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Sample records for exploring temporal transcription

  1. Bayesian experts in exploring reaction kinetics of transcription circuits.

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    Yoshida, Ryo; Saito, Masaya M; Nagao, Hiromichi; Higuchi, Tomoyuki

    2010-09-15

    Biochemical reactions in cells are made of several types of biological circuits. In current systems biology, making differential equation (DE) models simulatable in silico has been an appealing, general approach to uncover a complex world of biochemical reaction dynamics. Despite of a need for simulation-aided studies, our research field has yet provided no clear answers: how to specify kinetic values in models that are difficult to measure from experimental/theoretical analyses on biochemical kinetics. We present a novel non-parametric Bayesian approach to this problem. The key idea lies in the development of a Dirichlet process (DP) prior distribution, called Bayesian experts, which reflects substantive knowledge on reaction mechanisms inherent in given models and experimentally observable kinetic evidences to the subsequent parameter search. The DP prior identifies significant local regions of unknown parameter space before proceeding to the posterior analyses. This article reports that a Bayesian expert-inducing stochastic search can effectively explore unknown parameters of in silico transcription circuits such that solutions of DEs reproduce transcriptomic time course profiles. A sample source code is available at the URL http://daweb.ism.ac.jp/~yoshidar/lisdas/.

  2. Fluid consumption and taste novelty determines transcription temporal dynamics in the gustatory cortex.

    Science.gov (United States)

    Inberg, Sharon; Jacob, Eyal; Elkobi, Alina; Edry, Efrat; Rappaport, Akiva; Simpson, T Ian; Armstrong, J Douglas; Shomron, Noam; Pasmanik-Chor, Metsada; Rosenblum, Kobi

    2016-02-09

    Novel taste memories, critical for animal survival, are consolidated to form long term memories which are dependent on translation regulation in the gustatory cortex (GC) hours following acquisition. However, the role of transcription regulation in the process is unknown. Here, we report that transcription in the GC is necessary for taste learning in rats, and that drinking and its consequences, as well as the novel taste experience, affect transcription in the GC during taste memory consolidation. We show differential effects of learning on temporal dynamics in set of genes in the GC, including Arc/Arg3.1, known to regulate the homeostasis of excitatory synapses. We demonstrate that in taste learning, transcription programs were activated following the physiological responses (i.e., fluid consumption following a water restriction regime, reward, arousal of the animal, etc.) and the specific information about a given taste (i.e., taste novelty). Moreover, the cortical differential prolonged kinetics of mRNA following novel versus familiar taste learning may represent additional novelty related molecular response, where not only the total amount, but also the temporal dynamics of transcription is modulated by sensory experience of novel information.

  3. Temporal dynamics and transcriptional control using single-cell gene expression analysis.

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    Kouno, Tsukasa; de Hoon, Michiel; Mar, Jessica C; Tomaru, Yasuhiro; Kawano, Mitsuoki; Carninci, Piero; Suzuki, Harukazu; Hayashizaki, Yoshihide; Shin, Jay W

    2013-01-01

    Changes in environmental conditions lead to expression variation that manifest at the level of gene regulatory networks. Despite a strong understanding of the role noise plays in synthetic biological systems, it remains unclear how propagation of expression heterogeneity in an endogenous regulatory network is distributed and utilized by cells transitioning through a key developmental event. Here we investigate the temporal dynamics of a single-cell transcriptional network of 45 transcription factors in THP-1 human myeloid monocytic leukemia cells undergoing differentiation to macrophages. We systematically measure temporal regulation of expression and variation by profiling 120 single cells at eight distinct time points, and infer highly controlled regulatory modules through which signaling operates with stochastic effects. This reveals dynamic and specific rewiring as a cellular strategy for differentiation. The integration of both positive and negative co-expression networks further identifies the proto-oncogene MYB as a network hinge to modulate both the pro- and anti-differentiation pathways. Compared to averaged cell populations, temporal single-cell expression profiling provides a much more powerful technique to probe for mechanistic insights underlying cellular differentiation. We believe that our approach will form the basis of novel strategies to study the regulation of transcription at a single-cell level.

  4. Exploring Temporal Patterns of Stress in Adolescent Girls with Headache.

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    Björling, Elin A; Singh, Narayan

    2017-02-01

    As part of a larger study on perceived stress and headaches in 2009, momentary perceived stress, head pain levels and stress-related symptom data were collected. This paper explores a temporal analysis of the patterns of stress, as well as an analysis of momentary and retrospective stress-related symptoms compared by level of headache activity. Adolescent girls (N = 31) ages 14-18 were randomly cued by electronic diaries 7 times per day over a 21-day period responding to momentary questions about level of head pain, perceived stress and stress-related symptoms. Multivariate general linear modelling was used to determine significant differences among headache groups in relation to temporal patterns of stress. Significant headache group differences were found on retrospective and momentary stress-related symptom measures. A total of 2841 diary responses captured stress levels, head pain and related symptoms. The chronic headache (CH) group reported the highest levels of hourly and daily stress, followed by the moderate headache (MH) and low headache (LH) groups. Patterns of stress for the three headache groups were statistically distinct, illustrating increased stress in girls with more frequent head pain. This evidence suggests that because of increased stress, girls with recurrent head pain are likely a vulnerable population who may benefit from stress-reducing interventions. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  5. Exploring cellular memory molecules marking competent and active transcriptions

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    Liu De-Pei

    2007-05-01

    Full Text Available Abstract Background Development in higher eukaryotes involves programmed gene expression. Cell type-specific gene expression is established during this process and is inherited in succeeding cell cycles. Higher eukaryotes have evolved elegant mechanisms by which committed gene-expression states are transmitted through numerous cell divisions. Previous studies have shown that both DNase I-sensitive sites and the basal transcription factor TFIID remain on silenced mitotic chromosomes, suggesting that certain trans-factors might act as bookmarks, maintaining the information and transmitting it to the next generation. Results We used the mouse globin gene clusters as a model system to examine the retention of active information on M-phase chromosomes and its contribution to the persistence of transcriptional competence of these gene clusters in murine erythroleukemia cells. In cells arrested in mitosis, the erythroid-specific activator NF-E2p45 remained associated with its binding sites on the globin gene loci, while the other major erythroid factor, GATA-1, was removed from chromosome. Moreover, despite mitotic chromatin condensation, the distant regulatory regions and promoters of transcriptionally competent globin gene loci are marked by a preserved histone code consisting in active histone modifications such as H3 acetylation, H3-K4 dimethylation and K79 dimethylation. Further analysis showed that other active genes are also locally marked by the preserved active histone code throughout mitotic inactivation of transcription. Conclusion Our results imply that certain kinds of specific protein factors and active histone modifications function as cellular memory markers for both competent and active genes during mitosis, and serve as a reactivated core for the resumption of transcription when the cells exit mitosis.

  6. Temporal and spatial transcriptional fingerprints by antipsychotic or propsychotic drugs in mouse brain.

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    Kensuke Sakuma

    Full Text Available Various types of antipsychotics have been developed for the treatment of schizophrenia since the accidental discovery of the antipsychotic activity of chlorpromazine. Although all clinically effective antipsychotic agents have common properties to interact with the dopamine D2 receptor (D2R activation, their precise mechanisms of action remain elusive. Antipsychotics are well known to induce transcriptional changes of immediate early genes (IEGs, raising the possibility that gene expressions play an essential role to improve psychiatric symptoms. Here, we report that while different classes of antipsychotics have complex pharmacological profiles against D2R, they share common transcriptome fingerprint (TFP profile of IEGs in the murine brain in vivo by quantitative real-time PCR (qPCR. Our data showed that various types of antipsychotics with a profound interaction of D2R including haloperidol (antagonist, olanzapine (antagonist, and aripiprazole (partial agonist all share common spatial TFPs closely homologous to those of D2R antagonist sulpiride, and elicited greater transcriptional responses in the striatum than in the nucleus accumbens. Meanwhile, D2R agonist quinpirole and propsychotic NMDA antagonists such as MK-801 and phencyclidine (PCP exhibited the contrasting TFP profiles. Clozapine and propsychotic drug methamphetamine (MAP displayed peculiar TFPs that reflect their unique pharmacological property. Our results suggest that transcriptional responses are conserved across various types of antipsychotics clinically effective in positive symptoms of schizophrenia and also show that temporal and spatial TFPs may reflect the pharmacological features of the drugs. Thus, we propose that a TFP approach is beneficial to evaluate novel drug candidates for antipsychotic development.

  7. Exploring the spatio-temporal neural basis of face learning

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    Yang, Ying; Xu, Yang; Jew, Carol A.; Pyles, John A.; Kass, Robert E.; Tarr, Michael J.

    2017-01-01

    Humans are experts at face individuation. Although previous work has identified a network of face-sensitive regions and some of the temporal signatures of face processing, as yet, we do not have a clear understanding of how such face-sensitive regions support learning at different time points. To study the joint spatio-temporal neural basis of face learning, we trained subjects to categorize two groups of novel faces and recorded their neural responses using magnetoencephalography (MEG) throughout learning. A regression analysis of neural responses in face-sensitive regions against behavioral learning curves revealed significant correlations with learning in the majority of the face-sensitive regions in the face network, mostly between 150–250 ms, but also after 300 ms. However, the effect was smaller in nonventral regions (within the superior temporal areas and prefrontal cortex) than that in the ventral regions (within the inferior occipital gyri (IOG), midfusiform gyri (mFUS) and anterior temporal lobes). A multivariate discriminant analysis also revealed that IOG and mFUS, which showed strong correlation effects with learning, exhibited significant discriminability between the two face categories at different time points both between 150–250 ms and after 300 ms. In contrast, the nonventral face-sensitive regions, where correlation effects with learning were smaller, did exhibit some significant discriminability, but mainly after 300 ms. In sum, our findings indicate that early and recurring temporal components arising from ventral face-sensitive regions are critically involved in learning new faces. PMID:28570739

  8. Sequence mining and transcript profiling to explore cyst nematode parasitism

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    Recknor Justin

    2009-01-01

    currently known 6,860 H. glycines genes to a pool of 788 most promising candidate genes (including known parasitism genes and documented their expression profiles. Using our approach to pre-select genes likely involved in parasitism now allows detailed functional analyses in a manner not feasible for larger numbers of genes. The generation of the candidate pool described here is an important enabling advance because it will significantly facilitate the unraveling of fascinating plant-animal interactions and deliver knowledge that can be transferred to other pathogen-host systems. Ultimately, the exploration of true parasitism genes verified from the gene pool delineated here will identify weaknesses in the nematode life cycle that can be exploited by novel anti-nematode efforts.

  9. Temporal stability of novelty exploration in mice exposed to different open field tests.

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    Kalueff, Allan V; Keisala, Tiina; Minasyan, Anna; Kuuslahti, Marianne; Tuohimaa, Pentti

    2006-03-01

    We investigated behavioural activity and temporal distribution (patterning) of mouse exploration in different open field (OF) arenas. Mice of 129S1 (S1) strain were subjected in parallel to three different OF arenas (Experiment 1), two different OF arenas in two trials (Experiment 2) or two trials of the same OF test (Experiment 3). Overall, mice demonstrated a high degree of similarity in the temporal profile of novelty-induced horizontal and vertical exploration (regardless of the size, colour and shape of the OF), which remained stable in subsequent OF exposures. In Experiments 4 and 5, we tested F1 hybrid mice (BALB/c-S1; NMRI-S1), and Vitamin D receptor knockout mice (generated on S1 genetic background), again showing strikingly similar temporal patterns of their OF exploration, despite marked behavioural strain differences in anxiety and activity. These results suggest that mice are characterised by stability of temporal organization of their exploration in different OF novelty situations.

  10. Exploring the Temporality of Food Organizations in Liquid Modernity

    DEFF Research Database (Denmark)

    Hernes, Tor; Schmidt, Jonathan; Schultz, Majken

    study illustrates how their time enactment takes place along three dimensions. First, through what we call “malleable time”, including the contraction and dilation of time horizons. Second, through what we call “projective time”, signifying the outward enactment of time onto others. Third, through what....... Because food organizations are challenged to enact their time between natural time and human time while abiding by the constraints of industry, liquid modernity challenges their ability to enact multiple and sometimes contrasting temporalities. Drawing on data from a brewery and a dairy corporation, our...... we call “simultaneous time”, signifying the simultaneous enactment of different time horizons. We argue that time enactment poses its own set of dilemmas for managing food organizations, which are discussed, not just for food organizations, but in relation to other organizations confronted...

  11. Exploring the temporal stability of global road safety statistics.

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    Dimitriou, Loukas; Nikolaou, Paraskevas; Antoniou, Constantinos

    2018-02-08

    Given the importance of rigorous quantitative reasoning in supporting national, regional or global road safety policies, data quality, reliability, and stability are of the upmost importance. This study focuses on macroscopic properties of road safety statistics and the temporal stability of these statistics at a global level. A thorough investigation of two years of measurements was conducted to identify any unexpected gaps that could highlight the existence of inconsistent measurements. The database used in this research includes 121 member countries of the United Nation (UN-121) with a population of at least one million (smaller country data shows higher instability) and includes road safety and socioeconomic variables collected from a number of international databases (e.g. WHO and World Bank) for the years 2010 and 2013. For the fulfillment of the earlier stated goal, a number of data visualization and exploratory analyses (Hierarchical Clustering and Principal Component Analysis) were conducted. Furthermore, in order to provide a richer analysis of the data, we developed and compared the specification of a number of Structural Equation Models for the years 2010 and 2013. Different scenarios have been developed, with different endogenous variables (indicators of mortality rate and fatality risk) and structural forms. The findings of the current research indicate inconsistency phenomena in global statistics of different instances/years. Finally, the results of this research provide evidence on the importance of careful and systematic data collection for developing advanced statistical and econometric techniques and furthermore for developing road safety policies. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Spatial and temporal expression of the Grainyhead-like transcription factor family during murine development.

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    Auden, Alana; Caddy, Jacinta; Wilanowski, Tomasz; Ting, Stephen B; Cunningham, John M; Jane, Stephen M

    2006-10-01

    The Drosophila transcription factor Grainyhead (grh) is expressed in ectoderm-derived tissues where it regulates several key developmental events including cuticle formation, tracheal elongation and dorsal closure. Our laboratory has recently identified three novel mammalian homologues of the grh gene, Grainyhead-like 1, -2 and -3 (Grhl1-3) that rewrite the phylogeny of this family. Using gene targeting in mice, we have shown that Grhl3 is essential for neural tube closure, skin barrier formation and wound healing. Despite their extensive sequence homology, Grhl1 and Grhl2 are unable to compensate for loss of Grhl3 in these developmental processes. To explore this lack of redundancy, and to gain further insights into the functions of this gene family in mammalian development we have performed an extensive in situ hybridisation analysis. We demonstrate that, although all three Grhl genes are highly expressed in the developing epidermis, they display subtle differences in the timing and level of expression. Surprisingly, we also demonstrate differential expression patterns in non-ectoderm-derived tissues, including the heart, the lung, and the metanephric kidney. These findings expand our understanding of the unique role of Grhl3 in neurulation and epidermal morphogenesis, and provide a focus for further functional analysis of the Grhl genes during mouse embryogenesis.

  13. Fluid consumption and taste novelty determines transcription temporal dynamics in the gustatory cortex

    OpenAIRE

    Inberg, Sharon; Jacob, Eyal; Elkobi, Alina; Edry, Efrat; Rappaport, Akiva; Simpson, T. Ian; Armstrong, J. Douglas; Shomron, Noam; Pasmanik-Chor, Metsada; Rosenblum, Kobi

    2016-01-01

    Background Novel taste memories, critical for animal survival, are consolidated to form long term memories which are dependent on translation regulation in the gustatory cortex (GC) hours following acquisition. However, the role of transcription regulation in the process is unknown. Results Here, we report that transcription in the GC is necessary for taste learning in rats, and that drinking and its consequences, as well as the novel taste experience, affect transcription in the GC during ta...

  14. Temporally Regulated Neural Crest Transcription Factors Distinguish Neuroectodermal Tumors of Varying Malignancy and Differentiation

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    Timothy R. Gershon

    2005-06-01

    Full Text Available Neuroectodermal tumor cells, like neural crest (NC cells, are pluripotent, proliferative, and migratory. We tested the hypothesis that genetic programs essential to NC development are activated in neuroectodermal tumors. We examined the expression of transcription factors PAX3, PAX7, AP-2α, and SOX10 in human embryos and neuroectodermal tumors: neurofibroma, schwannoma, neuroblastoma, malignant nerve sheath tumor, melanoma, medulloblastoma, supratentorial primitive neuroectodermal tumor, and Ewing's sarcoma. We also examined the expression of P0, ERBB3, and STX, targets of SOX10, AP-2α, and PAX3, respectively. PAX3, AP-2α, and SOX10 were expressed sequentially in human NC development, whereas PAX7 was restricted to mesoderm. Tumors expressed PAX3, AP-2α, SOX10, and PAX7 in specific combinations. SOX10 and AP-2α were expressed in relatively differentiated neoplasms. The early NC marker, PAX3, and its homologue, PAX7, were detected in poorly differentiated tumors and tumors with malignant potential. Expression of NC transcription factors and target genes correlated. Transcription factors essential to NC development are thus present in neuroectodermal tumors. Correlation of specific NC transcription factors with phenotype, and with expression of specific downstream genes, provides evidence that these transcription factors actively influence gene expression and tumor behavior. These findings suggest that PAX3, PAX7, AP-2α, and SOX10 are potential markers of prognosis and targets for therapeutic intervention.

  15. The Transcriptional Repressor MYB2 Regulates Both Spatial and Temporal Patterns of Proanthocyandin and Anthocyanin Pigmentation in Medicago truncatula.

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    Jun, Ji Hyung; Liu, Chenggang; Xiao, Xirong; Dixon, Richard A

    2015-10-01

    Accumulation of anthocyanins and proanthocyanidins (PAs) is limited to specific cell types and developmental stages, but little is known about how antagonistically acting transcriptional regulators work together to determine temporal and spatial patterning of pigmentation at the cellular level, especially for PAs. Here, we characterize MYB2, a transcriptional repressor regulating both anthocyanin and PA biosynthesis in the model legume Medicago truncatula. MYB2 was strongly upregulated by MYB5, a major regulator of PA biosynthesis in M. truncatula and a component of MYB-basic helix loop helix-WD40 (MBW) activator complexes. Overexpression of MYB2 abolished anthocyanin and PA accumulation in M. truncatula hairy roots and Arabidopsis thaliana seeds, respectively. Anthocyanin deposition was expanded in myb2 mutant seedlings and flowers accompanied by increased anthocyanin content. PA mainly accumulated in the epidermal layer derived from the outer integument in the M. truncatula seed coat, starting from the hilum area. The area of PA accumulation and ANTHOCYANIDIN REDUCTASE expression was expanded into the seed body at the early stage of seed development in the myb2 mutant. Genetic, biochemical, and cell biological evidence suggests that MYB2 functions as part of a multidimensional regulatory network to define the temporal and spatial pattern of anthocyanin and PA accumulation linked to developmental processes. © 2015 American Society of Plant Biologists. All rights reserved.

  16. Fine temporal analysis of DHT transcriptional modulation of the ATM/Gadd45g signaling pathways in the mouse uterus.

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    Ivanga, Mahinè; Labrie, Yvan; Calvo, Ezequiel; Belleau, Pascal; Martel, Céline; Pelletier, Georges; Morissette, Jean; Labrie, Fernand; Durocher, Francine

    2009-03-01

    In rodents, the uterus of a mature female undergoes changes during the uterine cycle, under the control of steroid hormones. 5alpha-Dihydrotestosterone (DHT) is recognized to play an important role in the regulation of androgen action in normal endometrium. Using microarray technology, a screening analysis of genes responding to DHT in the uterus of ovariectomized mice, has allowed us to highlight multiple genes of the ATM/Gadd45g pathway that are modulated following exposure to DHT. Two phases of regulation were identified. In the early phase, the expression of genes involved in the G2/M arrest is rapidly increased, followed by the repression of genes of the G1/S checkpoint, and by the induction of transcriptional regulators. Later, i.e. from 12 to 24 hr, genes involved in G2/M transition, cytoarchitectural and lipid-related genes are stimulated by DHT while immunity-related genes appear to be differentially regulated by the hormone. These results show that a physiological dose of DHT induces the transcription of genes promoting the cell cycle progression in mice. Profile determination of temporal uterine gene expression at the transcriptional level enables us to suggest that the DHT modulation of genes involved in ATM/Gadd45g signaling in an ATM- or p53-independent manner, could play an important role in the cyclical changes of uterine cells in the mouse uterus.

  17. Temporal regulation of Drosophila salivary gland degeneration by the Broad-Complex transcription factors

    Czech Academy of Sciences Publication Activity Database

    Kuchárová-Mahmood, S.; Raška, Ivan; Mechler, B. M.; Farkaš, R.

    2002-01-01

    Roč. 140, - (2002), s. 67-78 ISSN 1047-8477 R&D Projects: GA ČR GA304/02/0342 Grant - others:GA-(SK) VEGA:2/7194/20 Institutional research plan: CEZ:AV0Z5039906; CEZ:MSM 111100003 Keywords : programmed cell death * BR-C transcription factors * drosophila Subject RIV: EA - Cell Biology Impact factor: 4.194, year: 2002

  18. Reconstructing Generalized Logical Networks of Transcriptional Regulation in Mouse Brain from Temporal Gene Expression Data

    Energy Technology Data Exchange (ETDEWEB)

    Song, Mingzhou (Joe) [New Mexico State University, Las Cruces; Lewis, Chris K. [New Mexico State University, Las Cruces; Lance, Eric [New Mexico State University, Las Cruces; Chesler, Elissa J [ORNL; Kirova, Roumyana [Bristol-Myers Squibb Pharmaceutical Research & Development, NJ; Langston, Michael A [University of Tennessee, Knoxville (UTK); Bergeson, Susan [Texas Tech University, Lubbock

    2009-01-01

    The problem of reconstructing generalized logical networks to account for temporal dependencies among genes and environmental stimuli from high-throughput transcriptomic data is addressed. A network reconstruction algorithm was developed that uses the statistical significance as a criterion for network selection to avoid false-positive interactions arising from pure chance. Using temporal gene expression data collected from the brains of alcohol-treated mice in an analysis of the molecular response to alcohol, this algorithm identified genes from a major neuronal pathway as putative components of the alcohol response mechanism. Three of these genes have known associations with alcohol in the literature. Several other potentially relevant genes, highlighted and agreeing with independent results from literature mining, may play a role in the response to alcohol. Additional, previously-unknown gene interactions were discovered that, subject to biological verification, may offer new clues in the search for the elusive molecular mechanisms of alcoholism.

  19. Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state.

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    Bartek Wilczynski

    Full Text Available Precise patterns of spatial and temporal gene expression are central to metazoan complexity and act as a driving force for embryonic development. While there has been substantial progress in dissecting and predicting cis-regulatory activity, our understanding of how information from multiple enhancer elements converge to regulate a gene's expression remains elusive. This is in large part due to the number of different biological processes involved in mediating regulation as well as limited availability of experimental measurements for many of them. Here, we used a Bayesian approach to model diverse experimental regulatory data, leading to accurate predictions of both spatial and temporal aspects of gene expression. We integrated whole-embryo information on transcription factor recruitment to multiple cis-regulatory modules, insulator binding and histone modification status in the vicinity of individual gene loci, at a genome-wide scale during Drosophila development. The model uses Bayesian networks to represent the relation between transcription factor occupancy and enhancer activity in specific tissues and stages. All parameters are optimized in an Expectation Maximization procedure providing a model capable of predicting tissue- and stage-specific activity of new, previously unassayed genes. Performing the optimization with subsets of input data demonstrated that neither enhancer occupancy nor chromatin state alone can explain all gene expression patterns, but taken together allow for accurate predictions of spatio-temporal activity. Model predictions were validated using the expression patterns of more than 600 genes recently made available by the BDGP consortium, demonstrating an average 15-fold enrichment of genes expressed in the predicted tissue over a naïve model. We further validated the model by experimentally testing the expression of 20 predicted target genes of unknown expression, resulting in an accuracy of 95% for temporal

  20. Object-Location Training Elicits an Overlapping but Temporally Distinct Transcriptional Profile from Contextual Fear Conditioning

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    Wimmer, Mathieu; Hawk, Joshua D.; Walsh, Jennifer L.; Giese, Karl P.; Abel, Ted

    2014-01-01

    Hippocampus-dependent learning is known to induce changes in gene expression, but information on gene expression differences between different learning paradigms that require the hippocampus is limited. The bulk of studies investigating RNA expression after learning use the contextual fear conditioning task, which couples a novel environment with a footshock. Although contextual fear conditioning has been useful in discovering gene targets, gene expression after spatial memory tasks has received less attention. In this study, we used the object-location memory task and studied gene expression at two time points after learning in a high-throughput manner using a microfluidic qPCR approach. We found that expression of the classic immediate-early genes changes after object-location training in a fashion similar to that observed after contextual fear conditioning. However, the temporal dynamics of gene expression are different between the two tasks, with object-location memory producing gene expression changes that last at least 2 hours. Our findings indicate that different training paradigms may give rise to distinct temporal dynamics of gene expression after learning. PMID:25242102

  1. Object-location training elicits an overlapping but temporally distinct transcriptional profile from contextual fear conditioning.

    Science.gov (United States)

    Poplawski, Shane G; Schoch, Hannah; Wimmer, Mathieu; Hawk, Joshua D; Walsh, Jennifer L; Giese, Karl P; Abel, Ted

    2014-12-01

    Hippocampus-dependent learning is known to induce changes in gene expression, but information on gene expression differences between different learning paradigms that require the hippocampus is limited. The bulk of studies investigating RNA expression after learning use the contextual fear conditioning task, which couples a novel environment with a footshock. Although contextual fear conditioning has been useful in discovering gene targets, gene expression after spatial memory tasks has received less attention. In this study, we used the object-location memory task and studied gene expression at two time points after learning in a high-throughput manner using a microfluidic qPCR approach. We found that expression of the classic immediate-early genes changes after object-location training in a fashion similar to that observed after contextual fear conditioning. However, the temporal dynamics of gene expression are different between the two tasks, with object-location memory producing gene expression changes that last at least 2 hours. Our findings indicate that different training paradigms may give rise to distinct temporal dynamics of gene expression after learning. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription

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    Newton Paul N

    2011-08-01

    Full Text Available Abstract Background Artemisinin resistance in Plasmodium falciparum malaria has emerged in Western Cambodia. This is a major threat to global plans to control and eliminate malaria as the artemisinins are a key component of antimalarial treatment throughout the world. To identify key features associated with the delayed parasite clearance phenotype, we employed DNA microarrays to profile the physiological gene expression pattern of the resistant isolates. Results In the ring and trophozoite stages, we observed reduced expression of many basic metabolic and cellular pathways which suggests a slower growth and maturation of these parasites during the first half of the asexual intraerythrocytic developmental cycle (IDC. In the schizont stage, there is an increased expression of essentially all functionalities associated with protein metabolism which indicates the prolonged and thus increased capacity of protein synthesis during the second half of the resistant parasite IDC. This modulation of the P. falciparum intraerythrocytic transcriptome may result from differential expression of regulatory proteins such as transcription factors or chromatin remodeling associated proteins. In addition, there is a unique and uniform copy number variation pattern in the Cambodian parasites which may represent an underlying genetic background that contributes to the resistance phenotype. Conclusions The decreased metabolic activities in the ring stages are consistent with previous suggestions of higher resilience of the early developmental stages to artemisinin. Moreover, the increased capacity of protein synthesis and protein turnover in the schizont stage may contribute to artemisinin resistance by counteracting the protein damage caused by the oxidative stress and/or protein alkylation effect of this drug. This study reports the first global transcriptional survey of artemisinin resistant parasites and provides insight to the complexities of the molecular basis

  3. Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster.

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    Wan, Cen; Lees, Jonathan G; Minneci, Federico; Orengo, Christine A; Jones, David T

    2017-10-01

    Accurate gene or protein function prediction is a key challenge in the post-genome era. Most current methods perform well on molecular function prediction, but struggle to provide useful annotations relating to biological process functions due to the limited power of sequence-based features in that functional domain. In this work, we systematically evaluate the predictive power of temporal transcription expression profiles for protein function prediction in Drosophila melanogaster. Our results show significantly better performance on predicting protein function when transcription expression profile-based features are integrated with sequence-derived features, compared with the sequence-derived features alone. We also observe that the combination of expression-based and sequence-based features leads to further improvement of accuracy on predicting all three domains of gene function. Based on the optimal feature combinations, we then propose a novel multi-classifier-based function prediction method for Drosophila melanogaster proteins, FFPred-fly+. Interpreting our machine learning models also allows us to identify some of the underlying links between biological processes and developmental stages of Drosophila melanogaster.

  4. Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster.

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    Cen Wan

    2017-10-01

    Full Text Available Accurate gene or protein function prediction is a key challenge in the post-genome era. Most current methods perform well on molecular function prediction, but struggle to provide useful annotations relating to biological process functions due to the limited power of sequence-based features in that functional domain. In this work, we systematically evaluate the predictive power of temporal transcription expression profiles for protein function prediction in Drosophila melanogaster. Our results show significantly better performance on predicting protein function when transcription expression profile-based features are integrated with sequence-derived features, compared with the sequence-derived features alone. We also observe that the combination of expression-based and sequence-based features leads to further improvement of accuracy on predicting all three domains of gene function. Based on the optimal feature combinations, we then propose a novel multi-classifier-based function prediction method for Drosophila melanogaster proteins, FFPred-fly+. Interpreting our machine learning models also allows us to identify some of the underlying links between biological processes and developmental stages of Drosophila melanogaster.

  5. The transcription factor FoxB mediates temporal loss of cellular competence for notochord induction in ascidian embryos.

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    Hashimoto, Hidehiko; Enomoto, Takashi; Enomoto, Atsushi; Kumano, Gaku; Nishida, Hiroki

    2011-06-01

    In embryos of the ascidian Halocynthia roretzi, the competence of isolated presumptive notochord blastomeres to respond to fibroblast growth factor (FGF) for induction of the primary notochord decays by 1 hour after cleavage from the 32- to 64-cell stage. This study analyzes the molecular mechanisms responsible for this loss of competence and provides evidence for a novel mechanism. A forkhead family transcription factor, FoxB, plays a role in competence decay by preventing the induction of notochord-specific Brachyury (Bra) gene expression by the FGF/MAPK signaling pathway. Unlike the mechanisms reported previously in other animals, no component in the FGF signal transduction cascade appeared to be lost or inactivated at the time of competence loss. Knockdown of FoxB functions allowed the isolated cells to retain their competence for a longer period, and to respond to FGF with expression of Bra beyond the stage at which competence was normally lost. FoxB acts as a transcription repressor by directly binding to the cis-regulatory element of the Bra gene. Our results suggest that FoxB prevents ectopic induction of the notochord fate within the cells that assume a default nerve cord fate, after the stage when notochord induction has been completed. The merit of this system is that embryos can use the same FGF signaling cascade again for another purpose in the same cell lineage at later stages by keeping the signaling cascade itself available. Temporally and spatially regulated FoxB expression in nerve cord cells was promoted by the ZicN transcription factor and absence of FGF/MAPK signaling.

  6. VAUD: A Visual Analysis Approach for Exploring Spatio-Temporal Urban Data.

    Science.gov (United States)

    Chen, Wei; Huang, Zhaosong; Wu, Feiran; Zhu, Minfeng; Guan, Huihua; Maciejewski, Ross

    2017-10-02

    Urban data is massive, heterogeneous, and spatio-temporal, posing a substantial challenge for visualization and analysis. In this paper, we design and implement a novel visual analytics approach, Visual Analyzer for Urban Data (VAUD), that supports the visualization, querying, and exploration of urban data. Our approach allows for cross-domain correlation from multiple data sources by leveraging spatial-temporal and social inter-connectedness features. Through our approach, the analyst is able to select, filter, aggregate across multiple data sources and extract information that would be hidden to a single data subset. To illustrate the effectiveness of our approach, we provide case studies on a real urban dataset that contains the cyber-, physical-, and socialinformation of 14 million citizens over 22 days.

  7. Exploring spatial-temporal dynamics of fire regime features in mainland Spain

    Science.gov (United States)

    Jiménez-Ruano, Adrián; Rodrigues Mimbrero, Marcos; de la Riva Fernández, Juan

    2017-10-01

    This paper explores spatial-temporal dynamics in fire regime features, such as fire frequency, burnt area, large fires and natural- and human-caused fires, as an essential part of fire regime characterization. Changes in fire features are analysed at different spatial - regional and provincial/NUTS3 - levels, together with summer and winter temporal scales, using historical fire data from Spain for the period 1974-2013. Temporal shifts in fire features are investigated by means of change point detection procedures - Pettitt test, AMOC (at most one change), PELT (pruned exact linear time) and BinSeg (binary segmentation) - at a regional level to identify changes in the time series of the features. A trend analysis was conducted using the Mann-Kendall and Sen's slope tests at both the regional and NUTS3 level. Finally, we applied a principal component analysis (PCA) and varimax rotation to trend outputs - mainly Sen's slope values - to summarize overall temporal behaviour and to explore potential links in the evolution of fire features. Our results suggest that most fire features show remarkable shifts between the late 1980s and the first half of the 1990s. Mann-Kendall outputs revealed negative trends in the Mediterranean region. Results from Sen's slope suggest high spatial and intra-annual variability across the study area. Fire activity related to human sources seems to be experiencing an overall decrease in the northwestern provinces, particularly pronounced during summer. Similarly, the Hinterland and the Mediterranean coast are gradually becoming less fire affected. Finally, PCA enabled trends to be synthesized into four main components: winter fire frequency (PC1), summer burnt area (PC2), large fires (PC3) and natural fires (PC4).

  8. Exploring spatial–temporal dynamics of fire regime features in mainland Spain

    Directory of Open Access Journals (Sweden)

    A. Jiménez-Ruano

    2017-10-01

    Full Text Available This paper explores spatial–temporal dynamics in fire regime features, such as fire frequency, burnt area, large fires and natural- and human-caused fires, as an essential part of fire regime characterization. Changes in fire features are analysed at different spatial – regional and provincial/NUTS3 – levels, together with summer and winter temporal scales, using historical fire data from Spain for the period 1974–2013. Temporal shifts in fire features are investigated by means of change point detection procedures – Pettitt test, AMOC (at most one change, PELT (pruned exact linear time and BinSeg (binary segmentation – at a regional level to identify changes in the time series of the features. A trend analysis was conducted using the Mann–Kendall and Sen's slope tests at both the regional and NUTS3 level. Finally, we applied a principal component analysis (PCA and varimax rotation to trend outputs – mainly Sen's slope values – to summarize overall temporal behaviour and to explore potential links in the evolution of fire features. Our results suggest that most fire features show remarkable shifts between the late 1980s and the first half of the 1990s. Mann–Kendall outputs revealed negative trends in the Mediterranean region. Results from Sen's slope suggest high spatial and intra-annual variability across the study area. Fire activity related to human sources seems to be experiencing an overall decrease in the northwestern provinces, particularly pronounced during summer. Similarly, the Hinterland and the Mediterranean coast are gradually becoming less fire affected. Finally, PCA enabled trends to be synthesized into four main components: winter fire frequency (PC1, summer burnt area (PC2, large fires (PC3 and natural fires (PC4.

  9. A temporal gate for viral enhancers to co-opt Toll-like-receptor transcriptional activation pathways upon acute infection.

    Directory of Open Access Journals (Sweden)

    Kai A Kropp

    2015-04-01

    Full Text Available Viral engagement with macrophages activates Toll-Like-Receptors (TLRs and viruses must contend with the ensuing inflammatory responses to successfully complete their replication cycle. To date, known counter-strategies involve the use of viral-encoded proteins that often employ mimicry mechanisms to block or redirect the host response to benefit the virus. Whether viral regulatory DNA sequences provide an opportunistic strategy by which viral enhancer elements functionally mimic innate immune enhancers is unknown. Here we find that host innate immune genes and the prototypical viral enhancer of cytomegalovirus (CMV have comparable expression kinetics, and positively respond to common TLR agonists. In macrophages but not fibroblasts we show that activation of NFκB at immediate-early times of infection is independent of virion-associated protein, M45. We find upon virus infection or transfection of viral genomic DNA the TLR-agonist treatment results in significant enhancement of the virus transcription-replication cycle. In macrophage time-course infection experiments we demonstrate that TLR-agonist stimulation of the viral enhancer and replication cycle is strictly delimited by a temporal gate with a determined half-maximal time for enhancer-activation of 6 h; after which TLR-activation blocks the viral transcription-replication cycle. By performing a systematic siRNA screen of 149 innate immune regulatory factors we identify not only anticipated anti-viral and pro-viral contributions but also new factors involved in the CMV transcription-replication cycle. We identify a central convergent NFκB-SP1-RXR-IRF axis downstream of TLR-signalling. Activation of the RXR component potentiated direct and indirect TLR-induced activation of CMV transcription-replication cycle; whereas chromatin binding experiments using wild-type and enhancer-deletion virus revealed IRF3 and 5 as new pro-viral host transcription factor interactions with the CMV enhancer in

  10. RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.

    Science.gov (United States)

    Castro-Mondragon, Jaime Abraham; Jaeger, Sébastien; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

    2017-07-27

    Transcription factor (TF) databases contain multitudes of binding motifs (TFBMs) from various sources, from which non-redundant collections are derived by manual curation. The advent of high-throughput methods stimulated the production of novel collections with increasing numbers of motifs. Meta-databases, built by merging these collections, contain redundant versions, because available tools are not suited to automatically identify and explore biologically relevant clusters among thousands of motifs. Motif discovery from genome-scale data sets (e.g. ChIP-seq) also produces redundant motifs, hampering the interpretation of results. We present matrix-clustering, a versatile tool that clusters similar TFBMs into multiple trees, and automatically creates non-redundant TFBM collections. A feature unique to matrix-clustering is its dynamic visualisation of aligned TFBMs, and its capability to simultaneously treat multiple collections from various sources. We demonstrate that matrix-clustering considerably simplifies the interpretation of combined results from multiple motif discovery tools, and highlights biologically relevant variations of similar motifs. We also ran a large-scale application to cluster ∼11 000 motifs from 24 entire databases, showing that matrix-clustering correctly groups motifs belonging to the same TF families, and drastically reduced motif redundancy. matrix-clustering is integrated within the RSAT suite (http://rsat.eu/), accessible through a user-friendly web interface or command-line for its integration in pipelines. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. Analysis of Transcriptional Signatures in Response to Listeria monocytogenes Infection Reveals Temporal Changes That Result from Type I Interferon Signaling

    Science.gov (United States)

    Potempa, Krzysztof; Graham, Christine M.; Moreira-Teixeira, Lucia; McNab, Finlay W.; Howes, Ashleigh; Stavropoulos, Evangelos; Pascual, Virginia; Banchereau, Jacques; Chaussabel, Damien; O’Garra, Anne

    2016-01-01

    Analysis of the mouse transcriptional response to Listeria monocytogenes infection reveals that a large set of genes are perturbed in both blood and tissue and that these transcriptional responses are enriched for pathways of the immune response. Further we identified enrichment for both type I and type II interferon (IFN) signaling molecules in the blood and tissues upon infection. Since type I IFN signaling has been reported widely to impair bacterial clearance we examined gene expression from blood and tissues of wild type (WT) and type I IFNαβ receptor-deficient (Ifnar1-/-) mice at the basal level and upon infection with L. monocytogenes. Measurement of the fold change response upon infection in the absence of type I IFN signaling demonstrated an upregulation of specific genes at day 1 post infection. A less marked reduction of the global gene expression signature in blood or tissues from infected Ifnar1-/- as compared to WT mice was observed at days 2 and 3 after infection, with marked reduction in key genes such as Oasg1 and Stat2. Moreover, on in depth analysis, changes in gene expression in uninfected mice of key IFN regulatory genes including Irf9, Irf7, Stat1 and others were identified, and although induced by an equivalent degree upon infection this resulted in significantly lower final gene expression levels upon infection of Ifnar1-/- mice. These data highlight how dysregulation of this network in the steady state and temporally upon infection may determine the outcome of this bacterial infection and how basal levels of type I IFN-inducible genes may perturb an optimal host immune response to control intracellular bacterial infections such as L. monocytogenes. PMID:26918359

  12. Exploring the utility of organo-polyoxometalate hybrids to inhibit SOX transcription factors.

    Science.gov (United States)

    Narasimhan, Kamesh; Micoine, Kevin; Lacôte, Emmanuel; Thorimbert, Serge; Cheung, Edwin; Hasenknopf, Bernold; Jauch, Ralf

    2014-01-01

    SOX transcription factors constitute an attractive target class for intervention with small molecules as they play a prominent role in the field of regenerative biomedicine and cancer biology. However, rationally engineering specific inhibitors that interfere with transcription factor DNA interfaces continues to be a monumental challenge in the field of transcription factor chemical biology. Polyoxometalates (POMs) are inorganic compounds that were previously shown to target the high-mobility group (HMG) of SOX proteins at nanomolar concentrations. In continuation of this work, we carried out an assessment of the selectivity of a panel of newly synthesized organo-polyoxometalate hybrids in targeting different transcription factor families to enable the usage of polyoxometalates as specific SOX transcription factor drugs. The residual DNA-binding activities of 15 different transcription factors were measured after treatment with a panel of diverse polyoxometalates. Polyoxometalates belonging to the Dawson structural class were found to be more potent inhibitors than the Keggin class. Further, organically modified Dawson polyoxometalates were found to be the most potent in inhibiting transcription factor DNA binding activity. The size of the polyoxometalates and its derivitization were found to be the key determinants of their potency. Polyoxometalates are highly potent, nanomolar range inhibitors of the DNA binding activity of the Sox-HMG family. However, binding assays involving a limited subset of structurally diverse polyoxometalates revealed a low selectivity profile against different transcription factor families. Further progress in achieving selectivity and deciphering structure-activity relationship of POMs require the identification of POM binding sites on transcription factors using elaborate approaches like X-ray crystallography and multidimensional NMR. In summary, our report reaffirms that transcription factors are challenging molecular architectures

  13. Exploring the utility of organo-polyoxometalate hybrids to inhibit SOX transcription factors

    Directory of Open Access Journals (Sweden)

    Kamesh Narasimhan

    2014-01-01

    Conclusion: Polyoxometalates are highly potent, nanomolar range inhibitors of the DNA binding activity of the Sox-HMG family. However, binding assays involving a limited subset of structurally diverse polyoxometalates revealed a low selectivity profile against different transcription factor families. Further progress in achieving selectivity and deciphering structure-activity relationship of POMs require the identification of POM binding sites on transcription factors using elaborate approaches like X-ray crystallography and multidimensional NMR. In summary, our report reaffirms that transcription factors are challenging molecular architectures and that future polyoxometalate chemistry must consider further modification strategies, to address the substantial challenges involved in achieving target selectivity.

  14. Transcript profiles uncover temporal and stress-induced changes of metabolic pathways in germinating sugar beet seeds

    Directory of Open Access Journals (Sweden)

    Windhövel Andrea

    2008-12-01

    Full Text Available Abstract Background With a cultivation area of 1.75 Mio ha and sugar yield of 16.7 Mio tons in 2006, sugar beet is a crop of great economic importance in Europe. The productivity of sugar beet is determined significantly by seed vigour and field emergence potential; however, little is known about the molecular mechanisms underlying these traits. Both traits exhibit large variations within sugar beet germplasm that have been difficult to ascribe to either environmental or genetic causes. Among potential targets for trait improvement, an enhancement of stress tolerance is considered because of the high negative influence of environmental stresses on trait parameters. Extending our knowledge of genetic and molecular determinants of sugar beet germination, stress response and adaptation mechanisms would facilitate the detection of new targets for breeding crop with an enhanced field emergence potential. Results To gain insight into the sugar beet germination we initiated an analysis of gene expression in a well emerging sugar beet hybrid showing high germination potential under various environmental conditions. A total of 2,784 ESTs representing 2,251 'unigenes' was generated from dry mature and germinating seeds. Analysis of the temporal expression of these genes during germination under non-stress conditions uncovered drastic transcriptional changes accompanying a shift from quiescent to metabolically active stages of the plant life cycle. Assay of germination under stressful conditions revealed 157 genes showing significantly different expression patterns in response to stress. As deduced from transcriptome data, stress adaptation mechanisms included an alteration in reserve mobilization pathways, an accumulation of the osmoprotectant glycine betaine, late embryogenesis abundant proteins and detoxification enzymes. The observed transcriptional changes are supposed to be regulated by ABA-dependent signal transduction pathway. Conclusion This study

  15. Towards operational hydrology for a thorough spatio-temporal exploration of the Critical Zone

    Science.gov (United States)

    Chatton, Eliot; Labasque, Thierry; Guillou, Aurélie; Aquilina, Luc; Bour, Olivier; Le Borgne, Tanguy; Longuevergne, Laurent

    2017-04-01

    Over the last century, the Critical Zone faced remarkable climate and land use changes increasing the pressures on the Hydrosphere and giving rise to numerous environmental consequences in terms of water quantity and quality. From now on, the Critical Zone must face the challenge to supply 9 billion people with quality food and safe drinking water in a context of global warming. For the Hydrosphere, this challenge could be addressed with a better understanding of the dynamics and resilience of aquatic environments (rivers, lakes, groundwaters, oceans). In view of the spatial and temporal variety and variability of flow dynamics and biogeochemical reactions occurring in the Hydrosphere a new investigation method is needed. This study approaches the concept of "operational hydrology" aiming to enhance either the spatio-temporal distribution and the quality of environmental data for a thorough exploration of the Hydrosphere. To illustrate our approach, we present natural and anthropogenic dissolved gas data (He, Ne, Ar, Kr, Xe, N2, O2, CO2, CH4, N2O, H2, BTEX, and some VOCs) measured in situ with a CF-MIMS (Chatton et al, 2016) installed in a mobile laboratory arranged in an all-terrain truck (CRITEX-Lab). This ongoing work focuses on groundwater and the field investigation of residence time distributions, recharge processes (origins), water flow paths and mixing, biogeochemical reactivity and contamination (sources). The rationale behind "operational hydrology" could be applied to the field measurement at high-frequency of many other environmental parameters (temperature, cations, anions, isotopes, micro-organisms) not only for the investigation of groundwaters but also rivers, lakes and oceans. Eliot Chatton, Thierry Labasque, Jérôme de La Bernardie, Nicolas Guihéneuf, Olivier Bour and Luc Aquilina; Field Continuous Measurement of Dissolved Gases with a CF-MIMS: Applications to the Physics and Biogeochemistry of Groundwater Flow; Environmental Science

  16. Sialotranscriptomics of Rhipicephalus zambeziensis reveals intricate expression profiles of secretory proteins and suggests tight temporal transcriptional regulation during blood-feeding.

    Science.gov (United States)

    de Castro, Minique Hilda; de Klerk, Daniel; Pienaar, Ronel; Rees, D Jasper G; Mans, Ben J

    2017-08-10

    Ticks secrete a diverse mixture of secretory proteins into the host to evade its immune response and facilitate blood-feeding, making secretory proteins attractive targets for the production of recombinant anti-tick vaccines. The largely neglected tick species, Rhipicephalus zambeziensis, is an efficient vector of Theileria parva in southern Africa but its available sequence information is limited. Next generation sequencing has advanced sequence availability for ticks in recent years and has assisted the characterisation of secretory proteins. This study focused on the de novo assembly and annotation of the salivary gland transcriptome of R. zambeziensis and the temporal expression of secretory protein transcripts in female and male ticks, before the onset of feeding and during early and late feeding. The sialotranscriptome of R. zambeziensis yielded 23,631 transcripts from which 13,584 non-redundant proteins were predicted. Eighty-six percent of these contained a predicted start and stop codon and were estimated to be putatively full-length proteins. A fifth (2569) of the predicted proteins were annotated as putative secretory proteins and explained 52% of the expression in the transcriptome. Expression analyses revealed that 2832 transcripts were differentially expressed among feeding time points and 1209 between the tick sexes. The expression analyses further indicated that 57% of the annotated secretory protein transcripts were differentially expressed. Dynamic expression profiles of secretory protein transcripts were observed during feeding of female ticks. Whereby a number of transcripts were upregulated during early feeding, presumably for feeding site establishment and then during late feeding, 52% of these were downregulated, indicating that transcripts were required at specific feeding stages. This suggested that secretory proteins are under stringent transcriptional regulation that fine-tunes their expression in salivary glands during feeding. No open

  17. Exploring the time course of face matching: temporal constraints impair unfamiliar face identification under temporally unconstrained viewing.

    Science.gov (United States)

    Ozbek, Müge; Bindemann, Markus

    2011-10-01

    The identification of unfamiliar faces has been studied extensively with matching tasks, in which observers decide if pairs of photographs depict the same person (identity matches) or different people (mismatches). In experimental studies in this field, performance is usually self-paced under the assumption that this will encourage best-possible accuracy. Here, we examined the temporal characteristics of this task by limiting display times and tracking observers' eye movements. Observers were required to make match/mismatch decisions to pairs of faces shown for 200, 500, 1000, or 2000ms, or for an unlimited duration. Peak accuracy was reached within 2000ms and two fixations to each face. However, intermixing exposure conditions produced a context effect that generally reduced accuracy on identity mismatch trials, even when unlimited viewing of faces was possible. These findings indicate that less than 2s are required for face matching when exposure times are variable, but temporal constraints should be avoided altogether if accuracy is truly paramount. The implications of these findings are discussed. Copyright © 2011 Elsevier Ltd. All rights reserved.

  18. Exploring the sequence-function relationship in transcriptional regulation by the lac O1 operator.

    Science.gov (United States)

    Maity, Tuhin S; Jha, Ramesh K; Strauss, Charlie E M; Dunbar, John

    2012-07-01

    Understanding how binding of a transcription factor to an operator is influenced by the operator sequence is an ongoing quest. It facilitates discovery of alternative binding sites as well as tuning of transcriptional regulation. We investigated the behavior of the Escherichia coli Lac repressor (LacI) protein with a large set of lac O(1) operator variants. The 114 variants examined contained a mean of 2.9 (range 0-4) mutations at positions -4, -2, +2 and +4 in the minimally required 17 bp operator. The relative affinity of LacI for the operators was examined by quantifying expression of a GFP reporter gene and Rosetta structural modeling. The combinations of mutations in the operator sequence created a wide range of regulatory behaviors. We observed variations in the GFP fluorescent signal among the operator variants of more than an order of magnitude under both uninduced and induced conditions. We found that a single nucleotide change may result in changes of up to six- and 12-fold in uninduced and induced GFP signals, respectively. Among the four positions mutated, we found that nucleotide G at position -4 is strongly correlated with strong repression. By Rosetta modeling, we found a significant correlation between the calculated binding energy and the experimentally observed transcriptional repression strength for many operators. However, exceptions were also observed, underscoring the necessity for further improvement in biophysical models of protein-DNA interactions. © 2012 The Authors Journal compilation © 2012 FEBS.

  19. Exploring Temporal Sequences of Regulatory Phases and Associated Interactions in Low- and High-Challenge Collaborative Learning Sessions

    Science.gov (United States)

    Sobocinski, Márta; Malmberg, Jonna; Järvelä, Sanna

    2017-01-01

    Investigating the temporal order of regulatory processes can explain in more detail the mechanisms behind success or lack of success during collaborative learning. The aim of this study is to explore the differences between high- and low-challenge collaborative learning sessions. This is achieved through examining how the three phases of…

  20. Exploring the bZIP transcription factor regulatory network in Neurospora crassa.

    Science.gov (United States)

    Tian, Chaoguang; Li, Jingyi; Glass, N Louise

    2011-03-01

    Transcription factors (TFs) are key nodes of regulatory networks in eukaryotic organisms, including filamentous fungi such as Neurospora crassa. The 178 predicted DNA-binding TFs in N. crassa are distributed primarily among six gene families, which represent an ancient expansion in filamentous ascomycete genomes; 98 TF genes show detectable expression levels during vegetative growth of N. crassa, including 35 that show a significant difference in expression level between hyphae at the periphery versus hyphae in the interior of a colony. Regulatory networks within a species genome include paralogous TFs and their respective target genes (TF regulon). To investigate TF network evolution in N. crassa, we focused on the basic leucine zipper (bZIP) TF family, which contains nine members. We performed baseline transcriptional profiling during vegetative growth of the wild-type and seven isogenic, viable bZIP deletion mutants. We further characterized the regulatory network of one member of the bZIP family, NCU03905. NCU03905 encodes an Ap1-like protein (NcAp-1), which is involved in resistance to multiple stress responses, including oxidative and heavy metal stress. Relocalization of NcAp-1 from the cytoplasm to the nucleus was associated with exposure to stress. A comparison of the NcAp-1 regulon with Ap1-like regulons in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans and Aspergillus fumigatus showed both conservation and divergence. These data indicate how N. crassa responds to stress and provide information on pathway evolution.

  1. Temporal transcription of the lactococcal temperate phage TP901-1 and DNA sequence of the early promoter region

    DEFF Research Database (Denmark)

    Madsen, Hans Peter Lynge; Hammer, Karin

    1998-01-01

    to a phage repressor, a single-stranded DNA-binding protein, a topoisomerase, a Cro-like protein and two other phage proteins of unknown function were detected. The gene arrangement in the early transcribed region of TP901-1 thus consists of two transcriptional units: one from PR containing four genes......, of which at least two (the integrase gene and putative repressor) are needed for lysogeny, and the divergent and longer transcriptional unit from PL, presumably encoding functions required for the lytic life cycle. ORFs with homology to proteins involved in DNA replication were identified on the latter......Transcriptional analysis by Northern blotting identified clusters of early, middle and late transcribed regions of the temperate lactococcal bacteriophage TP901-1 during one-step growth experiments. The latent period was found to be 65 min and the burst size 40 +/- 10. The eight early transcripts...

  2. RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria.

    Science.gov (United States)

    Novichkov, Pavel S; Kazakov, Alexey E; Ravcheev, Dmitry A; Leyn, Semen A; Kovaleva, Galina Y; Sutormin, Roman A; Kazanov, Marat D; Riehl, William; Arkin, Adam P; Dubchak, Inna; Rodionov, Dmitry A

    2013-11-01

    bacterial genomes. Analytical capabilities include exploration of: regulon content, structure and function; TF binding site motifs; conservation and variations in genome-wide regulatory networks across all taxonomic groups of Bacteria. RegPrecise 3.0 was selected as a core resource on transcriptional regulation of the Department of Energy Systems Biology Knowledgebase, an emerging software and data environment designed to enable researchers to collaboratively generate, test and share new hypotheses about gene and protein functions, perform large-scale analyses, and model interactions in microbes, plants, and their communities.

  3. Exploring the role of the posterior middle temporal gyrus in semantic cognition: Integration of anterior temporal lobe with executive processes.

    Science.gov (United States)

    Davey, James; Thompson, Hannah E; Hallam, Glyn; Karapanagiotidis, Theodoros; Murphy, Charlotte; De Caso, Irene; Krieger-Redwood, Katya; Bernhardt, Boris C; Smallwood, Jonathan; Jefferies, Elizabeth

    2016-08-15

    Making sense of the world around us depends upon selectively retrieving information relevant to our current goal or context. However, it is unclear whether selective semantic retrieval relies exclusively on general control mechanisms recruited in demanding non-semantic tasks, or instead on systems specialised for the control of meaning. One hypothesis is that the left posterior middle temporal gyrus (pMTG) is important in the controlled retrieval of semantic (not non-semantic) information; however this view remains controversial since a parallel literature links this site to event and relational semantics. In a functional neuroimaging study, we demonstrated that an area of pMTG implicated in semantic control by a recent meta-analysis was activated in a conjunction of (i) semantic association over size judgements and (ii) action over colour feature matching. Under these circumstances the same region showed functional coupling with the inferior frontal gyrus - another crucial site for semantic control. Structural and functional connectivity analyses demonstrated that this site is at the nexus of networks recruited in automatic semantic processing (the default mode network) and executively demanding tasks (the multiple-demand network). Moreover, in both task and task-free contexts, pMTG exhibited functional properties that were more similar to ventral parts of inferior frontal cortex, implicated in controlled semantic retrieval, than more dorsal inferior frontal sulcus, implicated in domain-general control. Finally, the pMTG region was functionally correlated at rest with other regions implicated in control-demanding semantic tasks, including inferior frontal gyrus and intraparietal sulcus. We suggest that pMTG may play a crucial role within a large-scale network that allows the integration of automatic retrieval in the default mode network with executively-demanding goal-oriented cognition, and that this could support our ability to understand actions and non

  4. Quantifying Temporal Autocorrelations for the Expression of Geobacter species mRNA Gene Transcripts at Variable Ammonium Levels during in situ U(VI) Bioremediation

    Science.gov (United States)

    Mouser, P. J.

    2010-12-01

    In order to develop decision-making tools for the prediction and optimization of subsurface bioremediation strategies, we must be able to link the molecular-scale activity of microorganisms involved in remediation processes with biogeochemical processes observed at the field-scale. This requires the ability to quantify changes in the in situ metabolic condition of dominant microbes and associate these changes to fluctuations in nutrient levels throughout the bioremediation process. It also necessitates a need to understand the spatiotemporal variability of the molecular-scale information to develop meaningful parameters and constraint ranges in complex bio-physio-chemical models. The expression of three Geobacter species genes (ammonium transporter (amtB), nitrogen fixation (nifD), and a housekeeping gene (recA)) were tracked at two monitoring locations that differed significantly in ammonium (NH4+) concentrations during a field-scale experiment where acetate was injected into the subsurface to simulate Geobacteraceae in a uranium-contaminated aquifer. Analysis of amtB and nifD mRNA transcript levels indicated that NH4+ was the primary form of fixed nitrogen during bioremediation. Overall expression levels of amtB were on average 8-fold higher at NH4+ concentrations of 300 μM or more than at lower NH4+ levels (average 60 μM). The degree of temporal correlation in Geobacter species mRNA expression levels was calculated at both locations using autocorrelation methods that describe the relationship between sample semi-variance and time lag. At the monitoring location with lower NH4+, a temporal correlation lag of 8 days was observed for both amtB and nifD transcript patterns. At the location where higher NH4+ levels were observed, no discernable temporal correlation lag above the sampling frequency (approximately every 2 days) was observed for amtB or nifD transcript fluctuations. Autocorrelation trends in recA expression levels at both locations indicated that

  5. The Transcriptional Repressor MYB2 Regulates Both Spatial and Temporal Patterns of Proanthocyandin and Anthocyanin Pigmentation in Medicago truncatula[OPEN

    Science.gov (United States)

    2015-01-01

    Accumulation of anthocyanins and proanthocyanidins (PAs) is limited to specific cell types and developmental stages, but little is known about how antagonistically acting transcriptional regulators work together to determine temporal and spatial patterning of pigmentation at the cellular level, especially for PAs. Here, we characterize MYB2, a transcriptional repressor regulating both anthocyanin and PA biosynthesis in the model legume Medicago truncatula. MYB2 was strongly upregulated by MYB5, a major regulator of PA biosynthesis in M. truncatula and a component of MYB-basic helix loop helix-WD40 (MBW) activator complexes. Overexpression of MYB2 abolished anthocyanin and PA accumulation in M. truncatula hairy roots and Arabidopsis thaliana seeds, respectively. Anthocyanin deposition was expanded in myb2 mutant seedlings and flowers accompanied by increased anthocyanin content. PA mainly accumulated in the epidermal layer derived from the outer integument in the M. truncatula seed coat, starting from the hilum area. The area of PA accumulation and ANTHOCYANIDIN REDUCTASE expression was expanded into the seed body at the early stage of seed development in the myb2 mutant. Genetic, biochemical, and cell biological evidence suggests that MYB2 functions as part of a multidimensional regulatory network to define the temporal and spatial pattern of anthocyanin and PA accumulation linked to developmental processes. PMID:26410301

  6. A Review Paper On Exploring Text Link And Spacial-Temporal Information In Social Media Networks

    Directory of Open Access Journals (Sweden)

    Dr. Mamta Madan

    2015-03-01

    Full Text Available ABSTRACT The objective of this paper is to have a literature review on the various methods to mine the knowledge from the social media by taking advantage of embedded heterogeneous information. Specifically we are trying to review different types of mining framework which provides us useful information from these networks that have heterogeneous data types including text spacial-temporal and data association LINK information. Firstly we will discuss the link mining to study the link structure with respect to Social Media SM. Secondly we summarize the various text mining models thirdly we shall review spacial as well the temporal models to extract or detect the frequent related topics from SM. Fourthly we will try to figure out few improvised models that take advantage of the link textual temporal and spacial information which motivates to discover progressive principles and fresh methodologies for DM Data Mining in social media networks SMNs.

  7. Escherichia coli under Ionic Silver Stress: An Integrative Approach to Explore Transcriptional, Physiological and Biochemical Responses.

    Directory of Open Access Journals (Sweden)

    Claire Saulou-Bérion

    Full Text Available For a better understanding of the systemic effect of sub-lethal micromolar concentrations of ionic silver on Escherichia coli, we performed a multi-level characterization of cells under Ag+-mediated stress using an integrative biology approach combining physiological, biochemical and transcriptomic data. Physiological parameters, namely bacterial growth and survival after Ag+ exposure, were first quantified and related to the accumulation of intracellular silver, probed for the first time by nano secondary ion mass spectroscopy at sub-micrometer lateral resolution. Modifications in E. coli biochemical composition were evaluated under Ag+-mediated stress by in situ synchrotron Fourier-transform infrared microspectroscopy and a comprehensive transcriptome response was also determined. Using multivariate statistics, correlations between the physiological parameters, the extracellular concentration of AgNO3 and the intracellular silver content, gene expression profiles and micro-spectroscopic data were investigated. We identified Ag+-dependent regulation of gene expression required for growth (e.g. transporter genes, transcriptional regulators, ribosomal proteins, for ionic silver transport and detoxification (e.g. copA, cueO, mgtA, nhaR and for coping with various types of stress (dnaK, pspA, metA,R, oxidoreductase genes. The silver-induced shortening of the acyl chain of fatty acids, mostly encountered in cell membrane, was highlighted by microspectroscopy and correlated with the down-regulated expression of genes involved in fatty acid transport (fadL and synthesis/modification of lipid A (lpxA and arnA. The increase in the disordered secondary structure of proteins in the presence of Ag+ was assessed through the conformational shift shown for amides I and II, and further correlated with the up-regulated expression of peptidase (hfq and chaperone (dnaJ, and regulation of transpeptidase expression (ycfS and ycbB. Interestingly, as these

  8. Exploring temporal and spatial variability of precipitation of Weizhou Island, South China Sea

    Directory of Open Access Journals (Sweden)

    Shulin Deng

    2017-02-01

    New hydrological insights: (1 Rainfall amounts had a non-homogeneous temporal distribution during periods of 1961–1990, 1981–2010 and 1961–2010 on Weizhou Island. (2 Large scale atmospheric circulation may be the major atmospheric driving force of precipitation changes. (3 Precipitation has a cyclical nature on Weizhou Island. (4 Precipitation pattern on Weizhou Island is also affected by oceanic climate. The results provide a scientific basis for water resource management on Weizhou Island.

  9. Exploring the Ecological Coherence between the Spatial and Temporal Patterns of Bacterioplankton in Boreal Lakes

    Directory of Open Access Journals (Sweden)

    Juan Pablo Niño-García

    2017-04-01

    Full Text Available One of the major contemporary challenges in microbial ecology has been to discriminate the reactive core from the random, unreactive components of bacterial communities. In previous work we used the spatial abundance distributions of bacterioplankton across boreal lakes of Québec to group taxa into four distinct categories that reflect either hydrology-mediated dispersal along the aquatic network or environmental selection mechanisms within lakes. Here, we test whether this categorization derived from the spatial distribution of taxa is maintained over time, by analyzing the temporal dynamics of the operational taxonomic units (OTUs within those spatially derived categories along an annual cycle in the oligotrophic lake Croche (Québec, Canada, and assessing the coherence in the patterns of abundance, occurrence, and environmental range of these OTUs over space and time. We report that the temporal dynamics of most taxa within a single lake are largely coherent with those derived from their spatial distribution over large spatial scales, suggesting that these properties must be intrinsic of particular taxa. We also identified a set of rare taxa cataloged as having a random occupancy based on their spatial distribution, but which showed clear seasonality and abundance peaks along the year, yet these comprised a very small fraction of the total rare OTUs. We conclude that the presence of most rare bacterioplankton taxa in boreal lakes is random, since both their temporal and spatial dynamics suggest links to passive downstream transport and persistence in freshwater networks, rather than environmental selection.

  10. SOLAP technology: Merging business intelligence with geospatial technology for interactive spatio-temporal exploration and analysis of data

    Science.gov (United States)

    Rivest, Sonia; Bédard, Yvan; Proulx, Marie-Josée; Nadeau, Martin; Hubert, Frederic; Pastor, Julien

    To support their analytical processes, today's organizations deploy data warehouses and client tools such as OLAP (On-Line Analytical Processing) to access, visualize, and analyze their integrated, aggregated and summarized data. Since a large part of these data have a spatial component, better client tools are required to take full advantage of the geometry of the spatial phenomena or objects being analyzed. With this regard, Spatial OLAP (SOLAP) technology offers promising possibilities. A SOLAP tool can be defined as "a type of software that allows rapid and easy navigation within spatial databases and that offers many levels of information granularity, many themes, many epochs and many display modes synchronized or not: maps, tables and diagrams" [Bédard, Y., Proulx, M.J., Rivest, S., 2005. Enrichissement du OLAP pour l'analyse géographique: exemples de réalisation et différentes possibilités technologiques. In: Bentayeb, F., Boussaid, O., Darmont, J., Rabaseda, S. (Eds.), Entrepôts de Données et Analyse en ligne, RNTI B_1. Paris: Cépaduès, pp. 1-20]. SOLAP tools offer a new user interface and are meant to be client applications sitting on top of multi-scale spatial data warehouses or datacubes. As they are based on the multidimensional paradigm, they facilitate the interactive spatio-temporal exploration of data. The purpose of this paper is to discuss how SOLAP concepts support spatio-temporal exploration of data and then to present the geovisualization, interactivity, and animation features of the SOLAP software developed by our research group. This paper first reviews the general concepts behind OLAP and SOLAP systems. This is followed by a discussion of how these SOLAP concepts support spatio-temporal exploration of data. In the subsequent section, SOLAP software is introduced along with features that enable geovisualization, interactivity and animation.

  11. Molecular and Electrophysiological Characterization of GABAergic Interneurons Expressing the Transcription Factor COUP-TFII in the Adult Human Temporal Cortex

    Science.gov (United States)

    Varga, Csaba; Tamas, Gabor; Barzo, Pal; Olah, Szabolcs; Somogyi, Peter

    2015-01-01

    Transcription factors contribute to the differentiation of cortical neurons, orchestrate specific interneuronal circuits, and define synaptic relationships. We have investigated neurons expressing chicken ovalbumin upstream promoter transcription factor II (COUP-TFII), which plays a role in the migration of GABAergic neurons. Whole-cell, patch-clamp recording in vitro combined with colocalization of molecular cell markers in the adult cortex differentiates distinct interneurons. The majority of strongly COUP-TFII-expressing neurons were in layers I–III. Most calretinin (CR) and/or cholecystokinin- (CCK) and/or reelin-positive interneurons were also COUP-TFII-positive. CR-, CCK-, or reelin-positive neurons formed 80%, 20%, or 17% of COUP-TFII-positive interneurons, respectively. About half of COUP-TFII-/CCK-positive interneurons were CR-positive, a quarter of them reelin-positive, but none expressed both. Interneurons positive for COUP-TFII fired irregular, accommodating and adapting trains of action potentials (APs) and innervated mostly small dendritic shafts and rarely spines or somata. Paired recording showed that a calretinin-/COUP-TFII-positive interneuron elicited inhibitory postsynaptic potentials (IPSPs) in a reciprocally connected pyramidal cell. Calbindin, somatostatin, or parvalbumin-immunoreactive interneurons and most pyramidal cells express no immunohistochemically detectable COUP-TFII. In layers V and VI, some pyramidal cells expressed a low level of COUP-TFII in the nucleus. In conclusion, COUP-TFII is expressed in a diverse subset of GABAergic interneurons predominantly innervating small dendritic shafts originating from both interneurons and pyramidal cells. PMID:25787832

  12. Honey bees as indicators of radionuclide contamination: exploring colony variability and temporal contaminant accumulation

    International Nuclear Information System (INIS)

    Haarmann, T.K.

    1997-01-01

    Two aspects of using honey bees, Apis mellifera, as indicators of environmental radionuclide contamination were investigated: colony variability and temporal contaminant accumulation. Two separate field experiments were conducted in areas with bioavailable radionuclide contamination. Bees were collected from colonies, analysed for concentrations of radionuclides, and the results were compared using graphical and statistical methods. The first experiment indicates that generally a low variability exists between samples collected within the same colony. A higher variability exists between samples collected from adjacent colonies. Levels of tritium and sodium-22 found in samples taken from similar colonies were inconsistent, while levels of cobalt-57, cobalt-60 and manganese-54 were consistent. A second experiment investigated the accumulation of radionuclides over time by comparing colonies that had been in the study area for different periods of time. This experiment demonstrated that there is indeed a significant accumulation of radionuclides within colonies

  13. Exploring spatial and temporal variations of cadmium concentrations in pacific oysters from british columbia.

    Science.gov (United States)

    Feng, Cindy Xin; Cao, Jiguo; Bendell, Leah

    2011-09-01

    Oysters from the Pacific Northwest coast of British Columbia, Canada, contain high levels of cadmium, in some cases exceeding some international food safety guidelines. A primary goal of this article is the investigation of the spatial and temporal variation in cadmium concentrations for oysters sampled from coastal British Columbia. Such information is important so that recommendations can be made as to where and when oysters can be cultured such that accumulation of cadmium within these oysters is minimized. Some modern statistical methods are applied to achieve this goal, including monotone spline smoothing, functional principal component analysis, and semi-parametric additive modeling. Oyster growth rates are estimated as the first derivatives of the monotone smoothing growth curves. Some important patterns in cadmium accumulation by oysters are observed. For example, most inland regions tend to have a higher level of cadmium concentration than most coastal regions, so more caution needs to be taken for shellfish aquaculture practices occurring in the inland regions. The semi-parametric additive modeling shows that oyster cadmium concentration decreases with oyster length, and oysters sampled at 7 m have higher average cadmium concentration than those sampled at 1 m. © 2010, The International Biometric Society.

  14. Exploring Spatio-temporal Dynamics of Cellular Automata for Pattern Recognition in Networks

    Science.gov (United States)

    Miranda, Gisele Helena Barboni; Machicao, Jeaneth; Bruno, Odemir Martinez

    2016-11-01

    Network science is an interdisciplinary field which provides an integrative approach for the study of complex systems. In recent years, network modeling has been used for the study of emergent phenomena in many real-world applications. Pattern recognition in networks has been drawing attention to the importance of network characterization, which may lead to understanding the topological properties that are related to the network model. In this paper, the Life-Like Network Automata (LLNA) method is introduced, which was designed for pattern recognition in networks. LLNA uses the network topology as a tessellation of Cellular Automata (CA), whose dynamics produces a spatio-temporal pattern used to extract the feature vector for network characterization. The method was evaluated using synthetic and real-world networks. In the latter, three pattern recognition applications were used: (i) identifying organisms from distinct domains of life through their metabolic networks, (ii) identifying online social networks and (iii) classifying stomata distribution patterns varying according to different lighting conditions. LLNA was compared to structural measurements and surpasses them in real-world applications, achieving improvement in the classification rate as high as 23%, 4% and 7% respectively. Therefore, the proposed method is a good choice for pattern recognition applications using networks and demonstrates potential for general applicability.

  15. Temporal and subjective work demands in office-based patient care: an exploration of the dimensions of physician work intensity.

    Science.gov (United States)

    Jacobson, C Jeff; Bolon, Shannon; Elder, Nancy; Schroer, Brian; Matthews, Gerald; Szaflarski, Jerzy P; Raphaelson, Marc; Horner, Ronnie D

    2011-01-01

    Physician work intensity (WI) during office-based patient care affects quality of care and patient safety as well as physician job-satisfaction and reimbursement. Existing, brief work intensity measures have been used in physician studies, but their validity in clinical settings has not been established. Document and describe subjective and temporal WI dimensions for physicians in office-based clinical settings. Examine these in relation to the measurement procedures and dimensions of the SWAT and NASA-TLX intensity measures. A focused ethnographic study using interviews and direct observations. Five family physicians, 5 general internists, 5 neurologists, and 4 surgeons. Through interviews, each physician was asked to describe low and high intensity work responsibilities, patients, and events. To document time and task allotments, physicians were observed during a routine workday. Notes and transcripts were analyzed using the editing method in which categories are obtained from the data. WI factors identified by physicians matched dimensions assessed by standard, generic instruments of work intensity. Physicians also reported WI factors outside of the direct patient encounter. Across specialties, physician time spent in direct contact with patients averaged 61% for office-based services. Brief work intensity measures such as the SWAT and NASA-TLX can be used to assess WI in the office-based clinical setting. However, because these measures define the physician work "task" in terms of effort in the presence of the patient (ie, intraservice time), substantial physician effort dedicated to pre- and postservice activities is not captured.

  16. Exploring the isotopic niche: isotopic variance, physiological incorporation, and the temporal dynamics of foraging

    Directory of Open Access Journals (Sweden)

    Justin Douglas Yeakel

    2016-01-01

    Full Text Available Consumer foraging behaviors are dynamic, changing in response to prey availability, seasonality, competition, and even the consumer's physiological state. The isotopic composition of a consumer is a product of these factors as well as the isotopic `landscape' of its prey, i.e. the isotopic mixing space. Stable isotope mixing models are used to back-calculate the most likely proportional contribution of a set of prey to a consumer's diet based on their respective isotopic distributions, however they are disconnected from ecological process. Here we build a mechanistic framework that links the ecological and physiological processes of an individual consumer to the isotopic distribution that describes its diet, and ultimately to the isotopic composition of its own tissues, defined as its `isotopic niche’. By coupling these processes, we systematically investigate under what conditions the isotopic niche of a consumer changes as a function of both the geometric properties of its mixing space and foraging strategies that may be static or dynamic over time. Results of our derivations reveal general insight into the conditions impacting isotopic niche width as a function of consumer specialization on prey, as well as the consumer's ability to transition between diets over time. We show analytically that moderate specialization on isotopically unique prey can serve to maximize a consumer's isotopic niche width, while temporally dynamic diets will tend to result in peak isotopic variance during dietary transitions. We demonstrate the relevance of our theoretical findings by examining a marine system composed of nine invertebrate species commonly consumed by sea otters. In general, our analytical framework highlights the complex interplay of mixing space geometry and consumer dietary behavior in driving expansion and contraction of the isotopic niche. Because this approach is established on ecological mechanism, it is well-suited for enhancing the

  17. Exploring the spatio-temporal interrelation between groundwater and surface water by using the self-organizing maps

    Science.gov (United States)

    Chen, I.-Ting; Chang, Li-Chiu; Chang, Fi-John

    2018-01-01

    In this study, we propose a soft-computing methodology to visibly explore the spatio-temporal groundwater variations of the Kuoping River basin in southern Taiwan. The self-organizing map (SOM) is implemented to investigate the interactive mechanism between surface water and groundwater over the river basin based on large high-dimensional data sets coupled with their occurrence times. We find that extracting the occurrence time from each 30-day moving average data set in the clustered neurons of the SOM is a crucial step to learn the spatio-temporal interaction between surface water and groundwater. We design 2-D Topological Bubble Map to summarize all the groundwater values of four aquifers in a neuron, which can visibly explore the major features of the groundwater in the vertical direction. The constructed SOM topological maps nicely display that: (1) the groundwater movement, in general, extends from the eastern area to the western, where groundwater in the eastern area can be easily recharged from precipitation in wet seasons and discharged into streams during dry seasons due to the high permeability in this area; (2) the water movements in the four aquifers of the study area are quite different, and the seasonal variations of groundwater in the second and third aquifers are larger than those of the others; and (3) the spatial distribution and seasonal variations of groundwater and surface water are comprehensively linked together over the constructed maps to present groundwater characteristics and the interrelation between groundwater and surface water. The proposed modeling methodology not only can classify the large complex high-dimensional data sets into visible topological maps to effectively facilitate the quantitative status of regional groundwater resources but can also provide useful elaboration for future groundwater management.

  18. Exploring the temporal development of childhood IgE profiles to allergen components

    Directory of Open Access Journals (Sweden)

    Önell Annica

    2012-12-01

    Full Text Available Abstract Background Children often develop allergies that may or not persist into adulthood. Although the different allergic symptoms over time have been well documented, the underlying pattern of sensitization to various proteins and subsequent allergy development is unexplored. The aim was to study the sensitization pattern to allergen components over time from infancy to adulthood in a group of infants with heredity for allergic diseases. Methods IgE profiles were monitored in a group of 67 children from 6 months to 18 years using a microarray chip (ImmunoCAP® ISAC containing 103 allergen components derived from 47 allergen sources. The chip IgE profile was compared with clinical history, skin prick test results and diagnoses (atopic dermatitis, asthma and allergic rhinoconjunctivitis at each time point for each child. Results IgE profiles were unique for each child and showed broad agreement with the results of skin prick tests and doctors’ diagnoses. In addition, close examination of the IgE profiles often revealed early indication of subsequent allergies. IgE profiles also facilitated the examination of cross-reactivity contra co-sensitization, thereby greatly enhancing the possibility for managing patients. Conclusion This explorative description indicates that sensitization pattern to allergen components differs over time as well as among allergic individuals when examined with microarray technology.

  19. A Hybrid Approach Combining the Multi-Temporal Scale Spatio-Temporal Network with the Continuous Triangular Model for Exploring Dynamic Interactions in Movement Data: A Case Study of Football

    Directory of Open Access Journals (Sweden)

    Pengdong Zhang

    2018-01-01

    Full Text Available Benefiting from recent advantages in location-aware technologies, movement data are becoming ubiquitous. Hence, numerous research topics with respect to movement data have been undertaken. Yet, the research of dynamic interactions in movement data is still in its infancy. In this paper, we propose a hybrid approach combining the multi-temporal scale spatio-temporal network (MTSSTN and the continuous triangular model (CTM for exploring dynamic interactions in movement data. The approach mainly includes four steps: first, the relative trajectory calculus (RTC is used to derive three types of interaction patterns; second, for each interaction pattern, a corresponding MTSSTN is generated; third, for each MTSSTN, the interaction intensity measures and three centrality measures (i.e., degree, betweenness and closeness are calculated; finally, the results are visualized at multiple temporal scales using the CTM and analyzed based on the generated CTM diagrams. Based on the proposed approach, three distinctive aims can be achieved for each interaction pattern at multiple temporal scales: (1 exploring the interaction intensities between any two individuals; (2 exploring the interaction intensities among multiple individuals, and (3 exploring the importance of each individual and identifying the most important individuals. The movement data obtained from a real football match are used as a case study to validate the effectiveness of the proposed approach. The results demonstrate that the proposed approach is useful in exploring dynamic interactions in football movement data and discovering insightful information.

  20. Visual exploration of big spatio-temporal urban data: a study of New York City taxi trips.

    Science.gov (United States)

    Ferreira, Nivan; Poco, Jorge; Vo, Huy T; Freire, Juliana; Silva, Cláudio T

    2013-12-01

    As increasing volumes of urban data are captured and become available, new opportunities arise for data-driven analysis that can lead to improvements in the lives of citizens through evidence-based decision making and policies. In this paper, we focus on a particularly important urban data set: taxi trips. Taxis are valuable sensors and information associated with taxi trips can provide unprecedented insight into many different aspects of city life, from economic activity and human behavior to mobility patterns. But analyzing these data presents many challenges. The data are complex, containing geographical and temporal components in addition to multiple variables associated with each trip. Consequently, it is hard to specify exploratory queries and to perform comparative analyses (e.g., compare different regions over time). This problem is compounded due to the size of the data-there are on average 500,000 taxi trips each day in NYC. We propose a new model that allows users to visually query taxi trips. Besides standard analytics queries, the model supports origin-destination queries that enable the study of mobility across the city. We show that this model is able to express a wide range of spatio-temporal queries, and it is also flexible in that not only can queries be composed but also different aggregations and visual representations can be applied, allowing users to explore and compare results. We have built a scalable system that implements this model which supports interactive response times; makes use of an adaptive level-of-detail rendering strategy to generate clutter-free visualization for large results; and shows hidden details to the users in a summary through the use of overlay heat maps. We present a series of case studies motivated by traffic engineers and economists that show how our model and system enable domain experts to perform tasks that were previously unattainable for them.

  1. Exploring transcriptional signalling mediated by OsWRKY13, a potential regulator of multiple physiological processes in rice

    Directory of Open Access Journals (Sweden)

    Li Xianghua

    2009-06-01

    Full Text Available Abstract Background Rice transcription regulator OsWRKY13 influences the functioning of more than 500 genes in multiple signalling pathways, with roles in disease resistance, redox homeostasis, abiotic stress responses, and development. Results To determine the putative transcriptional regulation mechanism of OsWRKY13, the putative cis-acting elements of OsWRKY13-influenced genes were analyzed using the whole genome expression profiling of OsWRKY13-activated plants generated with the Affymetrix GeneChip Rice Genome Array. At least 39 transcription factor genes were influenced by OsWRKY13, and 30 of them were downregulated. The promoters of OsWRKY13-upregulated genes were overrepresented with W-boxes for WRKY protein binding, whereas the promoters of OsWRKY13-downregulated genes were enriched with cis-elements putatively for binding of MYB and AP2/EREBP types of transcription factors. Consistent with the distinctive distribution of these cis-elements in up- and downregulated genes, nine WRKY genes were influenced by OsWRKY13 and the promoters of five of them were bound by OsWRKY13 in vitro; all seven differentially expressed AP2/EREBP genes and six of the seven differentially expressed MYB genes were suppressed by in OsWRKY13-activated plants. A subset of OsWRKY13-influenced WRKY genes were involved in host-pathogen interactions. Conclusion These results suggest that OsWRKY13-mediated signalling pathways are partitioned by different transcription factors. WRKY proteins may play important roles in the monitoring of OsWRKY13-upregulated genes and genes involved in pathogen-induced defence responses, whereas MYB and AP2/EREBP proteins may contribute most to the control of OsWRKY13-downregulated genes.

  2. Community Structure Analysis of Transcriptional Networks Reveals Distinct Molecular Pathways for Early- and Late-Onset Temporal Lobe Epilepsy with Childhood Febrile Seizures

    Science.gov (United States)

    Moreira-Filho, Carlos Alberto; Bando, Silvia Yumi; Bertonha, Fernanda Bernardi; Iamashita, Priscila; Silva, Filipi Nascimento; Costa, Luciano da Fontoura; Silva, Alexandre Valotta; Castro, Luiz Henrique Martins; Wen, Hung-Tzu

    2015-01-01

    Age at epilepsy onset has a broad impact on brain plasticity and epilepsy pathomechanisms. Prolonged febrile seizures in early childhood (FS) constitute an initial precipitating insult (IPI) commonly associated with mesial temporal lobe epilepsy (MTLE). FS-MTLE patients may have early disease onset, i.e. just after the IPI, in early childhood, or late-onset, ranging from mid-adolescence to early adult life. The mechanisms governing early (E) or late (L) disease onset are largely unknown. In order to unveil the molecular pathways underlying E and L subtypes of FS-MTLE we investigated global gene expression in hippocampal CA3 explants of FS-MTLE patients submitted to hippocampectomy. Gene coexpression networks (GCNs) were obtained for the E and L patient groups. A network-based approach for GCN analysis was employed allowing: i) the visualization and analysis of differentially expressed (DE) and complete (CO) - all valid GO annotated transcripts - GCNs for the E and L groups; ii) the study of interactions between all the system’s constituents based on community detection and coarse-grained community structure methods. We found that the E-DE communities with strongest connection weights harbor highly connected genes mainly related to neural excitability and febrile seizures, whereas in L-DE communities these genes are not only involved in network excitability but also playing roles in other epilepsy-related processes. Inversely, in E-CO the strongly connected communities are related to compensatory pathways (seizure inhibition, neuronal survival and responses to stress conditions) while in L-CO these communities harbor several genes related to pro-epileptic effects, seizure-related mechanisms and vulnerability to epilepsy. These results fit the concept, based on fMRI and behavioral studies, that early onset epilepsies, although impacting more severely the hippocampus, are associated to compensatory mechanisms, while in late MTLE development the brain is less able to

  3. Freely-available, true-color volume rendering software and cryohistology data sets for virtual exploration of the temporal bone anatomy.

    Science.gov (United States)

    Kahrs, Lüder Alexander; Labadie, Robert Frederick

    2013-01-01

    Cadaveric dissection of temporal bone anatomy is not always possible or feasible in certain educational environments. Volume rendering using CT and/or MRI helps understanding spatial relationships, but they suffer in nonrealistic depictions especially regarding color of anatomical structures. Freely available, nonstained histological data sets and software which are able to render such data sets in realistic color could overcome this limitation and be a very effective teaching tool. With recent availability of specialized public-domain software, volume rendering of true-color, histological data sets is now possible. We present both feasibility as well as step-by-step instructions to allow processing of publicly available data sets (Visible Female Human and Visible Ear) into easily navigable 3-dimensional models using free software. Example renderings are shown to demonstrate the utility of these free methods in virtual exploration of the complex anatomy of the temporal bone. After exploring the data sets, the Visible Ear appears more natural than the Visible Human. We provide directions for an easy-to-use, open-source software in conjunction with freely available histological data sets. This work facilitates self-education of spatial relationships of anatomical structures inside the human temporal bone as well as it allows exploration of surgical approaches prior to cadaveric testing and/or clinical implementation. Copyright © 2013 S. Karger AG, Basel.

  4. Time and Temporality in Early Childhood Educators' Work

    Science.gov (United States)

    Nuttall, Joce; Thomas, Louise

    2015-01-01

    This article reports on the persistence and significance of notions of time and temporality in interviews with early childhood educators in Victoria and Queensland, Australia, in two studies designed to explore the concept of "pedagogical leadership". Interpretive analysis of the interview transcripts of the 19 participants identified…

  5. Exploration

    International Nuclear Information System (INIS)

    Lohrenz, J.

    1992-01-01

    Oil and gas exploration is a unique kind of business. Businesses providing a vast and ever-changing panoply of products to markets are a focus of several disciplines' energetic study and analysis. The product inventory problem is robust, pertinent, and meaningful, and it merits the voluminous and protracted attention received from keen business practitioners. Prototypical business practitioners, be they trained by years of business hurly-burly, or sophisticated MBAs with arrays of mathematical algorithms and computers, are not normally prepared, however, to recognize the unique nature of exploration's inventories. Put together such a business practitioner with an explorationist and misunderstandings, hidden and open, are inevitable and predictably rife. The first purpose of this paper is to articulate the inherited inventory handling paradigms of business practitioners in relation to exploration's inventories. To do so, standard pedagogy in business administration is used and a case study of an exploration venture is presented. A second purpose is to show the burdens that the misunderstandings create. The result is not just business plans that go awry, but public policies that have effects opposite from those intended

  6. Use of a handheld low-cost sensor to explore the effect of urban design features on local-scale spatial and temporal air quality variability.

    Science.gov (United States)

    Miskell, Georgia; Salmond, Jennifer A; Williams, David E

    2018-04-01

    Portable low-cost instruments have been validated and used to measure ambient nitrogen dioxide (NO 2 ) at multiple sites over a small urban area with 20min time resolution. We use these results combined with land use regression (LUR) and rank correlation methods to explore the effects of traffic, urban design features, and local meteorology and atmosphere chemistry on small-scale spatio-temporal variations. We measured NO 2 at 45 sites around the downtown area of Vancouver, BC, in spring 2016, and constructed four different models: i) a model based on averaging concentrations observed at each site over the whole measurement period, and separate temporal models for ii) morning, iii) midday, and iv) afternoon. Redesign of the temporal models using the average model predictors as constants gave three 'hybrid' models that used both spatial and temporal variables. These accounted for approximately 50% of the total variation with mean absolute error±5ppb. Ranking sites by concentration and by change in concentration across the day showed a shift of high NO 2 concentrations across the central city from morning to afternoon. Locations could be identified in which NO 2 concentration was determined by the geography of the site, and others as ones in which the concentration changed markedly from morning to afternoon indicating the importance of temporal controls. Rank correlation results complemented LUR in identifying significant urban design variables that impacted NO 2 concentration. High variability across a relatively small space was partially described by predictor variables related to traffic (bus stop density, speed limits, traffic counts, distance to traffic lights), atmospheric chemistry (ozone, dew point), and environment (land use, trees). A high-density network recording continuously would be needed fully to capture local variations. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Spatial and temporal expression patterns of auxin response transcription factors in the syncytium induced by the beet cyst nematode Heterodera schachtii in Arabidopsis.

    Science.gov (United States)

    Hewezi, Tarek; Piya, Sarbottam; Richard, Geoffrey; Rice, J Hollis

    2014-09-01

    Plant-parasitic cyst nematodes induce the formation of a multinucleated feeding site in the infected root, termed the syncytium. Recent studies point to key roles of the phytohormone auxin in the regulation of gene expression and establishment of the syncytium. Nevertheless, information about the spatiotemporal expression patterns of the transcription factors that mediate auxin transcriptional responses during syncytium formation is limited. Here, we provide a gene expression map of 22 auxin response factors (ARFs) during the initiation, formation and maintenance stages of the syncytium induced by the cyst nematode Heterodera schachtii in Arabidopsis. We observed distinct and overlapping expression patterns of ARFs throughout syncytium development phases. We identified a set of ARFs whose expression is predominantly located inside the developing syncytium, whereas others are expressed in the neighbouring cells, presumably to initiate specific transcriptional programmes required for their incorporation within the developing syncytium. Our analyses also point to a role of certain ARFs in determining the maximum size of the syncytium. In addition, several ARFs were found to be highly expressed in fully developed syncytia, suggesting a role in maintaining the functional phenotype of mature syncytia. The dynamic distribution and overlapping expression patterns of various ARFs seem to be essential characteristics of ARF activity during syncytium development. © 2014 BSPP AND JOHN WILEY & SONS LTD.

  8. Project Temporalities

    DEFF Research Database (Denmark)

    Tryggestad, Kjell; Justesen, Lise; Mouritsen, Jan

    2013-01-01

    Purpose – The purpose of this paper is to explore how animals can become stakeholders in interaction with project management technologies and what happens with project temporalities when new and surprising stakeholders become part of a project and a recognized matter of concern to be taken...... into account. Design/methodology/approach – The paper is based on a qualitative case study of a project in the building industry. The authors use actor-network theory (ANT) to analyze the emergence of animal stakeholders, stakes and temporalities. Findings – The study shows how project temporalities can...... multiply in interaction with project management technologies and how conventional linear conceptions of project time may be contested with the emergence of new non-human stakeholders and temporalities. Research limitations/implications – The study draws on ANT to show how animals can become stakeholders...

  9. [Explore the spatial and temporal patterns of water pollution in the Yincungang canal of the Lake Taihu basin, China].

    Science.gov (United States)

    Yang, Xiao-Ying; Luo, Xing-Zhang; Zheng, Zheng; Fang, Shu-Bo

    2012-09-01

    Two high-density snap-shot samplings were conducted along the Yincungang canal, one important tributary of the Lake Tai, in April (low flow period) and June (high flow period) of 2010. Geostatistical analysis based on the river network distance was used to analyze the spatial and temporal patterns of the pollutant concentrations along the canal with an emphasis on chemical oxygen demand (COD) and total nitrogen (TN). Study results have indicated: (1) COD and TN concentrations display distinctly different spatial and temporal patterns between the low and high flow periods. COD concentration in June is lower than that in April, while TN concentration has the contrary trend. (2) COD load is relatively constant during the period between the two monitoring periods. The spatial correlation structure of COD is exponential for both April and June, and the change of COD concentration is mainly influenced by hydrological conditions. (3) Nitrogen load from agriculture increased significantly during the period between the two monitoring periods. Large amount of chaotic fertilizing by individual farmers has led to the loss of the spatial correlation among the observed TN concentrations. Hence, changes of TN concentration in June are under the dual influence of agricultural fertilizing and hydrological conditions. In the view of the complex hydrological conditions and serious water pollution in the Lake Taihu region, geostatistical analysis is potentially a useful tool for studying the characteristics of pollutant distribution and making predictions in the region.

  10. Exploring the potential of Sentinel-1 data for regional scale slope instability detection using multi-temporal interferometry

    Science.gov (United States)

    Wasowski, Janusz; Bovenga, Fabio; Nutricato, Raffaele; Nitti, Davide Oscar; Chiaradia, Maria Teresa; Refice, Alberto; Pasquariello, Guido

    2016-04-01

    Launched in 2014, the European Space Agency (ESA) Sentinel-1 satellite carrying a medium resolution (20 m) C-Band Synthetic Aperture Radar (SAR) sensor holds much promise for new applications of multi-temporal interferometry (MTI) in landslide assessment. Specifically, the regularity of acquisitions, timeliness of data delivery, shorter repeat cycle (currently 12 days with Sentinel-1A sensor), and flexible incidence angle geometry, all imply better practical utility of MTI relying on Sentinel-1 with respect to MTI based on data from earlier ESA's satellite radar C-band sensors (ERS1/2, ENVISAT). Furthermore, the upcoming launch of Sentinel-1B will cut down the repeat cycle to 6 days, thereby further improving temporal coherence and quality and coverage of MTI products. Taking advantage of the Interferometric Wide (IW) Swath acquisition mode of Sentinel-1 (images covering a 250 km swath on the ground), in this work we test the potential of such data for regional scale slope instability detection through MTI. Our test area includes the landslide-prone Apennine Mountains of Southern Italy. We rely on over 30 Sentinel-1 images, most of which acquired in 2015, and MTI processing through the SPINUA algorithm (Stable Points INterferometry in Un-urbanized Areas). The potential of MTI results based on Sentinel-1 data is assessed by comparing the detected ground surface displacements with the MTI results obtained for the same test area using the C-Band data acquired by ERS1/2 and ENVISAT in 1990s and 2000s. Although the initial results are encouraging, it seems evident that longer-term (few years) acquisitions of Sentinel-1 are necessary to reliably detect some extremely slow movements, which were observed in the last two decades and are likely to be still present in peri-urban areas of many hilltop towns in the Apennine Mts. The MTI results obtained from Sentinel-1 data are also locally compared with the MTI outcomes based on the high resolution (3 m) TerraSAR-X imagery

  11. Accidental hazardous material releases with human impacts in the United States: exploration of geographical distribution and temporal trends.

    Science.gov (United States)

    Sengul, Hatice; Santella, Nicholas; Steinberg, Laura J; Chermak, Christina

    2010-09-01

    To investigate the circumstances and geographic and temporal distributions of hazardous material releases and resulting human impacts in the United States. Releases with fatalities, injuries, and evacuations were identified from reports to the National Response Center between 1990 and 2008, correcting for data quality issues identified in previous studies. From more than 550,000 reports, 861 deaths, 16,348 injuries and 741,427 evacuations were identified. Injuries from releases of chemicals at fixed facilities and natural gas from pipelines have decreased whereas evacuations from petroleum releases at fixed facilities have increased. Results confirm recent advances in chemical and pipeline safety and suggest directions for further improvement including targeted training and inspections and adoption of inherently safer design principles.

  12. An Online Atlas for Exploring Spatio-Temporal Patterns of Cancer Mortality (1972-2011) and Incidence (1995-2008) in Taiwan.

    Science.gov (United States)

    Ku, Wen-Yuan; Liaw, Yung-Po; Huang, Jing-Yang; Nfor, Oswald Ndi; Hsu, Shu-Yi; Ko, Pei-Chieh; Lee, Wen-Chung; Chen, Chien-Jen

    2016-05-01

    Public health mapping and Geographical Information Systems (GIS) are already being used to locate the geographical spread of diseases. This study describes the construction of an easy-to-use online atlas of cancer mortality (1972-2011) and incidence (1995-2008) in Taiwan.Two sets of color maps were made based on "age-adjusted mortality by rate" and "age-adjusted mortality by rank." AJAX (Asynchronous JavaScript and XML), JSON (JavaScript Object Notation), and SVG (Scaling Vector Graphic) were used to create the online atlas. Spatio-temporal patterns of cancer mortality and incidence in Taiwan over the period from 1972 to 2011 and from 1995 to 2008.The constructed online atlas contains information on cancer mortality and incidence (http://taiwancancermap.csmu-liawyp.tw/). The common GIS functions include zoom and pan and identity tools. Users can easily customize the maps to explore the spatio-temporal trends of cancer mortality and incidence using different devices (such as personal computers, mobile phone, or pad). This study suggests an easy- to-use, low-cost, and independent platform for exploring cancer incidence and mortality. It is expected to serve as a reference tool for cancer prevention and risk assessment.This online atlas is a cheap and fast tool that integrates various cancer maps. Therefore, it can serve as a powerful tool that allows users to examine and compare spatio-temporal patterns of various maps. Furthermore, it is an-easy-to use tool for updating data and assessing risk factors of cancer in Taiwan.

  13. Exploration of spatio-temporal patterns of students' movement in field trip by visualizing the log data

    Science.gov (United States)

    Cho, Nahye; Kang, Youngok

    2018-05-01

    A numerous log data in addition to user input data are being generated as mobile and web users continue to increase recently, and the studies in order to explore the patterns and meanings of various movement activities by making use of these log data are also rising rapidly. On the other hand, in the field of education, people have recognized the importance of field trip as the creative education is highlighted. Also, the examples which utilize the mobile devices in the field trip in accordance to the development of information technology are growing. In this study, we try to explore the patterns of student's activity by visualizing the log data generated from high school students' field trip with mobile device.

  14. Homonormativity, Charternormativity, and Processes of Legitimation: Exploring the Affective-Spatio-Temporal-Fixed Dimensions of Marriage Equality and Charter Schools

    OpenAIRE

    Stern, Mark

    2015-01-01

    Over the past five years, marriage equality and charter schools have emerged at the forefront of political conversations about equality and rights. Some argue that these policies extend access to certain benefits and opportunities to historically oppressed communities, thus furthering liberalism and egalitarianism. In this article, I engage these arguments by exploring how and why people from dominant cultures come to support marriage equality or charter schools despite not directly benefitti...

  15. Exploring the determinants of phylogenetic diversity and assemblage structure in conifers across temporal, spatial, and taxonomic scales

    DEFF Research Database (Denmark)

    Eiserhardt, Wolf L.; Borchsenius, Finn; Sandel, Brody Steven

    -environmental models are important elements in this framework. Here, we integrate both types of data in order to explore the determinants of forest tree diversity using the conifers as a model group. Conifers are an old, diverse (ca. 650 spp. in 6 families) and widespread group of woody plants of high ecological...... and economic importance. They are better studied than most other globally distributed groups of forest trees, allowing integrative studies with high phylogenetic and spatial resolution. We analyse phylogenetic diversity, assemblage structure, and diversification rates for regional conifer assemblages...

  16. Kilometric Scale Modeling of the North West European Shelf Seas: Exploring the Spatial and Temporal Variability of Internal Tides

    Science.gov (United States)

    Guihou, K.; Polton, J.; Harle, J.; Wakelin, S.; O'Dea, E.; Holt, J.

    2018-01-01

    The North West European Shelf break acts as a barrier to the transport and exchange between the open ocean and the shelf seas. The strong spatial variability of these exchange processes is hard to fully explore using observations, and simulations generally are too coarse to simulate the fine-scale processes over the whole region. In this context, under the FASTNEt program, a new NEMO configuration of the North West European Shelf and Atlantic Margin at 1/60° (˜1.8 km) has been developed, with the objective to better understand and quantify the seasonal and interannual variability of shelf break processes. The capability of this configuration to reproduce the seasonal cycle in SST, the barotropic tide, and fine-resolution temperature profiles is assessed against a basin-scale (1/12°, ˜9 km) configuration and a standard regional configuration (7 km resolution). The seasonal cycle is well reproduced in all configurations though the fine-resolution allows the simulation of smaller scale processes. Time series of temperature at various locations on the shelf show the presence of internal waves with a strong spatiotemporal variability. Spectral analysis of the internal waves reveals peaks at the diurnal, semidiurnal, inertial, and quarter-diurnal bands, which are only realistically reproduced in the new configuration. Tidally induced pycnocline variability is diagnosed in the model and shown to vary with the spring neap cycle with mean displacement amplitudes in excess of 2 m for 30% of the stratified domain. With sufficiently fine resolution, internal tides are shown to be generated at numerous bathymetric features resulting in a complex pycnocline displacement superposition pattern.

  17. Exploring the efficacy of a 5-day course of transcranial direct current stimulation (TDCS) on depression and memory function in patients with well-controlled temporal lobe epilepsy.

    Science.gov (United States)

    Liu, Anli; Bryant, Andrew; Jefferson, Ashlie; Friedman, Daniel; Minhas, Preet; Barnard, Sarah; Barr, William; Thesen, Thomas; O'Connor, Margaret; Shafi, Mouhsin; Herman, Susan; Devinsky, Orrin; Pascual-Leone, Alvaro; Schachter, Steven

    2016-02-01

    Depression and memory dysfunction significantly impact the quality of life of patients with epilepsy. Current therapies for these cognitive and psychiatric comorbidities are limited. We explored the efficacy and safety of transcranial direct current stimulation (TDCS) for treating depression and memory dysfunction in patients with temporal lobe epilepsy (TLE). Thirty-seven (37) adults with well-controlled TLE were enrolled in a double-blinded, sham-controlled, randomized, parallel-group study of 5 days of fixed-dose (2 mA, 20 min) TDCS. Subjects were randomized to receive either real or sham TDCS, both delivered over the left dorsolateral prefrontal cortex. Patients received neuropsychological testing and a 20-minute scalp EEG at baseline immediately after the TDCS course and at 2- and 4-week follow-up. There was improvement in depression scores immediately after real TDCS, but not sham TDCS, as measured by changes in the Beck Depression Inventory (BDI change: -1.68 vs. 1.27, pTDCS as a safe and well-tolerated nonpharmacologic approach to improving depressive symptoms in patients with well-controlled TLE. However, there were no changes in memory function immediately following or persisting after a stimulation course. Further studies may determine optimal stimulation parameters for maximal mood benefit. Copyright © 2015. Published by Elsevier Inc.

  18. Temporal mood changes associated with different levels of adolescent drinking: using mobile phones and experience sampling methods to explore motivations for adolescent alcohol use.

    Science.gov (United States)

    Crooke, Alexander H D; Reid, Sophie C; Kauer, Sylvia D; McKenzie, Dean P; Hearps, Stephen J C; Khor, Angela S; Forbes, Andrew B

    2013-05-01

    Alcohol use during adolescence is associated with the onset of alcohol use disorders, mental health disorders, substance abuse as well as socially and physically damaging behaviours, the effects of which last well into adulthood. Nevertheless, alcohol use remains prevalent in this population. Understanding motivations behind adolescent alcohol consumption may help in developing more appropriate and effective interventions. This study aims to increase this understanding by exploring the temporal relationship between mood and different levels of alcohol intake in a sample of young people. Forty-one secondary school students used a purpose-designed mobile phone application to monitor their daily mood and alcohol use for 20 random days within a 31 day period. Generalised estimating equations were used to examine the relationship between differing levels of alcohol consumption (light, intermediate and heavy) and positive and negative mood three days before and after drinking episodes. While there was no relationship between light and heavy drinking and positive mood, there was an increase in positive mood before and after the drinking event for those that drank intermediate amounts. No statistically significant relationships were found between negative mood and any of the three drinking categories. Adolescents who drank in intermediate amounts on a single drinking occasion experienced an increase in positive mood over the three days leading up to and three days following a drinking event. These findings contribute to an understanding of the motivations that underpin adolescent alcohol use, which may help inform future interventions. © 2013 Australasian Professional Society on Alcohol and other Drugs.

  19. Exploring the Role of BET Bromodomain Proteins in AR Transcriptional Regulation: A Perpetuating Cycle of JQ1 Resistance in CRPC Therapy

    Science.gov (United States)

    2016-12-01

    Risk Gene in Metastatic Prostate Cancers with Novel Epigenetic Inhibitors. May19-20, 2016  What do you plan to do during the next reporting... Epigenetic Regulation of HOXB13 Transcriptional Networks Promotes Castration Resistant Prostate Cancer Growth (Manuscript under preparation...Release; Distribution Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT During the inevitable progression to castration resistant stage, prostate cancer

  20. Temporal contingency

    Science.gov (United States)

    Gallistel, C.R.; Craig, Andrew R.; Shahan, Timothy A.

    2015-01-01

    Contingency, and more particularly temporal contingency, has often figured in thinking about the nature of learning. However, it has never been formally defined in such a way as to make it a measure that can be applied to most animal learning protocols. We use elementary information theory to define contingency in such a way as to make it a measurable property of almost any conditioning protocol. We discuss how making it a measurable construct enables the exploration of the role of different contingencies in the acquisition and performance of classically and operantly conditioned behavior. PMID:23994260

  1. Temporal contingency.

    Science.gov (United States)

    Gallistel, C R; Craig, Andrew R; Shahan, Timothy A

    2014-01-01

    Contingency, and more particularly temporal contingency, has often figured in thinking about the nature of learning. However, it has never been formally defined in such a way as to make it a measure that can be applied to most animal learning protocols. We use elementary information theory to define contingency in such a way as to make it a measurable property of almost any conditioning protocol. We discuss how making it a measurable construct enables the exploration of the role of different contingencies in the acquisition and performance of classically and operantly conditioned behavior. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. Pavlovian Prisoner's Dilemma in one-dimensional cellular automata: analytical results, the quasi-regular phase, spatio-temporal patterns and parameter space exploration

    OpenAIRE

    Pereira, Marcelo Alves; Martinez, Alexandre Souto

    2009-01-01

    The Prisoner's Dilemma (PD) game is used in several fields due to the emergence of cooperation among selfish players. Here, we have considered a one-dimensional lattice, where each cell represents a player, that can cooperate or defect. This one-dimensional geometry allows us to retrieve the results obtained for regular lattices and to keep track of the system spatio-temporal evolution. Players play PD with their neighbors and update their state using the Pavlovian Evolutionary Strategy. If t...

  3. Normalization Strategies for Enhancing Spatio-Temporal Analysis of Social Media Responses during Extreme Events: A Case Study based on Analysis of Four Extreme Events using Socio-Environmental Data Explorer (SEDE)

    Science.gov (United States)

    Ajayakumar, J.; Shook, E.; Turner, V. K.

    2017-10-01

    With social media becoming increasingly location-based, there has been a greater push from researchers across various domains including social science, public health, and disaster management, to tap in the spatial, temporal, and textual data available from these sources to analyze public response during extreme events such as an epidemic outbreak or a natural disaster. Studies based on demographics and other socio-economic factors suggests that social media data could be highly skewed based on the variations of population density with respect to place. To capture the spatio-temporal variations in public response during extreme events we have developed the Socio-Environmental Data Explorer (SEDE). SEDE collects and integrates social media, news and environmental data to support exploration and assessment of public response to extreme events. For this study, using SEDE, we conduct spatio-temporal social media response analysis on four major extreme events in the United States including the "North American storm complex" in December 2015, the "snowstorm Jonas" in January 2016, the "West Virginia floods" in June 2016, and the "Hurricane Matthew" in October 2016. Analysis is conducted on geo-tagged social media data from Twitter and warnings from the storm events database provided by National Centers For Environmental Information (NCEI) for analysis. Results demonstrate that, to support complex social media analyses, spatial and population-based normalization and filtering is necessary. The implications of these results suggests that, while developing software solutions to support analysis of non-conventional data sources such as social media, it is quintessential to identify the inherent biases associated with the data sources, and adapt techniques and enhance capabilities to mitigate the bias. The normalization strategies that we have developed and incorporated to SEDE will be helpful in reducing the population bias associated with social media data and will be useful

  4. Direct Exploration of the Role of the Ventral Anterior Temporal Lobe in Semantic Memory: Cortical Stimulation and Local Field Potential Evidence From Subdural Grid Electrodes.

    Science.gov (United States)

    Shimotake, Akihiro; Matsumoto, Riki; Ueno, Taiji; Kunieda, Takeharu; Saito, Satoru; Hoffman, Paul; Kikuchi, Takayuki; Fukuyama, Hidenao; Miyamoto, Susumu; Takahashi, Ryosuke; Ikeda, Akio; Lambon Ralph, Matthew A

    2015-10-01

    Semantic memory is a crucial higher cortical function that codes the meaning of objects and words, and when impaired after neurological damage, patients are left with significant disability. Investigations of semantic dementia have implicated the anterior temporal lobe (ATL) region, in general, as crucial for multimodal semantic memory. The potentially crucial role of the ventral ATL subregion has been emphasized by recent functional neuroimaging studies, but the necessity of this precise area has not been selectively tested. The implantation of subdural electrode grids over this subregion, for the presurgical assessment of patients with partial epilepsy or brain tumor, offers the dual yet rare opportunities to record cortical local field potentials while participants complete semantic tasks and to stimulate the functionally identified regions in the same participants to evaluate the necessity of these areas in semantic processing. Across 6 patients, and utilizing a variety of semantic assessments, we evaluated and confirmed that the anterior fusiform/inferior temporal gyrus is crucial in multimodal, receptive, and expressive, semantic processing. © The Author 2014. Published by Oxford University Press.

  5. Deciphering Transcriptional Regulation

    DEFF Research Database (Denmark)

    Valen, Eivind

    The myriad of cells in the human body are all made from the same blueprint: the human genome. At the heart of this diversity lies the concept of gene regulation, the process in which it is decided which genes are used where and when. Genes do not function as on/off buttons, but more like a volume...... mostly near the start of the gene known as the promoter. This region contains patterns scattered in the DNA that the TFs can recognize and bind to. Such binding can prompt the assembly of the pre-initiation complex which ultimately leads to transcription of the gene. In order to achieve the regulation...... on what characterizes a hippocampus promoter. Pairing CAGE with TF binding site prediction we identi¿ed a likely key regulator of hippocampus. Finally, we developed a method for CAGE exploration. While the DeepCAGE library characterized a full 1.4 million transcription initiation events it did not capture...

  6. Temporal networks

    CERN Document Server

    Saramäki, Jari

    2013-01-01

    The concept of temporal networks is an extension of complex networks as a modeling framework to include information on when interactions between nodes happen. Many studies of the last decade examine how the static network structure affect dynamic systems on the network. In this traditional approach  the temporal aspects are pre-encoded in the dynamic system model. Temporal-network methods, on the other hand, lift the temporal information from the level of system dynamics to the mathematical representation of the contact network itself. This framework becomes particularly useful for cases where there is a lot of structure and heterogeneity both in the timings of interaction events and the network topology. The advantage compared to common static network approaches is the ability to design more accurate models in order to explain and predict large-scale dynamic phenomena (such as, e.g., epidemic outbreaks and other spreading phenomena). On the other hand, temporal network methods are mathematically and concept...

  7. Normalization Strategies for Enhancing Spatio-Temporal Analysis of Social Media Responses during Extreme Events: A Case Study based on Analysis of Four Extreme Events using Socio-Environmental Data Explorer (SEDE

    Directory of Open Access Journals (Sweden)

    J. Ajayakumar

    2017-10-01

    Full Text Available With social media becoming increasingly location-based, there has been a greater push from researchers across various domains including social science, public health, and disaster management, to tap in the spatial, temporal, and textual data available from these sources to analyze public response during extreme events such as an epidemic outbreak or a natural disaster. Studies based on demographics and other socio-economic factors suggests that social media data could be highly skewed based on the variations of population density with respect to place. To capture the spatio-temporal variations in public response during extreme events we have developed the Socio-Environmental Data Explorer (SEDE. SEDE collects and integrates social media, news and environmental data to support exploration and assessment of public response to extreme events. For this study, using SEDE, we conduct spatio-temporal social media response analysis on four major extreme events in the United States including the “North American storm complex” in December 2015, the “snowstorm Jonas” in January 2016, the “West Virginia floods” in June 2016, and the “Hurricane Matthew” in October 2016. Analysis is conducted on geo-tagged social media data from Twitter and warnings from the storm events database provided by National Centers For Environmental Information (NCEI for analysis. Results demonstrate that, to support complex social media analyses, spatial and population-based normalization and filtering is necessary. The implications of these results suggests that, while developing software solutions to support analysis of non-conventional data sources such as social media, it is quintessential to identify the inherent biases associated with the data sources, and adapt techniques and enhance capabilities to mitigate the bias. The normalization strategies that we have developed and incorporated to SEDE will be helpful in reducing the population bias associated with

  8. Temporal Patterns in Sheep Fetal Heart Rate Variability Correlate to Systemic Cytokine Inflammatory Response: A Methodological Exploration of Monitoring Potential Using Complex Signals Bioinformatics.

    Directory of Open Access Journals (Sweden)

    Christophe L Herry

    Full Text Available Fetal inflammation is associated with increased risk for postnatal organ injuries. No means of early detection exist. We hypothesized that systemic fetal inflammation leads to distinct alterations of fetal heart rate variability (fHRV. We tested this hypothesis deploying a novel series of approaches from complex signals bioinformatics. In chronically instrumented near-term fetal sheep, we induced an inflammatory response with lipopolysaccharide (LPS injected intravenously (n = 10 observing it over 54 hours; seven additional fetuses served as controls. Fifty-one fHRV measures were determined continuously every 5 minutes using Continuous Individualized Multi-organ Variability Analysis (CIMVA. CIMVA creates an fHRV measures matrix across five signal-analytical domains, thus describing complementary properties of fHRV. We implemented, validated and tested methodology to obtain a subset of CIMVA fHRV measures that matched best the temporal profile of the inflammatory cytokine IL-6. In the LPS group, IL-6 peaked at 3 hours. For the LPS, but not control group, a sharp increase in standardized difference in variability with respect to baseline levels was observed between 3 h and 6 h abating to baseline levels, thus tracking closely the IL-6 inflammatory profile. We derived fHRV inflammatory index (FII consisting of 15 fHRV measures reflecting the fetal inflammatory response with prediction accuracy of 90%. Hierarchical clustering validated the selection of 14 out of 15 fHRV measures comprising FII. We developed methodology to identify a distinctive subset of fHRV measures that tracks inflammation over time. The broader potential of this bioinformatics approach is discussed to detect physiological responses encoded in HRV measures.

  9. Biotransformation in the zebrafish embryo -temporal gene transcription changes of cytochrome P450 enzymes and internal exposure dynamics of the AhR binding xenobiotic benz[a]anthracene.

    Science.gov (United States)

    Kühnert, Agnes; Vogs, Carolina; Seiwert, Bettina; Aulhorn, Silke; Altenburger, Rolf; Hollert, Henner; Küster, Eberhard; Busch, Wibke

    2017-11-01

    Not much is known about the biotransformation capability of zebrafish (Danio rerio) embryos. For understanding possible toxicity differences to adult fish, it might be crucial to understand the biotransformation of chemicals in zebrafish embryos i.e. as part of toxicokinetics. The biotransformation capabilities were analysed for two different stages of zebrafish embryos in conjunction with the internal concentrations of a xenobiotic. Zebrafish embryos of the late cleavage/early blastula period (2-26 hpf) and the early pharyngula period (26-50 hpf) were exposed for 24 h to the AhR binding compound benz[a]anthracene (BaA). Time dependent changes in cyp transcription (cyp1a, cyp1b1, cyp1c1 and cyp1c2) as well as concentration & time-dependent courses of BaA in the fish embryo and the exposure medium were analysed. Additionally, the CYP mediated formation of biotransformation products was investigated. We found correlations between transcriptional responses and the internal concentration for both exposure types. These correlations were depending on the start of the exposure i.e. the age of the exposed embryo. While no significant induction of the examined gene transcripts was observed in the first 12 h of exposure beginning in the blastula period a correlation was apparent when exposure started later i.e. in the pharyngula period. A significant induction of cyp1a was detected already after 1.5 h of BaA exposure. Gene transcripts for cyp1b1, cyp1c1 and cyp1c2 showed expressions distinctly different from cyp1a and were, in general, less inducible by BaA in both exposure windows. The toxicokinetic analysis showed that the biotransformation capability was fivefold higher in the older fish embryos. Biotransformation products of phase I reactions were found between 32 hpf and 50 hpf and were tentatively identified as benz[a]anthracene-phenol and benz[a]anthracene-dihydrodiol-epoxide. In conclusion, not only duration but also onset of exposure in relation to the

  10. The transcriptional landscape

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2011-01-01

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

  11. Deciphering the Innate Lymphoid Cell Transcriptional Program

    Directory of Open Access Journals (Sweden)

    Cyril Seillet

    2016-10-01

    Full Text Available Innate lymphoid cells (ILCs are enriched at mucosal surfaces, where they provide immune surveillance. All ILC subsets develop from a common progenitor that gives rise to pre-committed progenitors for each of the ILC lineages. Currently, the temporal control of gene expression that guides the emergence of these progenitors is poorly understood. We used global transcriptional mapping to analyze gene expression in different ILC progenitors. We identified PD-1 to be specifically expressed in PLZF+ ILCp and revealed that the timing and order of expression of the transcription factors NFIL3, ID2, and TCF-1 was critical. Importantly, induction of ILC lineage commitment required only transient expression of NFIL3 prior to ID2 and TCF-1 expression. These findings highlight the importance of the temporal program that permits commitment of progenitors to the ILC lineage, and they expand our understanding of the core transcriptional program by identifying potential regulators of ILC development.

  12. Temporal networks

    Science.gov (United States)

    Holme, Petter; Saramäki, Jari

    2012-10-01

    A great variety of systems in nature, society and technology-from the web of sexual contacts to the Internet, from the nervous system to power grids-can be modeled as graphs of vertices coupled by edges. The network structure, describing how the graph is wired, helps us understand, predict and optimize the behavior of dynamical systems. In many cases, however, the edges are not continuously active. As an example, in networks of communication via e-mail, text messages, or phone calls, edges represent sequences of instantaneous or practically instantaneous contacts. In some cases, edges are active for non-negligible periods of time: e.g., the proximity patterns of inpatients at hospitals can be represented by a graph where an edge between two individuals is on throughout the time they are at the same ward. Like network topology, the temporal structure of edge activations can affect dynamics of systems interacting through the network, from disease contagion on the network of patients to information diffusion over an e-mail network. In this review, we present the emergent field of temporal networks, and discuss methods for analyzing topological and temporal structure and models for elucidating their relation to the behavior of dynamical systems. In the light of traditional network theory, one can see this framework as moving the information of when things happen from the dynamical system on the network, to the network itself. Since fundamental properties, such as the transitivity of edges, do not necessarily hold in temporal networks, many of these methods need to be quite different from those for static networks. The study of temporal networks is very interdisciplinary in nature. Reflecting this, even the object of study has many names-temporal graphs, evolving graphs, time-varying graphs, time-aggregated graphs, time-stamped graphs, dynamic networks, dynamic graphs, dynamical graphs, and so on. This review covers different fields where temporal graphs are considered

  13. Temporal naturalism

    Science.gov (United States)

    Smolin, Lee

    2015-11-01

    Two people may claim both to be naturalists, but have divergent conceptions of basic elements of the natural world which lead them to mean different things when they talk about laws of nature, or states, or the role of mathematics in physics. These disagreements do not much affect the ordinary practice of science which is about small subsystems of the universe, described or explained against a background, idealized to be fixed. But these issues become crucial when we consider including the whole universe within our system, for then there is no fixed background to reference observables to. I argue here that the key issue responsible for divergent versions of naturalism and divergent approaches to cosmology is the conception of time. One version, which I call temporal naturalism, holds that time, in the sense of the succession of present moments, is real, and that laws of nature evolve in that time. This is contrasted with timeless naturalism, which holds that laws are immutable and the present moment and its passage are illusions. I argue that temporal naturalism is empirically more adequate than the alternatives, because it offers testable explanations for puzzles its rivals cannot address, and is likely a better basis for solving major puzzles that presently face cosmology and physics. This essay also addresses the problem of qualia and experience within naturalism and argues that only temporal naturalism can make a place for qualia as intrinsic qualities of matter.

  14. Toward a clinic of temporality?

    Science.gov (United States)

    Rivasseau Jonveaux, Thérèse; Batt, Martine; Trognon, Alain

    2017-12-01

    The discovery of time cells has expanded our knowledge in the field of spatial and temporal information coding and the key role of the hippocampus. The internal clock model complemented with the attentional gate model allows a more in-depth understanding of the perception of time. The motor representation of duration is ensured by the basal ganglia, while the cerebellum synchronizes short duration for the movement. The right prefrontal cortex seemingly intervenes in the handling of temporal information in working memory. The temporal lobe ensures the comparison of durations, especially the right lobe for the reference durations and the medial lobe for the reproduction of durations in episodic memory. During normal aging, the hypothesis of slowing of the temporal processor is evoked when noting the perception of the acceleration of the passage of time that seemingly occurs with advancing age. The various studies pertaining specifically to time cognition, albeit heterogeneous in terms of methodology, attest to the wide-ranging disturbances of this cognitive field during the course of numerous disorders, whether psychiatric - depression and schizophrenia notably - or neurological. Hence, perturbations in temporality are observed in focal brain lesions and in subcortical disorders, such as Parkinson's disease or Huntington's chorea. Alzheimer's disease represents a particularly fertile field of exploration with regard to time cognition and temporality. The objectified deconstruction of temporal experience provides insights into the very processes of temporality and their nature: episodic, semantic and procedural. In addition to exploration based on elementary stimuli, one should also consider the time lived, i.e. that of the subject, to better understand cognition as it relates to time. While the temporal dimension permeates the whole cognitive field, it remains largely neglected: integration of a genuine time cognition and temporality clinic in daily practice remains

  15. ADHD and temporality

    DEFF Research Database (Denmark)

    Nielsen, Mikka

    According to the official diagnostic manual, ADHD is defined by symptoms of inattention, hyperactivity, and impulsivity and patterns of behaviour are characterized as failure to pay attention to details, excessive talking, fidgeting, or inability to remain seated in appropriate situations (DSM-5......). In this paper, however, I will ask if we can understand what we call ADHD in a different way than through the symptom descriptions and will advocate for a complementary, phenomenological understanding of ADHD as a certain being in the world – more specifically as a matter of a phenomenological difference...... in temporal experience and/or rhythm. Inspired by both psychiatry’s experiments with people diagnosed with ADHD and their assessment of time and phenomenological perspectives on mental disorders and temporal disorientation I explore the experience of ADHD as a disruption in the phenomenological experience...

  16. Physical interactions among plant MADS-box transcription factors and their biological relevance

    NARCIS (Netherlands)

    Nougalli Tonaco, I.A.

    2008-01-01

    The biological interpretation of the genome starts from transcription, and many different signaling pathways are integrated at this level. Transcription factors play a central role in the transcription process, because they select the down-stream genes and determine their spatial and temporal

  17. DNA residence time is a regulatory factor of transcription repression

    Science.gov (United States)

    Clauß, Karen; Popp, Achim P.; Schulze, Lena; Hettich, Johannes; Reisser, Matthias; Escoter Torres, Laura; Uhlenhaut, N. Henriette

    2017-01-01

    Abstract Transcription comprises a highly regulated sequence of intrinsically stochastic processes, resulting in bursts of transcription intermitted by quiescence. In transcription activation or repression, a transcription factor binds dynamically to DNA, with a residence time unique to each factor. Whether the DNA residence time is important in the transcription process is unclear. Here, we designed a series of transcription repressors differing in their DNA residence time by utilizing the modular DNA binding domain of transcription activator-like effectors (TALEs) and varying the number of nucleotide-recognizing repeat domains. We characterized the DNA residence times of our repressors in living cells using single molecule tracking. The residence times depended non-linearly on the number of repeat domains and differed by more than a factor of six. The factors provoked a residence time-dependent decrease in transcript level of the glucocorticoid receptor-activated gene SGK1. Down regulation of transcription was due to a lower burst frequency in the presence of long binding repressors and is in accordance with a model of competitive inhibition of endogenous activator binding. Our single molecule experiments reveal transcription factor DNA residence time as a regulatory factor controlling transcription repression and establish TALE-DNA binding domains as tools for the temporal dissection of transcription regulation. PMID:28977492

  18. Repression of meiotic genes by antisense transcription and by Fkh2 transcription factor in Schizosaccharomyces pombe.

    Science.gov (United States)

    Chen, Huei-Mei; Rosebrock, Adam P; Khan, Sohail R; Futcher, Bruce; Leatherwood, Janet K

    2012-01-01

    In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. Disruption of the antisense transcription of three of these mid-meiotic genes allowed vegetative sense transcription. These results suggest that antisense transcription represses sense transcription of meiotic genes in vegetative cells. Although the mechanism(s) of antisense mediated transcription repression need to be further explored, our data indicates that RNAi machinery is not required for repression. Previously, we and others used non-strand specific methods to study splicing regulation of meiotic genes and concluded that 28 mid-meiotic genes are spliced only in meiosis. We now demonstrate that the "unspliced" signal in vegetative cells comes from the antisense RNA, not from unspliced sense RNA, and we argue against the idea that splicing regulates these mid-meiotic genes. Most of these mid-meiotic genes are induced in mid-meiosis by the forkhead transcription factor Mei4. Interestingly, deletion of a different forkhead transcription factor, Fkh2, allows low levels of sense expression of some mid-meiotic genes in vegetative cells. We propose that vegetative expression of mid-meiotic genes is repressed at least two independent ways: antisense transcription and Fkh2 repression.

  19. Repression of Meiotic Genes by Antisense Transcription and by Fkh2 Transcription Factor in Schizosaccharomyces pombe

    Science.gov (United States)

    Chen, Huei-Mei; Rosebrock, Adam P.; Khan, Sohail R.; Futcher, Bruce; Leatherwood, Janet K.

    2012-01-01

    In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. Disruption of the antisense transcription of three of these mid-meiotic genes allowed vegetative sense transcription. These results suggest that antisense transcription represses sense transcription of meiotic genes in vegetative cells. Although the mechanism(s) of antisense mediated transcription repression need to be further explored, our data indicates that RNAi machinery is not required for repression. Previously, we and others used non-strand specific methods to study splicing regulation of meiotic genes and concluded that 28 mid-meiotic genes are spliced only in meiosis. We now demonstrate that the “unspliced” signal in vegetative cells comes from the antisense RNA, not from unspliced sense RNA, and we argue against the idea that splicing regulates these mid-meiotic genes. Most of these mid-meiotic genes are induced in mid-meiosis by the forkhead transcription factor Mei4. Interestingly, deletion of a different forkhead transcription factor, Fkh2, allows low levels of sense expression of some mid-meiotic genes in vegetative cells. We propose that vegetative expression of mid-meiotic genes is repressed at least two independent ways: antisense transcription and Fkh2 repression. PMID:22238674

  20. Repression of meiotic genes by antisense transcription and by Fkh2 transcription factor in Schizosaccharomyces pombe.

    Directory of Open Access Journals (Sweden)

    Huei-Mei Chen

    Full Text Available In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. Disruption of the antisense transcription of three of these mid-meiotic genes allowed vegetative sense transcription. These results suggest that antisense transcription represses sense transcription of meiotic genes in vegetative cells. Although the mechanism(s of antisense mediated transcription repression need to be further explored, our data indicates that RNAi machinery is not required for repression. Previously, we and others used non-strand specific methods to study splicing regulation of meiotic genes and concluded that 28 mid-meiotic genes are spliced only in meiosis. We now demonstrate that the "unspliced" signal in vegetative cells comes from the antisense RNA, not from unspliced sense RNA, and we argue against the idea that splicing regulates these mid-meiotic genes. Most of these mid-meiotic genes are induced in mid-meiosis by the forkhead transcription factor Mei4. Interestingly, deletion of a different forkhead transcription factor, Fkh2, allows low levels of sense expression of some mid-meiotic genes in vegetative cells. We propose that vegetative expression of mid-meiotic genes is repressed at least two independent ways: antisense transcription and Fkh2 repression.

  1. Transcription regulation by the Mediator complex.

    Science.gov (United States)

    Soutourina, Julie

    2018-04-01

    Alterations in the regulation of gene expression are frequently associated with developmental diseases or cancer. Transcription activation is a key phenomenon in the regulation of gene expression. In all eukaryotes, mediator of RNA polymerase II transcription (Mediator), a large complex with modular organization, is generally required for transcription by RNA polymerase II, and it regulates various steps of this process. The main function of Mediator is to transduce signals from the transcription activators bound to enhancer regions to the transcription machinery, which is assembled at promoters as the preinitiation complex (PIC) to control transcription initiation. Recent functional studies of Mediator with the use of structural biology approaches and functional genomics have revealed new insights into Mediator activity and its regulation during transcription initiation, including how Mediator is recruited to transcription regulatory regions and how it interacts and cooperates with PIC components to assist in PIC assembly. Novel roles of Mediator in the control of gene expression have also been revealed by showing its connection to the nuclear pore and linking Mediator to the regulation of gene positioning in the nuclear space. Clear links between Mediator subunits and disease have also encouraged studies to explore targeting of this complex as a potential therapeutic approach in cancer and fungal infections.

  2. Transcriptional regulation by competing transcription factor modules.

    Directory of Open Access Journals (Sweden)

    Rutger Hermsen

    2006-12-01

    Full Text Available Gene regulatory networks lie at the heart of cellular computation. In these networks, intracellular and extracellular signals are integrated by transcription factors, which control the expression of transcription units by binding to cis-regulatory regions on the DNA. The designs of both eukaryotic and prokaryotic cis-regulatory regions are usually highly complex. They frequently consist of both repetitive and overlapping transcription factor binding sites. To unravel the design principles of these promoter architectures, we have designed in silico prokaryotic transcriptional logic gates with predefined input-output relations using an evolutionary algorithm. The resulting cis-regulatory designs are often composed of modules that consist of tandem arrays of binding sites to which the transcription factors bind cooperatively. Moreover, these modules often overlap with each other, leading to competition between them. Our analysis thus identifies a new signal integration motif that is based upon the interplay between intramodular cooperativity and intermodular competition. We show that this signal integration mechanism drastically enhances the capacity of cis-regulatory domains to integrate signals. Our results provide a possible explanation for the complexity of promoter architectures and could be used for the rational design of synthetic gene circuits.

  3. High-density transcriptional initiation signals underline genomic islands in bacteria.

    Directory of Open Access Journals (Sweden)

    Qianli Huang

    Full Text Available Genomic islands (GIs, frequently associated with the pathogenicity of bacteria and having a substantial influence on bacterial evolution, are groups of "alien" elements which probably undergo special temporal-spatial regulation in the host genome. Are there particular hallmark transcriptional signals for these "exotic" regions? We here explore the potential transcriptional signals that underline the GIs beyond the conventional views on basic sequence composition, such as codon usage and GC property bias. It showed that there is a significant enrichment of the transcription start positions (TSPs in the GI regions compared to the whole genome of Salmonella enterica and Escherichia coli. There was up to a four-fold increase for the 70% GIs, implying high-density TSPs profile can potentially differentiate the GI regions. Based on this feature, we developed a new sliding window method GIST, Genomic-island Identification by Signals of Transcription, to identify these regions. Subsequently, we compared the known GI-associated features of the GIs detected by GIST and by the existing method Islandviewer to those of the whole genome. Our method demonstrates high sensitivity in detecting GIs harboring genes with biased GI-like function, preferred subcellular localization, skewed GC property, shorter gene length and biased "non-optimal" codon usage. The special transcriptional signals discovered here may contribute to the coordinate expression regulation of foreign genes. Finally, by using GIST, we detected many interesting GIs in the 2011 German E. coli O104:H4 outbreak strain TY-2482, including the microcin H47 system and gene cluster ycgXEFZ-ymgABC that activates the production of biofilm matrix. The aforesaid findings highlight the power of GIST to predict GIs with distinct intrinsic features to the genome. The heterogeneity of cumulative TSPs profiles may not only be a better identity for "alien" regions, but also provide hints to the special

  4. Extensive polycistronism and antisense transcription in the mammalian Hox clusters.

    Directory of Open Access Journals (Sweden)

    Gaëll Mainguy

    Full Text Available The Hox clusters play a crucial role in body patterning during animal development. They encode both Hox transcription factor and micro-RNA genes that are activated in a precise temporal and spatial sequence that follows their chromosomal order. These remarkable collinear properties confer functional unit status for Hox clusters. We developed the TranscriptView platform to establish high resolution transcriptional profiling and report here that transcription in the Hox clusters is far more complex than previously described in both human and mouse. Unannotated transcripts can represent up to 60% of the total transcriptional output of a cluster. In particular, we identified 14 non-coding Transcriptional Units antisense to Hox genes, 10 of which (70% have a detectable mouse homolog. Most of these Transcriptional Units in both human and mouse present conserved sizeable sequences (>40 bp overlapping Hox transcripts, suggesting that these Hox antisense transcripts are functional. Hox clusters also display at least seven polycistronic clusters, i.e., different genes being co-transcribed on long isoforms (up to 30 kb. This work provides a reevaluated framework for understanding Hox gene function and dys-function. Such extensive transcriptions may provide a structural explanation for Hox clustering.

  5. Temporal Glare

    DEFF Research Database (Denmark)

    Ritschel, Tobias; Ihrke, Matthias; Frisvad, Jeppe Revall

    2009-01-01

    Glare is a consequence of light scattered within the human eye when looking at bright light sources. This effect can be exploited for tone mapping since adding glare to the depiction of high-dynamic range (HDR) imagery on a low-dynamic range (LDR) medium can dramatically increase perceived contra...... to initially static HDR images. By conducting psychophysical studies, we validate that our method improves perceived brightness and that dynamic glare-renderings are often perceived as more attractive depending on the chosen scene.......Glare is a consequence of light scattered within the human eye when looking at bright light sources. This effect can be exploited for tone mapping since adding glare to the depiction of high-dynamic range (HDR) imagery on a low-dynamic range (LDR) medium can dramatically increase perceived contrast....... Even though most, if not all, subjects report perceiving glare as a bright pattern that fluctuates in time, up to now it has only been modeled as a static phenomenon. We argue that the temporal properties of glare are a strong means to increase perceived brightness and to produce realistic...

  6. WRKY transcription factors

    Science.gov (United States)

    Bakshi, Madhunita; Oelmüller, Ralf

    2014-01-01

    WRKY transcription factors are one of the largest families of transcriptional regulators found exclusively in plants. They have diverse biological functions in plant disease resistance, abiotic stress responses, nutrient deprivation, senescence, seed and trichome development, embryogenesis, as well as additional developmental and hormone-controlled processes. WRKYs can act as transcriptional activators or repressors, in various homo- and heterodimer combinations. Here we review recent progress on the function of WRKY transcription factors in Arabidopsis and other plant species such as rice, potato, and parsley, with a special focus on abiotic, developmental, and hormone-regulated processes. PMID:24492469

  7. Using temporal information to construct, update, and retrieve situation models of narratives

    NARCIS (Netherlands)

    Rinck, M.; Hähnel, A.; Becker, G.

    2001-01-01

    Four experiments explored how readers use temporal information to construct and update situation models and retrieve them from memory. In Experiment 1, readers spontaneously constructed temporal and spatial situation models of single sentences. In Experiment 2, temporal inconsistencies caused

  8. Quantum Temporal Imaging

    OpenAIRE

    Tsang, Mankei; Psaltis, Demetri

    2006-01-01

    The concept of quantum temporal imaging is proposed to manipulate the temporal correlation of entangled photons. In particular, we show that time correlation and anticorrelation can be converted to each other using quantum temporal imaging.

  9. Towards General Temporal Aggregation

    DEFF Research Database (Denmark)

    Boehlen, Michael H.; Gamper, Johann; Jensen, Christian Søndergaard

    2008-01-01

    associated with the management of temporal data. Indeed, temporal aggregation is complex and among the most difficult, and thus interesting, temporal functionality to support. This paper presents a general framework for temporal aggregation that accommodates existing kinds of aggregation, and it identifies...

  10. A biophysical model for transcription factories

    International Nuclear Information System (INIS)

    Canals-Hamann, Ana Z; Neves, Ricardo Pires das; Reittie, Joyce E; Iñiguez, Carlos; Soneji, Shamit; Enver, Tariq; Buckle, Veronica J; Iborra, Francisco J

    2013-01-01

    Transcription factories are nuclear domains where gene transcription takes place although the molecular basis for their formation and maintenance are unknown. In this study, we explored how the properties of chromatin as a polymer may contribute to the structure of transcription factories. We found that transcriptional active chromatin contains modifications like histone H4 acetylated at Lysine 16 (H4K16ac). Single fibre analysis showed that this modification spans the entire body of the gene. Furthermore, H4K16ac genes cluster in regions up to 500 Kb alternating active and inactive chromatin. The introduction of H4K16ac in chromatin induces stiffness in the chromatin fibre. The result of this change in flexibility is that chromatin could behave like a multi-block copolymer with repetitions of stiff-flexible (active-inactive chromatin) components. Copolymers with such structure self-organize through spontaneous phase separation into microdomains. Consistent with such model H4K16ac chromatin form foci that associates with nascent transcripts. We propose that transcription factories are the result of the spontaneous concentration of H4K16ac chromatin that are in proximity, mainly in cis

  11. Analyzing the temporal regulation of translation efficiency in mouse liver

    Directory of Open Access Journals (Sweden)

    Peggy Janich

    2016-06-01

    Full Text Available Mammalian physiology and behavior follow daily rhythms that are orchestrated by endogenous timekeepers known as circadian clocks. Rhythms in transcription are considered the main mechanism to engender rhythmic gene expression, but important roles for posttranscriptional mechanisms have recently emerged as well (reviewed in Lim and Allada (2013 [1]. We have recently reported on the use of ribosome profiling (RPF-seq, a method based on the high-throughput sequencing of ribosome protected mRNA fragments, to explore the temporal regulation of translation efficiency (Janich et al., 2015 [2]. Through the comparison of around-the-clock RPF-seq and matching RNA-seq data we were able to identify 150 genes, involved in ribosome biogenesis, iron metabolism and other pathways, whose rhythmicity is generated entirely at the level of protein synthesis. The temporal transcriptome and translatome data sets from this study have been deposited in NCBI's Gene Expression Omnibus under the accession number GSE67305. Here we provide additional information on the experimental setup and on important optimization steps pertaining to the ribosome profiling technique in mouse liver and to data analysis.

  12. How Would You Like to Aggregate Your Temporal Data?

    DEFF Research Database (Denmark)

    Böhlen, M. H.; Gamper, J.; Jensen, Christian Søndergaard

    2006-01-01

    concepts, and it discusses the abilities of five approaches to the design of temporal query languages with respect to temporal aggregation. Rather than providing focused, polished results, the paper?s aim is to explore the inherent support for temporal aggregation in an informal manner that may serve...

  13. Temporal Cyber Attack Detection.

    Energy Technology Data Exchange (ETDEWEB)

    Ingram, Joey Burton [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Draelos, Timothy J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Galiardi, Meghan [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Doak, Justin E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-11-01

    Rigorous characterization of the performance and generalization ability of cyber defense systems is extremely difficult, making it hard to gauge uncertainty, and thus, confidence. This difficulty largely stems from a lack of labeled attack data that fully explores the potential adversarial space. Currently, performance of cyber defense systems is typically evaluated in a qualitative manner by manually inspecting the results of the system on live data and adjusting as needed. Additionally, machine learning has shown promise in deriving models that automatically learn indicators of compromise that are more robust than analyst-derived detectors. However, to generate these models, most algorithms require large amounts of labeled data (i.e., examples of attacks). Algorithms that do not require annotated data to derive models are similarly at a disadvantage, because labeled data is still necessary when evaluating performance. In this work, we explore the use of temporal generative models to learn cyber attack graph representations and automatically generate data for experimentation and evaluation. Training and evaluating cyber systems and machine learning models requires significant, annotated data, which is typically collected and labeled by hand for one-off experiments. Automatically generating such data helps derive/evaluate detection models and ensures reproducibility of results. Experimentally, we demonstrate the efficacy of generative sequence analysis techniques on learning the structure of attack graphs, based on a realistic example. These derived models can then be used to generate more data. Additionally, we provide a roadmap for future research efforts in this area.

  14. The "fourth dimension" of gene transcription.

    Science.gov (United States)

    O'Malley, Bert W

    2009-05-01

    The three dimensions of space provide our relationship to position on the earth, but the fourth dimension of time has an equally profound influence on our lives. Everything from light and sound to weather and biology operate on the principle of measurable temporal periodicity. Consequently, a wide variety of time clocks affect all aspects of our existence. The annual (and biannual) cycles of activity, metabolism, and mating, the monthly physiological clocks of women and men, and the 24-h diurnal rhythms of humans are prime examples. Should it be surprising to us that the fourth dimension also impinges upon gene expression and that the genome itself is regulated by the fastest running of all biological clocks? Recent evidence substantiates the existence of such a ubiquitin-dependent transcriptional clock that is based upon the activation and destruction of transcriptional coactivators.

  15. The Transcription Factor Encyclopedia

    DEFF Research Database (Denmark)

    Yusuf, Dimas; Butland, Stefanie L; Swanson, Magdalena I

    2012-01-01

    mini review articles on pertinent human, mouse and rat TFs. Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written......ABSTRACT: Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130...

  16. Basal transcription machinery

    Indian Academy of Sciences (India)

    2007-03-29

    Mar 29, 2007 ... The holoenzyme of prokaryotic RNA polymerase consists of the core enzyme, made of two , , ' and subunits, which lacks promoter selectivity and a sigma () subunit which enables the core enzyme to initiate transcription in a promoter dependent fashion. A stress sigma factor s, in prokaryotes ...

  17. Machine Dictation and Transcription.

    Science.gov (United States)

    Harvey, Evelyn; And Others

    This instructional package contains both an instructor's manual and a student's manual for a course in machine dictation and transcription. The instructor's manual contains an overview with tips on teaching the course, letters for dictation, and a key to the letters. The student's manual contains an overview of the course and of the skills needed…

  18. Transcriptional Regulation in Haematopoiesis:

    DEFF Research Database (Denmark)

    Lauridsen, Felicia K B

    with the capacity to both self-renew and differentiate. This thesis is built upon two studies, which investigate two different aspects of the haematopoietic system; heterogeneity within the HSC compartment (presented in manuscript I), and the interplay between transcription factors controlling granulocyte/ monocyte...

  19. Temporal Coding of Volumetric Imagery

    Science.gov (United States)

    Llull, Patrick Ryan

    'Image volumes' refer to realizations of images in other dimensions such as time, spectrum, and focus. Recent advances in scientific, medical, and consumer applications demand improvements in image volume capture. Though image volume acquisition continues to advance, it maintains the same sampling mechanisms that have been used for decades; every voxel must be scanned and is presumed independent of its neighbors. Under these conditions, improving performance comes at the cost of increased system complexity, data rates, and power consumption. This dissertation explores systems and methods capable of efficiently improving sensitivity and performance for image volume cameras, and specifically proposes several sampling strategies that utilize temporal coding to improve imaging system performance and enhance our awareness for a variety of dynamic applications. Video cameras and camcorders sample the video volume (x,y,t) at fixed intervals to gain understanding of the volume's temporal evolution. Conventionally, one must reduce the spatial resolution to increase the framerate of such cameras. Using temporal coding via physical translation of an optical element known as a coded aperture, the compressive temporal imaging (CACTI) camera emonstrates a method which which to embed the temporal dimension of the video volume into spatial (x,y) measurements, thereby greatly improving temporal resolution with minimal loss of spatial resolution. This technique, which is among a family of compressive sampling strategies developed at Duke University, temporally codes the exposure readout functions at the pixel level. Since video cameras nominally integrate the remaining image volume dimensions (e.g. spectrum and focus) at capture time, spectral (x,y,t,lambda) and focal (x,y,t,z) image volumes are traditionally captured via sequential changes to the spectral and focal state of the system, respectively. The CACTI camera's ability to embed video volumes into images leads to exploration

  20. Transcriptional and post-transcriptional regulation of nucleotide excision repair genes in human cells

    Energy Technology Data Exchange (ETDEWEB)

    Lefkofsky, Hailey B. [Translational Oncology Program, University of Michigan Medical School, Ann Arbor, MI (United States); Veloso, Artur [Translational Oncology Program, University of Michigan Medical School, Ann Arbor, MI (United States); Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI (United States); Bioinformatics Program, Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI (United States); Ljungman, Mats, E-mail: ljungman@umich.edu [Translational Oncology Program, University of Michigan Medical School, Ann Arbor, MI (United States); Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI (United States); Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI (United States)

    2015-06-15

    Nucleotide excision repair (NER) removes DNA helix-distorting lesions induced by UV light and various chemotherapeutic agents such as cisplatin. These lesions efficiently block the elongation of transcription and need to be rapidly removed by transcription-coupled NER (TC-NER) to avoid the induction of apoptosis. Twenty-nine genes have been classified to code for proteins participating in nucleotide excision repair (NER) in human cells. Here we explored the transcriptional and post-transcriptional regulation of these NER genes across 13 human cell lines using Bru-seq and BruChase-seq, respectively. Many NER genes are relatively large in size and therefore will be easily inactivated by UV-induced transcription-blocking lesions. Furthermore, many of these genes produce transcripts that are rather unstable. Thus, these genes are expected to rapidly lose expression leading to a diminished function of NER. One such gene is ERCC6 that codes for the CSB protein critical for TC-NER. Due to its large gene size and high RNA turnover rate, the ERCC6 gene may act as dosimeter of DNA damage so that at high levels of damage, ERCC6 RNA levels would be diminished leading to the loss of CSB expression, inhibition of TC-NER and the promotion of cell death.

  1. DNA Topoisomerases in Transcription

    DEFF Research Database (Denmark)

    Rødgaard, Morten Terpager

    2015-01-01

    This Ph.D. thesis summarizes the main results of my studies on the interplay between DNA topoisomerases and transcription. The work was performed from 2011 to 2015 at Aarhus University in the Laboratory of Genome Research, and was supervised by associate professor Anni H. Andersen. Most of the ex......This Ph.D. thesis summarizes the main results of my studies on the interplay between DNA topoisomerases and transcription. The work was performed from 2011 to 2015 at Aarhus University in the Laboratory of Genome Research, and was supervised by associate professor Anni H. Andersen. Most...... topoisomerase-DNA cleavage complex. The second study is an investigation of how topoisomerases influence gene regulation by keeping the genome in an optimal topological state....

  2. Transcriptional networks controlling adipocyte differentiation

    DEFF Research Database (Denmark)

    Siersbæk, R; Mandrup, Susanne

    2011-01-01

    " of the transcription factor networks operating at specific time points during adipogenesis. Using such global "snapshots," we have demonstrated that dramatic remodeling of the chromatin template occurs within the first few hours following adipogenic stimulation and that many of the early transcription factors bind...... in a cooperative fashion to transcription factor hotspots. Such hotspots are likely to represent key chromatin nodes, where many adipogenic signaling pathways converge to drive the adipogenic transcriptional reprogramming....

  3. Advances in temporal logic

    CERN Document Server

    Fisher, Michael; Gabbay, Dov; Gough, Graham

    2000-01-01

    Time is a fascinating subject that has captured mankind's imagination from ancient times to the present. It has been, and continues to be studied across a wide range of disciplines, from the natural sciences to philosophy and logic. More than two decades ago, Pnueli in a seminal work showed the value of temporal logic in the specification and verification of computer programs. Today, a strong, vibrant international research community exists in the broad community of computer science and AI. This volume presents a number of articles from leading researchers containing state-of-the-art results in such areas as pure temporal/modal logic, specification and verification, temporal databases, temporal aspects in AI, tense and aspect in natural language, and temporal theorem proving. Earlier versions of some of the articles were given at the most recent International Conference on Temporal Logic, University of Manchester, UK. Readership: Any student of the area - postgraduate, postdoctoral or even research professor ...

  4. Indeterministic Temporal Logic

    Directory of Open Access Journals (Sweden)

    Trzęsicki Kazimierz

    2015-09-01

    Full Text Available The questions od determinism, causality, and freedom have been the main philosophical problems debated since the beginning of temporal logic. The issue of the logical value of sentences about the future was stated by Aristotle in the famous tomorrow sea-battle passage. The question has inspired Łukasiewicz’s idea of many-valued logics and was a motive of A. N. Prior’s considerations about the logic of tenses. In the scheme of temporal logic there are different solutions to the problem. In the paper we consider indeterministic temporal logic based on the idea of temporal worlds and the relation of accessibility between them.

  5. Full-fledged temporal processing: bridging the gap between deep linguistic processing and temporal extraction

    Directory of Open Access Journals (Sweden)

    Francisco Costa

    2013-07-01

    Full Text Available The full-fledged processing of temporal information presents specific challenges. These difficulties largely stem from the fact that the temporal meaning conveyed by grammatical means interacts with many extra-linguistic factors (world knowledge, causality, calendar systems, reasoning. This article proposes a novel approach to this problem, based on a hybrid strategy that explores the complementarity of the symbolic and probabilistic methods. A specialized temporal extraction system is combined with a deep linguistic processing grammar. The temporal extraction system extracts eventualities, times and dates mentioned in text, and also temporal relations between them, in line with the tasks of the recent TempEval challenges; and uses machine learning techniques to draw from different sources of information (grammatical and extra-grammatical even if it is not explicitly known how these combine to produce the final temporal meaning being expressed. In turn, the deep computational grammar delivers richer truth-conditional meaning representations of input sentences, which include a principled representation of temporal information, on which higher level tasks, including reasoning, can be based. These deep semantic representations are extended and improved according to the output of the aforementioned temporal extraction module. The prototype implemented shows performance results that increase the quality of the temporal meaning representations and are better than the performance of each of the two components in isolation.

  6. Selection Shapes Transcriptional Logic and Regulatory Specialization in Genetic Networks.

    Science.gov (United States)

    Fogelmark, Karl; Peterson, Carsten; Troein, Carl

    2016-01-01

    Living organisms need to regulate their gene expression in response to environmental signals and internal cues. This is a computational task where genes act as logic gates that connect to form transcriptional networks, which are shaped at all scales by evolution. Large-scale mutations such as gene duplications and deletions add and remove network components, whereas smaller mutations alter the connections between them. Selection determines what mutations are accepted, but its importance for shaping the resulting networks has been debated. To investigate the effects of selection in the shaping of transcriptional networks, we derive transcriptional logic from a combinatorially powerful yet tractable model of the binding between DNA and transcription factors. By evolving the resulting networks based on their ability to function as either a simple decision system or a circadian clock, we obtain information on the regulation and logic rules encoded in functional transcriptional networks. Comparisons are made between networks evolved for different functions, as well as with structurally equivalent but non-functional (neutrally evolved) networks, and predictions are validated against the transcriptional network of E. coli. We find that the logic rules governing gene expression depend on the function performed by the network. Unlike the decision systems, the circadian clocks show strong cooperative binding and negative regulation, which achieves tight temporal control of gene expression. Furthermore, we find that transcription factors act preferentially as either activators or repressors, both when binding multiple sites for a single target gene and globally in the transcriptional networks. This separation into positive and negative regulators requires gene duplications, which highlights the interplay between mutation and selection in shaping the transcriptional networks.

  7. Transcript structure and domain display: a customizable transcript visualization tool.

    Science.gov (United States)

    Watanabe, Kenneth A; Ma, Kaiwang; Homayouni, Arielle; Rushton, Paul J; Shen, Qingxi J

    2016-07-01

    Transcript Structure and Domain Display (TSDD) is a publicly available, web-based program that provides publication quality images of transcript structures and domains. TSDD is capable of producing transcript structures from GFF/GFF3 and BED files. Alternatively, the GFF files of several model organisms have been pre-loaded so that users only needs to enter the locus IDs of the transcripts to be displayed. Visualization of transcripts provides many benefits to researchers, ranging from evolutionary analysis of DNA-binding domains to predictive function modeling. TSDD is freely available for non-commercial users at http://shenlab.sols.unlv.edu/shenlab/software/TSD/transcript_display.html : jeffery.shen@unlv.nevada.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  8. Chondroblastoma of temporal bone

    Energy Technology Data Exchange (ETDEWEB)

    Tanohta, K.; Noda, M.; Katoh, H.; Okazaki, A.; Sugiyama, S.; Maehara, T.; Onishi, S.; Tanida, T.

    1986-07-01

    The case of a 55-year-old female with chondroblastoma arising from the left temporal bone is presented. Although 10 cases of temporal chondroblastoma have been reported, this is the first in which plain radiography, pluridirectional tomography, computed tomography (CT) and angiography were performed. We discuss the clinical and radiological aspects of this rare tumor.

  9. Chondroblastoma of temporal bone

    International Nuclear Information System (INIS)

    Tanohta, K.; Noda, M.; Katoh, H.; Okazaki, A.; Sugiyama, S.; Maehara, T.; Onishi, S.; Tanida, T.

    1986-01-01

    The case of a 55-year-old female with chondroblastoma arising from the left temporal bone is presented. Although 10 cases of temporal chondroblastoma have been reported, this is the first in which plain radiography, pluridirectional tomography, computed tomography (CT) and angiography were performed. We discuss the clinical and radiological aspects of this rare tumor. (orig.)

  10. Temporal Context, Preference, and Resistance to Change

    Science.gov (United States)

    Podlesnik, Christopher A.; Jimenez-Gomez, Corina; Thrailkill, Eric A.; Shahan, Timothy A.

    2011-01-01

    According to behavioral momentum theory, preference and relative resistance to change in concurrent chains schedules are correlated and reflect the relative conditioned value of discriminative stimuli. In the present study, we explore the generality of this relation by manipulating the temporal context within a concurrent-chains procedure through…

  11. Temporal Visualization for Legal Case Histories.

    Science.gov (United States)

    Harris, Chanda; Allen, Robert B.; Plaisant, Catherine; Shneiderman, Ben

    1999-01-01

    Discusses visualization of legal information using a tool for temporal information called "LifeLines." Explores ways "LifeLines" could aid in viewing the links between original case and direct and indirect case histories. Uses the case of Apple Computer, Inc. versus Microsoft Corporation and Hewlett Packard Company to…

  12. Nucleocytoplasmic shuttling of transcription factors

    DEFF Research Database (Denmark)

    Cartwright, P; Helin, K

    2000-01-01

    To elicit the transcriptional response following intra- or extracellular stimuli, the signals need to be transmitted to their site of action within the nucleus. The nucleocytoplasmic shuttling of transcription factors is a mechanism mediating this process. The activation and inactivation...... of the transcriptional response is essential for cells to progress through the cell cycle in a normal manner. The involvement of cytoplasmic and nuclear accessory molecules, and the general nuclear membrane transport components, are essential for this process. Although nuclear import and export for different...... transcription factor families are regulated by similar mechanisms, there are several differences that allow for the specific activation of each transcription factor. This review discusses the general import and export pathways found to be common amongst many different transcription factors, and highlights...

  13. Transcriptional Silencing of Retroviral Vectors

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Duch, M.; Pedersen, F.S.

    1996-01-01

    . Extinction of long-term vector expression has been observed after implantation of transduced hematopoietic cells as well as fibroblasts, myoblasts and hepatocytes. Here we review the influence of vector structure, integration site and cell type on transcriptional silencing. While down-regulation of proviral...... transcription is known from a number of cellular and animal models, major insight has been gained from studies in the germ line and embryonal cells of the mouse. Key elements for the transfer and expression of retroviral vectors, such as the viral transcriptional enhancer and the binding site for the t......RNA primer for reverse transcription may have a major influence on transcriptional silencing. Alterations of these elements of the vector backbone as well as the use of internal promoter elements from housekeeping genes may contribute to reduce transcriptional silencing. The use of cell culture and animal...

  14. DNA topology and transcription

    Science.gov (United States)

    Kouzine, Fedor; Levens, David; Baranello, Laura

    2014-01-01

    Chromatin is a complex assembly that compacts DNA inside the nucleus while providing the necessary level of accessibility to regulatory factors conscripted by cellular signaling systems. In this superstructure, DNA is the subject of mechanical forces applied by variety of molecular motors. Rather than being a rigid stick, DNA possesses dynamic structural variability that could be harnessed during critical steps of genome functioning. The strong relationship between DNA structure and key genomic processes necessitates the study of physical constrains acting on the double helix. Here we provide insight into the source, dynamics, and biology of DNA topological domains in the eukaryotic cells and summarize their possible involvement in gene transcription. We emphasize recent studies that might inspire and impact future experiments on the involvement of DNA topology in cellular functions. PMID:24755522

  15. Eukaryotic transcription factors

    DEFF Research Database (Denmark)

    Staby, Lasse; O'Shea, Charlotte; Willemoës, Martin

    2017-01-01

    Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains...... regions with function-related, short sequence motifs and molecular recognition features with structural propensities. This review focuses on molecular aspects of TFs, which represent paradigms of ID-related features. Through specific examples, we review how the ID-associated flexibility of TFs enables....... It is furthermore emphasized how classic biochemical concepts like allostery, conformational selection, induced fit, and feedback regulation are undergoing a revival with the appreciation of ID. The review also describes the most recent advances based on computational simulations of ID-based interaction mechanisms...

  16. An Optogenetic Platform for Real-Time, Single-Cell Interrogation of Stochastic Transcriptional Regulation.

    Science.gov (United States)

    Rullan, Marc; Benzinger, Dirk; Schmidt, Gregor W; Milias-Argeitis, Andreas; Khammash, Mustafa

    2018-05-17

    Transcription is a highly regulated and inherently stochastic process. The complexity of signal transduction and gene regulation makes it challenging to analyze how the dynamic activity of transcriptional regulators affects stochastic transcription. By combining a fast-acting, photo-regulatable transcription factor with nascent RNA quantification in live cells and an experimental setup for precise spatiotemporal delivery of light inputs, we constructed a platform for the real-time, single-cell interrogation of transcription in Saccharomyces cerevisiae. We show that transcriptional activation and deactivation are fast and memoryless. By analyzing the temporal activity of individual cells, we found that transcription occurs in bursts, whose duration and timing are modulated by transcription factor activity. Using our platform, we regulated transcription via light-driven feedback loops at the single-cell level. Feedback markedly reduced cell-to-cell variability and led to qualitative differences in cellular transcriptional dynamics. Our platform establishes a flexible method for studying transcriptional dynamics in single cells. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  17. An index guiding temporal planting policies for wind erosion reduction

    NARCIS (Netherlands)

    Zhao, C.X.; Zheng, D.W.; Stigter, C.J.; He, W.Q.; Tuo, D.B.; Zhao, P.

    2006-01-01

    Vegetation cover has spatial as well as temporal characteristics, but the latter are often neglected. Temporal cover characteristics were explored to recommend planting policies for returning arable land into land better protected from serious wind erosion during late autumn, winter, and

  18. Otosclerosis: Temporal Bone Pathology.

    Science.gov (United States)

    Quesnel, Alicia M; Ishai, Reuven; McKenna, Michael J

    2018-04-01

    Otosclerosis is pathologically characterized by abnormal bony remodeling, which includes bone resorption, new bone deposition, and vascular proliferation in the temporal bone. Sensorineural hearing loss in otosclerosis is associated with extension of otosclerosis to the cochlear endosteum and deposition of collagen throughout the spiral ligament. Persistent or recurrent conductive hearing loss after stapedectomy has been associated with incomplete footplate fenestration, poor incus-prosthesis connection, and incus resorption in temporal bone specimens. Human temporal bone pathology has helped to define the role of computed tomography imaging for otosclerosis, confirming that computed tomography is highly sensitive for diagnosis, yet limited in assessing cochlear endosteal involvement. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Exploration Review

    Science.gov (United States)

    Wilburn, D.R.; Stanley, K.A.

    2013-01-01

    This summary of international mineral exploration activities for 2012 draws upon information from industry sources, published literature and U.S. Geological Survey (USGS) specialists. The summary provides data on exploration budgets by region and mineral commodity, identifies significant mineral discoveries and areas of mineral exploration, discusses government programs affecting the mineral exploration industry and presents analyses of exploration activities performed by the mineral industry. Three sources of information are reported and analyzed in this annual review of international exploration for 2012: 1) budgetary statistics expressed in U.S. nominal dollars provided by SNL Metals Economics Group (MEG) of Halifax, Nova Scotia; 2) regional and site-specific exploration activities that took place in 2012 as compiled by the USGS and 3) regional events including economic, social and political conditions that affected exploration activities, which were derived from published sources and unpublished discussions with USGS and industry specialists.

  20. Exploration technology

    Energy Technology Data Exchange (ETDEWEB)

    Roennevik, H.C. [Saga Petroleum A/S, Forus (Norway)

    1996-12-31

    The paper evaluates exploration technology. Topics discussed are: Visions; the subsurface challenge; the creative tension; the exploration process; seismic; geology; organic geochemistry; seismic resolution; integration; drilling; value creation. 4 refs., 22 figs.

  1. Repository exploration

    International Nuclear Information System (INIS)

    Pentz, D.L.

    1984-01-01

    This paper discusses exploration objectives and requirements for a nuclear repository in the U.S.A. The importance of designing the exploration program to meet the system performance objectives is emphasized and some examples of the extent of exploration required before the License Application for Construction Authorization is granted are also discussed

  2. Nontraumatic temporal subcortical hemorrhage

    International Nuclear Information System (INIS)

    Weisberg, L.A.; Stazio, A.; Shamsnia, M.; Elliott, D.; Charity Hospital, New Orleans, LA

    1990-01-01

    Thirty patients with temporal hematomas were analyzed. Four with frontal extension survived. Of 6 with ganglionic extension, three had residual deficit. Of 8 with parietal extension, 4 had delayed deterioration and died, two patients recovered, and two with peritumoral hemorrhage due to glioblastoma multiforme died. Five patients with posterior temporal hematomas recovered. In 7 patients with basal-inferior temporal hematomas, angiography showed aneurysms in 3 cases, angiomas in 2 cases and no vascular lesion in 2 cases. Of 23 cases with negative angiography and no systemic cause for temporal hematoma, 12 patients were hypertensive and 11 were normotensive. Ten hypertensive patients without evidence of chronic vascular disease had the largest hematomas, extending into the parietal or ganglionic regions. Seven of these patients died; 3 had residual deficit. Eleven normotensive and two hypertensive patients with evidence of chronic vascular change had smaller hematomas. They survived with good functional recovery. (orig.)

  3. Temporal Lobe Seizure

    Science.gov (United States)

    ... functions, including having odd feelings — such as euphoria, deja vu or fear. Temporal lobe seizures are sometimes called ... sudden sense of unprovoked fear or joy A deja vu experience — a feeling that what's happening has happened ...

  4. Coordinated Evolution of Transcriptional and Post-Transcriptional Regulation for Mitochondrial Functions in Yeast Strains.

    Directory of Open Access Journals (Sweden)

    Xuepeng Sun

    Full Text Available Evolution of gene regulation has been proposed to play an important role in environmental adaptation. Exploring mechanisms underlying coordinated evolutionary changes at various levels of gene regulation could shed new light on how organism adapt in nature. In this study, we focused on regulatory differences between a laboratory Saccharomyces cerevisiae strain BY4742 and a pathogenic S. cerevisiae strain, YJM789. The two strains diverge in many features, including growth rate, morphology, high temperature tolerance, and pathogenicity. Our RNA-Seq and ribosomal footprint profiling data showed that gene expression differences are pervasive, and genes functioning in mitochondria are mostly divergent between the two strains at both transcriptional and translational levels. Combining functional genomics data from other yeast strains, we further demonstrated that significant divergence of expression for genes functioning in the electron transport chain (ETC was likely caused by differential expression of a transcriptional factor, HAP4, and that post-transcriptional regulation mediated by an RNA-binding protein, PUF3, likely led to expression divergence for genes involved in mitochondrial translation. We also explored mito-nuclear interactions via mitochondrial DNA replacement between strains. Although the two mitochondrial genomes harbor substantial sequence divergence, neither growth nor gene expression were affected by mitochondrial DNA replacement in both fermentative and respiratory growth media, indicating compatible mitochondrial and nuclear genomes between these two strains in the tested conditions. Collectively, we used mitochondrial functions as an example to demonstrate for the first time that evolution at both transcriptional and post-transcriptional levels could lead to coordinated regulatory changes underlying strain specific functional variations.

  5. SHEEP TEMPORAL BONE

    Directory of Open Access Journals (Sweden)

    Kesavan

    2016-03-01

    Full Text Available INTRODUCTION Human temporal bones are difficult to procure now a days due to various ethical issues. Sheep temporal bone is a good alternative due to morphological similarities, easy to procure and less cost. Many middle ear exercises can be done easily and handling of instruments is done in the procedures like myringoplasty, tympanoplasty, stapedotomy, facial nerve dissection and some middle ear implants. This is useful for resident training programme.

  6. Temporal Processing in Audition: Insights from Music.

    Science.gov (United States)

    Rajendran, Vani G; Teki, Sundeep; Schnupp, Jan W H

    2017-11-03

    Music is a curious example of a temporally patterned acoustic stimulus, and a compelling pan-cultural phenomenon. This review strives to bring some insights from decades of music psychology and sensorimotor synchronization (SMS) literature into the mainstream auditory domain, arguing that musical rhythm perception is shaped in important ways by temporal processing mechanisms in the brain. The feature that unites these disparate disciplines is an appreciation of the central importance of timing, sequencing, and anticipation. Perception of musical rhythms relies on an ability to form temporal predictions, a general feature of temporal processing that is equally relevant to auditory scene analysis, pattern detection, and speech perception. By bringing together findings from the music and auditory literature, we hope to inspire researchers to look beyond the conventions of their respective fields and consider the cross-disciplinary implications of studying auditory temporal sequence processing. We begin by highlighting music as an interesting sound stimulus that may provide clues to how temporal patterning in sound drives perception. Next, we review the SMS literature and discuss possible neural substrates for the perception of, and synchronization to, musical beat. We then move away from music to explore the perceptual effects of rhythmic timing in pattern detection, auditory scene analysis, and speech perception. Finally, we review the neurophysiology of general timing processes that may underlie aspects of the perception of rhythmic patterns. We conclude with a brief summary and outlook for future research. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  7. First Exon Length Controls Active Chromatin Signatures and Transcription

    Directory of Open Access Journals (Sweden)

    Nicole I. Bieberstein

    2012-07-01

    Full Text Available Here, we explore the role of splicing in transcription, employing both genome-wide analysis of human ChIP-seq data and experimental manipulation of exon-intron organization in transgenic cell lines. We show that the activating histone modifications H3K4me3 and H3K9ac map specifically to first exon-intron boundaries. This is surprising, because these marks help recruit general transcription factors (GTFs to promoters. In genes with long first exons, promoter-proximal levels of H3K4me3 and H3K9ac are greatly reduced; consequently, GTFs and RNA polymerase II are low at transcription start sites (TSSs and exhibit a second, promoter-distal peak from which transcription also initiates. In contrast, short first exons lead to increased H3K4me3 and H3K9ac at promoters, higher expression levels, accuracy in TSS usage, and a lower frequency of antisense transcription. Therefore, first exon length is predictive for gene activity. Finally, splicing inhibition and intron deletion reduce H3K4me3 levels and transcriptional output. Thus, gene architecture and splicing determines transcription quantity and quality as well as chromatin signatures.

  8. Intergenic disease-associated regions are abundant in novel transcripts.

    Science.gov (United States)

    Bartonicek, N; Clark, M B; Quek, X C; Torpy, J R; Pritchard, A L; Maag, J L V; Gloss, B S; Crawford, J; Taft, R J; Hayward, N K; Montgomery, G W; Mattick, J S; Mercer, T R; Dinger, M E

    2017-12-28

    Genotyping of large populations through genome-wide association studies (GWAS) has successfully identified many genomic variants associated with traits or disease risk. Unexpectedly, a large proportion of GWAS single nucleotide polymorphisms (SNPs) and associated haplotype blocks are in intronic and intergenic regions, hindering their functional evaluation. While some of these risk-susceptibility regions encompass cis-regulatory sites, their transcriptional potential has never been systematically explored. To detect rare tissue-specific expression, we employed the transcript-enrichment method CaptureSeq on 21 human tissues to identify 1775 multi-exonic transcripts from 561 intronic and intergenic haploblocks associated with 392 traits and diseases, covering 73.9 Mb (2.2%) of the human genome. We show that a large proportion (85%) of disease-associated haploblocks express novel multi-exonic non-coding transcripts that are tissue-specific and enriched for GWAS SNPs as well as epigenetic markers of active transcription and enhancer activity. Similarly, we captured transcriptomes from 13 melanomas, targeting nine melanoma-associated haploblocks, and characterized 31 novel melanoma-specific transcripts that include fusion proteins, novel exons and non-coding RNAs, one-third of which showed allelically imbalanced expression. This resource of previously unreported transcripts in disease-associated regions ( http://gwas-captureseq.dingerlab.org ) should provide an important starting point for the translational community in search of novel biomarkers, disease mechanisms, and drug targets.

  9. Laminar and Temporal Expression Dynamics of Coding and Noncoding RNAs in the Mouse Neocortex

    Directory of Open Access Journals (Sweden)

    Sofia Fertuzinhos

    2014-03-01

    Full Text Available The hallmark of the cerebral neocortex is its organization into six layers, each containing a characteristic set of cell types and synaptic connections. The transcriptional events involved in laminar development and function still remain elusive. Here, we employed deep sequencing of mRNA and small RNA species to gain insights into transcriptional differences among layers and their temporal dynamics during postnatal development of the mouse primary somatosensory neocortex. We identify a number of coding and noncoding transcripts with specific spatiotemporal expression and splicing patterns. We also identify signature trajectories and gene coexpression networks associated with distinct biological processes and transcriptional overlap between these processes. Finally, we provide data that allow the study of potential miRNA and mRNA interactions. Overall, this study provides an integrated view of the laminar and temporal expression dynamics of coding and noncoding transcripts in the mouse neocortex and a resource for studies of neurodevelopment and transcriptome.

  10. Dynamic usage of transcription start sites within core promoters

    DEFF Research Database (Denmark)

    Kawaji, Hideya; Frith, Martin C; Katayama, Shintaro

    2006-01-01

    BACKGROUND: Mammalian promoters do not initiate transcription at single, well defined base pairs, but rather at multiple, alternative start sites spread across a region. We previously characterized the static structures of transcription start site usage within promoters at the base pair level......, based on large-scale sequencing of transcript 5' ends. RESULTS: In the present study we begin to explore the internal dynamics of mammalian promoters, and demonstrate that start site selection within many mouse core promoters varies among tissues. We also show that this dynamic usage of start sites...... is associated with CpG islands, broad and multimodal promoter structures, and imprinting. CONCLUSION: Our results reveal a new level of biologic complexity within promoters--fine-scale regulation of transcription starting events at the base pair level. These events are likely to be related to epigenetic...

  11. Multiple promoters and alternative splicing: Hoxa5 transcriptional complexity in the mouse embryo.

    Directory of Open Access Journals (Sweden)

    Yan Coulombe

    2010-05-01

    Full Text Available The genomic organization of Hox clusters is fundamental for the precise spatio-temporal regulation and the function of each Hox gene, and hence for correct embryo patterning. Multiple overlapping transcriptional units exist at the Hoxa5 locus reflecting the complexity of Hox clustering: a major form of 1.8 kb corresponding to the two characterized exons of the gene and polyadenylated RNA species of 5.0, 9.5 and 11.0 kb. This transcriptional intricacy raises the question of the involvement of the larger transcripts in Hox function and regulation.We have undertaken the molecular characterization of the Hoxa5 larger transcripts. They initiate from two highly conserved distal promoters, one corresponding to the putative Hoxa6 promoter, and a second located nearby Hoxa7. Alternative splicing is also involved in the generation of the different transcripts. No functional polyadenylation sequence was found at the Hoxa6 locus and all larger transcripts use the polyadenylation site of the Hoxa5 gene. Some larger transcripts are potential Hoxa6/Hoxa5 bicistronic units. However, even though all transcripts could produce the genuine 270 a.a. HOXA5 protein, only the 1.8 kb form is translated into the protein, indicative of its essential role in Hoxa5 gene function. The Hoxa6 mutation disrupts the larger transcripts without major phenotypic impact on axial specification in their expression domain. However, Hoxa5-like skeletal anomalies are observed in Hoxa6 mutants and these defects can be explained by the loss of expression of the 1.8 kb transcript. Our data raise the possibility that the larger transcripts may be involved in Hoxa5 gene regulation.Our observation that the Hoxa5 larger transcripts possess a developmentally-regulated expression combined to the increasing sum of data on the role of long noncoding RNAs in transcriptional regulation suggest that the Hoxa5 larger transcripts may participate in the control of Hox gene expression.

  12. Transcriptional regulators of Na, K-ATPase subunits

    Directory of Open Access Journals (Sweden)

    Zhiqin eLi

    2015-10-01

    Full Text Available The Na,K-ATPase classically serves as an ion pump creating an electrochemical gradient across the plasma membrane that is essential for transepithelial transport, nutrient uptake and membrane potential. In addition, Na,K-ATPase also functions as a receptor, a signal transducer and a cell adhesion molecule. With such diverse roles, it is understandable that the Na,K-ATPase subunits, the catalytic alpha-subunit, the beta-subunit and the FXYD proteins, are controlled extensively during development and to accommodate physiological needs. The spatial and temporal expression of Na,K-ATPase is partially regulated at the transcriptional level. Numerous transcription factors, hormones, growth factors, lipids and extracellular stimuli modulate the transcription of the Na,K-ATPase subunits. Moreover, epigenetic mechanisms also contribute to the regulation of Na,K-ATPase expression. With the ever growing knowledge about diseases associated with the malfunction of Na,K-ATPase, this review aims at summarizing the best-characterized transcription regulators that modulate Na,K-ATPase subunit levels. As abnormal expression of Na,K-ATPase subunits have been observed in many carcinoma, we will also discuss transcription factors that are associated with epithelial-to-mesenchymal transition, a crucial step in the progression of many tumors to malignant disease.

  13. Temporal network epidemiology

    CERN Document Server

    Holme, Petter

    2017-01-01

    This book covers recent developments in epidemic process models and related data on temporally varying networks. It is widely recognized that contact networks are indispensable for describing, understanding, and intervening to stop the spread of infectious diseases in human and animal populations; “network epidemiology” is an umbrella term to describe this research field. More recently, contact networks have been recognized as being highly dynamic. This observation, also supported by an increasing amount of new data, has led to research on temporal networks, a rapidly growing area. Changes in network structure are often informed by epidemic (or other) dynamics, in which case they are referred to as adaptive networks. This volume gathers contributions by prominent authors working in temporal and adaptive network epidemiology, a field essential to understanding infectious diseases in real society.

  14. Temporal Concurrent Constraint Programming

    DEFF Research Database (Denmark)

    Valencia, Frank Dan

    Concurrent constraint programming (ccp) is a formalism for concurrency in which agents interact with one another by telling (adding) and asking (reading) information in a shared medium. Temporal ccp extends ccp by allowing agents to be constrained by time conditions. This dissertation studies...... temporal ccp by developing a process calculus called ntcc. The ntcc calculus generalizes the tcc model, the latter being a temporal ccp model for deterministic and synchronouss timed reactive systems. The calculus is built upon few basic ideas but it captures several aspects of timed systems. As tcc, ntcc...... structures, robotic devises, multi-agent systems and music applications. The calculus is provided with a denotational semantics that captures the reactive computations of processes in the presence of arbitrary environments. The denotation is proven to be fully-abstract for a substantial fragment...

  15. Empresas de trabajo temporal

    OpenAIRE

    Chico Abad, Virginia

    2015-01-01

    Las empresas de trabajo temporal han ido tomando mayor relevancia debido a la estructura de la sociedad y de la economía. La entrada en vigor de la ley 14/1994 por la que se regulan las empresas de trabajo temporal suposo la incorporación al ordenamiento jurífico español de un tipo de empresas cuya actuación se habia extendido en otros países del entorno europeo. La idea general gira en torno a la flexibilidad de un nuevo marco económico y organizativo y exige a las empresas una capa...

  16. Medial temporal lobe

    International Nuclear Information System (INIS)

    Silver, A.J.; Cross, D.T.; Friedman, D.P.; Bello, J.A.; Hilal, S.K.

    1989-01-01

    To better define the MR appearance of hippocampal sclerosis, the authors have reviewed over 500 MR coronal images of the temporal lobes. Many cysts were noted that analysis showed were of choroid-fissure (arachnoid) origin. Their association with seizures was low. A few nontumorous, static, medial temporal lesions, noted on T2-weighted coronal images, were poorly visualized on T1-weighted images and did not enhance with gadolinium. The margins were irregular, involved the hippocampus, and were often associated with focal atrophy. The lesions usually were associated with seizure disorders and specific electroencephalographic changes, and the authors believe they represented hippocampal sclerosis

  17. Preparing for opening night: temporal boundary objects in textually-mediated professional practice

    Directory of Open Access Journals (Sweden)

    Elisabeth Davies

    2004-01-01

    Full Text Available The authors report on two projects in which the role of documents as temporal boundary objects mediating information practices across multiple timelines was explored. It has been suggested that studying workplace documents will uncover the information practices of professionals beyond traditional information needs and uses studies. Two workplaces were studied: a professional theatre production and a midwifery clinic. Both settings are communities constructed partly through textual dynamics and both have a pre-production phase leading to an opening night. In the theatre setting, qualitative interviews with the cast and crew and document analysis of the prompt book were the means of data collection. The midwifery clinic setting was investigated by means of interviews and follow-ups with sixteen midwife-client pairs and document analysis of the antenatal record. Preliminary thematic analysis pertaining to time and information was conducted on interview transcripts and the relevant documents. It was possible to show several instances of both the prompt book and the antenatal record being treated as a timeline by the various professionals using them. The authors conclude with a discussion of the temporal aspects of professionals' information practices as revealed by these two projects and encourage further document-focused research.

  18. RNA-guided transcriptional regulation

    Science.gov (United States)

    Church, George M.; Mali, Prashant G.; Esvelt, Kevin M.

    2016-02-23

    Methods of modulating expression of a target nucleic acid in a cell are provided including introducing into the cell a first foreign nucleic acid encoding one or more RNAs complementary to DNA, wherein the DNA includes the target nucleic acid, introducing into the cell a second foreign nucleic acid encoding a nuclease-null Cas9 protein that binds to the DNA and is guided by the one or more RNAs, introducing into the cell a third foreign nucleic acid encoding a transcriptional regulator protein or domain, wherein the one or more RNAs, the nuclease-null Cas9 protein, and the transcriptional regulator protein or domain are expressed, wherein the one or more RNAs, the nuclease-null Cas9 protein and the transcriptional regulator protein or domain co-localize to the DNA and wherein the transcriptional regulator protein or domain regulates expression of the target nucleic acid.

  19. Transcriptional control of megakaryocyte development.

    Science.gov (United States)

    Goldfarb, A N

    2007-10-15

    Megakaryocytes are highly specialized cells that arise from a bipotent megakaryocytic-erythroid progenitor (MEP). This developmental leap requires coordinated activation of megakaryocyte-specific genes, radical changes in cell cycle properties, and active prevention of erythroid differentiation. These programs result from upregulation of megakaryocyte-selective transcription factors, downregulation of erythroid-selective transcription factors and ongoing mediation of common erythro-megakaryocytic transcription factors. Unlike most developmental programs, no single lineage-unique family of master regulators exerts executive control over the megakaryocytic plan. Rather, an assemblage of non-unique factors and signals converge to determine lineage and differentiation. In human megakaryopoiesis, hereditary disorders of platelet production have confirmed contributions from three distinct transcription factor families. Murine models have extended this repertoire to include multiple additional factors. At a mechanistic level, the means by which these non-unique factors collaborate in the establishment of a perfectly unique cell type remains a central question.

  20. Longitudinal evaluation of leukocyte transcripts in killer whales (Orcinus Orca)

    Science.gov (United States)

    Sitt, Tatjana; Bowen, Lizabeth; Lee, Chia-Shan; Blanchard, Myra; McBain, James; Dold, Christopher; Stott, Jeffrey L.

    2016-01-01

    Early identification of illness and/or presence of environmental and/or social stressors in free-ranging and domestic cetaceans is a priority for marine mammal health care professionals. Incorporation of leukocyte gene transcript analysis into the diagnostic tool kit has the potential to augment classical diagnostics based upon ease of sample storage and shipment, inducible nature and well-defined roles of transcription and associated downstream actions. Development of biomarkers that could serve to identify “insults” and potentially differentiate disease etiology would be of great diagnostic value. To this end, a modest number of peripheral blood leukocyte gene transcripts were selected for application to a domestic killer whale population with a focus on broad representation of inducible immunologically relevant genes. Normalized leukocyte transcript values, longitudinally acquired from 232 blood samples derived from 26 clinically healthy whales, were not visibly influenced temporally nor by sex or the specific Park in which they resided. Stability in leukocyte transcript number during periods of health enhances their potential use in diagnostics through identification of outliers. Transcript levels of two cytokine genes, IL-4 and IL-17, were highly variable within the group as compared to the other transcripts. IL-4 transcripts were typically absent. Analysis of transcript levels on the other genes of interest, on an individual animal basis, identified more outliers than were visible when analyzed in the context of the entire population. The majority of outliers (9 samples) were low, though elevated transcripts were identified for IL-17 from 2 animals and one each for Cox-2 and IL-10. The low number of outliers was not unexpected as sample selection was intentionally directed towards animals that were clinically healthy at the time of collection. Outliers may reflect animals experiencing subclinical disease that is transient and self-limiting. The

  1. Marking Time, Making Methods: Temporality and Untimely Dilemmas in the Sociology of Youth and Educational Change

    Science.gov (United States)

    McLeod, Julie

    2017-01-01

    This article explores how temporality and temporal regimes might be engaged in qualitative research in the sociology of education, proposing that such questions matter in relation to how research is done, not only to the topics and themes researched. The article shows how temporality enters into research designs, practices and imaginaries, arguing…

  2. Tc-MYBPA an Arabidopsis TT2-like transcription factor and functions in the regulation of proanthocyanidin synthesis in Theobroma cacao.

    Science.gov (United States)

    Liu, Yi; Shi, Zi; Maximova, Siela N; Payne, Mark J; Guiltinan, Mark J

    2015-06-25

    The flavan-3-ols catechin and epicatechin, and their polymerized oligomers, the proanthocyanidins (PAs, also called condensed tannins), accumulate to levels of up to 15 % of the total weight of dry seeds of Theobroma cacao L. These compounds have been associated with several health benefits in humans. They also play important roles in pest and disease defense throughout the plant. In Arabidopsis, the R2R3 type MYB transcription factor TT2 regulates the major genes leading to the synthesis of PA. To explore the transcriptional regulation of the PA synthesis pathway in cacao, we isolated and characterized an R2R3 type MYB transcription factor MYBPA from cacao. We examined the spatial and temporal gene expression patterns of the Tc-MYBPA gene and found it to be developmentally expressed in a manner consistent with its involvement in PAs and anthocyanin synthesis. Functional complementation of an Arabidopsis tt2 mutant with Tc-MYBPA suggested that it can functionally substitute the Arabidopsis TT2 gene. Interestingly, in addition to PA accumulation in seeds of the Tc-MYBPA expressing plants, we also observed an obvious increase of anthocyanidin accumulation in hypocotyls. We observed that overexpression of the Tc-MYBPA gene resulted in increased expression of several key genes encoding the major structural enzymes of the PA and anthocyanidin pathway, including DFR (dihydroflavanol reductase), LDOX (leucoanthocyanidin dioxygenase) and BAN (ANR, anthocyanidin reductase). We conclude that the Tc-MYBPA gene that encodes an R2R3 type MYB transcription factor is an Arabidopsis TT2 like transcription factor, and may be involved in the regulation of both anthocyanin and PA synthesis in cacao. This research may provide molecular tools for breeding of cacao varieties with improved disease resistance and enhanced flavonoid profiles for nutritional and pharmaceutical applications.

  3. Exploring spatio-temporal patterns in traffic congestion data

    DEFF Research Database (Denmark)

    Kveladze, Irma; Agerholm, Niels; Reinau, Kristian Hegner

    2017-01-01

    An efficient infrastructure is essential for economic development. However, economic growth has been closely connected to the increasing road transport. This increases traffic congestions significantly, and road network gets near or at its capacity limits. Hence, congestion has become a central...

  4. Exploration into the spatial and temporal mechanisms of bacterial polarity

    DEFF Research Database (Denmark)

    Ebersbach, Gitte; Jacobs-Wagner, Christine; Charbon, Gitte Ebersbach

    2007-01-01

    The recognition of bacterial asymmetry is not new: the first high-resolution microscopy studies revealed that bacteria come in a multitude of shapes and sometimes carry asymmetrically localized external structures such as flagella on the cell surface. Even so, the idea that bacteria could have...... polarity in bacteria....

  5. Transcription termination in the plasmid/virus hybrid pSSVx from Sulfolobus islandicus

    DEFF Research Database (Denmark)

    Contursi, Patrizia; Cannio, Raffaele; She, Qunxin

    2010-01-01

    The pSSVx from Sulfolobus islandicus, strain REY15/4, is a hybrid between a plasmid and a fusellovirus. A systematic study previously performed revealed the presence of nine major transcripts, the expression of which was differentially and temporally regulated over the growth cycle of S. islandicus....... In this study, two new transcripts were identified. Then, 3' termini of all the RNAs were mapped using adaptor RT-PCR and RNase protection assays, and termination/arrest positions were identified for each transcript. The majority of the identified ending positions were located in the close vicinity of a T...... and counter-transcripts might be responsible for the transcription termination at these T-track-minus loci in the closely spaced pSSVx genes....

  6. V(D)J recombination on minichromosomes is not affected by transcription.

    Science.gov (United States)

    Hsieh, C L; McCloskey, R P; Lieber, M R

    1992-08-05

    It has been shown previously by others that transcription is temporally correlated with the onset of V(D)J recombination at the endogenous antigen receptor loci. We have been interested in determining whether this temporal correlation indicates a causal connection between these two processes. We have compared V(D)J recombination minichromosome substrates that have transcripts running through the recombination zone with substrates that do not in a transient transfection assay. In this system, the substrates acquire a minichromosome conformation within the first several hours after transfection. We find that the substrates recombine equally well over a 100-fold range in transcriptional variation. In additional studies, we have taken substrates that have low levels of transcription and inhibited transcription further by methylating the substrate DNA or by treating the cells with a general transcription inhibitor (alpha-amanitin). Although these treatments decrease the level of expression an additional 10-100-fold, there is still no observable effect on V(D)J recombination. Based on these results, we conclude that transcription is not necessary for the V(D)J reaction mechanism and does not alter substrate structure at the DNA level or at the simplest levels of chromatin structure in a way that affects the reaction.

  7. National Capital Planning Commission Meeting Transcripts

    Data.gov (United States)

    National Capital Planning Commission — Transcripts of the monthly (with the exception of August) National Capital Planning Commission meeting transcripts are provided for research to confirm actions taken...

  8. Optimizing Temporal Queries

    DEFF Research Database (Denmark)

    Toman, David; Bowman, Ivan Thomas

    2003-01-01

    Recent research in the area of temporal databases has proposed a number of query languages that vary in their expressive power and the semantics they provide to users. These query languages represent a spectrum of solutions to the tension between clean semantics and efficient evaluation. Often, t...

  9. Temporal Concurrent Constraint Programming

    DEFF Research Database (Denmark)

    Nielsen, Mogens; Palamidessi, Catuscia; Valencia, Frank Dan

    2002-01-01

    The ntcc calculus is a model of non-deterministic temporal concurrent constraint programming. In this paper we study behavioral notions for this calculus. In the underlying computational model, concurrent constraint processes are executed in discrete time intervals. The behavioral notions studied...

  10. Temporal Photon Differentials

    DEFF Research Database (Denmark)

    Schjøth, Lars; Frisvad, Jeppe Revall; Erleben, Kenny

    2010-01-01

    The finite frame rate also used in computer animated films is cause of adverse temporal aliasing effects. Most noticeable of these is a stroboscopic effect that is seen as intermittent movement of fast moving illumination. This effect can be mitigated using non-zero shutter times, effectively...

  11. Temporal compressive sensing systems

    Science.gov (United States)

    Reed, Bryan W.

    2017-12-12

    Methods and systems for temporal compressive sensing are disclosed, where within each of one or more sensor array data acquisition periods, one or more sensor array measurement datasets comprising distinct linear combinations of time slice data are acquired, and where mathematical reconstruction allows for calculation of accurate representations of the individual time slice datasets.

  12. Information and Temporality

    Directory of Open Access Journals (Sweden)

    Christian Flender

    2016-09-01

    Full Text Available Being able to give reasons for what the world is and how it works is one of the defining characteristics of modernity. Mathematical reason and empirical observation brought science and engineering to unprecedented success. However, modernity has reached a post-state where an instrumental view of technology needs revision with reasonable arguments and evidence, i.e. without falling back to superstition and mysticism. Instrumentally, technology bears the potential to ease and to harm. Easing and harming can't be controlled like the initial development of technology is a controlled exercise for a specific, mostly easing purpose. Therefore, a revised understanding of information technology is proposed based upon mathematical concepts and intuitions as developed in quantum mechanics. Quantum mechanics offers unequaled opportunities because it raises foundational questions in a precise form. Beyond instrumentalism it enables to raise the question of essences as that what remains through time what it is. The essence of information technology is acausality. The time of acausality is temporality. Temporality is not a concept or a category. It is not epistemological. As an existential and thus more comprehensive and fundamental than a concept or a category temporality is ontological; it does not simply have ontic properties. Rather it exhibits general essences. Datability, significance, spannedness and openness are general essences of equiprimordial time (temporality.

  13. Temporal logic motion planning

    CSIR Research Space (South Africa)

    Seotsanyana, M

    2010-01-01

    Full Text Available In this paper, a critical review on temporal logic motion planning is presented. The review paper aims to address the following problems: (a) In a realistic situation, the motion planning problem is carried out in real-time, in a dynamic, uncertain...

  14. Experimental temporal quantum steering

    Czech Academy of Sciences Publication Activity Database

    Bartkiewicz, K.; Černoch, Antonín; Lemr, K.; Miranowicz, A.; Nori, F.

    2016-01-01

    Roč. 6, Nov (2016), 1-8, č. článku 38076. ISSN 2045-2322 R&D Projects: GA ČR GAP205/12/0382 Institutional support: RVO:68378271 Keywords : temporal quantum steering * EPR steering Subject RIV: BH - Optics, Masers, Lasers Impact factor: 4.259, year: 2016

  15. Communication, Technology, Temporality

    Directory of Open Access Journals (Sweden)

    Mark A. Martinez

    2012-08-01

    Full Text Available This paper proposes a media studies that foregrounds technological objects as communicative and historical agents. Specifically, I take the digital computer as a powerful catalyst of crises in communication theories and certain key features of modernity. Finally, the computer is the motor of “New Media” which is at once a set of technologies, a historical epoch, and a field of knowledge. As such the computer shapes “the new” and “the future” as History pushes its origins further in the past and its convergent quality pushes its future as a predominate medium. As treatment of information and interface suggest, communication theories observe computers, and technologies generally, for the mediated languages they either afford or foreclose to us. My project describes the figures information and interface for the different ways they can be thought of as aspects of communication. I treat information not as semantic meaning, formal or discursive language, but rather as a physical organism. Similarly an interface is not a relationship between a screen and a human visual intelligence, but is instead a reciprocal, affective and physical process of contact. I illustrate that historically there have been conceptions of information and interface complimentary to mine, fleeting as they have been in the face of a dominant temporality of mediation. I begin with a theoretically informed approach to media history, and extend it to a new theory of communication. In doing so I discuss a model of time common to popular, scientific, and critical conceptions of media technologies especially in theories of computer technology. This is a predominate model with particular rules of temporal change and causality for thinking about mediation, and limits the conditions of possibility for knowledge production about communication. I suggest a new model of time as integral to any event of observation and analysis, and that human mediation does not exhaust the

  16. DNA damage mediated transcription arrest: Step back to go forward.

    Science.gov (United States)

    Mullenders, Leon

    2015-12-01

    The disturbance of DNA helix conformation by bulky DNA damage poses hindrance to transcription elongating due to stalling of RNA polymerase at transcription blocking lesions. Stalling of RNA polymerase provokes the formation of R-loops, i.e. the formation of a DNA-RNA hybrid and a displaced single stranded DNA strand as well as displacement of spliceosomes. R-loops are processed into DNA single and double strand breaks by NER factors depending on TC-NER factors leading to genome instability. Moreover, stalling of RNA polymerase induces a strong signal for cell cycle arrest and apoptosis. These toxic and mutagenic effects are counteracted by a rapid recruitment of DNA repair proteins to perform transcription coupled nucleotide excision repair (TC-NER) to remove the blocking DNA lesions and to restore transcription. Recent studies have highlighted the role of backtracking of RNA polymerase to facilitate TC-NER and identified novel factors that play key roles in TC-NER and in restoration of transcription. On the molecular level these factors facilitate stability of the repair complex by promotion and regulation of various post-translational modifications of NER factors and chromatin substrate. In addition, the continuous flow of new factors that emerge from screening assays hints to several regulatory levels to safeguard the integrity of transcription elongation after disturbance by DNA damage that have yet to be explored. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development

    Directory of Open Access Journals (Sweden)

    Nick D.L. Owens

    2016-01-01

    Full Text Available Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack a comprehensive understanding of transcript kinetics, which limits quantitative biology. This is an acute challenge in embryonic development, where rapid changes in gene expression dictate cell fate decisions. By ultra-high-frequency sampling of Xenopus embryos and absolute normalization of sequence reads, we present smooth gene expression trajectories in absolute transcript numbers. During a developmental period approximating the first 8 weeks of human gestation, transcript kinetics vary by eight orders of magnitude. Ordering genes by expression dynamics, we find that “temporal synexpression” predicts common gene function. Remarkably, a single parameter, the characteristic timescale, can classify transcript kinetics globally and distinguish genes regulating development from those involved in cellular metabolism. Overall, our analysis provides unprecedented insight into the reorganization of maternal and embryonic transcripts and redefines our ability to perform quantitative biology.

  18. In silico comparative genomic analysis of GABAA receptor transcriptional regulation

    Directory of Open Access Journals (Sweden)

    Joyce Christopher J

    2007-06-01

    Full Text Available Abstract Background Subtypes of the GABAA receptor subunit exhibit diverse temporal and spatial expression patterns. In silico comparative analysis was used to predict transcriptional regulatory features in individual mammalian GABAA receptor subunit genes, and to identify potential transcriptional regulatory components involved in the coordinate regulation of the GABAA receptor gene clusters. Results Previously unreported putative promoters were identified for the β2, γ1, γ3, ε, θ and π subunit genes. Putative core elements and proximal transcriptional factors were identified within these predicted promoters, and within the experimentally determined promoters of other subunit genes. Conserved intergenic regions of sequence in the mammalian GABAA receptor gene cluster comprising the α1, β2, γ2 and α6 subunits were identified as potential long range transcriptional regulatory components involved in the coordinate regulation of these genes. A region of predicted DNase I hypersensitive sites within the cluster may contain transcriptional regulatory features coordinating gene expression. A novel model is proposed for the coordinate control of the gene cluster and parallel expression of the α1 and β2 subunits, based upon the selective action of putative Scaffold/Matrix Attachment Regions (S/MARs. Conclusion The putative regulatory features identified by genomic analysis of GABAA receptor genes were substantiated by cross-species comparative analysis and now require experimental verification. The proposed model for the coordinate regulation of genes in the cluster accounts for the head-to-head orientation and parallel expression of the α1 and β2 subunit genes, and for the disruption of transcription caused by insertion of a neomycin gene in the close vicinity of the α6 gene, which is proximal to a putative critical S/MAR.

  19. SEASTAR: systematic evaluation of alternative transcription start sites in RNA.

    Science.gov (United States)

    Qin, Zhiyi; Stoilov, Peter; Zhang, Xuegong; Xing, Yi

    2018-05-04

    Alternative first exons diversify the transcriptomes of eukaryotes by producing variants of the 5' Untranslated Regions (5'UTRs) and N-terminal coding sequences. Accurate transcriptome-wide detection of alternative first exons typically requires specialized experimental approaches that are designed to identify the 5' ends of transcripts. We developed a computational pipeline SEASTAR that identifies first exons from RNA-seq data alone then quantifies and compares alternative first exon usage across multiple biological conditions. The exons inferred by SEASTAR coincide with transcription start sites identified directly by CAGE experiments and bear epigenetic hallmarks of active promoters. To determine if differential usage of alternative first exons can yield insights into the mechanism controlling gene expression, we applied SEASTAR to an RNA-seq dataset that tracked the reprogramming of mouse fibroblasts into induced pluripotent stem cells. We observed dynamic temporal changes in the usage of alternative first exons, along with correlated changes in transcription factor expression. Using a combined sequence motif and gene set enrichment analysis we identified N-Myc as a regulator of alternative first exon usage in the pluripotent state. Our results demonstrate that SEASTAR can leverage the available RNA-seq data to gain insights into the control of gene expression and alternative transcript variation in eukaryotic transcriptomes.

  20. Farside explorer

    DEFF Research Database (Denmark)

    Mimoun, David; Wieczorek, Mark A.; Alkalai, Leon

    2012-01-01

    the primary differentiation and evolution of the Moon, it can be continuously monitored from the Earth-Moon L2 Lagrange point, and there is a complete lack of reflected solar illumination from the Earth. Farside Explorer will exploit these properties and make the first radio-astronomy measurements from...... the most radio-quiet region of near-Earth space, determine the internal structure and thermal evolution of the Moon, from crust to core, and quantify impact hazards in near-Earth space by the measurement of flashes generated by impact events. The Farside Explorer flight system includes two identical solar......Farside Explorer is a proposed Cosmic Vision medium-size mission to the farside of the Moon consisting of two landers and an instrumented relay satellite. The farside of the Moon is a unique scientific platform in that it is shielded from terrestrial radio-frequency interference, it recorded...

  1. Temporal Concurrent Constraint Programming

    DEFF Research Database (Denmark)

    Nielsen, Mogens; Valencia Posso, Frank Dan

    2002-01-01

    The ntcc calculus is a model of non-deterministic temporal concurrent constraint programming. In this paper we study behavioral notions for this calculus. In the underlying computational model, concurrent constraint processes are executed in discrete time intervals. The behavioral notions studied...... reflect the reactive interactions between concurrent constraint processes and their environment, as well as internal interactions between individual processes. Relationships between the suggested notions are studied, and they are all proved to be decidable for a substantial fragment of the calculus...

  2. Processivity and coupling in messenger RNA transcription.

    Directory of Open Access Journals (Sweden)

    Stuart Aitken

    2010-01-01

    Full Text Available The complexity of messenger RNA processing is now being uncovered by experimental techniques that are capable of detecting individual copies of mRNA in cells, and by quantitative real-time observations that reveal the kinetics. This processing is commonly modelled by permitting mRNA to be transcribed only when the promoter is in the on state. In this simple on/off model, the many processes involved in active transcription are represented by a single reaction. These processes include elongation, which has a minimum time for completion and processing that is not captured in the model.In this paper, we explore the impact on the mRNA distribution of representing the elongation process in more detail. Consideration of the mechanisms of elongation leads to two alternative models of the coupling between the elongating polymerase and the state of the promoter: Processivity allows polymerases to complete elongation irrespective of the promoter state, whereas coupling requires the promoter to be active to produce a full-length transcript. We demonstrate that these alternatives have a significant impact on the predicted distributions. Models are simulated by the Gillespie algorithm, and the third and fourth moments of the resulting distribution are computed in order to characterise the length of the tail, and sharpness of the peak. By this methodology, we show that the moments provide a concise summary of the distribution, showing statistically-significant differences across much of the feasible parameter range.We conclude that processivity is not fully consistent with the on/off model unless the probability of successfully completing elongation is low--as has been observed. The results also suggest that some form of coupling between the promoter and a rate-limiting step in transcription may explain the cell's inability to maintain high mRNA levels at low noise--a prediction of the on/off model that has no supporting evidence.

  3. The “Fourth Dimension” of Gene Transcription

    Science.gov (United States)

    O'Malley, Bert W.

    2009-01-01

    The three dimensions of space provide our relationship to position on the earth, but the fourth dimension of time has an equally profound influence on our lives. Everything from light and sound to weather and biology operate on the principle of measurable temporal periodicity. Consequently, a wide variety of time clocks affect all aspects of our existence. The annual (and biannual) cycles of activity, metabolism, and mating, the monthly physiological clocks of women and men, and the 24-h diurnal rhythms of humans are prime examples. Should it be surprising to us that the fourth dimension also impinges upon gene expression and that the genome itself is regulated by the fastest running of all biological clocks? Recent evidence substantiates the existence of such a ubiquitin-dependent transcriptional clock that is based upon the activation and destruction of transcriptional coactivators. PMID:19221049

  4. Genome-wide transcriptional reprogramming under drought stress

    KAUST Repository

    Chen, Hao

    2012-01-01

    Soil water deficit is one of the major factors limiting plant productivity. Plants cope with this adverse environmental condition by coordinating the up- or downregulation of an array of stress responsive genes. Reprogramming the expression of these genes leads to rebalanced development and growth that are in concert with the reduced water availability and that ultimately confer enhanced stress tolerance. Currently, several techniques have been employed to monitor genome-wide transcriptional reprogramming under drought stress. The results from these high throughput studies indicate that drought stress-induced transcriptional reprogramming is dynamic, has temporal and spatial specificity, and is coupled with the circadian clock and phytohormone signaling pathways. © 2012 Springer-Verlag Berlin Heidelberg. All rights are reserved.

  5. Uranium exploration

    International Nuclear Information System (INIS)

    De Voto, R.H.

    1984-01-01

    This paper is a review of the methodology and technology that are currently being used in varying degrees in uranium exploration activities worldwide. Since uranium is ubiquitous and occurs in trace amounts (0.2 to 5 ppm) in virtually all rocks of the crust of the earth, exploration for uranium is essentially the search of geologic environments in which geologic processes have produced unusual concentrations of uranium. Since the level of concentration of uranium of economic interest is dependent on the present and future price of uranium, it is appropriate here to review briefly the economic realities of uranium-fueled power generation. (author)

  6. Transcriptional Programs Controlling Perinatal Lung Maturation

    Science.gov (United States)

    Xu, Yan; Wang, Yanhua; Besnard, Valérie; Ikegami, Machiko; Wert, Susan E.; Heffner, Caleb; Murray, Stephen A.; Donahue, Leah Rae; Whitsett, Jeffrey A.

    2012-01-01

    The timing of lung maturation is controlled precisely by complex genetic and cellular programs. Lung immaturity following preterm birth frequently results in Respiratory Distress Syndrome (RDS) and Broncho-Pulmonary Dysplasia (BPD), which are leading causes of mortality and morbidity in preterm infants. Mechanisms synchronizing gestational length and lung maturation remain to be elucidated. In this study, we designed a genome-wide mRNA expression time-course study from E15.5 to Postnatal Day 0 (PN0) using lung RNAs from C57BL/6J (B6) and A/J mice that differ in gestational length by ∼30 hr (B6controlling lung maturation. We identified both temporal and strain dependent gene expression patterns during lung maturation. For time dependent changes, cell adhesion, vasculature development, and lipid metabolism/transport were major bioprocesses induced during the saccular stage of lung development at E16.5–E17.5. CEBPA, PPARG, VEGFA, CAV1 and CDH1 were found to be key signaling and transcriptional regulators of these processes. Innate defense/immune responses were induced at later gestational ages (E18.5–20.5), STAT1, AP1, and EGFR being important regulators of these responses. Expression of RNAs associated with the cell cycle and chromatin assembly was repressed during prenatal lung maturation and was regulated by FOXM1, PLK1, chromobox, and high mobility group families of transcription factors. Strain dependent lung mRNA expression differences peaked at E18.5. At this time, mRNAs regulating surfactant and innate immunity were more abundantly expressed in lungs of B6 (short gestation) than in A/J (long gestation) mice, while expression of genes involved in chromatin assembly and histone modification were expressed at lower levels in B6 than in A/J mice. The present study systemically mapped key regulators, bioprocesses, and transcriptional networks controlling lung maturation, providing the basis for new therapeutic strategies to enhance lung function in preterm

  7. College Explorer.

    Science.gov (United States)

    Ahl, David H.

    1985-01-01

    The "College Explorer" is a software package (for the 64K Apple II, IBM PC, TRS-80 model III and 4 microcomputers) which aids in choosing a college. The major features of this package (manufactured by The College Board) are described and evaluated. Sample input/output is included. (JN)

  8. Exploring Size.

    Science.gov (United States)

    Brand, Judith, Ed.

    1995-01-01

    "Exploring" is a magazine of science, art, and human perception that communicates ideas museum exhibits cannot demonstrate easily by using experiments and activities for the classroom. This issue concentrates on size, examining it from a variety of viewpoints. The focus allows students to investigate and discuss interconnections among…

  9. Single molecule transcription profiling with AFM

    International Nuclear Information System (INIS)

    Reed, Jason; Mishra, Bud; Pittenger, Bede; Magonov, Sergei; Troke, Joshua; Teitell, Michael A; Gimzewski, James K

    2007-01-01

    Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations

  10. Discriminative identification of transcriptional responses of promoters and enhancers after stimulus

    KAUST Repository

    Kleftogiannis, Dimitrios A.

    2016-10-17

    Promoters and enhancers regulate the initiation of gene expression and maintenance of expression levels in spatial and temporal manner. Recent findings stemming from the Cap Analysis of Gene Expression (CAGE) demonstrate that promoters and enhancers, based on their expression profiles after stimulus, belong to different transcription response subclasses. One of the most promising biological features that might explain the difference in transcriptional response between subclasses is the local chromatin environment. We introduce a novel computational framework, PEDAL, for distinguishing effectively transcriptional profiles of promoters and enhancers using solely histone modification marks, chromatin accessibility and binding sites of transcription factors and co-activators. A case study on data from MCF-7 cell-line reveals that PEDAL can identify successfully the transcription response subclasses of promoters and enhancers from two different stimulations. Moreover, we report subsets of input markers that discriminate with minimized classification error MCF-7 promoter and enhancer transcription response subclasses. Our work provides a general computational approach for identifying effectively cell-specific and stimulation-specific promoter and enhancer transcriptional profiles, and thus, contributes to improve our understanding of transcriptional activation in human.

  11. Anterior Temporal Lobe Morphometry Predicts Categorization Ability.

    Science.gov (United States)

    Garcin, Béatrice; Urbanski, Marika; Thiebaut de Schotten, Michel; Levy, Richard; Volle, Emmanuelle

    2018-01-01

    Categorization is the mental operation by which the brain classifies objects and events. It is classically assessed using semantic and non-semantic matching or sorting tasks. These tasks show a high variability in performance across healthy controls and the cerebral bases supporting this variability remain unknown. In this study we performed a voxel-based morphometry study to explore the relationships between semantic and shape categorization tasks and brain morphometric differences in 50 controls. We found significant correlation between categorization performance and the volume of the gray matter in the right anterior middle and inferior temporal gyri. Semantic categorization tasks were associated with more rostral temporal regions than shape categorization tasks. A significant relationship was also shown between white matter volume in the right temporal lobe and performance in the semantic tasks. Tractography revealed that this white matter region involved several projection and association fibers, including the arcuate fasciculus, inferior fronto-occipital fasciculus, uncinate fasciculus, and inferior longitudinal fasciculus. These results suggest that categorization abilities are supported by the anterior portion of the right temporal lobe and its interaction with other areas.

  12. Anterior Temporal Lobe Morphometry Predicts Categorization Ability

    Directory of Open Access Journals (Sweden)

    Béatrice Garcin

    2018-02-01

    Full Text Available Categorization is the mental operation by which the brain classifies objects and events. It is classically assessed using semantic and non-semantic matching or sorting tasks. These tasks show a high variability in performance across healthy controls and the cerebral bases supporting this variability remain unknown. In this study we performed a voxel-based morphometry study to explore the relationships between semantic and shape categorization tasks and brain morphometric differences in 50 controls. We found significant correlation between categorization performance and the volume of the gray matter in the right anterior middle and inferior temporal gyri. Semantic categorization tasks were associated with more rostral temporal regions than shape categorization tasks. A significant relationship was also shown between white matter volume in the right temporal lobe and performance in the semantic tasks. Tractography revealed that this white matter region involved several projection and association fibers, including the arcuate fasciculus, inferior fronto-occipital fasciculus, uncinate fasciculus, and inferior longitudinal fasciculus. These results suggest that categorization abilities are supported by the anterior portion of the right temporal lobe and its interaction with other areas.

  13. Transcriptional regulation of hepatic lipogenesis.

    Science.gov (United States)

    Wang, Yuhui; Viscarra, Jose; Kim, Sun-Joong; Sul, Hei Sook

    2015-11-01

    Fatty acid and fat synthesis in the liver is a highly regulated metabolic pathway that is important for very low-density lipoprotein (VLDL) production and thus energy distribution to other tissues. Having common features at their promoter regions, lipogenic genes are coordinately regulated at the transcriptional level. Transcription factors, such as upstream stimulatory factors (USFs), sterol regulatory element-binding protein 1C (SREBP1C), liver X receptors (LXRs) and carbohydrate-responsive element-binding protein (ChREBP) have crucial roles in this process. Recently, insights have been gained into the signalling pathways that regulate these transcription factors. After feeding, high blood glucose and insulin levels activate lipogenic genes through several pathways, including the DNA-dependent protein kinase (DNA-PK), atypical protein kinase C (aPKC) and AKT-mTOR pathways. These pathways control the post-translational modifications of transcription factors and co-regulators, such as phosphorylation, acetylation or ubiquitylation, that affect their function, stability and/or localization. Dysregulation of lipogenesis can contribute to hepatosteatosis, which is associated with obesity and insulin resistance.

  14. Structural insights into transcription complexes

    NARCIS (Netherlands)

    Berger, I.; Blanco, A.G.; Boelens, R.; Cavarelli, J.; Coll, M.; Folkers, G.E.; Nie, Y.; Pogenberg, V.; Schultz, P.; Wilmanns, M.; Moras, D.; Poterszman, A.

    2011-01-01

    Control of transcription allows the regulation of cell activity in response to external stimuli and research in the field has greatly benefited from efforts in structural biology. In this review, based on specific examples from the European SPINE2-COMPLEXES initiative, we illustrate the impact of

  15. Transcription factor-based biosensor

    Science.gov (United States)

    Dietrich, Jeffrey A; Keasling, Jay D

    2013-10-08

    The present invention provides for a system comprising a BmoR transcription factor, a .sigma..sup.54-RNA polymerase, and a pBMO promoter operatively linked to a reporter gene, wherein the pBMO promoter is capable of expression of the reporter gene with an activated form of the BmoR and the .sigma..sup.54-RNA polymerase.

  16. Navigating the transcriptional roadmap regulating plant secondary cell wall deposition

    Directory of Open Access Journals (Sweden)

    Steven Grant Hussey

    2013-08-01

    Full Text Available The current status of lignocellulosic biomass as an invaluable resource in industry, agriculture and health has spurred increased interest in understanding the transcriptional regulation of secondary cell wall (SCW biosynthesis. The last decade of research has revealed an extensive network of NAC, MYB and other families of transcription factors regulating Arabidopsis SCW biosynthesis, and numerous studies have explored SCW-related transcription factors in other dicots and monocots. Whilst the general structure of the Arabidopsis network has been a topic of several reviews, they have not comprehensively represented the detailed protein-DNA and protein-protein interactions described in the literature, and an understanding of network dynamics and functionality has not yet been achieved for SCW formation. Furthermore the methodologies employed in studies of SCW transcriptional regulation have not received much attention, especially in the case of non-model organisms. In this review, we have reconstructed the most exhaustive literature-based network representations to date of SCW transcriptional regulation in Arabidopsis. We include a manipulable Cytoscape representation of the Arabidopsis SCW transcriptional network to aid in future studies, along with a list of supporting literature for each documented interaction. Amongst other topics, we discuss the various components of the network, its evolutionary conservation in plants, putative modules and dynamic mechanisms that may influence network function, and the approaches that have been employed in network inference. Future research should aim to better understand network function and its response to dynamic perturbations, whilst the development and application of genome-wide approaches such as ChIP-seq and systems genetics are in progress for the study of SCW transcriptional regulation in non-model organisms.

  17. Epigenetics regulates transcription and pathogenesis in the parasite Trichomonas vaginalis.

    Science.gov (United States)

    Pachano, Tomas; Nievas, Yesica R; Lizarraga, Ayelen; Johnson, Patricia J; Strobl-Mazzulla, Pablo H; de Miguel, Natalia

    2017-06-01

    Trichomonas vaginalis is a common sexually transmitted parasite that colonizes the human urogenital tract. Infections range from asymptomatic to highly inflammatory, depending on the host and the parasite strain. Different T. vaginalis strains vary greatly in their adherence and cytolytic capacities. These phenotypic differences might be attributed to differentially expressed genes as a consequence of extra-genetic variation, such as epigenetic modifications. In this study, we explored the role of histone acetylation in regulating gene transcription and pathogenesis in T. vaginalis. Here, we show that histone 3 lysine acetylation (H3KAc) is enriched in nucleosomes positioned around the transcription start site of active genes (BAP1 and BAP2) in a highly adherent parasite strain; compared with the low acetylation abundance in contrast to that observed in a less-adherent strain that expresses these genes at low levels. Additionally, exposition of less-adherent strain with a specific histone deacetylases inhibitor, trichostatin A, upregulated the transcription of BAP1 and BAP2 genes in concomitance with an increase in H3KAc abundance and chromatin accessibility around their transcription start sites. Moreover, we demonstrated that the binding of initiator binding protein, the transcription factor responsible for the initiation of transcription of ~75% of known T. vaginalis genes, depends on the histone acetylation state around the metazoan-like initiator to which initiator binding protein binds. Finally, we found that trichostatin A treatment increased parasite aggregation and adherence to host cells. Our data demonstrated for the first time that H3KAc is a permissive histone modification that functions to mediate both transcription and pathogenesis of the parasite T. vaginalis. © 2017 John Wiley & Sons Ltd.

  18. Exploring quadrangulations

    KAUST Repository

    Peng, Chi-Han; Barton, Michael; Jiang, Caigui; Wonka, Peter

    2014-01-01

    Here we presented a framework to explore quad mesh topologies. The core of our work is a systematic enumeration algorithm that can generate all possible quadrangular meshes inside a defined boundary with an upper limit of v3-v5 pairs. The algorithm is orders of magnitude more efficient than previous work. The combination of topological enumeration and shape-space exploration demonstrates that mesh topology has a powerful influence on geometry. The Fig. 18. A gallery of different quadrilateral meshes for a Shuriken. The quadrilaterals of the model were colored in a postprocess. Topological variations have distinctive, interesting patterns of mesh lines. © 2014 ACM 0730-0301/2014/01-ART3 15.00.

  19. Exploring quadrangulations

    KAUST Repository

    Peng, Chi-Han

    2014-02-04

    Here we presented a framework to explore quad mesh topologies. The core of our work is a systematic enumeration algorithm that can generate all possible quadrangular meshes inside a defined boundary with an upper limit of v3-v5 pairs. The algorithm is orders of magnitude more efficient than previous work. The combination of topological enumeration and shape-space exploration demonstrates that mesh topology has a powerful influence on geometry. The Fig. 18. A gallery of different quadrilateral meshes for a Shuriken. The quadrilaterals of the model were colored in a postprocess. Topological variations have distinctive, interesting patterns of mesh lines. © 2014 ACM 0730-0301/2014/01-ART3 15.00.

  20. Cross-cultural caregiving and the temporal dimension.

    Science.gov (United States)

    Escandon, Socorro

    2013-11-01

    The caregiving research literature has explored and documented findings from psychological, clinical, and policy/program perspectives, but little is known regarding the contextual perspectives of caregiving. Temporal factors influence the structure and functioning of the caregiving family. The proposed paradigm adaptation extends a contextual perspective that addresses the exploration of the caregiving process as a temporal, dynamic, progressive process over time, in which decisions made by caregivers may not always be based on observable tasks but, nevertheless, may have important consequences. When cultures cross, attitudes and behaviors are modified, resulting from contact with a different set of values and beliefs. Cross-cultural research aims to explore these changes that take place over time. Future research should consider the inclusion of measures that assess the temporal aspect of caregiving and the acculturation considerations of family caregivers. These measures are especially needed because of the increased influence of international migration, economic globalization, and political conflicts in today's multicultural societies.

  1. Explorative Faktorenanalyse

    OpenAIRE

    Klopp, Eric

    2010-01-01

    Die explorative Faktorenanalyse (EFA) ist ein Verfahren aus der multivariaten Statistik. Mithilfe der Faktorenanalyse kann aus den Beobachtungen vieler manifester Variablen (z .B Items eines Fragebogens) auf wenige zugrunde liegende latente Variablen, die Faktoren genannt werden, geschlossen werden. Eine EFA führt zu einer Reduktion der Variablen auf wenige, den manifesten Variablen zugrunde liegende Faktoren. Der folgende Text gibt einen Überblick über die Grundlagen der EFA sowie der wichti...

  2. Spatio-Temporal Rule Mining

    DEFF Research Database (Denmark)

    Gidofalvi, Gyozo; Pedersen, Torben Bach

    2005-01-01

    Recent advances in communication and information technology, such as the increasing accuracy of GPS technology and the miniaturization of wireless communication devices pave the road for Location-Based Services (LBS). To achieve high quality for such services, spatio-temporal data mining techniques...... are needed. In this paper, we describe experiences with spatio-temporal rule mining in a Danish data mining company. First, a number of real world spatio-temporal data sets are described, leading to a taxonomy of spatio-temporal data. Second, the paper describes a general methodology that transforms...... the spatio-temporal rule mining task to the traditional market basket analysis task and applies it to the described data sets, enabling traditional association rule mining methods to discover spatio-temporal rules for LBS. Finally, unique issues in spatio-temporal rule mining are identified and discussed....

  3. Egocentric Temporal Action Proposals.

    Science.gov (United States)

    Shao Huang; Weiqiang Wang; Shengfeng He; Lau, Rynson W H

    2018-02-01

    We present an approach to localize generic actions in egocentric videos, called temporal action proposals (TAPs), for accelerating the action recognition step. An egocentric TAP refers to a sequence of frames that may contain a generic action performed by the wearer of a head-mounted camera, e.g., taking a knife, spreading jam, pouring milk, or cutting carrots. Inspired by object proposals, this paper aims at generating a small number of TAPs, thereby replacing the popular sliding window strategy, for localizing all action events in the input video. To this end, we first propose to temporally segment the input video into action atoms, which are the smallest units that may contain an action. We then apply a hierarchical clustering algorithm with several egocentric cues to generate TAPs. Finally, we propose two actionness networks to score the likelihood of each TAP containing an action. The top ranked candidates are returned as output TAPs. Experimental results show that the proposed TAP detection framework performs significantly better than relevant approaches for egocentric action detection.

  4. Spontaneous lateral temporal encephalocele.

    Science.gov (United States)

    Tuncbilek, Gokhan; Calis, Mert; Akalan, Nejat

    2013-01-01

    A spontaneous encephalocele is one that develops either because of embryological maldevelopment or from a poorly understood postnatal process that permits brain herniation to occur. We here report a rare case of lateral temporal encephalocele extending to the infratemporal fossa under the zygomatic arch. At birth, the infant was noted to have a large cystic mass in the right side of the face. After being operated on initially in another center in the newborn period, the patient was referred to our clinic with a diagnosis of temporal encephalocele. He was 6 months old at the time of admission. Computerized tomography scan and magnetic resonance imaging studies revealed a 8 × 9 cm fluid-filled, multiloculated cystic mass at the right infratemporal fossa. No intracranial pathology or connection is seen. The patient was operated on to reduce the distortion effect of the growing mass. The histopathological examination of the sac revealed well-differentiated mature glial tissue stained with glial fibrillary acid protein. This rare clinical presentation of encephaloceles should be taken into consideration during the evaluation of the lateral facial masses in the infancy period, and possible intracranial connection should be ruled out before surgery to avoid complications.

  5. Temporal Convergence for Knowledge Management

    Directory of Open Access Journals (Sweden)

    Christopher Phillip Martin

    2008-05-01

    Full Text Available Time and knowledge have tended to be conceptualised in conventional knowledge management systems as either ‘timeless’ recordings of procedures, or time-stamped records of past events and states. The concept of temporal convergence was previously developed to help apply knowledge-management theory to complex military processes such as commander’s intent, shared situation awareness, and self-synchronisation. This paper clarifies the concept and introduces several others in forming a framework to assist discussion and exploration of the types of knowledge required for complex endeavours, such as warfighting, characterised by opposition and uncertainty. The approach is grounded in a pragmatist philosophy and constructivist epistemology. Argument proceeds along mathematical lines from a basis that the types of knowledge most valuable to goal-directed agents in uncertain environments can be modelled as directed graph topologies. The framework is shown to be useful in describing and reasoning about the knowledge requirements and prerequisites for distributed decision-making through the sharing of situational knowledge and common intentions, with practical application to the planning and execution of operations. To the designers of knowledge management systems seeking to address this space, it presents a challenge that cannot be addressed merely by construction, storage, search and retrieval of documents and records pertaining to the past.

  6. Exploring Science Through Polar Exploration

    Science.gov (United States)

    Pfirman, S. L.; Bell, R. E.; Zadoff, L.; Kelsey, R.

    2003-12-01

    Exploring the Poles is a First Year Seminar course taught at Barnard College, Columbia University. First Year Seminars are required of incoming students and are designed to encourage critical analysis in a small class setting with focused discussion. The class links historical polar exploration with current research in order to: introduce non-scientists to the value of environmental science through polar literature; discuss issues related to venturing into the unknown that are of relevance to any discipline: self-reliance, leadership, preparation, decisions under uncertainty; show students the human face of science; change attitudes about science and scientists; use data to engage students in exploring/understanding the environment and help them learn to draw conclusions from data; integrate research and education. These goals are met by bringing analysis of early exploration efforts together with a modern understanding of the polar environment. To date to class has followed the efforts of Nansen in the Fram, Scott and Amundsen in their race to the pole, and Shackleton's Endurance. As students read turn-of-the-century expedition journals, expedition progress is progressively revealed on an interactive map showing the environmental context. To bring the exploration process to life, students are assigned to expedition teams for specific years and the fates of the student "expeditions" are based on their own decisions. For example, in the Arctic, they navigate coastal sea ice and become frozen into the ice north of Siberia, re-creating Nansen's polar drift. Fates of the teams varied tremendously: some safely emerged at Fram Strait in 4 years, while others nearly became hopelessly lost in the Beaufort Gyre. Students thus learn about variability in the current polar environment through first hand experience, enabling them to appreciate the experiences, decisions, and, in some cases, the luck, of polar explorers. Evaluation by the Columbia Center for New Media, Teaching

  7. Time matters: Temporal harmony and dissonance in nanotechnology networks

    DEFF Research Database (Denmark)

    Selin, Cynthia Lea

    2006-01-01

    the coding mediations that occur in the nanotechnology arena. The case of nanotechnology – due to its emergent properties, affinity with science fiction and inexhaustible promises – is taken up with an analytic exploration of network participants’ perspectives on time. Departing from empirical evidence...... within the nanotechnology arena, the focus is to explore the meanings and dilemmas implicated in disparate temporal horizons. Particular emphasis is placed on the effects of temporal diversity latent in discourses of the future as they relate to the formulation of a new technological domain....

  8. Space exploration

    CERN Document Server

    2009-01-01

    Space Exploration, is one book in the Britannica Illustrated Science Library Series that is correlated to the science curriculum in grades 5-8. The Britannica Illustrated Science Library is a visually compelling set that covers earth science, life science, and physical science in 16 volumes.  Created for ages 10 and up, each volume provides an overview on a subject and thoroughly explains it through detailed and powerful graphics-more than 1,000 per volume-that turn complex subjects into information that students can grasp.  Each volume contains a glossary with full definitions for vocabulary help and an index.

  9. Alternative staffing services. Contract transcription.

    Science.gov (United States)

    Tessier, C

    1992-03-01

    Contract medical transcription services can be of great assistance in meeting the demands for transcription, without jeopardizing patient, physician, or institutional confidentiality. You simply must require the contract service to provide at least the same degree of protection and preservation of confidentiality that you should require inhouse. To achieve this you must make these requirements explicit, comprehensive, comprehensible, believable, and enforceable. Discuss the requirements with prospective contractors. Review them at least annually with existing contractors and when contracts are due for renewal. Be sure to specify the consequence of breaching confidentiality, and if there are breaches, enforce the terms of the contract. Consult your institution's legal counsel both in developing the contract and in enforcing its provisions. Take into consideration your department's and institution's policies, AHIMA's statement on confidentiality, as well as local, state, and federal laws. Above all, never lose sight of the patient. Ultimately, it is not patient information that you are obligated to protect. It is the patient.

  10. The post-transcriptional operon

    DEFF Research Database (Denmark)

    Tenenbaum, Scott A.; Christiansen, Jan; Nielsen, Henrik

    2011-01-01

    model (PTO) is used to describe data from an assortment of methods (e.g. RIP-Chip, CLIP-Chip, miRNA profiling, ribosome profiling) that globally address the functionality of mRNA. Several examples of post-transcriptional operons have been documented in the literature and demonstrate the usefulness...... of the model in identifying new participants in cellular pathways as well as in deepening our understanding of cellular responses....

  11. Model Based Temporal Reasoning

    Science.gov (United States)

    Rabin, Marla J.; Spinrad, Paul R.; Fall, Thomas C.

    1988-03-01

    Systems that assess the real world must cope with evidence that is uncertain, ambiguous, and spread over time. Typically, the most important function of an assessment system is to identify when activities are occurring that are unusual or unanticipated. Model based temporal reasoning addresses both of these requirements. The differences among temporal reasoning schemes lies in the methods used to avoid computational intractability. If we had n pieces of data and we wanted to examine how they were related, the worst case would be where we had to examine every subset of these points to see if that subset satisfied the relations. This would be 2n, which is intractable. Models compress this; if several data points are all compatible with a model, then that model represents all those data points. Data points are then considered related if they lie within the same model or if they lie in models that are related. Models thus address the intractability problem. They also address the problem of determining unusual activities if the data do not agree with models that are indicated by earlier data then something out of the norm is taking place. The models can summarize what we know up to that time, so when they are not predicting correctly, either something unusual is happening or we need to revise our models. The model based reasoner developed at Advanced Decision Systems is thus both intuitive and powerful. It is currently being used on one operational system and several prototype systems. It has enough power to be used in domains spanning the spectrum from manufacturing engineering and project management to low-intensity conflict and strategic assessment.

  12. Multiple Temporalities, Layered Histories

    Directory of Open Access Journals (Sweden)

    Steven Pearson

    2017-11-01

    Full Text Available In Quotational Practices: Repeating the Future in Contemporary Art, Patrick Greaney asserts, “the past matters not only because of what actually happened but also because of the possibilities that were not realized and that still could be. Quotation evokes those possibilities. By repeating the past, artists and writers may be attempting to repeat that past’s unrealized futures.”[1]  In the information age, the Internet, for instance, provides us an expanded collection of visual information—quite literally available at our fingertips—summoning together aspects of the past and possibilities of the future into a boundless present. Sketchbook Revisions (2014–2015, a series of mixed-media paintings, represents my attempt to communicate the ways in which I experience my contemporary moment constructed from multiple temporalities excavated from my past. This body of work combines fragments of representational paintings created between 1995 and 2003 and nonrepresentational renderings produced between 2003 and 2014. Using traditional tracing paper and graphic color, I randomly select moments of my previous work to transfer and layer over selected areas of already-filled pages of a sketchbook I used from 2003 to 2004. These sketches depict objects I encountered in studio art classrooms and iconic architecture on the campus of McDaniel College, and often incorporate teaching notes. The final renditions of fragmented and layered histories enact the ways that we collectively experience multiple temporalities in the present. Quoting my various bodies of work, Sketchbook Revisions challenges both material and conceptual boundaries that determine fixed notions of artistic identity.

  13. Join Operations in Temporal Databases

    DEFF Research Database (Denmark)

    Gao, D.; Jensen, Christian Søndergaard; Snodgrass, R.T.

    2005-01-01

    Joins are arguably the most important relational operators. Poor implementations are tantamount to computing the Cartesian product of the input relations. In a temporal database, the problem is more acute for two reasons. First, conventional techniques are designed for the evaluation of joins...... with equality predicates rather than the inequality predicates prevalent in valid-time queries. Second, the presence of temporally varying data dramatically increases the size of a database. These factors indicate that specialized techniques are needed to efficiently evaluate temporal joins. We address...... this need for efficient join evaluation in temporal databases. Our purpose is twofold. We first survey all previously proposed temporal join operators. While many temporal join operators have been defined in previous work, this work has been done largely in isolation from competing proposals, with little...

  14. Knowledge acquisition for temporal abstraction.

    Science.gov (United States)

    Stein, A; Musen, M A; Shahar, Y

    1996-01-01

    Temporal abstraction is the task of detecting relevant patterns in data over time. The knowledge-based temporal-abstraction method uses knowledge about a clinical domain's contexts, external events, and parameters to create meaningful interval-based abstractions from raw time-stamped clinical data. In this paper, we describe the acquisition and maintenance of domain-specific temporal-abstraction knowledge. Using the PROTEGE-II framework, we have designed a graphical tool for acquiring temporal knowledge directly from expert physicians, maintaining the knowledge in a sharable form, and converting the knowledge into a suitable format for use by an appropriate problem-solving method. In initial tests, the tool offered significant gains in our ability to rapidly acquire temporal knowledge and to use that knowledge to perform automated temporal reasoning.

  15. [Temporal meaning of suffering].

    Science.gov (United States)

    Porée, J

    2015-09-01

    If we had to find a few simple words to express what a suffering human being experiences, no matter what ills are causing the suffering and no matter what circumstances underlie the ills themselves, we could unmistakably say that it is the experience of not being able to go on like this. Suffering can be described, in this same sense, as an alteration in temporality. However, describing suffering as such only makes sense if we already have a conception of normal temporality. Yet for this, philosophical tradition offers not one but four competing conceptions. In the present article, we begin by briefly presenting these different conceptions. We then show how each one sheds light, by way of contrast, on a phenomenon whose meaning thus appears to be essentially negative. But does this phenomenon have a negative meaning only? Doesn't it correspond as much to a transformation as an alteration of temporality? This is what we will strive to establish in the third part of the article by relating suffering to hope, in a paradoxical sense of the term. Of the four conceptions of time likely to shed a contrasting light on the upheavals that suffering introduces into our life experience, the one described by Aristotle in Physics is historically the first. In particular, the notion of succession originates therein. But this conception does not account for what makes time the unit of a past, a present, and a future. In Book XI of Confessions, St. Augustine situated this unit not in nature but in the human mind. Hence, his definition of time as a distension of the soul and the necessary division into physical time and psychic time it entails. Husserl's Lessons on the phenomenology of the consciousness of internal time lend credit to this division, but they illuminate only the internal constitution of the "present", which is at the heart of the psychological conception of time. In Being and Time, Heidegger breaks away from this long-standing tradition; in his view, physical time

  16. Temporal Representation in Semantic Graphs

    Energy Technology Data Exchange (ETDEWEB)

    Levandoski, J J; Abdulla, G M

    2007-08-07

    A wide range of knowledge discovery and analysis applications, ranging from business to biological, make use of semantic graphs when modeling relationships and concepts. Most of the semantic graphs used in these applications are assumed to be static pieces of information, meaning temporal evolution of concepts and relationships are not taken into account. Guided by the need for more advanced semantic graph queries involving temporal concepts, this paper surveys the existing work involving temporal representations in semantic graphs.

  17. Dynamic CRM occupancy reflects a temporal map of developmental progression.

    Science.gov (United States)

    Wilczyński, Bartek; Furlong, Eileen E M

    2010-06-22

    Development is driven by tightly coordinated spatio-temporal patterns of gene expression, which are initiated through the action of transcription factors (TFs) binding to cis-regulatory modules (CRMs). Although many studies have investigated how spatial patterns arise, precise temporal control of gene expression is less well understood. Here, we show that dynamic changes in the timing of CRM occupancy is a prevalent feature common to all TFs examined in a developmental ChIP time course to date. CRMs exhibit complex binding patterns that cannot be explained by the sequence motifs or expression of the TFs themselves. The temporal changes in TF binding are highly correlated with dynamic patterns of target gene expression, which in turn reflect transitions in cellular function during different stages of development. Thus, it is not only the timing of a TF's expression, but also its temporal occupancy in refined time windows, which determines temporal gene expression. Systematic measurement of dynamic CRM occupancy may therefore serve as a powerful method to decode dynamic changes in gene expression driving developmental progression.

  18. Production of the 2400 kb Duchenne muscular dystrophy (DMD) gene transcript; transcription time and cotranscriptional splicing

    Energy Technology Data Exchange (ETDEWEB)

    Tennyson, C.N.; Worton, R.G. [Univ. of Toronto and the Hospital for Sick Children, Ontario (Canada)

    1994-09-01

    The largest known gene in any organism is the human DMD gene which has 79 exons that span 2400 kb. The extreme nature of the DMD gene raises questions concerning the time required for transcription and whether splicing begins before transcription is complete. DMD gene transcription is induced as cultured human myoblasts differentiate to form multinucleated myotubes, providing a system for studying the kinetics of transcription and splicing. Using quantitative RT-PCR, transcript accumulation was monitored from four different regions within the gene following induction of expression. By comparing the accumulation of transcripts from the 5{prime} and 3{prime} ends of the gene we have shown that approximately 12 hours are required to transcribe 1770 kb of the gene, extrapolating to a time of 16 hours for the transcription unit expressed in muscle. Comparison of accumulation profiles for spliced and total transcript demonstrated that transcripts are spliced at the 5{prime} end before transcription is complete, providing strong evidence for cotranscriptional splicing of DMD gene transcripts. Finally, the rate of transcript accumulation was reduced at the 3{prime} end of the gene relative to the 5{prime} end, perhaps due to premature termination of transcription complexes as they traverse this enormous transcription unit. The lag between transcription initiation and the appearance of complete transcripts could be important in limiting transcript production in dividing cells and to the timing of mRNA appearance in differentiating muscle.

  19. Mutual interdependence of splicing and transcription elongation.

    Science.gov (United States)

    Brzyżek, Grzegorz; Świeżewski, Szymon

    2015-01-01

    Transcription and splicing are intrinsically linked, as splicing needs a pre-mRNA substrate to commence. The more nuanced view is that the rate of transcription contributes to splicing regulation. On the other hand there is accumulating evidence that splicing has an active role in controlling transcription elongation by DNA-dependent RNA polymerase II (RNAP II). We briefly review those mechanisms and propose a unifying model where splicing controls transcription elongation to provide an optimal timing for successive rounds of splicing.

  20. Geoelectrical exploration

    Directory of Open Access Journals (Sweden)

    Mostafa Said Barseem

    2015-12-01

    Full Text Available Sinai development is a goal of successive governments in Egypt. The present study is a geoelectrical exploration to find appropriate solutions of the problems affecting the land of a Research Station in Southeast Al Qantara. This research station is one of the Desert Research Center stations to facilitate the development of desert land for agriculture by introducing applied research. It suffers from some problems which can be summarized in the shortage of irrigation water and water logging. The appropriate solutions of these problems have been delineated by the results of 1D and 2D geoelectrical measurements. Electrical resistivity (ER revealed the subsurface sedimentary sequences and extension of subsurface layers in the horizontal and vertical directions, especially, the water bearing layer. Additionally it helped to choose the most suitable places to drill productive wells with a good condition.

  1. Exploration economics

    International Nuclear Information System (INIS)

    Mcgill, R.E.

    1992-01-01

    This paper deals with determining the economic viability of the play or prospect. At the outset, one point is important. Preexploration economists are important because they enable geologists to see if their assumptions will prove profitable. Their assumptions must consider the full range of possible outcomes, even if only some portion of that range may contain prospects or plays that are estimated to be profitable. Play economics are preferable to prospect economics because, being the sum of several prospects, they give a broader view of the investment opportunity. Finally, remember that play and prospect economics are always slightly optimistic. They seldom include all of the exploration and overhead changes that must ultimately be borne by the successful prospects

  2. HR Explorer

    CERN Document Server

    Möller, M

    1997-01-01

    At the European Laboratory for Particle Physics Research (CERN), Geneva Switzerland we are using OracleHR for managing our human resources since 1995. After the first year of production it became clear that there was a strong need for an easy-to-use Decision Support Tool exploring the data in OracleHR. This paper illustrates an approach which we have adopted to provide on-line management reporting, multi-dimensional analysis, drill-down and slicing & dicing of data, warehoused from OracleHR. The tool offers strong resource management and planning capabilities including career follow-up. The user management and security monitoring are implemented using the Oracle WebServer.

  3. Hydrocarbon exploration

    Energy Technology Data Exchange (ETDEWEB)

    Lerche, I. (South Carolina Univ., Columbia, SC (United States). Dept. of Geological Sciences)

    1993-01-01

    This special issue of the journal examines various aspects of the on-going search for hydrocarbons, ranging from frontier basins where little data are available, to more mature areas where considerable data are available. The incentives underlying the search for oil are roughly: the social, economic and industrial needs of a nation; the incentive of a corporation to be profitable; and the personal incentives of individuals in the oil industry and governments, which range from financial wealth to power and which are as diverse as the individuals who are involved. From a geopolitical perspective, the needs, requirements, goals, strategies, and philosophies of nations, and groups of nations, also impact on the oil exploration game. Strategies that have been employed have ranged from boycott to austerity and rationing, to physical intervention, to global ''flooding'' with oil by over-production. (author)

  4. Exploring ESASky

    Science.gov (United States)

    De Marchi, Guido; ESASky Team

    2017-06-01

    ESASky is a science-driven discovery portal for all ESA space astronomy missions. It also includes missions from international partners such as Suzaku and Chandra. The first public release of ESASky features interfaces for sky exploration and for single and multiple target searches. Using the application requires no prior-knowledge of any of the missions involved and gives users world-wide simplified access to high-level science-ready data products from space-based Astronomy missions, plus a number of ESA-produced source catalogues, including the Gaia Data Release 1 catalogue. We highlight here the latest features to be developed, including one that allows the user to project onto the sky the footprints of the JWST instruments, at any chosen position and orientation. This tool has been developed to aid JWST astronomers when they are defining observing proposals. We aim to include other missions and instruments in the near future.

  5. Spatio temporal media components for neurofeedback

    DEFF Research Database (Denmark)

    Jensen, Camilla Birgitte Falk; Petersen, Michael Kai; Larsen, Jakob Eg

    2013-01-01

    A class of Brain Computer Interfaces (BCI) involves interfaces for neurofeedback training, where a user can learn to self-regulate brain activity based on real-time feedback. These particular interfaces are constructed from audio-visual components and temporal settings, which appear to have...... a strong influence on the ability to control brain activity. Therefore, identifying the different interface components and exploring their individual effects might be key for constructing new interfaces that support more efficient neurofeedback training. We discuss experiments involving two different...

  6. Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max Embryos

    Directory of Open Access Journals (Sweden)

    Ruth Grene

    2013-05-01

    Full Text Available Soybean (Glycine max seeds are an important source of seed storage compounds, including protein, oil, and sugar used for food, feed, chemical, and biofuel production. We assessed detailed temporal transcriptional and metabolic changes in developing soybean embryos to gain a systems biology view of developmental and metabolic changes and to identify potential targets for metabolic engineering. Two major developmental and metabolic transitions were captured enabling identification of potential metabolic engineering targets specific to seed filling and to desiccation. The first transition involved a switch between different types of metabolism in dividing and elongating cells. The second transition involved the onset of maturation and desiccation tolerance during seed filling and a switch from photoheterotrophic to heterotrophic metabolism. Clustering analyses of metabolite and transcript data revealed clusters of functionally related metabolites and transcripts active in these different developmental and metabolic programs. The gene clusters provide a resource to generate predictions about the associations and interactions of unknown regulators with their targets based on “guilt-by-association” relationships. The inferred regulators also represent potential targets for future metabolic engineering of relevant pathways and steps in central carbon and nitrogen metabolism in soybean embryos and drought and desiccation tolerance in plants.

  7. Interplay between DNA supercoiling and transcription elongation.

    Science.gov (United States)

    Ma, Jie; Wang, Michelle

    2014-01-01

    Transcription-coupled DNA supercoiling has been shown to be an important regulator of transcription that is broadly present in the cell. Here we review experimental work which shows that RNA polymerase is a powerful torsional motor that can alter DNA topology and structure, and DNA supercoiling in turn directly affects transcription elongation.

  8. Auditory temporal processing in patients with temporal lobe epilepsy.

    Science.gov (United States)

    Lavasani, Azam Navaei; Mohammadkhani, Ghassem; Motamedi, Mahmoud; Karimi, Leyla Jalilvand; Jalaei, Shohreh; Shojaei, Fereshteh Sadat; Danesh, Ali; Azimi, Hadi

    2016-07-01

    Auditory temporal processing is the main feature of speech processing ability. Patients with temporal lobe epilepsy, despite their normal hearing sensitivity, may present speech recognition disorders. The present study was carried out to evaluate the auditory temporal processing in patients with unilateral TLE. The present study was carried out on 25 patients with epilepsy: 11 patients with right temporal lobe epilepsy and 14 with left temporal lobe epilepsy with a mean age of 31.1years and 18 control participants with a mean age of 29.4years. The two experimental and control groups were evaluated via gap-in-noise and duration pattern sequence tests. One-way ANOVA was run to analyze the data. The mean of the threshold of the GIN test in the control group was observed to be better than that in participants with LTLE and RTLE. Also, it was observed that the percentage of correct responses on the DPS test in the control group and in participants with RTLE was better than that in participants with LTLE. Patients with TLE have difficulties in temporal processing. Difficulties are more significant in patients with LTLE, likely because the left temporal lobe is specialized for the processing of temporal information. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Directing traffic on DNA-How transcription factors relieve or induce transcriptional interference.

    Science.gov (United States)

    Hao, Nan; Palmer, Adam C; Dodd, Ian B; Shearwin, Keith E

    2017-03-15

    Transcriptional interference (TI) is increasingly recognized as a widespread mechanism of gene control, particularly given the pervasive nature of transcription, both sense and antisense, across all kingdoms of life. Here, we discuss how transcription factor binding kinetics strongly influence the ability of a transcription factor to relieve or induce TI.

  10. Functional connectivity between right and left mesial temporal structures.

    Science.gov (United States)

    Lacuey, Nuria; Zonjy, Bilal; Kahriman, Emine S; Kaffashi, Farhad; Miller, Jonathan; Lüders, Hans O

    2015-09-01

    The aim of this study is to investigate functional connectivity between right and left mesial temporal structures using cerebrocerebral evoked potentials. We studied seven patients with drug-resistant focal epilepsy who were explored with stereotactically implanted depth electrodes in bilateral hippocampi. In all patients cerebrocerebral evoked potentials evoked by stimulation of the fornix were evaluated as part of a research project assessing fornix stimulation for control of hippocampal seizures. Stimulation of the fornix elicited responses in the ipsilateral hippocampus in all patients with a mean latency of 4.6 ms (range 2-7 ms). Two patients (29 %) also had contralateral hippocampus responses with a mean latency of 7.5 ms (range 5-12 ms) and without involvement of the contralateral temporal neocortex or amygdala. This study confirms the existence of connections between bilateral mesial temporal structures in some patients and explains seizure discharge spreading between homotopic mesial temporal structures without neocortical involvement.

  11. Financial times: Competing temporalities in the age of finance capitalism

    Directory of Open Access Journals (Sweden)

    Christian Kloeckner

    2018-05-01

    Full Text Available This special issue explores how finance deploys time, structures the future, and interacts with actors and institutions that sometimes function according to very different temporal regimes. Finance capitalism’s logic of recurrence, repetitive cycles, and successive ruptures has long been with us, but the essays in this special issue are particularly interested in how recent decades of intensified financialization have restructured temporal experience. They interrogate the production and dissemination of agency in an age of acceleration, risk, and uncertainty, asking how the temporality inscribed in financial transactions emerges from and simultaneously shapes individual and social practice. Topics covered range from the logic of finance and foundational concepts of financial theory to the intersection between objective structures and social practice, the role of literature, and finally questions of social insecurity, political action, and the possibility of resistance within a context of competing temporalities. In this introduction, the editors delineate some fundamental concepts and questions for our financial times.

  12. Was that Infinity or Affinity? Applying Insights from Translation Studies to Qualitative Research Transcription

    Directory of Open Access Journals (Sweden)

    Jen Ross

    2010-02-01

    Full Text Available Despite a small but compelling body of literature arguing that transcription represents a key moment of choice and the exercise of power in the research process, many qualitative researchers appear to believe (or at least proceed as if they believe that transcription is relatively unproblematic. Translation studies and its engagement with visibility, power, authenticity and fidelity has a lot to offer to qualitative researchers working critically with transcription theory and practice. This paper explores the translation studies theories of equivalence, overt and covert translation, foreignisation and domestication, and the remainder, and demonstrates some fertile connections between transcription and translation. These connections help us to think about some broader political and cultural issues in relation to transcription and academic discourse, the complexity of equivalence and the central role of the situated transcriber. URN: urn:nbn:de:0114-fqs100223

  13. Hedgehog signaling acts with the temporal cascade to promote neuroblast cell cycle exit.

    Directory of Open Access Journals (Sweden)

    Phing Chian Chai

    Full Text Available In Drosophila postembryonic neuroblasts, transition in gene expression programs of a cascade of transcription factors (also known as the temporal series acts together with the asymmetric division machinery to generate diverse neurons with distinct identities and regulate the end of neuroblast proliferation. However, the underlying mechanism of how this "temporal series" acts during development remains unclear. Here, we show that Hh signaling in the postembryonic brain is temporally regulated; excess (earlier onset of Hh signaling causes premature neuroblast cell cycle exit and under-proliferation, whereas loss of Hh signaling causes delayed cell cycle exit and excess proliferation. Moreover, the Hh pathway functions downstream of Castor but upstream of Grainyhead, two components of the temporal series, to schedule neuroblast cell cycle exit. Interestingly, hh is likely a target of Castor. Hence, Hh signaling provides a link between the temporal series and the asymmetric division machinery in scheduling the end of neurogenesis.

  14. Temporal grouping effects in musical short-term memory.

    Science.gov (United States)

    Gorin, Simon; Mengal, Pierre; Majerus, Steve

    2018-07-01

    Recent theoretical accounts of verbal and visuo-spatial short-term memory (STM) have proposed the existence of domain-general mechanisms for the maintenance of serial order information. These accounts are based on the observation of similar behavioural effects across several modalities, such as temporal grouping effects. Across two experiments, the present study aimed at extending these findings, by exploring a STM modality that has received little interest so far, STM for musical information. Given its inherent rhythmic, temporal and serial organisation, the musical domain is of interest for investigating serial order STM processes such as temporal grouping. In Experiment 1, the data did not allow to determine the presence or the absence of temporal grouping effects. In Experiment 2, we observed that temporal grouping of tone sequences during encoding improves short-term recognition for serially presented probe tones. Furthermore, the serial position curves included micro-primacy and micro-recency effects, which are the hallmark characteristic of temporal grouping. Our results suggest that the encoding of serial order information in musical STM may be supported by temporal positional coding mechanisms similar to those reported in the verbal domain.

  15. Space Exploration

    Science.gov (United States)

    Gallagher, Dennis

    2017-01-01

    New range Passage Tomb may be the first structure with known astronomical significance. It was built around 3,200 B.C. in Ireland. It's central passage allows light end-to-end for about 2 weeks around winter solstice. The Sun, Moon, Planets, and Stars held significance in early times due to the seasons, significance for food crops, and mythology. Citation: Corel Photography and Windows to the Universe The Greek may be among the first to pursue analytical interpretations of what they saw in the sky. In about 280 B.C. Aristarchus suggested Earth revolves around the Sun and estimated the distance between. Around 130 B.C. Hipparchus developed the first accurate star map. Today still seek to understand how the universe formed and how we came to be and are we alone. Understanding the causes and consequences of climate change using advanced space missions with major Earth science and applications research. center dotFire the public imagination and inspire students to pursue STEM fields. Train college and graduate students to create a U.S. technical workforce with employees that embody the values of competence, innovation, and service. center dotDrive the technical innovations that enable exploration and become the engine of National economic growth. center dotPartner domestically and internationally to leverage resources to extend the reach of research.

  16. Model Checking Discounted Temporal Properties

    NARCIS (Netherlands)

    de Alfaro, Luca; Faella, Marco; Henzinger, Thomas A.; Majumdar, Rupak; Stoelinga, Mariëlle Ida Antoinette

    2005-01-01

    Temporal logic is two-valued: a property is either true or false. When applied to the analysis of stochastic systems, or systems with imprecise formal models, temporal logic is therefore fragile: even small changes in the model can lead to opposite truth values for a specification. We present a

  17. Model Checking Discounted Temporal Properties

    NARCIS (Netherlands)

    de Alfaro, Luca; Faella, Marco; Henzinger, Thomas A.; Majumdar, Rupak; Stoelinga, Mariëlle Ida Antoinette; Jensen, K; Podelski, A.

    2004-01-01

    Temporal logic is two-valued: a property is either true or false. When applied to the analysis of stochastic systems, or systems with imprecise formal models, temporal logic is therefore fragile: even small changes in the model can lead to opposite truth values for a specification. We present a

  18. Negative transcriptional regulation of mitochondrial transcription factor A (TFAM) by nuclear TFAM

    International Nuclear Information System (INIS)

    Lee, Eun Jin; Kang, Young Cheol; Park, Wook-Ha; Jeong, Jae Hoon; Pak, Youngmi Kim

    2014-01-01

    Highlights: • TFAM localizes in nuclei and mitochondria of neuronal cells. • Nuclear TFAM does not bind the Tfam promoter. • Nuclear TFAM reduced the Tfam promoter activity via suppressing NRF-1 activity. • A novel self-negative feedback regulation of Tfam gene expression is explored. • FAM may play different roles depending on its subcellular localizations. - Abstract: The nuclear DNA-encoded mitochondrial transcription factor A (TFAM) is synthesized in cytoplasm and transported into mitochondria. TFAM enhances both transcription and replication of mitochondrial DNA. It is unclear, however, whether TFAM plays a role in regulating nuclear gene expression. Here, we demonstrated that TFAM was localized to the nucleus and mitochondria by immunostaining, subcellular fractionation, and TFAM-green fluorescent protein hybrid protein studies. In HT22 hippocampal neuronal cells, human TFAM (hTFAM) overexpression suppressed human Tfam promoter-mediated luciferase activity in a dose-dependent manner. The mitochondria targeting sequence-deficient hTFAM also repressed Tfam promoter activity to the same degree as hTFAM. It indicated that nuclear hTFAM suppressed Tfam expression without modulating mitochondrial activity. The repression required for nuclear respiratory factor-1 (NRF-1), but hTFAM did not bind to the NRF-1 binding site of its promoter. TFAM was co-immunoprecipitated with NRF-1. Taken together, we suggest that nuclear TFAM down-regulate its own gene expression as a NRF-1 repressor, showing that TFAM may play different roles depending on its subcellular localizations

  19. The Journey of a Transcription Factor

    DEFF Research Database (Denmark)

    Pireyre, Marie

    Plants have developed astonishing networks regulating their metabolism to adapt to their environment. The complexity of these networks is illustrated by the expansion of families of regulators such as transcription factors in the plant kingdom. Transcription factors specifically impact...... transcriptional networks by integrating exogenous and endogenous stimuli and regulating gene expression accordingly. Regulation of transcription factors and their activation is thus highly important to modulate the transcriptional programs and increase fitness of the plant in a given environment. Plant metabolism....... The biosynthetic machinery of GLS is governed by interplay of six MYB and three bHLH transcription factors. MYB28, MYB29 and MYB76 regulate methionine-derived GLS, and MYB51, MYB34 and MYB122 regulate tryptophan-derived GLS. The three bHLH transcription factors MYC2, MYC3 and MYC4 physically interact with all six...

  20. Unemployment in South Africa: Building a Spatio-temporal ...

    African Journals Online (AJOL)

    The spatial understanding of unemployment in South Africa is often limited to provinces. This paper explores ways to integrate unemployment data from 1991 to 2007 to obtain a spatially more detailed understanding of the phenomenon. Creating such a temporal GIS is challenging because of the changing administrative ...

  1. TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions

    KAUST Repository

    Schmeier, Sebastian

    2016-10-17

    Transcription factors (TFs) play a pivotal role in transcriptional regulation, making them crucial for cell survival and important biological functions. For the regulation of transcription, interactions of different regulatory proteins known as transcription co-factors (TcoFs) and TFs are essential in forming necessary protein complexes. Although TcoFs themselves do not bind DNA directly, their influence on transcriptional regulation and initiation, although indirect, has been shown to be significant, with the functionality of TFs strongly influenced by the presence of TcoFs. In the TcoF-DB v2 database, we collect information on TcoFs. In this article, we describe updates and improvements implemented in TcoF-DB v2. TcoF-DB v2 provides several new features that enables exploration of the roles of TcoFs. The content of the database has significantly expanded, and is enriched with information from Gene Ontology, biological pathways, diseases and molecular signatures. TcoF-DB v2 now includes many more TFs; has substantially increased the number of human TcoFs to 958, and now includes information on mouse (418 new TcoFs). TcoF-DB v2 enables the exploration of information on TcoFs and allows investigations into their influence on transcriptional regulation in humans and mice. TcoF-DB v2 can be accessed at http://tcofdb.org/.

  2. TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions

    KAUST Repository

    Schmeier, Sebastian; Alam, Tanvir; Essack, Magbubah; Bajic, Vladimir B.

    2016-01-01

    Transcription factors (TFs) play a pivotal role in transcriptional regulation, making them crucial for cell survival and important biological functions. For the regulation of transcription, interactions of different regulatory proteins known as transcription co-factors (TcoFs) and TFs are essential in forming necessary protein complexes. Although TcoFs themselves do not bind DNA directly, their influence on transcriptional regulation and initiation, although indirect, has been shown to be significant, with the functionality of TFs strongly influenced by the presence of TcoFs. In the TcoF-DB v2 database, we collect information on TcoFs. In this article, we describe updates and improvements implemented in TcoF-DB v2. TcoF-DB v2 provides several new features that enables exploration of the roles of TcoFs. The content of the database has significantly expanded, and is enriched with information from Gene Ontology, biological pathways, diseases and molecular signatures. TcoF-DB v2 now includes many more TFs; has substantially increased the number of human TcoFs to 958, and now includes information on mouse (418 new TcoFs). TcoF-DB v2 enables the exploration of information on TcoFs and allows investigations into their influence on transcriptional regulation in humans and mice. TcoF-DB v2 can be accessed at http://tcofdb.org/.

  3. Repression of Meiotic Genes by Antisense Transcription and by Fkh2 Transcription Factor in Schizosaccharomyces pombe

    OpenAIRE

    Chen, Huei-Mei; Rosebrock, Adam P.; Khan, Sohail R.; Futcher, Bruce; Leatherwood, Janet K.

    2012-01-01

    In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. Disruption of the antisense transcription of three of these mid-meiotic genes allowed vegetative sense transcription. These results suggest that antisense transcription ...

  4. Exploring Mars

    Science.gov (United States)

    Breuil, Stéphanie

    2016-04-01

    Mars is our neighbour planet and has always fascinated humans as it has been seen as a potential abode for life. Knowledge about Mars is huge and was constructed step by step through numerous missions. It could be difficult to describe these missions, the associated technology, the results, the questions they raise, that's why an activity is proposed, that directly interests students. Their production is presented in the poster. Step 1: The main Mars feature and the first Mars explorations using telescope are presented to students. It should be really interesting to present "Mars Canals" from Percival Lowell as it should also warn students against flawed interpretation. Moreover, this study has raised the big question about extra-terrestrial life on Mars for the first time. Using Google Mars is then a good way to show the huge knowledge we have on the planet and to introduce modern missions. Step 2: Students have to choose and describe one of the Mars mission from ESA and NASA. They should work in pairs. Web sites from ESA and NASA are available and the teacher makes sure the main missions will be studied. Step 3: Students have to collect different pieces of information about the mission - When? Which technology? What were the main results? What type of questions does it raise? They prepare an oral presentation in the form they want (role play, academic presentation, using a poster, PowerPoint). They also have to produce playing cards about the mission that could be put on a timeline. Step 4: As a conclusion, the different cards concerning different missions are mixed. Groups of students receive cards and they have to put them on a timeline as fast as possible. It is also possible to play the game "timeline".

  5. Temporal Ventriloquism Reveals Intact Audiovisual Temporal Integration in Amblyopia.

    Science.gov (United States)

    Richards, Michael D; Goltz, Herbert C; Wong, Agnes M F

    2018-02-01

    We have shown previously that amblyopia involves impaired detection of asynchrony between auditory and visual events. To distinguish whether this impairment represents a defect in temporal integration or nonintegrative multisensory processing (e.g., cross-modal matching), we used the temporal ventriloquism effect in which visual temporal order judgment (TOJ) is normally enhanced by a lagging auditory click. Participants with amblyopia (n = 9) and normally sighted controls (n = 9) performed a visual TOJ task. Pairs of clicks accompanied the two lights such that the first click preceded the first light, or second click lagged the second light by 100, 200, or 450 ms. Baseline audiovisual synchrony and visual-only conditions also were tested. Within both groups, just noticeable differences for the visual TOJ task were significantly reduced compared with baseline in the 100- and 200-ms click lag conditions. Within the amblyopia group, poorer stereo acuity and poorer visual acuity in the amblyopic eye were significantly associated with greater enhancement in visual TOJ performance in the 200-ms click lag condition. Audiovisual temporal integration is intact in amblyopia, as indicated by perceptual enhancement in the temporal ventriloquism effect. Furthermore, poorer stereo acuity and poorer visual acuity in the amblyopic eye are associated with a widened temporal binding window for the effect. These findings suggest that previously reported abnormalities in audiovisual multisensory processing may result from impaired cross-modal matching rather than a diminished capacity for temporal audiovisual integration.

  6. Efficient Temporal Action Localization in Videos

    KAUST Repository

    Alwassel, Humam

    2018-04-17

    State-of-the-art temporal action detectors inefficiently search the entire video for specific actions. Despite the encouraging progress these methods achieve, it is crucial to design automated approaches that only explore parts of the video which are the most relevant to the actions being searched. To address this need, we propose the new problem of action spotting in videos, which we define as finding a specific action in a video while observing a small portion of that video. Inspired by the observation that humans are extremely efficient and accurate in spotting and finding action instances in a video, we propose Action Search, a novel Recurrent Neural Network approach that mimics the way humans spot actions. Moreover, to address the absence of data recording the behavior of human annotators, we put forward the Human Searches dataset, which compiles the search sequences employed by human annotators spotting actions in the AVA and THUMOS14 datasets. We consider temporal action localization as an application of the action spotting problem. Experiments on the THUMOS14 dataset reveal that our model is not only able to explore the video efficiently (observing on average 17.3% of the video) but it also accurately finds human activities with 30.8% mAP (0.5 tIoU), outperforming state-of-the-art methods

  7. Trust, temporality and systems: how do patients understand patient safety in primary care? A qualitative study.

    Science.gov (United States)

    Rhodes, Penny; Campbell, Stephen; Sanders, Caroline

    2016-04-01

    Patient safety research has tended to focus on hospital settings, although most clinical encounters occur in primary care, and to emphasize practitioner errors, rather than patients' own understandings of safety. To explore patients' understandings of safety in primary care. Qualitative interviews were conducted with patients recruited from general practices in northwest England. Participants were asked basic socio-demographic information; thereafter, topics were largely introduced by interviewees themselves. Transcripts were coded and analysed using NVivo10 (qualitative data software), following a process of constant comparison. Thirty-eight people (14 men, 24 women) from 19 general practices in rural, small town and city locations were interviewed. Many of their concerns (about access, length of consultation, relationship continuity) have been discussed in terms of quality, but, in the interviews, were raised as matters of safety. Three broad themes were identified: (i) trust and psycho-social aspects of professional-patient relationships; (ii) choice, continuity, access, and the temporal underpinnings of safety; and (iii) organizational and systems-level tensions constraining safety. Conceptualizations of safety included common reliance on a bureaucratic framework of accreditation, accountability, procedural rules and regulation, but were also individual and context-dependent. For patients, safety is not just a property of systems, but personal and contingent and is realized in the interaction between doctor and patient. However, it is the systems approach that has dominated safety thinking, and patients' individualistic and relational conceptualizations are poorly accommodated within current service organization. © 2015 The Authors Health Expectations Published by John Wiley & Sons Ltd.

  8. A Model of the Spatio-temporal Dynamics of Drosophila Eye Disc Development.

    Science.gov (United States)

    Fried, Patrick; Sánchez-Aragón, Máximo; Aguilar-Hidalgo, Daniel; Lehtinen, Birgitta; Casares, Fernando; Iber, Dagmar

    2016-09-01

    Patterning and growth are linked during early development and have to be tightly controlled to result in a functional tissue or organ. During the development of the Drosophila eye, this linkage is particularly clear: the growth of the eye primordium mainly results from proliferating cells ahead of the morphogenetic furrow (MF), a moving signaling wave that sweeps across the tissue from the posterior to the anterior side, that induces proliferating cells anterior to it to differentiate and become cell cycle quiescent in its wake. Therefore, final eye disc size depends on the proliferation rate of undifferentiated cells and on the speed with which the MF sweeps across the eye disc. We developed a spatio-temporal model of the growing eye disc based on the regulatory interactions controlled by the signals Decapentaplegic (Dpp), Hedgehog (Hh) and the transcription factor Homothorax (Hth) and explored how the signaling patterns affect the movement of the MF and impact on eye disc growth. We used published and new quantitative data to parameterize the model. In particular, two crucial parameter values, the degradation rate of Hth and the diffusion coefficient of Hh, were measured. The model is able to reproduce the linear movement of the MF and the termination of growth of the primordium. We further show that the model can explain several mutant phenotypes, but fails to reproduce the previously observed scaling of the Dpp gradient in the anterior compartment.

  9. A Model of the Spatio-temporal Dynamics of Drosophila Eye Disc Development.

    Directory of Open Access Journals (Sweden)

    Patrick Fried

    2016-09-01

    Full Text Available Patterning and growth are linked during early development and have to be tightly controlled to result in a functional tissue or organ. During the development of the Drosophila eye, this linkage is particularly clear: the growth of the eye primordium mainly results from proliferating cells ahead of the morphogenetic furrow (MF, a moving signaling wave that sweeps across the tissue from the posterior to the anterior side, that induces proliferating cells anterior to it to differentiate and become cell cycle quiescent in its wake. Therefore, final eye disc size depends on the proliferation rate of undifferentiated cells and on the speed with which the MF sweeps across the eye disc. We developed a spatio-temporal model of the growing eye disc based on the regulatory interactions controlled by the signals Decapentaplegic (Dpp, Hedgehog (Hh and the transcription factor Homothorax (Hth and explored how the signaling patterns affect the movement of the MF and impact on eye disc growth. We used published and new quantitative data to parameterize the model. In particular, two crucial parameter values, the degradation rate of Hth and the diffusion coefficient of Hh, were measured. The model is able to reproduce the linear movement of the MF and the termination of growth of the primordium. We further show that the model can explain several mutant phenotypes, but fails to reproduce the previously observed scaling of the Dpp gradient in the anterior compartment.

  10. Semantics of Temporal Models with Multiple Temporal Dimensions

    DEFF Research Database (Denmark)

    Kraft, Peter; Sørensen, Jens Otto

    ending up with lexical data models. In particular we look upon the representations by sets of normalised tables, by sets of 1NF tables and by sets of N1NF/nested tables. At each translation step we focus on how the temporal semantic is consistently maintained. In this way we recognise the requirements...... for representation of temporal properties in different models and the correspondence between the models. The results rely on the assumptions that the temporal dimensions are interdependent and ordered. Thus for example the valid periods of existences of a property in a mini world are dependent on the transaction...... periods in which the corresponding recordings are valid. This is not the normal way of looking at temporal dimensions and we give arguments supporting our assumption....

  11. Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis.

    Science.gov (United States)

    Liang, Kaiwei; Woodfin, Ashley R; Slaughter, Brian D; Unruh, Jay R; Box, Andrew C; Rickels, Ryan A; Gao, Xin; Haug, Jeffrey S; Jaspersen, Sue L; Shilatifard, Ali

    2015-11-05

    Although it is established that some general transcription factors are inactivated at mitosis, many details of mitotic transcription inhibition (MTI) and its underlying mechanisms are largely unknown. We have identified mitotic transcriptional activation (MTA) as a key regulatory step to control transcription in mitosis for genes with transcriptionally engaged RNA polymerase II (Pol II) to activate and transcribe until the end of the gene to clear Pol II from mitotic chromatin, followed by global impairment of transcription reinitiation through MTI. Global nascent RNA sequencing and RNA fluorescence in situ hybridization demonstrate the existence of transcriptionally engaged Pol II in early mitosis. Both genetic and chemical inhibition of P-TEFb in mitosis lead to delays in the progression of cell division. Together, our study reveals a mechanism for MTA and MTI whereby transcriptionally engaged Pol II can progress into productive elongation and finish transcription to allow proper cellular division. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Differential transcript abundance and genotypic variation of four putative allergen-encoding gene families in melting peach

    NARCIS (Netherlands)

    Yang, Z.; Ma, Y.; Chen, L.; Xie, R.; Zhang, X.; Zhang, B.; Lu, M.; Wu, S.; Gilissen, L.J.W.J.; Ree, van R.; Gao, Z.

    2011-01-01

    We analysed the temporal and spatial transcript expression of the panel of 18 putative isoallergens from four gene families (Pru p 1–4) in the peach fruit, anther and leaf of two melting cultivars, to gain insight into their expression profiles and to identify the key family members. Genotypic

  13. Lytic Infection of Lactococcus lactis by Bacteriophages Tuc2009 and c2 Triggers Alternative Transcriptional Host Responses

    NARCIS (Netherlands)

    Ainsworth, S.; Zomer, A.L.; Mahony, J.; Sinderen, D. van

    2013-01-01

    Here we present an entire temporal transcriptional profile of Lactococcus lactis subsp. cremoris UC509.9 undergoing lytic infection with two distinct bacteriophages, Tuc2009 and c2. Furthermore, corresponding high-resolution whole-phage genome tiling arrays of both bacteriophages were performed

  14. Dispersal Ability Determines the Role of Environmental, Spatial and Temporal Drivers of Metacommunity Structure

    NARCIS (Netherlands)

    Padial, André A.; Ceschin, Fernanda; Declerck, Steven A. J.; De Meester, Luc; Bonecker, Cláudia C.; Lansac-Tôha, Fabio A.; Rodrigues, Liliana; Rodrigues, Luzia C.; Train, Sueli; Velho, Luiz F. M.; Bini, Luis M.

    2014-01-01

    Recently, community ecologists are focusing on the relative importance of local environmental factors and proxies to dispersal limitation to explain spatial variation in community structure. Albeit less explored, temporal processes may also be important in explaining species composition variation in

  15. Frequency Modulation of Transcriptional Bursting Enables Sensitive and Rapid Gene Regulation.

    Science.gov (United States)

    Li, Congxin; Cesbron, François; Oehler, Michael; Brunner, Michael; Höfer, Thomas

    2018-04-25

    Gene regulation is a complex non-equilibrium process. Here, we show that quantitating the temporal regulation of key gene states (transcriptionally inactive, active, and refractory) provides a parsimonious framework for analyzing gene regulation. Our theory makes two non-intuitive predictions. First, for transcription factors (TFs) that regulate transcription burst frequency, as opposed to amplitude or duration, weak TF binding is sufficient to elicit strong transcriptional responses. Second, refractoriness of a gene after a transcription burst enables rapid responses to stimuli. We validate both predictions experimentally by exploiting the natural, optogenetic-like responsiveness of the Neurospora GATA-type TF White Collar Complex (WCC) to blue light. Further, we demonstrate that differential regulation of WCC target genes is caused by different gene activation rates, not different TF occupancy, and that these rates are tuned by both the core promoter and the distance between TF-binding site and core promoter. In total, our work demonstrates the relevance of a kinetic, non-equilibrium framework for understanding transcriptional regulation. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  16. BRD4 localization to lineage-specific enhancers is associated with a distinct transcription factor repertoire

    OpenAIRE

    Najafova, Zeynab; Tirado-Magallanes, Roberto; Subramaniam, Malayannan; Hossan, Tareq; Schmidt, Geske; Nagarajan, Sankari; Baumgart, Simon J.; Mishra, Vivek?Kumar; Bedi, Upasana; Hesse, Eric; Knapp, Stefan; Hawse, John R.; Johnsen, Steven A.

    2016-01-01

    Proper temporal epigenetic regulation of gene expression is essential for cell fate determination and tissue development. The Bromodomain-containing Protein-4 (BRD4)was previously shown to control the transcription of defined subsets of genes in various cell systems. In this study we examined the role of BRD4 in promoting lineage-specific gene expression and show that BRD4 is essential for osteoblast differentiation. Genome-wide analyses demonstrate that BRD4 is rec...

  17. Promoter proximal polyadenylation sites reduce transcription activity

    DEFF Research Database (Denmark)

    Andersen, Pia Kjølhede; Lykke-Andersen, Søren; Jensen, Torben Heick

    2012-01-01

    Gene expression relies on the functional communication between mRNA processing and transcription. We previously described the negative impact of a point-mutated splice donor (SD) site on transcription. Here we demonstrate that this mutation activates an upstream cryptic polyadenylation (CpA) site......, which in turn causes reduced transcription. Functional depletion of U1 snRNP in the context of the wild-type SD triggers the same CpA event accompanied by decreased RNA levels. Thus, in accordance with recent findings, U1 snRNP can shield premature pA sites. The negative impact of unshielded pA sites...... on transcription requires promoter proximity, as demonstrated using artificial constructs and supported by a genome-wide data set. Importantly, transcription down-regulation can be recapitulated in a gene context devoid of splice sites by placing a functional bona fide pA site/transcription terminator within ∼500...

  18. Transcription and recombination: when RNA meets DNA.

    Science.gov (United States)

    Aguilera, Andrés; Gaillard, Hélène

    2014-08-01

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

  19. Specificity and robustness in transcription control networks.

    Science.gov (United States)

    Sengupta, Anirvan M; Djordjevic, Marko; Shraiman, Boris I

    2002-02-19

    Recognition by transcription factors of the regulatory DNA elements upstream of genes is the fundamental step in controlling gene expression. How does the necessity to provide stability with respect to mutation constrain the organization of transcription control networks? We examine the mutation load of a transcription factor interacting with a set of n regulatory response elements as a function of the factor/DNA binding specificity and conclude on theoretical grounds that the optimal specificity decreases with n. The predicted correlation between variability of binding sites (for a given transcription factor) and their number is supported by the genomic data for Escherichia coli. The analysis of E. coli genomic data was carried out using an algorithm suggested by the biophysical model of transcription factor/DNA binding. Complete results of the search for candidate transcription factor binding sites are available at http://www.physics.rockefeller.edu/~boris/public/search_ecoli.

  20. Transcriptional response of polycomb group genes to status epilepticus in mice is modified by prior exposure to epileptic preconditioning

    Directory of Open Access Journals (Sweden)

    James eReynolds

    2015-03-01

    Full Text Available Exposure of the brain to brief, non-harmful seizures can activate protective mechanisms that temporarily generate a damage-refractory state. This process, termed epileptic tolerance, is associated with large-scale down-regulation of gene expression. Polycomb group proteins are master controllers of gene silencing during development that are re-activated by injury to the brain. Here we explored the transcriptional response of genes associated with polycomb repressor complex (PRC 1 (Ring1A and Ring1B and Bmi1 and PRC2 (Ezh1, Ezh2 and Suz12, as well as additional transcriptional regulators Sirt1, Yy1 and Yy2, in a mouse model of status epilepticus. Findings were contrasted to changes after status epilepticus in mice previously given brief seizures to evoke tolerance. Real-time quantitative PCR showed status epilepticus prompted an early (1 h increase in expression of several genes in PRC1 and PRC2 in the hippocampus, followed by down-regulation of many of the same genes at later times points (4 , 8 and 24 h. Spatio-temporal differences were found among PRC2 genes in epileptic tolerance, including increased expression of Ezh2, Suz12 and Yy2 relative to the normal injury response to status epilepticus. In contrast, PRC1 complex genes including Ring 1B and Bmi1 displayed differential down-regulation in epileptic tolerance. The present study characterizes polycomb group gene expression following status epilepticus and shows prior seizure exposure produces select changes to PRC1 and PRC2 composition that may influence differential gene expression in epileptic tolerance.

  1. Temporal bone trauma and imaging

    International Nuclear Information System (INIS)

    Turetschek, K.; Czerny, C.; Wunderbaldinger, P.; Steiner, E.

    1997-01-01

    Fractures of the temporal bone result from direct trauma to the temporal bone or occur as one component of a severe craniocerebral injury. Complications of temporal trauma are hemotympanon, facial nerve paralysis, conductive or sensorineur hearing loss, and leakage of cerebrospinal fluid. Erly recognition and an appropiate therapy may improve or prevent permanent deficits related to such complications. Only 20-30% of temporal bone fractures can be visualized by plain films. CT has displaced plain radiography in the investigation of the otological trauma because subtle bony details are best evaluated by CT which even can be reformatted in multiple projections, regardless of the original plane of scanning. Associated epidural, subdural, and intracerebral hemorrhagic lesions are better defined by MRI. (orig.) [de

  2. Temporal dimension in cognitive models

    International Nuclear Information System (INIS)

    Decortis, F.; Cacciabue, P.C.

    1988-01-01

    Increased attention has been given to the role of humans in nuclear power plant safety, but one aspect seldom considered is the temporal dimension of human reasoning. Time is recognized as crucial in human reasoning and has been the subject of empirical studies where cognitive mechanisms and strategies to face the temporal dimension have been studied. The present study shows why temporal reasoning is essential in Human Reliability Analysis and how it could be introduced in a human model. Accounting for the time dimension in human behaviour is discussed first, with reference to proven field studies. Then, theoretical modelling of the temporal dimension in human reasoning and its relevance in simulation of cognitive activities of plant operator is discussed. Finally a Time Experience Model is presented

  3. Object-Location Training Elicits an Overlapping but Temporally Distinct Transcriptional Profile from Contextual Fear Conditioning

    OpenAIRE

    Poplawski, Shane G.; Schoch, Hannah; Wimmer, Mathieu; Hawk, Joshua D.; Walsh, Jennifer L.; Giese, Karl P.; Abel, Ted

    2014-01-01

    Hippocampus-dependent learning is known to induce changes in gene expression, but information on gene expression differences between different learning paradigms that require the hippocampus is limited. The bulk of studies investigating RNA expression after learning use the contextual fear conditioning task, which couples a novel environment with a footshock. Although contextual fear conditioning has been useful in discovering gene targets, gene expression after spatial memory tasks has recei...

  4. Suboptimal choice, reward-predictive signals, and temporal information.

    Science.gov (United States)

    Cunningham, Paul J; Shahan, Timothy A

    2018-01-01

    Suboptimal choice refers to preference for an alternative offering a low probability of food (suboptimal alternative) over an alternative offering a higher probability of food (optimal alternative). Numerous studies have found that stimuli signaling probabilistic food play a critical role in the development and maintenance of suboptimal choice. However, there is still much debate about how to characterize how these stimuli influence suboptimal choice. There is substantial evidence that the temporal information conveyed by a food-predictive signal governs its function as both a Pavlovian conditioned stimulus and as an instrumental conditioned reinforcer. Thus, we explore the possibility that food-predictive signals influence suboptimal choice via the temporal information they convey. Application of this temporal information-theoretic approach to suboptimal choice provides a formal, quantitative framework that describes how food-predictive signals influence suboptimal choice in a manner consistent with related phenomena in Pavlovian conditioning and conditioned reinforcement. Our reanalysis of previous data on suboptimal choice suggests that, generally speaking, preference in the suboptimal choice procedure tracks relative temporal information conveyed by food-predictive signals for the suboptimal and optimal alternatives. The model suggests that suboptimal choice develops when the food-predictive signal for the suboptimal alternative conveys more temporal information than that for the optimal alternative. Finally, incorporating a role for competition between temporal information provided by food-predictive signals and relative primary reinforcement rate provides a reasonable account of existing data on suboptimal choice. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  5. Transcriptional networks and chromatin remodeling controlling adipogenesis

    DEFF Research Database (Denmark)

    Siersbæk, Rasmus; Nielsen, Ronni; Mandrup, Susanne

    2012-01-01

    Adipocyte differentiation is tightly controlled by a transcriptional cascade, which directs the extensive reprogramming of gene expression required to convert fibroblast-like precursor cells into mature lipid-laden adipocytes. Recent global analyses of transcription factor binding and chromatin...... remodeling have revealed 'snapshots' of this cascade and the chromatin landscape at specific time-points of differentiation. These studies demonstrate that multiple adipogenic transcription factors co-occupy hotspots characterized by an open chromatin structure and specific epigenetic modifications....... Such transcription factor hotspots are likely to represent key signaling nodes which integrate multiple adipogenic signals at specific chromatin sites, thereby facilitating coordinated action on gene expression....

  6. Spatio-temporal data analytics for wind energy integration

    CERN Document Server

    Yang, Lei; Zhang, Junshan

    2014-01-01

    This SpringerBrief presents spatio-temporal data analytics for wind energy integration using stochastic modeling and optimization methods. It explores techniques for efficiently integrating renewable energy generation into bulk power grids. The operational challenges of wind, and its variability are carefully examined. A spatio-temporal analysis approach enables the authors to develop Markov-chain-based short-term forecasts of wind farm power generation. To deal with the wind ramp dynamics, a support vector machine enhanced Markov model is introduced. The stochastic optimization of economic di

  7. The histone chaperone TAF-I/SET/INHAT is required for transcription in vitro of chromatin templates.

    Science.gov (United States)

    Gamble, Matthew J; Erdjument-Bromage, Hediye; Tempst, Paul; Freedman, Leonard P; Fisher, Robert P

    2005-01-01

    To uncover factors required for transcription by RNA polymerase II on chromatin, we fractionated a mammalian cell nuclear extract. We identified the histone chaperone TAF-I (also known as INHAT [inhibitor of histone acetyltransferase]), which was previously proposed to repress transcription, as a potent activator of chromatin transcription responsive to the vitamin D3 receptor or to Gal4-VP16. TAF-I associates with chromatin in vitro and can substitute for the related protein NAP-1 in assembling chromatin onto cloned DNA templates in cooperation with the remodeling enzyme ATP-dependent chromatin assembly factor (ACF). The chromatin assembly and transcriptional activation functions are distinct, however, and can be dissociated temporally. Efficient transcription of chromatin assembled with TAF-I still requires the presence of TAF-I during the polymerization reaction. Conversely, TAF-I cannot stimulate transcript elongation when added after the other factors necessary for assembly of a preinitiation complex on naked DNA. Thus, TAF-I is required to facilitate transcription at a step after chromatin assembly but before transcript elongation.

  8. Transcriptional repression of BODENLOS by HD-ZIP transcription factor HB5 in Arabidopsis thaliana.

    NARCIS (Netherlands)

    Smet, De I.; Lau, S.; Ehrismann, J.S.; Axiotis, I.; Kolb, M.; Kientz, M.; Weijers, D.; Jürgens, G.

    2013-01-01

    In Arabidopsis thaliana, the phytohormone auxin is an important patterning agent during embryogenesis and post-embryonic development, exerting effects through transcriptional regulation. The main determinants of the transcriptional auxin response machinery are AUXIN RESPONSE FACTOR (ARF)

  9. "Healing is a Done Deal": Temporality and Metabolic Healing Among Evangelical Christians in Samoa.

    Science.gov (United States)

    Hardin, Jessica

    2016-01-01

    Drawing on fieldwork in independent Samoa, in this article, I analyze the temporal dimensions of evangelical Christian healing of metabolic disorders. I explore how those suffering with metabolic disorders draw from multiple time-based notions of healing, drawing attention to the limits of biomedicine in contrast with the effectiveness of Divine healing. By simultaneously engaging evangelical and biomedical temporalities, I argue that evangelical Christians create wellness despite sickness and, in turn, re-signify chronic suffering as a long-term process of Christian healing. Positioning biomedical temporality and evangelical temporality as parallel yet distinctive ways of practicing healing, therefore, influences health care choices.

  10. ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data.

    Science.gov (United States)

    Minas, Giorgos; Momiji, Hiroshi; Jenkins, Dafyd J; Costa, Maria J; Rand, David A; Finkenstädt, Bärbel

    2017-06-26

    Given the development of high-throughput experimental techniques, an increasing number of whole genome transcription profiling time series data sets, with good temporal resolution, are becoming available to researchers. The ReTrOS toolbox (Reconstructing Transcription Open Software) provides MATLAB-based implementations of two related methods, namely ReTrOS-Smooth and ReTrOS-Switch, for reconstructing the temporal transcriptional activity profile of a gene from given mRNA expression time series or protein reporter time series. The methods are based on fitting a differential equation model incorporating the processes of transcription, translation and degradation. The toolbox provides a framework for model fitting along with statistical analyses of the model with a graphical interface and model visualisation. We highlight several applications of the toolbox, including the reconstruction of the temporal cascade of transcriptional activity inferred from mRNA expression data and protein reporter data in the core circadian clock in Arabidopsis thaliana, and how such reconstructed transcription profiles can be used to study the effects of different cell lines and conditions. The ReTrOS toolbox allows users to analyse gene and/or protein expression time series where, with appropriate formulation of prior information about a minimum of kinetic parameters, in particular rates of degradation, users are able to infer timings of changes in transcriptional activity. Data from any organism and obtained from a range of technologies can be used as input due to the flexible and generic nature of the model and implementation. The output from this software provides a useful analysis of time series data and can be incorporated into further modelling approaches or in hypothesis generation.

  11. Bile Duct Exploration

    Science.gov (United States)

    ... Home / Health Library / Diagnostics & Testing / Bile Duct Exploration Bile Duct Exploration Common bile duct exploration is a ... Test Details Results and Follow-Up What is bile, and what is bile duct exploration? Bile is ...

  12. Heart morphogenesis gene regulatory networks revealed by temporal expression analysis.

    Science.gov (United States)

    Hill, Jonathon T; Demarest, Bradley; Gorsi, Bushra; Smith, Megan; Yost, H Joseph

    2017-10-01

    During embryogenesis the heart forms as a linear tube that then undergoes multiple simultaneous morphogenetic events to obtain its mature shape. To understand the gene regulatory networks (GRNs) driving this phase of heart development, during which many congenital heart disease malformations likely arise, we conducted an RNA-seq timecourse in zebrafish from 30 hpf to 72 hpf and identified 5861 genes with altered expression. We clustered the genes by temporal expression pattern, identified transcription factor binding motifs enriched in each cluster, and generated a model GRN for the major gene batteries in heart morphogenesis. This approach predicted hundreds of regulatory interactions and found batteries enriched in specific cell and tissue types, indicating that the approach can be used to narrow the search for novel genetic markers and regulatory interactions. Subsequent analyses confirmed the GRN using two mutants, Tbx5 and nkx2-5 , and identified sets of duplicated zebrafish genes that do not show temporal subfunctionalization. This dataset provides an essential resource for future studies on the genetic/epigenetic pathways implicated in congenital heart defects and the mechanisms of cardiac transcriptional regulation. © 2017. Published by The Company of Biologists Ltd.

  13. Decoding transcriptional enhancers: Evolving from annotation to functional interpretation.

    Science.gov (United States)

    Engel, Krysta L; Mackiewicz, Mark; Hardigan, Andrew A; Myers, Richard M; Savic, Daniel

    2016-09-01

    Deciphering the intricate molecular processes that orchestrate the spatial and temporal regulation of genes has become an increasingly major focus of biological research. The differential expression of genes by diverse cell types with a common genome is a hallmark of complex cellular functions, as well as the basis for multicellular life. Importantly, a more coherent understanding of gene regulation is critical for defining developmental processes, evolutionary principles and disease etiologies. Here we present our current understanding of gene regulation by focusing on the role of enhancer elements in these complex processes. Although functional genomic methods have provided considerable advances to our understanding of gene regulation, these assays, which are usually performed on a genome-wide scale, typically provide correlative observations that lack functional interpretation. Recent innovations in genome editing technologies have placed gene regulatory studies at an exciting crossroads, as systematic, functional evaluation of enhancers and other transcriptional regulatory elements can now be performed in a coordinated, high-throughput manner across the entire genome. This review provides insights on transcriptional enhancer function, their role in development and disease, and catalogues experimental tools commonly used to study these elements. Additionally, we discuss the crucial role of novel techniques in deciphering the complex gene regulatory landscape and how these studies will shape future research. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Post-transcriptional trafficking and regulation of neuronal gene expression.

    Science.gov (United States)

    Goldie, Belinda J; Cairns, Murray J

    2012-02-01

    Intracellular messenger RNA (mRNA) traffic and translation must be highly regulated, both temporally and spatially, within eukaryotic cells to support the complex functional partitioning. This capacity is essential in neurons because it provides a mechanism for rapid input-restricted activity-dependent protein synthesis in individual dendritic spines. While this feature is thought to be important for synaptic plasticity, the structures and mechanisms that support this capability are largely unknown. Certainly specialized RNA binding proteins and binding elements in the 3' untranslated region (UTR) of translationally regulated mRNA are important, but the subtlety and complexity of this system suggests that an intermediate "specificity" component is also involved. Small non-coding microRNA (miRNA) are essential for CNS development and may fulfill this role by acting as the guide strand for mediating complex patterns of post-transcriptional regulation. In this review we examine post-synaptic gene regulation, mRNA trafficking and the emerging role of post-transcriptional gene silencing in synaptic plasticity.

  15. Overlapping transcription structure of human cytomegalovirus

    Indian Academy of Sciences (India)

    Transcription of human cytomegalovirus UL/b′ region has been studied extensively for some genes. In this study, transcripts of the UL140 and UL141, two of the UL/b′ genes, were identified in late RNAs of three HCMV isolates using Northern blot hybridization, cDNA library screening and RACE-PCR. At least three ...

  16. Overlapping transcription structure of human cytomegalovirus ...

    Indian Academy of Sciences (India)

    2013-01-21

    Jan 21, 2013 ... Transcription of human cytomegalovirus UL/b′ region has been studied extensively for some genes. In this study, transcripts of the UL140 and UL141, two of the UL/b′ genes, were identified in late RNAs of three HCMV isolates using Northern blot hybridization, cDNA library screening and RACE-PCR.

  17. Transcription of Byzantine Chant - Problems, Possibilities, Formats

    DEFF Research Database (Denmark)

    Troelsgård, Christian

    2007-01-01

    Discusses the problems and possibilities for transsription of Byzantine chant on the basis of medieval musical manuscripts. A relatively 'neutral' style of transcription is suggested for musicological purposes.......Discusses the problems and possibilities for transsription of Byzantine chant on the basis of medieval musical manuscripts. A relatively 'neutral' style of transcription is suggested for musicological purposes....

  18. Regulation of transcription in hyperthermophilic archaea

    NARCIS (Netherlands)

    Brinkman, A.B.

    2002-01-01

    The aim of the research presented here was to insight in the mechanisms by which transcription in hyperthermophilic archaea is regulated. To accomplish this, we have aimed (I) to identify transcriptional regulatory proteins from hyperthermophilic archaea, (II) to characterize these

  19. 45 CFR 99.27 - Official transcript.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 1 2010-10-01 2010-10-01 false Official transcript. 99.27 Section 99.27 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION PROCEDURE FOR HEARINGS FOR THE CHILD CARE AND DEVELOPMENT FUND Hearing Procedures § 99.27 Official transcript. The Department will...

  20. RNA polymerase II collision interrupts convergent transcription

    DEFF Research Database (Denmark)

    Hobson, David J; Wei, Wu; Steinmetz, Lars M

    2012-01-01

    Antisense noncoding transcripts, genes-within-genes, and convergent gene pairs are prevalent among eukaryotes. The existence of such transcription units raises the question of what happens when RNA polymerase II (RNAPII) molecules collide head-to-head. Here we use a combination of biochemical...

  1. Temporal anteroinferior encephalocele: An underrecognized etiology of temporal lobe epilepsy?

    Science.gov (United States)

    Saavalainen, Taavi; Jutila, Leena; Mervaala, Esa; Kälviäinen, Reetta; Vanninen, Ritva; Immonen, Arto

    2015-10-27

    To report the increasing frequency with which temporal anteroinferior encephalocele is a cause of adult temporal lobe epilepsy, to illustrate the clinical and imaging characteristics of this condition, and to report its surgical treatment in a series of 23 adult patients. Epilepsy patients diagnosed with temporal anteroinferior encephalocele from January 2006 to December 2013 in a national epilepsy reference center were included in this noninterventional study. Twenty-three epilepsy patients (14 female, mean age 43.8 years) were diagnosed with temporal anteroinferior encephalocele in our institute. Thirteen patients had ≥2 encephaloceles; 7 cases presented bilaterally. The estimated frequency of this condition was 0.3% among MRI examinations performed due to newly diagnosed epilepsy (n = 6) and 1.9% among drug-resistant patients referred to our center (n = 17). Nine patients with local encephalocele disconnection (n = 4) or anterior temporal lobectomy and amygdalohippocampectomy (n = 5) have become seizure-free (Engel 1) for a mean 2.8 years (range 3 months-6.2 years) of follow-up. Three patients with local encephalocele disconnection were almost seizure-free or exhibited worthwhile improvement. Histologically, all 12 surgical patients had gliosis at the base of the encephalocele; some had cortical laminar disorganization (n = 5) or mild hippocampal degeneration (n = 1). The possibility of a temporal encephalocele should be considered when interpreting MRI examinations of patients with medically intractable focal epilepsy. These patients can significantly benefit from unitemporal epilepsy surgery, even in cases with bilateral encephaloceles. © 2015 American Academy of Neurology.

  2. The Temporality of Power and the Power of Temporality

    DEFF Research Database (Denmark)

    Costas, Jana; Grey, Christopher

    2014-01-01

    This paper extends existing understandings of power, resistance and subjectivity in professional service organizations by developing an analysis of how these relate to temporality. Drawing in particular on Hoy’s reading of the Foucauldian account of temporality, we conceive of disciplinary power...... regimes and resistance as inherently future-oriented, or, to use Ybema’s term, postalgic. In moving beyond the extant research focus on self-disciplined and/or counter-resistant professional selves, we draw attention to the imaginary future self as an employee response to disciplinary power. In contrast...

  3. [Children's oppositional behaviour, practice of parental authority and temporal anomie].

    Science.gov (United States)

    Gadeau, L

    2014-02-01

    This article examines the relationship between children's oppositional behaviour and the exercise of parental authority. It seeks to explore the value of a heuristic approach to psychic temporality in exercising parental authority. The study aims to better understand the role of psychic temporality in operations producing symbolic law. It goes on to describe a disorder of temporality, known as temporal anomie, which may be involved in a child's oppositional disorders. Psychiatric or psychological consultations motivated by oppositional disorders in children have increased steadily in the past fifteen years in France. The primary reason for consultation is in the form of difficulties for children in accepting the social rules or constraints, but also the difficulties of parenting while coping with the opposition of their children. This increase is made in connection with the works analysing the social and psychological effects imposed by modernity and its acceleration. Correspondingly, we find that some parents do not prioritize their educational requirements, do not know when or how to frustrate their child, or even if it is legitimate to expect from him/her a certain type of behaviour. They seem more preoccupied with the fear of not being loved by their child more than their duty to educate. A general trend suggests an alteration of psychological time, characterized by: a) a disinvestment of links between present and past for the enjoyment of the moment and its extension in the immediate future ; b) a difficulty in supporting educational responses causing frustration for the child ; c) a lack of continuity and constancy in educational requirements. The author proposes to define temporal anomie as the psychical time that weakens the consistency of educational responses. A link between psychological temporality and the symbolic law is discussed. Specifically, the study notes that: in intersubjective relations, mastery of psychological time by parents is an

  4. In vitro transcription in the presence of DNA oligonucleotides can generate strong anomalous initiation sites.

    Science.gov (United States)

    Chow, C W; Clark, M P; Rinaldo, J E; Chalkley, R

    1996-03-01

    In the present study, we have explored an unexpected observation in transcription initiation that is mediated by single-stranded oligonucleotides. Initially, our goal was to understand the function of different upstream regulatory elements/initiation sites in the rat xanthine dehydrogenase/oxidase (XDH/XO) promoter. We performed in vitro transcription with HeLa nuclear extracts in the presence of different double-stranded oligonucleotides against upstream elements as competitors. A new and unusual transcription initiation site was detected by primer extension. This new initiation site maps to the downstream region of the corresponding competitor. Subsequent analyses have indicated that the induction of a new transcription initiation site is anomalous which is due to the presence of a small amount of single-stranded oligonucleotide in the competitor. We found that this anomalous initiation site is insensitive to the orientation of the promoter and requires only a small amount of single-stranded oligonucleotide (< 2-fold molar excess relative to template). We surmise that a complementary interaction between the single-stranded oligonucleotide and transiently denatured promoter template may be responsible for this sequence-specific transcription initiation artifact. To study the regulation of transcription initiation by in vitro transcription approaches, we propose that one should probe the effect of removing transacting factors by adding an excess of a cognate oligonucleotide which does not bear exact sequence identity to the template.

  5. Temporal auditory processing in elders

    Directory of Open Access Journals (Sweden)

    Azzolini, Vanuza Conceição

    2010-03-01

    Full Text Available Introduction: In the trial of aging all the structures of the organism are modified, generating intercurrences in the quality of the hearing and of the comprehension. The hearing loss that occurs in consequence of this trial occasion a reduction of the communicative function, causing, also, a distance of the social relationship. Objective: Comparing the performance of the temporal auditory processing between elderly individuals with and without hearing loss. Method: The present study is characterized for to be a prospective, transversal and of diagnosis character field work. They were analyzed 21 elders (16 women and 5 men, with ages between 60 to 81 years divided in two groups, a group "without hearing loss"; (n = 13 with normal auditive thresholds or restricted hearing loss to the isolated frequencies and a group "with hearing loss" (n = 8 with neurosensory hearing loss of variable degree between light to moderately severe. Both the groups performed the tests of frequency (PPS and duration (DPS, for evaluate the ability of temporal sequencing, and the test Randon Gap Detection Test (RGDT, for evaluate the temporal resolution ability. Results: It had not difference statistically significant between the groups, evaluated by the tests DPS and RGDT. The ability of temporal sequencing was significantly major in the group without hearing loss, when evaluated by the test PPS in the condition "muttering". This result presented a growing one significant in parallel with the increase of the age group. Conclusion: It had not difference in the temporal auditory processing in the comparison between the groups.

  6. Biological data warehousing system for identifying transcriptional regulatory sites from gene expressions of microarray data.

    Science.gov (United States)

    Tsou, Ann-Ping; Sun, Yi-Ming; Liu, Chia-Lin; Huang, Hsien-Da; Horng, Jorng-Tzong; Tsai, Meng-Feng; Liu, Baw-Juine

    2006-07-01

    Identification of transcriptional regulatory sites plays an important role in the investigation of gene regulation. For this propose, we designed and implemented a data warehouse to integrate multiple heterogeneous biological data sources with data types such as text-file, XML, image, MySQL database model, and Oracle database model. The utility of the biological data warehouse in predicting transcriptional regulatory sites of coregulated genes was explored using a synexpression group derived from a microarray study. Both of the binding sites of known transcription factors and predicted over-represented (OR) oligonucleotides were demonstrated for the gene group. The potential biological roles of both known nucleotides and one OR nucleotide were demonstrated using bioassays. Therefore, the results from the wet-lab experiments reinforce the power and utility of the data warehouse as an approach to the genome-wide search for important transcription regulatory elements that are the key to many complex biological systems.

  7. Level and Temporal Trend of Perfluoroalkyl Acids in Greenlandic Inuit

    DEFF Research Database (Denmark)

    Long, Manhai; Bossi, Rossana; Bonefeld-Jørgensen, Eva Cecilie

    bears. However, until now, no data have been reported for PFAAs in Greenlandic Inuit. This study assesses the level and temporal trend of serum PFAAs in Greenlandic Inuit. Study design: Cross-section and temporal time trend survey. Methods: Serum PFAA levels were determined in 284 Inuit from different...... Greenlandic districts using liquid chromatography-tandem mass spectrometry with electrospray ionization. The temporal time trend of serum PFAAs in Nuuk Inuit during 19982005 and the correlation between serum PFAAs and legacy persistent organic pollutants (POPs) were explored. Results: Serum PFAA levels were...... higher in Nuuk Inuit than in non-Nuuk Inuit. Within the same district, higher PFAA levels were observed for males. An age-dependent, increasing trend of serum PFAA levels in the period from 19982005 was observed for Nuuk Inuit. For the pooled gender data, no significant association between PFAAs...

  8. Level and temporal trend of perfluoroalkyl acids in Greenlandic Inuit

    DEFF Research Database (Denmark)

    Long, Manhai; Bossi, Rossana; Bonefeld-Jørgensen, Eva Cecilie

    2012-01-01

    bears. However, until now, no data have been reported for PFAAs in Greenlandic Inuit. This study assesses the level and temporal trend of serum PFAAs in Greenlandic Inuit. Study design: Cross-section and temporal time trend survey. Methods: Serum PFAA levels were determined in 284 Inuit from different...... Greenlandic districts using liquid chromatography-tandem mass spectrometry with electrospray ionization. The temporal time trend of serum PFAAs in Nuuk Inuit during 19982005 and the correlation between serum PFAAs and legacy persistent organic pollutants (POPs) were explored. Results: Serum PFAA levels were...... higher in Nuuk Inuit than in non-Nuuk Inuit. Within the same district, higher PFAA levels were observed for males. An age-dependent, increasing trend of serum PFAA levels in the period from 19982005 was observed for Nuuk Inuit. For the pooled gender data, no significant association between PFAAs...

  9. Declarative Programming with Temporal Constraints, in the Language CG

    Directory of Open Access Journals (Sweden)

    Lorina Negreanu

    2015-01-01

    Full Text Available Specifying and interpreting temporal constraints are key elements of knowledge representation and reasoning, with applications in temporal databases, agent programming, and ambient intelligence. We present and formally characterize the language CG, which tackles this issue. In CG, users are able to develop time-dependent programs, in a flexible and straightforward manner. Such programs can, in turn, be coupled with evolving environments, thus empowering users to control the environment’s evolution. CG relies on a structure for storing temporal information, together with a dedicated query mechanism. Hence, we explore the computational complexity of our query satisfaction problem. We discuss previous implementation attempts of CG and introduce a novel prototype which relies on logic programming. Finally, we address the issue of consistency and correctness of CG program execution, using the Event-B modeling approach.

  10. Declarative Programming with Temporal Constraints, in the Language CG.

    Science.gov (United States)

    Negreanu, Lorina

    2015-01-01

    Specifying and interpreting temporal constraints are key elements of knowledge representation and reasoning, with applications in temporal databases, agent programming, and ambient intelligence. We present and formally characterize the language CG, which tackles this issue. In CG, users are able to develop time-dependent programs, in a flexible and straightforward manner. Such programs can, in turn, be coupled with evolving environments, thus empowering users to control the environment's evolution. CG relies on a structure for storing temporal information, together with a dedicated query mechanism. Hence, we explore the computational complexity of our query satisfaction problem. We discuss previous implementation attempts of CG and introduce a novel prototype which relies on logic programming. Finally, we address the issue of consistency and correctness of CG program execution, using the Event-B modeling approach.

  11. Temporal trade-offs in psychophysics.

    Science.gov (United States)

    Barack, David L; Gold, Joshua I

    2016-04-01

    Psychophysical techniques typically assume straightforward relationships between manipulations of real-world events, their effects on the brain, and behavioral reports of those effects. However, these relationships can be influenced by many complex, strategic factors that contribute to task performance. Here we discuss several of these factors that share two key features. First, they involve subjects making flexible use of time to process information. Second, this flexibility can reflect the rational regulation of information-processing trade-offs that can play prominent roles in particular temporal epochs: sensitivity to stability versus change for past information, speed versus accuracy for current information, and exploitation versus exploration for future goals. Understanding how subjects manage these trade-offs can be used to help design and interpret psychophysical studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Temporal Lobe Epilepsy in Children

    Science.gov (United States)

    Nickels, Katherine C.; Wong-Kisiel, Lily C.; Moseley, Brian D.; Wirrell, Elaine C.

    2012-01-01

    The temporal lobe is a common focus for epilepsy. Temporal lobe epilepsy in infants and children differs from the relatively homogeneous syndrome seen in adults in several important clinical and pathological ways. Seizure semiology varies by age, and the ictal EEG pattern may be less clear cut than what is seen in adults. Additionally, the occurrence of intractable seizures in the developing brain may impact neurocognitive function remote from the temporal area. While many children will respond favorably to medical therapy, those with focal imaging abnormalities including cortical dysplasia, hippocampal sclerosis, or low-grade tumors are likely to be intractable. Expedient workup and surgical intervention in these medically intractable cases are needed to maximize long-term developmental outcome. PMID:22957247

  13. LocExpress: a web server for efficiently estimating expression of novel transcripts.

    Science.gov (United States)

    Hou, Mei; Tian, Feng; Jiang, Shuai; Kong, Lei; Yang, Dechang; Gao, Ge

    2016-12-22

    The temporal and spatial-specific expression pattern of a transcript in multiple tissues and cell types can indicate key clues about its function. While several gene atlas available online as pre-computed databases for known gene models, it's still challenging to get expression profile for previously uncharacterized (i.e. novel) transcripts efficiently. Here we developed LocExpress, a web server for efficiently estimating expression of novel transcripts across multiple tissues and cell types in human (20 normal tissues/cells types and 14 cell lines) as well as in mouse (24 normal tissues/cell types and nine cell lines). As a wrapper to RNA-Seq quantification algorithm, LocExpress efficiently reduces the time cost by making abundance estimation calls increasingly within the minimum spanning bundle region of input transcripts. For a given novel gene model, such local context-oriented strategy allows LocExpress to estimate its FPKMs in hundreds of samples within minutes on a standard Linux box, making an online web server possible. To the best of our knowledge, LocExpress is the only web server to provide nearly real-time expression estimation for novel transcripts in common tissues and cell types. The server is publicly available at http://loc-express.cbi.pku.edu.cn .

  14. Temporal hypometabolism at the onset of cryptogenic temporal lobe epilepsy

    Energy Technology Data Exchange (ETDEWEB)

    Matheja, P.; Kuwert, T.; Weckesser, M.; Schober, O. [Dept. of Nuclear Medicine, Muenster Univ. (Germany); Luedemann, P.; Kellinghaus, C.; Diehl, B.; Ringelstein, E.B. [Dept. of Neurology, Muenster Univ. (Germany); Schuierer, G. [Dept. of Clinical Radiology, Muenster Univ. (Germany)

    2001-05-01

    Most patients with intractable temporal lobe epilepsy (TLE) exhibit temporal glucose hypometabolism. The reasons for the development of this abnormality are as yet unclear. The current notion is that an initial injury causes seizures, which in turn give rise to hypometabolism. The aim of this study was to assess whether temporal reductions in glucose metabolism in non-lesional TLE are the result of repeated seizures or whether hypometabolism represents an initial disturbance at the onset of disease. Glucose consumption was assessed with fluorine-18 fluorodeoxyglucose positron emission tomography ({sup 18}F-FDG PET) in 62 patients with cryptogenic non-refractory TLE in different stages of disease. Twelve subjects without neurological illness served as controls. Patients with onset of epilepsy at least 3 years prior to the PET scan were defined as having chronic TLE. Using this criterion, the whole patient cohort included 27 patients with de novo TLE and 35 patients with chronic TLE. The groups were matched for age and sex. The appearance of high-resolution magnetic resonance images of the brain was unremarkable in all patients. In the total cohort, number, duration and frequency of seizures had a significant relation to the magnitude of hypometabolism. Temporal hypometabolism was exhibited by 26 of the 62 patients (42%), including 8 out of 27 (30%) with newly diagnosed TLE and 18 out of 35 (51%) with chronic TLE. The disturbances were more extensive and more severe in patients with chronic TLE. It is concluded that temporal hypometabolism may already be present at the onset of TLE, but is less frequent and less severe in newly diagnosed than in chronic TLE. The metabolic disturbance correlates with the number of seizures. These findings suggest that an initial dysfunction is present in a considerable number of patients and that hypometabolism is worsened by continuing epileptic activity. (orig.)

  15. TEMPORAL QUERY PROCESSIG USING SQL SERVER

    OpenAIRE

    Vali Shaik, Mastan; Sujatha, P

    2017-01-01

    Most data sources in real-life are not static but change their information in time. This evolution of data in time can give valuable insights to business analysts. Temporal data refers to data, where changes over time or temporal aspects play a central role. Temporal data denotes the evaluation of object characteristics over time. One of the main unresolved problems that arise during the data mining process is treating data that contains temporal information. Temporal queries on time evolving...

  16. Temporality of Features in Near-Death Experience Narratives

    Directory of Open Access Journals (Sweden)

    Charlotte Martial

    2017-06-01

    Full Text Available Background: After an occurrence of a Near-Death Experience (NDE, Near-Death Experiencers (NDErs usually report extremely rich and detailed narratives. Phenomenologically, a NDE can be described as a set of distinguishable features. Some authors have proposed regular patterns of NDEs, however, the actual temporality sequence of NDE core features remains a little explored area.Objectives: The aim of the present study was to investigate the frequency distribution of these features (globally and according to the position of features in narratives as well as the most frequently reported temporality sequences of features.Methods: We collected 154 French freely expressed written NDE narratives (i.e., Greyson NDE scale total score ≥ 7/32. A text analysis was conducted on all narratives in order to infer temporal ordering and frequency distribution of NDE features.Results: Our analyses highlighted the following most frequently reported sequence of consecutive NDE features: Out-of-Body Experience, Experiencing a tunnel, Seeing a bright light, Feeling of peace. Yet, this sequence was encountered in a very limited number of NDErs.Conclusion: These findings may suggest that NDEs temporality sequences can vary across NDErs. Exploring associations and relationships among features encountered during NDEs may complete the rigorous definition and scientific comprehension of the phenomenon.

  17. Colon cancer associated transcripts in human cancers.

    Science.gov (United States)

    Chen, Yincong; Xie, Haibiao; Gao, Qunjun; Zhan, Hengji; Xiao, Huizhong; Zou, Yifan; Zhang, Fuyou; Liu, Yuchen; Li, Jianfa

    2017-10-01

    Long non-coding RNAs serve as important regulators in complicated cellular activities, including cell differentiation, proliferation and death. Dysregulation of long non-coding RNAs occurs in the formation and progression of cancers. The family of colon cancer associated transcripts, long non-coding RNAs colon cancer associated transcript-1 and colon cancer associated transcript-2 are known as oncogenes involved in various cancers. Colon cancer associated transcript-1 is a novel lncRNA located in 8q24.2, and colon cancer associated transcript-2 maps to the 8q24.21 region encompassing rs6983267. Colon cancer associated transcripts have close associations with clinical characteristics, such as lymph node metastasis, high TNM stage and short overall survival. Knockdown of them can reverse the malignant phenotypes of cancer cells, including proliferation, migration, invasion and apoptosis. Moreover, they can increase the expression level of c-MYC and oncogenic microRNAs via activating a series of complex mechanisms. In brief, the family of colon cancer associated transcripts may serve as potential biomarkers or therapeutic targets for human cancers. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  18. Temporal changes of the inner core from waveform doublets

    Science.gov (United States)

    Yang, Y.; Song, X.

    2017-12-01

    Temporal changes of the Earth's inner core have been detected from earthquake waveform doublets (repeating sources with similar waveforms at the same station). Using doublets from events up to the present in the South Sandwich Island (SSI) region recorded by the station COLA (Alaska), we confirmed systematic temporal variations in the travel time of the inner-core-refracted phase (PKIKP, the DF branch). The DF phase arrives increasingly earlier than outer core phases (BC and AB) by rate of approximately 0.07 s per decade since 1970s. If we assume that the temporal change is caused by a shift of the lateral gradient from the inner core rotation as in previous studies, we estimate the rotation rate of 0.2-0.4 degree per year. We also analyzed the topography of the inner core boundary (ICB) using SSI waveform doublets recorded by seismic stations in Eurasia and North America with reflected phase (PKiKP) and refracted phases. There are clear temporal changes in the waveforms of doublets for PKiKP under Africa and Central America. In addition, for doublets recorded by three nearby stations (AAK, AML, and UCH), we observed systematic change in the relative travel time of PKiKP and PKIKP. The temporal change of the (PKiKP - PKIKP) differential time is always negative for the event pairs if both events are before 2007, while it fluctuates to positive if the later event occurs after 2007. The rapid temporal changes in space and time may indicate localized processes (e.g., freezing and melting) of the ICB in the recent decades under Africa. We are exploring 4D models consistent with the temporal changes.

  19. Dissociable spatial and temporal effects of inhibition of return.

    Directory of Open Access Journals (Sweden)

    Zhiguo Wang

    Full Text Available Inhibition of return (IOR refers to the relative suppression of processing at locations that have recently been attended. It is frequently explored using a spatial cueing paradigm and is characterized by slower responses to cued than to uncued locations. The current study investigates the impact of IOR on overt visual orienting involving saccadic eye movements. Using a spatial cueing paradigm, our experiments have demonstrated that at a cue-target onset asynchrony (CTOA of 400 ms saccades to the vicinity of cued locations are not only delayed (temporal cost but also biased away (spatial effect. Both of these effects are basically no longer present at a CTOA of 1200 ms. At a shorter 200 ms CTOA, the spatial effect becomes stronger while the temporal cost is replaced by a temporal benefit. These findings suggest that IOR has a spatial effect that is dissociable from its temporal effect. Simulations using a neural field model of the superior colliculus (SC revealed that a theory relying on short-term depression (STD of the input pathway can explain most, but not all, temporal and spatial effects of IOR.

  20. Spatial-Temporal Event Detection from Geo-Tagged Tweets

    Directory of Open Access Journals (Sweden)

    Yuqian Huang

    2018-04-01

    Full Text Available As one of the most popular social networking services in the world, Twitter allows users to post messages along with their current geographic locations. Such georeferenced or geo-tagged Twitter datasets can benefit location-based services, targeted advertising and geosocial studies. Our study focused on the detection of small-scale spatial-temporal events and their textual content. First, we used Spatial-Temporal Density-Based Spatial Clustering of Applications with Noise (ST-DBSCAN to spatially-temporally cluster the tweets. Then, the word frequencies were summarized for each cluster and the potential topics were modeled by the Latent Dirichlet Allocation (LDA algorithm. Using two years of Twitter data from four college cities in the U.S., we were able to determine the spatial-temporal patterns of two known events, two unknown events and one recurring event, which then were further explored and modeled to identify the semantic content about the events. This paper presents our process and recommendations for both finding event-related tweets as well as understanding the spatial-temporal behaviors and semantic natures of the detected events.

  1. Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli.

    Science.gov (United States)

    Wang, Rui-Sheng; Jin, Guangxu; Zhang, Xiang-Sun; Chen, Luonan

    2009-04-29

    Transcriptional regulation is a fundamental process in biological systems, where transcription factors (TFs) have been revealed to play crucial roles. In recent years, in addition to TFs, an increasing number of non-coding RNAs (ncRNAs) have been shown to mediate post-transcriptional processes and regulate many critical pathways in both prokaryotes and eukaryotes. On the other hand, with more and more high-throughput biological data becoming available, it is possible and imperative to quantitatively study gene regulation in a systematic and detailed manner. Most existing studies for inferring transcriptional regulatory interactions and the activity of TFs ignore the possible post-transcriptional effects of ncRNAs. In this work, we propose a novel framework to infer the activity of regulators including both TFs and ncRNAs by exploring the expression profiles of target genes and (post)transcriptional regulatory relationships. We model the integrated regulatory system by a set of biochemical reactions which lead to a log-bilinear problem. The inference process is achieved by an iterative algorithm, in which two linear programming models are efficiently solved. In contrast to available related studies, the effects of ncRNAs on transcription process are considered in this work, and thus more reasonable and accurate reconstruction can be expected. In addition, the approach is suitable for large-scale problems from the viewpoint of computation. Experiments on two synthesized data sets and a model system of Escherichia coli (E. coli) carbon source transition from glucose to acetate illustrate the effectiveness of our model and algorithm. Our results show that incorporating the post-transcriptional regulation of ncRNAs into system model can mine the hidden effects from the regulation activity of TFs in transcription processes and thus can uncover the biological mechanisms in gene regulation in a more accurate manner. The software for the algorithm in this paper is available

  2. Microarray analysis of gender- and parasite-specific gene transcription in Strongyloides ratti

    NARCIS (Netherlands)

    Evans, Helen; Mello, Luciane V.; Fang, Yongxiang; Wit, Ernst; Thompson, Fiona J.; Viney, Mark E.; Paterson, Steve

    2008-01-01

    The molecular mechanisms by which parasitic nematodes reproduce and have adapted to life within a host are unclear. In the present study, microarray analysis was used to explore differential transcription among the different stages and sexes of Strongyloides ratti, a parasitic nematode of brown

  3. Analysis of the transcriptional responses in inflorescence buds of Jatropha curcas exposed to cytokinin treatment.

    Science.gov (United States)

    Chen, Mao-Sheng; Pan, Bang-Zhen; Wang, Gui-Juan; Ni, Jun; Niu, Longjian; Xu, Zeng-Fu

    2014-11-30

    Jatropha curcas L. is a potential biofuel plant. Application of exogenous cytokinin (6-benzyladenine, BA) on its inflorescence buds can significantly increase the number of female flowers, thereby improving seed yield. To investigate which genes and signal pathways are involved in the response to cytokinin in J. curcas inflorescence buds, we monitored transcriptional activity in inflorescences at 0, 3, 12, 24, and 48 h after BA treatment using a microarray. We detected 5,555 differentially expressed transcripts over the course of the experiment, which could be grouped into 12 distinct temporal expression patterns. We also identified 31 and 131 transcripts in J. curcas whose homologs in model plants function in flowering and phytohormonal signaling pathways, respectively. According to the transcriptional analysis of genes involved in flower development, we hypothesized that BA treatment delays floral organ formation by inhibiting the transcription of the A, B and E classes of floral organ-identity genes, which would allow more time to generate more floral primordia in inflorescence meristems, thereby enhancing inflorescence branching and significantly increasing flower number per inflorescence. BA treatment might also play an important role in maintaining the flowering signals by activating the transcription of GIGANTEA (GI) and inactivating the transcription of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and TERMINAL FLOWER 1b (TFL1b). In addition, exogenous cytokinin treatment could regulate the expression of genes involved in the metabolism and signaling of other phytohormones, indicating that cytokinin and other phytohormones jointly regulate flower development in J. curcas inflorescence buds. Our study provides a framework to better understand the molecular mechanisms underlying changes in flowering traits in response to cytokinin treatment in J. curcas inflorescence buds. The results provide valuable information related to the mechanisms of cross-talk among

  4. Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

    Directory of Open Access Journals (Sweden)

    Ciira wa Maina

    2014-05-01

    Full Text Available Gene transcription mediated by RNA polymerase II (pol-II is a key step in gene expression. The dynamics of pol-II moving along the transcribed region influence the rate and timing of gene expression. In this work, we present a probabilistic model of transcription dynamics which is fitted to pol-II occupancy time course data measured using ChIP-Seq. The model can be used to estimate transcription speed and to infer the temporal pol-II activity profile at the gene promoter. Model parameters are estimated using either maximum likelihood estimation or via Bayesian inference using Markov chain Monte Carlo sampling. The Bayesian approach provides confidence intervals for parameter estimates and allows the use of priors that capture domain knowledge, e.g. the expected range of transcription speeds, based on previous experiments. The model describes the movement of pol-II down the gene body and can be used to identify the time of induction for transcriptionally engaged genes. By clustering the inferred promoter activity time profiles, we are able to determine which genes respond quickly to stimuli and group genes that share activity profiles and may therefore be co-regulated. We apply our methodology to biological data obtained using ChIP-seq to measure pol-II occupancy genome-wide when MCF-7 human breast cancer cells are treated with estradiol (E2. The transcription speeds we obtain agree with those obtained previously for smaller numbers of genes with the advantage that our approach can be applied genome-wide. We validate the biological significance of the pol-II promoter activity clusters by investigating cluster-specific transcription factor binding patterns and determining canonical pathway enrichment. We find that rapidly induced genes are enriched for both estrogen receptor alpha (ERα and FOXA1 binding in their proximal promoter regions.

  5. Sleep is not just for the brain: transcriptional responses to sleep in peripheral tissues.

    Science.gov (United States)

    Anafi, Ron C; Pellegrino, Renata; Shockley, Keith R; Romer, Micah; Tufik, Sergio; Pack, Allan I

    2013-05-30

    Many have assumed that the primary function of sleep is for the brain. We evaluated the molecular consequences of sleep and sleep deprivation outside the brain, in heart and lung. Using microarrays we compared gene expression in tissue from sleeping and sleep deprived mice euthanized at the same diurnal times. In each tissue, nearly two thousand genes demonstrated statistically significant differential expression as a function of sleep/wake behavioral state. To mitigate the influence of an artificial deprivation protocol, we identified a subset of these transcripts as specifically sleep-enhanced or sleep-repressed by requiring that their expression also change over the course of unperturbed sleep. 3% and 6% of the assayed transcripts showed "sleep specific" changes in the lung and heart respectively. Sleep specific transcripts in these tissues demonstrated highly significant overlap and shared temporal dynamics. Markers of cellular stress and the unfolded protein response were reduced during sleep in both tissues. These results mirror previous findings in brain. Sleep-enhanced pathways reflected the unique metabolic functions of each tissue. Transcripts related to carbohydrate and sulfur metabolic processes were enhanced by sleep in the lung, and collectively favor buffering from oxidative stress. DNA repair and protein metabolism annotations were significantly enriched among the sleep-enhanced transcripts in the heart. Our results also suggest that sleep may provide a Zeitgeber, or synchronizing cue, in the lung as a large cluster of transcripts demonstrated systematic changes in inter-animal variability as a function of both sleep duration and circadian time. Our data support the notion that the molecular consequences of sleep/wake behavioral state extend beyond the brain to include peripheral tissues. Sleep state induces a highly overlapping response in both heart and lung. We conclude that sleep enhances organ specific molecular functions and that it has a

  6. Predictive modelling of gene expression from transcriptional regulatory elements.

    Science.gov (United States)

    Budden, David M; Hurley, Daniel G; Crampin, Edmund J

    2015-07-01

    Predictive modelling of gene expression provides a powerful framework for exploring the regulatory logic underpinning transcriptional regulation. Recent studies have demonstrated the utility of such models in identifying dysregulation of gene and miRNA expression associated with abnormal patterns of transcription factor (TF) binding or nucleosomal histone modifications (HMs). Despite the growing popularity of such approaches, a comparative review of the various modelling algorithms and feature extraction methods is lacking. We define and compare three methods of quantifying pairwise gene-TF/HM interactions and discuss their suitability for integrating the heterogeneous chromatin immunoprecipitation (ChIP)-seq binding patterns exhibited by TFs and HMs. We then construct log-linear and ϵ-support vector regression models from various mouse embryonic stem cell (mESC) and human lymphoblastoid (GM12878) data sets, considering both ChIP-seq- and position weight matrix- (PWM)-derived in silico TF-binding. The two algorithms are evaluated both in terms of their modelling prediction accuracy and ability to identify the established regulatory roles of individual TFs and HMs. Our results demonstrate that TF-binding and HMs are highly predictive of gene expression as measured by mRNA transcript abundance, irrespective of algorithm or cell type selection and considering both ChIP-seq and PWM-derived TF-binding. As we encourage other researchers to explore and develop these results, our framework is implemented using open-source software and made available as a preconfigured bootable virtual environment. © The Author 2014. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  7. Transcriptional mapping of rabies virus in vivo

    International Nuclear Information System (INIS)

    Flamand, A.; Delagneau, J.F.

    1978-01-01

    Synthesis of the proteins of rabies virus was studied in hamster cell infected with uv-irradiated virus. The uv target size of genes L, N, M 1 , and M 2 was measured during primary transcription. Except for N, the target size of the remaining genes was considerably larger than that of their physical sizes. The data fit the hypothesis that four genes occupy a single transcriptional unit and that transcription of rabies virus proceeds in the order N, M 1 , M 2 , and L

  8. CHD chromatin remodelers and the transcription cycle

    Science.gov (United States)

    Murawska, Magdalena

    2011-01-01

    It is well established that ATP-dependent chromatin remodelers modulate DNA access of transcription factors and RNA polymerases by “opening” or “closing” chromatin structure. However, this view is far too simplistic. Recent findings have demonstrated that these enzymes not only set the stage for the transcription machinery to act but also are actively involved at every step of the transcription process. As a consequence, they affect initiation, elongation, termination and RNA processing. In this review we will use the CHD family as a paradigm to illustrate the progress that has been made in revealing these new concepts. PMID:22223048

  9. NAC transcription factors: structurally distinct, functionally diverse

    DEFF Research Database (Denmark)

    Olsen, Addie Nina; Ernst, Heidi A; Leggio, Leila Lo

    2005-01-01

    level and localization, and to the first indications of NAC participation in transcription factor networks. The recent determination of the DNA and protein binding NAC domain structure offers insight into the molecular functions of the protein family. Research into NAC transcription factors has......NAC proteins constitute one of the largest families of plant-specific transcription factors, and the family is present in a wide range of land plants. Here, we summarize the biological and molecular functions of the NAC family, paying particular attention to the intricate regulation of NAC protein...

  10. Temporal aspects of copper homeostasis and its crosstalk with hormones

    Directory of Open Access Journals (Sweden)

    Lola ePeñarrubia

    2015-04-01

    Full Text Available To cope with the dual nature of copper as being essential and toxic for cells, plants temporarily adapt the expression of copper homeostasis components to assure its delivery to cuproproteins while avoiding the interference of potential oxidative damage derived from both copper uptake and photosynthetic reactions during light hours. The circadian clock participates in the temporal organization of coordination of plant nutrition adapting metabolic responses to the daily oscillations. This timely control improves plant fitness and reproduction and holds biotechnological potential to drive increased crop yields. Hormonal pathways, including those of abscisic acid, gibberellins, ethylene, auxins, and jasmonates are also under direct clock and light control, both in mono and dicotyledons. In this review, we focus on copper transport in Arabidopsis thaliana and Oryza sativa and the presumable role of hormones in metal homeostasis matching nutrient availability to growth requirements and preventing metal toxicity. The presence of putative hormone-dependent regulatory elements in the promoters of copper transporters genes suggests hormonal regulation to match special copper requirements during plant development. Spatial and temporal processes that can be affected by hormones include the regulation of copper uptake into roots, intracellular trafficking and compartmentalisation, and long-distance transport to developing vegetative and reproductive tissues. In turn, hormone biosynthesis and signalling are also influenced by copper availability, which suggests reciprocal regulation subjected to temporal control by the central oscillator of the circadian clock. This transcriptional regulatory network, coordinates environmental and hormonal signalling with developmental pathways to allow enhanced micronutrient acquisition efficiency.

  11. The Temporal Dynamics of Arc Expression Regulate Cognitive Flexibility.

    Science.gov (United States)

    Wall, Mark J; Collins, Dawn R; Chery, Samantha L; Allen, Zachary D; Pastuzyn, Elissa D; George, Arlene J; Nikolova, Viktoriya D; Moy, Sheryl S; Philpot, Benjamin D; Shepherd, Jason D; Müller, Jürgen; Ehlers, Michael D; Mabb, Angela M; Corrêa, Sonia A L

    2018-05-24

    Neuronal activity regulates the transcription and translation of the immediate-early gene Arc/Arg3.1, a key mediator of synaptic plasticity. Proteasome-dependent degradation of Arc tightly limits its temporal expression, yet the significance of this regulation remains unknown. We disrupted the temporal control of Arc degradation by creating an Arc knockin mouse (ArcKR) where the predominant Arc ubiquitination sites were mutated. ArcKR mice had intact spatial learning but showed specific deficits in selecting an optimal strategy during reversal learning. This cognitive inflexibility was coupled to changes in Arc mRNA and protein expression resulting in a reduced threshold to induce mGluR-LTD and enhanced mGluR-LTD amplitude. These findings show that the abnormal persistence of Arc protein limits the dynamic range of Arc signaling pathways specifically during reversal learning. Our work illuminates how the precise temporal control of activity-dependent molecules, such as Arc, regulates synaptic plasticity and is crucial for cognition. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  12. Osteoradionecrosis of the temporal bone

    International Nuclear Information System (INIS)

    Fujimori, Masato; Koyama, Yukiko; Enomoto, Fuyuki; Ichikawa, Ginichiro

    2002-01-01

    We report a case of temporal bone necrosis that emerged after radiotherapy for epipharyngeal carcinoma performed 13 years ago. The patient was a 51-year-old male. His major complaint was left facial swelling. The patient underwent chemotherapy and radiotherapy (Co 60, 6120 rad), as the treatment of that period, for epipharyngeal carcinoma from September 30, 1986 to January 31, 1987. He also underwent lobectomy of the left temporal lobe in brain surgery for left temporal lobe necrosis in August, 1989. After that operation, we saw constriction in his left external acoustic meatus and continued the follow-up. On October 22, 1999 he felt a left facial swelling. We found skin defects and ulcer formation in the front part of his left ear. Although we administered an antiseptic and antibiotic to the diseased area, his condition did not improve. He was hospitalized for the purpose of undergoing medical treatment on January 6, 2000. We found extensive skin necrosis and defects in his left auricular area. The corrupted temporal bone reached the zygomatic, the bone department external acoustic meatus and the mastoid process was exposing. We performed debridement of the diseased area on January 19, 2000. On February 23, we performed reconstruction by left trapezius muscle flap after debridement once again. One year after the operation, the flap was completely incorporated. (author)

  13. Temporal structures in shell models

    DEFF Research Database (Denmark)

    Okkels, F.

    2001-01-01

    The intermittent dynamics of the turbulent Gledzer, Ohkitani, and Yamada shell-model is completely characterized by a single type of burstlike structure, which moves through the shells like a front. This temporal structure is described by the dynamics of the instantaneous configuration of the shell...

  14. Temporal form in interaction design

    DEFF Research Database (Denmark)

    Vallgårda, Anna; Winther, Morten Trøstrup; Mørch, Nina

    2015-01-01

    temporal forms by letting a series of expert designers reflect upon them. We borrow a framework from Boorstin’s film theory in which he distinguishes between the voyeuristic, the vicarious, and the visceral experience. We show how to use rhythms, complexity, gentle or forceful behavior, etc., to create...

  15. Temporal factors in resource dilemmas

    NARCIS (Netherlands)

    Hendrickx, L; Poortinga, W; van der Kooij, R

    The conflict between present and future consumption lies at the heart of resource dilemmas (RDs), yet the role of time has received little attention in this research area. Emphasis was on factors related to the social rather than the temporal conflict inherent in an RD. We propose a model that deals

  16. Temporal scaling in information propagation

    Science.gov (United States)

    Huang, Junming; Li, Chao; Wang, Wen-Qiang; Shen, Hua-Wei; Li, Guojie; Cheng, Xue-Qi

    2014-06-01

    For the study of information propagation, one fundamental problem is uncovering universal laws governing the dynamics of information propagation. This problem, from the microscopic perspective, is formulated as estimating the propagation probability that a piece of information propagates from one individual to another. Such a propagation probability generally depends on two major classes of factors: the intrinsic attractiveness of information and the interactions between individuals. Despite the fact that the temporal effect of attractiveness is widely studied, temporal laws underlying individual interactions remain unclear, causing inaccurate prediction of information propagation on evolving social networks. In this report, we empirically study the dynamics of information propagation, using the dataset from a population-scale social media website. We discover a temporal scaling in information propagation: the probability a message propagates between two individuals decays with the length of time latency since their latest interaction, obeying a power-law rule. Leveraging the scaling law, we further propose a temporal model to estimate future propagation probabilities between individuals, reducing the error rate of information propagation prediction from 6.7% to 2.6% and improving viral marketing with 9.7% incremental customers.

  17. Osteoradionecrosis of the temporal bone

    Energy Technology Data Exchange (ETDEWEB)

    Fujimori, Masato; Koyama, Yukiko; Enomoto, Fuyuki; Ichikawa, Ginichiro [Juntendo Univ., Tokyo (Japan). School of Medicine

    2002-08-01

    We report a case of temporal bone necrosis that emerged after radiotherapy for epipharyngeal carcinoma performed 13 years ago. The patient was a 51-year-old male. His major complaint was left facial swelling. The patient underwent chemotherapy and radiotherapy (Co 60, 6120 rad), as the treatment of that period, for epipharyngeal carcinoma from September 30, 1986 to January 31, 1987. He also underwent lobectomy of the left temporal lobe in brain surgery for left temporal lobe necrosis in August, 1989. After that operation, we saw constriction in his left external acoustic meatus and continued the follow-up. On October 22, 1999 he felt a left facial swelling. We found skin defects and ulcer formation in the front part of his left ear. Although we administered an antiseptic and antibiotic to the diseased area, his condition did not improve. He was hospitalized for the purpose of undergoing medical treatment on January 6, 2000. We found extensive skin necrosis and defects in his left auricular area. The corrupted temporal bone reached the zygomatic, the bone department external acoustic meatus and the mastoid process was exposing. We performed debridement of the diseased area on January 19, 2000. On February 23, we performed reconstruction by left trapezius muscle flap after debridement once again. One year after the operation, the flap was completely incorporated. (author)

  18. Transition constraints for temporal attributes

    CSIR Research Space (South Africa)

    Ongoma, EAN

    2014-07-01

    Full Text Available Representing temporal data in conceptual data models and ontologies is required by various application domains. For it to be useful for modellers to represent the information precisely and reason over it, it is essential to have a language...

  19. Role of the GRAS transcription factor ATA/RAM1 in the transcriptional reprogramming of arbuscular mycorrhiza in Petunia hybrida.

    Science.gov (United States)

    Rich, Mélanie K; Courty, Pierre-Emmanuel; Roux, Christophe; Reinhardt, Didier

    2017-08-08

    Development of arbuscular mycorrhiza (AM) requires a fundamental reprogramming of root cells for symbiosis. This involves the induction of hundreds of genes in the host. A recently identified GRAS-type transcription factor in Petunia hybrida, ATA/RAM1, is required for the induction of host genes during AM, and for morphogenesis of the fungal endosymbiont. To better understand the role of RAM1 in symbiosis, we set out to identify all genes that depend on activation by RAM1 in mycorrhizal roots. We have carried out a transcript profiling experiment by RNAseq of mycorrhizal plants vs. non-mycorrhizal controls in wild type and ram1 mutants. The results show that the expression of early genes required for AM, such as the strigolactone biosynthetic genes and the common symbiosis signalling genes, is independent of RAM1. In contrast, genes that are involved at later stages of symbiosis, for example for nutrient exchange in cortex cells, require RAM1 for induction. RAM1 itself is highly induced in mycorrhizal roots together with many other transcription factors, in particular GRAS proteins. Since RAM1 has previously been shown to be directly activated by the common symbiosis signalling pathway through CYCLOPS, we conclude that it acts as an early transcriptional switch that induces many AM-related genes, among them genes that are essential for the development of arbuscules, such as STR, STR2, RAM2, and PT4, besides hundreds of additional RAM1-dependent genes the role of which in symbiosis remains to be explored. Taken together, these results indicate that the defect in the morphogenesis of the fungal arbuscules in ram1 mutants may be an indirect consequence of functional defects in the host, which interfere with nutrient exchange and possibly other functions on which the fungus depends.

  20. In silico and wet lab approaches to study transcriptional regulation

    NARCIS (Netherlands)

    Hestand, Matthew Scott

    2010-01-01

    Gene expression is a complicated process with multiple types of regulation, including binding of proteins termed transcription factors. This thesis looks at transcription factors and transcription factor binding site discovery through computational predictions and wet lab work to better elucidate

  1. Temporal motifs in time-dependent networks

    International Nuclear Information System (INIS)

    Kovanen, Lauri; Karsai, Márton; Kaski, Kimmo; Kertész, János; Saramäki, Jari

    2011-01-01

    Temporal networks are commonly used to represent systems where connections between elements are active only for restricted periods of time, such as telecommunication, neural signal processing, biochemical reaction and human social interaction networks. We introduce the framework of temporal motifs to study the mesoscale topological–temporal structure of temporal networks in which the events of nodes do not overlap in time. Temporal motifs are classes of similar event sequences, where the similarity refers not only to topology but also to the temporal order of the events. We provide a mapping from event sequences to coloured directed graphs that enables an efficient algorithm for identifying temporal motifs. We discuss some aspects of temporal motifs, including causality and null models, and present basic statistics of temporal motifs in a large mobile call network

  2. Comparison of Transcription Factor Binding Site Models

    KAUST Repository

    Bhuyan, Sharifulislam

    2012-05-01

    Modeling of transcription factor binding sites (TFBSs) and TFBS prediction on genomic sequences are important steps to elucidate transcription regulatory mechanism. Dependency of transcription regulation on a great number of factors such as chemical specificity, molecular structure, genomic and epigenetic characteristics, long distance interaction, makes this a challenging problem. Different experimental procedures generate evidence that DNA-binding domains of transcription factors show considerable DNA sequence specificity. Probabilistic modeling of TFBSs has been moderately successful in identifying patterns from a family of sequences. In this study, we compare performances of different probabilistic models and try to estimate their efficacy over experimental TFBSs data. We build a pipeline to calculate sensitivity and specificity from aligned TFBS sequences for several probabilistic models, such as Markov chains, hidden Markov models, Bayesian networks. Our work, containing relevant statistics and evaluation for the models, can help researchers to choose the most appropriate model for the problem at hand.

  3. Battles and hijacks: Noncoding transcription in plants

    KAUST Repository

    Ariel, Federico; Romero-Barrios, Natali; Jé gu, Teddy; Benhamed, Moussa; Crespi, Martin

    2015-01-01

    splicing, fine-tuning of miRNA activity, and the control of mRNA translation or accumulation. Recently, dual noncoding transcription by alternative RNA polymerases was implicated in epigenetic and chromatin conformation dynamics. This review integrates

  4. Salmonella Typhimurium transcription profiles in space flight

    Data.gov (United States)

    National Aeronautics and Space Administration — Salmonella transcription profiles were obtained from samples flown on space shuttle mission STS-115 and compared to profiles from Salmonella grown under identical...

  5. Transcript for Understanding Medical Words: A Tutorial

    Science.gov (United States)

    ... medlineplus.gov/medicalwordstranscript.html Transcript for Understanding Medical Words: A Tutorial To use the sharing features on ... get to what those mean in a minute. Word Roots Word Roots. Let's begin with body parts. ...

  6. JAXA's Space Exploration Scenario

    Science.gov (United States)

    Sato, N. S.

    2018-04-01

    Japan Aerospace Exploration Agency (JAXA) has been studying space exploration scenario, including human exploration for Japan since 2015, which encompasses goals, knowledge gap assessment, and architecture. assessment, and technology roadmap.

  7. A unified architecture of transcriptional regulatory elements

    DEFF Research Database (Denmark)

    Andersson, Robin; Sandelin, Albin Gustav; Danko, Charles G.

    2015-01-01

    Gene expression is precisely controlled in time and space through the integration of signals that act at gene promoters and gene-distal enhancers. Classically, promoters and enhancers are considered separate classes of regulatory elements, often distinguished by histone modifications. However...... and enhancers are considered a single class of functional element, with a unified architecture for transcription initiation. The context of interacting regulatory elements and the surrounding sequences determine local transcriptional output as well as the enhancer and promoter activities of individual elements....

  8. Transcriptional Waves in the Yeast Cell Cycle

    OpenAIRE

    Oliva, Anna; Rosebrock, Adam; Ferrezuelo, Francisco; Pyne, Saumyadipta; Chen, Haiying; Skiena, Steve; Futcher, Bruce; Leatherwood, Janet

    2005-01-01

    Many genes are regulated as an innate part of the eukaryotic cell cycle, and a complex transcriptional network helps enable the cyclic behavior of dividing cells. This transcriptional network has been studied in Saccharomyces cerevisiae (budding yeast) and elsewhere. To provide more perspective on these regulatory mechanisms, we have used microarrays to measure gene expression through the cell cycle of Schizosaccharomyces pombe (fission yeast). The 750 genes with the most significant oscillat...

  9. Linking Core Promoter Classes to Circadian Transcription.

    Directory of Open Access Journals (Sweden)

    Pål O Westermark

    2016-08-01

    Full Text Available Circadian rhythms in transcription are generated by rhythmic abundances and DNA binding activities of transcription factors. Propagation of rhythms to transcriptional initiation involves the core promoter, its chromatin state, and the basal transcription machinery. Here, I characterize core promoters and chromatin states of genes transcribed in a circadian manner in mouse liver and in Drosophila. It is shown that the core promoter is a critical determinant of circadian mRNA expression in both species. A distinct core promoter class, strong circadian promoters (SCPs, is identified in mouse liver but not Drosophila. SCPs are defined by specific core promoter features, and are shown to drive circadian transcriptional activities with both high averages and high amplitudes. Data analysis and mathematical modeling further provided evidence for rhythmic regulation of both polymerase II recruitment and pause release at SCPs. The analysis provides a comprehensive and systematic view of core promoters and their link to circadian mRNA expression in mouse and Drosophila, and thus reveals a crucial role for the core promoter in regulated, dynamic transcription.

  10. TAF(II)250: a transcription toolbox.

    Science.gov (United States)

    Wassarman, D A; Sauer, F

    2001-08-01

    Activation of RNA-polymerase-II-dependent transcription involves conversion of signals provided by gene-specific activator proteins into the synthesis of messenger RNA. This conversion requires dynamic structural changes in chromatin and assembly of general transcription factors (GTFs) and RNA polymerase II at core promoter sequence elements surrounding the transcription start site of genes. One hallmark of transcriptional activation is the interaction of DNA-bound activators with coactivators such as the TATA-box binding protein (TBP)-associated factors (TAF(II)s) within the GTF TFIID. TAF(II)250 possesses a variety of activities that are likely to contribute to the initial steps of RNA polymerase II transcription. TAF(II)250 is a scaffold for assembly of other TAF(II)s and TBP into TFIID, TAF(II)250 binds activators to recruit TFIID to particular promoters, TAF(II)250 regulates binding of TBP to DNA, TAF(II)250 binds core promoter initiator elements, TAF(II)250 binds acetylated lysine residues in core histones, and TAF(II)250 possesses protein kinase, ubiquitin-activating/conjugating and acetylase activities that modify histones and GTFs. We speculate that these activities achieve two goals--(1) they aid in positioning and stabilizing TFIID at particular promoters, and (2) they alter chromatin structure at the promoter to allow assembly of GTFs--and we propose a model for how TAF(II)250 converts activation signals into active transcription.

  11. Intrinsic terminators in Mycoplasma hyopneumoniae transcription.

    Science.gov (United States)

    Fritsch, Tiago Ebert; Siqueira, Franciele Maboni; Schrank, Irene Silveira

    2015-04-08

    Mycoplasma hyopneumoniae, an important pathogen of swine, exhibits a low guanine and cytosine (GC) content genome. M. hyopneumoniae genome is organised in long transcriptional units and promoter sequences have been mapped upstream of all transcription units. These analysis provided insights into the gene organisation and transcription initiation at the genome scale. However, the presence of transcriptional terminator sequences in the M. hyopneumoniae genome is poorly understood. In silico analyses demonstrated the presence of putative terminators in 82% of the 33 monocistronic units (mCs) and in 74% of the 116 polycistronic units (pCs) considering different classes of terminators. The functional activity of 23 intrinsic terminators was confirmed by RT-PCR and qPCR. Analysis of all terminators found by three software algorithms, combined with experimental results, allowed us to propose a pattern of RNA hairpin formation during the termination process and to predict the location of terminators in the M. hyopneumoniae genome sequence. The stem-loop structures of intrinsic terminators of mycoplasma diverge from the pattern of terminators found in other bacteria due the low content of guanine and cytosine. In M. hyopneumoniae, transcription can end after a transcriptional unit and before its terminator sequence and can also continue past the terminator sequence with RNA polymerases gradually releasing the RNA.

  12. MADS-box gene evolution - structure and transcription patterns

    DEFF Research Database (Denmark)

    Johansen, Bo; Pedersen, Louise Buchholt; Skipper, Martin

    2002-01-01

    Mads-box genes, ABC model, Evolution, Phylogeny, Transcription patterns, Gene structure, Conserved motifs......Mads-box genes, ABC model, Evolution, Phylogeny, Transcription patterns, Gene structure, Conserved motifs...

  13. Targeted HIV-1 Latency Reversal Using CRISPR/Cas9-Derived Transcriptional Activator Systems.

    Directory of Open Access Journals (Sweden)

    Julia K Bialek

    Full Text Available CRISPR/Cas9 technology is currently considered the most advanced tool for targeted genome engineering. Its sequence-dependent specificity has been explored for locus-directed transcriptional modulation. Such modulation, in particular transcriptional activation, has been proposed as key approach to overcome silencing of dormant HIV provirus in latently infected cellular reservoirs. Currently available agents for provirus activation, so-called latency reversing agents (LRAs, act indirectly through cellular pathways to induce viral transcription. However, their clinical performance remains suboptimal, possibly because reservoirs have diverse cellular identities and/or proviral DNA is intractable to the induced pathways. We have explored two CRISPR/Cas9-derived activator systems as targeted approaches to induce dormant HIV-1 proviral DNA. These systems recruit multiple transcriptional activation domains to the HIV 5' long terminal repeat (LTR, for which we have identified an optimal target region within the LTR U3 sequence. Using this target region, we demonstrate transcriptional activation of proviral genomes via the synergistic activation mediator complex in various in culture model systems for HIV latency. Observed levels of induction are comparable or indeed higher than treatment with established LRAs. Importantly, activation is complete, leading to production of infective viral particles. Our data demonstrate that CRISPR/Cas9-derived technologies can be applied to counteract HIV latency and may therefore represent promising novel approaches in the quest for HIV elimination.

  14. Molecular phylogenetic and expression analysis of the complete WRKY transcription factor family in maize.

    Science.gov (United States)

    Wei, Kai-Fa; Chen, Juan; Chen, Yan-Feng; Wu, Ling-Juan; Xie, Dao-Xin

    2012-04-01

    The WRKY transcription factors function in plant growth and development, and response to the biotic and abiotic stresses. Although many studies have focused on the functional identification of the WRKY transcription factors, much less is known about molecular phylogenetic and global expression analysis of the complete WRKY family in maize. In this study, we identified 136 WRKY proteins coded by 119 genes in the B73 inbred line from the complete genome and named them in an orderly manner. Then, a comprehensive phylogenetic analysis of five species was performed to explore the origin and evolutionary patterns of these WRKY genes, and the result showed that gene duplication is the major driving force for the origin of new groups and subgroups and functional divergence during evolution. Chromosomal location analysis of maize WRKY genes indicated that 20 gene clusters are distributed unevenly in the genome. Microarray-based expression analysis has revealed that 131 WRKY transcripts encoded by 116 genes may participate in the regulation of maize growth and development. Among them, 102 transcripts are stably expressed with a coefficient of variation (CV) value of WRKY genes with the CV value of >15% are further analysed to discover new organ- or tissue-specific genes. In addition, microarray analyses of transcriptional responses to drought stress and fungal infection showed that maize WRKY proteins are involved in stress responses. All these results contribute to a deep probing into the roles of WRKY transcription factors in maize growth and development and stress tolerance.

  15. Dynamic analysis of stochastic transcription cycles.

    Directory of Open Access Journals (Sweden)

    Claire V Harper

    2011-04-01

    Full Text Available In individual mammalian cells the expression of some genes such as prolactin is highly variable over time and has been suggested to occur in stochastic pulses. To investigate the origins of this behavior and to understand its functional relevance, we quantitatively analyzed this variability using new mathematical tools that allowed us to reconstruct dynamic transcription rates of different reporter genes controlled by identical promoters in the same living cell. Quantitative microscopic analysis of two reporter genes, firefly luciferase and destabilized EGFP, was used to analyze the dynamics of prolactin promoter-directed gene expression in living individual clonal and primary pituitary cells over periods of up to 25 h. We quantified the time-dependence and cyclicity of the transcription pulses and estimated the length and variation of active and inactive transcription phases. We showed an average cycle period of approximately 11 h and demonstrated that while the measured time distribution of active phases agreed with commonly accepted models of transcription, the inactive phases were differently distributed and showed strong memory, with a refractory period of transcriptional inactivation close to 3 h. Cycles in transcription occurred at two distinct prolactin-promoter controlled reporter genes in the same individual clonal or primary cells. However, the timing of the cycles was independent and out-of-phase. For the first time, we have analyzed transcription dynamics from two equivalent loci in real-time in single cells. In unstimulated conditions, cells showed independent transcription dynamics at each locus. A key result from these analyses was the evidence for a minimum refractory period in the inactive-phase of transcription. The response to acute signals and the result of manipulation of histone acetylation was consistent with the hypothesis that this refractory period corresponded to a phase of chromatin remodeling which significantly

  16. Sounding rockets explore the ionosphere

    International Nuclear Information System (INIS)

    Mendillo, M.

    1990-01-01

    It is suggested that small, expendable, solid-fuel rockets used to explore ionospheric plasma can offer insight into all the processes and complexities common to space plasma. NASA's sounding rocket program for ionospheric research focuses on the flight of instruments to measure parameters governing the natural state of the ionosphere. Parameters include input functions, such as photons, particles, and composition of the neutral atmosphere; resultant structures, such as electron and ion densities, temperatures and drifts; and emerging signals such as photons and electric and magnetic fields. Systematic study of the aurora is also conducted by these rockets, allowing sampling at relatively high spatial and temporal rates as well as investigation of parameters, such as energetic particle fluxes, not accessible to ground based systems. Recent active experiments in the ionosphere are discussed, and future sounding rocket missions are cited

  17. Temporal Regulation of fim Genes in Uropathogenic Escherichia coli during Infection of the Murine Urinary Tract

    Directory of Open Access Journals (Sweden)

    William R. Schwan

    2017-01-01

    Full Text Available Uropathogenic Escherichia coli (UPEC adhere to cells in the human urinary tract via type 1 pili that undergo phase variation where a 314-bp fimS DNA element flips between Phase-ON and Phase-OFF orientations through two site-specific recombinases, FimB and FimE. Three fim-lux operon transcriptional fusions were created and moved into the clinical UPEC isolate NU149 to determine their temporal regulation in UPEC growing in the urinary tract. Within murine urinary tracts, the UPEC strains demonstrated elevated transcription of fimA and fimB early in the infection, but lower transcription by the fifth day in murine kidneys. In contrast, fimE transcription was much lower than either fimA or fimB early, increased markedly at 24 h after inoculation, and then dropped five days after inoculation. Positioning of fimS was primarily in the Phase-ON position over the time span in UPEC infected bladders, whereas in UPEC infected murine kidneys the Phase-OFF orientation was favored by the fifth day after inoculation. Hemagglutination titers with guinea pig erythrocytes remained constant in UPEC growing in infected murine bladders but fell substantially in UPEC infected kidneys over time. Our results show temporal in vivo regulation of fim gene expression in different environmental niches when UPEC infects the murine urinary tract.

  18. Temporal context for authorship attribution

    DEFF Research Database (Denmark)

    Hansen, Niels Dalum; Lioma, Christina; Larsen, Birger

    2014-01-01

    A study of temporal aspects of authorship attribution - a task which aims to distinguish automatically between texts written by different authors by measuring textual features. This task is important in a number of areas, including plagiarism detection in secondary education, which we study...... world data from Danish secondary school students show 84% prediction accuracy when using all available material and 71.9% prediction accuracy when using only the five most recent writing samples from each student....

  19. Spatio-Temporal Data Construction

    Directory of Open Access Journals (Sweden)

    Hai Ha Le

    2013-08-01

    Full Text Available On the route to a spatio-temporal geoscience information system, an appropriate data model for geo-objects in space and time has been developed. In this model, geo-objects are represented as sequences of geometries and properties with continuous evolution in each time interval. Because geomodeling software systems usually model objects at specific time instances, we want to interpolate the geometry and properties from two models of an object with only geometrical constraints (no physical or mechanical constraints. This process is called spatio-temporal data construction or morphological interpolation of intermediate geometries. This paper is strictly related to shape morphing, shape deformation, cross-parameterization and compatible remeshing and is only concerned with geological surfaces. In this study, two main sub-solutions construct compatible meshes and find trajectories in which vertices of the mesh evolve. This research aims to find an algorithm to construct spatio-temporal data with some constraints from the geosciences, such as cutting surfaces by faulting or fracturing phenomena and evolving boundaries attached to other surfaces. Another goal of this research is the implementation of the algorithm in a software product, namely a gOcad plug-in. The four main procedures of the algorithm are cutting the surfaces, setting up constraints, partitioning and calculating the parameterizations and trajectories. The software has been tested to construct data for a salt dome and other surfaces in regard to the geological processes of faulting, deposition and erosion. The result of this research is an algorithm and software for the construction of spatio-temporal data.

  20. The Machinic Temporality of Metadata

    Directory of Open Access Journals (Sweden)

    Claudio Celis

    2015-03-01

    Full Text Available In 1990 Deleuze introduced the hypothesis that disciplinary societies are gradually being replaced by a new logic of power: control. Accordingly, Matteo Pasquinelli has recently argued that we are moving towards societies of metadata, which correspond to a new stage of what Deleuze called control societies. Societies of metadata are characterised for the central role that meta-information acquires both as a source of surplus value and as an apparatus of social control. The aim of this article is to develop Pasquinelli’s thesis by examining the temporal scope of these emerging societies of metadata. In particular, this article employs Guattari’s distinction between human and machinic times. Through these two concepts, this article attempts to show how societies of metadata combine the two poles of capitalist power formations as identified by Deleuze and Guattari, i.e. social subjection and machinic enslavement. It begins by presenting the notion of metadata in order to identify some of the defining traits of contemporary capitalism. It then examines Berardi’s account of the temporality of the attention economy from the perspective of the asymmetric relation between cyber-time and human time. The third section challenges Berardi’s definition of the temporality of the attention economy by using Guattari’s notions of human and machinic times. Parts four and five fall back upon Deleuze and Guattari’s notions of machinic surplus labour and machinic enslavement, respectively. The concluding section tries to show that machinic and human times constitute two poles of contemporary power formations that articulate the temporal dimension of societies of metadata.

  1. Temporal nonlocality in bistable perception

    Science.gov (United States)

    Atmanspacher, Harald; Filk, Thomas

    2012-12-01

    A novel conceptual framework for theoretical psychology is presented and illustrated for the example of bistable perception. A basic formal feature of this framework is the non-commutativity of operations acting on mental states. A corresponding model for the bistable perception of ambiguous stimuli, the Necker-Zeno model, is sketched and some empirical evidence for it so far is described. It is discussed how a temporal nonlocality of mental states, predicted by the model, can be understood and tested.

  2. Compressing spatio-temporal trajectories

    DEFF Research Database (Denmark)

    Gudmundsson, Joachim; Katajainen, Jyrki; Merrick, Damian

    2009-01-01

    such that the most common spatio-temporal queries can still be answered approximately after the compression has taken place. In the process, we develop an implementation of the Douglas–Peucker path-simplification algorithm which works efficiently even in the case where the polygonal path given as input is allowed...... to self-intersect. For a polygonal path of size n, the processing time is O(nlogkn) for k=2 or k=3 depending on the type of simplification....

  3. A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites

    KAUST Repository

    Kulakovskiy, Ivan V.; Belostotsky, A. A.; Kasianov, Artem S.; Esipova, Natalia G.; Medvedeva, Yulia; Eliseeva, Irina A.; Makeev, Vsevolod J.

    2011-01-01

    Motivation: Modern experimental methods provide substantial information on protein-DNA recognition. Studying arrangements of transcription factor binding sites (TFBSs) of interacting transcription factors (TFs) advances understanding

  4. Research on spatio-temporal database techniques for spatial information service

    Science.gov (United States)

    Zhao, Rong; Wang, Liang; Li, Yuxiang; Fan, Rongshuang; Liu, Ping; Li, Qingyuan

    2007-06-01

    Geographic data should be described by spatial, temporal and attribute components, but the spatio-temporal queries are difficult to be answered within current GIS. This paper describes research into the development and application of spatio-temporal data management system based upon GeoWindows GIS software platform which was developed by Chinese Academy of Surveying and Mapping (CASM). Faced the current and practical requirements of spatial information application, and based on existing GIS platform, one kind of spatio-temporal data model which integrates vector and grid data together was established firstly. Secondly, we solved out the key technique of building temporal data topology, successfully developed a suit of spatio-temporal database management system adopting object-oriented methods. The system provides the temporal data collection, data storage, data management and data display and query functions. Finally, as a case study, we explored the application of spatio-temporal data management system with the administrative region data of multi-history periods of China as the basic data. With all the efforts above, the GIS capacity of management and manipulation in aspect of time and attribute of GIS has been enhanced, and technical reference has been provided for the further development of temporal geographic information system (TGIS).

  5. Temporal ecology in the Anthropocene.

    Science.gov (United States)

    Wolkovich, E M; Cook, B I; McLauchlan, K K; Davies, T J

    2014-11-01

    Two fundamental axes - space and time - shape ecological systems. Over the last 30 years spatial ecology has developed as an integrative, multidisciplinary science that has improved our understanding of the ecological consequences of habitat fragmentation and loss. We argue that accelerating climate change - the effective manipulation of time by humans - has generated a current need to build an equivalent framework for temporal ecology. Climate change has at once pressed ecologists to understand and predict ecological dynamics in non-stationary environments, while also challenged fundamental assumptions of many concepts, models and approaches. However, similarities between space and time, especially related issues of scaling, provide an outline for improving ecological models and forecasting of temporal dynamics, while the unique attributes of time, particularly its emphasis on events and its singular direction, highlight where new approaches are needed. We emphasise how a renewed, interdisciplinary focus on time would coalesce related concepts, help develop new theories and methods and guide further data collection. The next challenge will be to unite predictive frameworks from spatial and temporal ecology to build robust forecasts of when and where environmental change will pose the largest threats to species and ecosystems, as well as identifying the best opportunities for conservation. © 2014 John Wiley & Sons Ltd/CNRS.

  6. Transcription Profiling of Bacillus subtilis Cells Infected with AR9, a Giant Phage Encoding Two Multisubunit RNA Polymerases.

    Science.gov (United States)

    Lavysh, Daria; Sokolova, Maria; Slashcheva, Marina; Förstner, Konrad U; Severinov, Konstantin

    2017-02-14

    Bacteriophage AR9 is a recently sequenced jumbo phage that encodes two multisubunit RNA polymerases. Here we investigated the AR9 transcription strategy and the effect of AR9 infection on the transcription of its host, Bacillus subtilis Analysis of whole-genome transcription revealed early, late, and continuously expressed AR9 genes. Alignment of sequences upstream of the 5' ends of AR9 transcripts revealed consensus sequences that define early and late phage promoters. Continuously expressed AR9 genes have both early and late promoters in front of them. Early AR9 transcription is independent of protein synthesis and must be determined by virion RNA polymerase injected together with viral DNA. During infection, the overall amount of host mRNAs is significantly decreased. Analysis of relative amounts of host transcripts revealed notable differences in the levels of some mRNAs. The physiological significance of up- or downregulation of host genes for AR9 phage infection remains to be established. AR9 infection is significantly affected by rifampin, an inhibitor of host RNA polymerase transcription. The effect is likely caused by the antibiotic-induced killing of host cells, while phage genome transcription is solely performed by viral RNA polymerases. IMPORTANCE Phages regulate the timing of the expression of their own genes to coordinate processes in the infected cell and maximize the release of viral progeny. Phages also alter the levels of host transcripts. Here we present the results of a temporal analysis of the host and viral transcriptomes of Bacillus subtilis infected with a giant phage, AR9. We identify viral promoters recognized by two virus-encoded RNA polymerases that are a unique feature of the phiKZ-related group of phages to which AR9 belongs. Our results set the stage for future analyses of highly unusual RNA polymerases encoded by AR9 and other phiKZ-related phages. Copyright © 2017 Lavysh et al.

  7. Temporal reasoning for decision support in medicine.

    Science.gov (United States)

    Augusto, Juan Carlos

    2005-01-01

    Handling time-related concepts is essential in medicine. During diagnosis it can make a substantial difference to know the temporal order in which some symptoms occurred or for how long they lasted. During prognosis the potential evolutions of a disease are conceived as a description of events unfolding in time. In therapy planning the different steps of treatment must be applied in a precise order, with a given frequency and for a certain span of time in order to be effective. This article offers a survey on the use of temporal reasoning for decision support-related tasks in medicine. Key publications of the area, mainly circumscribed to the latest two decades, are reviewed and classified according to three important stages of patient treatment requiring decision support: diagnosis, prognosis and therapy planning/management. Other complementary publications, like those on time-centered information storage and retrieval, are also considered as they provide valuable support to the above mentioned three stages. Key areas are highlighted and used to organize the latest contributions. The survey of previous research is followed by an analysis of what can still be improved and what is needed to make the next generation of decision support systems for medicine more effective. It can be observed that although the area has been considerably developed, there are still areas where more research is needed to make time-based systems of widespread use in decision support-related areas of medicine. Several suggestions for further exploration are proposed as a result of the survey.

  8. Evolving temporal association rules with genetic algorithms

    OpenAIRE

    Matthews, Stephen G.; Gongora, Mario A.; Hopgood, Adrian A.

    2010-01-01

    A novel framework for mining temporal association rules by discovering itemsets with a genetic algorithm is introduced. Metaheuristics have been applied to association rule mining, we show the efficacy of extending this to another variant - temporal association rule mining. Our framework is an enhancement to existing temporal association rule mining methods as it employs a genetic algorithm to simultaneously search the rule space and temporal space. A methodology for validating the ability of...

  9. Brain SPECT imaging in temporal lobe epilepsy

    International Nuclear Information System (INIS)

    Krausz, Y.; Yaffe, S.; Atlan, H.; Cohen, D.; Konstantini, S.; Meiner, Z.

    1991-01-01

    Temporal lobe epilepsy is diagnosed by clinical symptoms and signs and by localization of an epileptogenic focus. A brain SPECT study of two patients with temporal lobe epilepsy, using 99m Tc-HMPAO, was used to demonstrate a perfusion abnormality in the temporal lobe, while brain CT and MRI were non-contributory. The electroencephalogram, though abnormal, did not localize the diseased area. The potential role of the SPECT study in diagnosis and localization of temporal lobe epilepsy is discussed. (orig.)

  10. Convergent Transcription in the Butyrolactone Regulon in Streptomyces coelicolor Confers a Bistable Genetic Switch for Antibiotic Biosynthesis

    Science.gov (United States)

    Chatterjee, Anushree; Drews, Laurie; Mehra, Sarika; Takano, Eriko; Kaznessis, Yiannis N.; Hu, Wei-Shou

    2011-01-01

    cis-encoded antisense RNAs (cis asRNA) have been reported to participate in gene expression regulation in both eukaryotic and prokaryotic organisms. Its presence in Streptomyces coelicolor has also been reported recently; however, its role has yet to be fully investigated. Using mathematical modeling we explore the role of cis asRNA produced as a result of convergent transcription in scbA-scbR genetic switch. scbA and scbR gene pair, encoding repressor–amplifier proteins respectively, mediates the synthesis of a signaling molecule, the γ-butyrolactone SCB1 and controls the onset of antibiotic production. Our model considers that transcriptional interference caused by convergent transcription of two opposing RNA polymerases results in fatal collision and transcriptional termination, which suppresses transcription efficiency. Additionally, convergent transcription causes sense and antisense interactions between complementary sequences from opposing strands, rendering the full length transcript inaccessible for translation. We evaluated the role of transcriptional interference and the antisense effect conferred by convergent transcription on the behavior of scbA-scbR system. Stability analysis showed that while transcriptional interference affects the system, it is asRNA that confers scbA-scbR system the characteristics of a bistable switch in response to the signaling molecule SCB1. With its critical role of regulating the onset of antibiotic synthesis the bistable behavior offers this two gene system the needed robustness to be a genetic switch. The convergent two gene system with potential of transcriptional interference is a frequent feature in various genomes. The possibility of asRNA regulation in other such gene-pairs is yet to be examined. PMID:21765930

  11. A novel mode for transcription inhibition mediated by PNA-induced R-loops with a model in vitro system.

    Science.gov (United States)

    D'Souza, Alicia D; Belotserkovskii, Boris P; Hanawalt, Philip C

    2018-02-01

    The selective inhibition of transcription of a chosen gene by an artificial agent has numerous applications. Usually, these agents are designed to bind a specific nucleotide sequence in the promoter or within the transcribed region of the chosen gene. However, since optimal binding sites might not exist within the gene, it is of interest to explore the possibility of transcription inhibition when the agent is designed to bind at other locations. One of these possibilities arises when an additional transcription initiation site (e.g. secondary promoter) is present upstream from the primary promoter of the target gene. In this case, transcription inhibition might be achieved by inducing the formation of an RNA-DNA hybrid (R-loop) upon transcription from the secondary promoter. The R-loop could extend into the region of the primary promoter, to interfere with promoter recognition by RNA polymerase and thereby inhibit transcription. As a sequence-specific R-loop-inducing agent, a peptide nucleic acid (PNA) could be designed to facilitate R-loop formation by sequestering the non-template DNA strand. To investigate this mode for transcription inhibition, we have employed a model system in which a PNA binding site is localized between the T3 and T7 phage RNA polymerase promoters, which respectively assume the roles of primary and secondary promoters. In accord with our model, we have demonstrated that with PNA-bound DNA substrates, transcription from the T7 promoter reduces transcription from the T3 promoter by 30-fold, while in the absence of PNA binding there is no significant effect of T7 transcription upon T3 transcription. Copyright © 2018 Elsevier B.V. All rights reserved.

  12. Host transcription factors in the immediate pro-inflammatory response to the parasitic mite Psoroptes ovis.

    Directory of Open Access Journals (Sweden)

    Stewart T G Burgess

    Full Text Available BACKGROUND: Sheep scab, caused by infestation with the ectoparasitic mite Psoroptes ovis, results in the rapid development of cutaneous inflammation and leads to the crusted skin lesions characteristic of the disease. We described previously the global host transcriptional response to infestation with P. ovis, elucidating elements of the inflammatory processes which lead to the development of a rapid and profound immune response. However, the mechanisms by which this response is instigated remain unclear. To identify novel methods of intervention a better understanding of the early events involved in triggering the immune response is essential. The objective of this study was to gain a clearer understanding of the mechanisms and signaling pathways involved in the instigation of the immediate pro-inflammatory response. RESULTS: Through a combination of transcription factor binding site enrichment and pathway analysis we identified key roles for a number of transcription factors in the instigation of cutaneous inflammation. In particular, defined roles were elucidated for the transcription factors NF-kB and AP-1 in the orchestration of the early pro-inflammatory response, with these factors being implicated in the activation of a suite of inflammatory mediators. CONCLUSIONS: Interrogation of the host temporal response to P. ovis infestation has enabled the further identification of the mechanisms underlying the development of the immediate host pro-inflammatory response. This response involves key regulatory roles for the transcription factors NF-kB and AP-1. Pathway analysis demonstrated that the activation of these transcription factors may be triggered following a host LPS-type response, potentially involving TLR4-signalling and also lead to the intriguing possibility that this could be triggered by a P. ovis allergen.

  13. Constructing catalogue of temporal situations

    Directory of Open Access Journals (Sweden)

    Violetta Koseska-Toszewa

    2015-11-01

    Full Text Available Constructing catalogue of temporal situations The paper is aiming to create a common basis for description, comparing, and analysis natural languages. As a subject of comparison we have chosen temporal structures of some languages. For such a choice there exists a perfect tool, describing basic temporal phenomena, namely an ordering of states and events in time, certainty and uncertainty, independency of histories of separate objects, necessity and possibility. This tool is supported by the Petri nets formalism, which seems to be well suited for expressing the above mentioned phenomena. Petri nets are built form three primitive notions: of states, of events that begin or end the states, and so-called flow relation indicating succession of states and events. This simple constituents give rise to many possibilities of representing temporal phenomena; it turns out that such representations are sufficient for many (clearly, not necessarily all temporal situations appearing in natural languages. In description formalisms used till now there is no possibility of expressing such reality phenomena as temporal dependencies in compound statement, or combination of temporality and modality. Moreover, using these formalisms one cannot distinguish between two different sources of uncertainty of the speaker while describing the reality: one, due to the lack of knowledge of the speaker what is going on in outside world, the second, due to objective impossibility of foreseen ways in which some conflict situations will be (or already have been resolved. Petri net formalism seems to be perfectly suited for such differentiations. There are two main description principles that encompassed this paper. First, that assigns meaning to names of grammatical structures in different languages may lead to misunderstanding. Two grammatical structures with apparently close names may describe different reality. Additionally, some grammatical terms used in one language may be

  14. Recent behavioral history modifies coupling between cell activity and Arc gene transcription in hippocampal CA1 neurons.

    Science.gov (United States)

    Guzowski, John F; Miyashita, Teiko; Chawla, Monica K; Sanderson, Jennifer; Maes, Levi I; Houston, Frank P; Lipa, Peter; McNaughton, Bruce L; Worley, Paul F; Barnes, Carol A

    2006-01-24

    The ability of neurons to alter their transcriptional programs in response to synaptic input is of fundamental importance to the neuroplastic mechanisms underlying learning and memory. Because of technical limitations of conventional gene detection methods, the current view of activity-dependent neural transcription derives from experiments in which neurons are assumed quiescent until a signaling stimulus is given. The present study was designed to move beyond this static model by examining how earlier episodes of neural activity influence transcription of the immediate-early gene Arc. Using a sensitive FISH method that detects primary transcript at genomic alleles, the proportion of hippocampal CA1 neurons that activate transcription of Arc RNA was constant at approximately 40% in response to both a single novel exploration session and daily sessions repeated over 9 days. This proportion is similar to the percentage of active neurons defined electrophysiologically. However, this close correspondence was disrupted in rats exposed briefly, but repeatedly, to the same environment within a single day. Arc transcription in CA1 neurons declined dramatically after as few as four 5-min sessions, despite stable electrophysiological activity during all sessions. Additional experiments indicate that the decrement in Arc transcription occurred at the cellular, rather than synaptic level, and was not simply linked to habituation to novelty. Thus, the neural genomic response is governed by recent, but not remote, cell firing history in the behaving animal. This state-dependence of neuronal transcriptional coupling provides a mechanism of metaplasticity and may regulate capacity for synaptic modification in neural networks.

  15. Epilepsia temporal: relato de caso = Temporal epilepsy: case report

    Directory of Open Access Journals (Sweden)

    Souza, Taís Amara da Costa de

    2006-01-01

    Full Text Available Este trabalho tem o objetivo de divulgar um recurso terapêutico da epilepsia do lobo temporal por esclerose hipocampal: a cirurgia. Aproximadamente vinte e cinco mil pacientes com esta patologia são refratários aos tratamentos medicamentosos no sul do país e muitos chegam ao neurocirurgião com 30-40 anos de evolução, muitas vezes já mutilados em conseqüência das crises. Convulsões parciais originadas no lobo temporal são comuns, e grande parte originam-se em estruturas mesiais (esclerose mesial temporal – EMT. Como aí se encontram a sede de funções nobres do sistema nervoso – memória, aprendizagem, comportamento, entre outras –, os sintomas podem apresentar-se como alterações em qualquer uma delas. Ressaltamos a necessidade do correto diagnóstico e dos métodos para fazê-lo: através da anamnese, da ressonância magnética, do eletroencefalograma (EEG, do vídeo-EEG e por vezes através de sensores intracranianos (strips. Apesar de existirem métodos confiáveis para realizar o diagnóstico e tratamento cirúrgico com grande índice de sucesso, a desinformação dos profissionais que atendem pacientes com EMT acerca do assunto leva ao prolongamento de tratamentos clínico ineficiente e conseqüente seqüelas físicas, psicológicas e sociais

  16. Manuscript Transcription by Crowdsourcing: Transcribe Bentham

    Directory of Open Access Journals (Sweden)

    Martin Moyle

    2011-02-01

    Full Text Available Transcribe Bentham is testing the feasibility of outsourcing the work of manuscript transcription to members of the public. UCL Library Services holds 60,000 folios of manuscripts of the philosopher and jurist Jeremy Bentham (1748–1832. Transcribe Bentham will digitise 12,500 Bentham folios, and, through a wiki-based interface, allow volunteer transcribers to take temporary ownership of manuscript images and to create TEI-encoded transcription text for final approval by UCL experts. Approved transcripts will be stored and preserved, with the manuscript images, in UCL’s public Digital Collections repository. The project makes innovative use of traditional library material. It will stimulate public engagement with UCL’s scholarly archive collections and the challenges of palaeography and manuscript transcription; it will raise the profile of the work and thought of Jeremy Bentham; and it will create new digital resources for future use by professional researchers. Towards the end of the project, the transcription tool will be made available to other projects and services. This paper is based on a presentation given by the lead author at LIBER’s 39th Annual General Conference in Aarhus, Denmark, 2010.

  17. Structural Basis of Mitochondrial Transcription Initiation.

    Science.gov (United States)

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

    2017-11-16

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

  18. a Simple Spatially Weighted Measure of Temporal Stability for Data with Limited Temporal Observations

    Science.gov (United States)

    Piburn, J.; Stewart, R.; Morton, A.

    2017-10-01

    Identifying erratic or unstable time-series is an area of interest to many fields. Recently, there have been successful developments towards this goal. These new developed methodologies however come from domains where it is typical to have several thousand or more temporal observations. This creates a challenge when attempting to apply these methodologies to time-series with much fewer temporal observations such as for socio-cultural understanding, a domain where a typical time series of interest might only consist of 20-30 annual observations. Most existing methodologies simply cannot say anything interesting with so few data points, yet researchers are still tasked to work within in the confines of the data. Recently a method for characterizing instability in a time series with limitedtemporal observations was published. This method, Attribute Stability Index (ASI), uses an approximate entropy based method tocharacterize a time series' instability. In this paper we propose an explicitly spatially weighted extension of the Attribute StabilityIndex. By including a mechanism to account for spatial autocorrelation, this work represents a novel approach for the characterizationof space-time instability. As a case study we explore national youth male unemployment across the world from 1991-2014.

  19. The transcript release factor PTRF augments ribosomal gene transcription by facilitating reinitiation of RNA polymerase I

    Czech Academy of Sciences Publication Activity Database

    Jansa, Petr; Burek, C.; Sander, E. E.; Grummt, I.

    2001-01-01

    Roč. 29, č. 2 (2001), s. 423-429 ISSN 0305-1048 Institutional research plan: CEZ:AV0Z5052915 Keywords : rDNA transcription * PTRF * transcription reinitiation Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 6.373, year: 2001

  20. Transcription-induced DNA supercoiling: New roles of intranucleosomal DNA loops in DNA repair and transcription.

    Science.gov (United States)

    Gerasimova, N S; Pestov, N A; Kulaeva, O I; Clark, D J; Studitsky, V M

    2016-05-26

    RNA polymerase II (Pol II) transcription through chromatin is accompanied by formation of small intranucleosomal DNA loops. Pol II captured within a small loop drives accumulation of DNA supercoiling, facilitating further transcription. DNA breaks relieve supercoiling and induce Pol II arrest, allowing detection of DNA damage hidden in chromatin structure.

  1. Transcription factor FoxO1 is essential for enamel biomineralization.

    Directory of Open Access Journals (Sweden)

    Ross A Poché

    Full Text Available The Transforming growth factor β (Tgf-β pathway, by signaling via the activation of Smad transcription factors, induces the expression of many diverse downstream target genes thereby regulating a vast array of cellular events essential for proper development and homeostasis. In order for a specific cell type to properly interpret the Tgf-β signal and elicit a specific cellular response, cell-specific transcriptional co-factors often cooperate with the Smads to activate a discrete set of genes in the appropriate temporal and spatial manner. Here, via a conditional knockout approach, we show that mice mutant for Forkhead Box O transcription factor FoxO1 exhibit an enamel hypomaturation defect which phenocopies that of the Smad3 mutant mice. Furthermore, we determined that both the FoxO1 and Smad3 mutant teeth exhibit changes in the expression of similar cohort of genes encoding enamel matrix proteins required for proper enamel development. These data raise the possibility that FoxO1 and Smad3 act in concert to regulate a common repertoire of genes necessary for complete enamel maturation. This study is the first to define an essential role for the FoxO family of transcription factors in tooth development and provides a new molecular entry point which will allow researchers to delineate novel genetic pathways regulating the process of biomineralization which may also have significance for studies of human tooth diseases such as amelogenesis imperfecta.

  2. Embryonic maturation of epidermal Merkel cells is controlled by a redundant transcription factor network.

    Science.gov (United States)

    Perdigoto, Carolina N; Bardot, Evan S; Valdes, Victor J; Santoriello, Francis J; Ezhkova, Elena

    2014-12-01

    Merkel cell-neurite complexes are located in touch-sensitive areas of the mammalian skin and are involved in recognition of the texture and shape of objects. Merkel cells are essential for these tactile discriminations, as they generate action potentials in response to touch stimuli and induce the firing of innervating afferent nerves. It has been shown that Merkel cells originate from epidermal stem cells, but the cellular and molecular mechanisms of their development are largely unknown. In this study, we analyzed Merkel cell differentiation during development and found that it is a temporally regulated maturation process characterized by a sequential activation of Merkel cell-specific genes. We uncovered key transcription factors controlling this process and showed that the transcription factor Atoh1 is required for initial Merkel cell specification. The subsequent maturation steps of Merkel cell differentiation are controlled by cooperative function of the transcription factors Sox2 and Isl1, which physically interact and work to sustain Atoh1 expression. These findings reveal the presence of a robust transcriptional network required to produce functional Merkel cells that are required for tactile discrimination. © 2014. Published by The Company of Biologists Ltd.

  3. Systematic analysis of transcription start sites in avian development.

    Directory of Open Access Journals (Sweden)

    Marina Lizio

    2017-09-01

    Full Text Available Cap Analysis of Gene Expression (CAGE in combination with single-molecule sequencing technology allows precision mapping of transcription start sites (TSSs and genome-wide capture of promoter activities in differentiated and steady state cell populations. Much less is known about whether TSS profiling can characterize diverse and non-steady state cell populations, such as the approximately 400 transitory and heterogeneous cell types that arise during ontogeny of vertebrate animals. To gain such insight, we used the chick model and performed CAGE-based TSS analysis on embryonic samples covering the full 3-week developmental period. In total, 31,863 robust TSS peaks (>1 tag per million [TPM] were mapped to the latest chicken genome assembly, of which 34% to 46% were active in any given developmental stage. ZENBU, a web-based, open-source platform, was used for interactive data exploration. TSSs of genes critical for lineage differentiation could be precisely mapped and their activities tracked throughout development, suggesting that non-steady state and heterogeneous cell populations are amenable to CAGE-based transcriptional analysis. Our study also uncovered a large set of extremely stable housekeeping TSSs and many novel stage-specific ones. We furthermore demonstrated that TSS mapping could expedite motif-based promoter analysis for regulatory modules associated with stage-specific and housekeeping genes. Finally, using Brachyury as an example, we provide evidence that precise TSS mapping in combination with Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR-on technology enables us, for the first time, to efficiently target endogenous avian genes for transcriptional activation. Taken together, our results represent the first report of genome-wide TSS mapping in birds and the first systematic developmental TSS analysis in any amniote species (birds and mammals. By facilitating promoter-based molecular analysis and genetic

  4. The Intertwined Roles of DNA Damage and Transcription

    OpenAIRE

    Di Palo, Giacomo

    2016-01-01

    DNA damage and transcription are two interconnected events. Transcription can induce damage and scheduled DNA damage can be required for transcription. Here, we analyzed genome-wide distribution of 8oxodG-marked oxidative DNA damage obtained by OxiDIP-Seq, and we found a correlation with transcription of protein coding genes.

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

    Directory of Open Access Journals (Sweden)

    Rodrigo Lombraña

    2016-08-01

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

  6. Papercraft temporal bone in the first step of anatomy education.

    Science.gov (United States)

    Hiraumi, Harukazu; Sato, Hiroaki; Ito, Juichi

    2017-06-01

    (1) To compare temporal bone anatomy comprehension taught to speech therapy students with or without a papercraft model. (2) To explore the effect of papercraft simulation on the understanding of surgical approaches in first-year residents. (1) One-hundred and ten speech therapy students were divided into three classes. The first class was taught with a lecture only. The students in the second class were given a lecture and a papercraft modeling task without instruction. The third class modeled a papercraft with instruction after the lecture. The students were tested on their understanding of temporal bone anatomy. (2) A questionnaire on the understanding of surgical approaches was completed by 10 residents before and after the papercraft modeling. The papercraft models were cut with scissors to simulate surgical approaches. (1) The average scores were 4.4/8 for the first class, 4.3/8 for the second class, and 6.3/8 for the third class. The third class had significantly better results than the other classes (ppapercraft modeling and cutting were 2.6/7 and 4.9/7, respectively. The numerical rating scale score significantly improved (ppapercraft temporal bone model is effective in the first step of learning temporal bone anatomy and surgical approaches. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  7. Does Temporal Integration Occur for Unrecognizable Words in Visual Crowding?

    Science.gov (United States)

    Zhou, Jifan; Lee, Chia-Lin; Li, Kuei-An; Tien, Yung-Hsuan; Yeh, Su-Ling

    2016-01-01

    Visual crowding—the inability to see an object when it is surrounded by flankers in the periphery—does not block semantic activation: unrecognizable words due to visual crowding still generated robust semantic priming in subsequent lexical decision tasks. Based on the previous finding, the current study further explored whether unrecognizable crowded words can be temporally integrated into a phrase. By showing one word at a time, we presented Chinese four-word idioms with either a congruent or incongruent ending word in order to examine whether the three preceding crowded words can be temporally integrated to form a semantic context so as to affect the processing of the ending word. Results from both behavioral (Experiment 1) and Event-Related Potential (Experiment 2 and 3) measures showed congruency effect in only the non-crowded condition, which does not support the existence of unconscious multi-word integration. Aside from four-word idioms, we also found that two-word (modifier + adjective combination) integration—the simplest kind of temporal semantic integration—did not occur in visual crowding (Experiment 4). Our findings suggest that integration of temporally separated words might require conscious awareness, at least under the timing conditions tested in the current study. PMID:26890366

  8. Amnesia, rehearsal, and temporal distinctiveness models of recall.

    Science.gov (United States)

    Brown, Gordon D A; Della Sala, Sergio; Foster, Jonathan K; Vousden, Janet I

    2007-04-01

    Classical amnesia involves selective memory impairment for temporally distant items in free recall (impaired primacy) together with relative preservation of memory for recency items. This abnormal serial position curve is traditionally taken as evidence for a distinction between different memory processes, with amnesia being associated with selectively impaired long-term memory. However recent accounts of normal serial position curves have emphasized the importance of rehearsal processes in giving rise to primacy effects and have suggested that a single temporal distinctiveness mechanism can account for both primacy and recency effects when rehearsal is considered. Here we explore the pattern of strategic rehearsal in a patient with very severe amnesia. When the patient's rehearsal pattern is taken into account, a temporal distinctiveness model can account for the serial position curve in both amnesic and control free recall. The results are taken as consistent with temporal distinctiveness models of free recall, and they motivate an emphasis on rehearsal patterns in understanding amnesic deficits in free recall.

  9. Community ecology in 3D: Tensor decomposition reveals spatio-temporal dynamics of large ecological communities

    DEFF Research Database (Denmark)

    Frelat, Romain; Lindegren, Martin; Dencker, Tim Spaanheden

    2017-01-01

    it to multiple dimensions. This extension allows for the synchronized study of multiple ecological variables measured repeatedly in time and space. We applied this comprehensive approach to explore the spatio-temporal dynamics of 65 demersal fish species in the North Sea, a marine ecosystem strongly altered...... by human activities and climate change. Our case study demonstrates how tensor decomposition can successfully (i) characterize the main spatio-temporal patterns and trends in species abundances, (ii) identify sub-communities of species that share similar spatial distribution and temporal dynamics, and (iii...

  10. Battles and hijacks: Noncoding transcription in plants

    KAUST Repository

    Ariel, Federico

    2015-06-01

    Noncoding RNAs have emerged as major components of the eukaryotic transcriptome. Genome-wide analyses revealed the existence of thousands of long noncoding RNAs (lncRNAs) in several plant species. Plant lncRNAs are transcribed by the plant-specific RNA polymerases Pol IV and Pol V, leading to transcriptional gene silencing, as well as by Pol II. They are involved in a wide range of regulatory mechanisms impacting on gene expression, including chromatin remodeling, modulation of alternative splicing, fine-tuning of miRNA activity, and the control of mRNA translation or accumulation. Recently, dual noncoding transcription by alternative RNA polymerases was implicated in epigenetic and chromatin conformation dynamics. This review integrates the current knowledge on the regulatory mechanisms acting through plant noncoding transcription. © 2015 Elsevier Ltd.

  11. Phonemic Transcriptions in British and American Dictionaries

    Directory of Open Access Journals (Sweden)

    Rastislav Šuštaršič

    2005-06-01

    Full Text Available In view of recent criticisms concerning vowel symbols in some British English dictionaries (in particular by J. Windsor Lewis in JIPA (Windsor Lewis, 2003, with regard to the Oxford Dictionary of Pronunciation (Upton, 2001, this article extends the discussion on English phonemic transcriptions by including those that typically occur in standard American dictionaries, and by comparing the most common conventions of British and American dictionaries. In addition to symbols for both vowels and consonants, the paper also deals with the different representations of word accentuation and the issue of consistency regarding application of phonemic (systemic, broad, rather than phonetic (allophonic, narrow transcription. The different transcriptions are assessed from the points of view of their departures from the International Phonetic Alphabet, their overlapping with orthographic representation (spelling and their appropriateness in terms of reflecting actual pronunciation in standard British and/or American pronunciation.

  12. Crowdsourcing for quantifying transcripts: An exploratory study.

    Science.gov (United States)

    Azzam, Tarek; Harman, Elena

    2016-02-01

    This exploratory study attempts to demonstrate the potential utility of crowdsourcing as a supplemental technique for quantifying transcribed interviews. Crowdsourcing is the harnessing of the abilities of many people to complete a specific task or a set of tasks. In this study multiple samples of crowdsourced individuals were asked to rate and select supporting quotes from two different transcripts. The findings indicate that the different crowdsourced samples produced nearly identical ratings of the transcripts, and were able to consistently select the same supporting text from the transcripts. These findings suggest that crowdsourcing, with further development, can potentially be used as a mixed method tool to offer a supplemental perspective on transcribed interviews. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Transcription regulatory networks analysis using CAGE

    KAUST Repository

    Tegnér, Jesper N.

    2009-10-01

    Mapping out cellular networks in general and transcriptional networks in particular has proved to be a bottle-neck hampering our understanding of biological processes. Integrative approaches fusing computational and experimental technologies for decoding transcriptional networks at a high level of resolution is therefore of uttermost importance. Yet, this is challenging since the control of gene expression in eukaryotes is a complex multi-level process influenced by several epigenetic factors and the fine interplay between regulatory proteins and the promoter structure governing the combinatorial regulation of gene expression. In this chapter we review how the CAGE data can be integrated with other measurements such as expression, physical interactions and computational prediction of regulatory motifs, which together can provide a genome-wide picture of eukaryotic transcriptional regulatory networks at a new level of resolution. © 2010 by Pan Stanford Publishing Pte. Ltd. All rights reserved.

  14. Runx transcription factors in neuronal development

    Directory of Open Access Journals (Sweden)

    Shiga Takashi

    2008-08-01

    Full Text Available Abstract Runt-related (Runx transcription factors control diverse aspects of embryonic development and are responsible for the pathogenesis of many human diseases. In recent years, the functions of this transcription factor family in the nervous system have just begun to be understood. In dorsal root ganglion neurons, Runx1 and Runx3 play pivotal roles in the development of nociceptive and proprioceptive sensory neurons, respectively. Runx appears to control the transcriptional regulation of neurotrophin receptors, numerous ion channels and neuropeptides. As a consequence, Runx contributes to diverse aspects of the sensory system in higher vertebrates. In this review, we summarize recent progress in determining the role of Runx in neuronal development.

  15. Transcriptional inhibition by the retinoblastoma protein

    DEFF Research Database (Denmark)

    Fattaey, A; Helin, K; Harlow, E

    1993-01-01

    The retinoblastoma protein, pRB, appears to play a key role in coordinating the regulation of cell cycle position and transcriptional events. pRB undergoes specific cell-cycle-dependent phosphorylation, being underphosphorylated in G1 and heavily phosphorylated in S, G2, and M. The underphosphory......The retinoblastoma protein, pRB, appears to play a key role in coordinating the regulation of cell cycle position and transcriptional events. pRB undergoes specific cell-cycle-dependent phosphorylation, being underphosphorylated in G1 and heavily phosphorylated in S, G2, and M......-mediated transcription would be lost by mutation in the retinoblastoma gene in human tumours, by pRB's interaction with DNA tumour virus oncoproteins, or by phosphorylation during the cell cycle....

  16. Transcription as a Threat to Genome Integrity.

    Science.gov (United States)

    Gaillard, Hélène; Aguilera, Andrés

    2016-06-02

    Genomes undergo different types of sporadic alterations, including DNA damage, point mutations, and genome rearrangements, that constitute the basis for evolution. However, these changes may occur at high levels as a result of cell pathology and trigger genome instability, a hallmark of cancer and a number of genetic diseases. In the last two decades, evidence has accumulated that transcription constitutes an important natural source of DNA metabolic errors that can compromise the integrity of the genome. Transcription can create the conditions for high levels of mutations and recombination by its ability to open the DNA structure and remodel chromatin, making it more accessible to DNA insulting agents, and by its ability to become a barrier to DNA replication. Here we review the molecular basis of such events from a mechanistic perspective with particular emphasis on the role of transcription as a genome instability determinant.

  17. Molecular imaging of transcriptional regulation during inflammation

    Directory of Open Access Journals (Sweden)

    Carlsen Harald

    2010-04-01

    Full Text Available Abstract Molecular imaging enables non-invasive visualization of the dynamics of molecular processes within living organisms in vivo. Different imaging modalities as MRI, SPECT, PET and optic imaging are used together with molecular probes specific for the biological process of interest. Molecular imaging of transcription factor activity is done in animal models and mostly in transgenic reporter mice, where the transgene essentially consists of a promoter that regulates a reporter gene. During inflammation, the transcription factor NF-κB is widely involved in orchestration and regulation of the immune system and almost all imaging studies in this field has revolved around the role and regulation of NF-κB. We here present a brief introduction to experimental use and design of transgenic reporter mice and a more extensive review of the various studies where molecular imaging of transcriptional regulation has been applied during inflammation.

  18. Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control.

    Science.gov (United States)

    Celton, Jean-Marc; Gaillard, Sylvain; Bruneau, Maryline; Pelletier, Sandra; Aubourg, Sébastien; Martin-Magniette, Marie-Laure; Navarro, Lionel; Laurens, François; Renou, Jean-Pierre

    2014-07-01

    Characterizing the transcriptome of eukaryotic organisms is essential for studying gene regulation and its impact on phenotype. The realization that anti-sense (AS) and noncoding RNA transcription is pervasive in many genomes has emphasized our limited understanding of gene transcription and post-transcriptional regulation. Numerous mechanisms including convergent transcription, anti-correlated expression of sense and AS transcripts, and RNAi remain ill-defined. Here, we have combined microarray analysis and high-throughput sequencing of small RNAs (sRNAs) to unravel the complexity of transcriptional and potential post-transcriptional regulation in eight organs of apple (Malus × domestica). The percentage of AS transcript expression is higher than that identified in annual plants such as rice and Arabidopsis thaliana. Furthermore, we show that a majority of AS transcripts are transcribed beyond 3'UTR regions, and may cover a significant portion of the predicted sense transcripts. Finally we demonstrate at a genome-wide scale that anti-sense transcript expression is correlated with the presence of both short (21-23 nt) and long (> 30 nt) siRNAs, and that the sRNA coverage depth varies with the level of AS transcript expression. Our study provides a new insight on the functional role of anti-sense transcripts at the genome-wide level, and a new basis for the understanding of sRNA biogenesis in plants. © 2014 INRA. New Phytologist © 2014 New Phytologist Trust.

  19. Annotating temporal information in clinical narratives.

    Science.gov (United States)

    Sun, Weiyi; Rumshisky, Anna; Uzuner, Ozlem

    2013-12-01

    Temporal information in clinical narratives plays an important role in patients' diagnosis, treatment and prognosis. In order to represent narrative information accurately, medical natural language processing (MLP) systems need to correctly identify and interpret temporal information. To promote research in this area, the Informatics for Integrating Biology and the Bedside (i2b2) project developed a temporally annotated corpus of clinical narratives. This corpus contains 310 de-identified discharge summaries, with annotations of clinical events, temporal expressions and temporal relations. This paper describes the process followed for the development of this corpus and discusses annotation guideline development, annotation methodology, and corpus quality. Copyright © 2013 Elsevier Inc. All rights reserved.

  20. The transcriptional repressor DREAM is involved in thyroid gene expression

    International Nuclear Information System (INIS)

    D'Andrea, Barbara; Di Palma, Tina; Mascia, Anna; Motti, Maria Letizia; Viglietto, Giuseppe; Nitsch, Lucio; Zannini, Mariastella

    2005-01-01

    Downstream regulatory element antagonistic modulator (DREAM) was originally identified in neuroendocrine cells as a calcium-binding protein that specifically binds to downstream regulatory elements (DRE) on DNA, and represses transcription of its target genes. To explore the possibility that DREAM may regulate the endocrine activity of the thyroid gland, we analyzed its mRNA expression in undifferentiated and differentiated thyroid cells. We demonstrated that DREAM is expressed in the normal thyroid tissue as well as in differentiated thyroid cells in culture while it is absent in FRT poorly differentiated cells. In the present work, we also show that DREAM specifically binds to DRE sites identified in the 5' untranslated region (UTR) of the thyroid-specific transcription factors Pax8 and TTF-2/FoxE1 in a calcium-dependent manner. By gel retardation assays we demonstrated that thapsigargin treatment increases the binding of DREAM to the DRE sequences present in Pax8 and TTF-2/Foxe1 5' UTRs, and this correlates with a significant reduction of the expression of these genes. Interestingly, in poorly differentiated thyroid cells overexpression of exogenous DREAM strongly inhibits Pax8 expression. Moreover, we provide evidence that a mutated form of DREAM unable to bind Ca 2+ interferes with thyroid cell proliferation. Therefore, we propose that in thyroid cells DREAM is a mediator of the calcium-signaling pathway and it is involved in the regulation of thyroid cell function

  1. Geophysical Exploration. New site exploration method

    Energy Technology Data Exchange (ETDEWEB)

    Imai, Tsuneo; Otomo, Hideo; Sakayama, Toshihiko

    1988-07-25

    Geophysical exploration is used for geologic survey to serve purposes in civil engineering. New methods are being developed inside and outside Japan and are used to serve various purposes. This paper discusses recently developed techniques based on the measurement of seismic waves and electric potential. It also explains seismic tomography, radar tomography, and resistivity tomography which are included in the category of geotomography. At present, effort is being made to apply geophysical exploration technology to problems which were considered to be unsuitable for conventional exploration techniques. When such effort proceeds successfully, it is necessary to develop technology for presenting results quickly and exploration equipment which can work in various conditions. (10 figs, 15 refs)

  2. Ethnographies of Youth and Temporality

    DEFF Research Database (Denmark)

    Dalsgård, Anne Line; Frederiksen, Martin Demant; Højlund, Susanne

    As we experience and manipulate time—be it as boredom or impatience—it becomes an object: something materialized and social, something that affects perception, or something that may motivate reconsideration and change. The editors and contributors to this important new book, Ethnographies of Youth...... emotional unrest and violence but also creativity and hope are responses to troubling times. The chapters discuss notions of time and its “objectification” in diverse locales including the Georgian Republic, Brazil, Denmark, and Uganda. Based on long-term ethnographic fieldwork, the essays in Ethnographies...... of Youth and Temporality use youth as a prism to understand time and its subjective experience....

  3. Chondroblastoma of the temporal bone

    Energy Technology Data Exchange (ETDEWEB)

    Kobayashi, Yuko; Murakami, Ryusuke; Toba, Masahiro; Ichikawa, Taro [Dept. of Radiology, Nippon Medical School, Tokyo (Japan); Kanazawa, Ryuzaburo; Sanno, Naoko; Shimura, Toshiro [Dept. of Neurosurgery, Nippon Medical School, Tokyo (Japan); Sawada, Namie; Hosone, Masaru [Dept. of Pathology, Nippon Medical School, Tokyo (Japan); Kumazaki, Tatsuo [Dept. of Radiology, Nippon Medical School, Tokyo (Japan)

    2001-12-01

    A rare case of chondroblastoma arising from the temporal bone that occurred in a 60-year-old woman is reported. The tumor appeared well demarcated and osteolytic on the radiographs. CT scan clearly depicted marginal and central calcification in the tumor. MR imaging demonstrated two components in the tumor: a solid component with predominantly low signal intensities on both T1- and T2-weighted sequences, and a multilocular cystic component with T1- and T2-elongation and fluid-fluid levels on the T2-weighted images. Postcontrast MR imaging revealed marked enhancement in the solid component and the septa of the cystic component. (orig.)

  4. Harnessing transcription for bioproduction in cyanobacteria

    DEFF Research Database (Denmark)

    Stensjö, Karin; Vavitsas, Konstantinos; Tyystjärvi, Taina

    2018-01-01

    Sustainable production of biofuels and other valuable compounds is one of our future challenges. One tempting possibility is to use photosynthetic cyanobacteria as production factories. Currently, tools for genetic engineering of cyanobacteria are yet not good enough to exploit the full potential...... of cyanobacteria. A wide variety of expression systems will be required to adjust both the expression of heterologous enzyme(s) and metabolic routes to the best possible balance, allowing the optimal production of a particular substance. In bacteria, transcription, especially the initiation of transcription, has...

  5. Transcription and the aspect ratio of DNA

    DEFF Research Database (Denmark)

    Olsen, Kasper Wibeck; Bohr, Jakob

    2013-01-01

    analysis of transcription. It is shown that under certain reasonable assumptions transcription is only possible if the aspect ratio is in the regime corresponding to further twisting. We find this constraint to be in agreement with long-established crystallographic studies of DNA.......Two separate regimes exist for the aspect ratio of DNA. A low aspect regime where DNA will twist further under strain and a high aspect regime where DNA will untwist under strain. The question of the overall geometry, i.e. the aspect ratio, of DNA is revisited from the perspective of a geometrical...

  6. Towards Automatic Music Transcription: Extraction of MIDI-Data out of Polyphonic Piano Music

    Directory of Open Access Journals (Sweden)

    Jens Wellhausen

    2005-06-01

    Full Text Available Driven by the increasing amount of music available electronically the need of automatic search and retrieval systems for music becomes more and more important. In this paper an algorithm for automatic transcription of polyphonic piano music into MIDI data is presented, which is a very interesting basis for database applications and music analysis. The first part of the algorithm performs a note accurate temporal audio segmentation. The resulting segments are examined to extract the notes played in the second part. An algorithm for chord separation based on Independent Subspace Analysis is presented. Finally, the results are used to build a MIDI file.

  7. Towards automatic music transcription: note extraction based on independent subspace analysis

    Science.gov (United States)

    Wellhausen, Jens; Hoynck, Michael

    2005-01-01

    Due to the increasing amount of music available electronically the need of automatic search, retrieval and classification systems for music becomes more and more important. In this paper an algorithm for automatic transcription of polyphonic piano music into MIDI data is presented, which is a very interesting basis for database applications, music analysis and music classification. The first part of the algorithm performs a note accurate temporal audio segmentation. In the second part, the resulting segments are examined using Independent Subspace Analysis to extract sounding notes. Finally, the results are used to build a MIDI file as a new representation of the piece of music which is examined.

  8. Temporal regulation of foregut development by HTZ-1/H2A.Z and PHA-4/FoxA.

    Directory of Open Access Journals (Sweden)

    Dustin L Updike

    2006-09-01

    Full Text Available The histone variant H2A.Z is evolutionarily conserved and plays an essential role in mice, Drosophila, and Tetrahymena. The essential function of H2A.Z is unknown, with some studies suggesting a role in transcriptional repression and others in activation. Here we show that Caenorhabditis elegans HTZ-1/H2A.Z and the remodeling complex MYS-1/ESA1-SSL-1/SWR1 synergize with the FoxA transcription factor PHA-4 to coordinate temporal gene expression during foregut development. We observe dramatic genetic interactions between pha-4 and htz-1, mys-1, and ssl-1. A survey of transcription factors reveals that this interaction is specific, and thus pha-4 is acutely sensitive to reductions in these three proteins. Using a nuclear spot assay to visualize HTZ-1 in living embryos as organogenesis proceeds, we show that HTZ-1 is recruited to foregut promoters at the time of transcriptional onset, and this recruitment requires PHA-4. Loss of htz-1 by RNAi is lethal and leads to delayed expression of a subset of foregut genes. Thus, the effects of PHA-4 on temporal regulation can be explained in part by recruitment of HTZ-1 to target promoters. We suggest PHA-4 and HTZ-1 coordinate temporal gene expression by modulating the chromatin environment.

  9. A critique on nuclear factor-kappa B and signal transducer and activator of transcription 3: The key transcription factors in periodontal pathogenesis

    Directory of Open Access Journals (Sweden)

    Ranjith Ambili

    2017-01-01

    Full Text Available Periodontal disease is initiated by microorganisms in dental plaque, and host immunoinflammatory response to the microbial challenge helps in disease progression. Conventional periodontal therapy was mainly targeted on the elimination of microbial component. However, a better understanding of molecular aspects in host response will enable the clinicians to formulate effective host modulation therapy (HMT for the periodontal management. Inflammatory mediators were the main targets for HMT in the past. Transcription factors can regulate the production of multiple mediators simultaneously, and inhibition of these factors will be more beneficial than blocking individual molecule. Two important transcription factors implicated in chronic inflammatory diseases are nuclear factor kappa B (NF-κB and signal transducers and activators of transcription 3. The role of these factors in periodontal disease is a less explored area. This comprehensive review is aimed at unveiling the critical role of NF-κB and signal transducers and activators of transcription 3 in periodontal pathogenesis. An online search was performed using MEDLINE/PubMed database. All publications till 2016 related to NF-κB, signal transducer and activator of transcription 3 (STAT3, and inflammation were included in writing this review. A total of 27,390 references were published based on the search terms used. Out of these, 507 were related to the periodontal research published in English till 2016. Relevant papers were chosen after carefully reading the abstract. This review has attempted to comprehend the existing knowledge regarding the role of transcription factors NF-κB and STAT3 in periodontal disease. Moreover, it also provides a connecting molecular link for the periodontal medicine concept.

  10. Temporal dynamics of online petitions.

    Science.gov (United States)

    Böttcher, Lucas; Woolley-Meza, Olivia; Brockmann, Dirk

    2017-01-01

    Online petitions are an important avenue for direct political action, yet the dynamics that determine when a petition will be successful are not well understood. Here we analyze the temporal characteristics of online-petition signing behavior in order to identify systematic differences between popular petitions, which receive a high volume of signatures, and unpopular ones. We find that, in line with other temporal characterizations of human activity, the signing process is typically non-Poissonian and non-homogeneous in time. However, this process exhibits anomalously high memory for human activity, possibly indicating that synchronized external influence or contagion play and important role. More interestingly, we find clear differences in the characteristics of the inter-event time distributions depending on the total number of signatures that petitions receive, independently of the total duration of the petitions. Specifically, popular petitions that attract a large volume of signatures exhibit more variance in the distribution of inter-event times than unpopular petitions with only a few signatures, which could be considered an indication that the former are more bursty. However, petitions with large signature volume are less bursty according to measures that consider the time ordering of inter-event times. Our results, therefore, emphasize the importance of accounting for time ordering to characterize human activity.

  11. Generative Temporal Modelling of Neuroimaging - Decomposition and Nonparametric Testing

    DEFF Research Database (Denmark)

    Hald, Ditte Høvenhoff

    The goal of this thesis is to explore two improvements for functional magnetic resonance imaging (fMRI) analysis; namely our proposed decomposition method and an extension to the non-parametric testing framework. Analysis of fMRI allows researchers to investigate the functional processes...... of the brain, and provides insight into neuronal coupling during mental processes or tasks. The decomposition method is a Gaussian process-based independent components analysis (GPICA), which incorporates a temporal dependency in the sources. A hierarchical model specification is used, featuring both...... instantaneous and convolutive mixing, and the inferred temporal patterns. Spatial maps are seen to capture smooth and localized stimuli-related components, and often identifiable noise components. The implementation is freely available as a GUI/SPM plugin, and we recommend using GPICA as an additional tool when...

  12. little sister: An Afro-Temporal Solo-Play.

    Science.gov (United States)

    De Berry, Misty

    2017-07-03

    little sister: An Afro-Temporal Solo-Play is at once a memory-scape and a mytho-biography set to poetry, movement, and mixed media. A performance poem spanning from the Antebellum South to present-moment Chicago, it tells the story of a nomadic spirit named little-she who shape-shifts through the memories and imaginings of her sister, the narrator. Through the characters little-she and the narrator, the solo-performance explores embodied ways to rupture and relieve the impact of macro forms of violence in the micro realm of the everyday. To this end, little sister witnesses and disrupts the legacy of violence in the lives of queer Black women through a trans-temporal navigation of everyday encounters within familial, small groups and intimate partner spaces.

  13. Exploration and Mining Roadmap

    Energy Technology Data Exchange (ETDEWEB)

    none,

    2002-09-01

    This Exploration and Mining Technology Roadmap represents the third roadmap for the Mining Industry of the Future. It is based upon the results of the Exploration and Mining Roadmap Workshop held May 10 ñ 11, 2001.

  14. Audiovisual Temporal Perception in Aging: The Role of Multisensory Integration and Age-Related Sensory Loss.

    Science.gov (United States)

    Brooks, Cassandra J; Chan, Yu Man; Anderson, Andrew J; McKendrick, Allison M

    2018-01-01

    Within each sensory modality, age-related deficits in temporal perception contribute to the difficulties older adults experience when performing everyday tasks. Since perceptual experience is inherently multisensory, older adults also face the added challenge of appropriately integrating or segregating the auditory and visual cues present in our dynamic environment into coherent representations of distinct objects. As such, many studies have investigated how older adults perform when integrating temporal information across audition and vision. This review covers both direct judgments about temporal information (the sound-induced flash illusion, temporal order, perceived synchrony, and temporal rate discrimination) and judgments regarding stimuli containing temporal information (the audiovisual bounce effect and speech perception). Although an age-related increase in integration has been demonstrated on a variety of tasks, research specifically investigating the ability of older adults to integrate temporal auditory and visual cues has produced disparate results. In this short review, we explore what factors could underlie these divergent findings. We conclude that both task-specific differences and age-related sensory loss play a role in the reported disparity in age-related effects on the integration of auditory and visual temporal information.

  15. Audiovisual Temporal Perception in Aging: The Role of Multisensory Integration and Age-Related Sensory Loss

    Science.gov (United States)

    Brooks, Cassandra J.; Chan, Yu Man; Anderson, Andrew J.; McKendrick, Allison M.

    2018-01-01

    Within each sensory modality, age-related deficits in temporal perception contribute to the difficulties older adults experience when performing everyday tasks. Since perceptual experience is inherently multisensory, older adults also face the added challenge of appropriately integrating or segregating the auditory and visual cues present in our dynamic environment into coherent representations of distinct objects. As such, many studies have investigated how older adults perform when integrating temporal information across audition and vision. This review covers both direct judgments about temporal information (the sound-induced flash illusion, temporal order, perceived synchrony, and temporal rate discrimination) and judgments regarding stimuli containing temporal information (the audiovisual bounce effect and speech perception). Although an age-related increase in integration has been demonstrated on a variety of tasks, research specifically investigating the ability of older adults to integrate temporal auditory and visual cues has produced disparate results. In this short review, we explore what factors could underlie these divergent findings. We conclude that both task-specific differences and age-related sensory loss play a role in the reported disparity in age-related effects on the integration of auditory and visual temporal information. PMID:29867415

  16. Temporal expectancy in the context of a theory of visual attention.

    Science.gov (United States)

    Vangkilde, Signe; Petersen, Anders; Bundesen, Claus

    2013-10-19

    Temporal expectation is expectation with respect to the timing of an event such as the appearance of a certain stimulus. In this paper, temporal expectancy is investigated in the context of the theory of visual attention (TVA), and we begin by summarizing the foundations of this theoretical framework. Next, we present a parametric experiment exploring the effects of temporal expectation on perceptual processing speed in cued single-stimulus letter recognition with unspeeded motor responses. The length of the cue-stimulus foreperiod was exponentially distributed with one of six hazard rates varying between blocks. We hypothesized that this manipulation would result in a distinct temporal expectation in each hazard rate condition. Stimulus exposures were varied such that both the temporal threshold of conscious perception (t0 ms) and the perceptual processing speed (v letters s(-1)) could be estimated using TVA. We found that the temporal threshold t0 was unaffected by temporal expectation, but the perceptual processing speed v was a strikingly linear function of the logarithm of the hazard rate of the stimulus presentation. We argue that the effects on the v values were generated by changes in perceptual biases, suggesting that our perceptual biases are directly related to our temporal expectations.

  17. Visual temporal processing in dyslexia and the magnocellular deficit theory: the need for speed?

    Science.gov (United States)

    McLean, Gregor M T; Stuart, Geoffrey W; Coltheart, Veronika; Castles, Anne

    2011-12-01

    A controversial question in reading research is whether dyslexia is associated with impairments in the magnocellular system and, if so, how these low-level visual impairments might affect reading acquisition. This study used a novel chromatic flicker perception task to specifically explore temporal aspects of magnocellular functioning in 40 children with dyslexia and 42 age-matched controls (aged 7-11). The relationship between magnocellular temporal resolution and higher-level aspects of visual temporal processing including inspection time, single and dual-target (attentional blink) RSVP performance, go/no-go reaction time, and rapid naming was also assessed. The Dyslexia group exhibited significant deficits in magnocellular temporal resolution compared with controls, but the two groups did not differ in parvocellular temporal resolution. Despite the significant group differences, associations between magnocellular temporal resolution and reading ability were relatively weak, and links between low-level temporal resolution and reading ability did not appear specific to the magnocellular system. Factor analyses revealed that a collective Perceptual Speed factor, involving both low-level and higher-level visual temporal processing measures, accounted for unique variance in reading ability independently of phonological processing, rapid naming, and general ability.

  18. Temporal expectancy in the context of a theory of visual attention

    Science.gov (United States)

    Vangkilde, Signe; Petersen, Anders; Bundesen, Claus

    2013-01-01

    Temporal expectation is expectation with respect to the timing of an event such as the appearance of a certain stimulus. In this paper, temporal expectancy is investigated in the context of the theory of visual attention (TVA), and we begin by summarizing the foundations of this theoretical framework. Next, we present a parametric experiment exploring the effects of temporal expectation on perceptual processing speed in cued single-stimulus letter recognition with unspeeded motor responses. The length of the cue–stimulus foreperiod was exponentially distributed with one of six hazard rates varying between blocks. We hypothesized that this manipulation would result in a distinct temporal expectation in each hazard rate condition. Stimulus exposures were varied such that both the temporal threshold of conscious perception (t0 ms) and the perceptual processing speed (v letters s−1) could be estimated using TVA. We found that the temporal threshold t0 was unaffected by temporal expectation, but the perceptual processing speed v was a strikingly linear function of the logarithm of the hazard rate of the stimulus presentation. We argue that the effects on the v values were generated by changes in perceptual biases, suggesting that our perceptual biases are directly related to our temporal expectations. PMID:24018716

  19. Lateral head turning affects temporal memory.

    Science.gov (United States)

    Vicario, Carmelo Mario; Martino, Davide; Pavone, Enea Francesco; Fuggetta, Giorgio

    2011-08-01

    Spatial attention is a key factor in the exploration and processing of the surrounding environment, and plays a role in linking magnitudes such as space, time, and numbers. The present work evaluates whether shifting the coordinates of spatial attention through rotational head movements may affect the ability to estimate the duration of different time intervals. A computer-based implicit timing task was employed, in which participants were asked to concentrate and report verbally on colour changes of sequential stimuli displayed on a computer screen; subsequently, they were required to reproduce the temporal duration (ranging between 5 and 80 sec.) of the perceived stimuli using the computer keyboard. There was statistically significant overestimation of the 80-sec. intervals exclusively on the rightward rotation head posture, whereas head posture did not affect timing performances on shorter intervals. These findings support the hypothesis that the coordinates of spatial attention influence the ability to process time, consistent with the existence of common cortical metrics of space and time in healthy humans.

  20. Spatial and Temporal Patterns In Ecohydrological Separation

    Science.gov (United States)

    Jarvis, S. K.; Barnard, H. R.; Singha, K.; Harmon, R. E.; Szutu, D.

    2017-12-01

    The model of ecohydrological separation suggests that trees source water from a different subsurface pool than what is contributing to stream flow during dry periods, however diel fluctuations in stream flow and transpiration are tightly coupled. To better understand the mechanism of this coupling, this study examines spatiotemporal patterns in water isotopic relationships between tree, soil, and stream water. Preliminary analysis of data collected in 2015 show a trend in δ18O enrichment in xylem water, suggesting an increased reliance on enriched soil water not flowing to the stream as the growing season progresses, while xylem samples from 2016, a particularly wet year, do not have this trend. Variations in these temporal trends are explored with regard to distance from stream, aspect of hillslope, position in the watershed, size of the tree, and soil depth. Additionally, a near-stream site is examined at high resolution using water isotope data, sap flow, and electrical resistivity surveying to examine soil moisture and water use patterns across the riparian-hillslope transition.

  1. Automatic generation of pictorial transcripts of video programs

    Science.gov (United States)

    Shahraray, Behzad; Gibbon, David C.

    1995-03-01

    An automatic authoring system for the generation of pictorial transcripts of video programs which are accompanied by closed caption information is presented. A number of key frames, each of which represents the visual information in a segment of the video (i.e., a scene), are selected automatically by performing a content-based sampling of the video program. The textual information is recovered from the closed caption signal and is initially segmented based on its implied temporal relationship with the video segments. The text segmentation boundaries are then adjusted, based on lexical analysis and/or caption control information, to account for synchronization errors due to possible delays in the detection of scene boundaries or the transmission of the caption information. The closed caption text is further refined through linguistic processing for conversion to lower- case with correct capitalization. The key frames and the related text generate a compact multimedia presentation of the contents of the video program which lends itself to efficient storage and transmission. This compact representation can be viewed on a computer screen, or used to generate the input to a commercial text processing package to generate a printed version of the program.

  2. Mitochondrial transcription factor A protects human retinal ...

    African Journals Online (AJOL)

    Purpose: To investigate the impact of mitochondrial transcription factor A (TFAM), as a modulator of NF-κB, on proliferation of hypoxia-induced human retinal endothelial cell (HREC), and the probable mechanism. Methods: After exposure to hypoxia (1 % O2) for 5 days, cell proliferation and cell cycle of HREC were ...

  3. RNA Polymerase II–The Transcription Machine

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 12; Issue 3. RNA Polymerase II – The Transcription Machine - Nobel Prize in Chemistry 2006. Jiyoti Verma Aruna Naorem Anand Kumar Manimala Sen Parag Sadhale. General Article Volume 12 Issue 3 March 2007 pp 47-53 ...

  4. Polyphenol Compound as a Transcription Factor Inhibitor

    Directory of Open Access Journals (Sweden)

    Seyeon Park

    2015-10-01

    Full Text Available A target-based approach has been used to develop novel drugs in many therapeutic fields. In the final stage of intracellular signaling, transcription factor–DNA interactions are central to most biological processes and therefore represent a large and important class of targets for human therapeutics. Thus, we focused on the idea that the disruption of protein dimers and cognate DNA complexes could impair the transcriptional activation and cell transformation regulated by these proteins. Historically, natural products have been regarded as providing the primary leading compounds capable of modulating protein–protein or protein-DNA interactions. Although their mechanism of action is not fully defined, polyphenols including flavonoids were found to act mostly as site-directed small molecule inhibitors on signaling. There are many reports in the literature of screening initiatives suggesting improved drugs that can modulate the transcription factor interactions responsible for disease. In this review, we focus on polyphenol compound inhibitors against dimeric forms of transcription factor components of intracellular signaling pathways (for instance, c-jun/c-fos (Activator Protein-1; AP-1, c-myc/max, Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB and β-catenin/T cell factor (Tcf.

  5. Polyphenol Compound as a Transcription Factor Inhibitor.

    Science.gov (United States)

    Park, Seyeon

    2015-10-30

    A target-based approach has been used to develop novel drugs in many therapeutic fields. In the final stage of intracellular signaling, transcription factor-DNA interactions are central to most biological processes and therefore represent a large and important class of targets for human therapeutics. Thus, we focused on the idea that the disruption of protein dimers and cognate DNA complexes could impair the transcriptional activation and cell transformation regulated by these proteins. Historically, natural products have been regarded as providing the primary leading compounds capable of modulating protein-protein or protein-DNA interactions. Although their mechanism of action is not fully defined, polyphenols including flavonoids were found to act mostly as site-directed small molecule inhibitors on signaling. There are many reports in the literature of screening initiatives suggesting improved drugs that can modulate the transcription factor interactions responsible for disease. In this review, we focus on polyphenol compound inhibitors against dimeric forms of transcription factor components of intracellular signaling pathways (for instance, c-jun/c-fos (Activator Protein-1; AP-1), c-myc/max, Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and β-catenin/T cell factor (Tcf)).

  6. Cross-Family Transcription Factor Interactions

    NARCIS (Netherlands)

    Bemer, Marian; Dijk, van Aalt-Jan; Immink, Richard G.H.; Angenent, Gerco C.

    2017-01-01

    Specific and dynamic gene expression strongly depends on transcription factor (TF) activity and most plant TFs function in a combinatorial fashion. They can bind to DNA and control the expression of the corresponding gene in an additive fashion or cooperate by physical interactions, forming larger

  7. Corticosteroid receptors adopt distinct cyclical transcriptional signatures.

    Science.gov (United States)

    Le Billan, Florian; Amazit, Larbi; Bleakley, Kevin; Xue, Qiong-Yao; Pussard, Eric; Lhadj, Christophe; Kolkhof, Peter; Viengchareun, Say; Fagart, Jérôme; Lombès, Marc

    2018-05-07

    Mineralocorticoid receptors (MRs) and glucocorticoid receptors (GRs) are two closely related hormone-activated transcription factors that regulate major pathophysiologic functions. High homology between these receptors accounts for the crossbinding of their corresponding ligands, MR being activated by both aldosterone and cortisol and GR essentially activated by cortisol. Their coexpression and ability to bind similar DNA motifs highlight the need to investigate their respective contributions to overall corticosteroid signaling. Here, we decipher the transcriptional regulatory mechanisms that underlie selective effects of MRs and GRs on shared genomic targets in a human renal cellular model. Kinetic, serial, and sequential chromatin immunoprecipitation approaches were performed on the period circadian protein 1 ( PER1) target gene, providing evidence that both receptors dynamically and cyclically interact at the same target promoter in a specific and distinct transcriptional signature. During this process, both receptors regulate PER1 gene by binding as homo- or heterodimers to the same promoter region. Our results suggest a novel level of MR-GR target gene regulation, which should be considered for a better and integrated understanding of corticosteroid-related pathophysiology.-Le Billan, F., Amazit, L., Bleakley, K., Xue, Q.-Y., Pussard, E., Lhadj, C., Kolkhof, P., Viengchareun, S., Fagart, J., Lombès, M. Corticosteroid receptors adopt distinct cyclical transcriptional signatures.

  8. Transcriptional networks in epithelial-mesenchymal transition.

    Directory of Open Access Journals (Sweden)

    Christo Venkov

    Full Text Available Epithelial-mesenchymal transition (EMT changes polarized epithelial cells into migratory phenotypes associated with loss of cell-cell adhesion molecules and cytoskeletal rearrangements. This form of plasticity is seen in mesodermal development, fibroblast formation, and cancer metastasis.Here we identify prominent transcriptional networks active during three time points of this transitional process, as epithelial cells become fibroblasts. DNA microarray in cultured epithelia undergoing EMT, validated in vivo, were used to detect various patterns of gene expression. In particular, the promoter sequences of differentially expressed genes and their transcription factors were analyzed to identify potential binding sites and partners. The four most frequent cis-regulatory elements (CREs in up-regulated genes were SRY, FTS-1, Evi-1, and GC-Box, and RNA inhibition of the four transcription factors, Atf2, Klf10, Sox11, and SP1, most frequently binding these CREs, establish their importance in the initiation and propagation of EMT. Oligonucleotides that block the most frequent CREs restrain EMT at early and intermediate stages through apoptosis of the cells.Our results identify new transcriptional interactions with high frequency CREs that modulate the stability of cellular plasticity, and may serve as targets for modulating these transitional states in fibroblasts.

  9. Genetic characterization in symptomatic female DMD carriers: lack of relationship between X-inactivation, transcriptional DMD allele balancing and phenotype

    Directory of Open Access Journals (Sweden)

    Brioschi Simona

    2012-08-01

    Full Text Available Abstract Background Although Duchenne and Becker muscular dystrophies, X-linked recessive myopathies, predominantly affect males, a clinically significant proportion of females manifesting symptoms have also been reported. They represent an heterogeneous group characterized by variable degrees of muscle weakness and/or cardiac involvement. Though preferential inactivation of the normal X chromosome has long been considered the principal mechanism behind disease manifestation in these females, supporting evidence is controversial. Methods Eighteen females showing a mosaic pattern of dystrophin expression on muscle biopsy were recruited and classified as symptomatic (7 or asymptomatic (11, based on the presence or absence of muscle weakness. The causative DMD gene mutations were identified in all cases, and the X-inactivation pattern was assessed in muscle DNA. Transcriptional analysis in muscles was performed in all females, and relative quantification of wild-type and mutated transcripts was also performed in 9 carriers. Dystrophin protein was quantified by immunoblotting in 2 females. Results The study highlighted a lack of relationship between dystrophic phenotype and X-inactivation pattern in females; skewed X-inactivation was found in 2 out of 6 symptomatic carriers and in 5 out of 11 asymptomatic carriers. All females were characterized by biallelic transcription, but no association was found between X-inactivation pattern and allele transcriptional balancing. Either a prevalence of wild-type transcript or equal proportions of wild-type and mutated RNAs was observed in both symptomatic and asymptomatic females. Moreover, very similar levels of total and wild-type transcripts were identified in the two groups of carriers. Conclusions This is the first study deeply exploring the DMD transcriptional behaviour in a cohort of female carriers. Notably, no relationship between X-inactivation pattern and transcriptional behaviour of DMD gene was

  10. Transcriptional regulation of Caenorhabditis elegans FOXO/DAF-16 modulates lifespan.

    Science.gov (United States)

    Bansal, Ankita; Kwon, Eun-Soo; Conte, Darryl; Liu, Haibo; Gilchrist, Michael J; MacNeil, Lesley T; Tissenbaum, Heidi A

    2014-01-01

    Insulin/IGF-1 signaling plays a central role in longevity across phylogeny. In C. elegans, the forkhead box O (FOXO) transcription factor, DAF-16, is the primary target of insulin/IGF-1 signaling, and multiple isoforms of DAF-16 (a, b, and d/f) modulate lifespan, metabolism, dauer formation, and stress resistance. Thus far, across phylogeny modulation of mammalian FOXOs and DAF-16 have focused on post-translational regulation with little focus on transcriptional regulation. In C. elegans, we have previously shown that DAF-16d/f cooperates with DAF-16a to promote longevity. In this study, we generated transgenic strains expressing near-endogenous levels of either daf-16a or daf-16d/f, and examined temporal expression of the isoforms to further define how these isoforms contribute to lifespan regulation. Here, we show that DAF-16a is sensitive both to changes in gene dosage and to alterations in the level of insulin/IGF-1 signaling. Interestingly, we find that as worms age, the intestinal expression of daf-16d/f but not daf-16a is dramatically upregulated at the level of transcription. Preventing this transcriptional upregulation shortens lifespan, indicating that transcriptional regulation of daf-16d/f promotes longevity. In an RNAi screen of transcriptional regulators, we identify elt-2 (GATA transcription factor) and swsn-1 (core subunit of SWI/SNF complex) as key modulators of daf-16d/f gene expression. ELT-2 and another GATA factor, ELT-4, promote longevity via both DAF-16a and DAF-16d/f while the components of SWI/SNF complex promote longevity specifically via DAF-16d/f. Our findings indicate that transcriptional control of C. elegans FOXO/daf-16 is an essential regulatory event. Considering the conservation of FOXO across species, our findings identify a new layer of FOXO regulation as a potential determinant of mammalian longevity and age-related diseases such as cancer and diabetes.

  11. Transcriptator: An Automated Computational Pipeline to Annotate Assembled Reads and Identify Non Coding RNA.

    Directory of Open Access Journals (Sweden)

    Kumar Parijat Tripathi

    Full Text Available RNA-seq is a new tool to measure RNA transcript counts, using high-throughput sequencing at an extraordinary accuracy. It provides quantitative means to explore the transcriptome of an organism of interest. However, interpreting this extremely large data into biological knowledge is a problem, and biologist-friendly tools are lacking. In our lab, we developed Transcriptator, a web application based on a computational Python pipeline with a user-friendly Java interface. This pipeline uses the web services available for BLAST (Basis Local Search Alignment Tool, QuickGO and DAVID (Database for Annotation, Visualization and Integrated Discovery tools. It offers a report on statistical analysis of functional and Gene Ontology (GO annotation's enrichment. It helps users to identify enriched biological themes, particularly GO terms, pathways, domains, gene/proteins features and protein-protein interactions related informations. It clusters the transcripts based on functional annotations and generates a tabular report for functional and gene ontology annotations for each submitted transcript to the web server. The implementation of QuickGo web-services in our pipeline enable the users to carry out GO-Slim analysis, whereas the integration of PORTRAIT (Prediction of transcriptomic non coding RNA (ncRNA by ab initio methods helps to identify the non coding RNAs and their regulatory role in transcriptome. In summary, Transcriptator is a useful software for both NGS and array data. It helps the users to characterize the de-novo assembled reads, obtained from NGS experiments for non-referenced organisms, while it also performs the functional enrichment analysis of differentially expressed transcripts/genes for both RNA-seq and micro-array experiments. It generates easy to read tables and interactive charts for better understanding of the data. The pipeline is modular in nature, and provides an opportunity to add new plugins in the future. Web application is

  12. Asteroid exploration and utilization: The Hawking explorer

    Science.gov (United States)

    Carlson, Alan; Date, Medha; Duarte, Manny; Erian, Neil; Gafka, George; Kappler, Peter; Patano, Scott; Perez, Martin; Ponce, Edgar; Radovich, Brian

    1991-01-01

    The Earth is nearing depletion of its natural resources at a time when human beings are rapidly expanding the frontiers of space. The resources which may exist on asteroids could have enormous potential for aiding and enhancing human space exploration as well as life on Earth. With the possibly limitless opportunities that exist, it is clear that asteroids are the next step for human existence in space. This report comprises the efforts of NEW WORLDS, Inc. to develop a comprehensive design for an asteroid exploration/sample return mission. This mission is a precursor to proof-of-concept missions that will investigate the validity of mining and materials processing on an asteroid. Project STONER (Systematic Transfer of Near Earth Resources) is based on two utilization scenarios: (1) moving an asteroid to an advantageous location for use by Earth; and (2) mining an asteroids and transporting raw materials back to Earth. The asteroid explorer/sample return mission is designed in the context of both scenarios and is the first phase of a long range plane for humans to utilize asteroid resources. The report concentrates specifically on the selection of the most promising asteroids for exploration and the development of an exploration scenario. Future utilization as well as subsystem requirements of an asteroid sample return probe are also addressed.

  13. Modifiers of notch transcriptional activity identified by genome-wide RNAi

    Directory of Open Access Journals (Sweden)

    Firnhaber Christopher B

    2010-10-01

    Full Text Available Abstract Background The Notch signaling pathway regulates a diverse array of developmental processes, and aberrant Notch signaling can lead to diseases, including cancer. To obtain a more comprehensive understanding of the genetic network that integrates into Notch signaling, we performed a genome-wide RNAi screen in Drosophila cell culture to identify genes that modify Notch-dependent transcription. Results Employing complementary data analyses, we found 399 putative modifiers: 189 promoting and 210 antagonizing Notch activated transcription. These modifiers included several known Notch interactors, validating the robustness of the assay. Many novel modifiers were also identified, covering a range of cellular localizations from the extracellular matrix to the nucleus, as well as a large number of proteins with unknown function. Chromatin-modifying proteins represent a major class of genes identified, including histone deacetylase and demethylase complex components and other chromatin modifying, remodeling and replacement factors. A protein-protein interaction map of the Notch-dependent transcription modifiers revealed that a large number of the identified proteins interact physically with these core chromatin components. Conclusions The genome-wide RNAi screen identified many genes that can modulate Notch transcriptional output. A protein interaction map of the identified genes highlighted a network of chromatin-modifying enzymes and remodelers that regulate Notch transcription. Our results open new avenues to explore the mechanisms of Notch signal regulation and the integration of this pathway into diverse cellular processes.

  14. Spontaneous brain network activity: Analysis of its temporal complexity

    Directory of Open Access Journals (Sweden)

    Mangor Pedersen

    2017-06-01

    Full Text Available The brain operates in a complex way. The temporal complexity underlying macroscopic and spontaneous brain network activity is still to be understood. In this study, we explored the brain’s complexity by combining functional connectivity, graph theory, and entropy analyses in 25 healthy people using task-free functional magnetic resonance imaging. We calculated the pairwise instantaneous phase synchrony between 8,192 brain nodes for a total of 200 time points. This resulted in graphs for which time series of clustering coefficients (the “cliquiness” of a node and participation coefficients (the between-module connectivity of a node were estimated. For these two network metrics, sample entropy was calculated. The procedure produced a number of results: (1 Entropy is higher for the participation coefficient than for the clustering coefficient. (2 The average clustering coefficient is negatively related to its associated entropy, whereas the average participation coefficient is positively related to its associated entropy. (3 The level of entropy is network-specific to the participation coefficient, but not to the clustering coefficient. High entropy for the participation coefficient was observed in the default-mode, visual, and motor networks. These results were further validated using an independent replication dataset. Our work confirms that brain networks are temporally complex. Entropy is a good candidate metric to explore temporal network alterations in diseases with paroxysmal brain disruptions, including schizophrenia and epilepsy. In recent years, connectomics has provided significant insights into the topological complexity of brain networks. However, the temporal complexity of brain networks still remains somewhat poorly understood. In this study we used entropy analysis to demonstrate that the properties of network segregation (the clustering coefficient and integration (the participation coefficient are temporally complex

  15. Proteins mediating DNA loops effectively block transcription.

    Science.gov (United States)

    Vörös, Zsuzsanna; Yan, Yan; Kovari, Daniel T; Finzi, Laura; Dunlap, David

    2017-07-01

    Loops are ubiquitous topological elements formed when proteins simultaneously bind to two noncontiguous DNA sites. While a loop-mediating protein may regulate initiation at a promoter, the presence of the protein at the other site may be an obstacle for RNA polymerases (RNAP) transcribing a different gene. To test whether a DNA loop alters the extent to which a protein blocks transcription, the lac repressor (LacI) was used. The outcome of in vitro transcription along templates containing two LacI operators separated by 400 bp in the presence of LacI concentrations that produced both looped and unlooped molecules was visualized with scanning force microscopy (SFM). An analysis of transcription elongation complexes, moving for 60 s at an average of 10 nt/s on unlooped DNA templates, revealed that they more often surpassed LacI bound to the lower affinity O2 operator than to the highest affinity Os operator. However, this difference was abrogated in looped DNA molecules where LacI became a strong roadblock independently of the affinity of the operator. Recordings of transcription elongation complexes, using magnetic tweezers, confirmed that they halted for several minutes upon encountering a LacI bound to a single operator. The average pause lifetime is compatible with RNAP waiting for LacI dissociation, however, the LacI open conformation visualized in the SFM images also suggests that LacI could straddle RNAP to let it pass. Independently of the mechanism by which RNAP bypasses the LacI roadblock, the data indicate that an obstacle with looped topology more effectively interferes with transcription. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  16. Modelling oil exploration

    International Nuclear Information System (INIS)

    Padilla, V.R.

    1992-01-01

    The analysis of oil exploration models in this paper is developed in four parts. The way in which exploration has been dealt with in oil supply models is first described. Five recent models are then looked at, paying particular attention to the explanatory variables used when modelling exploration activities. This is followed by a discussion of the factors which have been shown by several empirical studies to determine exploration in less developed countries. Finally, the interdependence between institutional factors, oil prices and exploration effort is analysed with a view to drawing conclusions for modelling in the future. (UK)

  17. Marine Mineral Exploration

    DEFF Research Database (Denmark)

    in EEZ areas are fairly unknown; many areas need detailed mapping and mineral exploration, and the majority of coastal or island states with large EEZ areas have little experience in exploration for marine hard minerals. This book describes the systematic steps in marine mineral exploration....... Such exploration requires knowledge of mineral deposits and models of their formation, of geophysical and geochemical exploration methods, and of data evaluation and interpretation methods. These topics are described in detail by an international group of authors. A short description is also given of marine...

  18. Urban Space Explorer: A Visual Analytics System for Urban Planning.

    Science.gov (United States)

    Karduni, Alireza; Cho, Isaac; Wessel, Ginette; Ribarsky, William; Sauda, Eric; Dou, Wenwen

    2017-01-01

    Understanding people's behavior is fundamental to many planning professions (including transportation, community development, economic development, and urban design) that rely on data about frequently traveled routes, places, and social and cultural practices. Based on the results of a practitioner survey, the authors designed Urban Space Explorer, a visual analytics system that utilizes mobile social media to enable interactive exploration of public-space-related activity along spatial, temporal, and semantic dimensions.

  19. Hourly temporal distribution of wind

    Science.gov (United States)

    Deligiannis, Ilias; Dimitriadis, Panayiotis; Koutsoyiannis, Demetris

    2016-04-01

    The wind process is essential for hydrometeorology and additionally, is one of the basic renewable energy resources. Most stochastic forecast models are limited up to daily scales disregarding the hourly scale which is significant for renewable energy management. Here, we analyze hourly wind timeseries giving emphasis on the temporal distribution of wind within the day. We finally present a periodic model based on statistical as well as hydrometeorological reasoning that shows good agreement with data. Acknowledgement: This research is conducted within the frame of the undergraduate course "Stochastic Methods in Water Resources" of the National Technical University of Athens (NTUA). The School of Civil Engineering of NTUA provided moral support for the participation of the students in the Assembly.

  20. FGF signalling regulates chromatin organisation during neural differentiation via mechanisms that can be uncoupled from transcription.

    Directory of Open Access Journals (Sweden)

    Nishal S Patel

    Full Text Available Changes in higher order chromatin organisation have been linked to transcriptional regulation; however, little is known about how such organisation alters during embryonic development or how it is regulated by extrinsic signals. Here we analyse changes in chromatin organisation as neural differentiation progresses, exploiting the clear spatial separation of the temporal events of differentiation along the elongating body axis of the mouse embryo. Combining fluorescence in situ hybridisation with super-resolution structured illumination microscopy, we show that chromatin around key differentiation gene loci Pax6 and Irx3 undergoes both decompaction and displacement towards the nuclear centre coincident with transcriptional onset. Conversely, down-regulation of Fgf8 as neural differentiation commences correlates with a more peripheral nuclear position of this locus. During normal neural differentiation, fibroblast growth factor (FGF signalling is repressed by retinoic acid, and this vitamin A derivative is further required for transcription of neural genes. We show here that exposure to retinoic acid or inhibition of FGF signalling promotes precocious decompaction and central nuclear positioning of differentiation gene loci. Using the Raldh2 mutant as a model for retinoid deficiency, we further find that such changes in higher order chromatin organisation are dependent on retinoid signalling. In this retinoid deficient condition, FGF signalling persists ectopically in the elongating body, and importantly, we find that inhibiting FGF receptor (FGFR signalling in Raldh2-/- embryos does not rescue differentiation gene transcription, but does elicit both chromatin decompaction and nuclear position change. These findings demonstrate that regulation of higher order chromatin organisation during differentiation in the embryo can be uncoupled from the machinery that promotes transcription and, for the first time, identify FGF as an extrinsic signal that

  1. Memory for temporally dynamic scenes.

    Science.gov (United States)

    Ferguson, Ryan; Homa, Donald; Ellis, Derek

    2017-07-01

    Recognition memory was investigated for individual frames extracted from temporally continuous, visually rich film segments of 5-15 min. Participants viewed a short clip from a film in either a coherent or a jumbled order, followed by a recognition test of studied frames. Foils came either from an earlier or a later part of the film (Experiment 1) or from deleted segments selected from random cuts of varying duration (0.5 to 30 s) within the film itself (Experiment 2). When the foils came from an earlier or later part of the film (Experiment 1), recognition was excellent, with the hit rate far exceeding the false-alarm rate (.78 vs. 18). In Experiment 2, recognition was far worse, with the hit rate (.76) exceeding the false-alarm rate only for foils drawn from the longest cuts (15 and 30 s) and matching the false-alarm rate for the 5 s segments. When the foils were drawn from the briefest cuts (0.5 and 1.0 s), the false-alarm rate exceeded the hit rate. Unexpectedly, jumbling had no effect on recognition in either experiment. These results are consistent with the view that memory for complex visually temporal events is excellent, with the integrity unperturbed by disruption of the global structure of the visual stream. Disruption of memory was observed only when foils were drawn from embedded segments of duration less than 5 s, an outcome consistent with the view that memory at these shortest durations are consolidated with expectations drawn from the previous stream.

  2. A Temporal Map of Coaching.

    Science.gov (United States)

    Theeboom, Tim; Van Vianen, Annelies E M; Beersma, Bianca

    2017-01-01

    Economic pressures on companies, technological developments, and less stable career paths pose potential threats to the well-being of employees (e.g., stress, burn-out) and require constant adaptation. In the light of these challenges, it is not surprising that employees often seek the support of a coach. The role of a coach is to foster change by facilitating a coachees' movement through a self-regulatory cycle with the ultimate aim of stimulating sustained well-being and functioning. While meta-analytic research indicates that coaching interventions can be effectively applied to assist employees in dealing with change, the current literature on coaching lacks solid theoretical frameworks that are needed to build a cumulative knowledge-base and to inspire evidence-based practice. In this conceptual analysis, we examine the coaching process through a temporal lens. By doing so, we provide an integrated theoretical framework: a temporal map of coaching. In this framework, we link seminal concepts in psychology to the coaching process, and describe which competencies of coachees are crucial in the different stages of change that coaching aims to bring about. During the preparatory contemplation stage, targeting coachees' awareness by enhancing their mindfulness and environmental receptiveness is important. During the contemplation stage, coachees' willingness and perceived ability to change are central competencies. We propose that coaches should therefore foster intrinsic goal orientation and self-efficacy during this stage. During the planning stage, coaches should focus on goal-setting and implementation intentions. Finally, during the maintenance/termination stage, stimulating coachees' reflection is especially important in order to help them to integrate their learning experiences. The framework delineated in this paper contributes to the understanding of coaching as a tool to assist employees in dealing with the challenges of an increasingly dynamic work

  3. A Temporal Map of Coaching

    Directory of Open Access Journals (Sweden)

    Tim Theeboom

    2017-08-01

    Full Text Available Economic pressures on companies, technological developments, and less stable career paths pose potential threats to the well-being of employees (e.g., stress, burn-out and require constant adaptation. In the light of these challenges, it is not surprising that employees often seek the support of a coach. The role of a coach is to foster change by facilitating a coachees’ movement through a self-regulatory cycle with the ultimate aim of stimulating sustained well-being and functioning. While meta-analytic research indicates that coaching interventions can be effectively applied to assist employees in dealing with change, the current literature on coaching lacks solid theoretical frameworks that are needed to build a cumulative knowledge-base and to inspire evidence-based practice. In this conceptual analysis, we examine the coaching process through a temporal lens. By doing so, we provide an integrated theoretical framework: a temporal map of coaching. In this framework, we link seminal concepts in psychology to the coaching process, and describe which competencies of coachees are crucial in the different stages of change that coaching aims to bring about. During the preparatory contemplation stage, targeting coachees’ awareness by enhancing their mindfulness and environmental receptiveness is important. During the contemplation stage, coachees’ willingness and perceived ability to change are central competencies. We propose that coaches should therefore foster intrinsic goal orientation and self-efficacy during this stage. During the planning stage, coaches should focus on goal-setting and implementation intentions. Finally, during the maintenance/termination stage, stimulating coachees’ reflection is especially important in order to help them to integrate their learning experiences. The framework delineated in this paper contributes to the understanding of coaching as a tool to assist employees in dealing with the challenges of an

  4. High-order passive photonic temporal integrators.

    Science.gov (United States)

    Asghari, Mohammad H; Wang, Chao; Yao, Jianping; Azaña, José

    2010-04-15

    We experimentally demonstrate, for the first time to our knowledge, an ultrafast photonic high-order (second-order) complex-field temporal integrator. The demonstrated device uses a single apodized uniform-period fiber Bragg grating (FBG), and it is based on a general FBG design approach for implementing optimized arbitrary-order photonic passive temporal integrators. Using this same design approach, we also fabricate and test a first-order passive temporal integrator offering an energetic-efficiency improvement of more than 1 order of magnitude as compared with previously reported passive first-order temporal integrators. Accurate and efficient first- and second-order temporal integrations of ultrafast complex-field optical signals (with temporal features as fast as approximately 2.5ps) are successfully demonstrated using the fabricated FBG devices.

  5. SST: Single-Stream Temporal Action Proposals

    KAUST Repository

    Buch, Shyamal; Escorcia, Victor; Shen, Chuanqi; Ghanem, Bernard; Niebles, Juan Carlos

    2017-01-01

    Our paper presents a new approach for temporal detection of human actions in long, untrimmed video sequences. We introduce Single-Stream Temporal Action Proposals (SST), a new effective and efficient deep architecture for the generation of temporal action proposals. Our network can run continuously in a single stream over very long input video sequences, without the need to divide input into short overlapping clips or temporal windows for batch processing. We demonstrate empirically that our model outperforms the state-of-the-art on the task of temporal action proposal generation, while achieving some of the fastest processing speeds in the literature. Finally, we demonstrate that using SST proposals in conjunction with existing action classifiers results in improved state-of-the-art temporal action detection performance.

  6. SST: Single-Stream Temporal Action Proposals

    KAUST Repository

    Buch, Shyamal

    2017-11-09

    Our paper presents a new approach for temporal detection of human actions in long, untrimmed video sequences. We introduce Single-Stream Temporal Action Proposals (SST), a new effective and efficient deep architecture for the generation of temporal action proposals. Our network can run continuously in a single stream over very long input video sequences, without the need to divide input into short overlapping clips or temporal windows for batch processing. We demonstrate empirically that our model outperforms the state-of-the-art on the task of temporal action proposal generation, while achieving some of the fastest processing speeds in the literature. Finally, we demonstrate that using SST proposals in conjunction with existing action classifiers results in improved state-of-the-art temporal action detection performance.

  7. Method to determine transcriptional regulation pathways in organisms

    Science.gov (United States)

    Gardner, Timothy S.; Collins, James J.; Hayete, Boris; Faith, Jeremiah

    2012-11-06

    The invention relates to computer-implemented methods and systems for identifying regulatory relationships between expressed regulating polypeptides and targets of the regulatory activities of such regulating polypeptides. More specifically, the invention provides a new method for identifying regulatory dependencies between biochemical species in a cell. In particular embodiments, provided are computer-implemented methods for identifying a regulatory interaction between a transcription factor and a gene target of the transcription factor, or between a transcription factor and a set of gene targets of the transcription factor. Further provided are genome-scale methods for predicting regulatory interactions between a set of transcription factors and a corresponding set of transcriptional target substrates thereof.

  8. Post-transcription cleavage generates the 3' end of F17R transcripts in vaccinia virus

    International Nuclear Information System (INIS)

    D'Costa, Susan M.; Antczak, James B.; Pickup, David J.; Condit, Richard C.

    2004-01-01

    Most vaccinia virus intermediate and late mRNAs possess 3' ends that are extremely heterogeneous in sequence. However, late mRNAs encoding the cowpox A-type inclusion protein (ATI), the second largest subunit of the RNA polymerase, and the late telomeric transcripts possess homogeneous 3' ends. In the case of the ATI mRNA, it has been shown that the homogeneous 3' end is generated by a post-transcriptional endoribonucleolytic cleavage event. We have determined that the F17R gene also produces homogeneous transcripts generated by a post-transcriptional cleavage event. Mapping of in vivo mRNA shows that the major 3' end of the F17R transcript maps 1262 nt downstream of the F17R translational start site. In vitro transcripts spanning the in vivo 3' end are cleaved in an in vitro reaction using extracts from virus infected cells, and the site of cleavage is the same both in vivo and in vitro. Cleavage is not observed using extract from cells infected in the presence of hydroxyurea; therefore, the cleavage factor is either virus-coded or virus-induced during the post-replicative phase of virus replication. The cis-acting sequence responsible for cleavage is orientation specific and the factor responsible for cleavage activity has biochemical properties similar to the factor required for cleavage of ATI transcripts. Partially purified cleavage factor generates cleavage products of expected size when either the ATI or F17R substrates are used in vitro, strongly suggesting that cleavage of both transcripts is mediated by the same factor

  9. Characterization of neurons in the cortical white matter in human temporal lobe epilepsy.

    Science.gov (United States)

    Richter, Zsófia; Janszky, József; Sétáló, György; Horváth, Réka; Horváth, Zsolt; Dóczi, Tamás; Seress, László; Ábrahám, Hajnalka

    2016-10-01

    The aim of the present work was to characterize neurons in the archi- and neocortical white matter, and to investigate their distribution in mesial temporal sclerosis. Immunohistochemistry and quantification of neurons were performed on surgically resected tissue sections of patients with therapy-resistant temporal lobe epilepsy. Temporal lobe tissues of patients with tumor but without epilepsy and that from autopsy were used as controls. Neurons were identified with immunohistochemistry using antibodies against NeuN, calcium-binding proteins, transcription factor Tbr1 and neurofilaments. We found significantly higher density of neurons in the archi- and neocortical white matter of patients with temporal lobe epilepsy than in that of controls. Based on their morphology and neurochemical content, both excitatory and inhibitory cells were present among these neurons. A subset of neurons in the white matter was Tbr-1-immunoreactive and these neurons coexpressed NeuN and neurofilament marker SMI311R. No colocalization of Tbr1 was observed with the inhibitory neuronal markers, calcium-binding proteins. We suggest that a large population of white matter neurons comprises remnants of the subplate. Furthermore, we propose that a subset of white matter neurons was arrested during migration, highlighting the role of cortical maldevelopment in epilepsy associated with mesial temporal sclerosis. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

  10. Exploring the Limitations of Peripheral Blood Transcriptional Biomarkers in Predicting Influenza Vaccine Responsiveness

    Directory of Open Access Journals (Sweden)

    Luca Marchetti

    2017-01-01

    Full Text Available Systems biology has been recently applied to vaccinology to better understand immunological responses to the influenza vaccine. Particular attention has been paid to the identification of early signatures capable of predicting vaccine immunogenicity. Building from previous studies, we employed a recently established algorithm for signature-based clustering of expression profiles, SCUDO, to provide new insights into why blood-derived transcriptome biomarkers often fail to predict the seroresponse to the influenza virus vaccination. Specifically, preexisting immunity against one or more vaccine antigens, which was found to negatively affect the seroresponse, was identified as a confounding factor able to decouple early transcriptome from later antibody responses, resulting in the degradation of a biomarker predictive power. Finally, the broadly accepted definition of seroresponse to influenza virus vaccine, represented by the maximum response across the vaccine-targeted strains, was compared to a composite measure integrating the responses against all strains. This analysis revealed that composite measures provide a more accurate assessment of the seroresponse to multicomponent influenza vaccines.

  11. Can monaural temporal masking explain the ongoing precedence effect?

    Science.gov (United States)

    Freyman, Richard L; Morse-Fortier, Charlotte; Griffin, Amanda M; Zurek, Patrick M

    2018-02-01

    The precedence effect for transient sounds has been proposed to be based primarily on monaural processes, manifested by asymmetric temporal masking. This study explored the potential for monaural explanations with longer ("ongoing") sounds exhibiting the precedence effect. Transient stimuli were single lead-lag noise burst pairs; ongoing stimuli were trains of 63 burst pairs. Unlike with transients, monaural masking data for ongoing sounds showed no advantage for the lead, and are inconsistent with asymmetric audibility as an explanation for ongoing precedence. This result, along with supplementary measurements of interaural time discrimination, suggests different explanations for transient and ongoing precedence.

  12. Player Collaboration in the Explorative Sound Environment ToneInk

    DEFF Research Database (Denmark)

    Hansen, Anne-Marie S.; Andersen, Hans Jørgen; Raudaskoski, Pirkko Liisa

    2016-01-01

    mutual awareness, and in general were more passive when they needed to monitor a screen interface that supported the sound environment. Player collaboration was strongest when players negotiated rhythm, while the negotiation of melody was temporally offset and consisted of long individual explorations....

  13. Arousal, exploration and the locus coeruleus-norepinephrine system

    NARCIS (Netherlands)

    Jepma, Marieke

    2011-01-01

    The studies described in this thesis address a range of topics related to arousal, exploration, temporal attention, and the locus coeruleus-norepinephrine (LC-NE) system. Chapters 2 and 3 report two studies that investigated a recent theory about the role of the LC-NE system in the regulation of the

  14. International exploration by independent

    International Nuclear Information System (INIS)

    Bertragne, R.G.

    1992-01-01

    Recent industry trends indicate that the smaller U.S. independents are looking at foreign exploration opportunities as one of the alternatives for growth in the new age of exploration. Foreign finding costs per barrel usually are accepted to be substantially lower than domestic costs because of the large reserve potential of international plays. To get involved in overseas exploration, however, requires the explorationist to adapt to different cultural, financial, legal, operational, and political conditions. Generally, foreign exploration proceeds at a slower pace than domestic exploration because concessions are granted by a country's government, or are explored in partnership with a national oil company. First, the explorationist must prepare a mid- to long-term strategy, tailored to the goals and the financial capabilities of the company; next, is an ongoing evaluation of quality prospects in various sedimentary basins, and careful planning and conduct of the operations. To successfully explore overseas also requires the presence of a minimum number of explorationists and engineers thoroughly familiar with the various exploratory and operational aspects of foreign work. Ideally, these team members will have had a considerable amount of on-site experience in various countries and climates. Independents best suited for foreign expansion are those who have been financially successful in domestic exploration. When properly approached, foreign exploration is well within the reach of smaller U.S. independents, and presents essentially no greater risk than domestic exploration; however, the reward can be much larger and can catapult the company into the 'big leagues.'

  15. Cyclin D3 interacts with human activating transcription factor 5 and potentiates its transcription activity

    International Nuclear Information System (INIS)

    Liu Wenjin; Sun Maoyun; Jiang Jianhai; Shen Xiaoyun; Sun Qing; Liu Weicheng; Shen Hailian; Gu Jianxin

    2004-01-01

    The Cyclin D3 protein is a member of the D-type cyclins. Besides serving as cell cycle regulators, D-type cyclins have been reported to be able to interact with several transcription factors and modulate their transcriptional activations. Here we report that human activating transcription factor 5 (hATF5) is a new interacting partner of Cyclin D3. The interaction was confirmed by in vivo coimmunoprecipitation and in vitro binding analysis. Neither interaction between Cyclin D1 and hATF5 nor interaction between Cyclin D2 and hATF5 was observed. Confocal microscopy analysis showed that Cyclin D3 could colocalize with hATF5 in the nuclear region. Cyclin D3 could potentiate hATF5 transcriptional activity independently of its Cdk4 partner. But Cyclin D1 and Cyclin D2 had no effect on hATF5 transcriptional activity. These data provide a new clue to understand the new role of Cyclin D3 as a transcriptional regulator

  16. Temporal Lobe Epilepsy Surgery Failures: A Review

    Science.gov (United States)

    Harroud, Adil; Bouthillier, Alain; Weil, Alexander G.; Nguyen, Dang Khoa

    2012-01-01

    Patients with temporal lobe epilepsy (TLE) are refractory to antiepileptic drugs in about 30% of cases. Surgical treatment has been shown to be beneficial for the selected patients but fails to provide a seizure-free outcome in 20–30% of TLE patients. Several reasons have been identified to explain these surgical failures. This paper will address the five most common causes of TLE surgery failure (a) insufficient resection of epileptogenic mesial temporal structures, (b) relapse on the contralateral mesial temporal lobe, (c) lateral temporal neocortical epilepsy, (d) coexistence of mesial temporal sclerosis and a neocortical lesion (dual pathology); and (e) extratemporal lobe epilepsy mimicking TLE or temporal plus epilepsy. Persistence of epileptogenic mesial structures in the posterior temporal region and failure to distinguish mesial and lateral temporal epilepsy are possible causes of seizure persistence after TLE surgery. In cases of dual pathology, failure to identify a subtle mesial temporal sclerosis or regions of cortical microdysgenesis is a likely explanation for some surgical failures. Extratemporal epilepsy syndromes masquerading as or coexistent with TLE result in incomplete resection of the epileptogenic zone and seizure relapse after surgery. In particular, the insula may be an important cause of surgical failure in patients with TLE. PMID:22934162

  17. Optimization of temporal networks under uncertainty

    CERN Document Server

    Wiesemann, Wolfram

    2012-01-01

    Many decision problems in Operations Research are defined on temporal networks, that is, workflows of time-consuming tasks whose processing order is constrained by precedence relations. For example, temporal networks are used to model projects, computer applications, digital circuits and production processes. Optimization problems arise in temporal networks when a decision maker wishes to determine a temporal arrangement of the tasks and/or a resource assignment that optimizes some network characteristic (e.g. the time required to complete all tasks). The parameters of these optimization probl

  18. Geochemical exploration for uranium

    International Nuclear Information System (INIS)

    1988-01-01

    This Technical Report is designed mainly to introduce the methods and techniques of uranium geochemical exploration to exploration geologists who may not have had experience with geochemical exploration methods in their uranium programmes. The methods presented have been widely used in the uranium exploration industry for more than two decades. The intention has not been to produce an exhaustive, detailed manual, although detailed instructions are given for a field and laboratory data recording scheme and a satisfactory analytical method for the geochemical determination of uranium. Rather, the intention has been to introduce the concepts and methods of uranium exploration geochemistry in sufficient detail to guide the user in their effective use. Readers are advised to consult general references on geochemical exploration to increase their understanding of geochemical techniques for uranium

  19. Deconstructing transcriptional heterogeneity in pluripotent stem cells

    Science.gov (United States)

    Shalek, Alex K.; Satija, Rahul; DaleyKeyser, AJay; Li, Hu; Zhang, Jin; Pardee, Keith; Gennert, David; Trombetta, John J.; Ferrante, Thomas C.; Regev, Aviv; Daley, George Q.; Collins, James J.

    2014-01-01

    SUMMARY Pluripotent stem cells (PSCs) are capable of dynamic interconversion between distinct substates, but the regulatory circuits specifying these states and enabling transitions between them are not well understood. We set out to characterize transcriptional heterogeneity in PSCs by single-cell expression profiling under different chemical and genetic perturbations. Signaling factors and developmental regulators show highly variable expression, with expression states for some variable genes heritable through multiple cell divisions. Expression variability and population heterogeneity can be influenced by perturbation of signaling pathways and chromatin regulators. Strikingly, either removal of mature miRNAs or pharmacologic blockage of signaling pathways drives PSCs into a low-noise ground state characterized by a reconfigured pluripotency network, enhanced self-renewal, and a distinct chromatin state, an effect mediated by opposing miRNA families acting on the c-myc / Lin28 / let-7 axis. These data illuminate the nature of transcriptional heterogeneity in PSCs. PMID:25471879

  20. Computational Investigations of Post-Transcriptional Regulation

    DEFF Research Database (Denmark)

    Rasmussen, Simon Horskjær

    and miRNA regulation was studied by cross-linking immunoprecipitation (CLIP) and RBP double knockdown experiments. A comprehensive analysis of 107 CLIP datasets of 49 RBPs demonstrated that RBPs modulate miRNA regulation. Results suggest it is mediated by RBP-binding hotspots that likely...... investigated using high-throughput data. Analysis of IMP RIP-seq, iCLIP and RNA-seq datasets identified transcripts associated with cytoplasmic IMP ribonucleoproteins. Many of these transcripts were functionally involved in actin cytoskeletal remodeling. Further analyses of this data permitted estimation...... of a bipartite motif, composed of an AU-rich and a CA-rich domain. In addition, a regulatory motif discovery method was developed and applied to identify motifs using differential expression data and CLIP-data in the above investigations. This thesis increased the understanding of the role of RBPs in mi...

  1. Visual explorer facilitator's guide

    CERN Document Server

    Palus, Charles J

    2010-01-01

    Grounded in research and practice, the Visual Explorer™ Facilitator's Guide provides a method for supporting collaborative, creative conversations about complex issues through the power of images. The guide is available as a component in the Visual Explorer Facilitator's Letter-sized Set, Visual Explorer Facilitator's Post card-sized Set, Visual Explorer Playing Card-sized Set, and is also available as a stand-alone title for purchase to assist multiple tool users in an organization.

  2. A Herpesviral Immediate Early Protein Promotes Transcription Elongation of Viral Transcripts.

    Science.gov (United States)

    Fox, Hannah L; Dembowski, Jill A; DeLuca, Neal A

    2017-06-13

    Herpes simplex virus 1 (HSV-1) genes are transcribed by cellular RNA polymerase II (RNA Pol II). While four viral immediate early proteins (ICP4, ICP0, ICP27, and ICP22) function in some capacity in viral transcription, the mechanism by which ICP22 functions remains unclear. We observed that the FACT complex (comprised of SSRP1 and Spt16) was relocalized in infected cells as a function of ICP22. ICP22 was also required for the association of FACT and the transcription elongation factors SPT5 and SPT6 with viral genomes. We further demonstrated that the FACT complex interacts with ICP22 throughout infection. We therefore hypothesized that ICP22 recruits cellular transcription elongation factors to viral genomes for efficient transcription elongation of viral genes. We reevaluated the phenotype of an ICP22 mutant virus by determining the abundance of all viral mRNAs throughout infection by transcriptome sequencing (RNA-seq). The accumulation of almost all viral mRNAs late in infection was reduced compared to the wild type, regardless of kinetic class. Using chromatin immunoprecipitation sequencing (ChIP-seq), we mapped the location of RNA Pol II on viral genes and found that RNA Pol II levels on the bodies of viral genes were reduced in the ICP22 mutant compared to wild-type virus. In contrast, the association of RNA Pol II with transcription start sites in the mutant was not reduced. Taken together, our results indicate that ICP22 plays a role in recruiting elongation factors like the FACT complex to the HSV-1 genome to allow for efficient viral transcription elongation late in viral infection and ultimately infectious virion production. IMPORTANCE HSV-1 interacts with many cellular proteins throughout productive infection. Here, we demonstrate the interaction of a viral protein, ICP22, with a subset of cellular proteins known to be involved in transcription elongation. We determined that ICP22 is required to recruit the FACT complex and other transcription

  3. Reconstructing transcriptional regulatory networks through genomics data

    OpenAIRE

    Sun, Ning; Zhao, Hongyu

    2009-01-01

    One central problem in biology is to understand how gene expression is regulated under different conditions. Microarray gene expression data and other high throughput data have made it possible to dissect transcriptional regulatory networks at the genomics level. Owing to the very large number of genes that need to be studied, the relatively small number of data sets available, the noise in the data and the different natures of the distinct data types, network inference presents great challen...

  4. NUR TRANSCRIPTION FACTORS IN STRESS AND ADDICTION

    Directory of Open Access Journals (Sweden)

    Danae eCampos-Melo

    2013-12-01

    Full Text Available The Nur transcription factors Nur77 (NGFI-B, NR4A1, Nurr1 (NR4A2 and Nor-1 (NR4A3 are a sub-family of orphan members of the nuclear receptor superfamily. These transcription factors are products of immediate early genes, whose expression is rapidly and transiently induced in the central nervous system by several types of stimuli. Nur factors are present throughout the hypothalamus-pituitary-adrenal axis where are prominently induced in response to stress. Drugs of abuse and stress also induce the expression of Nur factors in nuclei of the motivation/reward circuit of the brain, indicating their participation in the process of drug addiction and in non-hypothalamic responses to stress. Repeated use of addictive drugs and chronic stress induce long-lasting dysregulation of the brain motivation/reward circuit, due to reprogramming of gene expression and enduring alterations in neuronal function. Here, we review the data supporting that Nur transcription factors are key players in the molecular basis of the dysregulation of neuronal circuits involved in chronic stress and addiction.

  5. The transcriptional regulatory network of Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Joaquín Sanz

    Full Text Available Under the perspectives of network science and systems biology, the characterization of transcriptional regulatory (TR networks beyond the context of model organisms offers a versatile tool whose potential remains yet mainly unexplored. In this work, we present an updated version of the TR network of Mycobacterium tuberculosis (M.tb, which incorporates newly characterized transcriptional regulations coming from 31 recent, different experimental works available in the literature. As a result of the incorporation of these data, the new network doubles the size of previous data collections, incorporating more than a third of the entire genome of the bacterium. We also present an exhaustive topological analysis of the new assembled network, focusing on the statistical characterization of motifs significances and the comparison with other model organisms. The expanded M.tb transcriptional regulatory network, considering its volume and completeness, constitutes an important resource for diverse tasks such as dynamic modeling of gene expression and signaling processes, computational reliability determination or protein function prediction, being the latter of particular relevance, given that the function of only a small percent of the proteins of M.tb is known.

  6. Evolution of transcriptional enhancers and animal diversity

    Science.gov (United States)

    Rubinstein, Marcelo; de Souza, Flávio S. J.

    2013-01-01

    Deciphering the genetic bases that drive animal diversity is one of the major challenges of modern biology. Although four decades ago it was proposed that animal evolution was mainly driven by changes in cis-regulatory DNA elements controlling gene expression rather than in protein-coding sequences, only now are powerful bioinformatics and experimental approaches available to accelerate studies into how the evolution of transcriptional enhancers contributes to novel forms and functions. In the introduction to this Theme Issue, we start by defining the general properties of transcriptional enhancers, such as modularity and the coexistence of tight sequence conservation with transcription factor-binding site shuffling as different mechanisms that maintain the enhancer grammar over evolutionary time. We discuss past and current methods used to identify cell-type-specific enhancers and provide examples of how enhancers originate de novo, change and are lost in particular lineages. We then focus in the central part of this Theme Issue on analysing examples of how the molecular evolution of enhancers may change form and function. Throughout this introduction, we present the main findings of the articles, reviews and perspectives contributed to this Theme Issue that together illustrate some of the great advances and current frontiers in the field. PMID:24218630

  7. Curated compendium of human transcriptional biomarker data.

    Science.gov (United States)

    Golightly, Nathan P; Bell, Avery; Bischoff, Anna I; Hollingsworth, Parker D; Piccolo, Stephen R

    2018-04-17

    One important use of genome-wide transcriptional profiles is to identify relationships between transcription levels and patient outcomes. These translational insights can guide the development of biomarkers for clinical application. Data from thousands of translational-biomarker studies have been deposited in public repositories, enabling reuse. However, data-reuse efforts require considerable time and expertise because transcriptional data are generated using heterogeneous profiling technologies, preprocessed using diverse normalization procedures, and annotated in non-standard ways. To address this problem, we curated 45 publicly available, translational-biomarker datasets from a variety of human diseases. To increase the data's utility, we reprocessed the raw expression data using a uniform computational pipeline, addressed quality-control problems, mapped the clinical annotations to a controlled vocabulary, and prepared consistently structured, analysis-ready data files. These data, along with scripts we used to prepare the data, are available in a public repository. We believe these data will be particularly useful to researchers seeking to perform benchmarking studies-for example, to compare and optimize machine-learning algorithms' ability to predict biomedical outcomes.

  8. The Mediator complex and transcription regulation

    Science.gov (United States)

    Poss, Zachary C.; Ebmeier, Christopher C.

    2013-01-01

    The Mediator complex is a multi-subunit assembly that appears to be required for regulating expression of most RNA polymerase II (pol II) transcripts, which include protein-coding and most non-coding RNA genes. Mediator and pol II function within the pre-initiation complex (PIC), which consists of Mediator, pol II, TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH and is approximately 4.0 MDa in size. Mediator serves as a central scaffold within the PIC and helps regulate pol II activity in ways that remain poorly understood. Mediator is also generally targeted by sequence-specific, DNA-binding transcription factors (TFs) that work to control gene expression programs in response to developmental or environmental cues. At a basic level, Mediator functions by relaying signals from TFs directly to the pol II enzyme, thereby facilitating TF-dependent regulation of gene expression. Thus, Mediator is essential for converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression). In this review, we summarize an expansive body of research on the Mediator complex, with an emphasis on yeast and mammalian complexes. We focus on the basics that underlie Mediator function, such as its structure and subunit composition, and describe its broad regulatory influence on gene expression, ranging from chromatin architecture to transcription initiation and elongation, to mRNA processing. We also describe factors that influence Mediator structure and activity, including TFs, non-coding RNAs and the CDK8 module. PMID:24088064

  9. Adaptive evolution of transcription factor binding sites

    Directory of Open Access Journals (Sweden)

    Berg Johannes

    2004-10-01

    Full Text Available Abstract Background The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks in the evolution of complex regulatory networks. We study a theoretical model for the sequence evolution of binding sites by point mutations. The approach is based on biophysical models for the binding of transcription factors to DNA. Hence we derive empirically grounded fitness landscapes, which enter a population genetics model including mutations, genetic drift, and selection. Results We show that the selection for factor binding generically leads to specific correlations between nucleotide frequencies at different positions of a binding site. We demonstrate the possibility of rapid adaptive evolution generating a new binding site for a given transcription factor by point mutations. The evolutionary time required is estimated in terms of the neutral (background mutation rate, the selection coefficient, and the effective population size. Conclusions The efficiency of binding site formation is seen to depend on two joint conditions: the binding site motif must be short enough and the promoter region must be long enough. These constraints on promoter architecture are indeed seen in eukaryotic systems. Furthermore, we analyse the adaptive evolution of genetic switches and of signal integration through binding cooperativity between different sites. Experimental tests of this picture involving the statistics of polymorphisms and phylogenies of sites are discussed.

  10. Transcription initiation complex structures elucidate DNA opening.

    Science.gov (United States)

    Plaschka, C; Hantsche, M; Dienemann, C; Burzinski, C; Plitzko, J; Cramer, P

    2016-05-19

    Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 Å and 3.6 Å, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH. Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE 'E-ribbon' domain. The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein-protein and protein-DNA contacts.

  11. Transcription of tandemly repetitive DNA: functional roles.

    Science.gov (United States)

    Biscotti, Maria Assunta; Canapa, Adriana; Forconi, Mariko; Olmo, Ettore; Barucca, Marco

    2015-09-01

    A considerable fraction of the eukaryotic genome is made up of satellite DNA constituted of tandemly repeated sequences. These elements are mainly located at centromeres, pericentromeres, and telomeres and are major components of constitutive heterochromatin. Although originally satellite DNA was thought silent and inert, an increasing number of studies are providing evidence on its transcriptional activity supporting, on the contrary, an unexpected dynamicity. This review summarizes the multiple structural roles of satellite noncoding RNAs at chromosome level. Indeed, satellite noncoding RNAs play a role in the establishment of a heterochromatic state at centromere and telomere. These highly condensed structures are indispensable to preserve chromosome integrity and genome stability, preventing recombination events, and ensuring the correct chromosome pairing and segregation. Moreover, these RNA molecules seem to be involved also in maintaining centromere identity and in elongation, capping, and replication of telomere. Finally, the abnormal variation of centromeric and pericentromeric DNA transcription across major eukaryotic lineages in stress condition and disease has evidenced the critical role that these transcripts may play and the potentially dire consequences for the organism.

  12. Repetitive Elements in Mycoplasma hyopneumoniae Transcriptional Regulation.

    Directory of Open Access Journals (Sweden)

    Amanda Malvessi Cattani

    Full Text Available Transcriptional regulation, a multiple-step process, is still poorly understood in the important pig pathogen Mycoplasma hyopneumoniae. Basic motifs like promoters and terminators have already been described, but no other cis-regulatory elements have been found. DNA repeat sequences have been shown to be an interesting potential source of cis-regulatory elements. In this work, a genome-wide search for tandem and palindromic repetitive elements was performed in the intergenic regions of all coding sequences from M. hyopneumoniae strain 7448. Computational analysis demonstrated the presence of 144 tandem repeats and 1,171 palindromic elements. The DNA repeat sequences were distributed within the 5' upstream regions of 86% of transcriptional units of M. hyopneumoniae strain 7448. Comparative analysis between distinct repetitive sequences found in related mycoplasma genomes demonstrated different percentages of conservation among pathogenic and nonpathogenic strains. qPCR assays revealed differential expression among genes showing variable numbers of repetitive elements. In addition, repeats found in 206 genes already described to be differentially regulated under different culture conditions of M. hyopneumoniae strain 232 showed almost 80% conservation in relation to M. hyopneumoniae strain 7448 repeats. Altogether, these findings suggest a potential regulatory role of tandem and palindromic DNA repeats in the M. hyopneumoniae transcriptional profile.

  13. Repetitive Elements in Mycoplasma hyopneumoniae Transcriptional Regulation.

    Science.gov (United States)

    Cattani, Amanda Malvessi; Siqueira, Franciele Maboni; Guedes, Rafael Lucas Muniz; Schrank, Irene Silveira

    2016-01-01

    Transcriptional regulation, a multiple-step process, is still poorly understood in the important pig pathogen Mycoplasma hyopneumoniae. Basic motifs like promoters and terminators have already been described, but no other cis-regulatory elements have been found. DNA repeat sequences have been shown to be an interesting potential source of cis-regulatory elements. In this work, a genome-wide search for tandem and palindromic repetitive elements was performed in the intergenic regions of all coding sequences from M. hyopneumoniae strain 7448. Computational analysis demonstrated the presence of 144 tandem repeats and 1,171 palindromic elements. The DNA repeat sequences were distributed within the 5' upstream regions of 86% of transcriptional units of M. hyopneumoniae strain 7448. Comparative analysis between distinct repetitive sequences found in related mycoplasma genomes demonstrated different percentages of conservation among pathogenic and nonpathogenic strains. qPCR assays revealed differential expression among genes showing variable numbers of repetitive elements. In addition, repeats found in 206 genes already described to be differentially regulated under different culture conditions of M. hyopneumoniae strain 232 showed almost 80% conservation in relation to M. hyopneumoniae strain 7448 repeats. Altogether, these findings suggest a potential regulatory role of tandem and palindromic DNA repeats in the M. hyopneumoniae transcriptional profile.

  14. Modulation of transcription factors by curcumin.

    Science.gov (United States)

    Shishodia, Shishir; Singh, Tulika; Chaturvedi, Madan M

    2007-01-01

    Curcumin is the active ingredient of turmeric that has been consumed as a dietary spice for ages. Turmeric is widely used in traditional Indian medicine to cure biliary disorders, anorexia, cough, diabetic wounds, hepatic disorders, rheumatism, and sinusitis. Extensive investigation over the last five decades has indicated that curcumin reduces blood cholesterol, prevents low-density lipoprotein oxidation, inhibits platelet aggregation, suppresses thrombosis and myocardial infarction, suppresses symptoms associated with type II diabetes, rheumatoid arthritis, multiple sclerosis, and Alzheimer's disease, inhibits HIV replication, enhances wound healing, protects from liver injury, increases bile secretion, protects from cataract formation, and protects from pulmonary toxicity and fibrosis. Evidence indicates that the divergent effects of curcumin are dependent on its pleiotropic molecular effects. These include the regulation of signal transduction pathways and direct modulation of several enzymatic activities. Most of these signaling cascades lead to the activation of transcription factors. Curcumin has been found to modulate the activity of several key transcription factors and, in turn, the cellular expression profiles. Curcumin has been shown to elicit vital cellular responses such as cell cycle arrest, apoptosis, and differentiation by activating a cascade of molecular events. In this chapter, we briefly review the effects of curcumin on transcription factors NF-KB, AP-1, Egr-1, STATs, PPAR-gamma, beta-catenin, nrf2, EpRE, p53, CBP, and androgen receptor (AR) and AR-related cofactors giving major emphasis to the molecular mechanisms of its action.

  15. Fatty Acid–Regulated Transcription Factors in the Liver

    Science.gov (United States)

    Jump, Donald B.; Tripathy, Sasmita; Depner, Christopher M.

    2014-01-01

    Fatty acid regulation of hepatic gene transcription was first reported in the early 1990s. Several transcription factors have been identified as targets of fatty acid regulation. This regulation is achieved by direct fatty acid binding to the transcription factor or by indirect mechanisms where fatty acids regulate signaling pathways controlling the expression of transcription factors or the phosphorylation, ubiquitination, or proteolytic cleavage of the transcription factor. Although dietary fatty acids are well-established regulators of hepatic transcription factors, emerging evidence indicates that endogenously generated fatty acids are equally important in controlling transcription factors in the context of glucose and lipid homeostasis. Our first goal in this review is to provide an up-to-date examination of the molecular and metabolic bases of fatty acid regulation of key transcription factors controlling hepatic metabolism. Our second goal is to link these mechanisms to nonalcoholic fatty liver disease (NAFLD), a growing health concern in the obese population. PMID:23528177

  16. To Your Health: NLM update transcript - Gun safety strategies

    Science.gov (United States)

    ... transcript040918.html To Your Health: NLM update Transcript Gun safety strategies : 04/09/2018 To use the ... on weekly topics. An evidence-based, public health gun safety strategy that is consistent with second amendment ...

  17. Determination of specificity influencing residues for key transcription factor families

    DEFF Research Database (Denmark)

    Patel, Ronak Y.; Garde, Christian; Stormo, Gary D.

    2015-01-01

    Transcription factors (TFs) are major modulators of transcription and subsequent cellular processes. The binding of TFs to specific regulatory elements is governed by their specificity. Considering the gap between known TFs sequence and specificity, specificity prediction frameworks are highly de...

  18. Comprehensive geophysical and geochemical method and prognosis criteria for the exploration of unconformity type uranium deposit in Russia

    International Nuclear Information System (INIS)

    Li Mao; Chen Zuyi

    2007-01-01

    According to the transcripts of the lectures by Russian experts during the investigation and training in Russia, the comprehensive geophysical and geochemical method and the prognosis criteria of Russia's unconformity type uranium deposit exploration are introduced in the paper. (authors)

  19. Genome-wide transcriptome study in wheat identified candidate genes related to processing quality, majority of them showing interaction (quality x development) and having temporal and spatial distributions.

    Science.gov (United States)

    Singh, Anuradha; Mantri, Shrikant; Sharma, Monica; Chaudhury, Ashok; Tuli, Rakesh; Roy, Joy

    2014-01-16

    The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The present wheat varieties require improvement in processing quality to meet the increasing demand of better quality food products. However, processing quality is very complex and controlled by many genes, which have not been completely explored. To identify the candidate genes whose expressions changed due to variation in processing quality and interaction (quality x development), genome-wide transcriptome studies were performed in two sets of diverse Indian wheat varieties differing for chapatti quality. It is also important to understand the temporal and spatial distributions of their expressions for designing tissue and growth specific functional genomics experiments. Gene-specific two-way ANOVA analysis of expression of about 55 K transcripts in two diverse sets of Indian wheat varieties for chapatti quality at three seed developmental stages identified 236 differentially expressed probe sets (10-fold). Out of 236, 110 probe sets were identified for chapatti quality. Many processing quality related key genes such as glutenin and gliadins, puroindolines, grain softness protein, alpha and beta amylases, proteases, were identified, and many other candidate genes related to cellular and molecular functions were also identified. The ANOVA analysis revealed that the expression of 56 of 110 probe sets was involved in interaction (quality x development). Majority of the probe sets showed differential expression at early stage of seed development i.e. temporal expression. Meta-analysis revealed that the majority of the genes expressed in one or a few growth stages indicating spatial distribution of their expressions. The differential expressions of a few candidate genes such as pre-alpha/beta-gliadin and gamma gliadin were validated by RT-PCR. Therefore, this study

  20. Genome-wide transcriptome study in wheat identified candidate genes related to processing quality, majority of them showing interaction (quality x development) and having temporal and spatial distributions

    Science.gov (United States)

    2014-01-01

    Background The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The present wheat varieties require improvement in processing quality to meet the increasing demand of better quality food products. However, processing quality is very complex and controlled by many genes, which have not been completely explored. To identify the candidate genes whose expressions changed due to variation in processing quality and interaction (quality x development), genome-wide transcriptome studies were performed in two sets of diverse Indian wheat varieties differing for chapatti quality. It is also important to understand the temporal and spatial distributions of their expressions for designing tissue and growth specific functional genomics experiments. Results Gene-specific two-way ANOVA analysis of expression of about 55 K transcripts in two diverse sets of Indian wheat varieties for chapatti quality at three seed developmental stages identified 236 differentially expressed probe sets (10-fold). Out of 236, 110 probe sets were identified for chapatti quality. Many processing quality related key genes such as glutenin and gliadins, puroindolines, grain softness protein, alpha and beta amylases, proteases, were identified, and many other candidate genes related to cellular and molecular functions were also identified. The ANOVA analysis revealed that the expression of 56 of 110 probe sets was involved in interaction (quality x development). Majority of the probe sets showed differential expression at early stage of seed development i.e. temporal expression. Meta-analysis revealed that the majority of the genes expressed in one or a few growth stages indicating spatial distribution of their expressions. The differential expressions of a few candidate genes such as pre-alpha/beta-gliadin and gamma gliadin were validated by RT

  1. Sleep is not just for the brain: transcriptional responses to sleep in peripheral tissues

    Science.gov (United States)

    2013-01-01

    Background Many have assumed that the primary function of sleep is for the brain. We evaluated the molecular consequences of sleep and sleep deprivation outside the brain, in heart and lung. Using microarrays we compared gene expression in tissue from sleeping and sleep deprived mice euthanized at the same diurnal times. Results In each tissue, nearly two thousand genes demonstrated statistically significant differential expression as a function of sleep/wake behavioral state. To mitigate the influence of an artificial deprivation protocol, we identified a subset of these transcripts as specifically sleep-enhanced or sleep-repressed by requiring that their expression also change over the course of unperturbed sleep. 3% and 6% of the assayed transcripts showed “sleep specific” changes in the lung and heart respectively. Sleep specific transcripts in these tissues demonstrated highly significant overlap and shared temporal dynamics. Markers of cellular stress and the unfolded protein response were reduced during sleep in both tissues. These results mirror previous findings in brain. Sleep-enhanced pathways reflected the unique metabolic functions of each tissue. Transcripts related to carbohydrate and sulfur metabolic processes were enhanced by sleep in the lung, and collectively favor buffering from oxidative stress. DNA repair and protein metabolism annotations were significantly enriched among the sleep-enhanced transcripts in the heart. Our results also suggest that sleep may provide a Zeitgeber, or synchronizing cue, in the lung as a large cluster of transcripts demonstrated systematic changes in inter-animal variability as a function of both sleep duration and circadian time. Conclusion Our data support the notion that the molecular consequences of sleep/wake behavioral state extend beyond the brain to include peripheral tissues. Sleep state induces a highly overlapping response in both heart and lung. We conclude that sleep enhances organ specific

  2. To bind or not to bind? Different temporal binding effects from voluntary pressing and releasing actions.

    Science.gov (United States)

    Zhao, Ke; Chen, Yu-Hsin; Yan, Wen-Jing; Fu, Xiaolan

    2013-01-01

    Binding effect refers to the perceptual attraction between an action and an outcome leading to a subjective compression of time. Most studies investigating binding effects exclusively employ the "pressing" action without exploring other types of actions. The present study addresses this issue by introducing another action, releasing action or the voluntary lifting of the finger/wrist, to investigate the differences between voluntary pressing and releasing actions. Results reveal that releasing actions led to robust yet short-lived temporal binding effects, whereas pressing condition had steady temporal binding effects up to super-seconds. The two actions also differ in sensitivity to changes in temporal contiguity and contingency, which could be attributed to the difference in awareness of action. Extending upon current models of "willed action," our results provide insights from a temporal point of view and support the concept of a dual system consisting of predictive motor control and top-down mechanisms.

  3. Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs.

    Science.gov (United States)

    Joshi, Anagha

    2014-12-30

    Transcriptional hotspots are defined as genomic regions bound by multiple factors. They have been identified recently as cell type specific enhancers regulating developmentally essential genes in many species such as worm, fly and humans. The in-depth analysis of hotspots across multiple cell types in same species still remains to be explored and can bring new biological insights. We therefore collected 108 transcription-related factor (TF) ChIP sequencing data sets in ten murine cell types and classified the peaks in each cell type in three groups according to binding occupancy as singletons (low-occupancy), combinatorials (mid-occupancy) and hotspots (high-occupancy). The peaks in the three groups clustered largely according to the occupancy, suggesting priming of genomic loci for mid occupancy irrespective of cell type. We then characterized hotspots for diverse structural functional properties. The genes neighbouring hotspots had a small overlap with hotspot genes in other cell types and were highly enriched for cell type specific function. Hotspots were enriched for sequence motifs of key TFs in that cell type and more than 90% of hotspots were occupied by pioneering factors. Though we did not find any sequence signature in the three groups, the H3K4me1 binding profile had bimodal peaks at hotspots, distinguishing hotspots from mono-modal H3K4me1 singletons. In ES cells, differentially expressed genes after perturbation of activators were enriched for hotspot genes suggesting hotspots primarily act as transcriptional activator hubs. Finally, we proposed that ES hotspots might be under control of SetDB1 and not DNMT for silencing. Transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes. In ES cells, they are predicted to act as transcriptional activator hubs and might be under SetDB1 control for silencing.

  4. Untangling the Effect of Fatty Acid Addition at Species Level Revealed Different Transcriptional Responses of the Biogas Microbial Community Members

    DEFF Research Database (Denmark)

    Treu, Laura; Campanaro, Stefano; Kougias, Panagiotis

    2016-01-01

    In the present study, RNA-sequencing was used to elucidate the change of anaerobic digestion metatranscriptome after long chain fatty acids (oleate) exposure. To explore the general transcriptional behavior of the microbiome, the analysis was first performed on shotgun reads without considering...

  5. Immediate and persistent transcriptional correlates of long-term sensitization training at different CNS loci in Aplysia californica.

    Directory of Open Access Journals (Sweden)

    Samantha Herdegen

    Full Text Available Repeated noxious stimulation produces long-term sensitization of defensive withdrawal reflexes in Aplysia californica, a form of long-term memory that requires changes in both transcription and translation. Previous work has identified 10 transcripts which are rapidly up-regulated after long-term sensitization training in the pleural ganglia. Here we use quantitative PCR to begin examining how these transcriptional changes are expressed in different CNS loci related to defensive withdrawal reflexes at 1 and 24 hours after long-term sensitization training. Specifically, we sample from a the sensory wedge of the pleural ganglia, which exclusively contains the VC nociceptor cell bodies that help mediate input to defensive withdrawal circuits, b the remaining pleural ganglia, which contain withdrawal interneurons, and c the pedal ganglia, which contain many motor neurons. Results from the VC cluster show different temporal patterns of regulation: 1 rapid but transient up-regulation of Aplysia homologs of C/EBP, C/EBPγ, and CREB1, 2 delayed but sustained up-regulation of BiP, Tolloid/BMP-1, and sensorin, 3 rapid and sustained up-regulation of Egr, GlyT2, VPS36, and an uncharacterized protein (LOC101862095, and 4 an unexpected lack of regulation of Aplysia homologs of calmodulin (CaM and reductase-related protein (RRP. Changes in the remaining pleural ganglia mirror those found in the VC cluster at 1 hour but with an attenuated level of regulation. Because these samples had almost no expression of the VC-specific transcript sensorin, our data suggests that sensitization training likely induces transcriptional changes in either defensive withdrawal interneurons or neurons unrelated to defensive withdrawal. In the pedal ganglia, we observed only a rapid but transient increase in Egr expression, indicating that long-term sensitization training is likely to induce transcriptional changes in motor neurons but raising the possibility of different

  6. A Psychophysical Investigation of Differences between Synchrony and Temporal Order Judgments

    Science.gov (United States)

    Love, Scott A.; Petrini, Karin; Cheng, Adam; Pollick, Frank E.

    2013-01-01

    Background Synchrony judgments involve deciding whether cues to an event are in synch or out of synch, while temporal order judgments involve deciding which of the cues came first. When the cues come from different sensory modalities these judgments can be used to investigate multisensory integration in the temporal domain. However, evidence indicates that that these two tasks should not be used interchangeably as it is unlikely that they measure the same perceptual mechanism. The current experiment further explores this issue across a variety of different audiovisual stimulus types. Methodology/Principal Findings Participants were presented with 5 audiovisual stimulus types, each at 11 parametrically manipulated levels of cue asynchrony. During separate blocks, participants had to make synchrony judgments or temporal order judgments. For some stimulus types many participants were unable to successfully make temporal order judgments, but they were able to make synchrony judgments. The mean points of subjective simultaneity for synchrony judgments were all video-leading, while those for temporal order judgments were all audio-leading. In the within participants analyses no correlation was found across the two tasks for either the point of subjective simultaneity or the temporal integration window. Conclusions Stimulus type influenced how the two tasks differed; nevertheless, consistent differences were found between the two tasks regardless of stimulus type. Therefore, in line with previous work, we conclude that synchrony and temporal order judgments are supported by different perceptual mechanisms and should not be interpreted as being representative of the same perceptual process. PMID:23349971

  7. A psychophysical investigation of differences between synchrony and temporal order judgments.

    Science.gov (United States)

    Love, Scott A; Petrini, Karin; Cheng, Adam; Pollick, Frank E

    2013-01-01

    Synchrony judgments involve deciding whether cues to an event are in synch or out of synch, while temporal order judgments involve deciding which of the cues came first. When the cues come from different sensory modalities these judgments can be used to investigate multisensory integration in the temporal domain. However, evidence indicates that that these two tasks should not be used interchangeably as it is unlikely that they measure the same perceptual mechanism. The current experiment further explores this issue across a variety of different audiovisual stimulus types. Participants were presented with 5 audiovisual stimulus types, each at 11 parametrically manipulated levels of cue asynchrony. During separate blocks, participants had to make synchrony judgments or temporal order judgments. For some stimulus types many participants were unable to successfully make temporal order judgments, but they were able to make synchrony judgments. The mean points of subjective simultaneity for synchrony judgments were all video-leading, while those for temporal order judgments were all audio-leading. In the within participants analyses no correlation was found across the two tasks for either the point of subjective simultaneity or the temporal integration window. Stimulus type influenced how the two tasks differed; nevertheless, consistent differences were found between the two tasks regardless of stimulus type. Therefore, in line with previous work, we conclude that synchrony and temporal order judgments are supported by different perceptual mechanisms and should not be interpreted as being representative of the same perceptual process.

  8. A psychophysical investigation of differences between synchrony and temporal order judgments.

    Directory of Open Access Journals (Sweden)

    Scott A Love

    Full Text Available BACKGROUND: Synchrony judgments involve deciding whether cues to an event are in synch or out of synch, while temporal order judgments involve deciding which of the cues came first. When the cues come from different sensory modalities these judgments can be used to investigate multisensory integration in the temporal domain. However, evidence indicates that that these two tasks should not be used interchangeably as it is unlikely that they measure the same perceptual mechanism. The current experiment further explores this issue across a variety of different audiovisual stimulus types. METHODOLOGY/PRINCIPAL FINDINGS: Participants were presented with 5 audiovisual stimulus types, each at 11 parametrically manipulated levels of cue asynchrony. During separate blocks, participants had to make synchrony judgments or temporal order judgments. For some stimulus types many participants were unable to successfully make temporal order judgments, but they were able to make synchrony judgments. The mean points of subjective simultaneity for synchrony judgments were all video-leading, while those for temporal order judgments were all audio-leading. In the within participants analyses no correlation was found across the two tasks for either the point of subjective simultaneity or the temporal integration window. CONCLUSIONS: Stimulus type influenced how the two tasks differed; nevertheless, consistent differences were found between the two tasks regardless of stimulus type. Therefore, in line with previous work, we conclude that synchrony and temporal order judgments are supported by different perceptual mechanisms and should not be interpreted as being representative of the same perceptual process.

  9. MRI lesion and epileptogenic focus in temporal lobe epilepsy

    International Nuclear Information System (INIS)

    Matsuda, Kazumi; Yagi, Kazuichi; Mihara, Tadahiro; Tottori, Takayasu; Watanabe, Yutaka; Seino, Masakazu

    1989-01-01

    The spatial relationship between a circumscribed lesion in the temporal lobe detected by MRI and an epileptogenic focus identified by ictal depth EEG along with a correlation of the MRI lesion with neuropathological findings were investigated in patients with medically intractable temporal lobe epilepsy but without any focal lesion on CT. Four parameters (an areal ratio of the temporal lobe against the hemisphere, area and calculated T1, T2 values of the hippocampus) were used to determine the abnormal MRI side. An agreement was reached in 67-72% of 18 patients between the abnormal values of the hippocampal area and of calculated T1, T2 and the side of the epileptogenic focus. In 14 of 17 patients, typical hippocampal sclerosis was demonstrated in resected tissue in accordance with the MRI lesions (atrophy and/or prolonged T2 of hippocampus). These results imply: 1)MRI abnormality thus defined may, if not all, indicate the side of the epileptogenic focus, and 2)also the presence of hippocampal sclerosis. It was emphasized that the MRI lesion would be a usable instrument to explore the causal relationship of hippocampal sclerosis to a generation of epileptogenic lesions as well as for presurgical evalution. (author)

  10. DNA Binding by the Ribosomal DNA Transcription Factor Rrn3 Is Essential for Ribosomal DNA Transcription*

    Science.gov (United States)

    Stepanchick, Ann; Zhi, Huijun; Cavanaugh, Alice H.; Rothblum, Katrina; Schneider, David A.; Rothblum, Lawrence I.

    2013-01-01

    The human homologue of yeast Rrn3 is an RNA polymerase I-associated transcription factor that is essential for ribosomal DNA (rDNA) transcription. The generally accepted model is that Rrn3 functions as a bridge between RNA polymerase I and the transcription factors bound to the committed template. In this model Rrn3 would mediate an interaction between the mammalian Rrn3-polymerase I complex and SL1, the rDNA transcription factor that binds to the core promoter element of the rDNA. In the course of studying the role of Rrn3 in recruitment, we found that Rrn3 was in fact a DNA-binding protein. Analysis of the sequence of Rrn3 identified a domain with sequence similarity to the DNA binding domain of heat shock transcription factor 2. Randomization, or deletion, of the amino acids in this region in Rrn3, amino acids 382–400, abrogated its ability to bind DNA, indicating that this domain was an important contributor to DNA binding by Rrn3. Control experiments demonstrated that these mutant Rrn3 constructs were capable of interacting with both rpa43 and SL1, two other activities demonstrated to be essential for Rrn3 function. However, neither of these Rrn3 mutants was capable of functioning in transcription in vitro. Moreover, although wild-type human Rrn3 complemented a yeast rrn3-ts mutant, the DNA-binding site mutant did not. These results demonstrate that DNA binding by Rrn3 is essential for transcription by RNA polymerase I. PMID:23393135

  11. DNA binding by the ribosomal DNA transcription factor rrn3 is essential for ribosomal DNA transcription.

    Science.gov (United States)

    Stepanchick, Ann; Zhi, Huijun; Cavanaugh, Alice H; Rothblum, Katrina; Schneider, David A; Rothblum, Lawrence I

    2013-03-29

    The human homologue of yeast Rrn3 is an RNA polymerase I-associated transcription factor that is essential for ribosomal DNA (rDNA) transcription. The generally accepted model is that Rrn3 functions as a bridge between RNA polymerase I and the transcription factors bound to the committed template. In this model Rrn3 would mediate an interaction between the mammalian Rrn3-polymerase I complex and SL1, the rDNA transcription factor that binds to the core promoter element of the rDNA. In the course of studying the role of Rrn3 in recruitment, we found that Rrn3 was in fact a DNA-binding protein. Analysis of the sequence of Rrn3 identified a domain with sequence similarity to the DNA binding domain of heat shock transcription factor 2. Randomization, or deletion, of the amino acids in this region in Rrn3, amino acids 382-400, abrogated its ability to bind DNA, indicating that this domain was an important contributor to DNA binding by Rrn3. Control experiments demonstrated that these mutant Rrn3 constructs were capable of interacting with both rpa43 and SL1, two other activities demonstrated to be essential for Rrn3 function. However, neither of these Rrn3 mutants was capable of functioning in transcription in vitro. Moreover, although wild-type human Rrn3 complemented a yeast rrn3-ts mutant, the DNA-binding site mutant did not. These results demonstrate that DNA binding by Rrn3 is essential for transcription by RNA polymerase I.

  12. Computed tomography of temporal bone fractures and temporal region anatomy in horses.

    Science.gov (United States)

    Pownder, S; Scrivani, P V; Bezuidenhout, A; Divers, T J; Ducharme, N G

    2010-01-01

    In people, specific classifications of temporal bone fractures are associated with clinical signs and prognosis. In horses, similar classifications have not been evaluated and might be useful establishing prognosis or understanding pathogenesis of certain types of trauma. We hypothesized associations between temporal bone fracture location and orientation in horses detected during computed tomography (CT) and frequency of facial nerve (CN7) deficit, vestibulocochlear nerve (CN8) deficit, or temporohyoid osteoarthropathy (THO). Complex temporal region anatomy may confound fracture identification, and consequently a description of normal anatomy was included. All horses undergoing temporal region CT at our hospital between July 1998 and May 2008. Data were collected retrospectively, examiners were blinded, and relationships were investigated among temporal bone fractures, ipsilateral THO, ipsilateral CN7, or ipsilateral CN8 deficits by Chi-square or Fischer's exact tests. Seventy-nine horses had CT examinations of the temporal region (158 temporal bones). Sixteen temporal bone fractures were detected in 14 horses. Cranial nerve deficits were seen with fractures in all parts of the temporal bone (petrosal, squamous, and temporal) and, temporal bone fractures were associated with CN7 and CN8 deficits and THO. No investigated fracture classification scheme, however, was associated with specific cranial nerve deficits. Without knowledge of the regional anatomy, normal structures may be mistaken for a temporal bone fracture or vice versa. Although no fracture classification scheme was associated with the assessed clinical signs, simple descriptive terminology (location and orientation) is recommended for reporting and facilitating future comparisons.

  13. An Algebraic Framework for Temporal Attribute Characteristics

    DEFF Research Database (Denmark)

    Böhlen, M. H.; Gamper, J.; Jensen, Christian Søndergaard

    2006-01-01

    Most real-world database applications manage temporal data, i.e., data with associated time references that capture a temporal aspect of the data, typically either when the data is valid or when the data is known. Such applications abound in, e.g., the financial, medical, and scientific domains...

  14. Schneiderian papilloma of the temporal bone

    NARCIS (Netherlands)

    van der Putten, L.; Bloemena, E.; Merkus, P.; Hensen, E.F.

    2013-01-01

    Temporal bone Schneiderian papilloma may present as a primary tumour originating from the middle ear and mastoid process, or an extension from sinonasal disease. Both forms are rare, this being only the 18th case of primary temporal bone Schneiderian papilloma described to date. Although the current

  15. Temporal logics and real time expert systems

    NARCIS (Netherlands)

    Blom, J.A.

    1996-01-01

    This paper introduces temporal logics. Due to the eternal compromise between expressive adequacy and reasoning efficiency that must decided upon in any application, full (first order logic or modal logic based) temporal logics are frequently not suitable. This is especially true in real time expert

  16. A Temporal Ratio Model of Memory

    Science.gov (United States)

    Brown, Gordon D. A.; Neath, Ian; Chater, Nick

    2007-01-01

    A model of memory retrieval is described. The model embodies four main claims: (a) temporal memory--traces of items are represented in memory partly in terms of their temporal distance from the present; (b) scale-similarity--similar mechanisms govern retrieval from memory over many different timescales; (c) local distinctiveness--performance on a…

  17. Quantifying temporal ventriloquism in audiovisual synchrony perception

    NARCIS (Netherlands)

    Kuling, I.A.; Kohlrausch, A.G.; Juola, J.F.

    2013-01-01

    The integration of visual and auditory inputs in the human brain works properly only if the components are perceived in close temporal proximity. In the present study, we quantified cross-modal interactions in the human brain for audiovisual stimuli with temporal asynchronies, using a paradigm from

  18. Correlated Temporal and Spectral Variability

    Science.gov (United States)

    Swank, Jean H.

    2007-01-01

    The variability of neutron star and black hole X-ray sources has several dimensions, because of the roles played by different important time-scales. The variations on time scales of hours, weeks, and months, ranging from 50% to orders of magnitude, arise out of changes in the flow in the disk. The most important driving forces for those changes are probably various possible instabilities in the disk, though there may be effects with other dominant causes. The changes in the rate of flow appear to be associated with changes in the flow's configuration, as the accreting material approaches the compact object, for there are generally correlated changes in both the Xray spectra and the character of the faster temporal variability. There has been a lot of progress in tracking these correlations, both for Z and Atoll neutron star low-mass X-ray binaries, and for black hole binaries. I will discuss these correlations and review briefly what they tell us about the physical states of the systems.

  19. Abscisic acid promotes proteasome-mediated degradation of the transcription coactivator NPR1 in Arabidopsis thaliana.

    Science.gov (United States)

    Ding, Yezhang; Dommel, Matthew; Mou, Zhonglin

    2016-04-01

    Proteasome-mediated turnover of the transcription coactivator NPR1 is pivotal for efficient activation of the broad-spectrum plant immune responses known as localized acquired resistance (LAR) and systemic acquired resistance (SAR) in adjacent and systemic tissues, respectively, and requires the CUL3-based E3 ligase and its adaptor proteins, NPR3 and NPR4, which are receptors for the signaling molecule salicylic acid (SA). It has been shown that SA prevents NPR1 turnover under non-inducing and LAR/SAR-inducing conditions, but how cellular NPR1 homeostasis is maintained remains unclear. Here, we show that the phytohormone abscisic acid (ABA) and SA antagonistically influence cellular NPR1 protein levels. ABA promotes NPR1 degradation via the CUL3(NPR) (3/) (NPR) (4) complex-mediated proteasome pathway, whereas SA may protect NPR1 from ABA-promoted degradation through phosphorylation. Furthermore, we demonstrate that the timing and strength of SA and ABA signaling are critical in modulating NPR1 accumulation and target gene expression. Perturbing ABA or SA signaling in adjacent tissues alters the temporal dynamic pattern of NPR1 accumulation and target gene transcription. Finally, we show that sequential SA and ABA treatment leads to dynamic changes in NPR1 protein levels and target gene expression. Our results revealed a tight correlation between sequential SA and ABA signaling and dynamic changes in NPR1 protein levels and NPR1-dependent transcription in plant immune responses. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  20. Polyphonic Piano Transcription with a Note-Based Music Language Model

    Directory of Open Access Journals (Sweden)

    Qi Wang

    2018-03-01

    Full Text Available This paper proposes a note-based music language model (MLM for improving note-level polyphonic piano transcription. The MLM is based on the recurrent structure, which could model the temporal correlations between notes in music sequences. To combine the outputs of the note-based MLM and acoustic model directly, an integrated architecture is adopted in this paper. We also propose an inference algorithm, in which the note-based MLM is used to predict notes at the blank onsets in the thresholding transcription results. The experimental results show that the proposed inference algorithm improves the performance of note-level transcription. We also observe that the combination of the restricted Boltzmann machine (RBM and recurrent structure outperforms a single recurrent neural network (RNN or long short-term memory network (LSTM in modeling the high-dimensional note sequences. Among all the MLMs, LSTM-RBM helps the system yield the best results on all evaluation metrics regardless of the performance of acoustic models.

  1. A light- and calcium-gated transcription factor for imaging and manipulating activated neurons.

    Science.gov (United States)

    Wang, Wenjing; Wildes, Craig P; Pattarabanjird, Tanyaporn; Sanchez, Mateo I; Glober, Gordon F; Matthews, Gillian A; Tye, Kay M; Ting, Alice Y

    2017-09-01

    Activity remodels neurons, altering their molecular, structural, and electrical characteristics. To enable the selective characterization and manipulation of these neurons, we present FLARE, an engineered transcription factor that drives expression of fluorescent proteins, opsins, and other genetically encoded tools only in the subset of neurons that experienced activity during a user-defined time window. FLARE senses the coincidence of elevated cytosolic calcium and externally applied blue light, which together produce translocation of a membrane-anchored transcription factor to the nucleus to drive expression of any transgene. In cultured rat neurons, FLARE gives a light-to-dark signal ratio of 120 and a high- to low-calcium signal ratio of 10 after 10 min of stimulation. Opsin expression permitted functional manipulation of FLARE-marked neurons. In adult mice, FLARE also gave light- and motor-activity-dependent transcription in the cortex. Due to its modular design, minute-scale temporal resolution, and minimal dark-state leak, FLARE should be useful for the study of activity-dependent processes in neurons and other cells that signal with calcium.

  2. Transcriptional Regulation During Zygotic Genome Activation in Zebrafish and Other Anamniote Embryos.

    Science.gov (United States)

    Wragg, J; Müller, F

    2016-01-01

    Embryo development commences with the fusion of two terminally differentiated haploid gametes into the totipotent fertilized egg, which through a series of major cellular and molecular transitions generate a pluripotent cell mass. The activation of the zygotic genome occurs during the so-called maternal to zygotic transition and prepares the embryo for zygotic takeover from maternal factors, in the control of the development of cellular lineages during differentiation. Recent advances in next generation sequencing technologies have allowed the dissection of the genomic and epigenomic processes mediating this transition. These processes include reorganization of the chromatin structure to a transcriptionally permissive state, changes in composition and function of structural and regulatory DNA-binding proteins, and changeover of the transcriptome as it is overhauled from that deposited by the mother in the oocyte to a zygotically transcribed complement. Zygotic genome activation in zebrafish occurs 10 cell cycles after fertilization and provides an ideal experimental platform for elucidating the temporal sequence and dynamics of establishment of a transcriptionally active chromatin state and helps in identifying the determinants of transcription activation at polymerase II transcribed gene promoters. The relatively large number of pluripotent cells generated by the fast cell divisions before zygotic transcription provides sufficient biomass for next generation sequencing technology approaches to establish the temporal dynamics of events and suggest causative relationship between them. However, genomic and genetic technologies need to be improved further to capture the earliest events in development, where cell number is a limiting factor. These technologies need to be complemented with precise, inducible genetic interference studies using the latest genome editing tools to reveal the function of candidate determinants and to confirm the predictions made by classic

  3. Microarray analysis of a salamander hopeful monster reveals transcriptional signatures of paedomorphic brain development

    Science.gov (United States)

    2010-01-01

    Background The Mexican axolotl (Ambystoma mexicanum) is considered a hopeful monster because it exhibits an adaptive and derived mode of development - paedomorphosis - that has evolved rapidly and independently among tiger salamanders. Unlike related tiger salamanders that undergo metamorphosis, axolotls retain larval morphological traits into adulthood and thus present an adult body plan that differs dramatically from the ancestral (metamorphic) form. The basis of paedomorphic development was investigated by comparing temporal patterns of gene transcription between axolotl and tiger salamander larvae (Ambystoma tigrinum tigrinum) that typically undergo a metamorphosis. Results Transcript abundances from whole brain and pituitary were estimated via microarray analysis on four different days post hatching (42, 56, 70, 84 dph) and regression modeling was used to independently identify genes that were differentially expressed as a function of time in both species. Collectively, more differentially expressed genes (DEGs) were identified as unique to the axolotl (n = 76) and tiger salamander (n = 292) than were identified as shared (n = 108). All but two of the shared DEGs exhibited the same temporal pattern of expression and the unique genes tended to show greater changes later in the larval period when tiger salamander larvae were undergoing anatomical metamorphosis. A second, complementary analysis that directly compared the expression of 1320 genes between the species identified 409 genes that differed as a function of species or the interaction between time and species. Of these 409 DEGs, 84% exhibited higher abundances in tiger salamander larvae at all sampling times. Conclusions Many of the unique tiger salamander transcriptional responses are probably associated with metamorphic biological processes. However, the axolotl also showed unique patterns of transcription early in development. In particular, the axolotl showed a genome-wide reduction in mRNA abundance

  4. Microarray analysis of a salamander hopeful monster reveals transcriptional signatures of paedomorphic brain development

    Directory of Open Access Journals (Sweden)

    Putta Srikrishna

    2010-06-01

    Full Text Available Abstract Background The Mexican axolotl (Ambystoma mexicanum is considered a hopeful monster because it exhibits an adaptive and derived mode of development - paedomorphosis - that has evolved rapidly and independently among tiger salamanders. Unlike related tiger salamanders that undergo metamorphosis, axolotls retain larval morphological traits into adulthood and thus present an adult body plan that differs dramatically from the ancestral (metamorphic form. The basis of paedomorphic development was investigated by comparing temporal patterns of gene transcription between axolotl and tiger salamander larvae (Ambystoma tigrinum tigrinum that typically undergo a metamorphosis. Results Transcript abundances from whole brain and pituitary were estimated via microarray analysis on four different days post hatching (42, 56, 70, 84 dph and regression modeling was used to independently identify genes that were differentially expressed as a function of time in both species. Collectively, more differentially expressed genes (DEGs were identified as unique to the axolotl (n = 76 and tiger salamander (n = 292 than were identified as shared (n = 108. All but two of the shared DEGs exhibited the same temporal pattern of expression and the unique genes tended to show greater changes later in the larval period when tiger salamander larvae were undergoing anatomical metamorphosis. A second, complementary analysis that directly compared the expression of 1320 genes between the species identified 409 genes that differed as a function of species or the interaction between time and species. Of these 409 DEGs, 84% exhibited higher abundances in tiger salamander larvae at all sampling times. Conclusions Many of the unique tiger salamander transcriptional responses are probably associated with metamorphic biological processes. However, the axolotl also showed unique patterns of transcription early in development. In particular, the axolotl showed a genome

  5. Validation, automatic generation and use of broad phonetic transcriptions

    NARCIS (Netherlands)

    Bael, Cristophe Patrick Jan Van

    2007-01-01

    Broad phonetic transcriptions represent the pronunciation of words as strings of characters from specifically designed symbol sets. In everyday life, broad phonetic transcriptions are often used as aids to pronounce (foreign) words. In addition, broad phonetic transcriptions are often used for

  6. DNA to DNA transcription might exist in eukaryotic cells

    OpenAIRE

    Li, Gao-De

    2016-01-01

    Till now, in biological sciences, the term, transcription, mainly refers to DNA to RNA transcription. But our recently published experimental findings obtained from Plasmodium falciparum strongly suggest the existence of DNA to DNA transcription in the genome of eukaryotic cells, which could shed some light on the functions of certain noncoding DNA in the human and other eukaryotic genomes.

  7. Transcription-associated quality control of mRNP

    DEFF Research Database (Denmark)

    Schmid, Manfred; Jensen, Torben Heick

    2013-01-01

    Although a prime purpose of transcription is to produce RNA, a substantial amount of transcript is nevertheless turned over very early in its lifetime. During transcription RNAs are matured by nucleases from longer precursors and activities are also employed to exert quality control over the RNA...

  8. Transcriptional profile of genes involved in ascorbate glutathione cycle in senescing leaves for an early senescence leaf (esl) rice mutant.

    Science.gov (United States)

    Li, Zhaowei; Su, Da; Lei, Bingting; Wang, Fubiao; Geng, Wei; Pan, Gang; Cheng, Fangmin

    2015-03-15

    To clarify the complex relationship between ascorbate-glutathione (AsA-GSH) cycle and H2O2-induced leaf senescence, the genotype-dependent difference in some senescence-related physiological parameters and the transcript levels and the temporal patterns of genes involved in the AsA-GSH cycle during leaf senescence were investigated using two rice genotypes, namely, the early senescence leaf (esl) mutant and its wild type. Meanwhile, the triggering effect of exogenous H2O2 on the expression of OsAPX genes was examined using detached leaves. The results showed that the esl mutant had higher H2O2 level than its wild type at the initial stage of leaf senescence. At transcriptional level, the association of expression of various genes involved in the AsA-GSH cycle with leaf senescence was isoform dependent. For OsAPXs, the transcripts of two cytosolic OsAPX genes (OsAPX1 and OsAPX2), thylakoid-bound OsAPX8, chloroplastic OsAPX7 and peroxisomal OsAPX4 exhibited remarkable genotype-dependent variation in their expression levels and temporal patterns during leaf senescence, there were significantly increasing transcripts of OsAXP1 and OsAPX7, severely repressed transcripts of OsAPX4 and OsAPX8 for the esl rice at the initial leaf senescence. In contrast, the repressing transcript of OsAPX8 was highly sensitive to the increasing H2O2 level in the senescing rice leaves, while higher H2O2 concentration resulted in the enhancing transcripts of two cytosolic OsAPX genes, OsAPX7 transcript was greatly variable with different H2O2 concentrations and incubating duration, suggesting that the different OsAPXs isoforms played a complementary role in perceiving and scavenging H2O2 accumulation at various H2O2 concentrations during leaf senescence. Higher H2O2 level, increased AsA level, higher activities of APX and glutathione reductase (GR), and relatively stable GSH content during the entire sampling period in the leaves of esl mutant implied that a close interrelationship existed

  9. Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus

    Directory of Open Access Journals (Sweden)

    Kovaleva Galina

    2011-06-01

    Full Text Available Abstract Background Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in bacteria is one of the critical tasks of modern genomics. The Shewanella genus is comprised of metabolically versatile gamma-proteobacteria, whose lifestyles and natural environments are substantially different from Escherichia coli and other model bacterial species. The comparative genomics approaches and computational identification of regulatory sites are useful for the in silico reconstruction of transcriptional regulatory networks in bacteria. Results To explore conservation and variations in the Shewanella transcriptional networks we analyzed the repertoire of transcription factors and performed genomics-based reconstruction and comparative analysis of regulons in 16 Shewanella genomes. The inferred regulatory network includes 82 transcription factors and their DNA binding sites, 8 riboswitches and 6 translational attenuators. Forty five regulons were newly inferred from the genome context analysis, whereas others were propagated from previously characterized regulons in the Enterobacteria and Pseudomonas spp.. Multiple variations in regulatory strategies between the Shewanella spp. and E. coli include regulon contraction and expansion (as in the case of PdhR, HexR, FadR, numerous cases of recruiting non-orthologous regulators to control equivalent pathways (e.g. PsrA for fatty acid degradation and, conversely, orthologous regulators to control distinct pathways (e.g. TyrR, ArgR, Crp. Conclusions We tentatively defined the first reference collection of ~100 transcriptional regulons in 16 Shewanella genomes. The resulting regulatory network contains ~600 regulated genes per genome that are mostly involved in metabolism of carbohydrates, amino acids, fatty acids, vitamins, metals, and stress responses. Several reconstructed regulons including NagR for N-acetylglucosamine catabolism were experimentally validated in S

  10. Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase.

    Science.gov (United States)

    Ahmed, Wareed; Sala, Claudia; Hegde, Shubhada R; Jha, Rajiv Kumar; Cole, Stewart T; Nagaraja, Valakunja

    2017-05-01

    Movement of the transcription machinery along a template alters DNA topology resulting in the accumulation of supercoils in DNA. The positive supercoils generated ahead of transcribing RNA polymerase (RNAP) and the negative supercoils accumulating behind impose severe topological constraints impeding transcription process. Previous studies have implied the role of topoisomerases in the removal of torsional stress and the maintenance of template topology but the in vivo interaction of functionally distinct topoisomerases with heterogeneous chromosomal territories is not deciphered. Moreover, how the transcription-induced supercoils influence the genome-wide recruitment of DNA topoisomerases remains to be explored in bacteria. Using ChIP-Seq, we show the genome-wide occupancy profile of both topoisomerase I and DNA gyrase in conjunction with RNAP in Mycobacterium tuberculosis taking advantage of minimal topoisomerase representation in the organism. The study unveils the first in vivo genome-wide interaction of both the topoisomerases with the genomic regions and establishes that transcription-induced supercoils govern their recruitment at genomic sites. Distribution profiles revealed co-localization of RNAP and the two topoisomerases on the active transcriptional units (TUs). At a given locus, topoisomerase I and DNA gyrase were localized behind and ahead of RNAP, respectively, correlating with the twin-supercoiled domains generated. The recruitment of topoisomerases was higher at the genomic loci with higher transcriptional activity and/or at regions under high torsional stress compared to silent genomic loci. Importantly, the occupancy of DNA gyrase, sole type II topoisomerase in Mtb, near the Ter domain of the Mtb chromosome validates its function as a decatenase.

  11. Exploring Lightning Jump Characteristics

    Science.gov (United States)

    Chronis, Themis; Carey, Larry D.; Schultz, Christopher J.; Schultz, Elise; Calhoun, Kristin; Goodman, Steven J.

    2014-01-01

    This study is concerned with the characteristics of storms exhibiting an abrupt temporal increase in the total lightning flash rate (i.e., lightning jump, LJ). An automated storm tracking method is used to identify storm "clusters" and total lightning activity from three different lightning detection systems over Oklahoma, northern Alabama and Washington, D.C. On average and for different employed thresholds, the clusters that encompass at least one LJ (LJ1) last longer, relate to higher Maximum Expected Size of Hail, Vertical Integrated Liquid and lightning flash rates (area-normalized) than the clusters that did not exhibit any LJ (LJ0). The respective mean values for LJ1 (LJ0) clusters are 80 min (35 min), 14 mm (8 mm), 25 kg per square meter (18 kg per square meter) and 0.05 flash per min per square kilometer (0.01 flash per min per square kilometer). Furthermore, the LJ1 clusters are also characterized by slower decaying autocorrelation functions, a result that implies a less "random" behavior in the temporal flash rate evolution. In addition, the temporal occurrence of the last LJ provides an estimate of the time remaining to the storm's dissipation. Depending of the LJ strength (i.e., varying thresholds), these values typically range between 20-60 min, with stronger jumps indicating more time until storm decay. This study's results support the hypothesis that the LJ is a proxy for the storm's kinematic and microphysical state rather than a coincidental value.

  12. Temporal dynamics of a subtropical urban forest in San Juan, Puerto Rico, 2001-2010

    Science.gov (United States)

    J. M. Tucker Lima; C. L. Staudhammer; T. J. Brandeis; F. J. Escobedo; W. Zipperer

    2013-01-01

    Several studies report urban tree growth and mortality rates as well as species composition, structural dynamics, and other characteristics of urban forests in mostly temperate, inland urban areas. Temporal dynamics of urban forests in subtropical and tropical forest regions are, until now, little explored and represent a new and important direction for study and...

  13. Evolution of bayesian-related research over time: a temporal text mining task

    CSIR Research Space (South Africa)

    de Waal, A

    2006-06-01

    Full Text Available Ronald Reagan’s Radio Addresses? Bayesian Analysis 2006, Volume 1, Number 2, pp. 189-383. 2. Mei Q and Zhai C, 2005. Discovering Evolutionary Theme Patterns from Text – An Exploration of Temporal Text Mining. KDD’05, August 21-24, 2005. Chicago...

  14. Temporal evolution of event-related desynchronization in acute stroke: A pilot study

    NARCIS (Netherlands)

    Tangwiriyasakul, Chayanin; Verhagen, Rens; Rutten, Wim; van Putten, Michel Johannes Antonius Maria

    2014-01-01

    Objective Assessment of event-related desynchronization (ERD) may assist in predicting recovery from stroke and rehabilitation, for instance in BCI applications. Here, we explore the temporal evolution of ERD during stroke recovery. Methods Ten stroke patients and eleven healthy controls were

  15. Visual Temporal Processing in Dyslexia and the Magnocellular Deficit Theory: The Need for Speed?

    Science.gov (United States)

    McLean, Gregor M. T.; Stuart, Geoffrey W.; Coltheart, Veronika; Castles, Anne

    2011-01-01

    A controversial question in reading research is whether dyslexia is associated with impairments in the magnocellular system and, if so, how these low-level visual impairments might affect reading acquisition. This study used a novel chromatic flicker perception task to specifically explore "temporal" aspects of magnocellular functioning…

  16. On the influence of interaural differences on temporal perception of masked noise bursts.

    NARCIS (Netherlands)

    Schimmel, O.V.; Kohlrausch, A.G.

    2006-01-01

    In this research, the influence of interaural differences on temporal positioning of the perceived onset of a dichotic broadband noise target in a diotic broadband noise masker was explored. Interaural time or level differences, a combination of these differences, and filtering with head-related

  17. Temporal self-splitting of optical pulses

    Science.gov (United States)

    Ding, Chaoliang; Koivurova, Matias; Turunen, Jari; Pan, Liuzhan

    2018-05-01

    We present mathematical models for temporally and spectrally partially coherent pulse trains with Laguerre-Gaussian and Hermite-Gaussian Schell-model statistics as extensions of the standard Gaussian Schell model for pulse trains. We derive propagation formulas of both classes of pulsed fields in linearly dispersive media and in temporal optical systems. It is found that, in general, both types of fields exhibit time-domain self-splitting upon propagation. The Laguerre-Gaussian model leads to multiply peaked pulses, while the Hermite-Gaussian model leads to doubly peaked pulses, in the temporal far field (in dispersive media) or at the Fourier plane of a temporal system. In both model fields the character of the self-splitting phenomenon depends both on the degree of temporal and spectral coherence and on the power spectrum of the field.

  18. Microsurgical techniques in temporal lobe epilepsy.

    Science.gov (United States)

    Alonso Vanegas, Mario A; Lew, Sean M; Morino, Michiharu; Sarmento, Stenio A

    2017-04-01

    Temporal lobe resection is the most prevalent epilepsy surgery procedure. However, there is no consensus on the best surgical approach to treat temporal lobe epilepsy. Complication rates are low and efficacy is very high regarding seizures after such procedures. However, there is still ample controversy regarding the best surgical approach to warrant maximum seizure control with minimal functional deficits. We describe the most frequently used microsurgical techniques for removal of both the lateral and mesial temporal lobe structures in the treatment of medically intractable temporal lobe epilepsy (TLE) due to mesial temporal sclerosis (corticoamygdalohippocampectomy and selective amygdalohippocampectomy). The choice of surgical technique appears to remain a surgeon's preference for the near future. Meticulous surgical technique and thorough three-dimensional microsurgical knowledge are essentials for obtaining the best results. Wiley Periodicals, Inc. © 2017 International League Against Epilepsy.

  19. Temporal maps and informativeness in associative learning.

    Science.gov (United States)

    Balsam, Peter D; Gallistel, C Randy

    2009-02-01

    Neurobiological research on learning assumes that temporal contiguity is essential for association formation, but what constitutes temporal contiguity has never been specified. We review evidence that learning depends, instead, on learning a temporal map. Temporal relations between events are encoded even from single experiences. The speed with which an anticipatory response emerges is proportional to the informativeness of the encoded relation between a predictive stimulus or event and the event it predicts. This principle yields a quantitative account of the heretofore undefined, but theoretically crucial, concept of temporal pairing, an account in quantitative accord with surprising experimental findings. The same principle explains the basic results in the cue competition literature, which motivated the Rescorla-Wagner model and most other contemporary models of associative learning. The essential feature of a memory mechanism in this account is its ability to encode quantitative information.

  20. MR imaging in temporal lobe epilepsy

    International Nuclear Information System (INIS)

    Fobben, E.S.; Zimmerman, R.A.; Sperling, M.R.; Kohn, M.I.; Atlas, S.W.; Hackney, D.B.; Goldberg, H.I.; Bilaniuk, L.T.; Grossman, R.I.

    1988-01-01

    MR imaging examinations of 31 patients undergoing temporal lobe resection for refractory partial epilepsy were reviewed retrospectively for the presence of signal abnormalities as well as atrophy. High-signal abnormalities were present in only two of the described 31 patients (6.5%). Pathologically, these represented mesial temporal sclerosis and a hamartoma. Of the remaining 29 cases, 13 showed pathologically varying degrees of mesial temporal sclerosis and gliosis and 16 were pathologically normal. Atrophy, as determined by gross asymmetry, sulcal and temporal horn enlargement, and computer volume measurements, was observed in 23 of 31 patients, correlating with the clinically affected side in 20 and the contralateral side in three. In this series, in contrast to others reported, focal MR signal abnormalities were not detected in the vast majority of patients with mesial temporal sclerosis