce changes in differentiation rates will alter the duration and susceptibility of organisms to stressors or disease. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Non coding extremities of the seven influenza virus type C vRNA segments: effect on transcription and replication by the type C and type A polymerase complexes

PubMed Central

Crescenzo-Chaigne, Bernadette; Barbezange, Cyril; van der Werf, Sylvie

2008-01-01

Background The transcription/replication of the influenza viruses implicate the terminal nucleotide sequences of viral RNA, which comprise sequences at the extremities conserved among the genomic segments as well as variable 3' and 5' non-coding (NC) regions. The plasmid-based system for the in vivo reconstitution of functional ribonucleoproteins, upon expression of viral-like RNAs together with the nucleoprotein and polymerase proteins has been widely used to analyze transcription/replication of influenza viruses. It was thus shown that the type A polymerase could transcribe and replicate type A, B, or C vRNA templates whereas neither type B nor type C polymerases were able to transcribe and replicate type A templates efficiently. Here we studied the importance of the NC regions from the seven segments of type C influenza virus for efficient transcription/replication by the type A and C polymerases. Results The NC sequences of the seven genomic segments of the type C influenza virus C/Johannesburg/1/66 strain were found to be more variable in length than those of the type A and B viruses. The levels of transcription/replication of viral-like vRNAs harboring the NC sequences of the respective type C virus segments flanking the CAT reporter gene were comparable in the presence of either type C or type A polymerase complexes except for the NS and PB2-like vRNAs. For the NS-like vRNA, the transcription/replication level was higher after introduction of a U residue at position 6 in the 5' NC region as for all other segments. For the PB2-like vRNA the CAT expression level was particularly reduced with the type C polymerase. Analysis of mutants of the 5' NC sequence in the PB2-like vRNA, the shortest 5' NC sequence among the seven segments, showed that additional sequences within the PB2 ORF were essential for the efficiency of transcription but not replication by the type C polymerase complex. Conclusion In the context of a PB2-like reporter vRNA template, the sequence upstream the polyU stretch plays a role in the transcription/replication process by the type C polymerase complex. PMID:18973655

Bone marrow cells stained by azide-conjugated Alexa fluors in the absence of an alkyne label.

PubMed

Lin, Guiting; Ning, Hongxiu; Banie, Lia; Qiu, Xuefeng; Zhang, Haiyang; Lue, Tom F; Lin, Ching-Shwun

2012-09-01

Thymidine analog 5-ethynyl-2'-deoxyuridine (EdU) has recently been introduced as an alternative to 5-bromo-2-deoxyuridine (BrdU) for cell labeling and tracking. Incorporation of EdU into replicating DNA can be detected by azide-conjugated fluors (eg, Alexa-azide) through a Cu(i)-catalyzed click reaction between EdU's alkyne moiety and azide. While this cell labeling method has proven to be valuable for tracking transplanted stem cells in various tissues, we have found that some bone marrow cells could be stained by Alexa-azide in the absence of EdU label. In intact rat femoral bone marrow, ~3% of nucleated cells were false-positively stained, and in isolated bone marrow cells, ~13%. In contrast to true-positive stains, which localize in the nucleus, the false-positive stains were cytoplasmic. Furthermore, while true-positive staining requires Cu(i), false-positive staining does not. Reducing the click reaction time or reducing the Alexa-azide concentration failed to improve the distinction between true- and false-positive staining. Hematopoietic and mesenchymal stem cell markers CD34 and Stro-1 did not co-localize with the false-positively stained cells, and these cells' identity remains unknown.

Peripheral re-localization of constitutive heterochromatin advances its replication timing and impairs maintenance of silencing marks.

PubMed

Heinz, Kathrin S; Casas-Delucchi, Corella S; Török, Timea; Cmarko, Dusan; Rapp, Alexander; Raska, Ivan; Cardoso, M Cristina

2018-05-10

The replication of the genome is a highly organized process, both spatially and temporally. Although a lot is known on the composition of the basic replication machinery, how its activity is regulated is mostly unknown. Several chromatin properties have been proposed as regulators, but a potential role of the nuclear DNA position remains unclear. We made use of the prominent structure and well-defined heterochromatic landscape of mouse pericentric chromosome domains as a well-studied example of late replicating constitutive heterochromatin. We established a method to manipulate its nuclear position and evaluated the effect on replication timing, DNA compaction and epigenetic composition. Using time-lapse microscopy, we observed that constitutive heterochromatin, known to replicate during late S-phase, was replicated in mid S-phase when repositioned to the nuclear periphery. Out-of-schedule replication resulted in deficient post-replicative maintenance of chromatin modifications, namely silencing marks. We propose that repositioned constitutive heterochromatin was activated in trans according to the domino model of origin firing by nearby (mid S) firing origins. In summary, our data provide, on the one hand, a novel approach to manipulate nuclear DNA position and, on the other hand, establish nuclear DNA position as a novel mechanism regulating DNA replication timing and epigenetic maintenance.

Replication profile of Saccharomyces cerevisiae chromosome VI.

PubMed

Friedman, K L; Brewer, B J; Fangman, W L

1997-11-01

An understanding of the replication programme at the genome level will require the identification and characterization of origins of replication through large, contiguous regions of DNA. As a step toward this goal, origin efficiencies and replication times were determined for 10 ARSs spanning most of the 270 kilobase (kb) chromosome VI of Saccharomyces cerevisiae. Chromosome VI shows a wide variation in the percentage of cell cycles in which different replication origins are utilized. Most of the origins are activated in only a fraction of cells, suggesting that the pattern of origin usage on chromosome VI varies greatly within the cell population. The replication times of fragments containing chromosome VI origins show a temporal pattern that has been recognized on other chromosomes--the telomeres replicate late in S phase, while the central region of the chromosome replicates early. As demonstrated here for chromosome VI, analysis of the direction of replication fork movement along a chromosome and determination of replication time by measuring a period of hemimethylation may provide an efficient means of surveying origin activity over large regions of the genome.

Cortical topography of intracortical inhibition influences the speed of decision making.

PubMed

Wilimzig, Claudia; Ragert, Patrick; Dinse, Hubert R

2012-02-21

The neocortex contains orderly topographic maps; however, their functional role remains controversial. Theoretical studies have suggested a role in minimizing computational costs, whereas empirical studies have focused on spatial localization. Using a tactile multiple-choice reaction time (RT) task before and after the induction of perceptual learning through repetitive sensory stimulation, we extend the framework of cortical topographies by demonstrating that the topographic arrangement of intracortical inhibition contributes to the speed of human perceptual decision-making processes. RTs differ among fingers, displaying an inverted U-shaped function. Simulations using neural fields show the inverted U-shaped RT distribution as an emergent consequence of lateral inhibition. Weakening inhibition through learning shortens RTs, which is modeled through topographically reorganized inhibition. Whereas changes in decision making are often regarded as an outcome of higher cortical areas, our data show that the spatial layout of interaction processes within representational maps contributes to selection and decision-making processes.

Cortical topography of intracortical inhibition influences the speed of decision making

PubMed Central

Wilimzig, Claudia; Ragert, Patrick; Dinse, Hubert R.

2012-01-01

The neocortex contains orderly topographic maps; however, their functional role remains controversial. Theoretical studies have suggested a role in minimizing computational costs, whereas empirical studies have focused on spatial localization. Using a tactile multiple-choice reaction time (RT) task before and after the induction of perceptual learning through repetitive sensory stimulation, we extend the framework of cortical topographies by demonstrating that the topographic arrangement of intracortical inhibition contributes to the speed of human perceptual decision-making processes. RTs differ among fingers, displaying an inverted U-shaped function. Simulations using neural fields show the inverted U-shaped RT distribution as an emergent consequence of lateral inhibition. Weakening inhibition through learning shortens RTs, which is modeled through topographically reorganized inhibition. Whereas changes in decision making are often regarded as an outcome of higher cortical areas, our data show that the spatial layout of interaction processes within representational maps contributes to selection and decision-making processes. PMID:22315409

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.

Natural Decrease in Texas Counties.

ERIC Educational Resources Information Center

Koebernick, Thomas E.; Markides, Kyriakos S.

In replication of other studies, the natural decrease of Texas population was examined in terms of the effect of migration and fertility. Utilizing Texas and U.S. vital statistics and the 1970 U.S. Census of Population, Texas population trends were analyzed for the 1968-72 period by dividing the 254 Texas counties into: (1) 65 natural decrease…

A semi-analytical method to estimate the effective slip length of spreading spherical-cap shaped droplets using Cox theory

NASA Astrophysics Data System (ADS)

Wörner, M.; Cai, X.; Alla, H.; Yue, P.

2018-03-01

The Cox–Voinov law on dynamic spreading relates the difference between the cubic values of the apparent contact angle (θ) and the equilibrium contact angle to the instantaneous contact line speed (U). Comparing spreading results with this hydrodynamic wetting theory requires accurate data of θ and U during the entire process. We consider the case when gravitational forces are negligible, so that the shape of the spreading drop can be closely approximated by a spherical cap. Using geometrical dependencies, we transform the general Cox law in a semi-analytical relation for the temporal evolution of the spreading radius. Evaluating this relation numerically shows that the spreading curve becomes independent from the gas viscosity when the latter is less than about 1% of the drop viscosity. Since inertia may invalidate the made assumptions in the initial stage of spreading, a quantitative criterion for the time when the spherical-cap assumption is reasonable is derived utilizing phase-field simulations on the spreading of partially wetting droplets. The developed theory allows us to compare experimental/computational spreading curves for spherical-cap shaped droplets with Cox theory without the need for instantaneous data of θ and U. Furthermore, the fitting of Cox theory enables us to estimate the effective slip length. This is potentially useful for establishing relationships between slip length and parameters in numerical methods for moving contact lines.

Effects of temporal integration on the shape of visual backward masking functions.

PubMed

Francis, Gregory; Cho, Yang Seok

2008-10-01

Many studies of cognition and perception use a visual mask to explore the dynamics of information processing of a target. Especially important in these applications is the time between the target and mask stimuli. A plot of some measure of target visibility against stimulus onset asynchrony is called a masking function, which can sometimes be monotonic increasing but other times is U-shaped. Theories of backward masking have long hypothesized that temporal integration of the target and mask influences properties of masking but have not connected the influence of integration with the shape of the masking function. With two experiments that vary the spatial properties of the target and mask, the authors provide evidence that temporal integration of the stimuli plays a critical role in determining the shape of the masking function. The resulting data both challenge current theories of backward masking and indicate what changes to the theories are needed to account for the new data. The authors further discuss the implication of the findings for uses of backward masking to explore other aspects of cognition.

Initiation of poliovirus plus-strand RNA synthesis in a membrane complex of infected HeLa cells

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

Takeda, N.; Kuhn, R.J.; Yang, C.F.

1986-10-01

An in vitro poliovirus RNA-synthesizing system derived from a crude membrance fraction of infected HeLa cells was used to analyze the mechanism of initiation of poliovirus plus-strand RNA synthesis. This system contains an activity that synthesizes the nucleotidyl proteins VPg-pU and VPg-pUpU. These molecules represent the 5'-terminal structure of nascent RNA molecules and of virion RNA. The membranous replication complex is also capable of synthesizing mucleotidyl proteins containing nine or more of the poliovirus 5'-proximal nucleotides as assayed by the formation of the RNase T/sub 1/-resistant oligonucleotide VPg-pUUAAAACAGp or by fingerprint analysis of the in vitro-synthesized /sup 32/P-RNA. Incubation ofmore » preformed VPg-pUpU with unlabeled nucleoside triphosphates resulted in the formation of VPg-pUUAAAACAGp. This reaction, which appeared to be an elongation of VPg-pUpU, was stimulated by the addition of a soluble fraction (S-10) obtained from uninfected HeLa cells. Preformed VPg-pU could be chased into VPg-pUpU in the presence of UTP. The data are consistent with a model that VPg-pU can function as a primer for poliovirus plus-strand RNA synthesis in the membranous replication complex and that the elongation reaction may be stimulated by a host cellular factor.« less

The predominant circular form of avocado sunblotch viroid accumulates in planta as a free RNA adopting a rod-shaped secondary structure unprotected by tightly bound host proteins.

PubMed

López-Carrasco, Amparo; Flores, Ricardo

2017-07-01

Avocado sunblotch viroid (ASBVd), the type member of the family Avsunviroidae, replicates and accumulates in chloroplasts. Whether this minimal non-protein-coding circular RNA of 246-250 nt exists in vivo as a free nucleic acid or closely associated with host proteins remains unknown. To tackle this issue, the secondary structures of the monomeric circular (mc) (+) and (-) strands of ASBVd have been examined in silico by searching those of minimal free energy, and in vitro at single-nucleotide resolution by selective 2'-hydroxyl acylation analysed by primer extension (SHAPE). Both approaches resulted in predominant rod-like secondary structures without tertiary interactions, with the mc (+) RNA being more compact than its (-) counterpart as revealed by non-denaturing polyacryamide gel electrophoresis. Moreover, in vivo SHAPE showed that the mc ASBVd (+) form accumulates in avocado leaves as a free RNA adopting a similar rod-shaped conformation unprotected by tightly bound host proteins. Hence, the mc ASBVd (+) RNA behaves in planta like the previously studied mc (+) RNA of potato spindle tuber viroid, the type member of nuclear viroids (family Pospiviroidae), indicating that two different viroids replicating and accumulating in distinct subcellular compartments, have converged into a common structural solution. Circularity and compact secondary structures confer to these RNAs, and probably to all viroids, the intrinsic stability needed to survive in their natural habitats. However, in vivo SHAPE has not revealed the (possibly transient or loose) interactions of the mc ASBVd (+) RNA with two host proteins observed previously by UV irradiation of infected avocado leaves.

Silencing of the pentose phosphate pathway genes influences DNA replication in human fibroblasts.

PubMed

Fornalewicz, Karolina; Wieczorek, Aneta; Węgrzyn, Grzegorz; Łyżeń, Robert

2017-11-30

Previous reports and our recently published data indicated that some enzymes of glycolysis and the tricarboxylic acid cycle can affect the genome replication process by changing either the efficiency or timing of DNA synthesis in human normal cells. Both these pathways are connected with the pentose phosphate pathway (PPP pathway). The PPP pathway supports cell growth by generating energy and precursors for nucleotides and amino acids. Therefore, we asked if silencing of genes coding for enzymes involved in the pentose phosphate pathway may also affect the control of DNA replication in human fibroblasts. Particular genes coding for PPP pathway enzymes were partially silenced with specific siRNAs. Such cells remained viable. We found that silencing of the H6PD, PRPS1, RPE genes caused less efficient enterance to the S phase and decrease in efficiency of DNA synthesis. On the other hand, in cells treated with siRNA against G6PD, RBKS and TALDO genes, the fraction of cells entering the S phase was increased. However, only in the case of G6PD and TALDO, the ratio of BrdU incorporation to DNA was significantly changed. The presented results together with our previously published studies illustrate the complexity of the influence of genes coding for central carbon metabolism on the control of DNA replication in human fibroblasts, and indicate which of them are especially important in this process. Copyright © 2017 Elsevier B.V. All rights reserved.

Impact of Climate Change on Food Security in Kenya

NASA Astrophysics Data System (ADS)

Yator, J. J.

2016-12-01

This study sought to address the existing gap on the impact of climate change on food security in support of policy measures to avert famine catastrophes. Fixed and random effects regressions for crop food security were estimated. The study simulated the expected impact of future climate change on food insecurity based on the Representative Concentration Pathways scenario (RCPs). The study makes use of county-level yields estimates (beans, maize, millet and sorghum) and daily climate data (1971 to 2010). Climate variability affects food security irrespective of how food security is defined. Rainfall during October-November-December (OND), as well as during March-April-May (MAM) exhibit an inverted U-shaped relationship with most food crops; the effects are most pronounced for maize and sorghum. Beans and Millet are found to be largely unresponsive to climate variability and also to time-invariant factors. OND rains and fall and summer temperature exhibit a U-shaped relationship with yields for most crops, while MAM rains temperature exhibits an inverted U-shaped relationship. However, winter temperatures exhibit a hill-shaped relationship with most crops. Project future climate change scenarios on crop productivity show that climate change will adversely affect food security, with up to 69% decline in yields by the year 2100. Climate variables have a non-linear relationship with food insecurity. Temperature exhibits an inverted U-shaped relationship with food insecurity, suggesting that increased temperatures will increase crop food insecurity. However, maize and millet, benefit from increased summer and winter temperatures. The simulated effects of different climate change scenarios on food insecurity suggest that adverse climate change will increase food insecurity in Kenya. The largest increases in food insecurity are predicted for the RCP 8.5Wm2, compared to RCP 4.5Wm2. Climate change is likely to have the greatest effects on maize insecurity, which is likely to increase by between 8.56% and 21% by the year 2100. There exists a need for policies that safeguard agriculture against the adverse effects of climate change to alleviate food insecurity in Kenya. Therefore, it is important that climate change mitigation is given much more priority in policy planning and also implementation.

The Emergence of Life as a First-Order Phase Transition

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

Mathis, Cole; Bhattacharya, Tanmoy; Walker, Sara Imari

It is well known that life on Earth alters its environment over evolutionary and geological timescales. An important open question is whether this is a result of evolutionary optimization or a universal feature of life. In the latter case, the origin of life would be coincident with a shift in environmental conditions. Here in this paper we present a model for the emergence of life in which replicators are explicitly coupled to their environment through the recycling of a finite supply of resources. The model exhibits a dynamic, first-order phase transition from nonlife to life, where the life phase ismore » distinguished by selection on replicators. We show that environmental coupling plays an important role in the dynamics of the transition. The transition corresponds to a redistribution of matter in replicators and their environment, driven by selection on replicators, exhibiting an explosive growth in diversity as replicators are selected. The transition is accurately tracked by the mutual information shared between replicators and their environment. In the absence of successfully repartitioning system resources, the transition fails to complete, leading to the possibility of many frustrated trials before life first emerges. Often, the replicators that initiate the transition are not those that are ultimately selected. The results are consistent with the view that life's propensity to shape its environment is indeed a universal feature of replicators, characteristic of the transition from nonlife to life. We discuss the implications of these results for understanding life's emergence and evolutionary transitions more broadly.« less

The Emergence of Life as a First-Order Phase Transition

DOE PAGES

Mathis, Cole; Bhattacharya, Tanmoy; Walker, Sara Imari

2017-03-01

It is well known that life on Earth alters its environment over evolutionary and geological timescales. An important open question is whether this is a result of evolutionary optimization or a universal feature of life. In the latter case, the origin of life would be coincident with a shift in environmental conditions. Here in this paper we present a model for the emergence of life in which replicators are explicitly coupled to their environment through the recycling of a finite supply of resources. The model exhibits a dynamic, first-order phase transition from nonlife to life, where the life phase ismore » distinguished by selection on replicators. We show that environmental coupling plays an important role in the dynamics of the transition. The transition corresponds to a redistribution of matter in replicators and their environment, driven by selection on replicators, exhibiting an explosive growth in diversity as replicators are selected. The transition is accurately tracked by the mutual information shared between replicators and their environment. In the absence of successfully repartitioning system resources, the transition fails to complete, leading to the possibility of many frustrated trials before life first emerges. Often, the replicators that initiate the transition are not those that are ultimately selected. The results are consistent with the view that life's propensity to shape its environment is indeed a universal feature of replicators, characteristic of the transition from nonlife to life. We discuss the implications of these results for understanding life's emergence and evolutionary transitions more broadly.« less

The Emergence of Life as a First-Order Phase Transition

NASA Astrophysics Data System (ADS)

Mathis, Cole; Bhattacharya, Tanmoy; Imari Walker, Sara

2017-03-01

It is well known that life on Earth alters its environment over evolutionary and geological timescales. An important open question is whether this is a result of evolutionary optimization or a universal feature of life. In the latter case, the origin of life would be coincident with a shift in environmental conditions. Here we present a model for the emergence of life in which replicators are explicitly coupled to their environment through the recycling of a finite supply of resources. The model exhibits a dynamic, first-order phase transition from nonlife to life, where the life phase is distinguished by selection on replicators. We show that environmental coupling plays an important role in the dynamics of the transition. The transition corresponds to a redistribution of matter in replicators and their environment, driven by selection on replicators, exhibiting an explosive growth in diversity as replicators are selected. The transition is accurately tracked by the mutual information shared between replicators and their environment. In the absence of successfully repartitioning system resources, the transition fails to complete, leading to the possibility of many frustrated trials before life first emerges. Often, the replicators that initiate the transition are not those that are ultimately selected. The results are consistent with the view that life's propensity to shape its environment is indeed a universal feature of replicators, characteristic of the transition from nonlife to life. We discuss the implications of these results for understanding life's emergence and evolutionary transitions more broadly.

Identification of a New Human Adenovirus Protein Encoded by a Novel Late l-Strand Transcription Unit▿

PubMed Central

Tollefson, Ann E.; Ying, Baoling; Doronin, Konstantin; Sidor, Peter D.; Wold, William S. M.

2007-01-01

A short open reading frame named the “U exon,” located on the adenovirus (Ad) l-strand (for leftward transcription) between the early E3 region and the fiber gene, is conserved in mastadenoviruses. We have observed that Ad5 mutants with large deletions in E3 that infringe on the U exon display a mild growth defect, as well as an aberrant Ad E2 DNA-binding protein (DBP) intranuclear localization pattern and an apparent failure to organize replication centers during late infection. Mutants in which the U exon DNA is reconstructed have a reversed phenotype. Chow et al. (L. T. Chow et al., J. Mol. Biol. 134:265-303, 1979) described mRNAs initiating in the region of the U exon and spliced to downstream sequences in the late DBP mRNA leader and the DBP-coding region. We have cloned this mRNA (as cDNA) from Ad5 late mRNA; the predicted protein is 217 amino acids, initiating in the U exon and continuing in frame in the DBP leader and in the DBP-coding region but in a different reading frame from DBP. Polyclonal and monoclonal antibodies generated against the predicted U exon protein (UXP) showed that UXP is ∼24K in size by immunoblot and is a late protein. At 18 to 24 h postinfection, UXP is strongly associated with nucleoli and is found throughout the nucleus; later, UXP is associated with the periphery of replication centers, suggesting a function relevant to Ad DNA replication or RNA transcription. UXP is expressed by all four species C Ads. When expressed in transient transfections, UXP complements the aberrant DBP localization pattern of UXP-negative Ad5 mutants. Our data indicate that UXP is a previously unrecognized protein derived from a novel late l-strand transcription unit. PMID:17881437

Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome

DOE PAGES

Wallen, Jamie R.; Zhang, Hao; Weis, Caroline; ...

2017-01-03

The physical organization of DNA enzymes at a replication fork enables efficient copying of two antiparallel DNA strands, yet dynamic protein interactions within the replication complex complicate replisome structural studies. We employed a combination of crystallographic, native mass spectrometry and small-angle X-ray scattering experiments to capture alternative structures of a model replication system encoded by bacteriophage T7. then, the two molecules of DNA polymerase bind the ring-shaped primase-helicase in a conserved orientation and provide structural insight into how the acidic C-terminal tail of the primase-helicase contacts the DNA polymerase to facilitate loading of the polymerase onto DNA. A third DNA polymerasemore » binds the ring in an offset manner that may enable polymerase exchange during replication. Alternative polymerase binding modes are also detected by small-angle X-ray scattering with DNA substrates present. The collective results unveil complex motions within T7 replisome higher-order structures that are underpinned by multivalent protein-protein interactions with functional implications.« less

Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome

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

Wallen, Jamie R.; Zhang, Hao; Weis, Caroline

The physical organization of DNA enzymes at a replication fork enables efficient copying of two antiparallel DNA strands, yet dynamic protein interactions within the replication complex complicate replisome structural studies. We employed a combination of crystallographic, native mass spectrometry and small-angle X-ray scattering experiments to capture alternative structures of a model replication system encoded by bacteriophage T7. then, the two molecules of DNA polymerase bind the ring-shaped primase-helicase in a conserved orientation and provide structural insight into how the acidic C-terminal tail of the primase-helicase contacts the DNA polymerase to facilitate loading of the polymerase onto DNA. A third DNA polymerasemore » binds the ring in an offset manner that may enable polymerase exchange during replication. Alternative polymerase binding modes are also detected by small-angle X-ray scattering with DNA substrates present. The collective results unveil complex motions within T7 replisome higher-order structures that are underpinned by multivalent protein-protein interactions with functional implications.« less

How and why multiple MCMs are loaded at origins of DNA replication.

PubMed

Das, Shankar P; Rhind, Nicholas

2016-07-01

Recent work suggests that DNA replication origins are regulated by the number of multiple mini-chromosome maintenance (MCM) complexes loaded. Origins are defined by the loading of MCM - the replicative helicase which initiates DNA replication and replication kinetics determined by origin's location and firing times. However, activation of MCM is heterogeneous; different origins firing at different times in different cells. Also, more MCMs are loaded in G1 than are used in S phase. These aspects of MCM biology are explained by the observation that multiple MCMs are loaded at origins. Having more MCMs at early origins makes them more likely to fire, effecting differences in origin efficiency that define replication timing. Nonetheless, multiple MCM loading raises new questions, such as how they are loaded, where these MCMs reside at origins, and how their presence affects replication timing. In this review, we address these questions and discuss future avenues of research. © 2016 WILEY Periodicals, Inc.

Replication of microchannel structures in WC-Co feedstock using elastomeric replica moulds by hot embossing process.

PubMed

Sahli, M; Gelin, J-C; Barrière, T

2015-10-01

Hot embossing is a net shaping process that is able to produce the micro-components of polymers with intrinsic and complex shapes at lower cost compared with machining and injection moulding. However, the emboss of hard metals, such as WC-Co, is more challenging due to their high thermal conductivity and ease of agglomeration. Thus, a WC-Co alloy mixed with a wax-based binder feedstock was selected. The formed feedstock exhibited pseudo-plastic flow and was successfully embossed (green part). Here, we developed a novel process that is used to replicate polymer microfluidic chips while simultaneously reducing the channel surface roughness of the mould insert, yielding optical-grade (less than 100 nm surface roughness) channels and reservoirs. This paper concerns the replication of metallic microfluidic mould inserts in WC-Co and the parameters associated with feedstock formation via a hot embossing process. A suitable formulation for micro-powder hot embossing has been established and characterised by thermogravimetric analyses and measurements of mixing torques to verify and quantify the homogeneity of the proposed feedstocks. The relative density of the samples increased with processing temperature, and almost fully dense materials were obtained. In this work, the effects of the sintering temperature on the physical properties were systematically analysed. The evolution of the metal surface morphology during the hot embossing process was also investigated. The results indicate that the feedstock can be used to manufacture micro-fluidic die mould cavities with a low roughness, proper dimensions and good shape retention. The shrinkage of the sintered part was approximately 19-24% compared with that of the brown part. Copyright © 2015 Elsevier B.V. All rights reserved.

Bunyaviridae and Their Replication. Part 2. Replication of Bunyaviridae

DTIC Science & Technology

1990-01-01

Ivatt RJ. Synthesis and processing of asparagine- mulates intracellularly: cellular process of the large glycopro- linked oligosaccharides . Anna Rev...the high-mannose rather than complex type, and no evidence for the presence of 0-linked oligosaccharides A- has been obtained (86,87,93,120,146). AA ’U...and Pulse -chase experiments revealed no precursor/prod- G2 has not been identified. However, an intergenic uct relationship between the 78- and 14-kd

S-phase arrest after vincristine treatment may promote hepatitis B virus replication

PubMed Central

Xu, Lei; Tu, Zeng; Xu, Ge; Hu, Jie-Li; Cai, Xue-Fei; Zhan, Xing-Xing; Wang, Yu-Wei; Huang, Yuan; Chen, Juan; Huang, Ai-Long

2015-01-01

AIM: To observe the effect of vincristine on hepatitis B virus (HBV) replication in vitro and to study its possible mechanisms. METHODS: Vincristine was added to the cultures of two cell lines stably expressing HBV. Then, the levels of hepatitis B surface antigen (HBsAg), hepatitis B e antigen (HBeAg), and hepatitis B core antigen (HBcAg) in the supernatants or cytoplasm were examined using by enzyme-linked immunosorbent assay and Western blot. The HBV pregenome RNA (pgRNA) was detected using reverse transcription-PCR and real-time fluorescent quantitative PCR (RT-qPCR), and viral DNA was detected using Southern blot and RT-qPCR. Cell proliferation after drug treatment was detected using the BrdU incorporation test and the trypan blue exclusion assay. Cell cycle and cell apoptosis were examined using flow cytometry and Western blot. RESULTS: Vincristine up-regulated HBV replication directly in vitro in a dose-dependent manner, and 24-h exposure to 0.1 μmol/L vincristine induced more than 4-fold and 3-fold increases in intracellular HBV DNA and the secretion of viral DNA, respectively. The expression of HBV pgRNA, intracellular HBsAg and HBcAg, and the secretion of HBeAg were also increased significantly after drug treatment. Most importantly, vincristine promoted the cell excretion of HBV nucleocapsids instead of HBV Dane particles, and the nucleocapsids are closely related to the HBV pathogenesis. Furthermore, vincristine inhibited the proliferation of cells stably expressing HBV. The higher the concentration of the drug, the more significant the inhibition of the cell proliferation and the stronger the HBV replication ability in cells. Flow cytometry indicated that cell cycle arrest at S-phase was responsible for the cell proliferation inhibition. CONCLUSION: Vincristine has a strong stimulatory effect on HBV replication and induces cell cycle arrest, and cell proliferation inhibition may be conducive to viral replication. PMID:25663769

Repeated Listening Increases the Liking for Music Regardless of Its Complexity: Implications for the Appreciation and Aesthetics of Music

PubMed Central

Madison, Guy; Schiölde, Gunilla

2017-01-01

Psychological and aesthetic theories predict that music is appreciated at optimal, peak levels of familiarity and complexity, and that appreciation of music exhibits an inverted U-shaped relationship with familiarity as well as complexity. Because increased familiarity conceivably leads to improved processing and less perceived complexity, we test whether there is an interaction between familiarity and complexity. Specifically, increased familiarity should render the music subjectively less complex, and therefore move the apex of the U curve toward greater complexity. A naturalistic listening experiment was conducted, featuring 40 music examples (ME) divided by experts into 4 levels of complexity prior to the main experiment. The MEs were presented 28 times each across a period of approximately 4 weeks, and individual ratings were assessed throughout the experiment. Ratings of liking increased monotonically with repeated listening at all levels of complexity; both the simplest and the most complex MEs were liked more as a function of listening time, without any indication of a U-shaped relation. Although the MEs were previously unknown to the participants, the strongest predictor of liking was familiarity in terms of having listened to similar music before, i.e., familiarity with musical style. We conclude that familiarity is the single most important variable for explaining differences in liking among music, regardless of the complexity of the music. PMID:28408864

Adiabatic decay of internal solitons due to Earth's rotation within the framework of the Gardner-Ostrovsky equation

NASA Astrophysics Data System (ADS)

Obregon, Maria; Raj, Nawin; Stepanyants, Yury

2018-03-01

The adiabatic decay of different types of internal wave solitons caused by the Earth's rotation is studied within the framework of the Gardner-Ostrovsky equation. The governing equation describing such processes includes quadratic and cubic nonlinear terms, as well as the Boussinesq and Coriolis dispersions: (ut + c ux + α u ux + α1 u2 ux + β uxxx)x = γ u. It is shown that at the early stage of evolution solitons gradually decay under the influence of weak Earth's rotation described by the parameter γ. The characteristic decay time is derived for different types of solitons for positive and negative coefficients of cubic nonlinearity α1 (both signs of that parameter may occur in the oceans). The coefficient of quadratic nonlinearity α determines only a polarity of solitary wave when α1 < 0 or the asymmetry of solitary waves of opposite polarity when α1 > 0. It is found that the adiabatic theory describes well the decay of solitons having bell-shaped profiles. In contrast to that, large amplitude table-top solitons, which can exist when α1 is negative, are structurally unstable. Under the influence of Earth's rotation, they transfer first to the bell-shaped solitons, which decay then adiabatically. Estimates of the characteristic decay time of internal solitons are presented for the real oceanographic conditions.

Results of using the NSTX-U Plasma Control System for scenario development

NASA Astrophysics Data System (ADS)

Boyer, M. D.; Battaglia, D. J.; Gates, D. A.; Gerhardt, S.; Menard, J.; Mueller, D.; Myers, C. E.; Ferron, J.; Sabbagh, S.; NSTX-U Team

2016-10-01

To best use the new capabilities of NSTX-U (e.g., higher toroidal field and additional, more distributed heating and current drive sources) and to achieve the operational goals of the program, major upgrades to the Plasma Control System have been made. These include improvements to vertical control, real-time equilibrium reconstruction, and plasma boundary shape control and the addition of flexible algorithms for beam modulation and gas injection to control the upgraded actuators in real-time, enabling their use in algorithms for stored energy and profile control. Control system commissioning activities have so far focused on vertical position and shape control. The upgraded controllers have been used to explore the vertical stability limits in inner wall limited and diverted discharges, and control of X-point and strike point locations has been demonstrated and is routinely used. A method for controlling the mid-plane inner gap, a challenge for STs, has also been added to improve reproducible control of diverted discharges. A supervisory shutdown handling algorithm has also been commissioned to ramp the plasma down and safely turn off actuators after an event such as loss of vertical control. Use of the upgrades has contributed to achieving 1MA, 0.65T scenarios with greater than 1s pulse length. Work supported by U.S. D.O.E. Contract No. DE-AC02-09CH11466.

Large-volume flux closure during plasmoid-mediated reconnection in coaxial helicity injection

DOE PAGES

Ebrahimi, F.; Raman, R.

2016-03-23

A large-volume flux closure during transient coaxial helicity injection (CHI) in NSTX-U is demonstrated through resistive magnetohydrodynamics (MHD) simulations. Several major improvements, including the improved positioning of the divertor poloidal field coils, are projected to improve the CHI start-up phase in NSTX-U. Simulations in the NSTX-U configuration with constant in time coil currents show that with strong flux shaping the injected open field lines (injector flux) rapidly reconnect and form large volume of closed flux surfaces. This is achieved by driving parallel current in the injector flux coil and oppositely directed currents in the flux shaping coils to form amore » narrow injector flux footprint and push the injector flux into the vessel. As the helicity and plasma are injected into the device, the oppositely directed field lines in the injector region are forced to reconnect through a local Sweet-Parker type reconnection, or to spontaneously reconnect when the elongated current sheet becomes MHD unstable to form plasmoids. In these simulations for the first time, it is found that the closed flux is over 70% of the initial injector flux used to initiate the discharge. Furthermore, these results could work well for the application of transient CHI in devices that employ super conducting coils to generate and sustain the plasma equilibrium.« less

Wongabel rhabdovirus accessory protein U3 targets the SWI/SNF chromatin remodeling complex.

PubMed

Joubert, D Albert; Rodriguez-Andres, Julio; Monaghan, Paul; Cummins, Michelle; McKinstry, William J; Paradkar, Prasad N; Moseley, Gregory W; Walker, Peter J

2015-01-15

Wongabel virus (WONV) is an arthropod-borne rhabdovirus that infects birds. It is one of the growing array of rhabdoviruses with complex genomes that encode multiple accessory proteins of unknown function. In addition to the five canonical rhabdovirus structural protein genes (N, P, M, G, and L), the 13.2-kb negative-sense single-stranded RNA (ssRNA) WONV genome contains five uncharacterized accessory genes, one overlapping the N gene (Nx or U4), three located between the P and M genes (U1 to U3), and a fifth one overlapping the G gene (Gx or U5). Here we show that WONV U3 is expressed during infection in insect and mammalian cells and is required for efficient viral replication. A yeast two-hybrid screen against a mosquito cell cDNA library identified that WONV U3 interacts with the 83-amino-acid (aa) C-terminal domain of SNF5, a component of the SWI/SNF chromatin remodeling complex. The interaction was confirmed by affinity chromatography, and nuclear colocalization was established by confocal microscopy. Gene expression studies showed that SNF5 transcripts are upregulated during infection of mosquito cells with WONV, as well as West Nile virus (Flaviviridae) and bovine ephemeral fever virus (Rhabdoviridae), and that SNF5 knockdown results in increased WONV replication. WONV U3 also inhibits SNF5-regulated expression of the cytokine gene CSF1. The data suggest that WONV U3 targets the SWI/SNF complex to block the host response to infection. The rhabdoviruses comprise a large family of RNA viruses infecting plants, vertebrates, and invertebrates. In addition to the major structural proteins (N, P, M, G, and L), many rhabdoviruses encode a diverse array of accessory proteins of largely unknown function. Understanding the role of these proteins may reveal much about host-pathogen interactions in infected cells. Here we examine accessory protein U3 of Wongabel virus, an arthropod-borne rhabdovirus that infects birds. We show that U3 enters the nucleus and interacts with SNF5, a component of the chromatin remodeling complex that is upregulated in response to infection and restricts viral replication. We also show that U3 inhibits SNF5-regulated expression of the cytokine colony-stimulating factor 1 (CSF1), suggesting that it targets the chromatin remodeling complex to block the host response to infection. This study appears to provide the first evidence of a virus targeting SNF5 to inhibit host gene expression. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Wongabel Rhabdovirus Accessory Protein U3 Targets the SWI/SNF Chromatin Remodeling Complex

PubMed Central

Joubert, D. Albert; Rodriguez-Andres, Julio; Monaghan, Paul; Cummins, Michelle; McKinstry, William J.; Paradkar, Prasad N.; Moseley, Gregory W.

2014-01-01

ABSTRACT Wongabel virus (WONV) is an arthropod-borne rhabdovirus that infects birds. It is one of the growing array of rhabdoviruses with complex genomes that encode multiple accessory proteins of unknown function. In addition to the five canonical rhabdovirus structural protein genes (N, P, M, G, and L), the 13.2-kb negative-sense single-stranded RNA (ssRNA) WONV genome contains five uncharacterized accessory genes, one overlapping the N gene (Nx or U4), three located between the P and M genes (U1 to U3), and a fifth one overlapping the G gene (Gx or U5). Here we show that WONV U3 is expressed during infection in insect and mammalian cells and is required for efficient viral replication. A yeast two-hybrid screen against a mosquito cell cDNA library identified that WONV U3 interacts with the 83-amino-acid (aa) C-terminal domain of SNF5, a component of the SWI/SNF chromatin remodeling complex. The interaction was confirmed by affinity chromatography, and nuclear colocalization was established by confocal microscopy. Gene expression studies showed that SNF5 transcripts are upregulated during infection of mosquito cells with WONV, as well as West Nile virus (Flaviviridae) and bovine ephemeral fever virus (Rhabdoviridae), and that SNF5 knockdown results in increased WONV replication. WONV U3 also inhibits SNF5-regulated expression of the cytokine gene CSF1. The data suggest that WONV U3 targets the SWI/SNF complex to block the host response to infection. IMPORTANCE The rhabdoviruses comprise a large family of RNA viruses infecting plants, vertebrates, and invertebrates. In addition to the major structural proteins (N, P, M, G, and L), many rhabdoviruses encode a diverse array of accessory proteins of largely unknown function. Understanding the role of these proteins may reveal much about host-pathogen interactions in infected cells. Here we examine accessory protein U3 of Wongabel virus, an arthropod-borne rhabdovirus that infects birds. We show that U3 enters the nucleus and interacts with SNF5, a component of the chromatin remodeling complex that is upregulated in response to infection and restricts viral replication. We also show that U3 inhibits SNF5-regulated expression of the cytokine colony-stimulating factor 1 (CSF1), suggesting that it targets the chromatin remodeling complex to block the host response to infection. This study appears to provide the first evidence of a virus targeting SNF5 to inhibit host gene expression. PMID:25392228

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

PubMed

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

2016-05-17

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

Evidence for a midlife crisis in great apes consistent with the U-shape in human well-being

PubMed Central

Weiss, Alexander; King, James E.; Inoue-Murayama, Miho; Matsuzawa, Tetsuro; Oswald, Andrew J.

2012-01-01

Recently, economists and behavioral scientists have studied the pattern of human well-being over the lifespan. In dozens of countries, and for a large range of well-being measures, including happiness and mental health, well-being is high in youth, falls to a nadir in midlife, and rises again in old age. The reasons for this U-shape are still unclear. Present theories emphasize sociological and economic forces. In this study we show that a similar U-shape exists in 508 great apes (two samples of chimpanzees and one sample of orangutans) whose well-being was assessed by raters familiar with the individual apes. This U-shaped pattern or “midlife crisis” emerges with or without use of parametric methods. Our results imply that human well-being’s curved shape is not uniquely human and that, although it may be partly explained by aspects of human life and society, its origins may lie partly in the biology we share with great apes. These findings have implications across scientific and social-scientific disciplines, and may help to identify ways of enhancing human and ape well-being. PMID:23169637

Daclatasvir Prevents Hepatitis C Virus Infectivity by Blocking Transfer of the Viral Genome to Assembly Sites.

PubMed

Boson, Bertrand; Denolly, Solène; Turlure, Fanny; Chamot, Christophe; Dreux, Marlène; Cosset, François-Loïc

2017-03-01

Daclatasvir is a direct-acting antiviral agent and potent inhibitor of NS5A, which is involved in replication of the hepatitis C virus (HCV) genome, presumably via membranous web shaping, and assembly of new virions, likely via transfer of the HCV RNA genome to viral particle assembly sites. Daclatasvir inhibits the formation of new membranous web structures and, ultimately, of replication complex vesicles, but also inhibits an early assembly step. We investigated the relationship between daclatasvir-induced clustering of HCV proteins, intracellular localization of viral RNAs, and inhibition of viral particle assembly. Cell-culture-derived HCV particles were produced from Huh7.5 hepatocarcinoma cells in presence of daclatasvir for short time periods. Infectivity and production of physical particles were quantified and producer cells were subjected to subcellular fractionation. Intracellular colocalization between core, E2, NS5A, NS4B proteins, and viral RNAs was quantitatively analyzed by confocal microscopy and by structured illumination microscopy. Short exposure of HCV-infected cells to daclatasvir reduced viral assembly and induced clustering of structural proteins with non-structural HCV proteins, including core, E2, NS4B, and NS5A. These clustered structures appeared to be inactive assembly platforms, likely owing to loss of functional connection with replication complexes. Daclatasvir greatly reduced delivery of viral genomes to these core clusters without altering HCV RNA colocalization with NS5A. In contrast, daclatasvir neither induced clustered structures nor inhibited HCV assembly in cells infected with a daclatasvir-resistant mutant (NS5A-Y93H), indicating that daclatasvir targets a mutual, specific function of NS5A inhibiting both processes. In addition to inhibiting replication complex biogenesis, daclatasvir prevents viral assembly by blocking transfer of the viral genome to assembly sites. This leads to clustering of HCV proteins because viral particles and replication complex vesicles cannot form or egress. This dual mode of action of daclatasvir could explain its efficacy in blocking HCV replication in cultured cells and in treatment of patients with HCV infection. Copyright © 2017 AGA Institute. Published by Elsevier Inc. All rights reserved.

Shape of the BMI-mortality association by cause of death, using generalized additive models: NHIS 1986-2006.

PubMed

Zajacova, Anna; Burgard, Sarah A

2012-03-01

Numerous studies have examined the association between body mass index (BMI) and mortality. The precise shape of their association, however, has not been established. We use nonparametric methods to determine the relationship between BMI and mortality. Data from the National Health Interview Survey-Linked Mortality Files 1986-2006 for adults aged 50 to 80 are analyzed using a Poisson approach to survival modeling within the generalized additive model (GAM) framework. The BMI-mortality association is more V shaped than U shaped, with the odds of dying rising steeply from the lowest risk point at BMIs of 23 to 26. The association varies considerably by time since interview and cause of death. For instance, the association has an inverted J shape for respiratory causes but is monotonically increasing for diabetes deaths. Our findings have implications for interpreting results from BMI-mortality studies and suggest caution in translating the findings into public health messages.

Are U-Shaped Developmental Trajectories Illusory?

ERIC Educational Resources Information Center

Vouloumanos, Athena

2011-01-01

Without criteria for what counts as a U/N-shaped developmental trajectory, it is not clear how many legitimate "Us" really exist. Many, if not all, "Us" may turn out to be illusions borne out of our sampling methods, task construal, and blurry lenses of description. (Contains 2 figures.)

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

PubMed

Lumian, Daniel S; McRae, Kateri

2017-09-01

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

Inverted-U-shaped correlation between dopamine receptor availability in striatum and sensation seeking

PubMed Central

Gjedde, Albert; Kumakura, Yoshitaka; Cumming, Paul; Linnet, Jakob; Møller, Arne

2010-01-01

Sensation seeking is a core personality trait that declines with age in both men and women, as do also both density and availability of the dopamine D2/3 receptors in striatum and cortical regions. In contrast, novelty seeking at a given age relates inversely to dopamine receptor availability. The simplest explanation of these findings is an inverted-U-shaped correlation between ratings of sensation seeking on the Zuckerman scale and dopamine D2/3 receptor availability. To test the claim of an inverted-U-shaped relation between ratings of the sensation-seeking personality and measures of dopamine receptor availability, we used PET to record [11C]raclopride binding in striatum of 18 healthy men. Here we report that an inverted-U shape significantly matched the receptor availability as a function of the Zuckerman score, with maximum binding potentials observed in the midrange of the scale. The inverted-U shape is consistent with a negative correlation between sensation seeking and the reactivity (“gain”) of dopaminergic neurotransmission to dopamine. The correlation reflects Zuckerman scores that are linearly linked to dopamine receptor densities in the striatum but nonlinearly linked to dopamine concentrations. Higher dopamine occupancy and dopamine concentrations explain the motivation that drives afflicted individuals to seek sensations, in agreement with reduced protection against addictive behavior that is characteristic of individuals with low binding potentials. PMID:20133675

Evidence That BRCA1- or BRCA2-Associated Cancers Are Not Inevitable

PubMed Central

Levin, Bess; Lech, Denise; Friedenson, Bernard

2012-01-01

Inheriting a BRCA1 or BRCA2 gene mutation can cause a deficiency in repairing complex DNA damage. This step leads to genomic instability and probably contributes to an inherited predisposition to breast and ovarian cancer. Complex DNA damage has been viewed as an integral part of DNA replication before cell division. It causes temporary replication blocks, replication fork collapse, chromosome breaks and sister chromatid exchanges (SCEs). Chemical modification of DNA may also occur spontaneously as a byproduct of normal processes. Pathways containing BRCA1 and BRCA2 gene products are essential to repair spontaneous complex DNA damage or to carry out SCEs if repair is not possible. This scenario creates a theoretical limit that effectively means there are spontaneous BRCA1/2-associated cancers that cannot be prevented or delayed. However, much evidence for high rates of spontaneous DNA mutation is based on measuring SCEs by using bromodeoxyuridine (BrdU). Here we find that the routine use of BrdU has probably led to overestimating spontaneous DNA damage and SCEs because BrdU is itself a mutagen. Evidence based on spontaneous chromosome abnormalities and epidemiologic data indicates strong effects from exogenous mutagens and does not support the inevitability of cancer in all BRCA1/2 mutation carriers. We therefore remove a theoretical argument that has limited efforts to develop chemoprevention strategies to delay or prevent cancers in BRCA1/2 mutation carriers. PMID:22972572

Linker Histone Phosphorylation Regulates Global Timing of Replication Origin Firing*S⃞

PubMed Central

Thiriet, Christophe; Hayes, Jeffrey J.

2009-01-01

Despite the presence of linker histone in all eukaryotes, the primary function(s) of this histone have been difficult to clarify. Knock-out experiments indicate that H1s play a role in regulation of only a small subset of genes but are an essential component in mouse development. Here, we show that linker histone (H1) is involved in the global regulation of DNA replication in Physarum polycephalum. We find that genomic DNA of H1 knock-down cells is more rapidly replicated, an effect due at least in part to disruption of the native timing of replication fork firing. Immunoprecipitation experiments demonstrate that H1 is transiently lost from replicating chromatin via a process facilitated by phosphorylation. Our results suggest that linker histones generate a chromatin environment refractory to replication and that their transient removal via protein phosphorylation during S phase is a critical step in the epigenetic regulation of replication timing. PMID:19015270

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

Social influence and political mobilization: Further evidence from a randomized experiment in the 2012 U.S. presidential election

PubMed Central

Bond, Robert M.; Bakshy, Eytan; Eckles, Dean; Fowler, James H.

2017-01-01

A large-scale experiment during the 2010 U.S. Congressional Election demonstrated a positive effect of an online get-out-the-vote message on real world voting behavior. Here, we report results from a replication of the experiment conducted during the U.S. Presidential Election in 2012. In spite of the fact that get-out-the-vote messages typically yield smaller effects during high-stakes elections due to saturation of mobilization efforts from many sources, a significant increase in voting was again observed. Voting also increased significantly among the close friends of those who received the message to go to the polls, and the total effect on the friends was likely larger than the direct effect, suggesting that understanding social influence effects is potentially even more important than understanding the direct effects of messaging. These results replicate earlier work and they add to growing evidence that online social networks can be instrumental for spreading offline behaviors. PMID:28445476

Social influence and political mobilization: Further evidence from a randomized experiment in the 2012 U.S. presidential election.

PubMed

Jones, Jason J; Bond, Robert M; Bakshy, Eytan; Eckles, Dean; Fowler, James H

2017-01-01

A large-scale experiment during the 2010 U.S. Congressional Election demonstrated a positive effect of an online get-out-the-vote message on real world voting behavior. Here, we report results from a replication of the experiment conducted during the U.S. Presidential Election in 2012. In spite of the fact that get-out-the-vote messages typically yield smaller effects during high-stakes elections due to saturation of mobilization efforts from many sources, a significant increase in voting was again observed. Voting also increased significantly among the close friends of those who received the message to go to the polls, and the total effect on the friends was likely larger than the direct effect, suggesting that understanding social influence effects is potentially even more important than understanding the direct effects of messaging. These results replicate earlier work and they add to growing evidence that online social networks can be instrumental for spreading offline behaviors.

ADARs, Viruses and Innate Immunity

PubMed Central

Samuel, Charles E.

2013-01-01

Double-stranded RNA (dsRNA) functions both as a substrate of ADARs and also as a molecular trigger of innate immune responses. ADARs, adenosine deaminases that act on RNA, catalyze the deamination of adenosine (A) to produce inosine (I) in dsRNA. ADARs thereby can destablize RNA structures, because the generated I:U mismatch pairs are less stable than A:U base pairs. Additionally, I is read as G instead of A by ribosomes during translation and by viral RNA-dependent RNA polymerases during RNA replication. Members of several virus families have the capacity to produce dsRNA during viral genome transcription and replication. Sequence changes (A-to-G, and U-to-C) characteristic of A-to-I editing occur during virus growth and persistence. Foreign viral dsRNA also mediates both the induction and the action of interferons. In this chapter our current understanding of the role and significance of ADARs in the context of innate immunity, and as determinants of the outcome of viral infection, will be considered. PMID:21809195

Structural Conversion of Aβ17–42 Peptides from Disordered Oligomers to U-Shape Protofilaments via Multiple Kinetic Pathways

PubMed Central

Cheon, Mookyung; Hall, Carol K.; Chang, Iksoo

2015-01-01

Discovering the mechanisms by which proteins aggregate into fibrils is an essential first step in understanding the molecular level processes underlying neurodegenerative diseases such as Alzheimer’s and Parkinson's. The goal of this work is to provide insights into the structural changes that characterize the kinetic pathways by which amyloid-β peptides convert from monomers to oligomers to fibrils. By applying discontinuous molecular dynamics simulations to PRIME20, a force field designed to capture the chemical and physical aspects of protein aggregation, we have been able to trace out the entire aggregation process for a system containing 8 Aβ17–42 peptides. We uncovered two fibrillization mechanisms that govern the structural conversion of Aβ17–42 peptides from disordered oligomers into protofilaments. The first mechanism is monomeric conversion templated by a U-shape oligomeric nucleus into U-shape protofilament. The second mechanism involves a long-lived and on-pathway metastable oligomer with S-shape chains, having a C-terminal turn, en route to the final U-shape protofilament. Oligomers with this C-terminal turn have been regarded in recent experiments as a major contributing element to cell toxicity in Alzheimer’s disease. The internal structures of the U-shape protofilaments from our PRIME20/DMD simulation agree well with those from solid state NMR experiments. The approach presented here offers a simple molecular-level framework to describe protein aggregation in general and to visualize the kinetic evolution of a putative toxic element in Alzheimer’s disease in particular. PMID:25955249

Learning Under Stress: The Inverted-U-Shape Function Revisited

ERIC Educational Resources Information Center

Salehi, Basira; Cordero, M. Isabel; Sandi, Carmen

2010-01-01

Although the relationship between stress intensity and memory function is generally believed to follow an inverted-U-shaped curve, strikingly this phenomenon has not been demonstrated under the same experimental conditions. We investigated this phenomenon for rats' performance in a hippocampus-dependent learning task, the radial arm water maze…

76 FR 36549 - Government-Owned Inventions; Availability for Licensing

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-22

... licensing in the U.S. in accordance with 35 U.S.C. 207 to achieve expeditious commercialization of results... enhancement modeling and shape likelihoods. The segmented vessels can be correctly classified into right... differential enhancement and shape with accuracy comparable to the reports from the Medical Image Computing and...

19 CFR 10.244 - Certificate of Origin.

Code of Federal Regulations, 2011 CFR

2011-04-01

... assembled from U.S. formed, dyed, printed and finished fabrics or fabric components, or U.S. formed knit-to... llama, alpaca or vicuña fabrics, fabric components, or knit-to-shape components, from Andean yarns 10... more yarns, fabrics, fabric components, or knit-to-shape components described in preference groups A...

19 CFR 10.244 - Certificate of Origin.

Code of Federal Regulations, 2010 CFR

2010-04-01

... assembled from U.S. formed, dyed, printed and finished fabrics or fabric components, or U.S. formed knit-to... llama, alpaca or vicuña fabrics, fabric components, or knit-to-shape components, from Andean yarns 10... more yarns, fabrics, fabric components, or knit-to-shape components described in preference groups A...

A Few Simple Classroom Experiments with a Permanent U-Shaped Magnet

ERIC Educational Resources Information Center

Babovic, Miloš; Babovic, Vukota

2017-01-01

A few simple experiments in the magnetic field of a permanent U-shaped magnet are described. Among them, pin oscillations inside the magnet are particularly interesting. These easy to perform and amusing measurements can help pupils understand magnetic phenomena and mutually connect knowledge of various physics branches.

U-SHAPED DOSE-RESPONSE CURVES: THEIR OCCURRENCE AND IMPLICATIONS FOR RISK ASSESSMENT

EPA Science Inventory

A class of curvilinear dose-response relationships in toxicological and epidemiological studies may be roughly described by "U-shaped curves. uch curves reflect an apparent reversal or inversion in the effect of an otherwise toxic agent at a low or intermediate region of the dose...

Shape selection in Landsat time series: a tool for monitoring forest dynamics.

PubMed

Moisen, Gretchen G; Meyer, Mary C; Schroeder, Todd A; Liao, Xiyue; Schleeweis, Karen G; Freeman, Elizabeth A; Toney, Chris

2016-10-01

We present a new methodology for fitting nonparametric shape-restricted regression splines to time series of Landsat imagery for the purpose of modeling, mapping, and monitoring annual forest disturbance dynamics over nearly three decades. For each pixel and spectral band or index of choice in temporal Landsat data, our method delivers a smoothed rendition of the trajectory constrained to behave in an ecologically sensible manner, reflecting one of seven possible 'shapes'. It also provides parameters summarizing the patterns of each change including year of onset, duration, magnitude, and pre- and postchange rates of growth or recovery. Through a case study featuring fire, harvest, and bark beetle outbreak, we illustrate how resultant fitted values and parameters can be fed into empirical models to map disturbance causal agent and tree canopy cover changes coincident with disturbance events through time. We provide our code in the r package ShapeSelectForest on the Comprehensive R Archival Network and describe our computational approaches for running the method over large geographic areas. We also discuss how this methodology is currently being used for forest disturbance and attribute mapping across the conterminous United States. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

Fabrication of Glass Microchannel via Glass Imprinting using a Vitreous Carbon Stamp for Flow Focusing Droplet Generator

PubMed Central

Refatul Haq, Muhammad; Kim, Youngkyu; Kim, Jun; Oh, Pyoung-hwa; Ju, Jonghyun; Kim, Seok-Min; Lim, Jiseok

2017-01-01

This study reports a cost-effective method of replicating glass microfluidic chips using a vitreous carbon (VC) stamp. A glass replica with the required microfluidic microstructures was synthesized without etching. The replication method uses a VC stamp fabricated by combining thermal replication using a furan-based, thermally-curable polymer with carbonization. To test the feasibility of this method, a flow focusing droplet generator with flow-focusing and channel widths of 50 µm and 100 µm, respectively, was successfully fabricated in a soda-lime glass substrate. Deviation between the geometries of the initial shape and the vitreous carbon mold occurred because of shrinkage during the carbonization process, however this effect could be predicted and compensated for. Finally, the monodispersity of the droplets generated by the fabricated microfluidic device was evaluated. PMID:29286341

20th Annual Systems Engineering Conference. Volume 2, Wednesday

DTIC Science & Technology

2017-10-26

Assurance Center (JFAC) 2017 Update u Mr. Thomas Hurt, Department of Defense 4B1 Tr a c k 2 m il le r Education & Training 19813 Shaping the... J . C . S. P. (2002, September). Agile requirements definition: A view from requirements engineering. In Proceedings of the International Workshop on...Management 52.2 (2005): 199-212. Web. 4. R. J . Calantone, and C . A. Di Benedetto. "Performance and Time to Market: Accelerating Cycle Time with

Counternarcotics Assistance: U.S. Agencies Have Allotted Billions in Andean Countries, but DOD Should Improve Its Reporting of Results

DTIC Science & Technology

2012-07-01

growing areas of the world, and replaced it with licit, high-value crops such as cacao , coffee, and oil palm. The U.S. strategy seeks to replicate...producing communities transition to cultivating licit crops. Licit crops fostered by USAID programs include cacao , palm oil, and coffee. Since...include cacao , coffee, and oil palm. Counternarcotics Assistance in the Andean Region U.S. agencies use a variety of funding sources

Novel Therapeutic Approach for Breast Cancer

DTIC Science & Technology

2006-06-01

replication, mda-7/IL-24 expression, growth inhibition and apoptosis induction. Injecting Ad.PEG-E1A-mda-7 into human breast cancer xenografts in athymic nude...CLASSIFICATION OF: 18 . NUMBER OF PAGES 19a. NAME OF RESPONSIBLE PERSON USAMRMC a. REPORT U b. ABSTRACT U c. THIS PAGE U UU 62 19b...breast cancer xenografts in athymic nude mice in vivo. Infection of this CRCA (designated Ad.PEG-E1A-mda-7) in normal mammary epithelial cells and

An interferon regulatory factor binding site in the U5 region of the bovine leukemia virus long terminal repeat stimulates Tax-independent gene expression.

PubMed

Kiermer, V; Van Lint, C; Briclet, D; Vanhulle, C; Kettmann, R; Verdin, E; Burny, A; Droogmans, L

1998-07-01

Bovine leukemia virus (BLV) replication is controlled by both cis- and trans-acting elements. The virus-encoded transactivator, Tax, is necessary for efficient transcription from the BLV promoter, although it is not present during the early stages of infection. Therefore, sequences that control Tax-independent transcription must play an important role in the initiation of viral gene expression. This study demonstrates that the R-U5 sequence of BLV stimulates Tax-independent reporter gene expression directed by the BLV promoter. R-U5 was also stimulatory when inserted immediately downstream from the transcription initiation site of a heterologous promoter. Progressive deletion analysis of this region revealed that a 46-bp element corresponding to the 5' half of U5 is principally responsible for the stimulation. This element exhibited enhancer activity when inserted upstream or downstream from the herpes simplex virus thymidine kinase promoter. This enhancer contains a binding site for the interferon regulatory factors IRF-1 and IRF-2. A 3-bp mutation that destroys the IRF recognition site caused a twofold decrease in Tax-independent BLV long terminal repeat-driven gene expression. These observations suggest that the IRF binding site in the U5 region of BLV plays a role in the initiation of virus replication.

Engineering anatomically shaped vascularized bone grafts with hASCs and 3D-printed PCL scaffolds.

PubMed

Temple, Joshua P; Hutton, Daphne L; Hung, Ben P; Huri, Pinar Yilgor; Cook, Colin A; Kondragunta, Renu; Jia, Xiaofeng; Grayson, Warren L

2014-12-01

The treatment of large craniomaxillofacial bone defects is clinically challenging due to the limited availability of transplantable autologous bone grafts and the complex geometry of the bones. The ability to regenerate new bone tissues that faithfully replicate the anatomy would revolutionize treatment options. Advances in the field of bone tissue engineering over the past few decades offer promising new treatment alternatives using biocompatible scaffold materials and autologous cells. This approach combined with recent advances in three-dimensional (3D) printing technologies may soon allow the generation of large, bioartificial bone grafts with custom, patient-specific architecture. In this study, we use a custom-built 3D printer to develop anatomically shaped polycaprolactone (PCL) scaffolds with varying internal porosities. These scaffolds are assessed for their ability to support induction of human adipose-derived stem cells (hASCs) to form vasculature and bone, two essential components of functional bone tissue. The development of functional tissues is assessed in vitro and in vivo. Finally, we demonstrate the ability to print large mandibular and maxillary bone scaffolds that replicate fine details extracted from patient's computed tomography scans. The findings of this study illustrate the capabilities and potential of 3D printed scaffolds to be used for engineering autologous, anatomically shaped, vascularized bone grafts. © 2014 Wiley Periodicals, Inc.

The Role of Replication in Activation of the DNA Damage Checkpoint

DTIC Science & Technology

2006-03-01

St AD Award Number : W81XWH-04-1-0311 TITLE: The Role of Replication in Activation of the DNA Damage Checkpoint PRINCIPAL INVESTIGATOR: Christopher...Van CONTRACTING ORGANIZATION: Stanford University Stanford, CA 94305 REPORT DATE: March 2006 TYPE OF REPORT: Annual Summary PREPARED FOR: U.S. Army...to comply with a collection of information if it does not display a currently valid OMB control number . PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE

Remotely replaceable tokamak plasma limiter tiles

DOEpatents

Tsuo, Simon , Langford, Alison A.

1989-01-01

U-shaped limiter tiles placed end-to-end over a pair of parallel runners secured to a wall have two rods which engage L-shaped slots in the runners. The short receiving legs of the L-shaped slots are perpendicular to the wall and open away from the wall, while long retaining legs are parallel to and adjacent the wall. A sliding bar between the runners has grooves with clips to retain the rods pressed into receiving legs of the L-shaped slots in the runners. Sliding the bar in the direction of retaining legs of the L-shaped slots latches the tiles in place over the runners. Resilient contact strips between the parallel arms of the U-shaped tiles and the wall assure thermal and electrical contact with the wall.

Evaluation of VIDAS Salmonella (SLM) easy Salmonella method for the detection of Salmonella in a variety of foods: collaborative study.

PubMed

Crowley, Erin; Bird, Patrick; Fisher, Kiel; Goetz, Katherine; Benzinger, M Joseph; Agin, James; Goins, David; Johnson, Ronald L

2011-01-01

The VIDAS Salmonella (SLM) Easy Salmonella method is a specific enzyme-linked fluorescent immunoassay performed in the automated VIDAS instrument. The VIDAS Easy Salmonella method is a simple 2-step enrichment procedure, using pre-enrichment followed by selective enrichment in a newly formulated broth, SX2 broth. This new method was compared in a multilaboratory collaborative study to the U.S. Food and Drug Administration's Bacteriological Analytical Manual, Chapter 5 method for five food matrixes (liquid egg, vanilla ice cream, spinach, raw shrimp, and peanut butter) and the U.S. Department of Agriculture's Microbiology Laboratory Guidebook 4.04 method for deli turkey. Each food type was artificially contaminated with Salmonella at three inoculation levels. A total of 15 laboratories representing government, academia, and industry, throughout the United States, participated. In this study, 1583 samples were analyzed, of which 792 were paired replicates and 791 were unpaired replicates. Of the 792 paired replicates, 285 were positive by both the VIDAS and reference methods. Of the 791 unpaired replicates, 341 were positive by the VIDAS method and 325 were positive by the cultural reference method. A Chi-square analysis of each of the six food types was performed at the three inoculation levels tested. For all foods evaluated, the VIDAS Easy SLM method demonstrated results comparable to those of the reference methods for the detection of Salmonella.

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

Electron impact fragmentation of adenine: partial ionization cross sections for positive fragments

NASA Astrophysics Data System (ADS)

van der Burgt, Peter J. M.; Finnegan, Sinead; Eden, Samuel

2015-07-01

Using computer-controlled data acquisition we have measured mass spectra of positive ions for electron impact on adenine, with electron energies up to 100 eV. Ion yield curves for 50 ions have been obtained and normalized by comparing their sum to the average of calculated total ionization cross sections. Appearance energies have been determined for 37 ions; for 20 ions for the first time. All appearance energies are consistent with the fragmentation pathways identified in the literature. Second onset energies have been determined for 12 fragment ions (for 11 ions for the first time), indicating the occurrence of more than one fragmentation process e.g. for 39 u (C2HN+) and 70 u (C2H4N3+). Matching ion yield shapes (118-120 u, 107-108 u, 91-92 u, and 54-56 u) provide new evidence supporting closely related fragmentation pathways and are attributed to hydrogen rearrangement immediately preceding the fragmentation. We present the first measurement of the ion yield curve of the doubly charged parent ion (67.5 u), with an appearance energy of 23.5 ± 1.0 eV. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey Solov'yov, Nigel Mason, Gustavo García, Eugene Surdutovich.

A Genome-Wide Association Study Identifies Five Loci Influencing Facial Morphology in Europeans

PubMed Central

Liu, Fan; van der Lijn, Fedde; Schurmann, Claudia; Zhu, Gu; Chakravarty, M. Mallar; Hysi, Pirro G.; Wollstein, Andreas; Lao, Oscar; de Bruijne, Marleen; Ikram, M. Arfan; van der Lugt, Aad; Rivadeneira, Fernando; Uitterlinden, André G.; Hofman, Albert; Niessen, Wiro J.; Homuth, Georg; de Zubicaray, Greig; McMahon, Katie L.; Thompson, Paul M.; Daboul, Amro; Puls, Ralf; Hegenscheid, Katrin; Bevan, Liisa; Pausova, Zdenka; Medland, Sarah E.; Montgomery, Grant W.; Wright, Margaret J.; Wicking, Carol; Boehringer, Stefan; Spector, Timothy D.; Paus, Tomáš; Martin, Nicholas G.; Biffar, Reiner; Kayser, Manfred

2012-01-01

Inter-individual variation in facial shape is one of the most noticeable phenotypes in humans, and it is clearly under genetic regulation; however, almost nothing is known about the genetic basis of normal human facial morphology. We therefore conducted a genome-wide association study for facial shape phenotypes in multiple discovery and replication cohorts, considering almost ten thousand individuals of European descent from several countries. Phenotyping of facial shape features was based on landmark data obtained from three-dimensional head magnetic resonance images (MRIs) and two-dimensional portrait images. We identified five independent genetic loci associated with different facial phenotypes, suggesting the involvement of five candidate genes—PRDM16, PAX3, TP63, C5orf50, and COL17A1—in the determination of the human face. Three of them have been implicated previously in vertebrate craniofacial development and disease, and the remaining two genes potentially represent novel players in the molecular networks governing facial development. Our finding at PAX3 influencing the position of the nasion replicates a recent GWAS of facial features. In addition to the reported GWA findings, we established links between common DNA variants previously associated with NSCL/P at 2p21, 8q24, 13q31, and 17q22 and normal facial-shape variations based on a candidate gene approach. Overall our study implies that DNA variants in genes essential for craniofacial development contribute with relatively small effect size to the spectrum of normal variation in human facial morphology. This observation has important consequences for future studies aiming to identify more genes involved in the human facial morphology, as well as for potential applications of DNA prediction of facial shape such as in future forensic applications. PMID:23028347

Copper Electrodeposition on a Magnesium Alloy (AZ80) with a U-Shaped Surface

PubMed Central

Huang, Ching An; Yeh, Yu Hu; Lin, Che Kuan; Hsieh, Chen Yun

2014-01-01

Cu electrodeposition was performed on a cylindrical AZ80 substrate with a U-shaped surface. A uniform deposition of Cu was achieved on an AZ80 electrode via galvanostatic etching, followed by Cu electrodeposition in an eco-friendly alkaline Cu plating bath. Improper wetting and lower rotational speeds of the AZ80 electrode resulted in an uneven Cu deposition at the inner upper site of the U-shaped surface during the Cu electroplating process. This wetting effect could be deduced from the variation in the anodic potential during the galvanostatic etching. The corrosion resistance of the Cu-deposited AZ80 electrode can be considerably improved after Ni electroplating. PMID:28788252

A quasi-hexagonal prism-shaped carbon nitride for photoreduction of carbon dioxide under visible light.

PubMed

He, Zhiqiao; Wang, Danfen; Tang, Juntao; Song, Shuang; Chen, Jianmeng; Tao, Xinyong

2017-03-01

A quasi-hexagonal prism-shaped carbon nitride (H-C 3 N 4 ) was synthesized from urea-derived C 3 N 4 (U-C 3 N 4 ) using an alkaline hydrothermal process. U-C 3 N 4 decomposition followed by hydrogen bond rearrangement of hydrolyzed products leads to the formation of a quasi-hexagonal prism-shaped structure. The H-C 3 N 4 catalysts displayed superior activity in the photoreduction of CO 2 with H 2 O compared to U-C 3 N 4 . The enhanced photocatalytic activities can be attributed to the promotion of incompletely coordinated nitrogen atom formation in the C 3 N 4 molecules. Graphical abstract ᅟ.

Using a single binge drinking question to identify Russian women at risk for an alcohol-exposed pregnancy.

PubMed

Balachova, Tatiana; Sobell, Linda Carter; Agrawal, Sangeeta; Isurina, Galina; Tsvetkova, Larissa; Volkova, Elena; Bohora, Som

2015-07-01

Low rates of contraception and at-risk drinking place many Russian women at risk of an alcohol-exposed pregnancy (AEP). The only realistic way to determine when women are at risk of AEP is by self-reports. A U.S. study found that a single binge-drinking question (SBD) effectively identified nearly all women whose drinking placed them at risk of AEP. The present study replicated the U.S. Participants were 689 non-pregnant Russian women of childbearing age who were at AEP risk. Their answers to SBD, "During the previous three months, how often did you have four or more drinks on one occasion", were compared with their reports of binge drinking on a 90-day Timeline Followback (TLFB) calendar. The SBD identified 99% of at-risk Russian women as binge drinkers, replicating U.S. Only 8% of the women were identified at-risk using a second AEP criterion of ≥8 drinks on average per week. Although Russian women did not report heavy weekly drinking and two-thirds did not meet AUDIT criteria for problem drinking, when they did drink, 40% of the time it was binge drinking. Almost all Russian women who were at risk of an AEP were identified by a single binge-drinking question. Results from this study suggest that Russian health care practitioners can use SBD to successfully screen women for AEP risk. SBD identified 99% of Russian women who were at AEP risk. Consequently, it is recommended that SBD be incorporated into routine health care screenings at OB/GYN clinic visits. Copyright © 2015 Elsevier Ltd. All rights reserved.

The temporal program of chromosome replication: genomewide replication in clb5{Delta} Saccharomyces cerevisiae.

PubMed

McCune, Heather J; Danielson, Laura S; Alvino, Gina M; Collingwood, David; Delrow, Jeffrey J; Fangman, Walton L; Brewer, Bonita J; Raghuraman, M K

2008-12-01

Temporal regulation of origin activation is widely thought to explain the pattern of early- and late-replicating domains in the Saccharomyces cerevisiae genome. Recently, single-molecule analysis of replication suggested that stochastic processes acting on origins with different probabilities of activation could generate the observed kinetics of replication without requiring an underlying temporal order. To distinguish between these possibilities, we examined a clb5Delta strain, where origin firing is largely limited to the first half of S phase, to ask whether all origins nonspecifically show decreased firing (as expected for disordered firing) or if only some origins ("late" origins) are affected. Approximately half the origins in the mutant genome show delayed replication while the remainder replicate largely on time. The delayed regions can encompass hundreds of kilobases and generally correspond to regions that replicate late in wild-type cells. Kinetic analysis of replication in wild-type cells reveals broad windows of origin firing for both early and late origins. Our results are consistent with a temporal model in which origins can show some heterogeneity in both time and probability of origin firing, but clustering of temporally like origins nevertheless yields a genome that is organized into blocks showing different replication times.

Chromosomal context and replication properties of ARS plasmids in Schizosaccharomyces pombe.

PubMed

Pratihar, Aditya S; Tripathi, Vishnu P; Yadav, Mukesh P; Dubey, Dharani D

2015-12-01

Short, specific DNA sequences called as Autonomously Replicating Sequence (ARS) elements function as plasmid as well as chromosomal replication origins in yeasts. As compared to ARSs, different chromosomal origins vary greatly in their efficiency and timing of replication probably due to their wider chromosomal context. The two Schizosaccharomyces pombe ARS elements, ars727 and ars2004, represent two extremities in their chromosomal origin activity - ars727 is inactive and late replicating, while ars2004 is a highly active, early-firing origin. To determine the effect of chromosomal context on the activity of these ARS elements, we have cloned them with their extended chromosomal context as well as in the context of each other in both orientations and analysed their replication efficiency by ARS and plasmid stability assays. We found that these ARS elements retain their origin activity in their extended/altered context. However, deletion of a 133-bp region of the previously reported ars727- associated late replication enforcing element (LRE) caused advancement in replication timing of the resulting plasmid. These results confirm the role of LRE in directing plasmid replication timing and suggest that the plasmid origin efficiency of ars2004 or ars727 remains unaltered by the extended chromosomal context.

Lipid overloading during liver regeneration causes delayed hepatocyte DNA replication by increasing ER stress in mice with simple hepatic steatosis.

PubMed

Hamano, Mina; Ezaki, Hisao; Kiso, Shinichi; Furuta, Kunimaro; Egawa, Mayumi; Kizu, Takashi; Chatani, Norihiro; Kamada, Yoshihiro; Yoshida, Yuichi; Takehara, Tetsuo

2014-02-01

Impaired fatty liver regeneration has already been reported in many genetic modification models. However, in diet-induced simple hepatic steatosis, which showed similar phenotype with clinical pathology, whether liver regeneration is impaired or not remains unclear. In this study, we evaluated liver regeneration in mice with diet-induced simple hepatic steatosis, and focused on excess lipid accumulation occurring during liver regeneration. Mice were fed high fat diet (HFD) or control diet for 9-10 weeks. We analyzed intrahepatic lipid accumulation, DNA replication, and various signaling pathways including cell proliferation and ER stress during liver regeneration after partial hepatectomy. In addition, some of mice were pretreated with tauroursodeoxycholic acid (TUDCA), a chemical chaperone which alleviates ER stress, and then we estimated TUDCA effects on liver regeneration. The peak of hepatocyte BrdU incorporation, the expression of proliferation cell nuclear antigen (PCNA) protein, and the expressions of cell cycle-related genes were observed in delayed time in HFD mice. The expression of phosphorylated Erk1/2 was also delayed in HFD mice. The amounts of liver triglyceride were at least twofold higher in HFD mice at each time point. Intrahepatic palmitic acid was increased especially in HFD mice. ER stress induced during liver regeneration was significantly higher in HFD mice. In HFD mice, pretreatment with TUDCA reduced ER stress and resulted in improvement of delayed liver regeneration. In simple hepatic steatosis, lipid overloading occurring during liver regeneration might be caused ER stress and results in delayed hepatocyte DNA replication.

Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq.

PubMed

Marchal, Claire; Sasaki, Takayo; Vera, Daniel; Wilson, Korey; Sima, Jiao; Rivera-Mulia, Juan Carlos; Trevilla-García, Claudia; Nogues, Coralin; Nafie, Ebtesam; Gilbert, David M

2018-05-01

This protocol is an extension to: Nat. Protoc. 6, 870-895 (2014); doi:10.1038/nprot.2011.328; published online 02 June 2011Cycling cells duplicate their DNA content during S phase, following a defined program called replication timing (RT). Early- and late-replicating regions differ in terms of mutation rates, transcriptional activity, chromatin marks and subnuclear position. Moreover, RT is regulated during development and is altered in diseases. Here, we describe E/L Repli-seq, an extension of our Repli-chip protocol. E/L Repli-seq is a rapid, robust and relatively inexpensive protocol for analyzing RT by next-generation sequencing (NGS), allowing genome-wide assessment of how cellular processes are linked to RT. Briefly, cells are pulse-labeled with BrdU, and early and late S-phase fractions are sorted by flow cytometry. Labeled nascent DNA is immunoprecipitated from both fractions and sequenced. Data processing leads to a single bedGraph file containing the ratio of nascent DNA from early versus late S-phase fractions. The results are comparable to those of Repli-chip, with the additional benefits of genome-wide sequence information and an increased dynamic range. We also provide computational pipelines for downstream analyses, for parsing phased genomes using single-nucleotide polymorphisms (SNPs) to analyze RT allelic asynchrony, and for direct comparison to Repli-chip data. This protocol can be performed in up to 3 d before sequencing, and requires basic cellular and molecular biology skills, as well as a basic understanding of Unix and R.

The Peculiar Light Curve of J1415+1320: A Case Study in Extreme Scattering Events

NASA Astrophysics Data System (ADS)

Vedantham, H. K.; Readhead, A. C. S.; Hovatta, T.; Koopmans, L. V. E.; Pearson, T. J.; Blandford, R. D.; Gurwell, M. A.; Lähteenmäki, A.; Max-Moerbeck, W.; Pavlidou, V.; Ravi, V.; Reeves, R. A.; Richards, J. L.; Tornikoski, M.; Zensus, J. A.

2017-08-01

The radio light curve of J1415+1320 (PKS 1413+135) shows time-symmetric and recurring U-shaped features across the centimeter-wave and millimeter-wave bands. The symmetry of these features points to lensing by an intervening object as the cause. U-shaped events in radio light curves in the centimeter-wave band have previously been attributed to Extreme scattering events (ESE). ESEs are thought to be the result of lensing by compact plasma structures in the Galactic interstellar medium, but the precise nature of these plasma structures remains unknown. Since the strength of a plasma lens evolves with wavelength λ as {λ }2, the presence of correlated variations at over a wide wavelength range casts doubt on the canonical ESE interpretation for J1415+1320. In this paper, we critically examine the evidence for plasma lensing in J1415+1320. We compute limits on the lensing strength and the associated free-free opacity of the putative plasma lenses. We compare the observed and model ESE light curves, and also derive a lower limit on the lens distance based on the effects of parallax due to the Earth’s orbit around the Sun. We conclude that plasma lensing is not a viable interpretation for J1415+1320's light curves and that symmetric U-shaped features in the radio light curves of extragalactic sources do not present prima facie evidence for ESEs. The methodology presented here is generic enough to be applicable to any plasma-lensing candidate.

Mitochondrial DNA copy number is associated with risk of head and neck squamous cell carcinoma in Chinese population.

PubMed

Wang, Lihua; Lv, Hong; Ji, Pei; Zhu, Xun; Yuan, Hua; Jin, Guangfu; Dai, Juncheng; Hu, Zhibin; Su, Yuxiong; Ma, Hongxia

2018-04-19

Mitochondria show the special role in cellular bioenergy and many essential physiological activities. Previous researches have suggested that variations of mitochondrial DNA copy number contribute to development of different types of carcinomas. However, the relationship of mtDNA copy number in peripheral blood leukocytes (PBLs) with the risk of head and neck squamous cell carcinoma (HNSCC) is still inconclusive. We investigated the association of mtDNA with HNSCC risk through a case-control study including 570 HNSCC cases and 597 cancer-free controls. mtDNA copy number in PBLs was measured by real-time qPCR. Logistic regression was performed to estimate the association between the mtDNA copy number in PBLs and HNSCC risk. A U-shaped relation between the mtDNA copy number and HNSCC risk was found. Compared with those in the second quartile group, the adjusted odds ratios (ORs) and 95% confidence interval (CI) for those in the first and the forth quartile groups were 1.95 (1.37-2.76) and 2.16 (1.53-3.04), respectively. Using restricted cubic spline analysis, we confirmed such a significant U-shaped relation. Furthermore, the U-shaped association remained significant in different subgroups stratified by age, gender, tobacco smoking, and alcohol consumption. Both extremely low and high mtDNA copy numbers had significant associations with the increased HNSCC risk. © 2018 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

In Vitro Replication of Chelonid Herpesvirus 5 in Organotypic Skin Cultures from Hawaiian Green Turtles (Chelonia mydas).

PubMed

Work, Thierry M; Dagenais, Julie; Weatherby, Tina M; Balazs, George H; Ackermann, Mathias

2017-09-01

Fibropapillomatosis (FP) is a tumor disease of marine turtles associated with chelonid herpesvirus 5 (ChHV5), which has historically been refractory to growth in tissue culture. Here we show, for the first time, de novo formation of ChHV5-positive intranuclear inclusions in cultured green turtle cells, which is indicative of active lytic replication of the virus. The minimal requirements to achieve lytic replication in cultured cells included (i) either in vitro cultures of ChHV5-positive tumor biopsy specimens (plugs) or organotypic cultures (rafts) consisting of ChHV5-positive turtle fibroblasts in collagen rafts seeded with turtle keratinocytes and (ii) keratinocyte maturation induced by raising raft or biopsy cultures to the air-liquid interface. Virus growth was confirmed by detailed electron microscopic studies that revealed intranuclear sun-shaped capsid factories, tubules, various stages of capsid formation, nuclear export by budding into the perinuclear space, tegument formation, and envelopment to complete de novo virus production. Membrane synthesis was also observed as a sign of active viral replication. Interestingly, cytoplasmic particles became associated with keratin filaments, a feature not seen in conventional monolayer cell cultures, in which most studies of herpesvirus replication have been performed. Our findings draw a rich and realistic picture of ChHV5 replication in cells derived from its natural host and may be crucial not only to better understand ChHV5 circulation but also to eventually complete Koch's postulates for FP. Moreover, the principles described here may serve as a model for culture of other viruses that are resistant to replication in conventional cell culture. IMPORTANCE A major challenge in virology is the study of viruses that cannot be grown in the laboratory. One example is chelonid herpesvirus 5 (ChHV5), which is associated with fibropapillomatosis, a globally distributed, debilitating, and fatal tumor disease of endangered marine turtles. Pathological examination shows that ChHV5 is shed in skin. Here we show that ChHV5 will grow in vitro if we replicate the complex three-dimensional structure of turtle skin. Moreover, lytic virus growth requires a close interplay between fibroblasts and keratinocytes. Finally, the morphogenesis of herpesviral growth in three-dimensional cultures reveals a far richer, and likely more realistic, array of capsid morphologies than that encountered in traditional monolayer cell cultures. Our findings have applications to other viruses, including those of humans. Copyright © 2017 American Society for Microbiology.

Something Borrowed, Something Learned? The Transatlantic Market in Education and Training Reform.

ERIC Educational Resources Information Center

Finegold, David, Ed.; And Others

The concentration of numerous case studies of British appropriation of U.S. education and training (ET) policies in a brief period of time (1986-90) provides a unique opportunity to improve understanding of the ET reform process and the role that international comparisons can play in shaping the domestic ET policy agenda. In this book, political…

Reversed flow fluidized-bed combustion apparatus

DOEpatents

Shang, Jer-Yu; Mei, Joseph S.; Wilson, John S.

1984-01-01

The present invention is directed to a fluidized-bed combustion apparatus provided with a U-shaped combustion zone. A cyclone is disposed in the combustion zone for recycling solid particulate material. The combustion zone configuration and the recycling feature provide relatively long residence times and low freeboard heights to maximize combustion of combustible material, reduce nitrogen oxides, and enhance sulfur oxide reduction.

Psychological detachment from work during non-work time: linear or curvilinear relations with mental health and work engagement?

PubMed

Shimazu, Akihito; Matsudaira, Ko; Jonge, Jan DE; Tosaka, Naoya; Watanabe, Kazuhiro; Takahashi, Masaya

2016-06-10

This study examined whether a higher level of psychological detachment during non-work time is associated with better employee mental health (Hypothesis 1), and examined whether psychological detachment has a curvilinear relation (inverted U-shaped pattern) with work engagement (Hypothesis 2). A large cross-sectional Internet survey was conducted among registered monitors of an Internet survey company in Japan. The questionnaire included scales for psychological detachment, employee mental health, and work engagement as well as for job characteristics and demographic variables as potential confounders. The hypothesized model was tested with moderated structural equation modeling techniques among 2,234 respondents working in the tertiary industries with regular employment. Results showed that psychological detachment had curvilinear relations with mental health as well as with work engagement. Mental health improved when psychological detachment increased from a low to higher levels but did not benefit any further from extremely high levels of psychological detachment. Work engagement showed the highest level at an intermediate level of detachment (inverted U-shaped pattern). Although high psychological detachment may enhance employee mental health, moderate levels of psychological detachment are most beneficial for his or her work engagement.

Psychological detachment from work during non-work time: linear or curvilinear relations with mental health and work engagement?

PubMed Central

SHIMAZU, Akihito; MATSUDAIRA, Ko; DE JONGE, Jan; TOSAKA, Naoya; WATANABE, Kazuhiro; TAKAHASHI, Masaya

2016-01-01

This study examined whether a higher level of psychological detachment during non-work time is associated with better employee mental health (Hypothesis 1), and examined whether psychological detachment has a curvilinear relation (inverted U-shaped pattern) with work engagement (Hypothesis 2). A large cross-sectional Internet survey was conducted among registered monitors of an Internet survey company in Japan. The questionnaire included scales for psychological detachment, employee mental health, and work engagement as well as for job characteristics and demographic variables as potential confounders. The hypothesized model was tested with moderated structural equation modeling techniques among 2,234 respondents working in the tertiary industries with regular employment. Results showed that psychological detachment had curvilinear relations with mental health as well as with work engagement. Mental health improved when psychological detachment increased from a low to higher levels but did not benefit any further from extremely high levels of psychological detachment. Work engagement showed the highest level at an intermediate level of detachment (inverted U-shaped pattern). Although high psychological detachment may enhance employee mental health, moderate levels of psychological detachment are most beneficial for his or her work engagement. PMID:26829972

El Habano and the world it has shaped: Cuba, Connecticut, and Indonesia.

PubMed

Stubbs, Jean

2010-01-01

In the half century since the 1959 Cuban Revolution, El Habano remains the premium cigar the world over; but both before and since 1959, the seed, agricultural and industrial know-how, and human capital have been transplanted to replicate that cigar in a process accentuated by upheavals and out-migration. The focus here is on a little-known facet of the interconnected island and offshore Havana cigar history, linking Cuba with Connecticut and Indonesia: from when tobacco was taken from the Americas to Indonesia and gave rise to the famed Sumatra cigar wrapper leaf; through the rise and demise of its sister shade wrapper in Connecticut, with Cuban and Sumatra seed, ultimately overshadowed by Indonesia; and the resulting challenges facing Cuba today. The article highlights the role of Dutch, U.S., British, and Swedish capital to explain why in 2009 the two major global cigar corporations, British Imperial Tobacco and Swedish Match, were lobbying Washington, respectively, for and against the embargo on Cuba. As the antismoking, antitobacco lobby gains ground internationally, the intriguing final question is whether the future lies with El Habano or smokeless Swedish snus.

The Shaped Charge Concept. Part 2. The History of Shaped Charges

DTIC Science & Technology

1990-09-01

research of Evans. Ubbel•ode. LAmurd-Jones, Devonihire, and An&ew. 1hW U.K. Mufied cadmium liners (which probably produce molten jets) msd steel liners...34 Mathematical Jet Theory of Lined Hollow Charges." BRL Report No. 370, U.S. Army Ballistic Research Laboratory. Aberdeen Proving Ground, MD, 18 June

Glucose Sensor Using U-Shaped Optical Fiber Probe with Gold Nanoparticles and Glucose Oxidase

PubMed Central

Chen, Kuan-Chieh; Li, Yu-Le; Wu, Chao-Wei

2018-01-01

In this study, we proposed a U-shaped optical fiber probe fabricated using a flame heating method. The probe was packaged in glass tube to reduce human factors during experimental testing of the probe as a glucose sensor. The U-shaped fiber probe was found to have high sensitivity in detecting the very small molecule. When the sensor was dipped in solutions with different refractive indexes, its wavelength or transmission loss changed. We used electrostatic self-assembly to bond gold nanoparticles and glucose oxidase (GOD) onto the sensor’s surface. The results over five cycles of the experiment showed that, as the glucose concentration increased, the refractive index of the sensor decreased and its spectrum wavelength shifted. The best wavelength sensitivity was 2.899 nm/%, and the linearity was 0.9771. The best transmission loss sensitivity was 5.101 dB/%, and the linearity was 0.9734. Therefore, the proposed U-shaped optical fiber probe with gold nanoparticles and GOD has good potential for use as a blood sugar sensor in the future. PMID:29659536

Glucose Sensor Using U-Shaped Optical Fiber Probe with Gold Nanoparticles and Glucose Oxidase.

PubMed

Chen, Kuan-Chieh; Li, Yu-Le; Wu, Chao-Wei; Chiang, Chia-Chin

2018-04-16

In this study, we proposed a U-shaped optical fiber probe fabricated using a flame heating method. The probe was packaged in glass tube to reduce human factors during experimental testing of the probe as a glucose sensor. The U-shaped fiber probe was found to have high sensitivity in detecting the very small molecule. When the sensor was dipped in solutions with different refractive indexes, its wavelength or transmission loss changed. We used electrostatic self-assembly to bond gold nanoparticles and glucose oxidase (GOD) onto the sensor’s surface. The results over five cycles of the experiment showed that, as the glucose concentration increased, the refractive index of the sensor decreased and its spectrum wavelength shifted. The best wavelength sensitivity was 2.899 nm/%, and the linearity was 0.9771. The best transmission loss sensitivity was 5.101 dB/%, and the linearity was 0.9734. Therefore, the proposed U-shaped optical fiber probe with gold nanoparticles and GOD has good potential for use as a blood sugar sensor in the future.

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

Torchia, B.S.; Call, L.M.; Migeon, B.R.

The relationship between the transcriptional state of a locus and the time when it replicates during DNA synthesis is increasingly apparent. Active autosomal genes tend to replicate early, whereas inactive ones are more permissive and frequently replicate later. Although the inactive X chromosome replicates later than its active homologue, little is known about the replication of X-linked genes. The authors have used FISH to examine the replication of loci on the active X chromosome that are not transcribed, either because the tissue analyzed was not the expressing tissue (F8C), because the locus is silent on all active X chromosomes (XIST),more » or because it has been mutated by expansion and methylation of a CpG island (FMR1). In this assay, an unreplicated locus is characterized by a single hybridization signal, and a replicated locus is characterized by a doublet hybridization signal. The percentage of doublets is used as a measure of relative time of replication in S phase. The results show that the FMR1 gene replicates relatively later in fragile X(fraX) males with the full mutation than in normal males, irrespective of the probe used. The F8C locus is late replicating in both normal and fraX males and replicates at nearly the same time on active and inactive X in females. The XIST locus replicates late in all the males studied and asynchronously in female cells. From the late replication of the locus on the active X in males, the authors deduce that the locus on the active X is the later replicating locus in female cells. They conclude that (1) the expansion of the FMR1 locus leads to late replication, (2) silence of the XIST gene in males is associated with late replication of the locus, and (3) this assay will be useful for further studies of the relationship between transcription and replication. 32 refs., 2 figs., 5 tabs.« less

Strategy for reflector pattern calculation - Let the computer do the work

NASA Technical Reports Server (NTRS)

Lam, P. T.; Lee, S.-W.; Hung, C. C.; Acosta, R.

1986-01-01

Using high frequency approximations, the secondary pattern of a reflector antenna can be calculated by numerically evaluating a radiation integral I(u,v). In recent years, tremendous effort has been expended to reducing I(u,v) to Fourier integrals. These reduction schemes are invariably reflector geometry dependent. Hence, different analyses/computer software development must be carried out for different reflector shapes/boundaries. It is pointed out, that, as the computer power improves, these reduction schemes are no longer necessary. Comparable accuracy and computation time can be achieved by evaluating I(u,v) by a brute force FFT described in this note. Furthermore, there is virtually no restriction on the reflector geometry by using the brute force FFT.

Strategy for reflector pattern calculation: Let the computer do the work

NASA Technical Reports Server (NTRS)

Lam, P. T.; Lee, S. W.; Hung, C. C.; Acousta, R.

1985-01-01

Using high frequency approximations, the secondary pattern of a reflector antenna can be calculated by numerically evaluating a radiation integral I(u,v). In recent years, tremendous effort has been expended to reducing I(u,v) to Fourier integrals. These reduction schemes are invariably reflector geometry dependent. Hence, different analyses/computer software development must be carried out for different reflector shapes/boundaries. it is pointed out, that, as the computer power improves, these reduction schemes are no longer necessary. Comparable accuracy and computation time can be achieved by evaluating I(u,v) by a brute force FFT described in this note. Furthermore, there is virtually no restriction on the reflector geometry by using the brute force FFT.

Human Activity Modeling and Simulation with High Biofidelity

DTIC Science & Technology

2013-01-01

Human activity Modeling and Simulation (M&S) plays an important role in simulation-based training and Virtual Reality (VR). However, human activity M...kinematics and motion mapping/creation; and (e) creation and replication of human activity in 3-D space with true shape and motion. A brief review is

Patterns and Prevalence of Core Profile Types in the WPPSI Standardization Sample.

ERIC Educational Resources Information Center

Glutting, Joseph J.; McDermott, Paul A.

1990-01-01

Found most representative subtest profiles for 1,200 children comprising standardization sample of Wechsler Preschool and Primary Scale of Intelligence (WPPSI). Grouped scaled scores from WPPSI subtests according to similar level and shape using sequential minimum-variance cluster analysis with independent replications. Obtained final solution of…

Going beyond the X

ERIC Educational Resources Information Center

Robertson, Carol

2018-01-01

How much do students really know about chromosomes? This article describes a partner activity and then a whole-class activity that use modeling to teach DNA replication, connect it to the shape of chromosomes during mitosis, and help students understand how daughter cells have the same DNA. Modeling is integral to science, helping students…

DNA adducts and liver DNA replication in rats during chronic exposure to N-nitrosodimethylamine (NDMA) and their relationships to the dose-dependence of NDMA hepatocarcinogenesis.

PubMed

Souliotis, Vassilis L; Henneman, John R; Reed, Carl D; Chhabra, Saranjit K; Diwan, Bhalchandra A; Anderson, Lucy M; Kyrtopoulos, Soterios A

2002-03-20

Exposure of rats to the hepatocarcinogen N-nitrosodimethylamine (NDMA) (0.2-2.64 ppm in the drinking water) for up to 180 days resulted in rapid accumulation of N7- and O6-methylguanine in liver and white blood cell DNA, maximum adduct levels being reached within 1-7 days, depending on the dose. The levels of both adducts remained constant up to treatment day 28, subsequently declining slowly to about 40% of maximal levels for the liver and 60% for white blood cells by day 180. In order to elucidate the role of DNA replication in NDMA hepatocarcinogenesis, changes in liver cell labeling index (LI) were also measured on treatment days 21, 120 and 180. Although the time- and dose-dependence of the observed effects were complex, a clear trend towards increased rates of hepatocyte LI, as indicated by BrdU incorporation, with increasing NDMA doses was evident, particularly above 1 ppm, a concentration above which NDMA hepatocarcinogenicity is known to increase sharply. In contrast, no increase in Kupffer cell DNA replication was found at any of the doses employed, in accordance with the low susceptibility of these cells to NDMA-induced carcinogenesis. No significant increase in the occurrence of necrotic or apoptotic cells was noted under the treatment conditions employed. These results suggest that, in addition to the accumulation of DNA damage, alterations in hepatocyte DNA replication during the chronic NDMA exposure may influence the dose-dependence of its carcinogenic efficacy.

Similarity in replication timing between polytene and diploid cells is associated with the organization of the Drosophila genome

PubMed Central

Goncharov, Fedor P.; Zhimulev, Igor F.

2018-01-01

Morphologically, polytene chromosomes of Drosophila melanogaster consist of compact “black” bands alternating with less compact “grey” bands and interbands. We developed a comprehensive approach that combines cytological mapping data of FlyBase-annotated genes and novel tools for predicting cytogenetic features of chromosomes on the basis of their protein composition and determined the genomic coordinates for all black bands of polytene chromosome 2R. By a PCNA immunostaining assay, we obtained the replication timetable for all the bands mapped. The results allowed us to compare replication timing between polytene chromosomes in salivary glands and chromosomes from cultured diploid cell lines and to observe a substantial similarity in the global replication patterns at the band resolution level. In both kinds of chromosomes, the intervals between black bands correspond to early replication initiation zones. Black bands are depleted of replication initiation events and are characterized by a gradient of replication timing; therefore, the time of replication completion correlates with the band length. The bands are characterized by low gene density, contain predominantly tissue-specific genes, and are represented by silent chromatin types in various tissues. The borders of black bands correspond well to the borders of topological domains as well as to the borders of the zones showing H3K27me3, SUUR, and LAMIN enrichment. In conclusion, the characteristic pattern of polytene chromosomes reflects partitioning of the Drosophila genome into two global types of domains with contrasting properties. This partitioning is conserved in different tissues and determines replication timing in Drosophila. PMID:29659604

Introduction to Intellectual Property: A U.S. Perspective.

PubMed

Murphy, Amanda; Stramiello, Michael; Lewis, Stacy; Irving, Tom

2015-03-27

This review introduces patents and trade secrets, the two mechanisms that U.S. law provides inventors to protect their inventions. These mechanisms are mutually exclusive: One demands disclosure and the other calls for concealment. Many biotechnology innovators opt for patents, which grant legal, time-limited monopolies to eligible inventions.To obtain a patent in the United States, an invention must be useful to the public and made or altered by the hand of man. It must then clear the hurdles of novelty and nonobviousness. If an invention can do that, obtaining a patent becomes a matter of form: Who qualifies as an inventor? Does the application demonstrate possession, stake a clear claim to the protection sought, and enable "ordinary" colleagues to replicate it? Has the inventor purposely withheld anything? This review addresses each of these hurdles as they apply to biotech inventions. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Introduction to Intellectual Property: A U.S. Perspective

PubMed Central

Murphy, Amanda; Stramiello, Michael; Lewis, Stacy; Irving, Tom

2015-01-01

This review introduces patents and trade secrets, the two mechanisms that U.S. law provides inventors to protect their inventions. These mechanisms are mutually exclusive: One demands disclosure and the other calls for concealment. Many biotechnology innovators opt for patents, which grant legal, time-limited monopolies to eligible inventions. To obtain a patent in the United States, an invention must be useful to the public and made or altered by the hand of man. It must then clear the hurdles of novelty and nonobviousness. If an invention can do that, obtaining a patent becomes a matter of form: Who qualifies as an inventor? Does the application demonstrate possession, stake a clear claim to the protection sought, and enable “ordinary” colleagues to replicate it? Has the inventor purposely withheld anything? This review addresses each of these hurdles as they apply to biotech inventions. PMID:25818665

Safety profile of a replication-deficient human adenovirus-vectored foot-and-mouth disease virus serotype A24 subunit vaccine in cattle.

PubMed

Barrera, J; Brake, D A; Kamicker, B J; Purcell, C; Kaptur, R; Schieber, T; Lechtenberg, K; Miller, T D; Ettyreddy, D; Brough, D E; Butman, B T; Colby, M; Neilan, J G

2018-04-01

The safety of a replication-deficient, human adenovirus-vectored foot-and-mouth disease virus (FMDV) serotype A24 Cruzeiro capsid-based subunit vaccine (AdtA24) was evaluated in five independent safety studies. The target animal safety studies were designed in compliance with United States (U.S.) regulatory requirements (Title 9, U.S. Code of Federal Regulation [9CFR]) and international standard guidelines (VICH Topic GL-44) for veterinary live vaccines. The first three studies were conducted in a total of 22 vaccinees and demonstrated that the AdtA24 master seed virus (MSV) was safe, did not revert to virulence and was not shed or spread from vaccinees to susceptible cattle or pigs. The fourth safety study conducted in 10 lactating cows using an AdtA24 vaccine serial showed that the vaccine was completely absent from milk. The fifth safety study was conducted under typical U.S. production field conditions in 500 healthy beef and dairy cattle using two AdtA24 vaccine serials. These results demonstrated that the vaccine was safe when used per the product label recommendations. Additional data collected during these five studies confirmed that AdtA24 vaccinees developed FMDV A24 and the HAd5 vaccine vector serum neutralization antibodies that test negative in a FMDV non-structural protein antibody test, confirming AdtA24 vaccine's capability to differentiate infected from vaccinated animals (DIVA). In conclusion, results from this comprehensive set of cattle studies demonstrated the safety of the replication-deficient AdtA24 vaccine and fulfilled safety-related requirements for U.S. regulatory requirements. © 2017 The Authors. Transboundary and Emerging Diseases Published by Blackwell Verlag GmbH.

Optimal firm growth under the threat of entry

PubMed Central

Kort, Peter M.; Wrzaczek, Stefan

2015-01-01

The paper studies the incumbent-entrant problem in a fully dynamic setting. We find that under an open-loop information structure the incumbent anticipates entry by overinvesting, whereas in the Markov perfect equilibrium the incumbent slightly underinvests in the period before the entry. The entry cost level where entry accommodation passes into entry deterrence is lower in the Markov perfect equilibrium. Further we find that the incumbent’s capital stock level needed to deter entry is hump shaped as a function of the entry time, whereas the corresponding entry cost, where the entrant is indifferent between entry and non-entry, is U-shaped. PMID:26435573

Cidofovir inhibits polyomavirus BK replication in human renal tubular cells downstream of viral early gene expression.

PubMed

Bernhoff, E; Gutteberg, T J; Sandvik, K; Hirsch, H H; Rinaldo, C H

2008-07-01

The human polyomavirus BK (BKV) causes nephropathy and hemorrhagic cystitis in kidney and bone marrow transplant patients, respectively. The anti-viral cidofovir (CDV) has been used in small case series but the effects on BKV replication are unclear, since polyomaviruses do not encode viral DNA polymerases. We investigated the effects of CDV on BKV(Dunlop) replication in primary human renal proximal tubule epithelial cells (RPTECs). CDV inhibited the generation of viral progeny in a dose-dependent manner yielding a 90% reduction at 40 microg/mL. Early steps such as receptor binding and entry seemed unaffected. Initial large T-antigen transcription and expression were also unaffected, but subsequent intra-cellular BKV DNA replication was reduced by >90%. Late viral mRNA and corresponding protein levels were also 90% reduced. In uninfected RPTECs, CDV 40 microg/mL reduced cellular DNA replication and metabolic activity by 7% and 11% in BrdU and WST-1 assays, respectively. BKV infection increased DNA replication to 142% and metabolic activity to 116%, respectively, which were reduced by CDV 40 microg/mL to levels of uninfected untreated RPTECs. Our results show that CDV inhibits BKV DNA replication downstream of large T-antigen expression and involves significant host cell toxicity. This should be considered in current treatment and drug development.

Diffusion of Energy Efficient Technology in Commercial Buildings: An Analysis of the Commercial Building Partnerships Program

NASA Astrophysics Data System (ADS)

Antonopoulos, Chrissi Argyro

This study presents findings from survey and interview data investigating replication of green building measures by Commercial Building Partnership (CBP) partners that worked directly with the Pacific Northwest National Laboratory (PNNL). PNNL partnered directly with 12 organizations on new and retrofit construction projects, which represented approximately 28 percent of the entire U.S. Department of Energy (DOE) CBP program. Through a feedback survey mechanism, along with personal interviews, quantitative and qualitative data were gathered relating to replication efforts by each organization. These data were analyzed to provide insight into two primary research areas: 1) CBP partners' replication efforts of green building approaches used in the CBP project to the rest of the organization's building portfolio, and, 2) the market potential for technology diffusion into the total U.S. commercial building stock, as a direct result of the CBP program. The first area of this research focused specifically on replication efforts underway or planned by each CBP program participant. The second area of this research develops a diffusion of innovations model to analyze potential broad market impacts of the CBP program on the commercial building industry in the United States. Findings from this study provided insight into motivations and objectives CBP partners had for program participation. Factors that impact replication include motivation, organizational structure and objectives firms have for implementation of energy efficient technologies. Comparing these factors between different CBP partners revealed patterns in motivation for constructing energy efficient buildings, along with better insight into market trends for green building practices. The optimized approach to the CBP program allows partners to develop green building parameters that fit the specific uses of their building, resulting in greater motivation for replication. In addition, the diffusion model developed for this analysis indicates that this method of market prediction may be used to adequately capture cumulative construction metrics for a whole-building analysis as opposed to individual energy efficiency measures used in green building.

Comet 67P/Churyumov-Gerasimenko: Non-Gravitational Forces Based on its Detailed Shape

NASA Astrophysics Data System (ADS)

Keller, Horst Uwe; Mottola, Stefano; Skorov, Yuri; Davidsson, Björn; Gutiérrez, Pedro; Jorda, Laurent; Maquet, Lucie

2015-11-01

Non-gravitational forces caused by sublimation on a cometary nucleus influence its orbital parameters and its rotational properties. Based on thermal models and rough estimates of the nucleus shape properties such as its mass and density can be derived [1, 2]. The uncertainty of the nucleus shape influences the quality of the results. Changes of the angular momentum of the nucleus rotation are more strongly influenced by details of the shape and surface. The long term observations of the nucleus of comet 67P/Churyumov-Gerasimenko by OSIRIS [3] during the rendezvous with ESA’s Rosetta spacecraft result in a very detailed shape model [3]. We use a shape model with > 105 facets to simulate the distributed forces due to sublimation and to calculate their exerted torques. The determination of the overall activity and its spatial and timely distribution over the nucleus remains a major challenge. Early observations revealed that the rotation period had changed from its last perihelion passage in 2009 [4]. The detailed shape model along with thermal modeling makes it possible to calculate the diurnal activity of the facets [6, 7]. The net torque integrated over the whole surface causes a change in the angular momentum. We also calculate the forces acting on the motion of the nucleus. This can be monitored by determinations of the spacecraft positions during the Rosetta mission. We will compare our results with the traditional approach to calculate the non-gravitational forces [8].[1, 2] Davidsson, B. J. R. & Gutiérrez, P. J., Icarus, 168, 392, 2004, Icarus, 176, 453, 2005[3] H. U. Keller, C. Barbieri, P. Lamy, H. Rickman, R. Rodrigo, K.-P. Wenzel, H. Sierks, M. A’Hearn, F. Angrilli, M. Angulo, et al., SSR, 128 (1-4): 433-506, 2007.[4] Preusker, F., Scholten, F., Matz, K.-D., et al., Astronomy & Astrophysics, accepted, 2015[5] S. Mottola, S. Lowry, C. Snodgrass, P. Lamy, I. Toth, et al. A&A, 569: L2, Sept. 2014.[6] H. U. Keller, S. Mottola, B. Davidsson, S. Schröder, Y. Skorov, E. Kührt, et al.. A&A, in press[7] H. U. Keller, S. Mottola, Y. V. Skorov, and L. Jorda, Astronomy and Astrophysics Letter , 2015.[8] B. G. Marsden, Z. Sekanina, and D. K. Yeomans, Astronomical Journal, 78: 211, Mar. 1973.

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

PubMed

Koren, Amnon; Tsai, Hung-Ji; Tirosh, Itay; Burrack, Laura S; Barkai, Naama; Berman, Judith

2010-08-19

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

Meta-analysis of genome-wide association studies identifies 8 novel loci involved in shape variation of human head hair.

PubMed

Liu, Fan; Chen, Yan; Zhu, Gu; Hysi, Pirro G; Wu, Sijie; Adhikari, Kaustubh; Breslin, Krystal; Pospiech, Ewelina; Hamer, Merel A; Peng, Fuduan; Muralidharan, Charanya; Acuna-Alonzo, Victor; Canizales-Quinteros, Samuel; Bedoya, Gabriel; Gallo, Carla; Poletti, Giovanni; Rothhammer, Francisco; Bortolini, Maria Catira; Gonzalez-Jose, Rolando; Zeng, Changqing; Xu, Shuhua; Jin, Li; Uitterlinden, André G; Ikram, M Arfan; van Duijn, Cornelia M; Nijsten, Tamar; Walsh, Susan; Branicki, Wojciech; Wang, Sijia; Ruiz-Linares, Andrés; Spector, Timothy D; Martin, Nicholas G; Medland, Sarah E; Kayser, Manfred

2018-02-01

Shape variation of human head hair shows striking variation within and between human populations, while its genetic basis is far from being understood. We performed a series of genome-wide association studies (GWASs) and replication studies in a total of 28 964 subjects from 9 cohorts from multiple geographic origins. A meta-analysis of three European GWASs identified 8 novel loci (1p36.23 ERRFI1/SLC45A1, 1p36.22 PEX14, 1p36.13 PADI3, 2p13.3 TGFA, 11p14.1 LGR4, 12q13.13 HOXC13, 17q21.2 KRTAP, and 20q13.33 PTK6), and confirmed 4 previously known ones (1q21.3 TCHH/TCHHL1/LCE3E, 2q35 WNT10A, 4q21.21 FRAS1, and 10p14 LINC00708/GATA3), all showing genome-wide significant association with hair shape (P < 5e-8). All except one (1p36.22 PEX14) were replicated with nominal significance in at least one of the 6 additional cohorts of European, Native American and East Asian origins. Three additional previously known genes (EDAR, OFCC1, and PRSS53) were confirmed at the nominal significance level. A multivariable regression model revealed that 14 SNPs from different genes significantly and independently contribute to hair shape variation, reaching a cross-validated AUC value of 0.66 (95% CI: 0.62-0.70) and an AUC value of 0.64 in an independent validation cohort, providing an improved accuracy compared with a previous model. Prediction outcomes of 2504 individuals from a multiethnic sample were largely consistent with general knowledge on the global distribution of hair shape variation. Our study thus delivers target genes and DNA variants for future functional studies to further evaluate the molecular basis of hair shape in humans. © The Author(s) 2017. Published by Oxford University Press.

Meta-analysis of genome-wide association studies identifies 8 novel loci involved in shape variation of human head hair

PubMed Central

Liu, Fan; Chen, Yan; Zhu, Gu; Hysi, Pirro G; Wu, Sijie; Adhikari, Kaustubh; Breslin, Krystal; Pośpiech, Ewelina; Hamer, Merel A; Peng, Fuduan; Muralidharan, Charanya; Acuna-Alonzo, Victor; Canizales-Quinteros, Samuel; Bedoya, Gabriel; Gallo, Carla; Poletti, Giovanni; Rothhammer, Francisco; Bortolini, Maria Catira; Gonzalez-Jose, Rolando; Zeng, Changqing; Xu, Shuhua; Jin, Li; Uitterlinden, André G; Ikram, M Arfan; van Duijn, Cornelia M; Nijsten, Tamar; Walsh, Susan; Branicki, Wojciech; Wang, Sijia; Ruiz-Linares, Andrés; Spector, Timothy D; Martin, Nicholas G; Medland, Sarah E; Kayser, Manfred

2018-01-01

Abstract Shape variation of human head hair shows striking variation within and between human populations, while its genetic basis is far from being understood. We performed a series of genome-wide association studies (GWASs) and replication studies in a total of 28 964 subjects from 9 cohorts from multiple geographic origins. A meta-analysis of three European GWASs identified 8 novel loci (1p36.23 ERRFI1/SLC45A1, 1p36.22 PEX14, 1p36.13 PADI3, 2p13.3 TGFA, 11p14.1 LGR4, 12q13.13 HOXC13, 17q21.2 KRTAP, and 20q13.33 PTK6), and confirmed 4 previously known ones (1q21.3 TCHH/TCHHL1/LCE3E, 2q35 WNT10A, 4q21.21 FRAS1, and 10p14 LINC00708/GATA3), all showing genome-wide significant association with hair shape (P < 5e-8). All except one (1p36.22 PEX14) were replicated with nominal significance in at least one of the 6 additional cohorts of European, Native American and East Asian origins. Three additional previously known genes (EDAR, OFCC1, and PRSS53) were confirmed at the nominal significance level. A multivariable regression model revealed that 14 SNPs from different genes significantly and independently contribute to hair shape variation, reaching a cross-validated AUC value of 0.66 (95% CI: 0.62–0.70) and an AUC value of 0.64 in an independent validation cohort, providing an improved accuracy compared with a previous model. Prediction outcomes of 2504 individuals from a multiethnic sample were largely consistent with general knowledge on the global distribution of hair shape variation. Our study thus delivers target genes and DNA variants for future functional studies to further evaluate the molecular basis of hair shape in humans. PMID:29220522

Optimization of surface morphology and scattering properties of TCO/AIT textured glass front electrode for thin film solar cells

NASA Astrophysics Data System (ADS)

Addonizio, M. L.; Fusco, L.; Antonaia, A.; Cominale, F.; Usatii, I.

2015-12-01

Aluminium induced texture (AIT) method has been used for obtaining highly textured glass substrate suitable for silicon based thin film solar cell technology. Wet etch step parameters of AIT process have been varied and effect of different etchants and different etching times on morphological and optical properties has been analyzed. The resulting morphology features (shape, size distribution, inclination angle) have been optimized in order to obtain the best scattering properties. ZnO:Ga (GZO) films have been deposited by sputtering technique on AIT-processed glass. Two different ZnO surface morphologies have been obtained, strongly depending on the underlying glass substrate morphology induced by different etching times. Very rough and porous texture (σrms ∼ 150 nm) was obtained on glass etched 2 min showing cauliflower-like structure, whereas a softer texture (σrms ∼ 78 nm) was obtained on glass etched 7 min giving wider and smoother U-shaped craters. The effect of different glass textures on optical confinement has been tested in amorphous silicon based p-i-n devices. Devices fabricated on GZO/high textured glass showed a quantum efficiency enhancement due to both an effective light trapping phenomenon and an effective anti-reflective optical behaviour. Short etching time produce smaller cavities (<1 μm) with deep U-shape characterized by high roughness, high inclination angle and low autocorrelation length. This surface morphology promoted a large light scattering phenomenon, as evidenced by haze value and by angular resolved scattering (ARS) behaviour, into a large range of diffraction angles, giving high probability of effective light trapping inside a PV device.

Internal initiation of influenza virus replication of viral RNA and complementary RNA in vitro.

PubMed

Zhang, Shijian; Wang, Jinlan; Wang, Qiang; Toyoda, Tetsuya

2010-12-24

Influenza virus transcription is a prototype of primer-dependent initiation. Its replication mechanism is thought to be primer-independent. The internal initiation and realignment model for influenza virus genome replication has been recently proposed (Deng, T., Vreede, F. T., and Brownlee, G. G. (2006) J. Virol. 80, 2337-2348). We obtained new results, which led us to propose a novel model for the initiation of viral RNA (vRNA) replication. In our study, we analyzed the initiation mechanisms of influenza virus vRNA and complementary RNA (cRNA) synthesis in vitro, using purified RNA polymerase (RdRp) and 84-nt model RNA templates. We found that, for vRNA → cRNA →, RdRp initiated replication from the second nucleotide of the 3'-end. Therefore, host RNA-specific ribonucleotidyltransferases are required to add one nucleotide (purine residues are preferred) to the 3'-end of vRNA to make the complete copy of vRNA. This hypothesis was experimentally proven using poly(A) polymerase. For cRNA → vRNA, the dinucleotide primer AG was synthesized from UC (fourth and fifth from the 3'-end) by RdRp pausing at the sixth U of UUU and realigning at the 3'-end of cRNA template; then RdRp was able to read through the entire template RNA. The RdRp initiation complex was not stable until it had read through the UUU of cRNA and the UUUU of vRNA at their respective 3'-ends. This was because primers overlapping with the first U of the clusters did not initiate transcription efficiently, and the initiation product of v84+G (the v84 template with an extra G at its 3'-end), AGC, realigned to the 3'-end.

Molecular architecture of the human GINS complex

PubMed Central

Boskovic, Jasminka; Coloma, Javier; Aparicio, Tomás; Zhou, Min; Robinson, Carol V; Méndez, Juan; Montoya, Guillermo

2007-01-01

Chromosomal DNA replication is strictly regulated through a sequence of steps that involve many macromolecular protein complexes. One of these is the GINS complex, which is required for initiation and elongation phases in eukaryotic DNA replication. The GINS complex consists of four paralogous subunits. At the G1/S transition, GINS is recruited to the origins of replication where it assembles with cell-division cycle protein (Cdc)45 and the minichromosome maintenance mutant (MCM)2–7 to form the Cdc45/Mcm2–7/GINS (CMG) complex, the presumed replicative helicase. We isolated the human GINS complex and have shown that it can bind to DNA. By using single-particle electron microscopy and three-dimensional reconstruction, we obtained a medium-resolution volume of the human GINS complex, which shows a horseshoe shape. Analysis of the protein interactions using mass spectrometry and monoclonal antibody mapping shows the subunit organization within the GINS complex. The structure and DNA-binding data suggest how GINS could interact with DNA and also its possible role in the CMG helicase complex. PMID:17557111

A conserved MCM single-stranded DNA binding element is essential for replication initiation.

PubMed

Froelich, Clifford A; Kang, Sukhyun; Epling, Leslie B; Bell, Stephen P; Enemark, Eric J

2014-04-01

The ring-shaped MCM helicase is essential to all phases of DNA replication. The complex loads at replication origins as an inactive double-hexamer encircling duplex DNA. Helicase activation converts this species to two active single hexamers that encircle single-stranded DNA (ssDNA). The molecular details of MCM DNA interactions during these events are unknown. We determined the crystal structure of the Pyrococcus furiosus MCM N-terminal domain hexamer bound to ssDNA and define a conserved MCM-ssDNA binding motif (MSSB). Intriguingly, ssDNA binds the MCM ring interior perpendicular to the central channel with defined polarity. In eukaryotes, the MSSB is conserved in several Mcm2-7 subunits, and MSSB mutant combinations in S. cerevisiae Mcm2-7 are not viable. Mutant Mcm2-7 complexes assemble and are recruited to replication origins, but are defective in helicase loading and activation. Our findings identify an important MCM-ssDNA interaction and suggest it functions during helicase activation to select the strand for translocation. DOI: http://dx.doi.org/10.7554/eLife.01993.001.

A conserved MCM single-stranded DNA binding element is essential for replication initiation

PubMed Central

Froelich, Clifford A; Kang, Sukhyun; Epling, Leslie B; Bell, Stephen P; Enemark, Eric J

2014-01-01

The ring-shaped MCM helicase is essential to all phases of DNA replication. The complex loads at replication origins as an inactive double-hexamer encircling duplex DNA. Helicase activation converts this species to two active single hexamers that encircle single-stranded DNA (ssDNA). The molecular details of MCM DNA interactions during these events are unknown. We determined the crystal structure of the Pyrococcus furiosus MCM N-terminal domain hexamer bound to ssDNA and define a conserved MCM-ssDNA binding motif (MSSB). Intriguingly, ssDNA binds the MCM ring interior perpendicular to the central channel with defined polarity. In eukaryotes, the MSSB is conserved in several Mcm2-7 subunits, and MSSB mutant combinations in S. cerevisiae Mcm2-7 are not viable. Mutant Mcm2-7 complexes assemble and are recruited to replication origins, but are defective in helicase loading and activation. Our findings identify an important MCM-ssDNA interaction and suggest it functions during helicase activation to select the strand for translocation. DOI: http://dx.doi.org/10.7554/eLife.01993.001 PMID:24692448

Disruption of a stem-loop structure located upstream of pseudoknot domain in Tobacco mosaic virus enhanced its infectivity and viral RNA accumulation.

PubMed

Guo, Song; Wong, Sek-Man

2018-06-01

A predicted stem-loop structure of 25 nucleotides, located in the coat protein (CP) gene and 3'-UTR sequences of Tobacco mosaic virus (TMV), was validated previously (Guo et al., 2015). In this study, both disrupted stem-loop and nucleotide deletion mutants of TMV replicated more rapidly in Nicotiana benthamiana protoplasts. The TMV mutant with a complete mirrored stem-loop structure showed similar level of viral RNA accumulation as TMV. Recovering the stem-loop structure also resulted in a similar replication level as TMV. All these mutants induced necrosis in N. benthamiana and assembled into typical rigid rod-shaped virions. TMV mutant without the stem-loop structure induced more local lesions in Chenopodium quinoa. When the putative stem-loop structure in Tomato mosaic virus (ToMV) was disrupted, the mutant also showed an enhanced virus replication. This suggests that the stem-loop structure of TMV is a new cis-acting element with a role in virus replication. Copyright © 2018 Elsevier Inc. All rights reserved.

Genome Dynamics in Legionella: The Basis of Versatility and Adaptation to Intracellular Replication

PubMed Central

Gomez-Valero, Laura; Buchrieser, Carmen

2013-01-01

Legionella pneumophila is a bacterial pathogen present in aquatic environments that can cause a severe pneumonia called Legionnaires’ disease. Soon after its recognition, it was shown that Legionella replicates inside amoeba, suggesting that bacteria replicating in environmental protozoa are able to exploit conserved signaling pathways in human phagocytic cells. Comparative, evolutionary, and functional genomics suggests that the Legionella–amoeba interaction has shaped this pathogen more than previously thought. A complex evolutionary scenario involving mobile genetic elements, type IV secretion systems, and horizontal gene transfer among Legionella, amoeba, and other organisms seems to take place. This long-lasting coevolution led to the development of very sophisticated virulence strategies and a high level of temporal and spatial fine-tuning of bacteria host–cell interactions. We will discuss current knowledge of the evolution of virulence of Legionella from a genomics perspective and propose our vision of the emergence of this human pathogen from the environment. PMID:23732852

Genome dynamics in Legionella: the basis of versatility and adaptation to intracellular replication.

PubMed

Gomez-Valero, Laura; Buchrieser, Carmen

2013-06-01

Legionella pneumophila is a bacterial pathogen present in aquatic environments that can cause a severe pneumonia called Legionnaires' disease. Soon after its recognition, it was shown that Legionella replicates inside amoeba, suggesting that bacteria replicating in environmental protozoa are able to exploit conserved signaling pathways in human phagocytic cells. Comparative, evolutionary, and functional genomics suggests that the Legionella-amoeba interaction has shaped this pathogen more than previously thought. A complex evolutionary scenario involving mobile genetic elements, type IV secretion systems, and horizontal gene transfer among Legionella, amoeba, and other organisms seems to take place. This long-lasting coevolution led to the development of very sophisticated virulence strategies and a high level of temporal and spatial fine-tuning of bacteria host-cell interactions. We will discuss current knowledge of the evolution of virulence of Legionella from a genomics perspective and propose our vision of the emergence of this human pathogen from the environment.

Space Science

NASA Image and Video Library

1999-04-01

NASA's Space Optics Manufacturing Center has been working to expand our view of the universe via sophisticated new telescopes. The Optics Center's goal is to develop low-cost, advanced space optics technologies for the NASA program in the 21st century - including the long-term goal of imaging Earth-like planets in distant solar systems. To reduce the cost of mirror fabrication, Marshall Space Flight Center (MSFC) has developed replication techniques, the machinery, and materials to replicate electro-formed nickel mirrors. The process allows fabricating precisely shaped mandrels to be used and reused as masters for replicating high-quality mirrors. MSFC's Space Optics Manufacturing Technology Center (SOMTC) has grinding and polishing equipment ranging from conventional spindles to custom-designed polishers. These capabilities allow us to grind precisely and polish a variety of optical devices, including x-ray mirror mandrels. This image shows Charlie Griffith polishing the half-meter mandrel at SOMTC.

The dynamics of genome replication using deep sequencing

PubMed Central

Müller, Carolin A.; Hawkins, Michelle; Retkute, Renata; Malla, Sunir; Wilson, Ray; Blythe, Martin J.; Nakato, Ryuichiro; Komata, Makiko; Shirahige, Katsuhiko; de Moura, Alessandro P.S.; Nieduszynski, Conrad A.

2014-01-01

Eukaryotic genomes are replicated from multiple DNA replication origins. We present complementary deep sequencing approaches to measure origin location and activity in Saccharomyces cerevisiae. Measuring the increase in DNA copy number during a synchronous S-phase allowed the precise determination of genome replication. To map origin locations, replication forks were stalled close to their initiation sites; therefore, copy number enrichment was limited to origins. Replication timing profiles were generated from asynchronous cultures using fluorescence-activated cell sorting. Applying this technique we show that the replication profiles of haploid and diploid cells are indistinguishable, indicating that both cell types use the same cohort of origins with the same activities. Finally, increasing sequencing depth allowed the direct measure of replication dynamics from an exponentially growing culture. This is the first time this approach, called marker frequency analysis, has been successfully applied to a eukaryote. These data provide a high-resolution resource and methodological framework for studying genome biology. PMID:24089142

Trajectories of attachment in older age: interpersonal trauma and its consequences.

PubMed

Bachem, Rahel; Levin, Yafit; Solomon, Zahava

2018-06-04

Previous studies suggest that attachment insecurities may increase after trauma exposure, an effect documented only at a group level. This study explores the heterogeneity of changes over time and examines the associations of the nature of the traumatic event (interpersonal and nonpersonal), and its consequences (posttraumatic stress disorder [PTSD] and loneliness) with attachment trajectories. Two groups of Israeli veterans participated: 164 former prisoners-of-war and 185 combat veterans. Attachment was assessed at four points (1991-2015). Risk factors were evaluated in 1991. Using latent growth mixture modeling, trajectories of attachment insecurities were explored. Three avoidance trajectories (stability, decrease, inverse u-shaped) and two anxiety trajectories (stability, decrease) were identified. The inverse u-shaped avoidance trajectory was associated with captivity, humiliation, loneliness, and PTSD, and stable avoidance was associated with loneliness. Stable anxiety was associated with captivity and loneliness. Attachment insecurities can change during aging and persist decades after a trauma. Trauma-related risk factors are related to more deleterious trajectories.

Relationship between DNA damage response, initiated by camptothecin or oxidative stress, and DNA replication, analyzed by quantitative 3D image analysis.

PubMed

Berniak, K; Rybak, P; Bernas, T; Zarębski, M; Biela, E; Zhao, H; Darzynkiewicz, Z; Dobrucki, J W

2013-10-01

A method of quantitative analysis of spatial (3D) relationship between discrete nuclear events detected by confocal microscopy is described and applied in analysis of a dependence between sites of DNA damage signaling (γH2AX foci) and DNA replication (EdU incorporation) in cells subjected to treatments with camptothecin (Cpt) or hydrogen peroxide (H2O2). Cpt induces γH2AX foci, likely reporting formation of DNA double-strand breaks (DSBs), almost exclusively at sites of DNA replication. This finding is consistent with the known mechanism of induction of DSBs by DNA topoisomerase I (topo1) inhibitors at the sites of collisions of the moving replication forks with topo1-DNA "cleavable complexes" stabilized by Cpt. Whereas an increased level of H2AX histone phosphorylation is seen in S-phase of cells subjected to H2O2, only a minor proportion of γH2AX foci coincide with DNA replication sites. Thus, the increased level of H2AX phosphorylation induced by H2O2 is not a direct consequence of formation of DNA lesions at the sites of moving DNA replication forks. These data suggest that oxidative stress induced by H2O2 and formation of the primary H2O2-induced lesions (8-oxo-7,8-dihydroguanosine) inhibits replication globally and triggers formation of γH2AX at various distances from replication forks. Quantitative analysis of a frequency of DNA replication sites and γH2AX foci suggests also that stalling of replicating forks by Cpt leads to activation of new DNA replication origins. © 2013 International Society for Advancement of Cytometry. Copyright © 2013 International Society for Advancement of Cytometry.

The Development of Project Information Packages for Effective Approaches in Compensatory Education. Final Report. Report No. UR-254.

ERIC Educational Resources Information Center

Tallmadge, G. Kasten

The project described herein represents an attempt by the U. S. Office of Education to take a more active role in the national dissemination and replication of those programs which have achieved the greatest success in producing reliably measured achievement benefits in reading and mathematical skills. With this general objective in mind, the U.…

Special Inspector General for Iraq Reconstruction

DTIC Science & Technology

2008-10-30

U.S. supervision on matters of law, policy, and gover - nance. This aspect of Iraq’s nascent normalcy has decreased GOI transparency for U.S...additional sleep- ing space for firefighters, fire support equipment, and covered parking.511 Tourism . In August 2008, the North Carolina...struction activities. The PRT aims to replicate this form of partnership in other PRT activities, especially in the tourism and agriculture sectors.573

Development and Demonstration of Adanced Tooling Alloys for Molds and Dies

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

Kevin M. McHugh; Enrique J. Lavernia

2006-01-01

This report summarizes research results in the project Development and Demonstration of Advanced Tooling Alloys for Molds and Dies. Molds, dies and related tooling are used to manufacture most of the plastic and metal products we use every day. Conventional fabrication of molds and dies involves a multiplicity of machining, benching and heat treatment unit operations. This approach is very expensive and time consuming. Rapid Solidifcation Process (RSP) Tooling is a spray-forming technology tailored for producing molds and dies. The appraoch combines rapid solidifcation processing and net-shape materials processing in a single step. An atomized spray of a tool-forming alloy,more » typically a tool steel, is deposited onto an easy-to-form tool pattern to replicate the pattern's shape and surface features. By so doing, the approach eliminates many machining operations in conventional mold making, significantly reducing cost, lead time and energy. Moreover, rapid solidification creates unique microstructural features by suppressing carbide precipitation and growth, and creating metastable phases. This can result in unique material properties following heat treatment. Spray-formed and aged tool steel dies have exhibited extended life compared to conventional dies in many forming operations such as forging, extrusion and die casting. RSP Tooling technolocy was commercialized with the formation of RSP Tooling, LLC in Solon, Oh.« less

A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease loci.

PubMed

Liu, Ying; Helms, Cynthia; Liao, Wilson; Zaba, Lisa C; Duan, Shenghui; Gardner, Jennifer; Wise, Carol; Miner, Andrew; Malloy, M J; Pullinger, Clive R; Kane, John P; Saccone, Scott; Worthington, Jane; Bruce, Ian; Kwok, Pui-Yan; Menter, Alan; Krueger, James; Barton, Anne; Saccone, Nancy L; Bowcock, Anne M

2008-03-28

A genome-wide association study was performed to identify genetic factors involved in susceptibility to psoriasis (PS) and psoriatic arthritis (PSA), inflammatory diseases of the skin and joints in humans. 223 PS cases (including 91 with PSA) were genotyped with 311,398 single nucleotide polymorphisms (SNPs), and results were compared with those from 519 Northern European controls. Replications were performed with an independent cohort of 577 PS cases and 737 controls from the U.S., and 576 PSA patients and 480 controls from the U.K.. Strongest associations were with the class I region of the major histocompatibility complex (MHC). The most highly associated SNP was rs10484554, which lies 34.7 kb upstream from HLA-C (P = 7.8x10(-11), GWA scan; P = 1.8x10(-30), replication; P = 1.8x10(-39), combined; U.K. PSA: P = 6.9x10(-11)). However, rs2395029 encoding the G2V polymorphism within the class I gene HCP5 (combined P = 2.13x10(-26) in U.S. cases) yielded the highest ORs with both PS and PSA (4.1 and 3.2 respectively). This variant is associated with low viral set point following HIV infection and its effect is independent of rs10484554. We replicated the previously reported association with interleukin 23 receptor and interleukin 12B (IL12B) polymorphisms in PS and PSA cohorts (IL23R: rs11209026, U.S. PS, P = 1.4x10(-4); U.K. PSA: P = 8.0x10(-4); IL12B:rs6887695, U.S. PS, P = 5x10(-5) and U.K. PSA, P = 1.3x10(-3)) and detected an independent association in the IL23R region with a SNP 4 kb upstream from IL12RB2 (P = 0.001). Novel associations replicated in the U.S. PS cohort included the region harboring lipoma HMGIC fusion partner (LHFP) and conserved oligomeric golgi complex component 6 (COG6) genes on chromosome 13q13 (combined P = 2x10(-6) for rs7993214; OR = 0.71), the late cornified envelope gene cluster (LCE) from the Epidermal Differentiation Complex (PSORS4) (combined P = 6.2x10(-5) for rs6701216; OR 1.45) and a region of LD at 15q21 (combined P = 2.9x10(-5) for rs3803369; OR = 1.43). This region is of interest because it harbors ubiquitin-specific protease-8 whose processed pseudogene lies upstream from HLA-C. This region of 15q21 also harbors the gene for SPPL2A (signal peptide peptidase like 2a) which activates tumor necrosis factor alpha by cleavage, triggering the expression of IL12 in human dendritic cells. We also identified a novel PSA (and potentially PS) locus on chromosome 4q27. This region harbors the interleukin 2 (IL2) and interleukin 21 (IL21) genes and was recently shown to be associated with four autoimmune diseases (Celiac disease, Type 1 diabetes, Grave's disease and Rheumatoid Arthritis).

Exploring the Roles of Nucleobase Desolvation and Shape Complementarity during the Misreplication of O6-Methylguanine

PubMed Central

Chavarria, Delia; Ramos-Serrano, Andrea; Hirao, Ichiro; Berdis, Anthony J.

2011-01-01

O6-methylguanine is a miscoding DNA lesion arising from the alkylation of guanine. This report uses the bacteriophage T4 DNA polymerase as a model to probe the roles hydrogen-bonding interactions, shape/size, and nucleobase desolvation during the replication of this miscoding lesion. This was accomplished by using transient kinetic techniques to monitor the kinetic parameters for incorporating and extending natural and non-natural nucleotides. In general, the efficiency of nucleotide incorporation does not depend on the hydrogen-bonding potential of the incoming nucleotide. Instead, nucleobase hydrophobicity and shape complementarity appear to be the preeminent factors controlling nucleotide incorporation. In addition, shape complementarity plays a large role in controlling the extension of various mispairs containing O6-methylguanine. This is evident as the rate constants for extension correlate with proper interglycosyl distances and symmetry between the base angles of the formed mispair. Base pairs not conforming to an acceptable geometry within the polymerase’s active site are refractory to elongation and are processed via exonuclease proofreading. The collective data set encompassing nucleotide incorporation, extension, and excision is used to generate a model accounting for the mutagenic potential of O6-methylguanine observed in vivo. In addition, kinetic studies monitoring the incorporation and extension of non-natural nucleotides identified an analog that displays high selectivity for incorporation opposite O6-methylguanine compared to unmodified purines. The unusual selectivity of this analog for replicating damaged DNA provides a novel biochemical tool to study translesion DNA synthesis. PMID:21819995

Re-Shaping the Faculty: Emergence and Development of "Permanent-Contingent" Roles through the Lens of Cultural-Historical Activity Theory

ERIC Educational Resources Information Center

Tkachenko, Oleksandr; Louis, Karen Seashore

2017-01-01

This study retrospectively examines the emergence and development of a new class of full-time non-tenure track employees in a large land grant research university in the U.S., which created the employment category in 1980. We employ cultural-historical activity theory (CHAT) to explore how this class of employees became institutionalized within…

Russia, China, and the United States in Central Asia: Prospects for Great Power Competition and Cooperation in the Shadow of the Georgian Crisis

DTIC Science & Technology

2009-02-01

energy, public health, and food safety) shape Chinese foreign relations with neighboring states. Professor Wishnick also writes about great power...Dismisses Georgia’s Leader as ‘Political Corpse’,” The New York Times, September 3, 2008, p. A10; Ellen Barry, “Russians with Pumpkins Protest Many U.S

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.

Single Cell Analysis of Human RAD18-Dependent DNA Post-Replication Repair by Alkaline Bromodeoxyuridine Comet Assay

PubMed Central

Mórocz, Mónika; Gali, Himabindu; Raskó, István; Downes, C. Stephen; Haracska, Lajos

2013-01-01

Damage to DNA can block replication progression resulting in gaps in the newly synthesized DNA. Cells utilize a number of post-replication repair (PRR) mechanisms such as the RAD18 controlled translesion synthesis or template switching to overcome the discontinuities formed opposite the DNA lesions and to complete DNA replication. Gaining more insights into the role of PRR genes promotes better understanding of DNA damage tolerance and of how their malfunction can lead to increased genome instability and cancer. However, a simple and efficient method to characterise gene specific PRR deficiencies at a single cell level has not been developed. Here we describe the so named BrdU comet PRR assay to test the contribution of human RAD18 to PRR at a single cell level, by which we kinetically characterized the consequences of the deletion of human RAD18 on the replication of UV-damaged DNA. Moreover, we demonstrate the capability of our method to evaluate PRR at a single cell level in unsynchronized cell population. PMID:23936422

Epstein-Barr virus nuclear antigen-1 is highly colocalized with interphase chromatin and its newly replicated regions in particular.

PubMed

Ito, Sayuri; Gotoh, Eisuke; Ozawa, Shigeru; Yanagi, Kazuo

2002-10-01

Epstein-Barr virus (EBV) nuclear antigen-1 (EBNA-1), which binds to both the EBV origin of replication (oriP) and metaphase chromosomes, is essential for the replication/retention and segregation/partition of oriP-containing plasmids. Here the chromosomal localization of EBNA-1 fused to green fluorescent protein (GFP-EBNA-1) is examined by confocal microscopy combined with a 'premature chromosome condensation' (PCC) procedure. Analyses show that GFP-EBNA-1 expressed in living cells that lack oriP plasmids is associated with cellular chromatin that has been condensed rapidly by the PCC procedure into identifiable forms that are unique to each phase of interphase as well as metaphase chromosomes. Studies of cellular chromosomal DNAs labelled with BrdU or Cy3-dUTP indicate that GFP-EBNA-1 colocalizes highly with the labelled, newly replicated regions of interphase chromatin in cells. These results suggest that EBNA-1 is associated not only with cellular metaphase chromosomes but also with condensing chromatin/chromosomes and probably with interphase chromatin, especially with its newly replicated regions.

The Human Cytomegalovirus IE2 and UL112-113 Proteins Accumulate in Viral DNA Replication Compartments That Initiate from the Periphery of Promyelocytic Leukemia Protein-Associated Nuclear Bodies (PODs or ND10)

PubMed Central

Ahn, Jin-Hyun; Jang, Won-Jong; Hayward, Gary S.

1999-01-01

During human cytomegalovirus (HCMV) infection, the periphery of promyelocytic leukemia protein (PML)-associated nuclear bodies (also known as PML oncogenic domains [PODs] or ND10) are sites for both input viral genome deposition and immediate-early (IE) gene transcription. At very early times after infection, the IE1 protein localizes to and subsequently disrupts PODs, whereas the IE2 protein localizes within or adjacent to PODs. This process appears to be required for efficient viral gene expression and DNA replication. We have investigated the initiation of viral DNA replication compartment formation by studying the localization of viral IE proteins, DNA replication proteins, and the PML protein during productive infection. Localization of IE2 adjacent to PODs between 2 and 6 h after infection was confirmed by confocal microscopy of human fibroblasts (HF cells) infected with both wild-type HCMV(Towne) and with an IE1-deletion mutant HCMV(CR208) that fails to disrupt PODs. In HCMV(Towne)-infected HF cells at 24 to 48 h, IE2 also accumulated in newly formed viral DNA replication compartments containing the polymerase processivity factor (UL44), the single-stranded DNA binding protein (SSB; UL57), the UL112-113 accessory protein, and newly incorporated bromodeoxyuridine (BrdU). Double labeling of the HCMV(CR208)-infected HF cells demonstrated that formation of viral DNA replication compartments initiates within granular structures that bud from the periphery of some of the PODs and subsequently coalesce into larger structures that are flanked by PODs. In transient DNA transfection assays, both the N terminus (codons 136 to 290) and the C terminus (codons 379 to 579) of IE2 exon 5, but not the central region between them, were found to be necessary for both the punctate distribution of IE2 and its association with PODs. Like IE2, the UL112-113 accessory replication protein was also distributed in a POD-associated pattern in both DNA-transfected and virus-infected cells beginning at 6 h. Furthermore, when all six replication core machinery proteins (polymerase complex, SSB, and helicase-primase complex) were expressed together in the presence of UL112-113, they also accumulated at POD-associated sites, suggesting that the UL112-113 protein (but not IE2) may play a role in recruitment of viral replication fork proteins into the periphery of PODs. These results show that (i) subsequent to accumulating at the periphery of PODs, IE2 is incorporated together with the core proteins into viral DNA replication compartments that initiate from the periphery of PODs and then grow to fill the space between groups of PODs, and (ii) the UL112-113 protein appears to have a key role in assembling and recruiting the core replication machinery proteins in the initial stages of viral replication compartment formation. PMID:10559364

Zinc Finger-Containing Cellular Transcription Corepressor ZBTB25 Promotes Influenza Virus RNA Transcription and Is a Target for Zinc Ejector Drugs.

PubMed

Chen, Shu-Chuan; Jeng, King-Song; Lai, Michael M C

2017-10-15

Influenza A virus (IAV) replication relies on an intricate interaction between virus and host cells. How the cellular proteins are usurped for IAV replication remains largely obscure. The aim of this study was to search for novel and potential cellular factors that participate in IAV replication. ZBTB25, a transcription repressor of a variety of cellular genes, was identified by an RNA interference (RNAi) genomic library screen. Depletion of ZBTB25 significantly reduced IAV production. Conversely, overexpression of ZBTB25 enhanced it. ZBTB25 interacted with the viral RNA-dependent RNA polymerase (RdRp) protein and modulated its transcription activity. In addition, ZBTB25 also functioned as a viral RNA (vRNA)-binding protein, binding preferentially to the U-rich sequence within the 5' untranslated region (UTR) of vRNA. Both protein-protein and protein-RNA interactions involving ZBTB25 facilitated viral RNA transcription and replication. In addition, ZBTB25 suppressed interferon production, further enhancing viral replication. ZBTB25-associated functions required an intact zinc finger domain and posttranslational SUMO-1 modification of ZBTB25. Furthermore, treatment with disulfiram (a zinc ejector) of ZBTB25-overexpressing cells showed significantly reduced IAV production as a result of reduced RNA synthesis. Our findings indicate that IAV usurps ZBTB25 for IAV RNA synthesis and serves as a novel and potential therapeutic antiviral target. IMPORTANCE IAV-induced seasonal influenza causes severe illness and death in high-risk populations. However, IAV has developed resistance to current antiviral drugs due to its high mutation rate. Therefore, development of drugs targeting cellular factors required for IAV replication is an attractive alternative for IAV therapy. Here, we discovered a cellular protein, ZBTB25, that enhances viral RdRp activity by binding to both viral RdRp and viral RNA to stimulate viral RNA synthesis. A unique feature of ZBTB25 in the regulation of viral replication is its dual transcription functions, namely, promoting viral RNA transcription through binding to the U-rich region of vRNA and suppressing cellular interferon production. ZBTB25 contains a zinc finger domain that is required for RNA-inhibitory activity by chelating zinc ions. Disulfiram treatment disrupts the zinc finger functions, effectively repressing IAV replication. Based on our findings, we demonstrate that ZBTB25 regulates IAV RNA transcription and replication and serves as a promising antiviral target for IAV treatment. Copyright © 2017 American Society for Microbiology.

Zinc Finger-Containing Cellular Transcription Corepressor ZBTB25 Promotes Influenza Virus RNA Transcription and Is a Target for Zinc Ejector Drugs

PubMed Central

Chen, Shu-Chuan; Jeng, King-Song

2017-01-01

ABSTRACT Influenza A virus (IAV) replication relies on an intricate interaction between virus and host cells. How the cellular proteins are usurped for IAV replication remains largely obscure. The aim of this study was to search for novel and potential cellular factors that participate in IAV replication. ZBTB25, a transcription repressor of a variety of cellular genes, was identified by an RNA interference (RNAi) genomic library screen. Depletion of ZBTB25 significantly reduced IAV production. Conversely, overexpression of ZBTB25 enhanced it. ZBTB25 interacted with the viral RNA-dependent RNA polymerase (RdRp) protein and modulated its transcription activity. In addition, ZBTB25 also functioned as a viral RNA (vRNA)-binding protein, binding preferentially to the U-rich sequence within the 5′ untranslated region (UTR) of vRNA. Both protein-protein and protein-RNA interactions involving ZBTB25 facilitated viral RNA transcription and replication. In addition, ZBTB25 suppressed interferon production, further enhancing viral replication. ZBTB25-associated functions required an intact zinc finger domain and posttranslational SUMO-1 modification of ZBTB25. Furthermore, treatment with disulfiram (a zinc ejector) of ZBTB25-overexpressing cells showed significantly reduced IAV production as a result of reduced RNA synthesis. Our findings indicate that IAV usurps ZBTB25 for IAV RNA synthesis and serves as a novel and potential therapeutic antiviral target. IMPORTANCE IAV-induced seasonal influenza causes severe illness and death in high-risk populations. However, IAV has developed resistance to current antiviral drugs due to its high mutation rate. Therefore, development of drugs targeting cellular factors required for IAV replication is an attractive alternative for IAV therapy. Here, we discovered a cellular protein, ZBTB25, that enhances viral RdRp activity by binding to both viral RdRp and viral RNA to stimulate viral RNA synthesis. A unique feature of ZBTB25 in the regulation of viral replication is its dual transcription functions, namely, promoting viral RNA transcription through binding to the U-rich region of vRNA and suppressing cellular interferon production. ZBTB25 contains a zinc finger domain that is required for RNA-inhibitory activity by chelating zinc ions. Disulfiram treatment disrupts the zinc finger functions, effectively repressing IAV replication. Based on our findings, we demonstrate that ZBTB25 regulates IAV RNA transcription and replication and serves as a promising antiviral target for IAV treatment. PMID:28768860

Inverted U-Shaped Dose-Response Curve of the Anxiolytic Effect of Cannabidiol during Public Speaking in Real Life.

PubMed

Zuardi, Antonio W; Rodrigues, Natália P; Silva, Angélica L; Bernardo, Sandra A; Hallak, Jaime E C; Guimarães, Francisco S; Crippa, José A S

2017-01-01

The purpose of this study was to investigate whether the anxiolytic effect of cannabidiol (CBD) in humans follows the same pattern of an inverted U-shaped dose-effect curve observed in many animal studies. Sixty healthy subjects of both sexes aged between 18 and 35 years were randomly assigned to five groups that received placebo, clonazepam (1 mg), and CBD (100, 300, and 900 mg). The subjects were underwent a test of public speaking in a real situation (TPSRS) where each subject had to speak in front of a group formed by the remaining participants. Each subject completed the anxiety and sedation factors of the Visual Analog Mood Scale and had their blood pressure and heart rate recorded. These measures were obtained in five experimental sessions with 12 volunteers each. Each session had four steps at the following times (minutes) after administration of the drug/placebo, as time 0: -5 (baseline), 80 (pre-test), 153 (speech), and 216 (post-speech). Repeated-measures analyses of variance showed that the TPSRS increased the subjective measures of anxiety, heart rate, and blood pressure. Student-Newman-Keuls test comparisons among the groups in each phase showed significant attenuation in anxiety scores relative to the placebo group in the group treated with clonazepam during the speech phase, and in the clonazepam and CBD 300 mg groups in the post-speech phase. Clonazepam was more sedative than CBD 300 and 900 mg and induced a smaller increase in systolic and diastolic blood pressure than CBD 300 mg. The results confirmed that the acute administration of CBD induced anxiolytic effects with a dose-dependent inverted U-shaped curve in healthy subjects, since the subjective anxiety measures were reduced with CBD 300 mg, but not with CBD 100 and 900 mg, in the post-speech phase.

Inverted U-Shaped Dose-Response Curve of the Anxiolytic Effect of Cannabidiol during Public Speaking in Real Life

PubMed Central

Zuardi, Antonio W.; Rodrigues, Natália P.; Silva, Angélica L.; Bernardo, Sandra A.; Hallak, Jaime E. C.; Guimarães, Francisco S.; Crippa, José A. S.

2017-01-01

The purpose of this study was to investigate whether the anxiolytic effect of cannabidiol (CBD) in humans follows the same pattern of an inverted U-shaped dose-effect curve observed in many animal studies. Sixty healthy subjects of both sexes aged between 18 and 35 years were randomly assigned to five groups that received placebo, clonazepam (1 mg), and CBD (100, 300, and 900 mg). The subjects were underwent a test of public speaking in a real situation (TPSRS) where each subject had to speak in front of a group formed by the remaining participants. Each subject completed the anxiety and sedation factors of the Visual Analog Mood Scale and had their blood pressure and heart rate recorded. These measures were obtained in five experimental sessions with 12 volunteers each. Each session had four steps at the following times (minutes) after administration of the drug/placebo, as time 0: -5 (baseline), 80 (pre-test), 153 (speech), and 216 (post-speech). Repeated-measures analyses of variance showed that the TPSRS increased the subjective measures of anxiety, heart rate, and blood pressure. Student-Newman-Keuls test comparisons among the groups in each phase showed significant attenuation in anxiety scores relative to the placebo group in the group treated with clonazepam during the speech phase, and in the clonazepam and CBD 300 mg groups in the post-speech phase. Clonazepam was more sedative than CBD 300 and 900 mg and induced a smaller increase in systolic and diastolic blood pressure than CBD 300 mg. The results confirmed that the acute administration of CBD induced anxiolytic effects with a dose-dependent inverted U-shaped curve in healthy subjects, since the subjective anxiety measures were reduced with CBD 300 mg, but not with CBD 100 and 900 mg, in the post-speech phase. PMID:28553229

Excess apoptosis of mononuclear cells contributes to the depressed cytomegalovirus-specific immunity in HIV-infected patients on HAART

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

Weinberg, Adriana; Jesser, Renee D.; Edelstein, Charles L.

2004-12-05

HIV-infected patients on highly active antiretroviral therapy (HAART) have persistently decreased cytomegalovirus (CMV)-specific proliferative responses [lymphocyte proliferation assay (LPA)] in spite of increases in CD4+ T cell counts. Here we demonstrate an association between apoptosis of unstimulated peripheral blood mononuclear cells (uPBMC) and decreased CMV-LPA. HAART recipients had more apoptosis of uPBMC than controls when measured by caspases 3, 8, and 9 activities and by annexin V binding. Patients with undetectable HIV replication maintained significantly higher apoptosis of CD4+ and CD14+ cells compared to controls. CMV-LPA decreased with higher apoptosis of uPBMC in patients only. This association was independent ofmore » CD4+ cell counts or HIV replication. Furthermore, rescuing PBMC from apoptosis with crmA, but not with TRAIL- or Fas-pathway blocking agents or with other caspase inhibitors, increased CMV-LPA in HAART recipients. This effect was not observed in uninfected controls, further indicating that the down regulatory effect of apoptosis on cell-mediated immunity (CMI) was specifically associated with the HIV-infected status.« less

Complex Dynamic Development of Poliovirus Membranous Replication Complexes

PubMed Central

Nair, Vinod; Hansen, Bryan T.; Hoyt, Forrest H.; Fischer, Elizabeth R.; Ehrenfeld, Ellie

2012-01-01

Replication of all positive-strand RNA viruses is intimately associated with membranes. Here we utilize electron tomography and other methods to investigate the remodeling of membranes in poliovirus-infected cells. We found that the viral replication structures previously described as “vesicles” are in fact convoluted, branching chambers with complex and dynamic morphology. They are likely to originate from cis-Golgi membranes and are represented during the early stages of infection by single-walled connecting and branching tubular compartments. These early viral organelles gradually transform into double-membrane structures by extension of membranous walls and/or collapsing of the luminal cavity of the single-membrane structures. As the double-membrane regions develop, they enclose cytoplasmic material. At this stage, a continuous membranous structure may have double- and single-walled membrane morphology at adjacent cross-sections. In the late stages of the replication cycle, the structures are represented mostly by double-membrane vesicles. Viral replication proteins, double-stranded RNA species, and actively replicating RNA are associated with both double- and single-membrane structures. However, the exponential phase of viral RNA synthesis occurs when single-membrane formations are predominant in the cell. It has been shown previously that replication complexes of some other positive-strand RNA viruses form on membrane invaginations, which result from negative membrane curvature. Our data show that the remodeling of cellular membranes in poliovirus-infected cells produces structures with positive curvature of membranes. Thus, it is likely that there is a fundamental divergence in the requirements for the supporting cellular membrane-shaping machinery among different groups of positive-strand RNA viruses. PMID:22072780

Examining the Shaping of Teachers' Pedagogical Orientation for the Use of Technology

ERIC Educational Resources Information Center

Prestridge, Sarah

2017-01-01

Teachers' current uses of technologies still tend to replicate traditional and/ or administrative practices, with research indicating that the pedagogies required for the effective integration of educational technologies are not yet in evidence amongst the majority of teachers. In order to conceptualise what could be considered effective…

Cytometry of DNA Replication and RNA Synthesis: Historical Perspective and Recent Advances Based on “Click Chemistry”

PubMed Central

Darzynkiewicz, Zbigniew; Traganos, Frank; Zhao, Hong; Halicka, H. Dorota; Li, Jiangwei

2011-01-01

This review covers progress in the development of cytometric methodologies designed to assess DNA replication and RNA synthesis. The early approaches utilizing autoradiography to detect incorporation of 3H- or 14C-labeled thymidine were able to identify the four fundamental phases of the cell cycle G1, S, G2, and M, and by analysis of the fraction of labeled mitosis (FLM), to precisely define the kinetics of cell progression through these phases. Analysis of 3H-uridine incorporation and RNA content provided the means to distinguish quiescent G0 from cycling G1 cells. Subsequent progress in analysis of DNA replication was based on the use of BrdU as a DNA precursor and its detection by the quenching of the fluorescence intensity of DNA-bound fluorochromes such as Hoechst 33358 or acridine orange as measured by flow cytometry. Several variants of this methodology have been designed and used in studies to detect anticancer drug-induced perturbations of cell cycle kinetics. The next phase of method development, which was particularly useful in studies of the cell cycle in vivo, including clinical applications, relied on immunocytochemical detection of incorporated halogenated DNA or RNA precursors. This approach however was hampered by the need for DNA denaturation, which made it difficult to concurrently detect other cell constituents for multiparametric analysis. The recently introduced “click chemistry” approach has no such limitation and is the method of choice for analysis of DNA replication and RNA synthesis. This method is based on the use of 5-ethynyl-2′deoxyuridine (EdU) as a DNA precursor or 5-ethynyluridine (EU) as an RNA precursor and their detection with fluorochrome-tagged azides utilizing a copper (I) catalyzed [3+2] cycloaddition. Several examples are presented that illustrate incorporation of EdU or EU in cells subjected to DNA damage detected as histone H2AX phosphorylation that have been analyzed by flow or laser scanning cytometry. PMID:21425239

A survey of pulse shape options for a revised plastic ablator ignition design

NASA Astrophysics Data System (ADS)

Clark, Daniel; Eder, David; Haan, Steven; Hinkel, Denise; Jones, Ogden; Marinak, Michael; Milovich, Jose; Peterson, Jayson; Robey, Harold; Salmonson, Jay; Smalyuk, Vladimir; Weber, Christopher

2014-10-01

Recent experimental results using the ``high foot'' pulse shape on the National Ignition Facility (NIF) have shown encouraging progress compared to earlier ``low foot'' experiments. These results strongly suggest that controlling ablation front instability growth can dramatically improve implosion performance, even in the presence of persistent, large, low-mode distortions. In parallel, Hydro. Growth Radiography experiments have so far validated the techniques used for modeling ablation front growth in NIF experiments. It is timely then to combine these two results and ask how current ignition pulse shapes could be modified so as to improve implosion performance, namely fuel compressibility, while maintaining the stability properties demonstrated with the high foot. This talk presents a survey of pulse shapes intermediate between the low and high foot extremes in search of a more optimal design. From the database of pulse shapes surveyed, a higher picket version of the original low foot pulse shape shows the most promise for improved compression without loss of stability. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

7 CFR 1755.870 - RUS specification for terminating cables.

Code of Federal Regulations, 2011 CFR

2011-01-01

... microseconds wave shape. (c) The shape of the generated wave shall be determined at a reduced voltage by... by the Director of the Federal Register in accordance with 5 U.S.C. 552(a) and 1 CFR part 51. Copies... references were approved by the Director of the Federal Register in accordance with 5 U.S.C. 552(a) and 1 CFR...

7 CFR 1755.870 - RUS specification for terminating cables.

Code of Federal Regulations, 2010 CFR

2010-01-01

... microseconds wave shape. (c) The shape of the generated wave shall be determined at a reduced voltage by... by the Director of the Federal Register in accordance with 5 U.S.C. 552(a) and 1 CFR part 51. Copies... references were approved by the Director of the Federal Register in accordance with 5 U.S.C. 552(a) and 1 CFR...

Defining the Optimal Selenium Dose for Prostate Cancer Risk Reduction: Insights from the U-Shaped Relationship Between Selenium Status, DNA Damage, and Apoptosis

USDA-ARS?s Scientific Manuscript database

Our work in dogs has revealed a U-shaped dose response between selenium status and prostatic DNA damage that remarkably parallels the relationship between dietary selenium and prostate cancer risk in men, suggesting that more selenium is not necessarily better. Herein, we extend this canine work to ...

Experimental investigation of the effect of variously-shaped ribs on local heat transfer on the outer wall of the turning portion of a U-channel inside solar air heater

NASA Astrophysics Data System (ADS)

Salameh, Tareq; Alami, Abdul Hai; Sunden, Bengt

2016-03-01

In the present work, an experimental investigation of convective heat transfer and pressure drop was carried out for the turning portion of a U-channel where the outer wall was equipped with ribs. The shape of the ribs was varied. The investigation aims to give guidelines for improving the thermo-hydraulic performance of a solar air heater at the turning portion of a U-channel. Both the U-channel and the ribs were made in acrylic material to allow optical access for measuring the surface temperature by using a high-resolution technique based on narrow band thermochromic liquid crystals (TLC R35C5 W) and a CCD camera placed to face the turning portion of the U-channel. The uncertainties were estimated to 5 and 7 % for the Nusselt number and friction factor, respectively. The pressure drop was approximately the same for all the considered shapes of the ribs while the dimpled rib case gave the highest heat transfer coefficient while the grooved rib presented the highest performance index.

Kid cleaves specific mRNAs at UUACU sites to rescue the copy number of plasmid R1

PubMed Central

Pimentel, Belén; Madine, Mark A; de la Cueva-Méndez, Guillermo

2005-01-01

Stability and copy number of extra-chromosomal elements are tightly regulated in prokaryotes and eukaryotes. Toxin Kid and antitoxin Kis are the components of the parD stability system of prokaryotic plasmid R1 and they can also function in eukaryotes. In bacteria, Kid was thought to become active only in cells that lose plasmid R1 and to cleave exclusively host mRNAs at UA(A/C/U) trinucleotide sites to eliminate plasmid-free cells. Instead, we demonstrate here that Kid becomes active in plasmid-containing cells when plasmid copy number decreases, cleaving not only host- but also a specific plasmid-encoded mRNA at the longer and more specific target sequence UUACU. This specific cleavage by Kid inhibits bacterial growth and, at the same time, helps to restore the plasmid copy number. Kid targets a plasmid RNA that encodes a repressor of the synthesis of an R1 replication protein, resulting in increased plasmid DNA replication. This mechanism resembles that employed by some human herpesviruses to regulate viral amplification during infection. PMID:16163387

Gene-gene interaction between COMT and MAOA potentially predicts the intelligence of attention-deficit hyperactivity disorder boys in China.

PubMed

Qian, Qiu-Jin; Yang, Li; Wang, Yu-Feng; Zhang, Hao-Bo; Guan, Li-Li; Chen, Yun; Ji, Ning; Liu, Lu; Faraone, S V

2010-05-01

The catechol-O-methyltransferase (COMT) gene contains a functional polymorphism (Val158Met) affecting the activity of the enzyme, and the monoamine oxidase A (MAOA) gene contains a VNTR polymorphism (MAOA-uVNTR) that affects the transcription of the gene. COMT and MAOA each contribute to the enzymatic degradation of dopamine and noradrenaline. Prefrontal cortical (PFC) function, which plays an important role in individual cognitive abilities, including intelligence, is modulated by dopamine. Since our previous association studies between attention deficit hyperactivity disorder (ADHD) and these two functional polymorphisms consistently showed the low activity alleles were preferentially transmitted to inattentive ADHD boys, the goal of the present study was to test the hypothesis that the interaction between COMT Val158Met and MAOA-uVNTR may affect the intelligence in a clinical sample of Chinese male ADHD subjects (n = 264). We found that the COMT x MAOA interaction significantly predicted full scale (FSIQ) and performance (PIQ) IQ scores (P = 0.039, 0.011); the MAOA-uVNTR significantly predicted FSIQ, PIQ and verbal IQ (VIQ) (P = 0.009, 0.019, 0.038); COMT Val158Met independently had no effect on any of the IQ scores. Only the COMT x MAOA interaction for PIQ remained significant after a Bonferroni correction. Among all combined genotypes, the valval-3R genotype predicted higher intelligence, (average 106.7 +/- 1.6, 95% C.I. 103.7-109.8 for FSIQ), and the valval-4R predicted lower intelligence (average 98.0 +/- 2.3, 95% C.I. 93.5-102.6 for FSIQ). These results suggest that there is an inverted U-shaped relationship between intelligence and dopaminergic activity in our sample. Our finding that gene-gene interaction between COMT and MAOA predicts the intelligence of ADHD boys in China is intriguing but requires replication in other samples.

Induction heating coupler and annealer

NASA Technical Reports Server (NTRS)

Fox, Robert L. (Inventor); Johnson, Samuel D. (Inventor); Copeland, Carl E. (Inventor); Coultrip, Robert H. (Inventor); Phillips, W. Morris (Inventor); Johnston, David F. (Inventor); Swaim, Robert J. (Inventor); Dinkins, James R. (Inventor)

1994-01-01

An induction heating device includes a handle having a hollow interior and two opposite ends, a wrist connected to one end of the handle, a U-shaped pole piece having- two spaced apart ends, a tank circuit including an induction coil wrapped around the pole piece and a capacitor connected to the induction coil, a head connected to the wrist and including a housing for receiving the U-shaped pole piece, the two spaced apart ends of the pole piece extending outwardly beyond the housing, and a power source connected to the tank circuit. When the tank circuit is energized and a susceptor is placed in juxtaposition to the ends of the U-shaped pole piece, the susceptor is heated by induction heating due to a magnetic flux passing between the two ends of the pole piece.

Induction heating coupler

NASA Technical Reports Server (NTRS)

Fox, Robert L. (Inventor); Copeland, Carl E. (Inventor); Swaim, Robert J. (Inventor); Coultrip, Robert H. (Inventor); Johnston, David F. (Inventor); Phillips, W. Morris (Inventor); Johnson, Samuel D. (Inventor); Dinkins, James R. (Inventor); Buckley, John D. (Inventor)

1994-01-01

An induction heating device includes a handle having a hollow interior and two opposite ends, a wrist connected to one end of the handle, a U-shaped pole piece having two spaced apart ends, a tank circuit including an induction coil wrapped around the pole piece and a capacitor connected to the induction coil, a head connected to the wrist and including a housing for receiving the U-shaped pole piece, the two spaced apart ends of the pole piece extending outwardely beyond the housing, and a power source connected to the tank circuit. When the tank circuit is energized and a susceptor is placed in juxtaposition to the ends of the U-shaped pole piece, the susceptor is heated by induction heating due to magnetic flux passing between the two ends of the pole piece.

Development of a new connection for precast concrete walls subjected to cyclic loading

NASA Astrophysics Data System (ADS)

Vaghei, Ramin; Hejazi, Farzad; Taheri, Hafez; Jaafar, Mohd Saleh; Aziz, Farah Nora Aznieta Abdul

2017-01-01

The Industrialized Building System (IBS) was recently introduced to minimize the time and cost of project construction. Accordingly, ensuring the integration of the connection of precast components in IBS structures is an important factor that ensures stability of buildings subjected to dynamic loads from earthquakes, vehicles, and machineries. However, structural engineers still lack knowledge on the proper connection and detailed joints of IBS structure construction. Therefore, this study proposes a special precast concrete wall-to-wall connection system for dynamic loads that resists multidirectional imposed loads and reduces vibration effects (PI2014701723). This system is designed to connect two adjacent precast wall panels by using two steel U-shaped channels (i.e., male and female joints). During casting, each joint is adapted for incorporation into a respective wall panel after considering the following conditions: one side of the steel channel opens into the thickness face of the panel; a U-shaped rubber is implemented between the two channels to dissipate the vibration effect; and bolts and nuts are used to create an extension between the two U-shaped male and female steel channels. The developed finite element model of the precast wall is subjected to cyclic loads to evaluate the performance of the proposed connection during an imposed dynamic load. Connection performance is then compared with conventional connections based on the energy dissipation, stress, deformation, and concrete damage in the plastic range. The proposed precast connection is capable of exceeding the energy absorption of precast walls subjected to dynamic load, thereby improving its resistance behavior in all principal directions.

An analytical solution of groundwater level fluctuation in a U-shaped leaky coastal aquifer

NASA Astrophysics Data System (ADS)

Huang, Fu-Kuo; Chuang, Mo-Hsiung; Wang, Shu-chuan

2017-04-01

Tide-induced groundwater level fluctuations in coastal aquifers have attracted much attention in past years, especially for the issues associated with the impact of the coastline shape, multi-layered leaky aquifer system, and anisotropy of aquifers. In this study, a homogeneous but anisotropic multi-layered leaky aquifer system with U-shaped coastline is considered, where the subsurface system consisting of an unconfined aquifer, a leaky confined aquifer, and a semi-permeable layer between them. The analytical solution of the model obtained herein may be considered as an extended work of two solutions; one was developed by Huang et al. (Huang et al. Tide-induced groundwater level fluctuation in a U-shaped coastal aquifer, J. Hydrol. 2015; 530: 291-305) for two-dimensional interacting tidal waves bounded by three water-land boundaries while the other was by Li and Jiao (Li and Jiao. Tidal groundwater level fluctuations in L-shaped leaky coastal aquifer system, J. Hydrol. 2002; 268: 234-243) for two-dimensional interacting tidal waves of leaky coastal aquifer system adjacent to a cross-shore estuary. In this research, the effects of leakage and storativity of the semi-permeable layer on the amplitude and phase shift of the tidal head fluctuation, and the influence of anisotropy of the aquifer are all examined for the U-shaped leaky coastal aquifer. Some existing solutions in literatures can be regarded as the special cases of the present solution if the aquifer system is isotropic and non-leaky. The results obtained will be beneficial to coastal development and management for water resources.

Not all triads are created equal: further support for the importance of visual and semantic proximity in object identification.

PubMed

Schweizer, Tom A; Dixon, Mike J; Desmarais, Geneviève; Smith, Stephen D

2002-01-01

Identification deficits were investigated in ELM, a temporal lobe stroke patient with category-specific deficits. We replicated previous work done on FS, a patient with category specific deficits as a result of herpes viral encephalitis. ELM was tested using novel, computer generated shapes that were paired with artifact labels. We paired semantically close or disparate labels to shapes and ELM attempted to learn these pairings. Overall, ELM's shape-label confusions were most detrimentally affected when we used labels that referred to objects that were visually and semantically close. However, as with FS, ELM had as many errors when shapes were paired with the labels "donut," "tire," and "washer" as he did when they were paired with visually and semantically close artifact labels. Two explanations are put forth to account for the anomalous performance by both patients on the triad of donut-tire-washer.

A role for the replication proteins PCNA, RF-C, polymerase epsilon and Cdc45 in transcriptional silencing in Saccharomyces cerevisiae.

PubMed Central

Ehrenhofer-Murray, A E; Kamakaka, R T; Rine, J

1999-01-01

Transcriptional silencing in the budding yeast Saccharomyces cerevisiae may be linked to DNA replication and cell cycle progression. In this study, we have surveyed the effect of 41 mutations in genes with a role in replication, the cell cycle, and DNA repair on silencing at HMR. Mutations in PCNA (POL30), RF-C (CDC44), polymerase epsilon (POL2, DPB2, DPB11), and CDC45 were found to restore silencing at a mutant HMR silencer allele that was still a chromosomal origin of replication. Replication timing experiments indicated that the mutant HMR locus was replicated late in S-phase, at the same time as wild-type HMR. Restoration of silencing by PCNA and CDC45 mutations required the origin recognition complex binding site of the HMR-E silencer. Several models for the precise role of these replication proteins in silencing are discussed. PMID:10545450

Silviculture affects composition, growth, and yield in mixed northern conifers: 40-year results from the Penobscot Experimental Forest

Treesearch

Paul E. Sendak; John C. Brissette; Robert M. Frank

2003-01-01

This long-term experiment in Maine, U.S.A., was designed to provide information on the best silvicultural practices for managing stands of mixed northern conifers in northeastern U.S.A. We evaluated growth and yield and changes in species composition, quality, and structure during the first 40 years of the experiment. Replicated treatments include the selection system...

Sharp and round shapes of seen objects have distinct influences on vowel and consonant articulation.

PubMed

Vainio, L; Tiainen, M; Tiippana, K; Rantala, A; Vainio, M

2017-07-01

The shape and size-related sound symbolism phenomena assume that, for example, the vowel [i] and the consonant [t] are associated with sharp-shaped and small-sized objects, whereas [ɑ] and [m] are associated with round and large objects. It has been proposed that these phenomena are mostly based on the involvement of articulatory processes in representing shape and size properties of objects. For example, [i] might be associated with sharp and small objects, because it is produced by a specific front-close shape of articulators. Nevertheless, very little work has examined whether these object properties indeed have impact on speech sound vocalization. In the present study, the participants were presented with a sharp- or round-shaped object in a small or large size. They were required to pronounce one out of two meaningless speech units (e.g., [i] or [ɑ]) according to the size or shape of the object. We investigated how a task-irrelevant object property (e.g., the shape when responses are made according to size) influences reaction times, accuracy, intensity, fundamental frequency, and formant 1 and formant 2 of vocalizations. The size did not influence vocal responses but shape did. Specifically, the vowel [i] and consonant [t] were vocalized relatively rapidly when the object was sharp-shaped, whereas [u] and [m] were vocalized relatively rapidly when the object was round-shaped. The study supports the view that the shape-related sound symbolism phenomena might reflect mapping of the perceived shape with the corresponding articulatory gestures.

Trajectory of Externalizing Child Behaviors in a KEEP Replication

ERIC Educational Resources Information Center

Uretsky, Mathew C.; Lee, Bethany R.; Greeno, Elizabeth J.; Barth, Richard P.

2017-01-01

Objective: The purpose of this study is to examine the correlates of child behavior change over time in a replication of the KEEP intervention. Method: The study sample was drawn from the treatment group of the Maryland replication of KEEP (n=65). Change over time was analyzed using multilevel linear mixed modeling. Results: Parents' use of…

Cyclin-dependent kinase regulates the length of S phase through TICRR/TRESLIN phosphorylation.

PubMed

Sansam, Courtney G; Goins, Duane; Siefert, Joseph C; Clowdus, Emily A; Sansam, Christopher L

2015-03-01

S-phase cyclin-dependent kinases (CDKs) stimulate replication initiation and accelerate progression through the replication timing program, but it is unknown which CDK substrates are responsible for these effects. CDK phosphorylation of the replication factor TICRR (TopBP1-interacting checkpoint and replication regulator)/TRESLIN is required for DNA replication. We show here that phosphorylated TICRR is limiting for S-phase progression. Overexpression of a TICRR mutant with phosphomimetic mutations at two key CDK-phosphorylated residues (TICRR(TESE)) stimulates DNA synthesis and shortens S phase by increasing replication initiation. This effect requires the TICRR region that is necessary for its interaction with MDM two-binding protein. Expression of TICRR(TESE) does not grossly alter the spatial organization of replication forks in the nucleus but does increase replication clusters and the number of replication forks within each cluster. In contrast to CDK hyperactivation, the acceleration of S-phase progression by TICRR(TESE) does not induce DNA damage. These results show that CDK can stimulate initiation and compress the replication timing program by phosphorylating a single protein, suggesting a simple mechanism by which S-phase length is controlled. © 2015 Sansam et al.; Published by Cold Spring Harbor Laboratory Press.

Consequences of Secondary Calibrations on Divergence Time Estimates.

PubMed

Schenk, John J

2016-01-01

Secondary calibrations (calibrations based on the results of previous molecular dating studies) are commonly applied in divergence time analyses in groups that lack fossil data; however, the consequences of applying secondary calibrations in a relaxed-clock approach are not fully understood. I tested whether applying the posterior estimate from a primary study as a prior distribution in a secondary study results in consistent age and uncertainty estimates. I compared age estimates from simulations with 100 randomly replicated secondary trees. On average, the 95% credible intervals of node ages for secondary estimates were significantly younger and narrower than primary estimates. The primary and secondary age estimates were significantly different in 97% of the replicates after Bonferroni corrections. Greater error in magnitude was associated with deeper than shallower nodes, but the opposite was found when standardized by median node age, and a significant positive relationship was determined between the number of tips/age of secondary trees and the total amount of error. When two secondary calibrated nodes were analyzed, estimates remained significantly different, and although the minimum and median estimates were associated with less error, maximum age estimates and credible interval widths had greater error. The shape of the prior also influenced error, in which applying a normal, rather than uniform, prior distribution resulted in greater error. Secondary calibrations, in summary, lead to a false impression of precision and the distribution of age estimates shift away from those that would be inferred by the primary analysis. These results suggest that secondary calibrations should not be applied as the only source of calibration in divergence time analyses that test time-dependent hypotheses until the additional error associated with secondary calibrations is more properly modeled to take into account increased uncertainty in age estimates.

Culture and Probability Judgment Accuracy: The Influence of Holistic Reasoning.

PubMed

Lechuga, Julia; Wiebe, John S

2011-08-01

A well-established phenomenon in the judgment and decision-making tradition is the overconfidence one places in the amount of knowledge that one possesses. Overconfidence or probability judgment accuracy varies not only individually but also across cultures. However, research efforts to explain cross-cultural variations in the overconfidence phenomenon have seldom been made. In Study 1, the authors compared the probability judgment accuracy of U.S. Americans (N = 108) and Mexican participants (N = 100). In Study 2, they experimentally primed culture by randomly assigning English/Spanish bilingual Mexican Americans (N = 195) to response language. Results of both studies replicated the cross-cultural variation of probability judgment accuracy previously observed in other cultural groups. U.S. Americans displayed less overconfidence when compared to Mexicans. These results were then replicated in bilingual participants, when culture was experimentally manipulated with language priming. Holistic reasoning did not account for the cross-cultural variation of overconfidence. Suggestions for future studies are discussed.

Disparities in prevalence, location, and shape characteristics of colorectal neoplasia between South Korean and U.S. patients.

PubMed

Cha, Jae Myung; Kozarek, Richard A; La Selva, Danielle; Gluck, Michael; Ross, Andrew; Chiorean, Michael; Koch, Johannes; Lin, Otto S

2015-12-01

Colon cancer screening is being introduced in many countries, but standard Western screening approaches may not be appropriate for Asian societies if differences in colon cancer epidemiology exist. Comparative analysis of colorectal neoplasia patterns in South Korean and Western subjects has implications for appropriate screening approaches in non-Western societies. The results of concurrent screening colonoscopies performed in average-risk patients 50 to 69 years old in 2 teaching hospitals, Kyung Hee University Hospital (Seoul, South Korea) and Virginia Mason Medical Center (Seattle, Wash), were compared with respect to prevalence, histologic features, anatomic distribution, and shape characteristics of colorectal neoplasia. The U.S. (n = 3460) and South Korean (n = 2193) cohorts were similar with regard to the prevalence of adenomas (28.5% vs 29.8%, respectively, P = .312) and advanced neoplasia (6.4% vs 5.4%, respectively, P = .102), but the proportion of proximal adenomas was greater in the U.S. cohort (62.8% vs 45.9%, P < .001). The prevalence of adenomas and advanced neoplasia was similar in male patients, but there was a greater prevalence of neoplasia (23.5% vs 18.8%, P = .006) and advanced neoplasia (5.1% vs 2.7%, P < .001) in U.S. women than South Korean women. When large (≥10 mm) adenomas were considered, proximal location and nonpolypoid (flat) shape were more common in the U.S. cohort (79.4% vs 37.1%, P = .003 and 43.5% vs 12.3%, P < .001, respectively). The overall prevalence of large flat adenomas in the U.S. cohort was 5 times that of the South Korean cohort (2.6% vs 0.5%, P < .001). Adjustment for sex ratio discrepancies (48.3% men in the U.S. cohort vs 60.8% in the South Korean cohort, P < .001) did not result in any significant changes in the conclusions. Compared with Westerners, South Koreans have a more distal distribution of adenomas and advanced neoplasia and lower prevalence of large flat adenomas. South Korean women have a lower prevalence of colorectal neoplasia than Western women. Such disparities suggest that Western screening strategies cannot be directly adopted by other countries, but need to be customized by society. Copyright © 2015 American Society for Gastrointestinal Endoscopy. Published by Elsevier Inc. All rights reserved.

Repliscan: a tool for classifying replication timing regions.

PubMed

Zynda, Gregory J; Song, Jawon; Concia, Lorenzo; Wear, Emily E; Hanley-Bowdoin, Linda; Thompson, William F; Vaughn, Matthew W

2017-08-07

Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density, and possible results make traditional ChIP-Seq analysis methods inappropriate for use with replication timing. To accurately detect and classify regions of replication across the genome, we present Repliscan. Repliscan robustly normalizes, automatically removes outlying and uninformative data points, and classifies Repli-seq signals into discrete combinations of replication signatures. The quality control steps and self-fitting methods make Repliscan generally applicable and more robust than previous methods that classify regions based on thresholds. Repliscan is simple and effective to use on organisms with different genome sizes. Even with analysis window sizes as small as 1 kilobase, reliable profiles can be generated with as little as 2.4x coverage.

Seabird diving behaviour reveals the functional significance of shelf-sea fronts as foraging hotspots

NASA Astrophysics Data System (ADS)

Cox, S. L.; Miller, P. I.; Embling, C. B.; Scales, K. L.; Bicknell, A. W. J.; Hosegood, P. J.; Morgan, G.; Ingram, S. N.; Votier, S. C.

2016-09-01

Oceanic fronts are key habitats for a diverse range of marine predators, yet how they influence fine-scale foraging behaviour is poorly understood. Here, we investigated the dive behaviour of northern gannets Morus bassanus in relation to shelf-sea fronts. We GPS (global positioning system) tracked 53 breeding birds and examined the relationship between 1901 foraging dives (from time-depth recorders) and thermal fronts (identified via Earth Observation composite front mapping) in the Celtic Sea, Northeast Atlantic. We (i) used a habitat-use availability analysis to determine whether gannets preferentially dived at fronts, and (ii) compared dive characteristics in relation to fronts to investigate the functional significance of these oceanographic features. We found that relationships between gannet dive probabilities and fronts varied by frontal metric and sex. While both sexes were more likely to dive in the presence of seasonally persistent fronts, links to more ephemeral features were less clear. Here, males were positively correlated with distance to front and cross-front gradient strength, with the reverse for females. Both sexes performed two dive strategies: shallow V-shaped plunge dives with little or no active swim phase (92% of dives) and deeper U-shaped dives with an active pursuit phase of at least 3 s (8% of dives). When foraging around fronts, gannets were half as likely to engage in U-shaped dives compared with V-shaped dives, independent of sex. Moreover, V-shaped dive durations were significantly shortened around fronts. These behavioural responses support the assertion that fronts are important foraging habitats for marine predators, and suggest a possible mechanistic link between the two in terms of dive behaviour. This research also emphasizes the importance of cross-disciplinary research when attempting to understand marine ecosystems.

Chromatin Heterogeneity and Distribution of Regulatory Elements in the Late-Replicating Intercalary Heterochromatin Domains of Drosophila melanogaster Chromosomes

PubMed Central

Khoroshko, Varvara A.; Levitsky, Viktor G.; Zykova, Tatyana Yu.; Antonenko, Oksana V.; Belyaeva, Elena S.; Zhimulev, Igor F.

2016-01-01

Late-replicating domains (intercalary heterochromatin) in the Drosophila genome display a number of features suggesting their organization is quite unique. Typically, they are quite large and encompass clusters of functionally unrelated tissue-specific genes. They correspond to the topologically associating domains and conserved microsynteny blocks. Our study aims at exploring further details of molecular organization of intercalary heterochromatin and has uncovered surprising heterogeneity of chromatin composition in these regions. Using the 4HMM model developed in our group earlier, intercalary heterochromatin regions were found to host chromatin fragments with a particular epigenetic profile. Aquamarine chromatin fragments (spanning 0.67% of late-replicating regions) are characterized as a class of sequences that appear heterogeneous in terms of their decompactization. These fragments are enriched with enhancer sequences and binding sites for insulator proteins. They likely mark the chromatin state that is related to the binding of cis-regulatory proteins. Malachite chromatin fragments (11% of late-replicating regions) appear to function as universal transitional regions between two contrasting chromatin states. Namely, they invariably delimit intercalary heterochromatin regions from the adjacent active chromatin of interbands. Malachite fragments also flank aquamarine fragments embedded in the repressed chromatin of late-replicating regions. Significant enrichment of insulator proteins CP190, SU(HW), and MOD2.2 was observed in malachite chromatin. Neither aquamarine nor malachite chromatin types appear to correlate with the positions of highly conserved non-coding elements (HCNE) that are typically replete in intercalary heterochromatin. Malachite chromatin found on the flanks of intercalary heterochromatin regions tends to replicate earlier than the malachite chromatin embedded in intercalary heterochromatin. In other words, there exists a gradient of replication progressing from the flanks of intercalary heterochromatin regions center-wise. The peculiar organization and features of replication in large late-replicating regions are discussed as possible factors shaping the evolutionary stability of intercalary heterochromatin. PMID:27300486

Future of the Particle Replication in Nonwetting Templates (PRINT) Technology

PubMed Central

Xu, Jing; Wong, Dominica H. C.; Byrne, James D.; Chen, Kai; Bowerman, Charles

2014-01-01

Particle replication in nonwetting templates (PRINT) is a continuous, roll-to-roll, high-resolution molding technology which allows the design and synthesis of precisely defined micro- and nanoparticles. This technology adapts the lithographic techniques from the microelectronics industry and marries these with the roll-to-roll processes from the photographic film industry to enable researchers to have unprecedented control over particle size, shape, chemical composition, cargo, modulus, and surface properties. In addition, PRINT is a GMP-compliant (GMP = good manufacturing practice) platform amenable for particle fabrication on a large scale. Herein, we describe some of our most recent work involving the PRINT technology for application in the biomedical and material sciences. PMID:23670869

Aberrant localization of lamin B receptor (LBR) in cellular senescence in human cells

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

Arai, Rumi; En, Atsuki; Ukekawa, Ryo

2016-05-13

5-Bromodeoxyuridine (BrdU), a thymidine analogue, induces cellular senescence in mammalian cells. BrdU induces cellular senescence probably through the regulation of chromatin because BrdU destabilizes or disrupts nucleosome positioning and decondenses heterochromatin. Since heterochromatin is tethered to the nuclear periphery through the interaction with the nuclear envelope proteins, we examined the localization of the several nuclear envelope proteins such as lamins, lamin-interacting proteins, nuclear pore complex proteins, and nuclear transport proteins in senescent cells. We have shown here that lamin B receptor (LBR) showed a change in localization in both BrdU-induced and replicative senescent cells.

Northrop Grumman Corporation's modified U.S. Navy F-5E Shaped Sonic Boom Demonstration (SSBD) aircraft flies over Lake Isabella, Calif., on Aug. 4, 2003

NASA Image and Video Library

2003-08-04

Northrop Grumman Corporation's modified U.S. Navy F-5E Shaped Sonic Boom Demonstration (SSBD) aircraft flies over Lake Isabella, California on Aug. 4, 2003. NASA Dryden provided range, air and ground data-gathering support for the SSBD project, which is part of DARPA's Quiet Supersonic Platform (QSP) program.

"Shaping Communities" as a Christian Practice and Popular Religion: Their Implications for Latina/o Religious Education in the United States

ERIC Educational Resources Information Center

Lee, Michael G.

2008-01-01

This article sets Dorothy Bass' Christian practices movement in critical dialogue with U.S. Latina/o popular religion in order to explore ways that these distinctive sets of practices could enrich one another. Then, it focuses on "shaping communities" as a Christian practice and correlates it with the U.S. Latina/o popular religious…

The State of the Cities, 2000: Megaforces Shaping the Future of the Nation's Cities. Fourth Annual Report.

ERIC Educational Resources Information Center

Department of Housing and Urban Development, Washington, DC.

This report, fourth in a series, recounts the most recent data on indicators of the social and economic vitality of U.S. cities and positions the Administration's urban policy agenda to address challenges confronting cities. This year the report identifies four megaforces that are shaping the future of U.S. cities and presents findings showing…

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

NASA Astrophysics Data System (ADS)

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

2016-08-01

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

Disruption of PCNA-lamins A/C interactions by prelamin A induces DNA replication fork stalling.

PubMed

Cobb, Andrew M; Murray, Thomas V; Warren, Derek T; Liu, Yiwen; Shanahan, Catherine M

2016-09-02

The accumulation of prelamin A is linked to disruption of cellular homeostasis, tissue degeneration and aging. Its expression is implicated in compromised genome stability and increased levels of DNA damage, but to date there is no complete explanation for how prelamin A exerts its toxic effects. As the nuclear lamina is important for DNA replication we wanted to investigate the relationship between prelamin A expression and DNA replication fork stability. In this study we report that the expression of prelamin A in U2OS cells induced both mono-ubiquitination of proliferating cell nuclear antigen (PCNA) and subsequent induction of Pol η, two hallmarks of DNA replication fork stalling. Immunofluorescence microscopy revealed that cells expressing prelamin A presented with high levels of colocalisation between PCNA and γH2AX, indicating collapse of stalled DNA replication forks into DNA double-strand breaks. Subsequent protein-protein interaction assays showed prelamin A interacted with PCNA and that its presence mitigated interactions between PCNA and the mature nuclear lamina. Thus, we propose that the cytotoxicity of prelamin A arises in part, from it actively competing against mature lamin A to bind PCNA and that this destabilises DNA replication to induce fork stalling which in turn contributes to genomic instability.

De novo identification of replication-timing domains in the human genome by deep learning.

PubMed

Liu, Feng; Ren, Chao; Li, Hao; Zhou, Pingkun; Bo, Xiaochen; Shu, Wenjie

2016-03-01

The de novo identification of the initiation and termination zones-regions that replicate earlier or later than their upstream and downstream neighbours, respectively-remains a key challenge in DNA replication. Building on advances in deep learning, we developed a novel hybrid architecture combining a pre-trained, deep neural network and a hidden Markov model (DNN-HMM) for the de novo identification of replication domains using replication timing profiles. Our results demonstrate that DNN-HMM can significantly outperform strong, discriminatively trained Gaussian mixture model-HMM (GMM-HMM) systems and other six reported methods that can be applied to this challenge. We applied our trained DNN-HMM to identify distinct replication domain types, namely the early replication domain (ERD), the down transition zone (DTZ), the late replication domain (LRD) and the up transition zone (UTZ), using newly replicated DNA sequencing (Repli-Seq) data across 15 human cells. A subsequent integrative analysis revealed that these replication domains harbour unique genomic and epigenetic patterns, transcriptional activity and higher-order chromosomal structure. Our findings support the 'replication-domain' model, which states (1) that ERDs and LRDs, connected by UTZs and DTZs, are spatially compartmentalized structural and functional units of higher-order chromosomal structure, (2) that the adjacent DTZ-UTZ pairs form chromatin loops and (3) that intra-interactions within ERDs and LRDs tend to be short-range and long-range, respectively. Our model reveals an important chromatin organizational principle of the human genome and represents a critical step towards understanding the mechanisms regulating replication timing. Our DNN-HMM method and three additional algorithms can be freely accessed at https://github.com/wenjiegroup/DNN-HMM The replication domain regions identified in this study are available in GEO under the accession ID GSE53984. shuwj@bmi.ac.cn or boxc@bmi.ac.cn Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Central safety factor and β N control on NSTX-U via beam power and plasma boundary shape modification, using TRANSP for closed loop simulations

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

Boyer, M. D.; Andre, R.; Gates, D. A.

The high-performance operational goals of NSTX-U will require development of advanced feedback control algorithms, including control of ßN and the safety factor profile. In this work, a novel approach to simultaneously controlling ßN and the value of the safety factor on the magnetic axis, q0, through manipulation of the plasma boundary shape and total beam power, is proposed. Simulations of the proposed scheme show promising results and motivate future experimental implementation and eventual integration into a more complex current profile control scheme planned to include actuation of individual beam powers, density, and loop voltage. As part of this work, amore » flexible framework for closed loop simulations within the high-fidelity code TRANSP was developed. The framework, used here to identify control-design-oriented models and to tune and test the proposed controller, exploits many of the predictive capabilities of TRANSP and provides a means for performing control calculations based on user-supplied data (controller matrices, target waveforms, etc.). The flexible framework should enable high-fidelity testing of a variety of control algorithms, thereby reducing the amount of expensive experimental time needed to implement new control algorithms on NSTX-U and other devices.« less

Central safety factor and βN control on NSTX-U via beam power and plasma boundary shape modification, using TRANSP for closed loop simulations

NASA Astrophysics Data System (ADS)

Boyer, M. D.; Andre, R.; Gates, D. A.; Gerhardt, S.; Goumiri, I. R.; Menard, J.

2015-05-01

The high-performance operational goals of NSTX-U will require development of advanced feedback control algorithms, including control of βN and the safety factor profile. In this work, a novel approach to simultaneously controlling βN and the value of the safety factor on the magnetic axis, q0, through manipulation of the plasma boundary shape and total beam power, is proposed. Simulations of the proposed scheme show promising results and motivate future experimental implementation and eventual integration into a more complex current profile control scheme planned to include actuation of individual beam powers, density, and loop voltage. As part of this work, a flexible framework for closed loop simulations within the high-fidelity code TRANSP was developed. The framework, used here to identify control-design-oriented models and to tune and test the proposed controller, exploits many of the predictive capabilities of TRANSP and provides a means for performing control calculations based on user-supplied data (controller matrices, target waveforms, etc). The flexible framework should enable high-fidelity testing of a variety of control algorithms, thereby reducing the amount of expensive experimental time needed to implement new control algorithms on NSTX-U and other devices.

Analysis of the temporal program of replication initiation in yeast chromosomes.

PubMed

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

1995-01-01

The multiple origins of eukaryotic chromosomes vary in the time of their initiation during S phase. In the chromosomes of Saccharomyces cerevisiae the presence of a functional telomere causes nearby origins to delay initiation until the second half of S phase. The key feature of telomeres that causes the replication delay is the telomeric sequence (C(1-3)A/G(1-3)T) itself and not the proximity of the origin to a DNA end. A second group of late replicating origins has been found at an internal position on chromosome XIV. Four origins, spanning approximately 140 kb, initiate replication in the second half of S phase. At least two of these internal origins maintain their late replication time on circular plasmids. Each of these origins can be separated into two functional elements: those sequences that provide origin function and those that impose late activation. Because the assay for determining replication time is costly and laborious, it has not been possible to analyze in detail these 'late' elements. We report here the development of two new assays for determining replication time. The first exploits the expression of the Escherichia coli dam methylase in yeast and the characteristic period of hemimethylation that transiently follows the passage of a replication fork. The second uses quantitative hybridization to detect two-fold differences in the amount of specific restriction fragments as a function of progress through S phase. The novel aspect of this assay is the creation in vivo of a non-replicating DNA sequence by site-specific pop-out recombination. This non-replicating fragment acts as an internal control for copy number within and between samples. Both of these techniques are rapid and much less costly than the more conventional density transfer experiments that require CsCl gradients to detect replicated DNA. With these techniques it should be possible to identify the sequences responsible for late initiation, to search for other late replicating regions in the genome, and to begin to analyze the effect that altering the temporal program has on chromosome function.

FISH-detected delay in replication timing of mutated FMR1 alleles on both active and inactive X-chromosomes.

PubMed

Yeshaya, J; Shalgi, R; Shohat, M; Avivi, L

1999-01-01

X-chromosome inactivation and the size of the CGG repeat number are assumed to play a role in the clinical, physical, and behavioral phenotype of female carriers of a mutated FMR1 allele. In view of the tight relationship between replication timing and the expression of a given DNA sequence, we have examined the replication timing of FMR1 alleles on active and inactive X-chromosomes in cell samples (lymphocytes or amniocytes) of 25 females: 17 heterozygous for a mutated FMR1 allele with a trinucleotide repeat number varying from 58 to a few hundred, and eight homozygous for a wild-type allele. We have applied two-color fluorescence in situ hybridization (FISH) with FMR1 and X-chromosome alpha-satellite probes to interphase cells of the various genotypes: the alpha-satellite probe was used to distinguish between early replicating (active) and late replicating (inactive) X-chromosomes, and the FMR1 probe revealed the replication pattern of this locus. All samples, except one with a large trinucleotide expansion, showed an early replicating FMR1 allele on the active X-chromosome and a late replicating allele on the inactive X-chromosome. In samples of mutation carriers, both the early and the late alleles showed delayed replication compared with normal alleles, regardless of repeat size. We conclude therefore that: (1) the FMR1 locus is subjected to X-inactivation; (2) mutated FMR1 alleles, regardless of repeat size, replicate later than wild-type alleles on both the active and inactive X-chromosomes; and (3) the delaying effect of the trinucleotide expansion, even with a low repeat size, is superimposed on the delay in replication associated with X-inactivation.

PARP12 suppresses Zika virus infection through PARP-dependent degradation of NS1 and NS3 viral proteins.

PubMed

Li, Lili; Zhao, Hui; Liu, Ping; Li, Chunfeng; Quanquin, Natalie; Ji, Xue; Sun, Nina; Du, Peishuang; Qin, Cheng-Feng; Lu, Ning; Cheng, Genhong

2018-06-19

Zika virus infection stimulates a type I interferon (IFN) response in host cells, which suppresses viral replication. Type I IFNs exert antiviral effects by inducing the expression of hundreds of IFN-stimulated genes (ISGs). To screen for antiviral ISGs that restricted Zika virus replication, we individually knocked out 21 ISGs in A549 lung cancer cells and identified PARP12 as a strong inhibitor of Zika virus replication. Our findings suggest that PARP12 mediated the ADP-ribosylation of NS1 and NS3, nonstructural viral proteins that are involved in viral replication and modulating host defense responses. This modification of NS1 and NS3 triggered their proteasome-mediated degradation. These data increase our understanding of the antiviral activity of PARP12 and suggest a molecular basis for the potential development of therapeutics against Zika virus. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

DNA polymerase η modulates replication fork progression and DNA damage responses in platinum-treated human cells

NASA Astrophysics Data System (ADS)

Sokol, Anna M.; Cruet-Hennequart, Séverine; Pasero, Philippe; Carty, Michael P.

2013-11-01

Human cells lacking DNA polymerase η (polη) are sensitive to platinum-based cancer chemotherapeutic agents. Using DNA combing to directly investigate the role of polη in bypass of platinum-induced DNA lesions in vivo, we demonstrate that nascent DNA strands are up to 39% shorter in human cells lacking polη than in cells expressing polη. This provides the first direct evidence that polη modulates replication fork progression in vivo following cisplatin and carboplatin treatment. Severe replication inhibition in individual platinum-treated polη-deficient cells correlates with enhanced phosphorylation of the RPA2 subunit of replication protein A on serines 4 and 8, as determined using EdU labelling and immunofluorescence, consistent with formation of DNA strand breaks at arrested forks in the absence of polη. Polη-mediated bypass of platinum-induced DNA lesions may therefore represent one mechanism by which cancer cells can tolerate platinum-based chemotherapy.

Monoclonal Antibody Testing for Cancer Metastasis

NASA Technical Reports Server (NTRS)

1993-01-01

Malignant cells are characterized by the ability to invade surrounding normal tissues. Tumor invasion is abetted by proteolytic enzymes that have been correlated with recurrent disease and metastasis. These enzymes are involved in a cascade of proteolytic interactions with other enzymes and inhibitors which allow cancer cells to dissolve surrounding extracellular matrix, thereby enabling the cells to rapidly invade adjacent tissues and migrate to metastatic sites distant from the primary tumor. Among these proteases are the plasminogen activators (PA), collagenase IV, faminase, and in some cases cathepsin D, which together mediate key steps in the invasion process of metastasis. Cells which have the selective advantage for invasion and metastasis are those capable of regulating their proteolytic activity and proliferation. Cells in the process of invasion would be probably down-regulated for proliferation, but subsequent to attachment and adhesion at a distant site, would then be in a proliferative mode, up-regulating DNA replication. Urokinase (uPA) can be present in the tissues in several molecular forms. The inactive proenzyme is a single chain protein (scuPA) that is cleaved at Lys. 158 to form the double chain, high molecular weight active form (HMW-uPA) of 54 kD. A low molecular weight form (LMW-uPA) can also be produced by cleavage of the HMW-U PA at Lys. 135 - Lys. 136 giving a 35 kD active enzyme. Recently, it has been shown that the HMW active form of urokinase, bound to the tumor cell membrane, is responsible for the local lysis of the extracellular matrix, hence the tissue invasion mechanism for metastasis (Andreasen et al, 19861. Receptor- (membrane) bound uPA is twice as efficient (catalytically) as free fluid-phase uPA. Tho unbound uPA and the LMW form is not responsible for most of the local dissolution of extracellular matrix in the immediate vicinity of the metastatic tumor cell. High levels of urokinase (greater than 3.49 ng/mg of total protein) extracted from breast tumor tissues have recently been shown, together with plasminogen activator inhibitor 1 (PAI-1), to be a good prognostic indicator for high risk of recurrence and shorter patient survival times. In this project, we have attempted to develop immunocytochemical methodologies for the clinical assessment of the expression of urokinase plasminogen activator, which has been implicated to be important for initial steps in tumor invasion, and to relate it to cell proliferation and DNA replication at the single-cell level.

Linguistic Relativity in Japanese and English: Is Language the Primary Determinant in Object Classification?

ERIC Educational Resources Information Center

Mazuka, Reiko; Friedman, Ronald S.

2000-01-01

Tested claims by Lucy (1992a, 1992b) that differences between the number marking systems used by Yucatec Maya and English lead speakers of these languages to differentially attend to either the material composition or the shape of objects. Replicated Lucy's critical objects' classification experiments using speakers of English and Japanese.…

Going Underground: A Field Investigation and Lab Activity on Karst Topography and Water Systems

ERIC Educational Resources Information Center

O'Dell, Gary; Gonzalez-Espada, Wilson

2011-01-01

Students learn science best with activities that mirror the way scientists work. This article describes how geologists investigate groundwater flow systems in areas of karst topography--geologic formations shaped by dissolving bedrock--and provides a way for students to replicate this research. Students also use electric current to model water…

How Funding Shapes the Growth of Charter Management Organizations: Is the Tail Wagging the Dog?

ERIC Educational Resources Information Center

Wohlstetter, Priscilla; Smith, Joanna; Farrell, Caitlin; Hentschke, Guilbert C.; Hirman, Jennifer

2011-01-01

The Obama administration's education reform agenda has included an increased emphasis on the role of charter schools generally and a specific emphasis on charter management organizations (CMOs) in replicating best practices and helping "turn around" the lowest performing 5% of the nation's public schools. Through interviews with more than 50…

Sugeno-Fuzzy Expert System Modeling for Quality Prediction of Non-Contact Machining Process

NASA Astrophysics Data System (ADS)

Sivaraos; Khalim, A. Z.; Salleh, M. S.; Sivakumar, D.; Kadirgama, K.

2018-03-01

Modeling can be categorised into four main domains: prediction, optimisation, estimation and calibration. In this paper, the Takagi-Sugeno-Kang (TSK) fuzzy logic method is examined as a prediction modelling method to investigate the taper quality of laser lathing, which seeks to replace traditional lathe machines with 3D laser lathing in order to achieve the desired cylindrical shape of stock materials. Three design parameters were selected: feed rate, cutting speed and depth of cut. A total of twenty-four experiments were conducted with eight sequential runs and replicated three times. The results were found to be 99% of accuracy rate of the TSK fuzzy predictive model, which suggests that the model is a suitable and practical method for non-linear laser lathing process.

A study of an adaptive replication framework for orchestrated composite web services.

PubMed

Mohamed, Marwa F; Elyamany, Hany F; Nassar, Hamed M

2013-01-01

Replication is considered one of the most important techniques to improve the Quality of Services (QoS) of published Web Services. It has achieved impressive success in managing resource sharing and usage in order to moderate the energy consumed in IT environments. For a robust and successful replication process, attention should be paid to suitable time as well as the constraints and capabilities in which the process runs. The replication process is time-consuming since outsourcing some new replicas into other hosts is lengthy. Furthermore, nowadays, most of the business processes that might be implemented over the Web are composed of multiple Web services working together in two main styles: Orchestration and Choreography. Accomplishing a replication over such business processes is another challenge due to the complexity and flexibility involved. In this paper, we present an adaptive replication framework for regular and orchestrated composite Web services. The suggested framework includes a number of components for detecting unexpected and unhappy events that might occur when consuming the original published web services including failure or overloading. It also includes a specific replication controller to manage the replication process and select the best host that would encapsulate a new replica. In addition, it includes a component for predicting the incoming load in order to decrease the time needed for outsourcing new replicas, enhancing the performance greatly. A simulation environment has been created to measure the performance of the suggested framework. The results indicate that adaptive replication with prediction scenario is the best option for enhancing the performance of the replication process in an online business environment.

Recessive resistance to Bean common mosaic virus conferred by the bc-1 and bc-2 genes in common bean (Phaseolus vulgaris L.) affects long distance movement of the virus.

PubMed

Feng, Xue; Orellana, Gardenia; Myers, James; Karasev, Alexander V

2018-04-12

Recessive resistance to Bean common mosaic virus (BCMV) in common bean (Phaseolus vulgaris L.) is governed by four genes that include one strain-nonspecific helper gene bc-u, and three strain-specific genes bc-1, bc-2, and bc-3. The bc-3 gene was identified as an eIF4E translation initiation factor gene mediating resistance through disruption of the interaction between this protein and the VPg protein of the virus. The mode of action of bc-1 and bc-2 in expression of BCMV resistance is unknown, although bc-1 gene was found to affect systemic spread of a related potyvirus, Bean common mosaic necrosis virus. To investigate the possible role of both bc-1 and bc-2 genes in replication, cell-to-cell, and long distance movement of BCMV in P. vulgaris, we tested virus spread of eight BCMV isolates representing pathogroups I, IV, VI, VII, and VIII, in a set of bean differentials expressing different combinations of six resistance alleles including bc-u, bc-1, bc-1 2 , bc-2, bc-2 2 , and bc-3. All studied BCMV isolates were able to replicate and spread in inoculated leaves of bean cultivars harboring bc-u, bc-1, bc-1 2 , bc-2, and bc-2 2 alleles and their combinations, while no BCMV replication was found in inoculated leaves of 'IVT7214' carrying the bc-u, bc-2 and bc-3 genes, except for isolate 1755a capable of overcoming the resistance conferred by bc-2 and bc-3. In contrast, the systemic spread of all BCMV isolates from pathogroups I, IV,VI, VII, and VIII was impaired in common bean cultivars carrying bc-1, bc-1 2 , bc-2, and bc-2 2 alleles. The data suggest that bc-1 and bc-2 recessive resistance genes have no effect on the replication and cell-to-cell movement of BCMV, but affect systemic spread of BCMV in common bean. The BCMV resistance conferred by bc-1 and bc-2 and affecting systemic spread was found only partially effective when these two genes were expressed singly. The efficiency of the restriction of the systemic spread of the virus was greatly enhanced when the alleles of bc-1 and bc-2 genes were combined together.

Abrupt shape transition at neutron number N =60 : B (E 2 ) values in 94,96,98Sr from fast γ -γ timing

NASA Astrophysics Data System (ADS)

Régis, J.-M.; Jolie, J.; Saed-Samii, N.; Warr, N.; Pfeiffer, M.; Blanc, A.; Jentschel, M.; Köster, U.; Mutti, P.; Soldner, T.; Simpson, G. S.; Drouet, F.; Vancraeyenest, A.; de France, G.; Clément, E.; Stezowski, O.; Ur, C. A.; Urban, W.; Regan, P. H.; Podolyák, Zs.; Larijani, C.; Townsley, C.; Carroll, R.; Wilson, E.; Fraile, L. M.; Mach, H.; Paziy, V.; Olaizola, B.; Vedia, V.; Bruce, A. M.; Roberts, O. J.; Smith, J. F.; Scheck, M.; Kröll, T.; Hartig, A.-L.; Ignatov, A.; Ilieva, S.; Lalkovski, S.; Korten, W.; Mǎrginean, N.; Otsuka, T.; Shimizu, N.; Togashi, T.; Tsunoda, Y.

2017-05-01

Lifetimes of low-lying yrast states in neutron-rich 94,96,98Sr have been measured by Germanium-gated γ -γ fast timing with LaBr 3 (Ce ) detectors using the EXILL&FATIMA spectrometer at the Institut Laue-Langevin. Sr fission products were generated using cold-neutron-induced fission of 235U and stopped almost instantaneously within the thick target. The experimental B (E 2 ) values are compared with results of Monte Carlo shell-model calculations made without truncation on the occupation numbers of the orbits spanned by eight proton and eight neutron orbits and show good agreement. Similarly to the Zr isotopes, the abrupt shape transition in the Sr isotopes near neutron number N =60 is identified as being caused by many-proton excitations to its g9 /2 orbit.

Polymerization of non-complementary RNA: systematic symmetric nucleotide exchanges mainly involving uracil produce mitochondrial RNA transcripts coding for cryptic overlapping genes.

PubMed

Seligmann, Hervé

2013-03-01

Usual DNA→RNA transcription exchanges T→U. Assuming different systematic symmetric nucleotide exchanges during translation, some GenBank RNAs match exactly human mitochondrial sequences (exchange rules listed in decreasing transcript frequencies): C↔U, A↔U, A↔U+C↔G (two nucleotide pairs exchanged), G↔U, A↔G, C↔G, none for A↔C, A↔G+C↔U, and A↔C+G↔U. Most unusual transcripts involve exchanging uracil. Independent measures of rates of rare replicational enzymatic DNA nucleotide misinsertions predict frequencies of RNA transcripts systematically exchanging the corresponding misinserted nucleotides. Exchange transcripts self-hybridize less than other gene regions, self-hybridization increases with length, suggesting endoribonuclease-limited elongation. Blast detects stop codon depleted putative protein coding overlapping genes within exchange-transcribed mitochondrial genes. These align with existing GenBank proteins (mainly metazoan origins, prokaryotic and viral origins underrepresented). These GenBank proteins frequently interact with RNA/DNA, are membrane transporters, or are typical of mitochondrial metabolism. Nucleotide exchange transcript frequencies increase with overlapping gene densities and stop densities, indicating finely tuned counterbalancing regulation of expression of systematic symmetric nucleotide exchange-encrypted proteins. Such expression necessitates combined activities of suppressor tRNAs matching stops, and nucleotide exchange transcription. Two independent properties confirm predicted exchanged overlap coding genes: discrepancy of third codon nucleotide contents from replicational deamination gradients, and codon usage according to circular code predictions. Predictions from both properties converge, especially for frequent nucleotide exchange types. Nucleotide exchanging transcription apparently increases coding densities of protein coding genes without lengthening genomes, revealing unsuspected functional DNA coding potential. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Monitoring transients in low inductance circuits

DOEpatents

Guilford, Richard P.; Rosborough, John R.

1987-01-01

A pair of flat cable transmission lines are monitored for transient current spikes by using a probe connected to a current transformer by a pickup loop and monitoring the output of the current transformer. The approach utilizes a U-shaped pickup probe wherein the pair of flat cable transmission lines are received between the legs of the U-shaped probe. The U-shaped probe is preferably formed of a flat coil conductor adhered to one side of a flexible substrate. On the other side of the flexible substrate there is a copper foil shield. The copper foil shield is connected to one end of the flat conductor coil and connected to one leg of the pickup loop which passes through the current transformer. The other end of the flat conductor coil is connected to the other leg of the pickup loop.

Short Sleep Times Predict Obesity in Internal Medicine Clinic Patients

PubMed Central

Buscemi, Dolores; Kumar, Ashwani; Nugent, Rebecca; Nugent, Kenneth

2007-01-01

Study Objectives: Epidemiological studies have demonstrated an association between short sleep times and obesity as defined by body mass index (BMI). We wanted to determine whether this association occurs in patients with chronic medical diagnoses since the number of confounding factors is likely higher in patients than the general population. Methods: Two hundred patients attending internal medicine clinics completed a survey regarding sleep habits, lifestyle characteristics, and medical diagnoses. An independent surveyor collected the information on the questionnaires and reviewed the medical records. Height and weight were measured by clinic personnel. Data were analyzed with multivariate logistic regression. Results: Subjects with short sleep times (< 7 hours) had an increased likelihood of obesity as defined by a BMI ≥ 30 kg/m2 when compared to the reference group of (8, 9] hours (odds ratio 2.93; 95% confidence interval, 1.06–8.09). There was a U-shaped relationship between obesity and sleep time in women but not in men. Young age (18 to 49 years), not smoking, drinking alcohol, hypertension, diabetes, and sleep apnea were also associated with obesity in the overall model. Conclusions: This study demonstrates an association between short sleep times and obesity in undifferentiated patients attending an internal medicine clinic using models adjusting for age, lifestyle characteristics, and some medical diagnoses. The U-shaped relationship in women suggests that sleep patterns may have gender specific associations. These observations provide the background for therapeutic trials in weight loss in patients with established medical problems. Citation: Buscemi D; Kumar A; Nugent R; Nugent K. Short sleep times predict obesity in internal medicine clinic patients. J Clin Sleep Med 2007;3(7):681–688. PMID:18198800

Plant communities, soil carbon, and soil nitrogen properties in a successional gradient of sub-alpine meadows on the eastern Tibetan plateau of China.

PubMed

Li, Wen-Jin; Li, Jin-Hua; Knops, Johannes M H; Wang, Gang; Jia, Ju-Jie; Qin, Yan-Yan

2009-10-01

To assess the recovery trajectory and self-maintenance of restored ecosystems, a successional gradient (1, 3, 5, 15, and 30 years after abandonment) was established in a sub-alpine meadow of the eastern Tibetan Plateau in China. Plant communities and soil carbon and nitrogen properties were investigated and analyzed. Regression analyses were used to assess the models (linear or quadratic) relating measures of species richness, soil carbon and nitrogen properties to fallow time. We found that species richness (S) increased over the first 20 years but decreased thereafter, and aboveground biomass showed a linear increase along the fallow time gradient. The richness of different functional groups (forb, grass and legume) changed little along the fallow time gradient, but their corresponding above ground biomass showed the U-shaped, humped or linear pattern. Soil microbial carbon (MBC) and nitrogen (MBN) in the upper 20 cm showed a U-shaped pattern along the fallow time gradient. However, soil organic carbon (C(org)) and total nitrogen (TN) in the soil at depth greater than 20 cm showed significant patterns of linear decline along the fallow time gradient. The threshold models of species richness reflected best the recovery over the 15 year fallow period. These results indicated that fallow time had a greater influence on development of the plant community than soil processes in abandoned fields in sub-alpine meadow ecosystem. These results also suggested that although the succession process did not significantly increase soil C, an increase in microbial biomass at the latter stage of succession could promote the decomposability of plant litter. Therefore, abandoned fields in sub-alpine meadow ecosystem may have a high resilience and strong rehabilitating capability under natural recovery condition.

Nonisothermal glass molding for the cost-efficient production of precision freeform optics

NASA Astrophysics Data System (ADS)

Vu, Anh-Tuan; Kreilkamp, Holger; Dambon, Olaf; Klocke, Fritz

2016-07-01

Glass molding has become a key replication-based technology to satisfy intensively growing demands of complex precision optics in the today's photonic market. However, the state-of-the-art replicative technologies are still limited, mainly due to their insufficiency to meet the requirements of mass production. This paper introduces a newly developed nonisothermal glass molding in which a complex-shaped optic is produced in a very short process cycle. The innovative molding technology promises a cost-efficient production because of increased mold lifetime, less energy consumption, and high throughput from a fast process chain. At the early stage of the process development, the research focuses on an integration of finite element simulation into the process chain to reduce time and labor-intensive cost. By virtue of numerical modeling, defects including chill ripples and glass sticking in the nonisothermal molding process can be predicted and the consequent effects are avoided. In addition, the influences of process parameters and glass preforms on the surface quality, form accuracy, and residual stress are discussed. A series of experiments was carried out to validate the simulation results. The successful modeling, therefore, provides a systematic strategy for glass preform design, mold compensation, and optimization of the process parameters. In conclusion, the integration of simulation into the entire nonisothermal glass molding process chain will significantly increase the manufacturing efficiency as well as reduce the time-to-market for the mass production of complex precision yet low-cost glass optics.

Rice MEL2, the RNA recognition motif (RRM) protein, binds in vitro to meiosis-expressed genes containing U-rich RNA consensus sequences in the 3'-UTR.

PubMed

Miyazaki, Saori; Sato, Yutaka; Asano, Tomoya; Nagamura, Yoshiaki; Nonomura, Ken-Ichi

2015-10-01

Post-transcriptional gene regulation by RNA recognition motif (RRM) proteins through binding to cis-elements in the 3'-untranslated region (3'-UTR) is widely used in eukaryotes to complete various biological processes. Rice MEIOSIS ARRESTED AT LEPTOTENE2 (MEL2) is the RRM protein that functions in the transition to meiosis in proper timing. The MEL2 RRM preferentially associated with the U-rich RNA consensus, UUAGUU[U/A][U/G][A/U/G]U, dependently on sequences and proportionally to MEL2 protein amounts in vitro. The consensus sequences were located in the putative looped structures of the RNA ligand. A genome-wide survey revealed a tendency of MEL2-binding consensus appearing in 3'-UTR of rice genes. Of 249 genes that conserved the consensus in their 3'-UTR, 13 genes spatiotemporally co-expressed with MEL2 in meiotic flowers, and included several genes whose function was supposed in meiosis; such as Replication protein A and OsMADS3. The proteome analysis revealed that the amounts of small ubiquitin-related modifier-like protein and eukaryotic translation initiation factor3-like protein were dramatically altered in mel2 mutant anthers. Taken together with transcriptome and gene ontology results, we propose that the rice MEL2 is involved in the translational regulation of key meiotic genes on 3'-UTRs to achieve the faithful transition of germ cells to meiosis.

Overview of Initial NSTX-U Experimental Operations

NASA Astrophysics Data System (ADS)

Battaglia, Devon; the NSTX-U Team

2016-10-01

Initial operation of the National Spherical Torus Experiment Upgrade (NSTX-U) has satisfied a number of commissioning milestones, including demonstration of discharges that exceed the field and pulse length of NSTX. ELMy H-mode operation at the no-wall βN limit is obtained with Boronized wall conditioning. Peak H-mode parameters include: Ip = 1 MA, BT0 = 0.63 T, WMHD = 330 kJ, βN = 4, βN/li = 6, κ = 2.3, τE , tot >50 ms. Access to high-performance H-mode scenarios with long MHD-quiescent periods is enabled by the resilient timing of the L-H transition via feedback control of the diverting time and shape, and correction of the dominant n =1 error fields during the Ip ramp. Stationary L-mode discharges have been realized up to 1 MA with 2 s discharges achieved at Ip = 650 kA. The long-pulse L-mode discharges enabled by the new central solenoid supported initial experiments on error field measurements and correction, plasma shape control, controlled discharge ramp-down, L-mode transport and fast ion physics. Increased off-axis current drive and reduction of fast ion instabilities has been observed with the new, more tangential neutral beamline. The initial results support that access to increased field, current and heating at low-aspect-ratio expands the regimes available to develop scenarios, diagnostics and predictive models that inform the design and optimization of future burning plasma tokamak devices, including ITER. Work Supported by U.S. DOE Contract No. DE-AC02-09CH11466.

Experimental evaluation of a new morphological approximation of the articular surfaces of the ankle joint.

PubMed

Belvedere, Claudio; Siegler, Sorin; Ensini, Andrea; Toy, Jason; Caravaggi, Paolo; Namani, Ramya; Giannini, Giulia; Durante, Stefano; Leardini, Alberto

2017-02-28

The mechanical characteristics of the ankle such as its kinematics and load transfer properties are influenced by the geometry of the articulating surfaces. A recent, image-based study found that these surfaces can be approximated by a saddle-shaped, skewed, truncated cone with its apex oriented laterally. The goal of this study was to establish a reliable experimental technique to study the relationship between the geometry of the articular surfaces of the ankle and its mobility and stability characteristics and to use this technique to determine if morphological approximations of the ankle surfaces based on recent discoveries, produce close to normal behavior. The study was performed on ten cadavers. For each specimen, a process based on medical imaging, modeling and 3D printing was used to produce two subject specific artificial implantable sets of the ankle surfaces. One set was a replica of the natural surfaces. The second approximated the ankle surfaces as an original saddle-shaped truncated cone with apex oriented laterally. Testing under cyclic loading conditions was then performed on each specimen following a previously established technique to determine its mobility and stability characteristics under three different conditions: natural surfaces; artificial surfaces replicating the natural surface morphology; and artificial approximation based on the saddle-shaped truncated cone concept. A repeated measure analysis of variance was then used to compare between the three conditions. The results show that (1): the artificial surfaces replicating natural morphology produce close to natural mobility and stability behavior thus establishing the reliability of the technique; and (2): the approximated surfaces based on saddle-shaped truncated cone concept produce mobility and stability behavior close to the ankle with natural surfaces. Copyright © 2017 Elsevier Ltd. All rights reserved.

The United States Army Concept Capability Plan for Combating Weapons of Mass Destruction for the Futer Modular Force 2015-2024

DTIC Science & Technology

2009-03-25

development and pest control, also have deleterious dual use potential. By replicating themselves after introduction into a target population, a small...N national NATO North Atlantic Treaty Organization NEBC network-enabled battle command NMSCWMD National Military Strategy for Combating...within the continental U.S., Alaska, Hawaii, the District of Columbia, the Commonwealth of Puerto Rico, the U.S. Virgin Islands, Guam, American Samoa

A Genome-Wide Association Study of Psoriasis and Psoriatic Arthritis Identifies New Disease Loci

PubMed Central

Liu, Ying; Helms, Cynthia; Liao, Wilson; Zaba, Lisa C.; Duan, Shenghui; Gardner, Jennifer; Wise, Carol; Miner, Andrew; Malloy, M. J.; Pullinger, Clive R.; Kane, John P.; Saccone, Scott; Worthington, Jane; Bruce, Ian; Kwok, Pui–Yan; Menter, Alan; Krueger, James; Barton, Anne; Saccone, Nancy L.; Bowcock, Anne M.

2008-01-01

A genome-wide association study was performed to identify genetic factors involved in susceptibility to psoriasis (PS) and psoriatic arthritis (PSA), inflammatory diseases of the skin and joints in humans. 223 PS cases (including 91 with PSA) were genotyped with 311,398 single nucleotide polymorphisms (SNPs), and results were compared with those from 519 Northern European controls. Replications were performed with an independent cohort of 577 PS cases and 737 controls from the U.S., and 576 PSA patients and 480 controls from the U.K.. Strongest associations were with the class I region of the major histocompatibility complex (MHC). The most highly associated SNP was rs10484554, which lies 34.7 kb upstream from HLA-C (P = 7.8×10−11, GWA scan; P = 1.8×10−30, replication; P = 1.8×10−39, combined; U.K. PSA: P = 6.9×10−11). However, rs2395029 encoding the G2V polymorphism within the class I gene HCP5 (combined P = 2.13×10−26 in U.S. cases) yielded the highest ORs with both PS and PSA (4.1 and 3.2 respectively). This variant is associated with low viral set point following HIV infection and its effect is independent of rs10484554. We replicated the previously reported association with interleukin 23 receptor and interleukin 12B (IL12B) polymorphisms in PS and PSA cohorts (IL23R: rs11209026, U.S. PS, P = 1.4×10−4; U.K. PSA: P = 8.0×10−4; IL12B:rs6887695, U.S. PS, P = 5×10−5 and U.K. PSA, P = 1.3×10−3) and detected an independent association in the IL23R region with a SNP 4 kb upstream from IL12RB2 (P = 0.001). Novel associations replicated in the U.S. PS cohort included the region harboring lipoma HMGIC fusion partner (LHFP) and conserved oligomeric golgi complex component 6 (COG6) genes on chromosome 13q13 (combined P = 2×10−6 for rs7993214; OR = 0.71), the late cornified envelope gene cluster (LCE) from the Epidermal Differentiation Complex (PSORS4) (combined P = 6.2×10−5 for rs6701216; OR 1.45) and a region of LD at 15q21 (combined P = 2.9×10−5 for rs3803369; OR = 1.43). This region is of interest because it harbors ubiquitin-specific protease-8 whose processed pseudogene lies upstream from HLA-C. This region of 15q21 also harbors the gene for SPPL2A (signal peptide peptidase like 2a) which activates tumor necrosis factor alpha by cleavage, triggering the expression of IL12 in human dendritic cells. We also identified a novel PSA (and potentially PS) locus on chromosome 4q27. This region harbors the interleukin 2 (IL2) and interleukin 21 (IL21) genes and was recently shown to be associated with four autoimmune diseases (Celiac disease, Type 1 diabetes, Grave's disease and Rheumatoid Arthritis). PMID:18369459

On the shape of the hospital industry long run average cost curve.

PubMed Central

Finkler, S A

1979-01-01

Empirical studies of the hospital industry have produced conflicting results with respect to the shape of the industry's long run average cost (LRAC) curve. Some of the studies have found a classical U-shaped curve. Others have produced results indicating that the LRAC curve is much closer to being L-shaped. Some theoretical support exists for both sets of findings. While classical theory predicts that the LRAC curve will be U-shaped, Alchian has presented theoretical arguments explaining why such curves would be L-shaped. This paper reconciles the results of these studies. The basis for the reconciliation is recognition of the failure of individual hospitals to produce all their individual product lines at efficient volumes. Such inefficient production is feasible and perhaps common, given the incentive structure which exists under current cost reimbursement systems. The implication of this paper is that large hospitals may have a greater potential for scale economies than has previously been recognized. PMID:528221

On the shape of the hospital industry long run average cost curve.

PubMed

Finkler, S A

1979-01-01

Empirical studies of the hospital industry have produced conflicting results with respect to the shape of the industry's long run average cost (LRAC) curve. Some of the studies have found a classical U-shaped curve. Others have produced results indicating that the LRAC curve is much closer to being L-shaped. Some theoretical support exists for both sets of findings. While classical theory predicts that the LRAC curve will be U-shaped, Alchian has presented theoretical arguments explaining why such curves would be L-shaped. This paper reconciles the results of these studies. The basis for the reconciliation is recognition of the failure of individual hospitals to produce all their individual product lines at efficient volumes. Such inefficient production is feasible and perhaps common, given the incentive structure which exists under current cost reimbursement systems. The implication of this paper is that large hospitals may have a greater potential for scale economies than has previously been recognized.

Relative resistance of HIV-1 founder viruses to control by interferon-alpha

PubMed Central

2013-01-01

Background Following mucosal human immunodeficiency virus type 1 (HIV-1) transmission, type 1 interferons (IFNs) are rapidly induced at sites of initial virus replication in the mucosa and draining lymph nodes. However, the role played by IFN-stimulated antiviral activity in restricting HIV-1 replication during the initial stages of infection is not clear. We hypothesized that if type 1 IFNs exert selective pressure on HIV-1 replication in the earliest stages of infection, the founder viruses that succeed in establishing systemic infection would be more IFN-resistant than viruses replicating during chronic infection, when type 1 IFNs are produced at much lower levels. To address this hypothesis, the relative resistance of virus isolates derived from HIV-1-infected individuals during acute and chronic infection to control by type 1 IFNs was analysed. Results The replication of plasma virus isolates generated from subjects acutely infected with HIV-1 and molecularly cloned founder HIV-1 strains could be reduced but not fully suppressed by type 1 IFNs in vitro. The mean IC50 value for IFNα2 (22 U/ml) was lower than that for IFNβ (346 U/ml), although at maximally-inhibitory concentrations both IFN subtypes inhibited virus replication to similar extents. Individual virus isolates exhibited differential susceptibility to inhibition by IFNα2 and IFNβ, likely reflecting variation in resistance to differentially up-regulated IFN-stimulated genes. Virus isolates from subjects acutely infected with HIV-1 were significantly more resistant to in vitro control by IFNα than virus isolates generated from the same individuals during chronic, asymptomatic infection. Viral IFN resistance declined rapidly after the acute phase of infection: in five subjects, viruses derived from six-month consensus molecular clones were significantly more sensitive to the antiviral effects of IFNs than the corresponding founder viruses. Conclusions The establishment of systemic HIV-1 infection by relatively IFNα-resistant founder viruses lends strong support to the hypothesis that IFNα plays an important role in the control of HIV-1 replication during the earliest stages of infection, prior to systemic viral spread. These findings suggest that it may be possible to harness the antiviral activity of type 1 IFNs in prophylactic and potentially also therapeutic strategies to combat HIV-1 infection. PMID:24299076

Northrop Grumman Corporation's modified U.S. Navy F-5E Shaped Sonic Boom Demonstration (SSBD) aircraft flies over the company's Palmdale, Calif. facilities on Aug. 2, 2003

NASA Image and Video Library

2003-08-02

Northrop Grumman Corporation's modified U.S. Navy F-5E Shaped Sonic Boom Demonstration (SSBD) aircraft flies over the company's Palmdale, California facilities on Aug. 2, 2003. NASA Dryden provided range, air and ground data-gathering support for the SSBD project, which is part of DARPA's Quiet Supersonic Platform (QSP) program.

Immunogenic HSV-mediated oncolysis shapes the antitumor immune response and contributes to therapeutic efficacy.

PubMed

Workenhe, Samuel T; Simmons, Graydon; Pol, Jonathan G; Lichty, Brian D; Halford, William P; Mossman, Karen L

2014-01-01

Within the oncolytic virus field, the extent of virus replication that is essential for immune stimulation to control tumor growth remains unresolved. Using infected cell protein 0 (ICP0)-defective oncolytic Herpes simplex virus type 1 (HSV-1) and HSV-2 viruses (dICP0 and dNLS) that show differences in their in vitro replication and cytotoxicity, we investigated the inherent features of oncolytic HSV viruses that are required for potent antitumor activity. In vitro, the HSV-2 vectors showed rapid cytotoxicity despite lower viral burst sizes compared to HSV-1 vectors. In vivo, although both of the dICP0 vectors initially replicated to a similar level, HSV-1 dICP0 was rapidly cleared from the tumors. In spite of this rapid clearance, HSV-1 dICP0 treatment conferred significant survival benefit. HSV-1 dICP0-treated tumors showed significantly higher levels of danger-associated molecular patterns that correlated with higher numbers of antigen-presenting cells within the tumor and increased antigen-specific CD8+ T-cell levels in the peripheral blood. This study suggests that, at least in the context of oncolytic HSV, the initial stages of immunogenic virus replication leading to activation of antitumor immunity are more important than persistence of a replicating virus within the tumor. This knowledge provides important insight for the design of therapeutically successful oncolytic viruses.

Recent human evolution has shaped geographical differences in susceptibility to disease

PubMed Central

2011-01-01

Background Searching for associations between genetic variants and complex diseases has been a very active area of research for over two decades. More than 51,000 potential associations have been studied and published, a figure that keeps increasing, especially with the recent explosion of array-based Genome-Wide Association Studies. Even if the number of true associations described so far is high, many of the putative risk variants detected so far have failed to be consistently replicated and are widely considered false positives. Here, we focus on the world-wide patterns of replicability of published association studies. Results We report three main findings. First, contrary to previous results, genes associated to complex diseases present lower degrees of genetic differentiation among human populations than average genome-wide levels. Second, also contrary to previous results, the differences in replicability of disease associated-loci between Europeans and East Asians are highly correlated with genetic differentiation between these populations. Finally, highly replicated genes present increased levels of high-frequency derived alleles in European and Asian populations when compared to African populations. Conclusions Our findings highlight the heterogeneous nature of the genetic etiology of complex disease, confirm the importance of the recent evolutionary history of our species in current patterns of disease susceptibility and could cast doubts on the status as false positives of some associations that have failed to replicate across populations. PMID:21261943

The U-shaped association of body mass index with mortality: Influence of the traits height, intelligence, and education.

PubMed

Jørgensen, Terese Sara Høj; Osler, Merete; Ängquist, Lars Henrik; Zimmermann, Esther; Christensen, Gunhild Tidemann; Sørensen, Thorkild I A

2016-10-01

The U-shaped association between body mass index (BMI) and mortality may depend on other traits with permanent health effects. Whether the association between BMI and mortality depends on levels of health-related traits known to be inversely associated with mortality throughout adult life such as height, intelligence, and education was investigated. The study was based on a cohort of young men with data on weight, height, intelligence test score, and education from the Danish Conscription Database. In total, 346,500 men born 1939 to 1959 were followed until December 2013. The association between BMI and mortality was analyzed using Cox-regression models including interactions between BMI and height, intelligence, and education, respectively. BMI and mortality showed the U-shaped association from the start of the follow-up period, and it persisted through the subsequent 56 years. As expected, the mortality was inversely associated with height, intelligence, and education, but the U shape of the association between BMI and mortality was unaffected by the levels of these traits except at higher BMI values, where the slopes were steeper for men with higher levels of height, intelligence, and education. High and low BMI was associated with higher mortality throughout life regardless of the levels of height, intelligence, and education. © 2016 The Obesity Society.

Effect of zinc bacitracin and phytase on growth performance, nutrient digestibility, carcass and meat traits of broilers.

PubMed

Attia, Y A; Bovera, F; Abd El-Hamid, A E; Tag El-Din, A E; Al-Harthi, M A; El-Shafy, A S

2016-06-01

A total of 336 one-day-old Hubbard broiler chickens were randomly distributed among 8 groups, each containing six replicates (7 chickens/replicate). From 1 to 40 days of age, the groups fed the same starter, grower and finisher diets. The control group was unsupplemented; zinc bacitracin (ZnB) group received the antibiotic at 0.5 g/kg; fungal phytase (FP) groups received 250, 500 and 1000 U/kg diet of Aspergillus niger phytase (FP_250, FP_500 and FP_1000 groups), respectively; bacterial phyatse (BP) groups received 250, 500 and 1000 U/kg diet of Escherichia coli phytase (BP_250EP, BP_500EP and BP_1000EP groups) respectively. Considering the whole experimental period, body weight gain was unaffected by ZnB and different concentrations of bacterial and fungal phytase; however, the feed conversion ratio of the group fed a diet supplemented with 500 U of BP was better (p < 0.01) than those fed with a diet supplemented with 500 U of FP. BP_250 group had a higher (p < 0.05) apparent digestibility of ether extract compared to FP_250 group. In conclusion, bacterial phytase at 500 U may enhance performance of broiler chickens fed during days 1-40 of age and yield similar growth performance and economic efficiency to those of eB-supplemented groups. Journal of Animal Physiology and Animal Nutrition © 2015 Blackwell Verlag GmbH.

Spatio-temporal re-organization of replication foci accompanies replication domain consolidation during human pluripotent stem cell lineage specification

PubMed Central

Wilson, Korey A.; Elefanty, Andrew G.; Stanley, Edouard G.; Gilbert, David M.

2016-01-01

ABSTRACT Lineage specification of both mouse and human pluripotent stem cells (PSCs) is accompanied by spatial consolidation of chromosome domains and temporal consolidation of their replication timing. Replication timing and chromatin organization are both established during G1 phase at the timing decision point (TDP). Here, we have developed live cell imaging tools to track spatio-temporal replication domain consolidation during differentiation. First, we demonstrate that the fluorescence ubiquitination cell cycle indicator (Fucci) system is incapable of demarcating G1/S or G2/M cell cycle transitions. Instead, we employ a combination of fluorescent PCNA to monitor S phase progression, cytokinesis to demarcate mitosis, and fluorescent nucleotides to label early and late replication foci and track their 3D organization into sub-nuclear chromatin compartments throughout all cell cycle transitions. We find that, as human PSCs differentiate, the length of S phase devoted to replication of spatially clustered replication foci increases, coincident with global compartmentalization of domains into temporally clustered blocks of chromatin. Importantly, re-localization and anchorage of domains was completed prior to the onset of S phase, even in the context of an abbreviated PSC G1 phase. This approach can also be employed to investigate cell fate transitions in single PSCs, which could be seen to differentiate preferentially from G1 phase. Together, our results establish real-time, live-cell imaging methods for tracking cell cycle transitions during human PSC differentiation that can be applied to study chromosome domain consolidation and other aspects of lineage specification. PMID:27433885

Surface roughness measurements

NASA Technical Reports Server (NTRS)

Howard, Thomas G.

1994-01-01

The Optics Division is currently in the research phase of producing grazing-incidence mirrors to be used in x-ray detector applications. The traditional method of construction involves labor-intensive glass grinding. This also culminates in a relatively heavy mirror. For lower resolution applications, the mirrors may be of a replicated design which involves milling a mandrel as a negative of the final shape and electroplating the cylindrical mirror onto it. The mirror is then separated from the mandrel by cooling. The mandrel will shrink more than the 'shell' (mirror) allowing it to be pulled from the mandrel. Ulmer (2) describes this technique and its variations in more detail. To date, several mirrors have been tested at MSFC by the Optical Fabrication Branch by focusing x-ray energy onto a detector with limited success. Little is known about the surface roughness of the actual mirror. Hence, the attempt to gather data on these surfaces. The test involves profiling the surface of a sample, replicating the surface as described above, and then profiling the replicated surface.

Rates of spontaneous mutation.

PubMed Central

Drake, J W; Charlesworth, B; Charlesworth, D; Crow, J F

1998-01-01

Rates of spontaneous mutation per genome as measured in the laboratory are remarkably similar within broad groups of organisms but differ strikingly among groups. Mutation rates in RNA viruses, whose genomes contain ca. 10(4) bases, are roughly 1 per genome per replication for lytic viruses and roughly 0.1 per genome per replication for retroviruses and a retrotransposon. Mutation rates in microbes with DNA-based chromosomes are close to 1/300 per genome per replication; in this group, therefore, rates per base pair vary inversely and hugely as genome sizes vary from 6 x 10(3) to 4 x 10(7) bases or base pairs. Mutation rates in higher eukaryotes are roughly 0.1-100 per genome per sexual generation but are currently indistinguishable from 1/300 per cell division per effective genome (which excludes the fraction of the genome in which most mutations are neutral). It is now possible to specify some of the evolutionary forces that shape these diverse mutation rates. PMID:9560386

A “dry and wet hybrid” lithography technique for multilevel replication templates: Applications to microfluidic neuron culture and two-phase global mixing

PubMed Central

Paul, Debjani; Saias, Laure; Pedinotti, Jean-Cedric; Chabert, Max; Magnifico, Sebastien; Pallandre, Antoine; De Lambert, Bertrand; Houdayer, Claude; Brugg, Bernard; Peyrin, Jean-Michel; Viovy, Jean-Louis

2011-01-01

A broad range of microfluidic applications, ranging from cell culture to protein crystallization, requires multilevel devices with different heights and feature sizes (from micrometers to millimeters). While state-of-the-art direct-writing techniques have been developed for creating complex three-dimensional shapes, replication molding from a multilevel template is still the preferred method for fast prototyping of microfluidic devices in the laboratory. Here, we report on a “dry and wet hybrid” technique to fabricate multilevel replication molds by combining SU-8 lithography with a dry film resist (Ordyl). We show that the two lithography protocols are chemically compatible with each other. Finally, we demonstrate the hybrid technique in two different microfluidic applications: (1) a neuron culture device with compartmentalization of different elements of a neuron and (2) a two-phase (gas-liquid) global micromixer for fast mixing of a small amount of a viscous liquid into a larger volume of a less viscous liquid. PMID:21559239

SARS-CoV replicates in primary human alveolar type II cell cultures but not in type I-like cells

PubMed Central

Mossel, Eric C.; Wang, Jieru; Jeffers, Scott; Edeen, Karen E.; Wang, Shuanglin; Cosgrove, Gregory P.; Funk, C. Joel; Manzer, Rizwan; Miura, Tanya A.; Pearson, Leonard D.; Holmes, Kathryn V.; Mason, Robert J.

2008-01-01

Severe acute respiratory syndrome (SARS) is a disease characterized by diffuse alveolar damage. We isolated alveolar type II cells and maintained them in a highly differentiated state. Type II cell cultures supported SARS-CoV replication as evidenced by RT-PCR detection of viral subgenomic RNA and an increase in virus titer. Virus titers were maximal by 24 hours and peaked at approximately 105 pfu/mL. Two cell types within the cultures were infected. One cell type was type II cells, which were positive for SP-A, SP-C, cytokeratin, a type II cell-specific monoclonal antibody, and Ep-CAM. The other cell type was composed of spindle-shaped cells that were positive for vimentin and collagen III and likely fibroblasts. Viral replication was not detected in type I-like cells or macrophages. Hence, differentiated adult human alveolar type II cells were infectible but alveolar type I-like cells and alveolar macrophages did not support productive infection. PMID:18022664

In Search of the Perfect Phenotype: An Analysis of Linkage and Association Studies of Reading and Reading-Related Processes

PubMed Central

Skiba, Thomas; Landi, Nicole; Wagner, Richard

2011-01-01

Reading ability and specific reading disability (SRD) are complex traits involving several cognitive processes and are shaped by a complex interplay of genetic and environmental forces. Linkage studies of these traits have identified several susceptibility loci. Association studies have gone further in detecting candidate genes that might underlie these signals. These results have been obtained in samples of mainly European ancestry, which vary in their languages, inclusion criteria, and phenotype assessments. Such phenotypic heterogeneity across samples makes understanding the relationship between reading (dis)ability and reading-related processes and the genetic factors difficult; in addition, it may negatively influence attempts at replication. In moving forward, the identification of preferable phenotypes for future sample collection may improve the replicability of findings. This review of all published linkage and association results from the past 15 years was conducted to determine if certain phenotypes produce more replicable and consistent results than others. PMID:21243420

Detection of flow limitation in obstructive sleep apnea with an artificial neural network.

PubMed

Norman, Robert G; Rapoport, David M; Ayappa, Indu

2007-09-01

During sleep, the development of a plateau on the inspiratory airflow/time contour provides a non-invasive indicator of airway collapsibility. Humans recognize this abnormal contour easily, and this study replicates this with an artificial neural network (ANN) using a normalized shape. Five 10 min segments were selected from each of 18 sleep records (respiratory airflow measured with a nasal cannula) with varying degrees of sleep disordered breathing. Each breath was visually scored for shape, and breaths split randomly into a training and test set. Equally spaced, peak amplitude normalized flow values (representing breath shape) formed the only input to a back propagation ANN. Following training, breath-by-breath agreement of the ANN with the manual classification was tabulated for the training and test sets separately. Agreement of the ANN was 89% in the training set and 70.6% in the test set. When the categories of 'probably normal' and 'normal', and 'probably flow limited' and 'flow limited' were combined, the agreement increased to 92.7% and 89.4% respectively, similar to the intra- and inter-rater agreements obtained by a visual classification of these breaths. On a naive dataset, the agreement of the ANN to visual classification was 57.7% overall and 82.4% when the categories were collapsed. A neural network based only on the shape of inspiratory airflow succeeded in classifying breaths as to the presence/absence of flow limitation. This approach could be used to provide a standardized, reproducible and automated means of detecting elevated upper airway resistance.

All you need is shape: Predicting shear banding in sand with LS-DEM

NASA Astrophysics Data System (ADS)

Kawamoto, Reid; Andò, Edward; Viggiani, Gioacchino; Andrade, José E.

2018-02-01

This paper presents discrete element method (DEM) simulations with experimental comparisons at multiple length scales-underscoring the crucial role of particle shape. The simulations build on technological advances in the DEM furnished by level sets (LS-DEM), which enable the mathematical representation of the surface of arbitrarily-shaped particles such as grains of sand. We show that this ability to model shape enables unprecedented capture of the mechanics of granular materials across scales ranging from macroscopic behavior to local behavior to particle behavior. Specifically, the model is able to predict the onset and evolution of shear banding in sands, replicating the most advanced high-fidelity experiments in triaxial compression equipped with sequential X-ray tomography imaging. We present comparisons of the model and experiment at an unprecedented level of quantitative agreement-building a one-to-one model where every particle in the more than 53,000-particle array has its own avatar or numerical twin. Furthermore, the boundary conditions of the experiment are faithfully captured by modeling the membrane effect as well as the platen displacement and tilting. The results show a computational tool that can give insight into the physics and mechanics of granular materials undergoing shear deformation and failure, with computational times comparable to those of the experiment. One quantitative measure that is extracted from the LS-DEM simulations that is currently not available experimentally is the evolution of three dimensional force chains inside and outside of the shear band. We show that the rotations on the force chains are correlated to the rotations in stress principal directions.

Segment-specific expression of alkaline phosphatase in the Tubifex embryo requires DNA replication and mRNA synthesis.

PubMed

Kitamura, Kaoru; Shimizu, Takashi

2002-04-15

During embryogenesis of the oligochaete annelid Tubifex, segments VII and VIII specifically express mesodermal alkaline phosphatase (ALP) activity in the ventrolateral region. In this study, using specific inhibitors, we examined whether this segment-specific expression of ALP activity depends on DNA replication and RNA transcription. BrdU-incorporation experiments showed that presumptive ALP-expressing cells undergo the last round of DNA replication at 12-24 hr prior to emergence of ALP activity. When this DNA replication was inhibited by aphidicolin, ALP development was completely abrogated in the ventrolateral mesoderm. Similar inhibition of ALP development was also observed in alpha-amanitin-injected embryos. While injection of alpha-amanitin at 24 hr prior to the emergence of ALP activity exerted inhibitory effects on ALP development, injection at 14 hr was no longer effective. In contrast, ALP activity developed normally in cytochalasin-D-treated embryos in which cytokinesis was prevented from occurring for 36 hs prior to appearance of ALP activity. These results suggest that the segment-specific development of ALP activity in the Tubifex embryo depends on DNA replication and mRNA transcription, both of which occur long before the emergence of ALP activity. Copyright 2002 Wiley-Liss, Inc.

Uracil recognition by replicative DNA polymerases is limited to the archaea, not occurring with bacteria and eukarya.

PubMed

Wardle, Josephine; Burgers, Peter M J; Cann, Isaac K O; Darley, Kate; Heslop, Pauline; Johansson, Erik; Lin, Li-Jung; McGlynn, Peter; Sanvoisin, Jonathan; Stith, Carrie M; Connolly, Bernard A

2008-02-01

Family B DNA polymerases from archaea such as Pyrococcus furiosus, which live at temperatures approximately 100 degrees C, specifically recognize uracil in DNA templates and stall replication in response to this base. Here it is demonstrated that interaction with uracil is not restricted to hyperthermophilic archaea and that the polymerase from mesophilic Methanosarcina acetivorans shows identical behaviour. The family B DNA polymerases replicate the genomes of archaea, one of the three fundamental domains of life. This publication further shows that the DNA replicating polymerases from the other two domains, bacteria (polymerase III) and eukaryotes (polymerases delta and epsilon for nuclear DNA and polymerase gamma for mitochondrial) are also unable to recognize uracil. Uracil occurs in DNA as a result of deamination of cytosine, either in G:C base-pairs or, more rapidly, in single stranded regions produced, for example, during replication. The resulting G:U mis-pairs/single stranded uracils are promutagenic and, unless repaired, give rise to G:C to A:T transitions in 50% of the progeny. The confinement of uracil recognition to polymerases of the archaeal domain is discussed in terms of the DNA repair pathways necessary for the elimination of uracil.

An analysis of metropolitan land-use by machine processing of earth resources technology satellite data

NASA Technical Reports Server (NTRS)

Mausel, P. W.; Todd, W. J.; Baumgardner, M. F.

1976-01-01

A successful application of state-of-the-art remote sensing technology in classifying an urban area into its broad land use classes is reported. This research proves that numerous urban features are amenable to classification using ERTS multispectral data automatically processed by computer. Furthermore, such automatic data processing (ADP) techniques permit areal analysis on an unprecedented scale with a minimum expenditure of time. Also, classification results obtained using ADP procedures are consistent, comparable, and replicable. The results of classification are compared with the proposed U. S. G. S. land use classification system in order to determine the level of classification that is feasible to obtain through ERTS analysis of metropolitan areas.