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Sample records for factors tfs play

  1. Prognostic Value of EMT-inducing Transcription Factors (EMT-TFs) in Metastatic Breast Cancer: A Systematic Review and Meta-analysis.

    Science.gov (United States)

    Imani, Saber; Hosseinifard, Hossein; Cheng, Jingliang; Wei, Chunli; Fu, Junjiang

    2016-06-23

    The epithelial-to-mesenchymal transition (EMT) is a vital control point in metastatic breast cancer (MBC). TWIST1, SNAIL1, SLUG, and ZEB1, as key EMT-inducing transcription factors (EMT-TFs), are involved in MBC through different signaling cascades. This updated meta-analysis was conducted to assess the correlation between the expression of EMT-TFs and prognostic value in MBC patients. A total of 3,218 MBC patients from fourteen eligible studies were evaluated. The pooled hazard ratios (HR) for EMT-TFs suggested that high EMT-TF expression was significantly associated with poor prognosis in MBC patients (HRs = 1.72; 95% confidence intervals (CIs) = 1.53-1.93; P = 0.001). In addition, the overexpression of SLUG was the most impactful on the risk of MBC compared with TWIST1 and SNAIL1, which sponsored fixed models. Strikingly, the increased risk of MBC was less associated with ZEB1 expression. However, the EMT-TF expression levels significantly increased the risk of MBC in the Asian population (HR = 2.11, 95% CI = 1.70-2.62) without any publication bias (t = 1.70, P = 0.11). These findings suggest that the overexpression of potentially TWIST1, SNAIL1 and especially SLUG play a key role in the aggregation of MBC treatment as well as in the improvement of follow-up plans in Asian MBC patients.

  2. MicroRNA-34a targets epithelial to mesenchymal transition-inducing transcription factors (EMT-TFs) and inhibits breast cancer cell migration and invasion.

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    Imani, Saber; Wei, Chunli; Cheng, Jingliang; Khan, Md Asaduzzaman; Fu, Shangyi; Yang, Luquan; Tania, Mousumi; Zhang, Xianqin; Xiao, Xiuli; Zhang, Xianning; Fu, Junjiang

    2017-03-28

    MicroRNA-34a (miR-34a) plays an essential role against tumorigenesis and progression of cancer metastasis. Here, we analyzed the expression, targets and functional effects of miR-34a on epithelial to mesenchymal transition-inducing transcription factors (EMT-TFs), such as TWIST1, SLUG and ZEB1/2, and an EMT-inducing protein NOTCH1 in breast cancer (BC) cell migration and invasion and its correlation with tumorigenesis and clinical outcomes. Expression of miR-34a is downregulated in human metastatic breast cancers (MBC) compared to normal breast tissues and is negatively correlated with clinicopathological features of MBC patients. Ectopic expression of miR-34a in MBC cell-line BT-549 significantly inhibits cell migration and invasion, but exhibits no clear effect on BC cell growth. We found that miR-34a is able to inactivate EMT signaling pathway with mediatory of NOTCH1, TWIST1, and ZEB1 upon 3'-UTR activity in MBC cell lines, but has no inhibitory effects on SLUG and ZEB2. Furthermore, we investigated the synergistic effects of Thymoquinone (TQ) and miR-34a together on the expression of EMT-associated proteins. Results showed that co-delivery of miR-34a and TQ is able to inactivate EMT signaling pathway by directly targeting TWIST1 and ZEB1 in BT-549 cell line, indicating that they might be a promising therapeutic combination against breast cancer metastasis. Epigenetic inactivation of the EMT-TFs/miR-34a pathway can potentially alter the equilibrium of these regulations, facilitating EMT and metastasis in BC. Altogether, our findings suggest that miR-34a alone could serve as a potential therapeutic agent for MBC, and together with TQ, their therapeutic potential is synergistically enhanced.

  3. Adaptive Forgetting Factor Fictitious Play

    CERN Document Server

    Smyrnakis, Michalis

    2011-01-01

    It is now well known that decentralised optimisation can be formulated as a potential game, and game-theoretical learning algorithms can be used to find an optimum. One of the most common learning techniques in game theory is fictitious play. However fictitious play is founded on an implicit assumption that opponents' strategies are stationary. We present a novel variation of fictitious play that allows the use of a more realistic model of opponent strategy. It uses a heuristic approach, from the online streaming data literature, to adaptively update the weights assigned to recently observed actions. We compare the results of the proposed algorithm with those of stochastic and geometric fictitious play in a simple strategic form game, a vehicle target assignment game and a disaster management problem. In all the tests the rate of convergence of the proposed algorithm was similar or better than the variations of fictitious play we compared it with. The new algorithm therefore improves the performance of game-t...

  4. Teachers and Children Playing with Factorization

    DEFF Research Database (Denmark)

    Valente, Andrea; Marchetti, Emanuela

    2013-01-01

    adventure game and a logic puzzle game. The game design was informed by the results obtained in a 1 year field study exploring and assessing techniques for transposing dynamic and complex domain-specific knowledge into games. Empirical results suggest that children may prefer different forms of play, mainly...... based upon the work conducted by Rogoff (1990) and Säljö (2010). Rogoff (1990) proposes the notion of apprenticeship in thinking, discussing how children learn new skills engaging into goal-directed activities with adults, who support them when reaching their zone of proximal development, defined...... is that we show how a computer game can effectively turn an abstract concept into a virtual artefact, that learners can then probe in a playful way, as well as study empirically, to explore alternative hypothesis circa its workings and verify them through experiments. This allows the learners to move from...

  5. Establishment and optimization for TALE-TFs construction%TALE-TFs构建方法的建立及优化

    Institute of Scientific and Technical Information of China (English)

    王媛媛; 苏攀柯; 黄爱龙; 胡接力

    2015-01-01

    Objective To optimize the method of transcription activator‐like effector transcription factors (TALE‐TFs) con‐struction ,some improvement and adaption were made based on the traditional methods .Methods We first constructed the basic tandem fragments with different length ,including trimer ,tetramer ,pentamer and hexamer by Golden Gate cloning technique and PCR ,then the procedure with the highest efficacy was chosen to construct our TALE‐TFs .To determine the function of the TALE‐TFs ,the plasmid pminCMV with the specific binding sequence of TALE‐TFs was constructed by fragment substitution reaction (FSR) .The transcription activating function of TALE‐TFs was confirmed by the intensity of red fluorescence ,after TALE‐TFs , pEGFP‐N1 and pminCMV plasmid were co‐transfected into 293HEK cells .Results An optimized method for TALE‐TFs construc‐tion and functional assay was established .Conclusion This method can potentially be wildly used in fields that the expression of some constitutively expressed genes needs to be modified .%目的:在传统方案的基础上建立一种经济有效且易于操作的类转录激活效应子转录因子(TALE‐TFs)的构建和功能检测方案。方法采用基于PCR的Golden gate克隆法分别尝试构建类转录激活效应物(TALEs)的六聚体、五聚体、四聚体和三聚体,比较构建结果,选择最优效果方案进行TALE‐TFs的构建。采用片段置换反应(FSR)构建了含有 TALE‐TFs结合片段的RFP质粒pminCMV ,并与TALE‐TFs进行共转染,观察红色荧光验证TALE‐TFs的转录活性。结果 TALEs中所含的串联重复模块越少,获得的构建产物越多。共转染时,TALE‐TFs使得pminCMV成功启动表达。结论该研究为不同条件下实验方案的选择提供了依据,并利用含有TALE‐TF结合片段和红色荧光的质粒建立了快捷直观的转录活性验证方法。

  6. Convergent evolution of RFX transcription factors and ciliary genes predated the origin of metazoans

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    Chen Nansheng

    2010-05-01

    Full Text Available Abstract Background Intraflagellar transport (IFT genes, which are critical for the development and function of cilia and flagella in metazoans, are tightly regulated by the Regulatory Factor X (RFX transcription factors (TFs. However, how and when their evolutionary relationship was established remains unknown. Results We have identified evidence suggesting that RFX TFs and IFT genes evolved independently and their evolution converged before the first appearance of metazoans. Both ciliary genes and RFX TFs exist in all metazoans as well as some unicellular eukaryotes. However, while RFX TFs and IFT genes are found simultaneously in all sequenced metazoan genomes, RFX TFs do not co-exist with IFT genes in most pre-metazoans and thus do not regulate them in these organisms. For example, neither the budding yeast nor the fission yeast possesses cilia although both have well-defined RFX TFs. Conversely, most unicellular eukaryotes, including the green alga Chlamydomonas reinhardtii, have typical cilia and well conserved IFT genes but lack RFX TFs. Outside of metazoans, RFX TFs and IFT genes co-exist only in choanoflagellates including M. brevicollis, and only one fungus Allomyces macrogynus of the 51 sequenced fungus genomes. M. brevicollis has two putative RFX genes and a full complement of ciliary genes. Conclusions The evolution of RFX TFs and IFT genes were independent in pre-metazoans. We propose that their convergence in evolution, or the acquired transcriptional regulation of IFT genes by RFX TFs, played a pivotal role in the establishment of metazoan.

  7. The Play Factor: Effect of Social Skills Group Play Therapy on Adolescent African-American Males

    Science.gov (United States)

    Earls, Melissa K.

    2009-01-01

    The purpose of this study was to examine the effectiveness of Social Skills Group Play Therapy on remedying the social skills deficits of adolescent African-American males. Additionally, the study investigated whether age and grade level impacted the outcome of the intervention. The participants were adolescent African-American males ages 10 to…

  8. Perceived migraine triggers: do dietary factors play a role?

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    F. Camboim Rockett

    Full Text Available The present cross-sectional study was designed to assess the frequency of 36 possible triggering factors precipitating a migraine crisis (hormonal, environmental, and dietary in adult outpatients suffering from migraine attacks. A group of 123 migraine sufferers, aged 43.2 ± 13.9 (mean ± SD years, including 114 (92.7% women, 68.3% having migraine without aura, 68.3% reporting pain severe enough to require drug prophylaxis, and 29.3% presenting with hypertension, were evaluated. The most common triggers were stress and fasting, and environmental and hormonal factors were frequently found to precipitate a crisis. More than 90% of the patients reported susceptibility to 5 or more factors, and only 2.4% did not complain about any dietary factor. The large number of triggers detected in the present study emphasises the importance of awareness and avoidance of these factors in the management of patients with migraine.

  9. Do intercultural factors play a role in exacerbating psychiatric symptoms?

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    Ong, Yong Lock; Yap, Hwa Ling

    2013-01-01

    We report the case of a 29-year-old mixed-race woman suffering from recurrent major depressive episodes, with suicidal ideation and risk, involving several inpatient admissions. A comorbid diagnosis of borderline personality disorder was also recorded in one of her previous inpatient admissions. During her last inpatient admission, a multidisciplinary case discussion and review of the patient's life highlighted several possible intercultural trigger factors that could have contributed to the exacerbation of her psychiatric illness. We emphasise the need to explore intercultural predisposing and precipitating factors for a more complete psychodynamic understanding of psychiatric illnesses among the multiracial population of Singapore. This also adds to the discussion on the management of such patients with the option of formal in-depth psychotherapy in adjunct to medication. This may prevent recurrent relapses, modify suicide intent and reduce the necessity for inpatient treatment, which will be cost-effective and result in efficacious treatment.

  10. Genome-Wide Identification of the Transcription Factors Involved in Citrus Fruit Ripening from the Transcriptomes of a Late-Ripening Sweet Orange Mutant and Its Wild Type.

    Science.gov (United States)

    Wu, Juxun; Fu, Lili; Yi, Hualin

    2016-01-01

    Fruit ripening is a genetically programmed process. Transcription factors (TFs) play key roles in plant development and ripening by temporarily and spatially regulating the transcription of their target genes. In this study, a total of 159 TFs were identified from a spontaneous late-ripening mutant 'Fengwan' (C. sinensis L. Osbeck) sweet orange (MT) and its wild-type counterpart ('Fengjie 72-1', WT) along the ripening period via the Transcription Factor Prediction of PlantTFDB 3.0. Fifty-two differentially expressed TFs were identified between MT and WT; 92 and 120 differentially expressed TFs were identified in WT and MT, respectively. The Venn diagram analysis showed that 16 differentially expressed TFs were identified between MT and WT and during the ripening of WT and MT. These TFs were primarily assigned to the families of C2H2, Dof, bHLH, ERF, MYB, NAC and LBD. Particularly, the number of TFs of the ERF family was the greatest between MT and WT. According to the results of the WGCNA analysis, a weighted correlation network analysis tool, several important TFs correlated to abscisic acid (ABA), citric acid, fructose, glucose and sucrose were identified, such as RD26, NTT, GATA7 and MYB21/62/77. Hierarchical cluster analysis and the expression analysis conducted at five fruit ripening stages further validated the pivotal TFs that potentially function during orange fruit development and ripening.

  11. Interactions of transcription factors with chromatin.

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    van Bakel, Harm

    2011-01-01

    Sequence-specific transcription factors (TFs) play a central role in regulating transcription initiation by directing the recruitment and activity of the general transcription machinery and accessory factors. It is now well established that many of the effects exerted by TFs in eukaryotes are mediated through interactions with a host of coregulators that modify the chromatin state, resulting in a more open (in case of activation) or closed conformation (in case of repression). The relationship between TFs and chromatin is a two-way street, however, as chromatin can in turn influence the recognition and binding of target sequences by TFs. The aim of this chapter is to highlight how this dynamic interplay between TF-directed remodelling of chromatin and chromatin-adjusted targeting of TF binding determines where and how transcription is initiated, and to what degree it is productive.

  12. Exploring the Functional Disorder and Corresponding Key Transcription Factors in Intraductal Papillary Mucinous Neoplasms Progression

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    Guiying Bai

    2015-01-01

    Full Text Available This study has analyzed the gene expression patterns of an IPMN microarray dataset including normal pancreatic ductal tissue (NT, intraductal papillary mucinous adenoma (IPMA, intraductal papillary mucinous carcinoma (IPMC, and invasive ductal carcinoma (IDC samples. And eight clusters of differentially expressed genes (DEGs with similar expression pattern were detected by k-means clustering. Then a survey map of functional disorder in IPMN progression was established by functional enrichment analysis of these clusters. In addition, transcription factors (TFs enrichment analysis was used to detect the key TFs in each cluster of DEGs, and three TFs (FLI1, ERG, and ESR1 were found to significantly regulate DEGs in cluster 1, and expression of these three TFs was validated by qRT-PCR. All these results indicated that these three TFs might play key roles in the early stages of IPMN progression.

  13. Viola Playing May Be a Strong Aggravating Factor for Temporomandibular Disorder

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    Mahmut Alpayci

    2014-12-01

    Full Text Available Temporomandibular disorder (TMD is the general term used to describe the symptoms originated from temporomandibular joint region. The most common symptom of the disorder is pain during mandibular movement. Etiology of TMD is multifactorial. Several factors such as trauma, occlusal discrepancies, stress, parafunctions, hypermobility, and heredity can make one more vulnerable to this disorder. It has been reported that viola playing might be a predisposing factor for TMD. In this article, we present a 24 year old male patient suffering from TMD symptoms exacerbated by viola playing and emphasize that viola playing may be a powerful aggravating factor for TMD.

  14. Contributing Factors on Malaysia Preschool Teachers' Belief, Attitude and Competence in Using Play Activities

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    Jantan, Hafsah Binti; Bin Hamdan, Abdul Rahim; Yahya, Fauziah Hj; Saleh, Halimatussadiah Binti; Ong, Mohd Hanafi Bin Azman

    2015-01-01

    This study focused on preschool teachers' belief, attitude, knowledge and competence in using play in Malaysia. Its purpose is to find out indicators significantly contribute to belief, attitude, knowledge and competence in play of preschool teachers in Malaysia. The method used was factor analysis in order to confirm indicators in each variable…

  15. Young Mothers' Play with Their Toddlers: Individual Variability as a Function of Psychosocial Factors

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    Driscoll, Joan Riley; Easterbrooks, M. Ann

    2007-01-01

    There is no one style of parenting which characterizes young mothers as a group. In addition, life circumstances play an important role in shaping maternal behaviour. The aim of this study was to identify patterns of maternal play behaviour and contextual (social and personal) factors associated with these different patterns. In this study, 107…

  16. Genetic mapping and comparative expression analysis of transcription factors in cotton.

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    Chen, Xuemei; Jin, Xin; Li, Ximei; Lin, Zhongxu

    2015-01-01

    Transcription factors (TFs) play an important role in the regulation of plant growth and development. The study of the structure and function of TFs represents a research frontier in plant molecular biology. The findings of these studies will provide significant information regarding genetic improvement traits in crops. Currently, a large number of TFs have been cloned, and their function has been verified. However, relatively few studies that genetically map TFs in cotton are available. To genetically map TFs in cotton in this study, specific primers were designed for TF genes that were published in the Plant Transcription Factor Database. A total of 977 TF primers were obtained, and 31 TF polymorphic loci were mapped on 15 cotton chromosomes. These polymorphic loci were clearly preferentially distributed on chromosomes 5, 11, 19 and 20; and TFs from the same family mapped to homologous cotton chromosomes. In-silico mapping verified that many mapped TFs were mapped on their corresponding chromosomes or their homologous chromosomes' corresponding chromosomes in the diploid genomes. QTL mapping for fiber quality revealed that TF-Ghi005602-2 mapped on Chr19 was associated with fiber length. Eighty-five TF genes were selected for RT-PCR analysis, and 4 TFs were selected for qRT-PCR analysis, revealing unique expression patterns across different stages of fiber development between the mapping parents. Our data offer an overview of the chromosomal distribution of TFs in cotton, and the comparative expression analysis between Gossypium hirsutum and G. barbadense provides a rough understanding of the regulation of TFs during cotton fiber development.

  17. Data in support of FSH induction of IRS-2 in human granulosa cells: Mapping the transcription factor binding sites in human IRS-2 promoter

    OpenAIRE

    Surleen Kaur; Anjali, G.; Priya Bhardwaj; Jyoti Taneja; Rita Singh

    2015-01-01

    Insulin receptor substrate-2 (IRS-2) plays critical role in the regulation of various metabolic processes by insulin and IGF-1. The defects in its expression and/or function are linked to diseases like polycystic ovary syndrome (PCOS), insulin resistance and cancer. To predict the transcription factors (TFs) responsible for the regulation of human IRS-2 gene expression, the transcription factor binding sites (TFBS) and the corresponding TFs were investigated by analysis of IRS-2 promoter sequ...

  18. Validation of a Seven-Factor Structure for the Motives for Playing Drinking Games Measure.

    Science.gov (United States)

    Zamboanga, Byron L; Audley, Shannon; Olthuis, Janine V; Blumenthal, Heidemarie; Tomaso, Cara C; Bui, Ngoc; Borsari, Brian

    2017-04-01

    Playing drinking games can be characterized as a high-risk drinking activity because games are typically designed to promote heavy alcohol consumption. While research suggests that young adults are motivated to play drinking games for a variety of reasons (e.g., for thrills/fun, for the competition), the Motives for Playing Drinking Games measure has received limited empirical attention. We examined the psychometric properties of this measure with a confirmation sample of young adults recruited from Amazon's MTurk ( N = 1,809, ages 18-25 years, 47% men; 41% not currently enrolled in college) and a validation sample of college students ( N = 671; ages 18-23 years; 26% men). Contrary to the 8-factor model obtained by Johnson and Sheets in a study published in 2004, examination of the factor structure with our confirmation sample yielded a revised 7-factor model that was invariant across race/ethnicity and college student status. This model was also validated with the college student sample. In the confirmation sample, enhancement/thrills and sexual pursuit motives for playing drinking games were positively associated with gaming frequency/consumption and negative gaming consequences. Furthermore, conformity motives for playing drinking games were positively associated with negative gaming consequences, while competition motives were positively associated with gaming frequency. These findings have significant implications for research and prevention/intervention efforts.

  19. Viola Playing May Be a Strong Aggravating Factor for Temporomandibular Disorder

    OpenAIRE

    Mahmut Alpayci

    2014-01-01

    Temporomandibular disorder (TMD) is the general term used to describe the symptoms originated from temporomandibular joint region. The most common symptom of the disorder is pain during mandibular movement. Etiology of TMD is multifactorial. Several factors such as trauma, occlusal discrepancies, stress, parafunctions, hypermobility, and heredity can make one more vulnerable to this disorder. It has been reported that viola playing might be a predisposing factor for TMD. In this article, we p...

  20. Factors That Play a Role in the Academic Resilience of Academicians

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    Ömer KUTLU

    2016-12-01

    Full Text Available In academic life, it is possible for all students to experience different obstacles, hardships and setbacks. While some students fail to negotiate their way through these difficulties, many are successful. In this context, the purpose of this study is to reveal the factors that play a role in the academic resilience of academicians. In this context, a qualitative study was employed, with semi-structured interviews conducted with 11 academicians from the Educational Sciences Faculty of Ankara University, Turkey. Eligibility criteria required academicians to have had a risk factor in their life. The academicians were also selected on the basis of their title and years of experience to sustain variety. In order to conduct interviews, an interview guide was prepared by the researchers. The questions in the interview guide for this study were linked to risk factors, and internal and external protective factors. Descriptive analysis was used to analyze collected data. According to the findings, mainly risk factors which academically resilient academicians had experienced were poverty, and negative environmental conditions. On the other hand, this study revealed that internal factors such as self-esteem, decisiveness, curiosity and external factors such as family support, qualified teachers, and peer relations helped them to overcome their risk factors.

  1. Serum response factor play a regulative role in the gene expression in heart failure

    Institute of Scientific and Technical Information of China (English)

    Xiaoxia WU; Guang ZHI; Tao WAN; Jiajin WU

    2005-01-01

    To investigate the relationship between transcription factor and the change of protein expression levels in heart failure. Methods Bioinformatic method was used to analyze the data of binding-sites on the 5 ' flaking regions of four genes whose mRNA level changed in failing heart from three databases about nucleic acid-EMBL, transcriptional regulation factor-TRANSFAC and protein-SWISS-PORT.The expression level of selected transcription factor was determined by immunohischemical method.Results Nine transcription factors were inferred to influence the proteins' levels in occurrence and development of heart failure.Serum response factor (SRF) was selected from the nine factors and assayed. The results showed that there was a higher level of SRF in healthy group than in chronic heart failure (CHF), and the level was associated with the degree of CHF. It was also found that there was a relative higher level of SRF in the acute myocardial infarction (AMI) than that in CHF, but which was lower than the healthy. Conclusion It showed that SRF had a quantitative change in the development of heart failure, and suggested SRF might play an important regulative role in heart failure. The expression changes of proteins related to myocardial function might be regulated by the quantitative change of transcription factor(s).

  2. Transcription factors as tools to engineer enhanced drought stress tolerance in plants.

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    Hussain, Syed Sarfraz; Kayani, Mahmood Akhtar; Amjad, Muhammad

    2011-01-01

    Plant growth and productivity are greatly affected by abiotic stresses such as drought, salinity, and temperature. Drought stress is one of the major limitations to crop productivity worldwide due to its multigene nature, making the production of transgenic crops a challenging prospect. To develop crop plant with enhanced tolerance of drought stress, a basic understanding of physiological, biochemical, and gene regulatory networks is essential. In the signal transduction network that leads from the perception of stress signals to the expression of stress-responsive genes, transcription factors (TFs) play an essential role. Because TFs, as opposed to most structural genes, tend to control multiple pathways steps, they have emerged as powerful tools for the manipulation of complex metabolic pathways in plants. One such class of TFs is DREB/CBF that binds to drought responsive cis-acting elements. Transgenic plants have been developed with enhanced stress tolerance by manipulating the expression of DREB/CBF. Recently the functions of an increasing number of plant TFs are being elucidated and increased understanding of these factors in controlling drought stress response has lead to practical approaches for engineering stress tolerance in plants. The utility of the various TFs in plant stress research we review is illustrated by several published examples. The manipulation of native plant regularity networks therefore represents a new era for genetically modified crops. This review focuses on the recent understanding, latest advancements related to TFs and present status of their deployment in developing stress tolerant transgenic plants.

  3. A Factor-Based Exploration of Player´s Continuation Desire in Free-to-Play Mobile Games

    DEFF Research Database (Denmark)

    Stankevicius, Deividas; Jady, Hawraa Amira; Drachen, Anders

    2015-01-01

    the perceived user experience factors relevant for Continuation Desire and then attempts to predict play-ers’ intention to continue playing. Structural Equation Mod-eling analysis was performed to validate the model and to predict the intention of continuation desire. At the same time, exploring why people...... continue playing, based on ex-periments using Candy Crush Saga, one of the most popular Free-to-Play mobile games worldwide. The findings indi-cate that motivation is an important factor of Continuation Desire in Free-to-Play mobile games, with engagement, en-joyment and flow being less important...

  4. The transcription factor NFATp plays a key role in susceptibility to TB in mice.

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    Laura E Via

    Full Text Available In T cells, the transcription factor nuclear factor of activated T cells p (NFATp is a key regulator of the cytokine genes tumor necrosis factor (TNF and interferon-γ (IFN-γ. Here, we show that NFATp-deficient (NFATp(-/- mice have a dramatic and highly significant increase in mortality after Mycobacterium tuberculosis (MTb infection as compared to mortality of control animals after MTb infection. Animals deficient in NFATp have significantly impaired levels of TNF and IFN-γ transcription and protein expression in naïve or total CD4(+ T cells, but display wild-type levels of TNF mRNA or protein from MTb-stimulated dendritic cells (DC. The rapid mortality and disease severity observed in MTb-infected NFATp(-/- mice is associated with dysregulated production of TNF and IFN-γ in the lungs, as well as with increased levels of TNF, in their serum. Furthermore, global blocking of TNF production by injection of a TNF neutralizaing agent at 6 weeks, but not 12 weeks, post-MTb-infection further decreased the survival rate of both wild-type and NFATp(-/- mice, indicating an early role for TNF derived from cells from the monocyte lineage in containment of infection. These results thus demonstrate that NFATp plays a critical role in immune containment of TB disease in vivo, through the NFATp-dependent expression of TNF and IFN-γ in T cells.

  5. Kruppel-like factor KLF8 plays a critical role in adipocyte differentiation.

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    Haemi Lee

    Full Text Available KLF8 (Krüppel-like factor 8 is a zinc-finger transcription factor known to play an essential role in the regulation of the cell cycle, apoptosis, and differentiation. However, its physiological roles and functions in adipogenesis remain unclear. In the present study, we show that KLF8 acts as a key regulator controlling adipocyte differentiation. In 3T3-L1 preadipocytes, we found that KLF8 expression was induced during differentiation, which was followed by expression of peroxisome proliferator-activated receptor γ (PPARγ and CCAAT/enhancer-binding protein α (C/EBPα. Adipocyte differentiation was significantly attenuated by the addition of siRNA against KLF8, whereas overexpression of KLF8 resulted in enhanced differentiation. Furthermore, luciferase reporter assays demonstrated that overexpression of KLF8 induced PPARγ2 and C/EBPα promoter activity, suggesting that KLF8 is an upstream regulator of PPARγ and C/EBPα. The KLF8 binding sites were localized by site mutation analysis to -191 region in C/EBPα promoter and -303 region in PPARγ promoter, respectively. Taken together, these data reveal that KLF8 is a key component of the transcription factor network that controls terminal differentiation during adipogenesis.

  6. Prediction of nucleosome positioning based on transcription factor binding sites.

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    Xianfu Yi

    Full Text Available BACKGROUND: The DNA of all eukaryotic organisms is packaged into nucleosomes, the basic repeating units of chromatin. The nucleosome consists of a histone octamer around which a DNA core is wrapped and the linker histone H1, which is associated with linker DNA. By altering the accessibility of DNA sequences, the nucleosome has profound effects on all DNA-dependent processes. Understanding the factors that influence nucleosome positioning is of great importance for the study of genomic control mechanisms. Transcription factors (TFs have been suggested to play a role in nucleosome positioning in vivo. PRINCIPAL FINDINGS: Here, the minimum redundancy maximum relevance (mRMR feature selection algorithm, the nearest neighbor algorithm (NNA, and the incremental feature selection (IFS method were used to identify the most important TFs that either favor or inhibit nucleosome positioning by analyzing the numbers of transcription factor binding sites (TFBSs in 53,021 nucleosomal DNA sequences and 50,299 linker DNA sequences. A total of nine important families of TFs were extracted from 35 families, and the overall prediction accuracy was 87.4% as evaluated by the jackknife cross-validation test. CONCLUSIONS: Our results are consistent with the notion that TFs are more likely to bind linker DNA sequences than the sequences in the nucleosomes. In addition, our results imply that there may be some TFs that are important for nucleosome positioning but that play an insignificant role in discriminating nucleosome-forming DNA sequences from nucleosome-inhibiting DNA sequences. The hypothesis that TFs play a role in nucleosome positioning is, thus, confirmed by the results of this study.

  7. Mechanical factors play an important role in pectus excavatum with thoracic scoliosis

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    Wang Yuncang

    2012-11-01

    Full Text Available Abstract Background This study investigated the incidence, imaging characteristics and mechanical factors in scoliotic patients with pectus excavatum. Methods A total of 142 scoliostic patients with pectus excavatum were evaluated prior to operation. The evaluation included a complete physical exam, phenotype and severity of the pectus excavatum, incidence and severity of scoliosis, and analysis of radiological images, including calculation of the Haller index. Results Twenty five out of 142 patients (17.61% with pectus excavatum had scoliosis with a Cobb angle >10 degrees, and in 80.00% of the cases the spinal column was bent to the right. Seventeen patients had bent-to-the-right spines that involved the 6th to 10 th thoracic vertebrae. We found that 23 out of 25 patients with a Cobb angle more than 10° were teenagers and adults. The incidence of scoliosis was only 6.06% in the children under 11 years whereas it was 21.79% in the teenage group. Conclusions Mechanical forces appear to play a role in the coexistence of pectus excavatum and scoliosis. There is a relationship between age, severity (Haller index, asymmetry and scoliosis. The heart and mediastinum play a role in providing an outward force to the left of the sternum which may be an important reason for the coexistence of pectus excavatum and scoliosis, but the correlation needs further proof.

  8. Factors influencing player preferences for heroic roles in role-playing games.

    Science.gov (United States)

    Hsu, Shang Hwa; Kao, Ching-Han; Wu, Muh-Cherng

    2007-04-01

    Two studies were conducted to investigate whether player personality or social cognition influence preferences for heroic roles in role-playing games (RPG). In Study 1, 149 teenager subjects were categorized into five groups according to the Guilford Personality Inventory. Heroes were clustered into three types based on their attributes. The analysis of variance (ANOVA) results indicated that each personality group did not display distinctive preference for any particular heroic type. However, of the three heroic types teenagers most strongly preferred, Justice Warrior was followed, in order of preference, by Visionary Leader and Saint. In Study 2, the influence of three player social cognition factors (similarity, proximity, and familiarity) on player preference for heroic roles was studied. Multiple regression analysis results indicated that similarity and familiarity predicted player preferences for heroic roles.

  9. Factors affecting exercise intensity in professional rugby league match-play.

    Science.gov (United States)

    Kempton, Thomas; Coutts, Aaron J

    2016-06-01

    To examine the effects of match-related and individual player characteristics on running performance in professional rugby league matches. Longitudinal observational study. Global positioning system (GPS) and technical performance measures (attacking involvements and tackles made) were collected from 23 players competing in the National Rugby League (NRL) over 24 matches during a season. The GPS data were categorised into relative total distance (mmin(-1)) and relative high-speed running distance (HSR mmin(-1), >14.4kmh(-1)). Each match was classified according to season phase, location, recovery length, opposition strength and result. Individual player fitness status was obtained from a 1.2-km shuttle run test conducted prior to the start of the season. Two separate linear mixed models were constructed to examine the influence of match-related and individual player characteristics on relative total and HSR distances. Matches played away from home, early in the season and following short recovery cycles were associated with reduced relative total and HSR distances. Matches won contained less relative total and HSR distance; whereas only HSR distance was higher against weaker opposition. The total time the ball was out of play reduced relative total but not HSR distances. The number of defensive but not attacking involvements influenced both physical performance measures. Finally, player fitness was positively related to both relative total and HSR distances. There appears to be a complex interplay of factors affecting match-running performance in rugby league. The results underline the importance of considering contextual factors when analysing rugby league match-activity profiles. Copyright © 2015 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

  10. Structure, Function and Networks of Transcription Factors Involved in Abiotic Stress Responses

    Directory of Open Access Journals (Sweden)

    Karen Skriver

    2013-03-01

    Full Text Available Transcription factors (TFs are master regulators of abiotic stress responses in plants. This review focuses on TFs from seven major TF families, known to play functional roles in response to abiotic stresses, including drought, high salinity, high osmolarity, temperature extremes and the phytohormone ABA. Although ectopic expression of several TFs has improved abiotic stress tolerance in plants, fine-tuning of TF expression and protein levels remains a challenge to avoid crop yield loss. To further our understanding of TFs in abiotic stress responses, emerging gene regulatory networks based on TFs and their direct targets genes are presented. These revealed components shared between ABA-dependent and independent signaling as well as abiotic and biotic stress signaling. Protein structure analysis suggested that TFs hubs of large interactomes have extended regions with protein intrinsic disorder (ID, referring to their lack of fixed tertiary structures. ID is now an emerging topic in plant science. Furthermore, the importance of the ubiquitin-proteasome protein degradation systems and modification by sumoylation is also apparent from the interactomes. Therefore; TF interaction partners such as E3 ubiquitin ligases and TF regions with ID represent future targets for engineering improved abiotic stress tolerance in crops.

  11. Hypoxia-inducible factor plays a gut-injurious role in intestinal ischemia reperfusion injury.

    Science.gov (United States)

    Kannan, Kolenkode B; Colorado, Iriana; Reino, Diego; Palange, David; Lu, Qi; Qin, Xiaofa; Abungu, Billy; Watkins, Anthony; Caputo, Francis J; Xu, Da-Zhong; Semenza, Gregg L; Deitch, Edwin A; Feinman, Rena

    2011-05-01

    Gut injury and loss of normal intestinal barrier function are key elements in the paradigm of gut-origin systemic inflammatory response syndrome, acute lung injury, and multiple organ dysfunction syndrome (MODS). As hypoxia-inducible factor (HIF-1) is a critical determinant of the physiological and pathophysiological response to hypoxia and ischemia, we asked whether HIF-1 plays a proximal role in the induction of gut injury and subsequent lung injury. Using partially HIF-1α-deficient mice in an isolated superior mesenteric artery occlusion (SMAO) intestinal ischemia reperfusion (I/R) injury model (45 min SMAO followed by 3 h of reperfusion), we showed a direct relationship between HIF-1 activation and intestinal I/R injury. Specifically, partial HIF-1α deficiency attenuated SMAO-induced increases in intestinal permeability, lipid peroxidation, mucosal caspase-3 activity, and IL-1β mRNA levels. Furthermore, partial HIF-1α deficiency prevented the induction of ileal mucosal inducible nitric oxide synthase (iNOS) protein levels after SMAO and iNOS deficiency ameliorated SMAO-induced villus injury. Resistance to SMAO-induced gut injury was also associated with resistance to lung injury, as reflected by decreased levels of myeloperoxidase, IL-6 and IL-10 in the lungs of HIF-1α(+/-) mice. In contrast, a short duration of SMAO (15 min) followed by 3 h of reperfusion neither induced mucosal HIF-1α protein levels nor caused significant gut and lung injury in wild-type or HIF-1α(+/-) mice. This study indicates that intestinal HIF-1 activation is a proximal regulator of I/R-induced gut mucosal injury and gut-induced lung injury. However, the duration and severity of the gut I/R insult dictate whether HIF-1 plays a gut-protective or deleterious role.

  12. A high-affinity inhibitor of yeast carboxypeptidase Y is encoded by TFS1 and shows homology to a family of lipid binding proteins

    DEFF Research Database (Denmark)

    Bruun, A W; Svendsen, I; Sørensen, S O;

    1998-01-01

    degree of specificity, showing a 200-fold higher Ki toward a carboxypeptidase from Candida albicans which is highly homologous to carboxypeptidase Y. The TFS1 gene product shows extensive similarity to a class of proteins termed "21-23-kDa lipid binding proteins", members of which are found in several...

  13. Transcription Factor ets-2 Plays an Important Role in the Pathogenesis of Pulmonary Fibrosis

    Science.gov (United States)

    Baran, Christopher P.; Fischer, Sara N.; Nuovo, Gerard J.; Kabbout, Mohamed N.; Hitchcock, Charles L.; Bringardner, Benjamin D.; McMaken, Sara; Newland, Christie A.; Cantemir-Stone, Carmen Z.; Phillips, Gary S.; Ostrowski, Michael C.

    2011-01-01

    Ets-2 is a ubiquitous transcription factor activated after phosphorylation at threonine-72. Previous studies highlighted the importance of phosphorylated ets-2 in lung inflammation and extracellular matrix remodeling, two pathways involved in pulmonary fibrosis. We hypothesized that phosphorylated ets-2 played an important role in pulmonary fibrosis, and we sought to determine the role of ets-2 in its pathogenesis. We challenged ets-2 (A72/A72) transgenic mice (harboring a mutated form of ets-2 at phosphorylation site threonine-72) and ets-2 (wild-type/wild-type [WT/WT]) control mice with sequential intraperitoneal injections of bleomycin, followed by quantitative measurements of lung fibrosis and inflammation and primary cell in vitro assays. Concentrations of phosphorylated ets-2 were detected via the single and dual immunohistochemical staining of murine lungs and lung sections from patients with idiopathic pulmonary fibrosis. Ets-2 (A72/A72) mice were protected from bleomycin-induced pulmonary fibrosis, compared with ets-2 (WT/WT) mice. This protection was characterized by decreased lung pathological abnormalities and the fibrotic gene expression of Type I collagen, Type III collagen, α–smooth muscle actin, and connective tissue growth factor. Immunohistochemical staining of lung sections from bleomycin-treated ets-2 (WT/WT) mice and from patients with idiopathic pulmonary fibrosis demonstrated increased staining of phosphorylated ets-2 that colocalized with Type I collagen expression and to fibroblastic foci. Lastly, primary lung fibroblasts from ets-2 (A72/A72) mice exhibited decreased expression of Type I collagen in response to stimulation with TGF-β, compared with fibroblasts from ets-2 (WT/WT) mice. These data indicate the importance of phosphorylated ets-2 in the pathogenesis of pulmonary fibrosis through the expression of Type I collagen and (myo)fibroblast activation. PMID:21562315

  14. Epidermal growth factor receptor plays an anabolic role in bone metabolism in vivo.

    Science.gov (United States)

    Zhang, Xianrong; Tamasi, Joseph; Lu, Xin; Zhu, Ji; Chen, Haiyan; Tian, Xiaoyan; Lee, Tang-Cheng; Threadgill, David W; Kream, Barbara E; Kang, Yibin; Partridge, Nicola C; Qin, Ling

    2011-05-01

    While the epidermal growth factor receptor (EGFR)-mediated signaling pathway has been shown to have vital roles in many developmental and pathologic processes, its functions in the development and homeostasis of the skeletal system has been poorly defined. To address its in vivo role, we constructed transgenic and pharmacologic mouse models and used peripheral quantitative computed tomography (pQCT), micro-computed tomography (µCT) and histomorphometry to analyze their trabecular and cortical bone phenotypes. We initially deleted the EGFR in preosteoblasts/osteoblasts using a Cre/loxP system (Col-Cre Egfr(f/f)), but no bone phenotype was observed because of incomplete deletion of the Egfr genomic locus. To further reduce the remaining osteoblastic EGFR activity, we introduced an EGFR dominant-negative allele, Wa5, and generated Col-Cre Egfr(Wa5/f) mice. At 3 and 7 months of age, both male and female mice exhibited a remarkable decrease in tibial trabecular bone mass with abnormalities in trabecular number and thickness. Histologic analyses revealed decreases in osteoblast number and mineralization activity and an increase in osteoclast number. Significant increases in trabecular pattern factor and structural model index indicate that trabecular microarchitecture was altered. The femurs of these mice were shorter and smaller with reduced cortical area and periosteal perimeter. Moreover, colony-forming unit-fibroblast (CFU-F) assay indicates that these mice had fewer bone marrow mesenchymal stem cells and committed progenitors. Similarly, administration of an EGFR inhibitor into wild-type mice caused a significant reduction in trabecular bone volume. In contrast, Egfr(Dsk5/+) mice with a constitutively active EGFR allele displayed increases in trabecular and cortical bone content. Taken together, these data demonstrate that the EGFR signaling pathway is an important bone regulator and that it primarily plays an anabolic role in bone metabolism. Copyright © 2011

  15. TAK1 plays a major role in growth factor-induced phenotypic modulation of airway smooth muscle

    NARCIS (Netherlands)

    Pera, Tonio; Sami, Riham; Zaagsma, Johan; Meurs, Herman

    2011-01-01

    Pera T, Sami R, Zaagsma J, Meurs H. TAK1 plays a major role in growth factor-induced phenotypic modulation of airway smooth muscle. Am J Physiol Lung Cell Mol Physiol 301: L822-L828, 2011. First published August 26, 2011; doi:10.1152/ajplung.00017.2011.-Increased airway smooth muscle (ASM) mass is a

  16. The repertoire of DNA-binding transcription factors in prokaryotes: functional and evolutionary lessons.

    Science.gov (United States)

    Perez-Rueda, Ernesto; Martinez-Nuñez, Mario Alberto

    2012-01-01

    The capabilities of organisms to contend with environmental changes depend on their genes and their ability to regulate their expression. DNA-binding transcription factors (TFs) play a central role in this process, because they regulate gene expression positively and/or negatively, depending on the operator context and ligand-binding status. In this review, we summarise recent findings regarding the function and evolution of TFs in prokaryotes. We consider the abundance of TFs in bacteria and archaea, the role of DNA-binding domains and their partner domains, and the effects of duplication events in the evolution of regulatory networks. Finally, a comprehensive picture for how regulatory networks have evolved in prokaryotes is provided.

  17. A Genome-Scale Resource for the Functional Characterization of Arabidopsis Transcription Factors

    Directory of Open Access Journals (Sweden)

    Jose L. Pruneda-Paz

    2014-07-01

    Full Text Available Extensive transcriptional networks play major roles in cellular and organismal functions. Transcript levels are in part determined by the combinatorial and overlapping functions of multiple transcription factors (TFs bound to gene promoters. Thus, TF-promoter interactions provide the basic molecular wiring of transcriptional regulatory networks. In plants, discovery of the functional roles of TFs is limited by an increased complexity of network circuitry due to a significant expansion of TF families. Here, we present the construction of a comprehensive collection of Arabidopsis TFs clones created to provide a versatile resource for uncovering TF biological functions. We leveraged this collection by implementing a high-throughput DNA binding assay and identified direct regulators of a key clock gene (CCA1 that provide molecular links between different signaling modules and the circadian clock. The resources introduced in this work will significantly contribute to a better understanding of the transcriptional regulatory landscape of plant genomes.

  18. Playing a Musical Instrument as a Protective Factor against Dementia and Cognitive Impairment: A Population-Based Twin Study

    Directory of Open Access Journals (Sweden)

    M. Alison Balbag

    2014-01-01

    Full Text Available Increasing evidence supports that playing a musical instrument may benefit cognitive development and health at young ages. Whether playing an instrument provides protection against dementia has not been established. In a population-based cotwin control study, we examined the association between playing a musical instrument and whether or not the twins developed dementia or cognitive impairment. Participation in playing an instrument was taken from informant-based reports of twins’ leisure activities. Dementia diagnoses were based on a complete clinical workup using standard diagnostic criteria. Among 157 twin pairs discordant for dementia and cognitive impairment, 27 pairs were discordant for playing an instrument. Controlling for sex, education, and physical activity, playing a musical instrument was significantly associated with less likelihood of dementia and cognitive impairment (odds ratio [OR] = 0.36 [95% confidence interval 0.13–0.99]. These findings support further consideration of music as a modifiable protective factor against dementia and cognitive impairment.

  19. Linking hydraulic traits to tropical forest function in a size-structured and trait-driven model (TFS v.1-Hydro)

    Science.gov (United States)

    Christoffersen, Bradley O.; Gloor, Manuel; Fauset, Sophie; Fyllas, Nikolaos M.; Galbraith, David R.; Baker, Timothy R.; Kruijt, Bart; Rowland, Lucy; Fisher, Rosie A.; Binks, Oliver J.; Sevanto, Sanna; Xu, Chonggang; Jansen, Steven; Choat, Brendan; Mencuccini, Maurizio; McDowell, Nate G.; Meir, Patrick

    2016-11-01

    Forest ecosystem models based on heuristic water stress functions poorly predict tropical forest response to drought partly because they do not capture the diversity of hydraulic traits (including variation in tree size) observed in tropical forests. We developed a continuous porous media approach to modeling plant hydraulics in which all parameters of the constitutive equations are biologically interpretable and measurable plant hydraulic traits (e.g., turgor loss point πtlp, bulk elastic modulus ɛ, hydraulic capacitance Cft, xylem hydraulic conductivity ks,max, water potential at 50 % loss of conductivity for both xylem (P50,x) and stomata (P50,gs), and the leaf : sapwood area ratio Al : As). We embedded this plant hydraulics model within a trait forest simulator (TFS) that models light environments of individual trees and their upper boundary conditions (transpiration), as well as providing a means for parameterizing variation in hydraulic traits among individuals. We synthesized literature and existing databases to parameterize all hydraulic traits as a function of stem and leaf traits, including wood density (WD), leaf mass per area (LMA), and photosynthetic capacity (Amax), and evaluated the coupled model (called TFS v.1-Hydro) predictions, against observed diurnal and seasonal variability in stem and leaf water potential as well as stand-scaled sap flux. Our hydraulic trait synthesis revealed coordination among leaf and xylem hydraulic traits and statistically significant relationships of most hydraulic traits with more easily measured plant traits. Using the most informative empirical trait-trait relationships derived from this synthesis, TFS v.1-Hydro successfully captured individual variation in leaf and stem water potential due to increasing tree size and light environment, with model representation of hydraulic architecture and plant traits exerting primary and secondary controls, respectively, on the fidelity of model predictions. The plant

  20. PlnTFDB: an integrative plant transcription factor database

    Directory of Open Access Journals (Sweden)

    Ruzicic Slobodan

    2007-02-01

    Full Text Available Abstract Background Transcription factors (TFs are key regulatory proteins that enhance or repress the transcriptional rate of their target genes by binding to specific promoter regions (i.e. cis-acting elements upon activation or de-activation of upstream signaling cascades. TFs thus constitute master control elements of dynamic transcriptional networks. TFs have fundamental roles in almost all biological processes (development, growth and response to environmental factors and it is assumed that they play immensely important functions in the evolution of species. In plants, TFs have been employed to manipulate various types of metabolic, developmental and stress response pathways. Cross-species comparison and identification of regulatory modules and hence TFs is thought to become increasingly important for the rational design of new plant biomass. Up to now, however, no computational repository is available that provides access to the largely complete sets of transcription factors of sequenced plant genomes. Description PlnTFDB is an integrative plant transcription factor database that provides a web interface to access large (close to complete sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress, Populus trichocarpa (poplar, Oryza sativa (rice, Chlamydomonas reinhardtii and Ostreococcus tauri. It also provides an access point to its daughter databases of a species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB. Information including protein sequences, coding regions, genomic sequences, expressed sequence tags (ESTs, domain architecture and scientific literature is provided for each family. Conclusion We have created lists of putatively complete sets of transcription factors and other transcriptional regulators for five plant genomes. They are publicly available through http://plntfdb.bio.uni-potsdam.de. Further data will be

  1. Factors influencing the degree and pattern of parental involvement in play therapy for sexually abused children.

    Science.gov (United States)

    Hill, Andrew

    2009-01-01

    Although much has been written about the role of therapists in children's recovery from child sexual abuse, relatively little attention has been paid to the role of nonoffending parents. This study investigated the work of a team of therapists who sometimes included such parents in therapy sessions with children. The study sought to understand what factors were influencing the degree and pattern of parental involvement and to understand what effect these patterns of parental involvement were having on the process and outcomes of therapy. The study successfully identified a range of factors influencing the patterns of parental involvement, but more research will be needed to understand the effect on outcomes.

  2. Transcription factor families in Arabidopsis: major progress and outstanding issues for future research.

    Science.gov (United States)

    Qu, Li-Jia; Zhu, Yu-Xian

    2006-10-01

    Transcription factors (TFs) are a group of proteins that control cellular processes by regulating the expression of downstream target genes. Recent progress has been made in the cloning and characterization of Arabidopsis TFs on the genome scale, especially on the cloning of open reading frames (ORFs), sequence analysis and the expression profiling of different TF families. Huge difference in numbers of subfamily members were found for Arabidopsis MYB, C2H2 (Zn), C3H-type 1 (Zn), C3H-type 2 (Zn) TFs by independent research groups, mainly because of differences in bioinformatic search stringency. However, the Arabidopsis and rice genomes contain very different numbers of TFs in the WRKY, NAC, bZIP, MADS, ALFIN-like, GRAS and C2C2 (Zn)-dof families, indicating a possible divergence of biological functions from dicots to monocots. TFs have also been found to play key roles in the biosynthesis and signaling of plant hormones, in cell growth and differentiation, and in photomorphogenesis.

  3. Climate factors play a limited role for past adaptation strategies in West Africa

    DEFF Research Database (Denmark)

    Mertz, Ole; Mbow, Cheikh; Nielsen, Jonas Østergaard;

    2010-01-01

    The Sudano-Sahelian zone of West Africa has experienced recurrent droughts since the mid-1970s and today there is considerable concern for how this region will be able to adapt to future climate change. To develop well targeted adaptation strategies, the relative importance of climate factors...... to be reflected in national adaptation strategies in the region....

  4. Climate factors play a limited role for past adaptation strategies in West Africa

    DEFF Research Database (Denmark)

    Mertz, Ole; Mbow, Cheikh; Nielsen, Jonas Østergaard

    2010-01-01

    The Sudano-Sahelian zone of West Africa has experienced recurrent droughts since the mid-1970s and today there is considerable concern for how this region will be able to adapt to future climate change. To develop well targeted adaptation strategies, the relative importance of climate factors as ...

  5. Mechanical factors play an important role in pectus excavatum with thoracic scoliosis

    OpenAIRE

    Wang Yuncang; Chen Gang; Xie Liang; Tang Jiming; Ben Xiaosong; Zhang Dongkun; Xiao Pu; Zhou Haiyu; Zhou Zihao; Ye Xiong

    2012-01-01

    Abstract Background This study investigated the incidence, imaging characteristics and mechanical factors in scoliotic patients with pectus excavatum. Methods A total of 142 scoliostic patients with pectus excavatum were evaluated prior to operation. The evaluation included a complete physical exam, phenotype and severity of the pectus excavatum, incidence and severity of scoliosis, and analysis of radiological images, including calculation of the Haller index. Results Twenty five out of 142 ...

  6. TRANSCRIPTION FACTOR Bmsage PLAYS A CRUCIAL ROLE IN SILK GLAND GENERATION IN SILKWORM, Bombyx mori.

    Science.gov (United States)

    Xin, Hu-hu; Zhang, Deng-pan; Chen, Rui-ting; Cai, Zi-zheng; Lu, Yan; Liang, Shuang; Miao, Yun-gen

    2015-10-01

    Salivary gland secretion is altered in Drosophila embryos with loss of function of the sage gene. Saliva has a reduced volume and an increased electron density according to transmission electron microscopy, resulting in regions of tube dilation and constriction with intermittent tube closure. However, the precise functions of Bmsage in silkworm (Bombyx mori) are unknown, although its sequence had been deposited in SilkDB. From this, Bmsage is inferred to be a transcription factor that regulates the synthesis of silk fibroin and interacts with another silk gland-specific transcription factor, namely, silk gland factor-1. In this study, we introduced a germline mutation of Bmsage using the Cas9/sgRNA system, a genome-editing technology, resulting in deletion of Bmsage from the genome of B. mori. Of the 15 tested samples, seven displayed alterations at the target site. The mutagenesis efficiency was about 46.7% and there were no obvious off-target effects. In the screened homozygous mutants, silk glands developed poorly and the middle and posterior silk glands (MSG and PSG) were absent, which was significantly different from the wild type. The offspring of G0 mosaic silkworms had indel mutations causing 2- or 9-bp deletions at the target site, but exhibited the same abnormal silk gland structure. Mutant larvae containing different open-reading frames of Bmsage had the same silk gland phenotype. This illustrated that the mutant phenotype was due to Bmsage knockout. We conclude that Bmsage participates in embryonic development of the silk gland.

  7. Genetic variation in insulin-like growth factor 2 may play a role in ovarian cancer risk

    DEFF Research Database (Denmark)

    Pearce, Celeste Leigh; Doherty, Jennifer A; Van Den Berg, David J

    2011-01-01

    The insulin-like growth factor (IGF) signaling axis plays an important role in cancer biology. We hypothesized that genetic variation in this pathway may influence risk of ovarian cancer. A three-center study of non-Hispanic whites including 1880 control women, 1135 women with invasive epithelial...... as an important gene for ovarian cancer; additional genotyping is warranted to further confirm these associations with IGF2 and to narrow down the region harboring the causal SNP....

  8. Which factors play a role in clinical decision-making in subfertility?

    Science.gov (United States)

    van der Steeg, Jan W; Steures, Pieternel; Eijkemans, Marinus J C; Habbema, J Dik F; Bossuyt, Patrick M M; Hompes, Peter G A; van der Veen, Fulco; Mol, Ben W J

    2006-04-01

    Sixteen vignettes of subfertile couples were constructed by varying fertility history, post-coital test, sperm motility, FSH concentration and Chlamydia antibody titre (CAT). Thirty-five gynaecologists estimated probabilities of treatment-independent pregnancy, intrauterine insemination (IUI) and IVF. Thereafter, they chose IUI, IVF or no treatment. The relative contribution of each factor to probability estimates and to subsequent treatment decisions was calculated. Duration of subfertility and maternal age were the most important contributors for gynaecologists' estimates of treatment-independent pregnancy [relative contribution (RC) 41, 26%]. Maternal age and FSH concentration were the most important contributors in the estimates for IUI (RC: 51, 25%) and for IVF (RC: 64, 31%). The decision to start IVF was mainly determined by maternal age, duration of subfertility, FSH concentration and CAT. The relative contribution of maternal age and duration of subfertility was in concordance with existing prediction models, whereas previous pregnancy and FSH concentration were under- and overestimated respectively. In conclusion, maternal age, duration of subfertility and FSH concentration are the main factors in clinical decision-making in subfertility. Gynaecologists overestimate the importance of FSH concentration, but underestimate that of a previous pregnancy, as compared with their importance reported in prediction models and guidelines.

  9. Stress-induced growth-differentiation factor 15 plays an intriguing role in cardiovascular diseases

    Institute of Scientific and Technical Information of China (English)

    LIU Hai-tao; WANG Hai-chang; TAO Ling; LI Cheng-xiang; LI Fei; ZHANG Yu-yang; LIU Bo-wu

    2013-01-01

    Objective To provide an overview of the current knowledge of growth-differentiation factor 15 (GDF-15) in heart disease.Data sources To identify relevant publications,we searched PubMED database combining the textual terms of heart,cardiac,cardiovascular disease with GDF-15.Study selection Well-controlled,relatively large-scale,retrospective studies as well as meaningful individual cases were all selected as materials.Results GDF-15 is a distant member of the transforming growth factor-β cytokine superfamily.In myocardium,GDF-15 is weakly expressed under physiological conditions.However,its expression level is increased in response to pathological stress.Growing evidence indicate that elevated levels of GDF-15 is a promising prognostic biomarker in cardiovascular diseases.Moreover,GDF-15 exhibits the properties of endogenous anti-hypertrophy of cardiomyocytes and protecting the heart suffering from ischemia and reperfusion insult.Conclusion Ve GDF-15 may be a promising biomarker for evaluation and management of patient with cardiovascular diseases,and have potential protective properties on myocardium.

  10. Prefoldin Plays a Role as a Clearance Factor in Preventing Proteasome Inhibitor-induced Protein Aggregation*

    Science.gov (United States)

    Abe, Akira; Takahashi-Niki, Kazuko; Takekoshi, Yuka; Shimizu, Takashi; Kitaura, Hirotake; Maita, Hiroshi; Iguchi-Ariga, Sanae M. M.; Ariga, Hiroyoshi

    2013-01-01

    Prefoldin is a molecular chaperone composed of six subunits, PFD1–6, and prevents misfolding of newly synthesized nascent polypeptides. Although it is predicted that prefoldin, like other chaperones, modulates protein aggregation, the precise function of prefoldin against protein aggregation under physiological conditions has never been elucidated. In this study, we first established an anti-prefoldin monoclonal antibody that recognizes the prefoldin complex but not its subunits. Using this antibody, it was found that prefoldin was localized in the cytoplasm with dots in co-localization with polyubiquitinated proteins and that the number and strength of dots were increased in cells that had been treated with lactacystin, a proteasome inhibitor, and thapsigargin, an inducer of endoplasmic reticulum stress. Knockdown of prefoldin increased the level of SDS-insoluble ubiquitinated protein and reduced cell viability in lactacystin and thapsigargin-treated cells. Opposite results were obtained in prefoldin-overexpressed cells. It has been reported that mice harboring a missense mutation L110R of MM-1α/PFD5 exhibit neurodegeneration in the cerebellum. Although the prefoldin complex containing L110R MM-1α was properly formed in vitro and in cells derived from L110R MM-1α mice, the levels of ubiquitinated proteins and cytotoxicity were higher in L110R MM-1α cells than in wild-type cells under normal conditions and were increased by lactacystin and thapsigargin treatment, and growth of L110R MM-1α cells was attenuated. Furthermore, the polyubiquitinated protein aggregation level was increased in the brains of L110R MM-1α mice. These results suggest that prefoldin plays a role in quality control against protein aggregation and that dysfunction of prefoldin is one of the causes of neurodegenerative diseases. PMID:23946485

  11. Fibroblast growth factor receptor 2 plays an essential role in telencephalic progenitors.

    Science.gov (United States)

    Ever, Leah; Zhao, Rui-Jing; Eswarakumar, Veraragavan P; Gaiano, Nicholas

    2008-01-01

    We used loss-of-function analysis to determine the role of fibroblast growth factor receptor 2 (FGFR2) in telencephalic progenitors, and also to examine interactions between FGFR and Notch signaling. While the telencephalon of FGFR2 mutants appears grossly normal, mutant telencephalic progenitors exhibit altered proliferative behavior in vivo and in vitro. Based upon our prior finding that Notch1 activation increased neurosphere frequency in FGF2, we tested whether this effect is mediated by FGFR1 or FGFR2. We found that Notch1 activation increased neurosphere frequency in cells mutant for either FGFR1 or FGFR2, but had no effect on the reduced size of neurospheres mutant for those receptors. Additional analyses revealed biochemical changes in the adult neocortex mutant for the IIIc isoform of FGFR2, and essential roles for FGFR2 in nasopharynx, eyelid, and cornea development.

  12. Does epidermal growth factor play a role in the action of sucralfate?

    DEFF Research Database (Denmark)

    Nexø, Ebba; Poulsen, Steen Seier

    1987-01-01

    the effector system of EGF. We conclude that Sucralfate does not change the binding of EGF to its receptor, but it is able to bind EGF in a pH dependent manner and at pH below 4.5 virtually all EGF is bound to Sucralfate. In vivo studies in rats with acid-induced gastric ulcers show that sucralfate carries EGF......Epidermal growth factor (EGF) is a mitogenic peptide synthesized in the submandibular glands and released in saliva. EGF is able to prevent the development of gastrointestinal ulcers in the rat and to accelerate their healing. The present work was undertaken to examine whether Sucralfate acts via...... to the ulcer, and that EGF is available for a longer period of time (3 hours) when EGF and Sucralfate are is given together than when EGF is given alone....

  13. A novel ethylene responsive factor CitERF13 plays a role in photosynthesis regulation.

    Science.gov (United States)

    Xie, Xiu-Lan; Xia, Xiao-Jian; Kuang, Sheng; Zhang, Xi-Li; Yin, Xue-Ren; Yu, Jing-Quan; Chen, Kun-Song

    2017-03-01

    Ethylene responsive factors (ERFs) act as critical downstream components of the ethylene signalling pathway in regulating plant development and stress responses. However little is known about its role in regulation of photosynthesis. Here, we identified an ethylene-inducible ERF gene in citrus, CitERF13. Transient over-expression of CitERF13 in N. tabacum leaves, resulted in a significant decrease in net photosynthetic rate. Closer examination of photosynthetic activity of PSII and PSI indicated that CitERF13 overexpression led to declines of Fv/Fm, Y(II) and Y(I). However, change in NPQ was less pronounced. CitERF13 overexpression also significantly reduced Vc,max, Jmax and AQY, indicating inhibition of the Calvin cycle. The expression of photosynthesis-related genes was suppressed to a variable extent in leaf blades transiently over-expressing CitERF13. CitERF13 transient overexpression in tobacco or citrus both resulted in a decline of Chlorophyll content and CitERF13 overexpressing tobacco leaf disc was more susceptible to chlorosis in response to MV-mediated oxidative stress. The results suggest that CitERF13 is potentially involved in suppressing photosynthesis through multiple pathways, for instance, inhibiting photochemical activity of photosynthesis, CO2 carboxylation capacity and chlorophyll metabolism. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  14. Plant transcription factors from the homeodomain-leucine zipper family I. Role in development and stress responses.

    Science.gov (United States)

    Perotti, María Florencia; Ribone, Pamela Anahí; Chan, Raquel Lía

    2017-05-01

    In front of stressful conditions plants display adaptation mechanisms leading to changes in their morphology, physiology, development and molecular composition. Transcription factors (TFs) play crucial roles in these complex adaptation processes. This work is focused in the homeodomain-leucine zipper I (HD-Zip I) family of TFs, unique to plants. First discovered in 1991, they were identified and isolated from monocotyledonous and dicotyledonous plants showing high structural similarity and diversified functions. These TFs have, besides the homeodomain and leucine zipper, conserved motifs in their carboxy-termini allowing the interaction with the basal machinery and with other regulatory proteins. The model dicotyledonous plant Arabidopsis thaliana has 17 HD-Zip I members; most of them regulated by external stimuli and hormones. These TFs are involved in key developmental processes like root and stem elongation, rosette leaves morphology determination, inflorescence stem branching, flowering and pollen hydration. Moreover, they are key players in responses to environmental stresses and illumination conditions. Several HD-Zip I encoding genes from different species were protected in patents because their overexpression or mutation generates improved agronomical phenotypes. Here we discuss many aspects about these TFs including structural features, biological functions and their utilization as biotechnological tools to improve crops. © 2017 IUBMB Life, 69(5):280-289, 2017. © 2017 International Union of Biochemistry and Molecular Biology.

  15. Yes and Lyn play a role in nuclear translocation of the epidermal growth factor receptor.

    Science.gov (United States)

    Iida, M; Brand, T M; Campbell, D A; Li, C; Wheeler, D L

    2013-02-07

    The epidermal growth factor receptor (EGFR) is a central regulator of tumor progression in human cancers. Cetuximab is an anti-EGFR antibody that has been approved for use in oncology. Previously we investigated mechanisms of resistance to cetuximab using a model derived from the non-small cell lung cancer line NCI-H226. We demonstrated that cetuximab-resistant clones (Ctx(R)) had increased nuclear localization of the EGFR. This process was mediated by Src family kinases (SFKs), and nuclear EGFR had a role in resistance to cetuximab. To better understand SFK-mediated nuclear translocation of EGFR, we investigated which SFK member(s) controlled this process as well as the EGFR tyrosine residues that are involved. Analyses of mRNA and protein expression indicated upregulation of the SFK members Yes (v-Yes-1 yamaguchi sarcoma viral oncogene) and Lyn (v-yes-1 Yamaguchi sarcoma viral-related oncogene homolog) in all Ctx(R) clones. Further, immunoprecipitation analysis revealed that EGFR interacts with Yes and Lyn in Ctx(R) clones, but not in cetuximab-sensitive (Ctx(S)) parental cells. Using RNAi interference, we found that knockdown of either Yes or Lyn led to loss of EGFR translocation to the nucleus. Conversely, overexpression of Yes or Lyn in low nuclear EGFR-expressing Ctx(S) parental cells led to increased nuclear EGFR. Chromatin immunoprecipitation (ChIP) assays confirmed nuclear EGFR complexes associated with the promoter of the known EGFR target genes B-Myb and iNOS. Further, all Ctx(R) clones exhibited upregulation of B-Myb and iNOS at the mRNA and protein levels. siRNAs directed at Yes or Lyn led to decreased binding of EGFR complexes to the B-Myb and iNOS promoters based on ChIP analyses. SFKs have been shown to phosphorylate EGFR on tyrosines 845 and 1101 (Y845 and Y1101), and mutation of Y1101, but not Y845, impaired nuclear entry of the EGFR. Taken together, our findings demonstrate that Yes and Lyn phosphorylate EGFR at Y1101, which influences EGFR

  16. Transcription Factor Zbtb20 Controls Regional Specification of Mammalian Archicortex

    DEFF Research Database (Denmark)

    Rosenthal, Eva Helga

    2010-01-01

    Combinatorial expression of sets of transcription factors (TFs) along the mammalian cortex controls its subdivision into functional areas. Unlike neocortex, only few recent data suggest genetic mechanisms controlling the regionalization of the archicortex. TF Emx2 plays a crucial role in patterning...... later on becoming restricted exclusively to postmitotic neurons of hippocampus (Hi) proper, dentate gyrus (DG), and two transitory zones, subiculum (S) and retrosplenial cortex (Rsp). Analysis of Zbtb20-/- mice revealed altered cortical patterning at the border between neocortex and archicortex...

  17. Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors.

    Science.gov (United States)

    Ishihama, Akira; Shimada, Tomohiro; Yamazaki, Yukiko

    2016-03-18

    Bacterial genomes are transcribed by DNA-dependent RNA polymerase (RNAP), which achieves gene selectivity through interaction with sigma factors that recognize promoters, and transcription factors (TFs) that control the activity and specificity of RNAP holoenzyme. To understand the molecular mechanisms of transcriptional regulation, the identification of regulatory targets is needed for all these factors. We then performed genomic SELEX screenings of targets under the control of each sigma factor and each TF. Here we describe the assembly of 156 SELEX patterns of a total of 116 TFs performed in the presence and absence of effector ligands. The results reveal several novel concepts: (i) each TF regulates more targets than hitherto recognized; (ii) each promoter is regulated by more TFs than hitherto recognized; and (iii) the binding sites of some TFs are located within operons and even inside open reading frames. The binding sites of a set of global regulators, including cAMP receptor protein, LeuO and Lrp, overlap with those of the silencer H-NS, suggesting that certain global regulators play an anti-silencing role. To facilitate sharing of these accumulated SELEX datasets with the research community, we compiled a database, 'Transcription Profile of Escherichia coli' (www.shigen.nig.ac.jp/ecoli/tec/). © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Do environmental factors play a role in the aetiology of carcinoma in situ testis and the testicular dysgenesis syndrome?

    DEFF Research Database (Denmark)

    Sonne, Si Brask; Hoei-Hansen, C E; Fisher, J S

    2004-01-01

    development, and may be provoked by external factors such as endocrine disruptors in addition to genetic predisposition. Testicular germ cell tumours (TGCTs), considered the most severe symptom of TDS, have increased in incidence during the last 60 years, to become the most common malignancy in young...... (DBP) suggesting that ubiquitously present environmental endocrine disruptors may play a role in the aetiology of human TDS. So far, no animal model has been able to mimick all the symptoms of TDS including TGCTs although CIS-like cells have been found in a spontaneous testicular neoplasm in a rabbit....

  19. A Factor-Based Exploration of Player´s Continuation Desire in Free-to-Play Mobile Games

    DEFF Research Database (Denmark)

    Stankevicius, Deividas; Jady, Hawraa Amira; Drachen, Anders

    2015-01-01

    experience, motivation and enjoyment, yet difficult to measure. These concepts were conceptualized into different factors and thereby it was identified which of them are re-lated. This resulted in a synthesized model that was based on the Theory of Planned Behavior model. This model takes into account......This paper explores the concept of Continuation Desire fur-ther by investigating the behavioral intent of players’ desire to keep playing. User experience is a complex, multifaceted topic, which is commonly studied through different aspects namely engagement, continuation desire, immersion, flow...

  20. 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/.

  1. Play Matters

    DEFF Research Database (Denmark)

    Sicart (Vila), Miguel Angel

    , but not necessarily fun. Play can be dangerous, addictive, and destructive. Along the way, Sicart considers playfulness, the capacity to use play outside the context of play; toys, the materialization of play--instruments but also play pals; playgrounds, play spaces that enable all kinds of play; beauty......, the aesthetics of play through action; political play -- from Maradona's goal against England in the 1986 World Cup to the hactivist activities of Anonymous; the political, aesthetic, and moral activity of game design; and why play and computers get along so well....

  2. Playful Interventions Increase Knowledge about Healthy Habits and Cardiovascular Risk Factors in Children: The CARDIOKIDS Randomized Study

    Science.gov (United States)

    Cecchetto, Fátima H.; Pena, Daniela B.; Pellanda, Lucia C.

    2017-01-01

    Background Childhood obesity is an important health problem worldwide. In this context, there is a need for the development and evaluation of innovative educational interventions targeting prevention and formation of health habits. Objectives To ascertain the impact of ludic workshops on children’s knowledge, self-care, and body weight. Methods This was a randomized, clinical study with 79 students aged 7-11 years, conducted from March to November 2012. Anthropometric measurements were collected and two questionnaires (Typical Day of Physical Activities and Food Intake, in Portuguese, and the CARDIOKIDS, a questionnaire of knowledge about cardiovascular risk factors) were applied at baseline, at the end of intervention, and three months thereafter. The intervention consisted of eight playful workshops, which involved the presentation of a play. Results Seventy-nine students were randomized to the intervention (n = 40) or the control group (n = 39). Mean age was 10.0 ± 1.1 years. After eight weeks, the intervention group showed significant improvement in the knowledge score (p < 0.001). There was an increase in physical activity scores in both groups, but with no difference between the groups at the end of intervention (p = 0.209). A reduction in the BMI percentile was observed in the intervention group, but there was no significant statistical difference between the two groups after the intervention. Conclusions Playful interventions may improve knowledge and physical activity levels in children and, when combined with other strategies, may be beneficial to prevent child obesity and improve self-care. PMID:28746521

  3. A formal anthropological view of motivation models of problematic MMO play: achievement, social, and immersion factors in the context of culture.

    Science.gov (United States)

    Snodgrass, Jeffrey G; Dengah, H J Francois; Lacy, Michael G; Fagan, Jesse

    2013-04-01

    Yee (2006) found three motivational factors-achievement, social, and immersion-underlying play in massively multiplayer online role-playing games ("MMORPGs" or "MMOs" for short). Subsequent work has suggested that these factors foster problematic or addictive forms of play in online worlds. In the current study, we used an online survey of respondents (N = 252), constructed and also interpreted in reference to ethnography and interviews, to examine problematic play in the World of Warcraft (WoW; Blizzard Entertainment, 2004-2013). We relied on tools from psychological anthropology to reconceptualize each of Yee's three motivational factors in order to test for the possible role of culture in problematic MMO play: (a) For achievement, we examined how "cultural consonance" with normative understandings of success might structure problematic forms of play; (b) for social, we analyzed the possibility that developing overvalued virtual relationships that are cutoff from offline social interactions might further exacerbate problematic play; and (c) in relation to immersion, we examined how "dissociative" blurring of actual- and virtual-world identities and experiences might contribute to problematic patterns. Our results confirmed that compared to Yee's original motivational factors, these culturally sensitive measures better predict problematic forms of play, pointing to the important role of sociocultural factors in structuring online play.

  4. An active factor from tomato root exudates plays an important role in efficient establishment of mycorrhizal symbiosis.

    Directory of Open Access Journals (Sweden)

    Shubin Sun

    Full Text Available Root exudates play an important role in the early signal exchange between host plants and arbuscular mycorrhizal fungi. M161, a pre-mycorrhizal infection (pmi mutant of the tomoto (Solanum lycopersicum cultivar Micro-Tom, fails to establish normal arbuscular mycorrhizal symbioses, and produces exudates that are unable to stimulate hyphal growth and branching of Glomus intraradices. Here, we report the identification of a purified active factor (AF that is present in the root exudates of wild-type tomato, but absent in those of M161. A complementation assay using the dual root organ culture system showed that the AF could induce fungal growth and branching at the pre-infection stage and, subsequently, the formation of viable new spores in the M161 background. Since the AF-mediated stimulation of hyphal growth and branching requires the presence of the M161 root, our data suggest that the AF is essential but not sufficient for hyphal growth and branching. We propose that the AF, which remains to be chemically determined, represents a plant signal molecule that plays an important role in the efficient establishment of mycorrhizal symbioses.

  5. Scaffolding, Analysis and Materials: Contributing Factors in an Unexpected Finding of Advanced Infant/Toddler Pretend Play?

    Science.gov (United States)

    Morrissey, Anne-Marie

    2014-01-01

    As part of a longitudinal study, infant/toddler pretend play development and maternal play modelling were investigated in dyadic context. A total of 21 children were videotaped in monthly play sessions with their mothers, from age 8 to 17 months. Child and mother pretend play frequencies and levels were measured using Brown's Pretend Play…

  6. Scaffolding, Analysis and Materials: Contributing Factors in an Unexpected Finding of Advanced Infant/Toddler Pretend Play?

    Science.gov (United States)

    Morrissey, Anne-Marie

    2014-01-01

    As part of a longitudinal study, infant/toddler pretend play development and maternal play modelling were investigated in dyadic context. A total of 21 children were videotaped in monthly play sessions with their mothers, from age 8 to 17 months. Child and mother pretend play frequencies and levels were measured using Brown's Pretend Play…

  7. NAC transcription factors play an important role in ethylene biosynthesis, reception and signaling of tomato fruit ripening.

    Science.gov (United States)

    Kou, Xiaohong; Liu, Chen; Han, Lihua; Wang, Shuang; Xue, Zhaohui

    2016-06-01

    NAC proteins comprise a large family of transcription factors that play important roles in diverse physiological processes during development. To explore the role of NAC transcription factors in the ripening of fruits, we predicted the secondary and tertiary structure as well as regulative function of the SNAC4 (SlNAC48, Accession number: NM 001279348.2) and SNAC9 (SlNAC19, Accession number: XM 004236996.2) transcription factors in tomato. We found that the tertiary structure of SNAC9 was similar to that of ATNAP, which played an important role in the fruit senescence and was required for ethylene stimulation. Likewise, the bio-function prediction results indicated that SNAC4 and SNAC9 participated in various plant hormone signaling and senescence processes. More information about SNACs was obtained by the application of VIGS (virus-induced gene silencing). The silencing of SNAC4 and SNAC9 dramatically repressed the LeACS2, LeACS4 and LeACO1 expression, which consequently led to the inhibition of the ripening process. The silencing of SNACs down-regulated the mRNA levels of the ethylene perception genes and, at the same time, suppressed the expression of ethylene signaling-related genes except for LeERF2 which was induced by the silencing of SNAC4. The expressions of LeRIN were different in two silenced fruits. In addition, the silencing of SNAC4 reduced its mRNA level, while the silencing of SNAC9 induced its expression. Furthermore, the silencing of LeACS4, LeACO1 and LeERF2 reduced the expression of SNAC4 and SNAC9, while the silencing of NR induced the expression of all of them. In particular, these results indicate that SNAC transcription factors bind to the promoter of the ethylene synthesis genes in vitro. This experimental evidence demonstrates that SNAC4 and SNAC9 could positively regulate the tomato fruit ripening process by functioning upstream of ethylene synthesis genes. These outcomes will be helpful to provide a theoretical foundation for further

  8. Playful Gaming.

    Science.gov (United States)

    Makedon, Alexander

    A philosophical analysis of play and games is undertaken in this paper. Playful gaming, which is shown to be a synthesis of play and games, is utilized as a category for undertaking the examination of play and games. The significance of playful gaming to education is demonstrated through analyses of Plato's, Dewey's, Sartre's, and Marcuse's…

  9. Assessing long-term return to play after hip arthroscopy in football players evaluating risk factors for good prognosis.

    Science.gov (United States)

    Barastegui, D; Seijas, R; Alvarez-Diaz, P; Rivera, E; Alentorn-Geli, E; Steinbacher, G; Cuscó, X; Cugat, R

    2017-05-17

    Groin pain is the third most common disease in football players and has often been associated with hip pathology such as femoroacetabular impingement and labral lesions. Hip arthroscopy offers possibilities of function restoration via minimally invasive procedures. The aim of this study is to evaluate professional football player's injuries and their return to play after hip arthroscopy for FAI and labral injuries. Patients that underwent hip arthroscopy between 2009 and 2014 were selected retrospectively. From this population, only professional soccer players competing at national level were included (Tegner 10). Arthroscopic surgery was proposed in patients with persistent pain. All patients were assessed for VAS score preoperatively and at 3, 6, 12 and 24 months post-op. HOS (sport and DLA) and mHHS tests were performed at the same time periods. All patients were men with a mean age of 26.5 ± 7.1 years old. Preoperative VAS (7.4 ± 1.3), HOS ADL (67.7 ± 5.5), HOS sport (37.6 ± 18.7) and mHHS (72.5 ± 8.8) showed improved scores during long-term follow-up. Time to return to play was 10.8 months (SD ± 4.3), with range between 4 and 20 months. Mean follow-up was 45.4 ± 15.6 months (range from 26 to 72 months). No differences were observed between non-active and active patients at final follow-up with respect to chondral lesions, but significant differences were observed with reference to management of the labrum (p = 0.031), where a higher rate of labrectomies existed among inactive patients and a higher rate of suture among active patients. Hip arthroscopy is a safe procedure with very good return to play results, but for optimized return to football one should consider patient age at the time of surgery, the condition of the labrum and low scores on the Harris Hip Score (mHHS) and HOS (sport version) as predictive factors for poor prognosis. Level of evidence IV.

  10. Perceived migraine triggers: do dietary factors play a role? Factores desencadenantes de migraña: ¿los factores dietéticos tienen influencia?

    Directory of Open Access Journals (Sweden)

    F. Camboim Rockett

    2012-04-01

    Full Text Available The present cross-sectional study was designed to assess the frequency of 36 possible triggering factors precipitating a migraine crisis (hormonal, environmental, and dietary in adult outpatients suffering from migraine attacks. A group of 123 migraine sufferers, aged 43.2 ± 13.9 (mean ± SD years, including 114 (92.7% women, 68.3% having migraine without aura, 68.3% reporting pain severe enough to require drug prophylaxis, and 29.3% presenting with hypertension, were evaluated. The most common triggers were stress and fasting, and environmental and hormonal factors were frequently found to precipitate a crisis. More than 90% of the patients reported susceptibility to 5 or more factors, and only 2.4% did not complain about any dietary factor. The large number of triggers detected in the present study emphasises the importance of awareness and avoidance of these factors in the management of patients with migraine.El presente es un estudio transversal que fue diseñado para estimar la frecuencia de 36 posibles factores desencadenantes de iniciar una crisis de migraña (hormonales, ambientales y dietéticos en pacientes adultos ambulatoriales que sufren ataques de migraña. Fue evaluado un grupo de 123 adultos que sufre de migraña, con edades entre 43,2 ± 13,9 (media ± DE, incluyendo 114 (92,7% mujeres con migraña sin aura, 68,3% de las cuales informaron sentir dolor suficiente como para requerir profilaxis con fármacos y 29,3% con hipertensión. Los factores desencadenantes más comunes fueron el estrés y el ayuno; factores ambientales y hormonales fueron también desencadenantes frecuentes. Más del 90% de los pacientes informaron susceptibilidad a 5 o más factores, y sólo el 2,4% no informó de ningún factor dietético. El gran número de factores desencadenantes detectados en el presente estudio enfatiza la importancia del cuidado y la prevención de estos factores en el manejo de pacientes con migraña.

  11. The transcription factor encyclopedia.

    Science.gov (United States)

    Yusuf, Dimas; Butland, Stefanie L; Swanson, Magdalena I; Bolotin, Eugene; Ticoll, Amy; Cheung, Warren A; Zhang, Xiao Yu Cindy; Dickman, Christopher T D; Fulton, Debra L; Lim, Jonathan S; Schnabl, Jake M; Ramos, Oscar H P; Vasseur-Cognet, Mireille; de Leeuw, Charles N; Simpson, Elizabeth M; Ryffel, Gerhart U; Lam, Eric W-F; Kist, Ralf; Wilson, Miranda S C; Marco-Ferreres, Raquel; Brosens, Jan J; Beccari, Leonardo L; Bovolenta, Paola; Benayoun, Bérénice A; Monteiro, Lara J; Schwenen, Helma D C; Grontved, Lars; Wederell, Elizabeth; Mandrup, Susanne; Veitia, Reiner A; Chakravarthy, Harini; Hoodless, Pamela A; Mancarelli, M Michela; Torbett, Bruce E; Banham, Alison H; Reddy, Sekhar P; Cullum, Rebecca L; Liedtke, Michaela; Tschan, Mario P; Vaz, Michelle; Rizzino, Angie; Zannini, Mariastella; Frietze, Seth; Farnham, Peggy J; Eijkelenboom, Astrid; Brown, Philip J; Laperrière, David; Leprince, Dominique; de Cristofaro, Tiziana; Prince, Kelly L; Putker, Marrit; del Peso, Luis; Camenisch, Gieri; Wenger, Roland H; Mikula, Michal; Rozendaal, Marieke; Mader, Sylvie; Ostrowski, Jerzy; Rhodes, Simon J; Van Rechem, Capucine; Boulay, Gaylor; Olechnowicz, Sam W Z; Breslin, Mary B; Lan, Michael S; Nanan, Kyster K; Wegner, Michael; Hou, Juan; Mullen, Rachel D; Colvin, Stephanie C; Noy, Peter John; Webb, Carol F; Witek, Matthew E; Ferrell, Scott; Daniel, Juliet M; Park, Jason; Waldman, Scott A; Peet, Daniel J; Taggart, Michael; Jayaraman, Padma-Sheela; Karrich, Julien J; Blom, Bianca; Vesuna, Farhad; O'Geen, Henriette; Sun, Yunfu; Gronostajski, Richard M; Woodcroft, Mark W; Hough, Margaret R; Chen, Edwin; Europe-Finner, G Nicholas; Karolczak-Bayatti, Magdalena; Bailey, Jarrod; Hankinson, Oliver; Raman, Venu; LeBrun, David P; Biswal, Shyam; Harvey, Christopher J; DeBruyne, Jason P; Hogenesch, John B; Hevner, Robert F; Héligon, Christophe; Luo, Xin M; Blank, Marissa Cathleen; Millen, Kathleen Joyce; Sharlin, David S; Forrest, Douglas; Dahlman-Wright, Karin; Zhao, Chunyan; Mishima, Yuriko; Sinha, Satrajit; Chakrabarti, Rumela; Portales-Casamar, Elodie; Sladek, Frances M; Bradley, Philip H; Wasserman, Wyeth W

    2012-01-01

    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 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 and vetted by experts in the field. TFe is available at http://www.cisreg.ca/tfe.

  12. 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...

  13. Revisiting epidermal growth factor receptor in glioblastoma multiforme: Does it play a role in response to therapy?

    Directory of Open Access Journals (Sweden)

    Priyanka Soni

    2014-01-01

    Full Text Available Background and Aim: Glioblastoma multiforme (GBM are the most aggressive class of cancer of central nervous system with hallmark characteristics that include rampant proliferation, necrosis, and endothelial proliferation. Epidermal growth factor receptor (EGFR has been implicated as the primary contributor to glioblastoma initiation and succession. The present study was designed to evaluate EGFR protein expression in GBM as predictor of response to therapy and survival. Materials and Methods: Epidermal growth factor receptor was assessed by immunohistochemistry as a percentage of positive tumor cells in hot spots (10 high-power fields. The study group comprised of 35 cases of GBM. All cases underwent surgical resection and subsequently underwent radiotherapy (n = 17 or radiotherapy with adjuvant temozolomide chemotherapy (n = 18. Immediate response to therapy was assessed at 3 months using World Health Organization response evaluation criteria in solid tumors criteria and cases followed up for survival. Results: Twenty-four cases (68.6% expressed EGFR while 11/35 (31.4% cases were negative. Response to therapy was evident in 21/35 cases (60.0% and 14/35 were (40.0% nonresponders. Mean EGFR protein expression in responders was 37.23 ± 33.70 and in nonresponders was 59.5 ± 39.46 (P = 0.542. The percentage of responders which were EGFR negative was 72.7% and while response in EGFR positive cases was observed in 54.2%. Mean survival in EGFR positive and negative GBM was 394.37 ± 189.11 and 420.54 ± 191.23 days, respectively. Conclusion: The EGFR negative cases appear to respond better to therapy, however, the difference is not statistically significant (P = 0.298. Further, EGFR protein expression does not play a definitive role in predicting survival. This is an original study evaluating EGFR in terms of therapeutic response.

  14. The RNA-binding protein CsrA plays a central role in positively regulating virulence factors in Erwinia amylovora.

    Science.gov (United States)

    Ancona, Veronica; Lee, Jae Hoon; Zhao, Youfu

    2016-11-15

    The GacS/GacA two-component system (also called GrrS/GrrA) is a global regulatory system which is highly conserved among gamma-proteobacteria. This system positively regulates non-coding small regulatory RNA csrB, which in turn binds to the RNA-binding protein CsrA. However, how GacS/GacA-Csr system regulates virulence traits in E. amylovora remains unknown. Results from mutant characterization showed that the csrB mutant was hypermotile, produced higher amount of exopolysaccharide amylovoran, and had increased expression of type III secretion (T3SS) genes in vitro. In contrast, the csrA mutant exhibited complete opposite phenotypes, including non-motile, reduced amylovoran production and expression of T3SS genes. Furthermore, the csrA mutant did not induce hypersensitive response on tobacco or cause disease on immature pear fruits, indicating that CsrA is a positive regulator of virulence factors. These findings demonstrated that CsrA plays a critical role in E. amylovora virulence and suggested that negative regulation of virulence by GacS/GacA acts through csrB sRNA, which binds to CsrA and neutralizes its positive effect on T3SS gene expression, flagellar formation and amylovoran production. Future research will be focused on determining the molecular mechanism underlying the positive regulation of virulence traits by CsrA.

  15. The RNA-binding protein CsrA plays a central role in positively regulating virulence factors in Erwinia amylovora

    Science.gov (United States)

    Ancona, Veronica; Lee, Jae Hoon; Zhao, Youfu

    2016-01-01

    The GacS/GacA two-component system (also called GrrS/GrrA) is a global regulatory system which is highly conserved among gamma-proteobacteria. This system positively regulates non-coding small regulatory RNA csrB, which in turn binds to the RNA-binding protein CsrA. However, how GacS/GacA-Csr system regulates virulence traits in E. amylovora remains unknown. Results from mutant characterization showed that the csrB mutant was hypermotile, produced higher amount of exopolysaccharide amylovoran, and had increased expression of type III secretion (T3SS) genes in vitro. In contrast, the csrA mutant exhibited complete opposite phenotypes, including non-motile, reduced amylovoran production and expression of T3SS genes. Furthermore, the csrA mutant did not induce hypersensitive response on tobacco or cause disease on immature pear fruits, indicating that CsrA is a positive regulator of virulence factors. These findings demonstrated that CsrA plays a critical role in E. amylovora virulence and suggested that negative regulation of virulence by GacS/GacA acts through csrB sRNA, which binds to CsrA and neutralizes its positive effect on T3SS gene expression, flagellar formation and amylovoran production. Future research will be focused on determining the molecular mechanism underlying the positive regulation of virulence traits by CsrA. PMID:27845410

  16. Aesthetic Play

    DEFF Research Database (Denmark)

    Bang, Jytte Susanne

    2012-01-01

    to the children’s complex life-worlds. Further, this leads to an analysis of music-play activities as play with an art-form (music), which includes aesthetic dimensions and gives the music-play activities its character of being aesthetic play. Following Lev Vygotsky’s insight that art is a way of building life...

  17. Playful Interventions Increase Knowledge about Healthy Habits and Cardiovascular Risk Factors in Children: The CARDIOKIDS Randomized Study.

    Science.gov (United States)

    Cecchetto, Fátima H; Pena, Daniela B; Pellanda, Lucia C

    2017-07-20

    Childhood obesity is an important health problem worldwide. In this context, there is a need for the development and evaluation of innovative educational interventions targeting prevention and formation of health habits. To ascertain the impact of ludic workshops on children's knowledge, self-care, and body weight. This was a randomized, clinical study with 79 students aged 7-11 years, conducted from March to November 2012. Anthropometric measurements were collected and two questionnaires (Typical Day of Physical Activities and Food Intake, in Portuguese, and the CARDIOKIDS, a questionnaire of knowledge about cardiovascular risk factors) were applied at baseline, at the end of intervention, and three months thereafter. The intervention consisted of eight playful workshops, which involved the presentation of a play. Seventy-nine students were randomized to the intervention (n = 40) or the control group (n = 39). Mean age was 10.0 ± 1.1 years. After eight weeks, the intervention group showed significant improvement in the knowledge score (p teatro. Setenta e nove estudantes foram randomizados para o grupo intervenção (n = 40) ou para o grupo controle (n = 39). A idade média foi 10 ± 1,1 anos. Após oito semanas, o grupo intervenção mostrou uma melhora significativa no escore de conhecimento (p < 0,01). Houve um aumento nos escores de atividade física em ambos os grupos, mas sem diferença entre os grupos no final da intervenção (p=0,209). Observou-se uma redução no percentil do IMC no grupo intervenção, mas não houve diferença estatística entre os grupos após a intervenção. Intervenções lúdicas podem melhorar o conhecimento e níveis de atividade física em crianças e, quando combinadas com outras estratégias, podem ser benéficas na prevenção da obesidade e melhoria do autocuidado.

  18. Differential contribution of transcription factors to Arabidopsis thaliana defence against Spodoptera littoralis.

    Directory of Open Access Journals (Sweden)

    Fabian eSchweizer

    2013-02-01

    Full Text Available In response to insect herbivory, Arabidopsis plants activate the synthesis of the phytohormone jasmonate-isoleucine (JA-Ile, which binds to a complex consisting of the receptor COI1 and JAZ repressors. Upon proteasome-mediated JAZ degradation, basic helix-loop-helix transcription factors (TFs MYC2, MYC3, and MYC4 become activated and this results in the expression of defence genes. Although the jasmonate (JA pathway is known to be essential for the massive transcriptional reprogramming that follows herbivory, there is however little information on other TFs that are required for defence against herbivores and whether they contribute significantly to JA-dependent defence gene expression. By transcriptome profiling, we identified 41 TFs that were induced in response to herbivory by the generalist Spodoptera littoralis. Among them, nine genes, including WRKY18, WRKY40, ANAC019, ANAC055, ZAT10, ZAT12, AZF2, ERF13, and RRTF1, were found to play a significant role in resistance to S. littoralis herbivory. However, compared to the triple mutant myc234 that is as sensitive as coi1-1 to herbivory, knockout lines of these nine TFs were only partially more sensitive to S. littoralis and showed only minor gene expression changes at the whole genome level. Data thus reveal that MYC2, MYC3, and MYC4 are master regulators of Arabidopsis resistance to a generalist herbivore and identify new genes involved in insect defence.

  19. A Qualitative Exploration of Factors Affecting Group Cohesion and Team Play in Multiplayer Online Battle Arenas (MOBAs)

    OpenAIRE

    Taylor, Jacqui

    2016-01-01

    Previous research examining the social psychology of video-gaming has tended to focus on Massively Multiplayer Online Role Playing Game (MMORPG) environments, such as World of Warcraft. Although many online group processes have been examined using this game, this genre does not enforce cooperative play and studies tend to be based on very large groups. Newer genres are being developed and played which have so far not been studied. The genre known as Multiplayer Online Battle Arenas (MOBAs) ar...

  20. Does Performance in Digital Reading Relate to Computer Game Playing? A Study of Factor Structure and Gender Patterns in 15-Year-Olds' Reading Literacy Performance

    Science.gov (United States)

    Rasmusson, Maria; Åberg-Bengtsson, Lisbeth

    2015-01-01

    Data from a Swedish PISA-sample were used (1) to identify a digital reading factor, (2) to investigate gender differences in this factor (if found), and (3) to explore how computer game playing might relate to digital reading performance and gender. The analyses were conducted with structural equation modeling techniques. In addition to an overall…

  1. Aesthetic Play

    DEFF Research Database (Denmark)

    Bang, Jytte Susanne

    2012-01-01

    The present article explores the role of music-related artefacts and technologies in children’s lives. More specifically, it analyzes how four 10- to 11-year old girls use CDs and DVD games in their music-play activities and which developmental themes and potentials may accrue from such activities...... to the children’s complex life-worlds. Further, this leads to an analysis of music-play activities as play with an art-form (music), which includes aesthetic dimensions and gives the music-play activities its character of being aesthetic play. Following Lev Vygotsky’s insight that art is a way of building life...

  2. Playful Membership

    DEFF Research Database (Denmark)

    Åkerstrøm Andersen, Niels; Pors, Justine Grønbæk

    2014-01-01

    This article studies the implications of current attempts by organizations to adapt to a world of constant change by introducing the notion of playful organizational membership. To this end we conduct a brief semantic history of organizational play and argue that when organizations play, employees...... are expected to engage in playful exploration of alternative selves. Drawing on Niklas Luhmann's theory of time and decision-making and Gregory Bateson's theory of play, the article analyses three empirical examples of how games play with conceptions of time. We explore how games represent an organizational...... desire to reach out - not just to the future - but to futures beyond the future presently imaginable. The article concludes that playful membership is membership through which employees are expected to develop a surplus of potential identities and continuously cross boundaries between real and virtual...

  3. Large-scale screening of transcription factor-promoter interactions in spruce reveals a transcriptional network involved in vascular development.

    Science.gov (United States)

    Duval, Isabelle; Lachance, Denis; Giguère, Isabelle; Bomal, Claude; Morency, Marie-Josée; Pelletier, Gervais; Boyle, Brian; MacKay, John J; Séguin, Armand

    2014-06-01

    This research aimed to investigate the role of diverse transcription factors (TFs) and to delineate gene regulatory networks directly in conifers at a relatively high-throughput level. The approach integrated sequence analyses, transcript profiling, and development of a conifer-specific activation assay. Transcript accumulation profiles of 102 TFs and potential target genes were clustered to identify groups of coordinately expressed genes. Several different patterns of transcript accumulation were observed by profiling in nine different organs and tissues: 27 genes were preferential to secondary xylem both in stems and roots, and other genes were preferential to phelloderm and periderm or were more ubiquitous. A robust system has been established as a screening approach to define which TFs have the ability to regulate a given promoter in planta. Trans-activation or repression effects were observed in 30% of TF-candidate gene promoter combinations. As a proof of concept, phylogenetic analysis and expression and trans-activation data were used to demonstrate that two spruce NAC-domain proteins most likely play key roles in secondary vascular growth as observed in other plant species. This study tested many TFs from diverse families in a conifer tree species, which broadens the knowledge of promoter-TF interactions in wood development and enables comparisons of gene regulatory networks found in angiosperms and gymnosperms.

  4. Spatial expression of transcription factors in Drosophila embryonic organ development.

    Science.gov (United States)

    Hammonds, Ann S; Bristow, Christopher A; Fisher, William W; Weiszmann, Richard; Wu, Siqi; Hartenstein, Volker; Kellis, Manolis; Yu, Bin; Frise, Erwin; Celniker, Susan E

    2013-12-20

    Site-specific transcription factors (TFs) bind DNA regulatory elements to control expression of target genes, forming the core of gene regulatory networks. Despite decades of research, most studies focus on only a small number of TFs and the roles of many remain unknown. We present a systematic characterization of spatiotemporal gene expression patterns for all known or predicted Drosophila TFs throughout embryogenesis, the first such comprehensive study for any metazoan animal. We generated RNA expression patterns for all 708 TFs by in situ hybridization, annotated the patterns using an anatomical controlled vocabulary, and analyzed TF expression in the context of organ system development. Nearly all TFs are expressed during embryogenesis and more than half are specifically expressed in the central nervous system. Compared to other genes, TFs are enriched early in the development of most organ systems, and throughout the development of the nervous system. Of the 535 TFs with spatially restricted expression, 79% are dynamically expressed in multiple organ systems while 21% show single-organ specificity. Of those expressed in multiple organ systems, 77 TFs are restricted to a single organ system either early or late in development. Expression patterns for 354 TFs are characterized for the first time in this study. We produced a reference TF dataset for the investigation of gene regulatory networks in embryogenesis, and gained insight into the expression dynamics of the full complement of TFs controlling the development of each organ system.

  5. Playing-related musculoskeletal problems in children learning instrumental music: the association between problem location and gender, age, and music exposure factors.

    Science.gov (United States)

    Ranelli, Sonia; Straker, Leon; Smith, Anne

    2011-09-01

    Playing-related musculoskeletal problems (PRMP) are common in adult musicians, and risk factors include gender, music exposure, and particularly instrument type. Emerging evidence suggests PRMP are common in children and adolescents and that risk factors may be similar. The aim of this study was to determine the prevalence of PRMP, both symptoms and disorders, and PRMP location in children and adolescents as well as the associations with gender, age, and music exposure factors such as type and number of instruments and playing time. This study surveyed 731 children (460 females), aged 7 to 17 years, studying instrumental music in government schools in Perth, Australia. Lifetime and monthly symptoms, monthly disorders (inability to play an instrument as usual), and PRMP location were examined. Chi-squared analyses were used to evaluate associations between gender, age, music exposure, and PRMP outcomes. Logistic regression evaluated the independent association of these potential risk factors with PRMP prevalence and location. RESULTS) Sixty-seven percent of students reported PRMP symptoms at some point, 56% reported them within the last month, and 30% reported an inability to play as usual within the last month. After adjustment for gender and age, the type of instrument played (upper and lower strings, woodwind, and brass) was significantly associated with all PRMP (pmusic exposure are associated with PRMP risk and need to be addressed to ensure musicians' personal well-being and musical longevity.

  6. Why people continue to play online games: in search of critical design factors to increase customer loyalty to online contents.

    Science.gov (United States)

    Choi, Dongseong; Kim, Jinwoo

    2004-02-01

    As people increasingly play online games, numerous new features have been proposed to increase players' log-on time at online gaming sites. However, few studies have investigated why people continue to play certain online games or which design features are most closely related to the amount of time spent by players at particular online gaming sites. This study proposes a theoretical model using the concepts of customer loyalty, flow, personal interaction, and social interaction to explain why people continue to play online network games. The study then conducts a large-scale survey to validate the model. Finally, it analyzes current online games to identify design features that are closely related to the theoretical concepts. The results indicate that people continue to play online games if they have optimal experiences while playing the games. This optimal experience can be attained if the player has effective personal interaction with the system or pleasant social interactions with other people connected to the Internet. Personal interaction can be facilitated by providing appropriate goals, operators and feedback; social interaction can be facilitated through appropriate communication places and tools. This paper ends with the implications of applying the study results to other domains such as e-commerce and cyber communities.

  7. Playful Literacy

    DEFF Research Database (Denmark)

    Froes, Isabel

    2017-01-01

    these practices, which compose the taxonomy of tablet play. My contribution lies in identifying and proposing a series of theoretical concepts that complement recent theories related to play and digital literacy studies. The data collected through observations informed some noteworthy aspects, including how...... with tablets’ physical and digital affordances shape children’s digital play. This thesis presents how young children’s current practices when playing with tablets inform digital experiences in Denmark and Japan. Through an interdisciplinary lens and a grounded theory approach, I have identified and mapped...... vocabulary in children’s digital play experiences. These early digital experiences set the rules for the playgrounds and assert digital tablets as twenty-first-century toys, shaping young children’s playful literacy....

  8. Statistics for Transcription Factor Binding Sites

    OpenAIRE

    2008-01-01

    Transcription factors (TFs) play a key role in gene regulation. They interact with specific binding sites or motifs on the DNA sequence and regulate expression of genes downstream of these binding sites. In silico prediction of potential binding of a TF to a binding site is an important task in computational biology. From a statistical point of view, the DNA sequence is a long text consisting of four different letters ('A','C','G', and 'T'). The binding of a TF to the sequence corresponds to ...

  9. Pretend play.

    Science.gov (United States)

    Weisberg, Deena Skolnick

    2015-01-01

    Pretend play is a form of playful behavior that involves nonliteral action. Although on the surface this activity appears to be merely for fun, recent research has discovered that children's pretend play has connections to important cognitive and social skills, such as symbolic thinking, theory of mind, and counterfactual reasoning. The current article first defines pretend play and then reviews the arguments and evidence for these three connections. Pretend play has a nonliteral correspondence to reality, hence pretending may provide children with practice with navigating symbolic relationships, which may strengthen their language skills. Pretend play and theory of mind reasoning share a focus on others' mental states in order to correctly interpret their behavior, hence pretending and theory of mind may be mutually supportive in development. Pretend play and counterfactual reasoning both involve representing nonreal states of affairs, hence pretending may facilitate children's counterfactual abilities. These connections make pretend play an important phenomenon in cognitive science: Studying children's pretend play can provide insight into these other abilities and their developmental trajectories, and thereby into human cognitive architecture and its development.

  10. Playful Interaction

    DEFF Research Database (Denmark)

    2003-01-01

    The video Playful Interaction describes a future architectural office, and envisions ideas and concepts for playful interactions between people, materials and appliances in a pervasive and augmented working environment. The video both describes existing developments, technologies and designs...... as well as ideas not yet implemented such as playful modes of interaction with an augmented ball. Playful Interaction has been used as a hybrid of a vision video and a video prototype (1). Externally the video has been used to visualising our new ideas, and internally the video has also worked to inspire...

  11. Mediatized play

    DEFF Research Database (Denmark)

    Johansen, Stine Liv

    Children’s play must nowadays be understood as a mediatized field in society and culture. Media – understood in a very broad sense - holds severe explanatory power in describing and understanding the practice of play, since play happens both with, through and inspired by media of different sorts....... In this presentation the case of ‘playing soccer’ will be outlined through its different mediated manifestations, including soccer games and programs on TV, computer games, magazines, books, YouTube videos and soccer trading cards....

  12. Play practices and play moods

    DEFF Research Database (Denmark)

    Karoff, Helle Skovbjerg

    2013-01-01

    The aim of this article is to develop a view of play as a relation between play practices and play moods based on an empirical study of children's everyday life and by using Bateson's term of ‘framing’ [(1955/2001). In Steps to an ecology of mind (pp. 75–80). Chicago: University of Chicago Press......], Schmidt's notion of ‘commonness’ [(2005). Om respekten. København: Danmarks Pædagogiske Universitets Forlag; (2011). On respect. Copenhagen: Danish School of Education University Press] and Heidegger's term ‘mood’ [(1938/1996). Time and being. Cornwall: Wiley-Blackwell.]. Play mood is a state of being...... in which we are open and ready, both to others and their production of meaning and to new opportunities for producing meaning. This play mood is created when we engage with the world during play practices. The article points out four types of play moods – devotion, intensity, tension and euphorica – which...

  13. Construction of pancreatic cancer double-factor regulatory network based on chip data on the transcriptional level.

    Science.gov (United States)

    Zhao, Li-Li; Zhang, Tong; Liu, Bing-Rong; Liu, Tie-Fu; Tao, Na; Zhuang, Li-Wei

    2014-05-01

    Transcription factor (TF) and microRNA (miRNA) have been discovered playing crucial roles in cancer development. However, the effect of TFs and miRNAs in pancreatic cancer pathogenesis remains vague. We attempted to reveal the possible mechanism of pancreatic cancer based on transcription level. Using GSE16515 datasets downloaded from gene expression omnibus database, we first identified the differentially expressed genes (DEGs) in pancreatic cancer by the limma package in R. Then the DEGs were mapped into DAVID to conduct the kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis. TFs and miRNAs that DEGs significantly enriched were identified by Fisher's test, and then the pancreatic cancer double-factor regulatory network was constructed. In our study, total 1117 DEGs were identified and they significantly enriched in 4 KEGG pathways. A double-factor regulatory network was established, including 29 DEGs, 24 TFs, 25 miRNAs. In the network, LAMC2, BRIP1 and miR155 were identified which may be involved in pancreatic cancer development. In conclusion, the double-factor regulatory network was found to play an important role in pancreatic cancer progression and our results shed new light on the molecular mechanism of pancreatic cancer.

  14. Playful Organizations

    DEFF Research Database (Denmark)

    Pors, Justine Grønbæk; Åkerstrøm Andersen, Niels

    2015-01-01

    and undecidability. With an empirical point of departure in Danish public school policy and two concrete examples of games utilised in school development, the article analyses how play is a way for organisations to simultaneously decide and also avoid making a decision, thus keeping flexibility and possibilities...... intact. In its final sections, the article discusses what happens to conditions of decision-making when organisations do not just see undecidability as a given condition, but as a limited resource indispensable for change and renewal. The article advances discussions of organisational play by exploring......This article explores how organisational play becomes a managerial tool to increase and benefit from undecidability. The article draws on Niklas Luhmann's concept of decision and on Gregory Bateson's theory of play to create a conceptual framework for analysing the relation between decision...

  15. Water and playing facilities as a factor increasing the efficiency of educational and training process of young athletes.

    Directory of Open Access Journals (Sweden)

    Sitnikova N.S.

    2011-03-01

    Full Text Available It is shown the role of water-game activities to enhance the efficiency of teaching and training process for athletes 10-16 years in the preparatory period and their effects on young athletes. It is proposed a set of exercises and games in the water for a sprinter. The basis of systems put different games, relay races, dynamic and static exercises, exercises on the recovery. Proved that the water-play classes young athletes develop harmoniously reinforce the emotional and physiological quality, improve health and increase the intellectual level.

  16. Regulation of Axillary Meristem Initiation by Transcription Factors and Plant Hormones.

    Science.gov (United States)

    Yang, Minglei; Jiao, Yuling

    2016-01-01

    One distinctive feature of plant post-embryonic development is that plants can undergo reiterative growth and continuous organogenesis throughout their lifetimes. Axillary meristems (AMs) in leaf axils play a central role in this growth and differences in meristem initiation and development produce the diversity of plant architecture. Studies in the past 15 years have shown that several transcription factors (TFs) and phytohormones affect AM initiation. In this review, we highlight recent research using systems biology approaches to examine the regulatory hierarchies underlying AM initiation and the role of auxins and cytokinins in AM initiation and development. This research revealed a developmental mechanism in which phytohormone signals act with a gene regulatory network containing multiple TFs to contribute to the initiation of AMs.

  17. Group play

    DEFF Research Database (Denmark)

    Tychsen, Anders; Hitchens, Michael; Brolund, Thea

    2008-01-01

    of group dynamics, the influence of the fictional game characters and the comparative play experience between the two formats. The results indicate that group dynamics and the relationship between the players and their digital characters, are integral to the quality of the gaming experience in multiplayer......Role-playing games (RPGs) are a well-known game form, existing in a number of formats, including tabletop, live action, and various digital forms. Despite their popularity, empirical studies of these games are relatively rare. In particular there have been few examinations of the effects...... of the various formats used by RPGs on the gaming experience. This article presents the results of an empirical study, examining how multi-player tabletop RPGs are affected as they are ported to the digital medium. Issues examined include the use of disposition assessments to predict play experience, the effect...

  18. Characterization and stress-induced expression analysis of Alfin-like transcription factors in Brassica rapa.

    Science.gov (United States)

    Kayum, Md Abdul; Park, Jong-In; Ahmed, Nasar Uddin; Jung, Hee-Jeong; Saha, Gopal; Kang, Jong-Goo; Nou, Ill-Sup

    2015-08-01

    The Alfin-like (AL) transcription factors (TFs) family is involved in many developmental processes, including the growth and development of roots, root hair elongation, meristem development, etc. However, stress resistance-related function and the regulatory mechanism of these TFs have yet to be elucidated. This study identified 15 Brassica rapa AL (BrAL) TFs from BRAD database, analyzed the sequences and profiled their expression first time in response to Fusarium oxysporum f. sp. conglutinans and Pectobacterium carotovorum subsp. carotovorum in fection, cold, salt and drought stresses in B. rapa. Structural and phylogenetic analyses of 15 BrAL TFs revealed four distinct groups (groups I-IV) with AL TFs of Arabidopsis thaliana. In the expression analyses, ten BrAL TFs showed responsive expression after F. oxysporum f. sp. conglutinans infection, while all BrAL TFs showed responses under cold, salt and drought stresses in B. rapa. Interestingly, ten BrAL TFs showed responses to both biotic and abiotic stress factors tested here. The differentially expressed BrAL TFs thus represent potential resources for molecular breeding of Brassica crops resistant against abiotic and biotic stresses. Our findings will also help to elucidate the complex regulatory mechanism of AL TFs in stress resistance and provide a foundation for further functional genomics studies and applications.

  19. Postphenomenological Play

    DEFF Research Database (Denmark)

    Hammar, Emil

    This paper aims to identify an understanding of digital games in virtual environments by using Don Ihde’s (1990) postphenomenological approach to how technology mediates the world to human beings in conjunction with Hans-Georg Gadamer’s (1993) notion of play . Through this tentatively proposed...... amalgamation of theories I point towards an alternative understanding of the relationship between play and game as not only dialectic, but also as socially and ethically relevant qua the design and implementation of the game as technology....

  20. Which factors may play a pivotal role on determining the type of psychiatric disorder in children and adolescents with epilepsy?

    Science.gov (United States)

    Thome-Souza, Sigride; Kuczynski, Evelyn; Assumpção, Francisco; Rzezak, Patricia; Fuentes, Daniel; Fiore, Lia; Valente, Kette D

    2004-12-01

    Physicians have become aware of the high prevalence of psychiatric disorders (PDs) in children and adolescents with epilepsy; however, there are many controversies as to which factors may have an important role in the different types of PD. This study was designed to assess the main PD; verify the age of onset compared with the age of diagnosis of the PD; and determine which factors may be correlated with the type of PD described. For this purpose, a multidisciplinary team evaluated children and adolescents (4-18 years) with epilepsy and analyzed patient-related factors such as age (grouped according to Piaget's cognitive scale: 13 years), sex, family history of PDs, and cognitive status. With respect to epilepsy features, we considered age of onset, duration, seizure control at the time of psychiatric evaluation, refractoriness, antiepileptic drugs (mono- vs polytherapy), seizure type (generalized vs focal), and epilepsy type (idiopathic vs symptomatic/probably symptomatic). Depression occurred in 36.4% and attention-deficit hyperactivity disorder (ADHD) in 29.1%, these being the most frequent PDs in this series. Focal epilepsy was significantly more frequent in children and adolescents with PDs. As to the type of PD, age was an important factor, with a predominance of ADHD in children and depression in adolescents (P<0.0001). Family history was contributory for depression, but not for others PDs (P<0.0001). Depression remained underdiagnosed and untreated for a longer period. Impact of early diagnosis and treatment remains unknown.

  1. A Factor-Based Exploration of Player´s Continuation Desire in Free-to-Play Mobile Games

    DEFF Research Database (Denmark)

    Stankevicius, Deividas; Jady, Hawraa Amira; Drachen, Anders;

    2015-01-01

    experience, motivation and enjoyment, yet difficult to measure. These concepts were conceptualized into different factors and thereby it was identified which of them are re-lated. This resulted in a synthesized model that was based on the Theory of Planned Behavior model. This model takes into account...

  2. A petunia ocs element binding factor, PhOBF1, plays an important role in antiviral RNA silencing

    Science.gov (United States)

    Virus-induced gene silencing (VIGS) is a common strategy of reverse genetics for characterizing function of genes in plant. The detailed mechanism governing RNA silencing efficiency triggered by virus is largely unclear. Here, we revealed that a petunia (Petunia hybrida) ocs element binding factor, ...

  3. Clay Play

    Science.gov (United States)

    Rogers, Liz; Steffan, Dana

    2009-01-01

    This article describes how to use clay as a potential material for young children to explore. As teachers, the authors find that their dialogue about the potential of clay as a learning medium raises many questions: (1) What makes clay so enticing? (2) Why are teachers noticing different play and conversation around the clay table as compared to…

  4. Environmental Contaminants and microRNA Regulation: Transcription Factors as Regulators of Toxicant-Altered microRNA Expression

    Science.gov (United States)

    Sollome, James; Martin, Elizabeth; Sethupathy, Praveen; Fry, Rebecca C.

    2016-01-01

    MicroRNAs (miRNAs) regulate gene expression by binding mRNA transcripts and inhibiting translation and/or inducing degradation of the associated transcripts. Expression levels of miRNAs have been shown to be altered in response to environmental toxicants, thus impacting cellular function and influencing disease risk. Transcription factors (TFs) are known to be altered in response to environmental toxicants and play a critical role in the regulation of miRNA expression. To date, environmentally-responsive TFs that are important for regulating miRNAs remain understudied. In a state-of-the-art analysis, we utilized in silico bioinformatic analysis to characterize potential transcriptional regulators of environmentally-responsive miRNAs. Using the miRStart database, genomic sequences of promoter regions for all available human miRNAs (n=847) were identified and promoter regions were defined as −1000/+500 base pairs from the transcription start site. Subsequently, the promoter region sequences of environmentally-responsive miRNAs (n=128) were analyzed using enrichment analysis to determine overrepresented TF binding sites (TFBS). While most (56/73) TFs differed across environmental contaminants, a set of 17 TFs was enriched for promoter binding among miRNAs responsive to numerous environmental contaminants. Of these, one TF was common to miRNAs altered by the majority of environmental contaminants, namely SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 3 (SMARCA3). These identified TFs represent candidate common transcriptional regulators of miRNAs perturbed by environmental toxicants. PMID:27292125

  5. Macrophage Migration Inhibitory Factor Plays a Critical Role in Mediating Protection against the Helminth Parasite Taenia crassiceps

    OpenAIRE

    Rodríguez-Sosa, Miriam; Rosas, Lucia E.; David, John R; Bojalil, Rafael; Satoskar, Abhay R.; Terrazas, Luis I.

    2003-01-01

    To determine the role of endogenous migration inhibitory factor (MIF) in regulation of immune response during murine cysticercosis caused by the helminth parasite Taenia crassiceps, we analyzed the course of T. crassiceps infection in MIF−/− BALB/c mice. MIF−/− mice were highly susceptible to T. crassiceps and developed significantly higher parasite loads compared to similarly infected MIF+/+ mice. Throughout the course of infection, Taenia crassiceps soluble antigen-stimulated spleen cells f...

  6. Play and Positive Group Dynamics

    Science.gov (United States)

    Thompson, Pam; White, Samantha

    2010-01-01

    Play is an important part of a child's life and essential to learning and development (Vygotsky, 1978). It is vital that students participate in play and that play be conducted in a restorative manner. Play allows a variety of group dynamics to emerge. Irvin Yalom (1995) identifies 11 curative factors of the group experience. These factors include…

  7. The alternative sigma factor σ(B) plays a crucial role in adaptive strategies of Clostridium difficile during gut infection.

    Science.gov (United States)

    Kint, Nicolas; Janoir, Claire; Monot, Marc; Hoys, Sandra; Soutourina, Olga; Dupuy, Bruno; Martin-Verstraete, Isabelle

    2017-02-15

    Clostridium difficile is a major cause of diarrhoea associated with antibiotherapy. Exposed to stresses in the gut, C. difficile can survive by inducing protection, detoxification and repair systems. In several firmicutes, most of these systems are controlled by the general stress response involving σ(B) . In this work, we studied the role of σ(B) in the physiopathology of C. difficile. We showed that the survival of the sigB mutant during the stationary phase was reduced. Using a transcriptome analysis, we showed that σ(B) controls the expression of ∼25% of genes including genes involved in sporulation, metabolism, cell surface biogenesis and the management of stresses. By contrast, σ(B) does not control toxin gene expression. In agreement with the up-regulation of sporulation genes, the sporulation efficiency is higher in the sigB mutant than in the wild-type strain. sigB inactivation also led to increased sensitivity to acidification, cationic antimicrobial peptides, nitric oxide and ROS. In addition, we showed for the first time that σ(B) also plays a crucial role in oxygen tolerance in this strict anaerobe. Finally, we demonstrated that the fitness of colonisation by the sigB mutant is greatly affected in a dixenic mouse model of colonisation when compared to the wild-type strain.

  8. Chromatin properties of regulatory DNA probed by manipulation of transcription factors.

    Science.gov (United States)

    Sharov, Alexei A; Nishiyama, Akira; Qian, Yong; Dudekula, Dawood B; Longo, Dan L; Schlessinger, David; Ko, Minoru S H

    2014-08-01

    Transcription factors (TFs) bind to DNA and regulate the transcription of nearby genes. However, only a small fraction of TF binding sites have such regulatory effects. Here we search for the predictors of functional binding sites by carrying out a systematic computational screening of a variety of contextual factors (histone modifications, nuclear lamin-bindings, and cofactor bindings). We used regression analysis to test if contextual factors are associated with upregulation or downregulation of neighboring genes following the induction or knockdown of the 9 TFs in mouse embryonic stem (ES) cells. Functional TF binding sites appeared to be either active (i.e., bound by P300, CHD7, mediator, cohesin, and SWI/SNF) or repressed (i.e., with H3K27me3 histone marks and bound by Polycomb factors). Active binding sites mediated the downregulation of nearby genes upon knocking down the activating TFs or inducing repressors. Repressed TF binding sites mediated the upregulation of nearby genes (e.g., poised developmental regulators) upon inducing TFs. In addition, repressed binding sites mediated repressive effects of TFs, identified by the downregulation of target genes after the induction of TFs or by the upregulation of target genes after the knockdown of TFs. The contextual factors associated with functions of DNA-bound TFs were used to improve the identification of candidate target genes regulated by TFs.

  9. Chromatin Properties of Regulatory DNA Probed by Manipulation of Transcription Factors

    Science.gov (United States)

    Sharov, Alexei A.; Nishiyama, Akira; Qian, Yong; Dudekula, Dawood B.; Longo, Dan L.; Schlessinger, David

    2014-01-01

    Abstract Transcription factors (TFs) bind to DNA and regulate the transcription of nearby genes. However, only a small fraction of TF binding sites have such regulatory effects. Here we search for the predictors of functional binding sites by carrying out a systematic computational screening of a variety of contextual factors (histone modifications, nuclear lamin-bindings, and cofactor bindings). We used regression analysis to test if contextual factors are associated with upregulation or downregulation of neighboring genes following the induction or knockdown of the 9 TFs in mouse embryonic stem (ES) cells. Functional TF binding sites appeared to be either active (i.e., bound by P300, CHD7, mediator, cohesin, and SWI/SNF) or repressed (i.e., with H3K27me3 histone marks and bound by Polycomb factors). Active binding sites mediated the downregulation of nearby genes upon knocking down the activating TFs or inducing repressors. Repressed TF binding sites mediated the upregulation of nearby genes (e.g., poised developmental regulators) upon inducing TFs. In addition, repressed binding sites mediated repressive effects of TFs, identified by the downregulation of target genes after the induction of TFs or by the upregulation of target genes after the knockdown of TFs. The contextual factors associated with functions of DNA-bound TFs were used to improve the identification of candidate target genes regulated by TFs. PMID:24918633

  10. c-ETS transcription factors play an essential role in the licensing of human MCM4 origin of replication.

    Science.gov (United States)

    Sidhu, Kaveri; Kumar, Vijay

    2015-11-01

    In metazoans, DNA replication is a highly regulated and ordered process that occurs during the S phase of cell cycle. It begins with the licensing of origins of replication usually found in close proximity of actively transcribing genes owing perhaps to a profound influence of transcription factors on the epigenetic signatures and architecture of chromatin. Here we show that ETS transcription factors are novel regulators of MCM4 origin, whose binding sites are localized between two divergently transcribing MCM4 and PRKDC genes. c-ETS1 and c-ETS2 were recruited to the MCM4 origin respectively during the S and G1 phases of cell cycle. c-ETS2 binding was facilitated by an active chromatin distinguished by acetylated histone H3 orchestrated by histone acetyl transferase GCN5 and followed by HBO1 mediated histone H4 acetylation. Interestingly, c-ETS2 overexpression led to increased BrdU incorporation in the S phase cells while its down-regulation by RNA interference compromised the loading of pre-replicative complex at the origin. Conversely, the recruitment of c-ETS1 at the origin coincided with histone H3 methylation signature characteristic of closed chromatin conformation. As expected, enforced expression of c-ETS1 severely compromised DNA replication whereas its down-regulation enhanced DNA replication as evident from increased BrdU incorporation. Thus, c-ETS transcription factors appear to be key regulators of MCM4 origin where c-ETS2 seems to promote DNA replication whereas c-ETS1 functions as a negative regulator. © 2015 Elsevier B.V. All rights reserved.

  11. Inheritance and memory of stress-induced epigenome change: roles played by the ATF-2 family of transcription factors

    Science.gov (United States)

    Seong, Ki-Hyeon; Maekawa, Toshio; Ishii, Shunsuke

    2012-01-01

    Data on the inheritance-of-stress effect have been accumulating and some mechanistic insights, such as epigenetic regulation, have also been suggested. In particular, the modern view of Lamarckian inheritance appears to be affected by the finding that stress-induced epigenetic changes can be inherited. This review summarizes the current data on the inheritance of stress effect and possible mechanisms involved in this process. In particular, we focus on the stress-induced epigenetic changes mediated by the ATF-2 family of transcription factors. PMID:22380515

  12. Group play

    DEFF Research Database (Denmark)

    Tychsen, Anders; Hitchens, Michael; Brolund, Thea

    2008-01-01

    Role-playing games (RPGs) are a well-known game form, existing in a number of formats, including tabletop, live action, and various digital forms. Despite their popularity, empirical studies of these games are relatively rare. In particular there have been few examinations of the effects of the v......Role-playing games (RPGs) are a well-known game form, existing in a number of formats, including tabletop, live action, and various digital forms. Despite their popularity, empirical studies of these games are relatively rare. In particular there have been few examinations of the effects...... of the various formats used by RPGs on the gaming experience. This article presents the results of an empirical study, examining how multi-player tabletop RPGs are affected as they are ported to the digital medium. Issues examined include the use of disposition assessments to predict play experience, the effect...... RPGs, with the first being of greater importance to digital games and the latter to the tabletop version....

  13. Spatial Factors Play a Major Role as Determinants of Endemic Ground Beetle Beta Diversity of Madeira Island Laurisilva

    Science.gov (United States)

    Boieiro, Mário; Carvalho, José C.; Cardoso, Pedro; Aguiar, Carlos A. S.; Rego, Carla; de Faria e Silva, Israel; Amorim, Isabel R.; Pereira, Fernando; Azevedo, Eduardo B.; Borges, Paulo A. V.; Serrano, Artur R. M.

    2013-01-01

    The development in recent years of new beta diversity analytical approaches highlighted valuable information on the different processes structuring ecological communities. A crucial development for the understanding of beta diversity patterns was also its differentiation in two components: species turnover and richness differences. In this study, we evaluate beta diversity patterns of ground beetles from 26 sites in Madeira Island distributed throughout Laurisilva – a relict forest restricted to the Macaronesian archipelagos. We assess how the two components of ground beetle beta diversity (βrepl – species turnover and βrich - species richness differences) relate with differences in climate, geography, landscape composition matrix, woody plant species richness and soil characteristics and the relative importance of the effects of these variables at different spatial scales. We sampled 1025 specimens from 31 species, most of which are endemic to Madeira Island. A spatially explicit analysis was used to evaluate the contribution of pure environmental, pure spatial and environmental spatially structured effects on variation in ground beetle species richness and composition. Variation partitioning showed that 31.9% of species turnover (βrepl) and 40.7% of species richness variation (βrich) could be explained by the environmental and spatial variables. However, different environmental variables controlled the two types of beta diversity: βrepl was influenced by climate, disturbance and soil organic matter content whilst βrich was controlled by altitude and slope. Furthermore, spatial variables, represented through Moran’s eigenvector maps, played a significant role in explaining both βrepl and βrich, suggesting that both dispersal ability and Madeira Island complex orography are crucial for the understanding of beta diversity patterns in this group of beetles. PMID:23724065

  14. Cardiovascular risk in lupus nephritis: Do renal disease-related and other traditional risk factors play a role?

    Directory of Open Access Journals (Sweden)

    Inoshi Atukorala

    2015-01-01

    Full Text Available This study was performed to evaluate the prevalence of thickened carotid intima media thickness (CIMT in a Sri Lankan cohort of lupus nephritis (LN patients and to identify associations between traditional cardiovascular disease (CVD and LN-related risk factors with increased CIMT. Consecutive patients with biopsy-proven LN were evaluated for conventional CVD risk factors, renal parameters and extent of organ involvement in this cross-sectional study. Current disease activity and damage were assessed by the British Isles Lupus Activity Group (BILAG score and the Systemic Lupus International Collaborative Clinics/American College of Rheumatology (SLICC/ACR damage index, respectively. CIMT was assessed by B Mode grey scale ultrasonography. Increased CIMT was defined as CIMT more than the 75th percentile based on cutoffs from the "Carotid Atherosclerosis Progression Study." Forty patients (98% female, with a mean age of 38 years (age range of 20-50 and of South Asian descent, were evaluated. The mean duration of disease of 6.15 years (SD = 4.66. The overall prevalence of cardiovascular events was low and included previous acute coronary syndromes in 7.5%, stable angina in 5%, cerebrovascular accidents in 7.5% and transient ischemic attacks in 2.5% of the patients; 72.5% had hypertension (HTN [mean blood pressure (BP 140/80 mm Hg]; 32.5% had dyslipidemias (mean serum cholesterol 5.9; SD = 5.6 and 25% had diabetes (mean blood sugar 103.7; SD = 15.6. Forty percent were obese and 20% were overweight (Asian cutoffs. Increased CIMT (57.5% and atherosclerotic plaques (15.36% indicated a high CVD risk in this cohort. Diabetes (P = 0.016, HTN (P = 0.002, dyslipidemia (P = 0.002 and obesity (P = 0.048 were associated with thickened CIMT. The only LN-related risk factor associated with thickened CIMT (P <0.05 was the SLICC/ACR damage index. The independent predictors of thickened CIMT determined by logistic regression analysis were HTN and dyslipidemia.

  15. Playing Possum

    Directory of Open Access Journals (Sweden)

    Enrico Euli

    2016-07-01

    Full Text Available Our society is drenched in the catastrophe; where the growth of financial crisis, environmental cataclysm and militarization represents its gaudiest and mortifying phenomena. Humans struggle with depression, sense of impotence, anguish towards a future considered a threat.  A possibility to keep us alive can be represented by the enhancement of our ability in ‘playing Possum’, an exercise of desisting and renitence: to firmly say ‘no’. To say no to a world that proposes just one way of being and living free, that imposes as the only unavoidable possible destiny.

  16. Playful Technology

    DEFF Research Database (Denmark)

    Johansen, Stine Liv; Eriksson, Eva

    2013-01-01

    In this paper, the design of future services for children in Danish public libraries is discussed, in the light of new challenges and opportunities in relation to new media and technologies. The Danish government has over the last few years initiated and described a range of initiatives regarding...... in the library, the changing role of the librarians and the library space. We argue that intertwining traditional library services with new media forms and engaging play is the core challenge for future design in physical public libraries, but also that it is through new media and technology that new...

  17. Playful Technology

    DEFF Research Database (Denmark)

    Johansen, Stine Liv; Eriksson, Eva

    2013-01-01

    in the library, the changing role of the librarians and the library space. We argue that intertwining traditional library services with new media forms and engaging play is the core challenge for future design in physical public libraries, but also that it is through new media and technology that new......In this paper, the design of future services for children in Danish public libraries is discussed, in the light of new challenges and opportunities in relation to new media and technologies. The Danish government has over the last few years initiated and described a range of initiatives regarding...

  18. What factors play a role in preventing self-immolation?Results from a case-control study in Iran

    Directory of Open Access Journals (Sweden)

    Hosein Karim

    2015-07-01

    Full Text Available Abstract: Background: To investigate factors related to prevention of self-immolation in west of Iran. Methods: In a case-control study, 30 consecutive cases of deliberate self-inflicted burns admitted to the regional burn center (Imam Khomeini hospital in Kermanshah province, Iran were compared with controls selected from the community and matched by sex, age,district-county of residence, and rural vs urban living environment. The following characteristics relevant to preventing self immolation were collected from all cases and controls: main domestic fuel used in the household, awareness about complications of burn injuries, and use of counseling services. Results: Descriptive analyses revealed that kerosene was the main domestic fuel in the household for 83% of cases. Not surprisingly, the main means of self-immolation in 93% of the patients was kerosene, with other fuels such as petrol and domestic gas used in remaining cases. The majority of cases and controls were aware of the potential complications of burn injuries. Use of counseling services was more common in controls. Conclusions: All three aspects of preventing self-immolation – having kerosene and other fuels in the home, being aware of the complications of burn injuries, and using counseling services were present in both the cases and controls. This suggests a large portion of residents in rural Iran are potential self-immolation victims. Increasing preventive strategies may reduce risk of suicide by self-immolation.

  19. Fas-associated factor 1 plays a negative regulatory role in the antibacterial immunity of Locusta migratoria.

    Science.gov (United States)

    He, Z; Wang, P; Shi, H; Si, F; Hao, Y; Chen, B

    2013-08-01

    Insect immune responses are precisely regulated to maintain immune balance. In this study, the Fas-associated factor 1 (FAF1) gene of Locusta migratoria manilensis, a homologue of the caspar gene that functions as a specific negative regulator in the antibacterial immunity pathway, was cloned. Gene expression analysis showed that FAF1 was expressed throughout the developmental stages and in all tested tissues, but its transcription levels varied significantly. Thus, FAF1 appears to be tightly regulated and is probably involved in multiple physiological processes. In addition, the antimicrobial peptide gene prolixicin was cloned and characterized. After bacterial challenge, prolixicin was rapidly up-regulated, whereas FAF1 was markedly down-regulated. This result was consistent with the observation that prolixicin was hyperactivated when FAF1 was suppressed by RNA interference. Moreover, after bacterial infection, the survival rate of FAF1-knockdown locusts was much higher than that of the wild-type. Taken together, these findings strongly suggest that FAF1 shares a similar function as caspar in Drosophila and may be involved in the negative regulation of antibacterial immunity in locusts.

  20. La teoría de las funciones semióticas (tfs), instrumentos de mediación y el análisis del objeto variación lineal

    OpenAIRE

    2007-01-01

    La teoría de instrucción matemática significativa basada en el modelo ontológico semiótico de la cognición matemática denominado Teoría de las Funciones Semióticas (TFS ) proporciona un marco unificado para el estudio de las diversas formas de conocimiento matemático y sus respectivas interacciones en el seno de los sistemas didácticos ( Godino, 1998 ). Presentamos un desarrollo de esta teoría consistente en la descomposición de un objeto, para nuestro modelo, la Variación Lineal, en unidades...

  1. Playing cards.

    Science.gov (United States)

    1977-01-01

    Mrs. Zahia Marzouk, vice-president of the Alexandria Family Planning Association and a living legend of Egyptian family planning, does not believe in talking about problems. She is far too busy learning from people and teaching them. Her latest brainstorm is a set of playing cards designed to help girls and women to read and learn about family planning at the same time. The 5 packs of cards, representing familiar words and sounds, and each with a family planning joker, took Mrs. Marzouk 6 months to design and paint by hand. They have now been printed, packed into packets provided by UNICEF, and distributed to some 2000 literacy groups in factories and family planning clinics. Each woman who succeeds in learning to read is encouraged to teach 4 others. They then go to the family planning clinic to be examined and gain a certificate. For the teacher who has made them proficient there is a special prize. Girls at El Brinth village outside Alexandria are pictured playing cards at the family planning center where they are learning various skills including how to read.

  2. Comprehensive human transcription factor binding site map for combinatory binding motifs discovery.

    Directory of Open Access Journals (Sweden)

    Arnoldo J Müller-Molina

    Full Text Available To know the map between transcription factors (TFs and their binding sites is essential to reverse engineer the regulation process. Only about 10%-20% of the transcription factor binding motifs (TFBMs have been reported. This lack of data hinders understanding gene regulation. To address this drawback, we propose a computational method that exploits never used TF properties to discover the missing TFBMs and their sites in all human gene promoters. The method starts by predicting a dictionary of regulatory "DNA words." From this dictionary, it distills 4098 novel predictions. To disclose the crosstalk between motifs, an additional algorithm extracts TF combinatorial binding patterns creating a collection of TF regulatory syntactic rules. Using these rules, we narrowed down a list of 504 novel motifs that appear frequently in syntax patterns. We tested the predictions against 509 known motifs confirming that our system can reliably predict ab initio motifs with an accuracy of 81%-far higher than previous approaches. We found that on average, 90% of the discovered combinatorial binding patterns target at least 10 genes, suggesting that to control in an independent manner smaller gene sets, supplementary regulatory mechanisms are required. Additionally, we discovered that the new TFBMs and their combinatorial patterns convey biological meaning, targeting TFs and genes related to developmental functions. Thus, among all the possible available targets in the genome, the TFs tend to regulate other TFs and genes involved in developmental functions. We provide a comprehensive resource for regulation analysis that includes a dictionary of "DNA words," newly predicted motifs and their corresponding combinatorial patterns. Combinatorial patterns are a useful filter to discover TFBMs that play a major role in orchestrating other factors and thus, are likely to lock/unlock cellular functional clusters.

  3. Classifying transcription factor targets and discovering relevant biological features

    Directory of Open Access Journals (Sweden)

    DeLisi Charles

    2008-05-01

    Full Text Available Abstract Background An important goal in post-genomic research is discovering the network of interactions between transcription factors (TFs and the genes they regulate. We have previously reported the development of a supervised-learning approach to TF target identification, and used it to predict targets of 104 transcription factors in yeast. We now include a new sequence conservation measure, expand our predictions to include 59 new TFs, introduce a web-server, and implement an improved ranking method to reveal the biological features contributing to regulation. The classifiers combine 8 genomic datasets covering a broad range of measurements including sequence conservation, sequence overrepresentation, gene expression, and DNA structural properties. Principal Findings (1 Application of the method yields an amplification of information about yeast regulators. The ratio of total targets to previously known targets is greater than 2 for 11 TFs, with several having larger gains: Ash1(4, Ino2(2.6, Yaf1(2.4, and Yap6(2.4. (2 Many predicted targets for TFs match well with the known biology of their regulators. As a case study we discuss the regulator Swi6, presenting evidence that it may be important in the DNA damage response, and that the previously uncharacterized gene YMR279C plays a role in DNA damage response and perhaps in cell-cycle progression. (3 A procedure based on recursive-feature-elimination is able to uncover from the large initial data sets those features that best distinguish targets for any TF, providing clues relevant to its biology. An analysis of Swi6 suggests a possible role in lipid metabolism, and more specifically in metabolism of ceramide, a bioactive lipid currently being investigated for anti-cancer properties. (4 An analysis of global network properties highlights the transcriptional network hubs; the factors which control the most genes and the genes which are bound by the largest set of regulators. Cell-cycle and

  4. A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity

    Directory of Open Access Journals (Sweden)

    Ana C. D’Alessio

    2015-11-01

    Full Text Available Hundreds of transcription factors (TFs are expressed in each cell type, but cell identity can be induced through the activity of just a small number of core TFs. Systematic identification of these core TFs for a wide variety of cell types is currently lacking and would establish a foundation for understanding the transcriptional control of cell identity in development, disease, and cell-based therapy. Here, we describe a computational approach that generates an atlas of candidate core TFs for a broad spectrum of human cells. The potential impact of the atlas was demonstrated via cellular reprogramming efforts where candidate core TFs proved capable of converting human fibroblasts to retinal pigment epithelial-like cells. These results suggest that candidate core TFs from the atlas will prove a useful starting point for studying transcriptional control of cell identity and reprogramming in many human cell types.

  5. DNA-binding specificities of human transcription factors.

    Science.gov (United States)

    Jolma, Arttu; Yan, Jian; Whitington, Thomas; Toivonen, Jarkko; Nitta, Kazuhiro R; Rastas, Pasi; Morgunova, Ekaterina; Enge, Martin; Taipale, Mikko; Wei, Gonghong; Palin, Kimmo; Vaquerizas, Juan M; Vincentelli, Renaud; Luscombe, Nicholas M; Hughes, Timothy R; Lemaire, Patrick; Ukkonen, Esko; Kivioja, Teemu; Taipale, Jussi

    2013-01-17

    Although the proteins that read the gene regulatory code, transcription factors (TFs), have been largely identified, it is not well known which sequences TFs can recognize. We have analyzed the sequence-specific binding of human TFs using high-throughput SELEX and ChIP sequencing. A total of 830 binding profiles were obtained, describing 239 distinctly different binding specificities. The models represent the majority of human TFs, approximately doubling the coverage compared to existing systematic studies. Our results reveal additional specificity determinants for a large number of factors for which a partial specificity was known, including a commonly observed A- or T-rich stretch that flanks the core motifs. Global analysis of the data revealed that homodimer orientation and spacing preferences, and base-stacking interactions, have a larger role in TF-DNA binding than previously appreciated. We further describe a binding model incorporating these features that is required to understand binding of TFs to DNA.

  6. Transcriptome-Based Analysis of Dof Family Transcription Factors and Their Responses to Abiotic Stress in Tea Plant (Camellia sinensis

    Directory of Open Access Journals (Sweden)

    Hui Li

    2016-01-01

    Full Text Available Tea plant (Camellia sinensis (L. O. Kuntze is affected by abiotic stress during its growth and development. DNA-binding with one finger (Dof transcription factors (TFs play important roles in abiotic stress tolerance of plants. In this study, a total of 29 putative Dof TFs were identified based on transcriptome of tea plant, and the conserved domains and common motifs of these CsDof TFs were predicted and analyzed. The 29 CsDof proteins were divided into 7 groups (A, B1, B2, C1, C2.1, C2.2, and D2, and the interaction networks of Dof proteins in C. sinensis were established according to the data in Arabidopsis. Gene expression was analyzed in “Yingshuang” and “Huangjinya” under four experimental stresses by qRT-PCR. CsDof genes were expressed differentially and related to different abiotic stress conditions. In total, our results might suggest that there is a potential relationship between CsDof factors and tea plant stress resistance.

  7. Simplified method to predict mutual interactions of human transcription factors based on their primary structure

    KAUST Repository

    Schmeier, Sebastian

    2011-07-05

    Background: Physical interactions between transcription factors (TFs) are necessary for forming regulatory protein complexes and thus play a crucial role in gene regulation. Currently, knowledge about the mechanisms of these TF interactions is incomplete and the number of known TF interactions is limited. Computational prediction of such interactions can help identify potential new TF interactions as well as contribute to better understanding the complex machinery involved in gene regulation. Methodology: We propose here such a method for the prediction of TF interactions. The method uses only the primary sequence information of the interacting TFs, resulting in a much greater simplicity of the prediction algorithm. Through an advanced feature selection process, we determined a subset of 97 model features that constitute the optimized model in the subset we considered. The model, based on quadratic discriminant analysis, achieves a prediction accuracy of 85.39% on a blind set of interactions. This result is achieved despite the selection for the negative data set of only those TF from the same type of proteins, i.e. TFs that function in the same cellular compartment (nucleus) and in the same type of molecular process (transcription initiation). Such selection poses significant challenges for developing models with high specificity, but at the same time better reflects real-world problems. Conclusions: The performance of our predictor compares well to those of much more complex approaches for predicting TF and general protein-protein interactions, particularly when taking the reduced complexity of model utilisation into account. © 2011 Schmeier et al.

  8. Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution

    Directory of Open Access Journals (Sweden)

    Singh Rama S

    2008-08-01

    Full Text Available Abstract Background Much of the morphological diversity in eukaryotes results from differential regulation of gene expression in which transcription factors (TFs play a central role. The nematode Caenorhabditis elegans is an established model organism for the study of the roles of TFs in controlling the spatiotemporal pattern of gene expression. Using the fully sequenced genomes of three Caenorhabditid nematode species as well as genome information from additional more distantly related organisms (fruit fly, mouse, and human we sought to identify orthologous TFs and characterized their patterns of evolution. Results We identified 988 TF genes in C. elegans, and inferred corresponding sets in C. briggsae and C. remanei, containing 995 and 1093 TF genes, respectively. Analysis of the three gene sets revealed 652 3-way reciprocal 'best hit' orthologs (nematode TF set, approximately half of which are zinc finger (ZF-C2H2 and ZF-C4/NHR types and HOX family members. Examination of the TF genes in C. elegans and C. briggsae identified the presence of significant tandem clustering on chromosome V, the majority of which belong to ZF-C4/NHR family. We also found evidence for lineage-specific duplications and rapid evolution of many of the TF genes in the two species. A search of the TFs conserved among nematodes in Drosophila melanogaster, Mus musculus and Homo sapiens revealed 150 reciprocal orthologs, many of which are associated with important biological processes and human diseases. Finally, a comparison of the sequence, gene interactions and function indicates that nematode TFs conserved across phyla exhibit significantly more interactions and are enriched in genes with annotated mutant phenotypes compared to those that lack orthologs in other species. Conclusion Our study represents the first comprehensive genome-wide analysis of TFs across three nematode species and other organisms. The findings indicate substantial conservation of transcription

  9. The Transcription Factor Interferon Regulatory Factor-1 (IRF1) Plays a Key Role in the Terminal Effector Pathways of Human Preterm Labor.

    Science.gov (United States)

    Lim, Ratana; Tran, Ha Thi; Liong, Stella; Barker, Gillian; Lappas, Martha

    2016-02-01

    Preterm birth is the largest single cause of neonatal death and morbidity. By activating cytokine- and Toll-like receptor (TLR)-signaling pathways, infection and/or inflammation are strongly associated with preterm delivery. Interferon regulatory factor-1 (IRF1) is an important regulator of the inflammatory response. The aims of this study were to establish the effect of 1) labor on IRF1 expression in human fetal membranes and myometrium, 2) prolabor mediators on IRF1 expression and activity, and 3) IRF1 small interfering RNA on the expression of prolabor mediators. IRF1 expression was higher in fetal membranes and myometrium after spontaneous term labor and in preterm fetal membranes with infection. The proinflammatory cytokine IL1B, the bacterial product fsl-1, and viral analog polyinosinic:polycytidylic acid (poly [I:C]) significantly increased IRF1 mRNA expression and transcriptional activity in human primary myometrial cells. In addition, IL1B increased IRF1 activity in primary amnion cells. IRF1 silencing in myometrial cells decreased IL1B-, fsl-1-, and poly (I:C)-induced cytokine (IL6, TNF, IL1B) and chemokine (CXCL8, CCL2) mRNA expression and IL6, CXCL8, and CCL2 release. IL1B-, fsl-1-, and poly (I:C)-induced PTGS2 mRNA expression and IL1B-induced prostaglandin release was also decreased by IRF1 silencing. In conclusion, IRF1 upregulation in fetal membranes and myometrium after term labor indicates a proinflammatory role for IRF1 in human parturition. IRF1 is involved in TLR- and cytokine-mediated signaling in human myometrium. These data provide new insights into the mechanisms associated with inflammation- and infection-associated preterm birth. IRF1 inhibitors as therapeutics for the management of spontaneous preterm birth warrants further investigation. © 2016 by the Society for the Study of Reproduction, Inc.

  10. Transcriptional profiling of Medicago truncatula under salt stress identified a novel CBF transcription factor MtCBF4 that plays an important role in abiotic stress responses

    Directory of Open Access Journals (Sweden)

    Su Zhen

    2011-07-01

    Full Text Available Abstract Background Salt stress hinders the growth of plants and reduces crop production worldwide. However, different plant species might possess different adaptive mechanisms to mitigate salt stress. We conducted a detailed pathway analysis of transcriptional dynamics in the roots of Medicago truncatula seedlings under salt stress and selected a transcription factor gene, MtCBF4, for experimental validation. Results A microarray experiment was conducted using root samples collected 6, 24, and 48 h after application of 180 mM NaCl. Analysis of 11 statistically significant expression profiles revealed different behaviors between primary and secondary metabolism pathways in response to external stress. Secondary metabolism that helps to maintain osmotic balance was induced. One of the highly induced transcription factor genes was successfully cloned, and was named MtCBF4. Phylogenetic analysis revealed that MtCBF4, which belongs to the AP2-EREBP transcription factor family, is a novel member of the CBF transcription factor in M. truncatula. MtCBF4 is shown to be a nuclear-localized protein. Expression of MtCBF4 in M. truncatula was induced by most of the abiotic stresses, including salt, drought, cold, and abscisic acid, suggesting crosstalk between these abiotic stresses. Transgenic Arabidopsis over-expressing MtCBF4 enhanced tolerance to drought and salt stress, and activated expression of downstream genes that contain DRE elements. Over-expression of MtCBF4 in M. truncatula also enhanced salt tolerance and induced expression level of corresponding downstream genes. Conclusion Comprehensive transcriptomic analysis revealed complex mechanisms exist in plants in response to salt stress. The novel transcription factor gene MtCBF4 identified here played an important role in response to abiotic stresses, indicating that it might be a good candidate gene for genetic improvement to produce stress-tolerant plants.

  11. Identification of Transcription Factors for Lineage-Specific ESC Differentiation

    Science.gov (United States)

    Yamamizu, Kohei; Piao, Yulan; Sharov, Alexei A.; Zsiros, Veronika; Yu, Hong; Nakazawa, Kazu; Schlessinger, David; Ko, Minoru S.H.

    2013-01-01

    Summary A network of transcription factors (TFs) determines cell identity, but identity can be altered by overexpressing a combination of TFs. However, choosing and verifying combinations of TFs for specific cell differentiation have been daunting due to the large number of possible combinations of ∼2,000 TFs. Here, we report the identification of individual TFs for lineage-specific cell differentiation based on the correlation matrix of global gene expression profiles. The overexpression of identified TFs—Myod1, Mef2c, Esx1, Foxa1, Hnf4a, Gata2, Gata3, Myc, Elf5, Irf2, Elf1, Sfpi1, Ets1, Smad7, Nr2f1, Sox11, Dmrt1, Sox9, Foxg1, Sox2, or Ascl1—can direct efficient, specific, and rapid differentiation into myocytes, hepatocytes, blood cells, and neurons. Furthermore, transfection of synthetic mRNAs of TFs generates their appropriate target cells. These results demonstrate both the utility of this approach to identify potent TFs for cell differentiation, and the unanticipated capacity of single TFs directly guides differentiation to specific lineage fates. PMID:24371809

  12. Arabidopsis Small Rubber Particle Protein Homolog SRPs Play Dual Roles as Positive Factors for Tissue Growth and Development and in Drought Stress Responses.

    Science.gov (United States)

    Kim, Eun Yu; Park, Ki Youl; Seo, Young Sam; Kim, Woo Taek

    2016-04-01

    Lipid droplets (LDs) act as repositories for fatty acids and sterols, which are used for various cellular processes such as energy production and membrane and hormone synthesis. LD-associated proteins play important roles in seed development and germination, but their functions in postgermination growth are not well understood. Arabidopsis (Arabidopsis thaliana) contains three SRP homologs (SRP1, SRP2, and SRP3) that share sequence identities with small rubber particle proteins of the rubber tree (Hevea brasiliensis). In this report, the possible cellular roles of SRPs in postgermination growth and the drought tolerance response were investigated. Arabidopsis SRPs appeared to be LD-associated proteins and displayed polymerization properties in vivo and in vitro. SRP-overexpressing transgenic Arabidopsis plants (35S:SRP1, 35S:SRP2, and 35S:SRP3) exhibited higher vegetative and reproductive growth and markedly better tolerance to drought stress than wild-type Arabidopsis. In addition, constitutive over-expression of SRPs resulted in increased numbers of large LDs in postgermination seedlings. In contrast, single (srp1, 35S:SRP2-RNAi, and srp3) and triple (35S:SRP2-RNAi/srp1srp3) loss-of-function mutant lines exhibited the opposite phenotypes. Our results suggest that Arabidopsis SRPs play dual roles as positive factors in postgermination growth and the drought stress tolerance response. The possible relationships between LD-associated proteins and the drought stress response are discussed. © 2016 American Society of Plant Biologists. All Rights Reserved.

  13. The Transcription Factor Encyclopedia

    DEFF Research Database (Denmark)

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

    2012-01-01

    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...

  14. Prostaglandin E2 and Transforming Growth FactorPlay a Critical Role in Suppression of Allergic Airway Inflammation by Adipose-Derived Stem Cells.

    Directory of Open Access Journals (Sweden)

    Kyu-Sup Cho

    Full Text Available The role of soluble factors in the suppression of allergic airway inflammation by adipose-derived stem cells (ASCs remains to be elucidated. Moreover, the major soluble factors responsible for the immunomodulatory effects of ASCs in allergic airway diseases have not been well documented. We evaluated the effects of ASCs on allergic inflammation in asthmatic mice treated with a prostaglandin E2 (PGE2 inhibitor or transforming growth factor-β (TGF-β neutralizing antibodies.Asthmatic mice were injected intraperitoneally with a PGE2 inhibitor or TGF-β neutralizing antibodies at approximately the same time as ASCs injection and were compared with non-treated controls. In asthmatic mice, ASCs significantly reduced airway hyperresponsiveness, the number of total inflammatory cells and eosinophils in the bronchoalveolar lavage fluid (BALF, eosinophilic inflammation, goblet cell hyperplasia, and serum total and allergen-specific IgE and IgG1. ASCs significantly inhibited Th2 cytokines, such as interleukin (IL-4, IL-5, and IL-13, and enhanced the Th1 cytokine (Interferon-γ and regulatory cytokines (IL-10 and TGF-β in the BALF and lung draining lymph nodes (LLNs. ASCs engraftment caused significant increases in the regulatory T cell (Treg and IL-10+ T cell populations in LLNs. However, blocking PGE2 or TGF-β eliminated the immunosuppressive effect of ASCs in allergic airway inflammation.ASCs are capable of secreting PGE2 and TGF-β, which may play a role in inducing Treg expansion. Furthermore, treatment with a PGE2 inhibitor or TGF-β neutralizing antibodies eliminated the beneficial effect of ASCs treatment in asthmatic mice, suggesting that PGE2 and TGF-β are the major soluble factors responsible for suppressing allergic airway inflammation.

  15. Real sequence effects on the search dynamics of transcription factors on DNA

    DEFF Research Database (Denmark)

    Bauer, Maximilian; Rasmussen, Emil S.; Lomholt, Michael A.

    2015-01-01

    Recent experiments show that transcription factors (TFs) indeed use the facilitated diffusion mechanism to locate their target sequences on DNA in living bacteria cells: TFs alternate between sliding motion along DNA and relocation events through the cytoplasm. From simulations and theoretical...

  16. Transcription Factor Networks in Drosophila melanogaster

    Directory of Open Access Journals (Sweden)

    David Y. Rhee

    2014-09-01

    Full Text Available Specific cellular fates and functions depend on differential gene expression, which occurs primarily at the transcriptional level and is controlled by complex regulatory networks of transcription factors (TFs. TFs act through combinatorial interactions with other TFs, cofactors, and chromatin-remodeling proteins. Here, we define protein-protein interactions using a coaffinity purification/mass spectrometry method and study 459 Drosophila melanogaster transcription-related factors, representing approximately half of the established catalog of TFs. We probe this network in vivo, demonstrating functional interactions for many interacting proteins, and test the predictive value of our data set. Building on these analyses, we combine regulatory network inference models with physical interactions to define an integrated network that connects combinatorial TF protein interactions to the transcriptional regulatory network of the cell. We use this integrated network as a tool to connect the functional network of genetic modifiers related to mastermind, a transcriptional cofactor of the Notch pathway.

  17. A seed-specific AP2-domain transcription factor from soybean plays a certain role in regulation of seed ger-mination

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Plant seed development and germination are under strict temporal and spatial regulation, and tran-scription factors play important roles in this regulation. In the present study we identified an EST ex-pressed specifically in the developing soybean seeds. The full length of the gene was obtained through further RACE analysis and the gene was named GmSGR. Sequence analysis revealed that this gene belonged to the AP2/ERF transcription factor family. Its AP2 domain had the highest similarity with that of the A-3 member AtABI4 of DREB subgroup in the AP2/ERF family in Arabidopsis. GmSGR did not exhibit transcriptional activation activity in the yeast assay system. GmSGR was overexpressed in Arabidopsis and the germination rates of the transgenic seeds were significantly higher than that of the wild type seeds under higher concentrations of ABA and glucose respectively. However, the germina-tion rates of the transgenic seeds were lower than that of control under salt stress. The expression of AtEm6 and AtRD29B was higher in the seedlings of the transgenic plants than that in the wild-type seedlings. These results suggest that GmSGR may confer reduced ABA sensitivity and enhanced salt sensitivity to the transgenic seeds through regulating the expression of AtEm6 and AtRD29B genes.

  18. Motivations for play in computer role-playing games

    DEFF Research Database (Denmark)

    Tychsen, Anders; Hitchens, Michael; Brolund, Thea

    2008-01-01

    In this paper the motivations for play in the context of single-and multi-player digital Role-Playing Games (RPGs) are examined. Survey data were drawn from respondents online and participants in a related experimental study. The results indicate that motivations for play are not simple constructs......, but rather composed of multiple motivational drivers that are heavily interrelated and act in concert. Character uniqueness and Discovery & Immersion were the highest ranked motivational categories. Different levels of detail in motivations for playing single-/multi- Player RPGs were located......, with mechanistic/tactical play and character-based/social play being the two overall motivational factors. Copyright 2008 ACM....

  19. A Phylogenetically Conserved Group of Nuclear Factor-Y Transcription Factors Interact to Control Nodulation in Legumes.

    Science.gov (United States)

    Baudin, Maël; Laloum, Tom; Lepage, Agnès; Rípodas, Carolina; Ariel, Federico; Frances, Lisa; Crespi, Martin; Gamas, Pascal; Blanco, Flavio Antonio; Zanetti, Maria Eugenia; de Carvalho-Niebel, Fernanda; Niebel, Andreas

    2015-12-01

    The endosymbiotic association between legumes and soil bacteria called rhizobia leads to the formation of a new root-derived organ called the nodule in which differentiated bacteria convert atmospheric nitrogen into a form that can be assimilated by the host plant. Successful root infection by rhizobia and nodule organogenesis require the activation of symbiotic genes that are controlled by a set of transcription factors (TFs). We recently identified Medicago truncatula nuclear factor-YA1 (MtNF-YA1) and MtNF-YA2 as two M. truncatula TFs playing a central role during key steps of the Sinorhizobium meliloti-M. truncatula symbiotic interaction. NF-YA TFs interact with NF-YB and NF-YC subunits to regulate target genes containing the CCAAT box consensus sequence. In this study, using a yeast two-hybrid screen approach, we identified the NF-YB and NF-YC subunits able to interact with MtNF-YA1 and MtNF-YA2. In yeast (Saccharomyces cerevisiae) and in planta, we further demonstrated by both coimmunoprecipitation and bimolecular fluorescence complementation that these NF-YA, -B, and -C subunits interact and form a stable NF-Y heterotrimeric complex. Reverse genetic and chromatin immunoprecipitation-PCR approaches revealed the importance of these newly identified NF-YB and NF-YC subunits for rhizobial symbiosis and binding to the promoter of MtERN1 (for Ethylene Responsive factor required for Nodulation), a direct target gene of MtNF-YA1 and MtNF-YA2. Finally, we verified that a similar trimer is formed in planta by the common bean (Phaseolus vulgaris) NF-Y subunits, revealing the existence of evolutionary conserved NF-Y protein complexes to control nodulation in leguminous plants. This sheds light on the process whereby an ancient heterotrimeric TF mainly controlling cell division in animals has acquired specialized functions in plants.

  20. The TGF-β/Smad repressor TG-interacting factor 1 (TGIF1 plays a role in radiation-induced intestinal injury independently of a Smad signaling pathway.

    Directory of Open Access Journals (Sweden)

    Mohammad Hneino

    Full Text Available Despite advances in radiation delivery protocols, exposure of normal tissues during the course of radiation therapy remains a limiting factor of cancer treatment. If the canonical TGF-β/Smad pathway has been extensively studied and implicated in the development of radiation damage in various organs, the precise modalities of its activation following radiation exposure remain elusive. In the present study, we hypothesized that TGF-β1 signaling and target genes expression may depend on radiation-induced modifications in Smad transcriptional co-repressors/inhibitors expressions (TGIF1, SnoN, Ski and Smad7. In endothelial cells (HUVECs and in a model of experimental radiation enteropathy in mice, radiation exposure increases expression of TGF-β/Smad pathway and of its target gene PAI-1, together with the overexpression of Smad co-repressor TGIF1. In mice, TGIF1 deficiency is not associated with changes in the expression of radiation-induced TGF-β pathway-related transcripts following localized small intestinal irradiation. In HUVECs, TGIF1 overexpression or silencing has no influence either on the radiation-induced Smad activation or the Smad3-dependent PAI-1 overexpression. However, TGIF1 genetic deficiency sensitizes mice to radiation-induced intestinal damage after total body or localized small intestinal radiation exposure, demonstrating that TGIF1 plays a role in radiation-induced intestinal injury. In conclusion, the TGF-β/Smad co-repressor TGIF1 plays a role in radiation-induced normal tissue damage by a Smad-independent mechanism.

  1. Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin.

    Science.gov (United States)

    Pérez-Rueda, Ernesto; Janga, Sarath Chandra

    2010-06-01

    Archaea, which represent a large fraction of the phylogenetic diversity of organisms, are prokaryotes with eukaryote-like basal transcriptional machinery. This organization makes the study of their DNA-binding transcription factors (TFs) and their transcriptional regulatory networks particularly interesting. In addition, there are limited experimental data regarding their TFs. In this work, 3,918 TFs were identified and exhaustively analyzed in 52 archaeal genomes. TFs represented less than 5% of the gene products in all the studied species comparable with the number of TFs identified in parasites or intracellular pathogenic bacteria, suggesting a deficit in this class of proteins. A total of 75 families were identified, of which HTH_3, AsnC, TrmB, and ArsR families were universally and abundantly identified in all the archaeal genomes. We found that archaeal TFs are significantly small compared with other protein-coding genes in archaea as well as bacterial TFs, suggesting that a large fraction of these small-sized TFs could supply the probable deficit of TFs in archaea, by possibly forming different combinations of monomers similar to that observed in eukaryotic transcriptional machinery. Our results show that although the DNA-binding domains of archaeal TFs are similar to bacteria, there is an underrepresentation of ligand-binding domains in smaller TFs, which suggests that protein-protein interactions may act as mediators of regulatory feedback, indicating a chimera of bacterial and eukaryotic TFs' functionality. The analysis presented here contributes to the understanding of the details of transcriptional apparatus in archaea and provides a framework for the analysis of regulatory networks in these organisms.

  2. The Theobroma cacao B3 domain transcription factor TcLEC2 plays a duel role in control of embryo development and maturation.

    Science.gov (United States)

    Zhang, Yufan; Clemens, Adam; Maximova, Siela N; Guiltinan, Mark J

    2014-04-24

    The Arabidopsis thaliana LEC2 gene encodes a B3 domain transcription factor, which plays critical roles during both zygotic and somatic embryogenesis. LEC2 exerts significant impacts on determining embryogenic potential and various metabolic processes through a complicated genetic regulatory network. An ortholog of the Arabidopsis Leafy Cotyledon 2 gene (AtLEC2) was characterized in Theobroma cacao (TcLEC2). TcLEC2 encodes a B3 domain transcription factor preferentially expressed during early and late zygotic embryo development. The expression of TcLEC2 was higher in dedifferentiated cells competent for somatic embryogenesis (embryogenic calli), compared to non-embryogenic calli. Transient overexpression of TcLEC2 in immature zygotic embryos resulted in changes in gene expression profiles and fatty acid composition. Ectopic expression of TcLEC2 in cacao leaves changed the expression levels of several seed related genes. The overexpression of TcLEC2 in cacao explants greatly increased the frequency of regeneration of stably transformed somatic embryos. TcLEC2 overexpressing cotyledon explants exhibited a very high level of embryogenic competency and when cultured on hormone free medium, exhibited an iterative embryogenic chain-reaction. Our study revealed essential roles of TcLEC2 during both zygotic and somatic embryo development. Collectively, our evidence supports the conclusion that TcLEC2 is a functional ortholog of AtLEC2 and that it is involved in similar genetic regulatory networks during cacao somatic embryogenesis. To our knowledge, this is the first detailed report of the functional analysis of a LEC2 ortholog in a species other then Arabidopsis. TcLEC2 could potentially be used as a biomarker for the improvement of the SE process and screen for elite varieties in cacao germplasm.

  3. Transcription factor σB plays an important role in the production of extracellular membrane-derived vesicles in Listeria monocytogenes.

    Directory of Open Access Journals (Sweden)

    Jung Hwa Lee

    Full Text Available Gram-negative bacteria produce extracellular outer membrane vesicles (OMVs that interact with host cells. Unlike Gram-negative bacteria, less is known about the production and role of extracellular membrane vesicles (MVs in Gram-positive bacteria. The food-borne pathogen Listeria monocytogenes can survive under extreme environmental and energy stress conditions and the transcription factor σ(B is involved in this survival ability. Here, we first determined the production of MVs from L. monocytogenes and evaluated whether general stress transcription factor σ(B affected production of MVs in L. monocytogenes. L. monocytogenes secreted MVs during in vitro broth culture. The wild-type strain actively produced MVs approximately nine times more and also produced more intact shapes of MVs than those of the isogenic ΔsigB mutant. A proteomic analysis showed that 130 and 89 MV proteins were identified in the wild-type and ΔsigB mutant strains, respectively. Wild-type strain-derived MVs contained proteins regulated by σ(B such as transporters (OpuCA and OpuCC, stress response (Kat, metabolism (LacD, translation (InfC, and cell division protein (FtsZ. Gene Ontology (GO enrichment analysis showed that wild-type-derived MV proteins corresponded to several GO terms, including response to stress (heat, acid, and bile resistance and extracellular polysaccharide biosynthetic process, but not the ΔsigB mutant. Internalin B (InlB was almost three times more contained in MVs derived from the wild-type strain than in MVs derived from the ΔsigB mutant. Taken together, these results suggest that σ(B plays a pivotal role in the production of MVs and protein profiles contained in MVs. L. monocytogenes MVs may contribute to host infection and survival ability under various stressful conditions.

  4. Identification and characterization of wheat drought-responsive MYB transcription factors involved in the regulation of cuticle biosynthesis

    Science.gov (United States)

    Bi, Huihui; Luang, Sukanya; Li, Yuan; Bazanova, Natalia; Morran, Sarah; Song, Zhihong; Perera, M. Ann; Hrmova, Maria; Borisjuk, Nikolai; Lopato, Sergiy

    2016-01-01

    A plant cuticle forms a hydrophobic layer covering plant organs, and plays an important role in plant development and protection from environmental stresses. We examined epicuticular structure, composition, and a MYB-based regulatory network in two Australian wheat cultivars, RAC875 and Kukri, with contrasting cuticle appearance (glaucousness) and drought tolerance. Metabolomics and microscopic analyses of epicuticular waxes revealed that the content of β-diketones was the major compositional and structural difference between RAC875 and Kukri. The content of β-diketones remained the same while those of alkanes and primary alcohols were increased by drought in both cultivars, suggesting that the interplay of all components rather than a single one defines the difference in drought tolerance between cultivars. Six wheat genes encoding MYB transcription factors (TFs) were cloned; four of them were regulated in flag leaves of both cultivars by rapid dehydration and/or slowly developing cyclic drought. The involvement of selected MYB TFs in the regulation of cuticle biosynthesis was confirmed by a transient expression assay in wheat cell culture, using the promoters of wheat genes encoding cuticle biosynthesis-related enzymes and the SHINE1 (SHN1) TF. Two functional MYB-responsive elements, specifically recognized by TaMYB74 but not by other MYB TFs, were localized in the TdSHN1 promoter. Protein structural determinants underlying the binding specificity of TaMYB74 for functional DNA cis-elements were defined, using 3D protein molecular modelling. A scheme, linking drought-induced expression of the investigated TFs with downstream genes that participate in the synthesis of cuticle components, is proposed. PMID:27489236

  5. Theory on the mechanisms of combinatorial binding of transcription factors with DNA

    CERN Document Server

    Murugan, R

    2016-01-01

    We develop a theoretical framework on the mechanism of combinatorial binding of transcription factors (TFs) with their specific binding sites on DNA. We consider three possible mechanisms viz. monomer, hetero-oligomer and coordinated recruitment pathways. In the monomer pathway, combinatorial TFs search for their targets in an independent manner and the protein-protein interactions among them will be insignificant. The protein-protein interactions are very strong so that the hetero-oligomer complex of TFs as a whole searches for the cognate sites in case of hetero-oligomer pathway. The TF which arrived first will recruit the adjacent TFs in a sequential manner in the recruitment pathway. The free energy released from the protein-protein interactions among TFs will be in turn utilized to stabilize the TFs-DNA complex. Such coordinated binding of TFs in fact emerges as the cooperative effect. Monomer and hetero-oligomer pathways are efficient only when few TFs are involved in the combinatorial regulation. Detai...

  6. Identification of 32 full-length NAC transcription factors in ramie (Boehmeria nivea L. Gaud) and characterization of the expression pattern of these genes.

    Science.gov (United States)

    Liu, Touming; Zhu, Siyuan; Tang, Qingming; Tang, Shouwei

    2014-08-01

    NAM, ATAF, and CUC (NAC) genes are plant-specific transcription factors (TFs) that play key roles in plant growth, development, and stress tolerance. To date, none of the ramie NAC (BnNAC) genes had been identified, even though ramie is one of the most important natural fiber crops. In order to mine the BnNAC TFs and identify their potential function, the search for BnNAC genes against two pools of unigenes de novo assembled from the RNA-seq in our two previous studies was performed, and a total of 32 full-length BnNAC genes were identified in this study. Forty-seven function-known NAC proteins published in other species, in concert with these 32 BnNAC proteins were subjected to phylogenetic analysis, and the result showed that all the 79 NAC proteins can be divided into eight groups (NAC-I-VIII). Among the 32 BnNAC genes, 24, 2, and 1 gene showed higher expression in stem xylem, leaf, and flower, respectively. Furthermore, the expression of 14, 11 and 4 BnNAC genes was regulated by drought, cadmium stress, and infection by root lesion nematode, respectively. Interestingly, there were five BnNAC TFs which showed high homology with the NAC TFs of other species involved in regulating the secondary wall synthesis, and their expressions were not regulated by drought and cadmium stress. These results suggested that the BnNAC family might have a functional diversity. The identification of these 32 full-length BnNAC genes and the characterization of their expression pattern provide a basis for future clarification of their functions in ramie growth and development.

  7. Molecular interactions of the γ-clade homeodomain-leucine zipper class I transcription factors during the wheat response to water deficit.

    Science.gov (United States)

    Harris, John C; Sornaraj, Pradeep; Taylor, Mathew; Bazanova, Natalia; Baumann, Ute; Lovell, Ben; Langridge, Peter; Lopato, Sergiy; Hrmova, Maria

    2016-03-01

    The γ-clade of class I homeodomain-leucine zipper (HD-Zip I) transcription factors (TFs) constitute members which play a role in adapting plant growth to conditions of water deficit. Given the importance of wheat (Triticum aestivum L.) as a global food crop and the impact of water deficit upon grain yield, we focused on functional aspects of wheat drought responsive HD-Zip I TFs. While the wheat γ-clade HD-Zip I TFs share significant sequence similarities with homologous genes from other plants, the clade-specific features in transcriptional response to abiotic stress were detected. We demonstrate that wheat TaHDZipI-3, TaHDZipI-4, and TaHDZipI-5 genes respond differentially to a variety of abiotic stresses, and that proteins encoded by these genes exhibit pronounced differences in oligomerisation, strength of DNA binding, and trans-activation of an artificial promoter. Three-dimensional molecular modelling of the protein-DNA interface was conducted to address the ambiguity at the central nucleotide in the pseudo-palindromic cis-element CAATNATTG that is recognised by all three HD-Zip I proteins. The co-expression of these genes in the same plant tissues together with the ability of HD-Zip I TFs of the γ-clade to hetero-dimerise suggests a role in the regulatory mechanisms of HD-Zip I dependent transcription. Our findings highlight the complexity of TF networks involved in plant responses to water deficit. A better understanding of the molecular complexity at the protein level during crop responses to drought will enable adoption of efficient strategies for production of cereal plants with enhanced drought tolerance.

  8. Queixas musculoesqueléticas em músicos: prevalência e fatores de risco Playing-related musculoskeletal complaints among musicians: prevalence and risk factors

    Directory of Open Access Journals (Sweden)

    Annemarie Frank

    2007-06-01

    Full Text Available Disfunções musculoesqueléticas relacionadas à prática instrumental são freqüentes entre músicos, atingindo acima de 70% dos componentes de orquestras. O exercício da música como profissão requer ampla diferenciação e produtividade de capacidades tanto psicológicas, mentais, como também físicas. Muitos fatores de risco contribuem para o surgimento de queixas musculoesqueléticas durante a prática musical, entre eles: a técnica individual, as condições físicas do músico e o instrumento em si. Podem ocorrer distúrbios reumatológicos, neurológicos, dermatológicos e psicológicos, assim como problemas de visão e audição e do complexo orofacial. As queixas no aparelho motor manifestam-se, muitas vezes, como dor, fraqueza ou tensão. Os diagnósticos do membro superior mais freqüentemente estabelecidos são as tendinopatias, mialgias e a síndrome do superuso. O médico e o terapeuta responsáveis devem conhecer as atividades e cargas do músico profissional, para que sejam proporcionadas avaliação e estratégia terapêutica adequadas.Playing-related musculoskeletal complaints are often found among musicians, taking a toll in more than 70% of professional musicians in orchestras. Professional musical performance requires a high level of differenciation and efficiency of psychological, mental and physical skills. Many risk factors can contribute to the development of musculoskeletal conditions in this special population, like the individual technique, physical fitness of the musician and the instrument itself. Many rheumatic, neurological, dermatological, and psychiatric problems are reported, as well as dysfunctions of the visual, auditive and oral system. The musculoskeletal complaints often manifest as pain, weakness or tension, and the most common diagnoses of the upper limb are tendinopathies, myalgia and overuse syndromes. It is necessary for the skilfull physician and physical therapist to have a thorough knowledge

  9. Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes

    NARCIS (Netherlands)

    Mokry, M.; Hatzis, P.; Schuijers, J.; Lansu, N.; Ruzius, F.P.; Clevers, H.; Cuppen, E.

    2012-01-01

    Routine methods for assaying steady-state mRNA levels such as RNA-seq and micro-arrays are commonly used as readouts to study the role of transcription factors (TFs) in gene expression regulation. However, cellular RNA levels do not solely depend on activity of TFs and subsequent transcription by

  10. Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes

    NARCIS (Netherlands)

    Mokry, Michal; Hatzis, Pantelis; Schuijers, Jurian; Lansu, Nico; Ruzius, Frans-Paul; Clevers, Hans; Cuppen, Edwin

    2012-01-01

    Routine methods for assaying steady-state mRNA levels such as RNA-seq and micro-arrays are commonly used as readouts to study the role of transcription factors (TFs) in gene expression regulation. However, cellular RNA levels do not solely depend on activity of TFs and subsequent transcription by RN

  11. Transcriptional profiling of intrinsic PNS factors in the postnatal mouse.

    Science.gov (United States)

    Smith, Robin P; Lerch-Haner, Jessica K; Pardinas, Jose R; Buchser, William J; Bixby, John L; Lemmon, Vance P

    2011-01-01

    Neurons in the peripheral nervous system (PNS) display a higher capacity to regenerate after injury than those in the central nervous system, suggesting cell specific transcriptional modules underlying axon growth and inhibition. We report a systems biology based search for PNS specific transcription factors (TFs). Messenger RNAs enriched in dorsal root ganglion (DRG) neurons compared to cerebellar granule neurons (CGNs) were identified using subtractive hybridization and DNA microarray approaches. Network and transcription factor binding site enrichment analyses were used to further identify TFs that may be differentially active. Combining these techniques, we identified 32 TFs likely to be enriched and/or active in the PNS. Twenty-five of these TFs were then tested for an ability to promote CNS neurite outgrowth in an overexpression screen. Real-time PCR and immunohistochemical studies confirmed that one representative TF, STAT3, is intrinsic to PNS neurons, and that constitutively active STAT3 is sufficient to promote CGN neurite outgrowth.

  12. 哺乳动物转录因子DNA结合谱%DNA-binding profiles of mammalian transcription factors

    Institute of Scientific and Technical Information of China (English)

    谷光明; 王进科

    2012-01-01

    The differential gene expression is the molecular base of development and responses to stimuli of organisms. Transcription factors (TFs) play important regulatory roles in this kind of differential gene expression. Therefore, to elucidate how these TFs regulate the complex differential gene expression, it is necessary to identify all target genes of them and construct the gene transcription regulatory network controlled by them. DNA binding is a key step for TFs regulating gene transcription. Therefore, in order to identify their target genes, it is indispensable to identify all possible DNA sequences that can be recognized and bound by TFs at the molecular level of their interactions with DNA, i.e., construction of the DNA-binding profiles of TFs. In recent years, along with the development of DNA microarray and high-throughput DNA sequencing techniques, there appeared some revolutionary new techniques for constructing DNA-binding profiles of TFs, which greatly promotes studies in this field. These techniques include ChlP-chip and ChlP-Seq for constructing in vivo DNA-binding profiles of TFs, dsDNA microarray, SELEX-SAGE, Bind-n-Seq, MMP-SELEX, EMSA-Seq, and HiTS-FLIP for constructing in vitro DNA-binding profiles of TFs. This paper reviewed these techniques.%基因差异表达是生物发育和对刺激作出应答的分子基础,转录因子在这种基因差异表达中发挥着重要的调控作用.因此,要弄清楚转录因子调控基因差异表达的机理,就必须鉴定出它们全部的靶基因并构建其操纵的转录调控网络.对基因组DNA的序列特异性结合是转录因子调控基因转录的关键环节.因此,要鉴定转录因子的靶基因,就必须从它们与DNA相互作用的分子水平,鉴定它们能够识别并结合的全部DNA序列,即转录因子DNA结合谱.近年来随着DNA微阵列芯片和高通量DNA测序技术的产生和快速发展,出现了建立转录因子体内及体外DNA结合谱的一系列革命性的

  13. ScreeninG of transcription factors from Magnaporthe oryzae which are speciaLLy expressed in its earLy infection staGe%稻瘟病菌中侵染初期特异表达的转录因子筛选

    Institute of Scientific and Technical Information of China (English)

    孟秀利; 李亚; 周波; 鲁国东

    2014-01-01

    稻瘟病是威胁水稻产量的重要病害,弄清楚稻瘟病菌与水稻的互作对于防控稻瘟病具有重要的意义。转录因子是调控基因表达的重要因子,对于调控稻瘟病菌的生长发育和致病性具有重要作用。为了寻找在稻瘟病菌侵染初期特异表达的转录因子,我们首先从稻瘟病菌数据库中找到486个假定的转录因子,然后通过RT-PCR方法筛选出30个在侵染时期特异表达的转录因子。这些转录因子根据结构域的不同可以分为10种类型。具体来讲,9个属于Zn2Cys6类转录因子,4个属于C2H2 zinc finger类转录因子,6个属于HMG类转录因子,携带Transcription factor jumonji和 NucLeic acid-binding,OB-foLd结构域的转录因子分别含有3个,而携带Winged heLix repressor DNA-binding结构域、ssDNA-binding transcriptionaL reguLator结构域、Homeodomain-Like结构域、zinc finger MIZ-type结构域和 zinc finger DHHC-type结构域的转录因子分别含有1个。%Rice bLast is an important disease which threatens the product of rice. It is significant to study the interac-tion between rice and Magnaporthe oryzae. Transcription factors( TFs)can pLay an important roLe in reguLating the ex-pression of genes. The purpose of this articLe is to screen TFs which can speciaLLy express in the earLy stage of infec-tion. 486 TFs were seLected and studied from the genome database of Magnaporthe oryzae and 30 TFs of them were found speciaLLy expressed in the earLy stage of infection by RT-PCR. The 30 TFs were divided into 10 types based on their protein domains. 9 TFs contain Zn2Cys6 domain and 4 TFs contain C2H2 zinc finger domain. 6 TFs contain HMG domain. 3 TFs contain Winged heLix repressor DNA-binding domain or NucLeic acid-binding OB-foLd domain. There are onLy one TF that contains Winged heLix repressor DNA-binding domain,ssDNA-binding transcriptionaL reg-uLator domain,Homeodomain-Like domain,zinc finger MIZ-type domain or zinc

  14. Water deficit-induced changes in transcription factor expression in maize seedlings

    Science.gov (United States)

    Plants tolerate water deficits by regulating gene networks controlling cellular and physiological traits to modify growth and development. Transcription factor (TFs) directed regulation of transcription within these gene networks is key to eliciting appropriate responses. In this study, reverse tran...

  15. Musical Instrument Choice and Playing History in Post-Secondary Level Music Students: Some Descriptive Data, Some Causes and Some Background Factors

    Science.gov (United States)

    Chen, Simy Meng-Yu; Howard, Robert W.

    2004-01-01

    Why do musicians specialize in the specific instruments that they do? Research has shown effects of such factors as the perceived masculinity/femininity of instruments and musician's personality but there are little background data on other factors. The present study had two major aims. The first aim was to gather some useful background data on…

  16. Determination and inference of eukaryotic transcription factor sequence specificity.

    Science.gov (United States)

    Weirauch, Matthew T; Yang, Ally; Albu, Mihai; Cote, Atina G; Montenegro-Montero, Alejandro; Drewe, Philipp; Najafabadi, Hamed S; Lambert, Samuel A; Mann, Ishminder; Cook, Kate; Zheng, Hong; Goity, Alejandra; van Bakel, Harm; Lozano, Jean-Claude; Galli, Mary; Lewsey, Mathew G; Huang, Eryong; Mukherjee, Tuhin; Chen, Xiaoting; Reece-Hoyes, John S; Govindarajan, Sridhar; Shaulsky, Gad; Walhout, Albertha J M; Bouget, François-Yves; Ratsch, Gunnar; Larrondo, Luis F; Ecker, Joseph R; Hughes, Timothy R

    2014-09-11

    Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are currently known for only ∼1% of eukaryotic TFs. Broadly sampling DNA-binding domain (DBD) types from multiple eukaryotic clades, we determined DNA sequence preferences for >1,000 TFs encompassing 54 different DBD classes from 131 diverse eukaryotes. We find that closely related DBDs almost always have very similar DNA sequence preferences, enabling inference of motifs for ∼34% of the ∼170,000 known or predicted eukaryotic TFs. Sequences matching both measured and inferred motifs are enriched in chromatin immunoprecipitation sequencing (ChIP-seq) peaks and upstream of transcription start sites in diverse eukaryotic lineages. SNPs defining expression quantitative trait loci in Arabidopsis promoters are also enriched for predicted TF binding sites. Importantly, our motif "library" can be used to identify specific TFs whose binding may be altered by human disease risk alleles. These data present a powerful resource for mapping transcriptional networks across eukaryotes.

  17. SM-TF: A structural database of small molecule-transcription factor complexes.

    Science.gov (United States)

    Xu, Xianjin; Ma, Zhiwei; Sun, Hongmin; Zou, Xiaoqin

    2016-06-30

    Transcription factors (TFs) are the proteins involved in the transcription process, ensuring the correct expression of specific genes. Numerous diseases arise from the dysfunction of specific TFs. In fact, over 30 TFs have been identified as therapeutic targets of about 9% of the approved drugs. In this study, we created a structural database of small molecule-transcription factor (SM-TF) complexes, available online at http://zoulab.dalton.missouri.edu/SM-TF. The 3D structures of the co-bound small molecule and the corresponding binding sites on TFs are provided in the database, serving as a valuable resource to assist structure-based drug design related to TFs. Currently, the SM-TF database contains 934 entries covering 176 TFs from a variety of species. The database is further classified into several subsets by species and organisms. The entries in the SM-TF database are linked to the UniProt database and other sequence-based TF databases. Furthermore, the druggable TFs from human and the corresponding approved drugs are linked to the DrugBank. © 2016 Wiley Periodicals, Inc.

  18. Do psychological factors play a crucial role in sport performance? – Research on personality and psychological variables of athletes in Hungary

    OpenAIRE

    Gyomber, Noemi; Kovacs, Krisztina; Lenart, Agota

    2016-01-01

    ABSTRACT: Contemporary research aims to investigate background factors that contribute to successful sport performance. Of these factors the psychological well-being and mental health status should be underlined that have gained a significant role, particularly in the frames of sport psychological counseling. The aim of the present study is to seek for interrelations of psychological variables and sport performance of young athletes, and to reveal what advantages might be ut...

  19. TF-finder: A software package for identifying transcription factors involved in biological processes using microarray data and existing knowledge base

    Directory of Open Access Journals (Sweden)

    Cui Xiaoqi

    2010-08-01

    Full Text Available Abstract Background Identification of transcription factors (TFs involved in a biological process is the first step towards a better understanding of the underlying regulatory mechanisms. However, due to the involvement of a large number of genes and complicated interactions in a gene regulatory network (GRN, identification of the TFs involved in a biology process remains to be very challenging. In reality, the recognition of TFs for a given a biological process can be further complicated by the fact that most eukaryotic genomes encode thousands of TFs, which are organized in gene families of various sizes and in many cases with poor sequence conservation except for small conserved domains. This poses a significant challenge for identification of the exact TFs involved or ranking the importance of a set of TFs to a process of interest. Therefore, new methods for recognizing novel TFs are desperately needed. Although a plethora of methods have been developed to infer regulatory genes using microarray data, it is still rare to find the methods that use existing knowledge base in particular the validated genes known to be involved in a process to bait/guide discovery of novel TFs. Such methods can replace the sometimes-arbitrary process of selection of candidate genes for experimental validation and significantly advance our knowledge and understanding of the regulation of a process. Results We developed an automated software package called TF-finder for recognizing TFs involved in a biological process using microarray data and existing knowledge base. TF-finder contains two components, adaptive sparse canonical correlation analysis (ASCCA and enrichment test, for TF recognition. ASCCA uses positive target genes to bait TFS from gene expression data while enrichment test examines the presence of positive TFs in the outcomes from ASCCA. Using microarray data from salt and water stress experiments, we showed TF-finder is very efficient in recognizing

  20. Children's Empowerment in Play

    Science.gov (United States)

    Canning, Natalie

    2007-01-01

    This article examines the level of empowerment and autonomy children can create in their play experiences. It examines the play discourses that children build and maintain and considers the importance of play contexts in supporting children's emotional and social development. These aspects of play are often unseen or misunderstood by the adult…

  1. The Play of Psychotherapy

    Science.gov (United States)

    Marks-Tarlow, Terry

    2012-01-01

    The author reviews the role of play within psychotherapy. She does not discuss the formal play therapy especially popular for young children, nor play from the Jungian perspective that encourages the use of the sand tray with adults. Instead, she focuses on the informal use of play during psychotherapy as it is orchestrated intuitively. Because…

  2. Two people playing together: some thoughts on play, playing, and playfulness in psychoanalytic work.

    Science.gov (United States)

    Vliegen, Nicole

    2009-01-01

    Children's play and the playfulness of adolescents and adults are important indicators of personal growth and development. When a child is not able to play, or an adolescent/adult is not able to be playful with thoughts and ideas, psychotherapy can help to find a more playful and creative stance. Elaborating Winnicott's (1968, p. 591) statement that "psychotherapy has to do with two people playing together," three perspectives on play in psychotherapy are discussed. In the first point of view, the child gets in touch with and can work through aspects of his or her inner world, while playing in the presence of the therapist. The power of play is then rooted in the playful communication with the self In a second perspective, in play the child is communicating aspects of his or her inner world to the therapist as a significant other. In a third view, in "playing together" child and therapist are coconstructing new meanings. These three perspectives on play are valid at different moments of a therapy process or for different children, depending on the complex vicissitudes of the child's constitution, life experiences, development, and psychic structure. Concerning these three perspectives, a parallel can be drawn between the therapist's attitude toward the child's play and the way the therapist responds to the verbal play of an adolescent or adult. We illustrate this with the case of Jacob, a late adolescent hardly able to play with ideas.

  3. Applying Play to Therapy.

    Science.gov (United States)

    Ritter, Patricia S.; Fokes, Joann

    The objectives of this paper are (1) to present the relationship of play to language and cognition, (2) to describe the stages of play and discuss recent literature about the characteristics of play, and (3) to describe the use of play with the multifaceted goals of cognition, pragmatics, semantics, syntax, and morphology as an intervention…

  4. TOBFAC: the database of tobacco transcription factors

    Directory of Open Access Journals (Sweden)

    Brannock Jennifer F

    2008-01-01

    Full Text Available Abstract Background Regulation of gene expression at the level of transcription is a major control point in many biological processes. Transcription factors (TFs can activate and/or repress the transcriptional rate of target genes and vascular plant genomes devote approximately 7% of their coding capacity to TFs. Global analysis of TFs has only been performed for three complete higher plant genomes – Arabidopsis (Arabidopsis thaliana, poplar (Populus trichocarpa and rice (Oryza sativa. Presently, no large-scale analysis of TFs has been made from a member of the Solanaceae, one of the most important families of vascular plants. To fill this void, we have analysed tobacco (Nicotiana tabacum TFs using a dataset of 1,159,022 gene-space sequence reads (GSRs obtained by methylation filtering of the tobacco genome. An analytical pipeline was developed to isolate TF sequences from the GSR data set. This involved multiple (typically 10–15 independent searches with different versions of the TF family-defining domain(s (normally the DNA-binding domain followed by assembly into contigs and verification. Our analysis revealed that tobacco contains a minimum of 2,513 TFs representing all of the 64 well-characterised plant TF families. The number of TFs in tobacco is higher than previously reported for Arabidopsis and rice. Results TOBFAC: the database of tobacco transcription factors, is an integrative database that provides a portal to sequence and phylogeny data for the identified TFs, together with a large quantity of other data concerning TFs in tobacco. The database contains an individual page dedicated to each of the 64 TF families. These contain background information, domain architecture via Pfam links, a list of all sequences and an assessment of the minimum number of TFs in this family in tobacco. Downloadable phylogenetic trees of the major families are provided along with detailed information on the bioinformatic pipeline that was used to find

  5. The ubiquitous transcription factor CTCF promotes lineage-specific epigenomic remodeling and establishment of transcriptional networks driving cell differentiation.

    Science.gov (United States)

    Dubois-Chevalier, Julie; Staels, Bart; Lefebvre, Philippe; Eeckhoute, Jérôme

    2015-01-01

    Cell differentiation relies on tissue-specific transcription factors (TFs) that cooperate to establish unique transcriptomes and phenotypes. However, the role of ubiquitous TFs in these processes remains poorly defined. Recently, we have shown that the CCCTC-binding factor (CTCF) is required for adipocyte differentiation through epigenomic remodelling of adipose tissue-specific enhancers and transcriptional activation of Peroxisome proliferator-activated receptor gamma (PPARG), the main driver of the adipogenic program (PPARG), and its target genes. Here, we discuss how these findings, together with the recent literature, illuminate a functional role for ubiquitous TFs in lineage-determining transcriptional networks.

  6. Genome-Wide Identification and Evolutionary Analysis of the Animal Specific ETS Transcription Factor Family

    OpenAIRE

    Wang, Zhipeng; Zhang, Qin

    2009-01-01

    The ETS proteins are a family of transcription factors (TFs) that regulate a variety of biological processes. We made genome-wide analyses to explore the classification of the ETS gene family. We identified 207 ETS genes which encode 321 ETS TFs from ten animal species. Of the 321 ETS TFs, 155 contain only an ETS domain, about 50% contain a ETS_PEA3_N or a SAM_PNT domain in addition to an ETS domain, the rest (only four) contain a second ETS domain or a second ETS_PEA3_N domain or an another ...

  7. Generation of mouse ES cell lines engineered for the forced induction of transcription factors

    OpenAIRE

    Correa-Cerro, Lina S.; Piao, Yulan; Sharov, Alexei A; Nishiyama, Akira; Cadet, Jean S.; Yu, Hong; Sharova, Lioudmila V.; Xin, Li; Hoang, Hien G.; Thomas, Marshall; Qian, Yong; Dudekula, Dawood B.; Meyers, Emily; Binder, Bernard Y.; Mowrer, Gregory

    2011-01-01

    Here we report the generation and characterization of 84 mouse ES cell lines with doxycycline-controllable transcription factors (TFs) which, together with the previous 53 lines, cover 7–10% of all TFs encoded in the mouse genome. Global gene expression profiles of all 137 lines after the induction of TFs for 48 hrs can associate each TF with the direction of ES cell differentiation, regulatory pathways, and mouse phenotypes. These cell lines and microarray data provide building blocks for a ...

  8. Generation of mouse ES cell lines engineered for the forced induction of transcription factors

    Science.gov (United States)

    Correa-Cerro, Lina S.; Piao, Yulan; Sharov, Alexei A.; Nishiyama, Akira; Cadet, Jean S.; Yu, Hong; Sharova, Lioudmila V.; Xin, Li; Hoang, Hien G.; Thomas, Marshall; Qian, Yong; Dudekula, Dawood B.; Meyers, Emily; Binder, Bernard Y.; Mowrer, Gregory; Bassey, Uwem; Longo, Dan L.; Schlessinger, David; Ko, Minoru S. H.

    2011-01-01

    Here we report the generation and characterization of 84 mouse ES cell lines with doxycycline-controllable transcription factors (TFs) which, together with the previous 53 lines, cover 7–10% of all TFs encoded in the mouse genome. Global gene expression profiles of all 137 lines after the induction of TFs for 48 hrs can associate each TF with the direction of ES cell differentiation, regulatory pathways, and mouse phenotypes. These cell lines and microarray data provide building blocks for a variety of future biomedical research applications as a community resource. PMID:22355682

  9. Transcription factors involved in the regulation of natural killer cell development and function: an update

    Directory of Open Access Journals (Sweden)

    Martha Elia Luevano

    2012-10-01

    Full Text Available Natural Killer (NK cells belong to the innate immune system and are key effectors in the immune response against cancer and infection. Recent studies have contributed to the knowledge of events controlling NK cell fate. The use of knockout mice has enabled the discovery of key transcription factors (TFs essential for NK cell development and function. Yet, unwrapping the downstream targets of these TFs and their influence on NK cells remains a challenge. In this review we discuss the latest TFs described to be involved in the regulation of NK cell development and maturation.

  10. Prunus transcription factors: Breeding perspectives

    Directory of Open Access Journals (Sweden)

    Valmor João Bianchi

    2015-06-01

    Full Text Available Many plant processes depend on differential gene expression, which is generally controlled by complex proteins called transcription factors (TFs. In peach, 1,533 TFs have been identified, accounting for about 5.5% of the 27,852 protein-coding genes. These TFs are the reference for the rest of the Prunus species. TF studies in Prunus have been performed on the gene expression analysis of different agronomic traits, including control of the flowering process, fruit quality, and biotic and abiotic stress resistance. These studies, using quantitative RT-PCR, have mainly been performed in peach, and to a lesser extent in other species, including almond, apricot, black cherry, Fuji cherry, Japanese apricot, plum, and sour and sweet cherry. Other tools have also been used in TF studies, including cDNA-AFLP, LC-ESI-MS, RNA and DNA blotting or mapping. More recently, new tools assayed include microarray and high-throughput DNA sequencing (DNA-Seq and RNA sequencing (RNA-Seq. New functional genomics opportunities include genome resequencing and the well-known synteny among Prunus genomes and transcriptomes. These new functional studies should be applied in breeding programs in the development of molecular markers. With the genome sequences available, some strategies that have been used in model systems (such as SNP genotyping assays and genotyping-by-sequencing may be applicable in the functional analysis of Prunus TFs as well. In addition, the knowledge of the gene functions and position in the peach reference genome of the TFs represents an additional advantage. These facts could greatly facilitate the isolation of genes via QTL (quantitative trait loci map-based cloning in the different Prunus species, following the association of these TFs with the identified QTLs using the peach reference genome.

  11. Simplified Method for Predicting a Functional Class of Proteins in Transcription Factor Complexes

    KAUST Repository

    Piatek, Marek J.

    2013-07-12

    Background:Initiation of transcription is essential for most of the cellular responses to environmental conditions and for cell and tissue specificity. This process is regulated through numerous proteins, their ligands and mutual interactions, as well as interactions with DNA. The key such regulatory proteins are transcription factors (TFs) and transcription co-factors (TcoFs). TcoFs are important since they modulate the transcription initiation process through interaction with TFs. In eukaryotes, transcription requires that TFs form different protein complexes with various nuclear proteins. To better understand transcription regulation, it is important to know the functional class of proteins interacting with TFs during transcription initiation. Such information is not fully available, since not all proteins that act as TFs or TcoFs are yet annotated as such, due to generally partial functional annotation of proteins. In this study we have developed a method to predict, using only sequence composition of the interacting proteins, the functional class of human TF binding partners to be (i) TF, (ii) TcoF, or (iii) other nuclear protein. This allows for complementing the annotation of the currently known pool of nuclear proteins. Since only the knowledge of protein sequences is required in addition to protein interaction, the method should be easily applicable to many species.Results:Based on experimentally validated interactions between human TFs with different TFs, TcoFs and other nuclear proteins, our two classification systems (implemented as a web-based application) achieve high accuracies in distinguishing TFs and TcoFs from other nuclear proteins, and TFs from TcoFs respectively.Conclusion:As demonstrated, given the fact that two proteins are capable of forming direct physical interactions and using only information about their sequence composition, we have developed a completely new method for predicting a functional class of TF interacting protein partners

  12. CORRELATION OF MRI GRADING OF BONE STRESS INJURIES WITH CLINICAL RISK FACTORS AND RETURN TO PLAY: A 5-YEAR PROSPECTIVE STUDY IN COLLEGIATE TRACK AND FIELD ATHLETES

    Science.gov (United States)

    Nattiv, Aurelia; Kennedy, Gannon; Barrack, Michelle T.; Abdelkerim, Ashraf; Goolsby, Marci A.; Arends, Julie C.; Seeger, Leanne L.

    2015-01-01

    Background Bone stress injuries are common in track and field athletes. Knowledge of risk factors and correlation of these to magnetic resonance imaging (MRI) grading could be helpful in determining recovery time. Purpose To examine the relationships between MRI grading of bone stress injury with clinical risk factors and time to return to sport in collegiate track and field athletes. Study Design Prospective cohort over 5 years. Methods Two hundred and eleven male and female collegiate track and field and cross-country athletes were followed prospectively through their competitive seasons. All athletes had a pre-participation history, physical exam, and anthropometric measurements obtained annually. An additional questionnaire was completed regarding nutritional behaviors, menstrual patterns and prior injuries, as well as a 3-day diet record. Dual energy X-ray absorptiometry was obtained at baseline and each year of participation in the study. Athletes with clinical evidence of bone stress injuries had plain radiographs. If radiographs were negative, MRI was obtained. Bone stress injuries were evaluated by two independent radiologists utilizing an MRI grading system. MRI grading and risk factors were evaluated to identify predictors of time to return to sport. Results Thirty-four (12 males, 22 females) of the 211 collegiate athletes sustained 61 bone stress injuries during the 5-year study period. The average prospective assessment for participants was 2.1 years. MRI grade and total body bone mineral density (BMD) emerged as significant and independent predictors of time to return to sport in the multiple regression model. Specifically, the higher the MRI grade, the longer the recovery time (psport. Conclusions Higher MRI grade, lower BMD, and skeletal sites of predominant trabecular bone structure were independently associated with delayed recovery of bone stress injuries in track and field athletes. Knowledge of these risk factors, as well as nutritional and

  13. Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes.

    Science.gov (United States)

    Li, Xu; Wang, Wenqi; Wang, Jiadong; Malovannaya, Anna; Xi, Yuanxin; Li, Wei; Guerra, Rudy; Hawke, David H; Qin, Jun; Chen, Junjie

    2015-01-21

    The current knowledge on how transcription factors (TFs), the ultimate targets and executors of cellular signalling pathways, are regulated by protein-protein interactions remains limited. Here, we performed proteomics analyses of soluble and chromatin-associated complexes of 56 TFs, including the targets of many signalling pathways involved in development and cancer, and 37 members of the Forkhead box (FOX) TF family. Using tandem affinity purification followed by mass spectrometry (TAP/MS), we performed 214 purifications and identified 2,156 high-confident protein-protein interactions. We found that most TFs form very distinct protein complexes on and off chromatin. Using this data set, we categorized the transcription-related or unrelated regulators for general or specific TFs. Our study offers a valuable resource of protein-protein interaction networks for a large number of TFs and underscores the general principle that TFs form distinct location-specific protein complexes that are associated with the different regulation and diverse functions of these TFs.

  14. The play grid

    DEFF Research Database (Denmark)

    Fogh, Rune; Johansen, Asger

    2013-01-01

    In this paper we propose The Play Grid, a model for systemizing different play types. The approach is psychological by nature and the actual Play Grid is based, therefore, on two pairs of fundamental and widely acknowledged distinguishing characteristics of the ego, namely: extraversion vs...... at the Play Grid. Thus, the model has four quadrants, each of them describing one of four play types: the Assembler, the Director, the Explorer, and the Improviser. It is our hope that the Play Grid can be a useful design tool for making entertainment products for children....

  15. Play-level distributions of estimates of recovery factors for a miscible carbon dioxide enhanced oil recovery method used in oil reservoirs in the conterminous United States

    Science.gov (United States)

    Attanasi, E.D.; Freeman, P.A.

    2016-03-02

    In a U.S. Geological Survey (USGS) study, recovery-factor estimates were calculated by using a publicly available reservoir simulator (CO2 Prophet) to estimate how much oil might be recovered with the application of a miscible carbon dioxide (CO2) enhanced oil recovery (EOR) method to technically screened oil reservoirs located in onshore and State offshore areas in the conterminous United States. A recovery factor represents the percentage of an oil reservoir’s original oil in place estimated to be recoverable by the application of a miscible CO2-EOR method. The USGS estimates were calculated for 2,018 clastic and 1,681 carbonate candidate reservoirs in the “Significant Oil and Gas Fields of the United States Database” prepared by Nehring Associates, Inc. (2012).

  16. Play-level distributions of estimates of recovery factors for a miscible carbon dioxide enhanced oil recovery method used in oil reservoirs in the conterminous United States

    Science.gov (United States)

    Attanasi, E.D.; Freeman, P.A.

    2016-03-02

    In a U.S. Geological Survey (USGS) study, recovery-factor estimates were calculated by using a publicly available reservoir simulator (CO2 Prophet) to estimate how much oil might be recovered with the application of a miscible carbon dioxide (CO2) enhanced oil recovery (EOR) method to technically screened oil reservoirs located in onshore and State offshore areas in the conterminous United States. A recovery factor represents the percentage of an oil reservoir’s original oil in place estimated to be recoverable by the application of a miscible CO2-EOR method. The USGS estimates were calculated for 2,018 clastic and 1,681 carbonate candidate reservoirs in the “Significant Oil and Gas Fields of the United States Database” prepared by Nehring Associates, Inc. (2012).

  17. Increased growth factors play a role in wound healing promoted by noninvasive oxygen-ozone therapy in diabetic patients with foot ulcers.

    Science.gov (United States)

    Zhang, Jing; Guan, Meiping; Xie, Cuihua; Luo, Xiangrong; Zhang, Qian; Xue, Yaoming

    2014-01-01

    Management of diabetic foot ulcers (DFUs) is a great challenge for clinicians. Although the oxygen-ozone treatment improves the diabetic outcome, there are few clinical trials to verify the efficacy and illuminate the underlying mechanisms of oxygen-ozone treatment on DFUs. In the present study, a total of 50 type 2 diabetic patients complicated with DFUs, Wagner stage 2~4, were randomized into control group treated by standard therapy only and ozone group treated by standard therapy plus oxygen-ozone treatment. The therapeutic effects were graded into 4 levels from grade 0 (no change) to grade 3 (wound healing). The wound sizes were measured at baseline and day 20, respectively. Tissue biopsies were performed at baseline and day 11. The expressions of vascular endothelial growth factor (VEGF), transforming growth factor-β (TGF-β), and platelet-derived growth factor (PDGF) proteins in the pathologic specimens were determined by immunohistochemical examinations. The effective rate of ozone group was significantly higher than that of control group (92% versus 64%, P ozone group than in control group (P ozone group than in control group. Ozone therapy promotes the wound healing of DFUs via potential induction of VEGF, TGF-β, and PDGF at early stage of the treatment. (Clinical trial registry number is ChiCTR-TRC-14004415).

  18. Correlation of MRI grading of bone stress injuries with clinical risk factors and return to play: a 5-year prospective study in collegiate track and field athletes.

    Science.gov (United States)

    Nattiv, Aurelia; Kennedy, Gannon; Barrack, Michelle T; Abdelkerim, Ashraf; Goolsby, Marci A; Arends, Julie C; Seeger, Leanne L

    2013-08-01

    Bone stress injuries are common in track and field athletes. Knowledge of risk factors and correlation of these to magnetic resonance imaging (MRI) grading could be helpful in determining recovery time. To examine the relationships between MRI grading of bone stress injuries with clinical risk factors and time to return to sport in collegiate track and field athletes. Cohort study (prognosis); Level of evidence, 2. A total of 211 male and female collegiate track and field and cross-country athletes were followed prospectively through their competitive seasons. All athletes had preparticipation history, physical examination, and anthropometric measurements obtained annually. An additional questionnaire was completed regarding nutritional behaviors, menstrual patterns, and prior injuries, as well as a 3-day diet record. Dual-energy X-ray absorptiometry was performed at baseline and each year of participation in the study. Athletes with clinical evidence of bone stress injuries had plain radiographs. If radiograph findings were negative, MRI was performed. Bone stress injuries were evaluated by 2 independent radiologists utilizing an MRI grading system. The MRI grading and risk factors were evaluated to identify predictors of time to return to sport. Thirty-four of the athletes (12 men, 22 women) sustained 61 bone stress injuries during the 5-year study period. The mean prospective assessment for participants was 2.7 years. In the multiple regression model, MRI grade and total-body bone mineral density (BMD) emerged as significant and independent predictors of time to return to sport. Specifically, the higher the MRI grade (P = .004) and lower the BMD (P = .030), the longer the recovery time. Location of the bone injury at predominantly trabecular sites of the femoral neck, pubic bone, and sacrum was also associated with a prolonged time to return to sport. Female athletes with oligomenorrhea and amenorrhea had bone stress injuries of higher MRI grades compared with

  19. Leukaemia-associated Rho guanine nucleotide exchange factor (LARG) plays an agonist specific role in platelet function through RhoA activation.

    Science.gov (United States)

    Zou, Siying; Teixeira, Alexandra M; Yin, Mingzhu; Xiang, Yaozu; Xavier-Ferrucio, Juliana; Zhang, Ping-Xia; Hwa, John; Min, Wang; Krause, Diane S

    2016-08-30

    Leukemia-Associated RhoGEF (LARG) is highly expressed in platelets, which are essential for maintaining normal haemostasis. We studied the function of LARG in murine and human megakaryocytes and platelets with Larg knockout (KO), shRNA-mediated knockdown and small molecule-mediated inhibition. We found that LARG is important for human, but not murine, megakaryocyte maturation. Larg KO mice exhibit macrothrombocytopenia, internal bleeding in the ovaries and prolonged bleeding times. KO platelets have impaired aggregation, α-granule release and integrin α2bβ3 activation in response to thrombin and thromboxane, but not to ADP. The same agonist-specific reductions in platelet aggregation occur in human platelets treated with a LARG inhibitor. Larg KO platelets have reduced RhoA activation and myosin light chain phosphorylation, suggesting that Larg plays an agonist-specific role in platelet signal transduction. Using two different in vivo assays, Larg KO mice are protected from in vivo thrombus formation. Together, these results establish that LARG regulates human megakaryocyte maturation, and is critical for platelet function in both humans and mice.

  20. Role-Playing Mitosis.

    Science.gov (United States)

    Wyn, Mark A.; Stegink, Steven J.

    2000-01-01

    Introduces a role playing activity that actively engages students in the learning process of mitosis. Students play either chromosomes carrying information, or cells in the cell membrane. (Contains 11 references.) (Author/YDS)

  1. Play the Tuberculosis Game

    Science.gov (United States)

    ... Questionnaire Tuberculosis Play Tuberculosis Experiments & Discoveries About the game Discover and experience some of the classic methods ... last will in Paris. Play the Blood Typing Game Try to save some patients and learn about ...

  2. Play the MRI Game

    Science.gov (United States)

    ... Teachers' Questionnaire MRI Play MRI the Magnetic Miracle Game About the game In the MRI imaging technique, strong magnets and ... last will in Paris. Play the Blood Typing Game Try to save some patients and learn about ...

  3. Play the Electrocardiogram Game

    Science.gov (United States)

    ... and Work Teachers' Questionnaire Electrocardiogram Play the ECG Game About the game ECG is used for diagnosing heart conditions by ... last will in Paris. Play the Blood Typing Game Try to save some patients and learn about ...

  4. Learning Through Play

    Science.gov (United States)

    ... play, such as using play dough, LEGOs, and board games. Toys such as puzzles, pegboards, beads, and lacing ... Building sets, books, bicycles, roller skates, ice skates, board games, checkers, beginning sports • Middle Schoolers and Adolescents: Athletics, ...

  5. Children, Time, and Play

    DEFF Research Database (Denmark)

    Elkind, David; Rinaldi, Carla; Flemmert Jensen, Anne;

    Proceedings from the conference "Children, Time, and Play". Danish University of Education, January 30th 2003.......Proceedings from the conference "Children, Time, and Play". Danish University of Education, January 30th 2003....

  6. Role-Playing Mitosis.

    Science.gov (United States)

    Wyn, Mark A.; Stegink, Steven J.

    2000-01-01

    Introduces a role playing activity that actively engages students in the learning process of mitosis. Students play either chromosomes carrying information, or cells in the cell membrane. (Contains 11 references.) (Author/YDS)

  7. Play at Work

    DEFF Research Database (Denmark)

    Meier Sørensen, Bent; Spoelstra, Sverre

    2012-01-01

    for business and the other insists that work and play are largely indistinguishable in the postindustrial organization. Our field study of a design and communications company in Denmark shows that organizational play can be much more than just functional to the organization. We identify three ways in which......The interest in organizational play is growing, both in popular business discourse and organization studies. As the presumption that play is dysfunctional for organizations is increasingly discarded, the existing positions may be divided into two camps; one proposes ‘serious play’ as an engine...... workplaces engage in play: play as a (serious) continuation of work, play as a (critical) intervention into work and play as an (uninvited) usurpation of work....

  8. Increased Growth Factors Play a Role in Wound Healing Promoted by Noninvasive Oxygen-Ozone Therapy in Diabetic Patients with Foot Ulcers

    Directory of Open Access Journals (Sweden)

    Jing Zhang

    2014-01-01

    Full Text Available Management of diabetic foot ulcers (DFUs is a great challenge for clinicians. Although the oxygen-ozone treatment improves the diabetic outcome, there are few clinical trials to verify the efficacy and illuminate the underlying mechanisms of oxygen-ozone treatment on DFUs. In the present study, a total of 50 type 2 diabetic patients complicated with DFUs, Wagner stage 2~4, were randomized into control group treated by standard therapy only and ozone group treated by standard therapy plus oxygen-ozone treatment. The therapeutic effects were graded into 4 levels from grade 0 (no change to grade 3 (wound healing. The wound sizes were measured at baseline and day 20, respectively. Tissue biopsies were performed at baseline and day 11. The expressions of vascular endothelial growth factor (VEGF, transforming growth factor-β (TGF-β, and platelet-derived growth factor (PDGF proteins in the pathologic specimens were determined by immunohistochemical examinations. The effective rate of ozone group was significantly higher than that of control group (92% versus 64%, P<0.05. The wound size reduction was significantly more in ozone group than in control group (P<0.001. After treatment, the expressions of VEGF, TGF-β, and PDGF proteins at day 11 were significantly higher in ozone group than in control group. Ozone therapy promotes the wound healing of DFUs via potential induction of VEGF, TGF-β, and PDGF at early stage of the treatment. (Clinical trial registry number is ChiCTR-TRC-14004415.

  9. Playing with social identities

    DEFF Research Database (Denmark)

    Winther-Lindqvist, Ditte Alexandra

    2013-01-01

    This chapter offers support for Vygotsky’s claim that all play involves both an imagined situation as well as rules. Synthesising Schousboe’s comprehensive model of spheres of realities in playing (see Chapter 1, this volume) with Lev Vygotskys insight that all playing involve rules as well...

  10. Toddlers: Learning by Playing

    Science.gov (United States)

    ... Feeding Your 1- to 2-Year-Old Toddlers: Learning by Playing KidsHealth > For Parents > Toddlers: Learning by Playing Print A A A What's in ... child's play, but toddlers are hard at work learning important physical skills as they gain muscle control, ...

  11. Playing against the Game

    Science.gov (United States)

    Remmele, Bernd

    2017-01-01

    The paper first outlines a differentiation of play/game-motivations that include "negative" attitudes against the play/game itself like cheating or spoilsporting. This problem is of particular importance in concern of learning games because they are not "played" for themselves--at least in the first place--but due to an…

  12. Play the Mosquito Game

    Science.gov (United States)

    ... and Work Teachers' Questionnaire Malaria Play the Mosquito Game Play the Parasite Game About the games Malaria is one of the world's most common ... last will in Paris. Play the Blood Typing Game Try to save some patients and learn about ...

  13. (Steering) interactive play behavior

    NARCIS (Netherlands)

    Delden, van Robertus Wilhelmus

    2017-01-01

    Play is a powerful means to have an impact on the cognitive, social-emotional, and/or motor skills development. The introduction of technology brings new possibilities to provide engaging and entertaining whole-body play activities. Technology mediates the play activities and in this way changes how

  14. (Steering) interactive play behavior

    NARCIS (Netherlands)

    van Delden, Robertus Wilhelmus

    2017-01-01

    Play is a powerful means to have an impact on the cognitive, social-emotional, and/or motor skills development. The introduction of technology brings new possibilities to provide engaging and entertaining whole-body play activities. Technology mediates the play activities and in this way changes how

  15. Socioeconomic factors play a more important role in childhood vaccination coverage than parental perceptions: a cross-sectional study in Greece.

    Science.gov (United States)

    Danis, K; Georgakopoulou, T; Stavrou, T; Laggas, D; Panagiotopoulos, T

    2010-02-17

    To identify predictive factors of complete and age-appropriate vaccination status in Greece, we conducted a cross-sectional study, using stratified cluster sampling, among children attending the first year of the Greek Grammar school (about 6 years of age) and their parents/guardians. Almost 88% (N=3878) of pupils in the selected clusters (school classrooms) provided their vaccination booklet and their parents/guardians completed a questionnaire regarding beliefs and attitudes towards immunization. Belonging to a minority group, having other siblings and perceiving long distance to immunization site as a barrier were independent predictors of both incomplete and delayed vaccination status in the final logistic regression model. Maternal age >or=30 years and the perception that natural disease is preferable to vaccination were associated with complete vaccination, whereas paternal education of high school or higher was the other independent determinant of age-appropriate immunization. Socioeconomic factors rather than parental beliefs and attitudes towards immunization explained underimmunization. Further interventions are warranted to enhance vaccine coverage in high-risk groups identified in this study. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

  16. Increments and duplication events of enzymes and transcription factors influence metabolic and regulatory diversity in prokaryotes.

    Directory of Open Access Journals (Sweden)

    Mario Alberto Martínez-Núñez

    Full Text Available In this work, the content of enzymes and DNA-binding transcription factors (TFs in 794 non-redundant prokaryotic genomes was evaluated. The identification of enzymes was based on annotations deposited in the KEGG database as well as in databases of functional domains (COG and PFAM and structural domains (Superfamily. For identifications of the TFs, hidden Markov profiles were constructed based on well-known transcriptional regulatory families. From these analyses, we obtained diverse and interesting results, such as the negative rate of incremental changes in the number of detected enzymes with respect to the genome size. On the contrary, for TFs the rate incremented as the complexity of genome increased. This inverse related performance shapes the diversity of metabolic and regulatory networks and impacts the availability of enzymes and TFs. Furthermore, the intersection of the derivatives between enzymes and TFs was identified at 9,659 genes, after this point, the regulatory complexity grows faster than metabolic complexity. In addition, TFs have a low number of duplications, in contrast to the apparent high number of duplications associated with enzymes. Despite the greater number of duplicated enzymes versus TFs, the increment by which duplicates appear is higher in TFs. A lower proportion of enzymes among archaeal genomes (22% than in the bacterial ones (27% was also found. This low proportion might be compensated by the interconnection between the metabolic pathways in Archaea. A similar proportion was also found for the archaeal TFs, for which the formation of regulatory complexes has been proposed. Finally, an enrichment of multifunctional enzymes in Bacteria, as a mechanism of ecological adaptation, was detected.

  17. Increments and duplication events of enzymes and transcription factors influence metabolic and regulatory diversity in prokaryotes.

    Science.gov (United States)

    Martínez-Núñez, Mario Alberto; Poot-Hernandez, Augusto Cesar; Rodríguez-Vázquez, Katya; Perez-Rueda, Ernesto

    2013-01-01

    In this work, the content of enzymes and DNA-binding transcription factors (TFs) in 794 non-redundant prokaryotic genomes was evaluated. The identification of enzymes was based on annotations deposited in the KEGG database as well as in databases of functional domains (COG and PFAM) and structural domains (Superfamily). For identifications of the TFs, hidden Markov profiles were constructed based on well-known transcriptional regulatory families. From these analyses, we obtained diverse and interesting results, such as the negative rate of incremental changes in the number of detected enzymes with respect to the genome size. On the contrary, for TFs the rate incremented as the complexity of genome increased. This inverse related performance shapes the diversity of metabolic and regulatory networks and impacts the availability of enzymes and TFs. Furthermore, the intersection of the derivatives between enzymes and TFs was identified at 9,659 genes, after this point, the regulatory complexity grows faster than metabolic complexity. In addition, TFs have a low number of duplications, in contrast to the apparent high number of duplications associated with enzymes. Despite the greater number of duplicated enzymes versus TFs, the increment by which duplicates appear is higher in TFs. A lower proportion of enzymes among archaeal genomes (22%) than in the bacterial ones (27%) was also found. This low proportion might be compensated by the interconnection between the metabolic pathways in Archaea. A similar proportion was also found for the archaeal TFs, for which the formation of regulatory complexes has been proposed. Finally, an enrichment of multifunctional enzymes in Bacteria, as a mechanism of ecological adaptation, was detected.

  18. Increments and Duplication Events of Enzymes and Transcription Factors Influence Metabolic and Regulatory Diversity in Prokaryotes

    Science.gov (United States)

    Martínez-Núñez, Mario Alberto; Poot-Hernandez, Augusto Cesar; Rodríguez-Vázquez, Katya; Perez-Rueda, Ernesto

    2013-01-01

    In this work, the content of enzymes and DNA-binding transcription factors (TFs) in 794 non-redundant prokaryotic genomes was evaluated. The identification of enzymes was based on annotations deposited in the KEGG database as well as in databases of functional domains (COG and PFAM) and structural domains (Superfamily). For identifications of the TFs, hidden Markov profiles were constructed based on well-known transcriptional regulatory families. From these analyses, we obtained diverse and interesting results, such as the negative rate of incremental changes in the number of detected enzymes with respect to the genome size. On the contrary, for TFs the rate incremented as the complexity of genome increased. This inverse related performance shapes the diversity of metabolic and regulatory networks and impacts the availability of enzymes and TFs. Furthermore, the intersection of the derivatives between enzymes and TFs was identified at 9,659 genes, after this point, the regulatory complexity grows faster than metabolic complexity. In addition, TFs have a low number of duplications, in contrast to the apparent high number of duplications associated with enzymes. Despite the greater number of duplicated enzymes versus TFs, the increment by which duplicates appear is higher in TFs. A lower proportion of enzymes among archaeal genomes (22%) than in the bacterial ones (27%) was also found. This low proportion might be compensated by the interconnection between the metabolic pathways in Archaea. A similar proportion was also found for the archaeal TFs, for which the formation of regulatory complexes has been proposed. Finally, an enrichment of multifunctional enzymes in Bacteria, as a mechanism of ecological adaptation, was detected. PMID:23922780

  19. Playing with social identities

    DEFF Research Database (Denmark)

    Winther-Lindqvist, Ditte Alexandra

    2013-01-01

    This chapter offers support for Vygotsky’s claim that all play involves both an imagined situation as well as rules. Synthesising Schousboe’s comprehensive model of spheres of realities in playing (see Chapter 1, this volume) with Lev Vygotskys insight that all playing involve rules as well...... as pretence, children’s play is understood as an activity involving rules of the social order (roles and positions) as well as identification processes (imagined situations). The theoretical argumentation builds on empirical examples obtained in two different Danish day-care centres. The chapter is informed...... by ethnographic observations and draws on illustrative examples with symbolic group play as well as game-play with rules (soccer) among 5 year old boys. Findings suggest that day-care children’s play, involves negotiation of roles, positioning and identification, and rules – and that these negotiations...

  20. Systematic investigation of transcription factors critical in the protection against cerebral ischemia by Danhong injection

    Science.gov (United States)

    Wei, Junying; Zhang, Yanqiong; Jia, Qiang; Liu, Mingwei; Li, Defeng; Zhang, Yi; Song, Lei; Hu, Yanzhen; Xian, Minghua; Yang, Hongjun; Ding, Chen; Huang, Luqi

    2016-01-01

    Systematic investigations of complex pathological cascades during ischemic brain injury help to elucidate novel therapeutic targets against cerebral ischemia. Although some transcription factors (TFs) involved in cerebral ischemia, systematic surveys of their changes during ischemic brain injury have not been reported. Moreover, some multi-target agents effectively protected against ischemic stroke, but their mechanisms, especially the targets of TFs, are still unclear. Therefore, a comprehensive approach by integrating network pharmacology strategy and a new concatenated tandem array of consensus transcription factor response elements method to systematically investigate the target TFs critical in the protection against cerebral ischemia by a medication was first reported, and then applied to a multi-target drug, Danhong injection (DHI). High-throughput nature and depth of coverage, as well as high quantitative accuracy of the developed approach, make it more suitable for analyzing such multi-target agents. Results indicated that pre-B-cell leukemia transcription factor 1 and cyclic AMP-dependent transcription factor 1, along with six other TFs, are putative target TFs for DHI-mediated protection against cerebral ischemia. This study provides, for the first time, a systematic investigation of the target TFs critical to DHI-mediated protection against cerebral ischemia, as well as reveals more potential therapeutic targets for ischemic stroke. PMID:27431009

  1. TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins

    KAUST Repository

    Schaefer, Ulf

    2010-10-21

    The initiation and regulation of transcription in eukaryotes is complex and involves a large number of transcription factors (TFs), which are known to bind to the regulatory regions of eukaryotic DNA. Apart from TF-DNA binding, protein-protein interaction involving TFs is an essential component of the machinery facilitating transcriptional regulation. Proteins that interact with TFs in the context of transcription regulation but do not bind to the DNA themselves, we consider transcription co-factors (TcoFs). The influence of TcoFs 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. While the role of TFs and their interaction with regulatory DNA regions has been well-studied, the association between TFs and TcoFs has so far been given less attention. Here, we present a resource that is comprised of a collection of human TFs and the TcoFs with which they interact. Other proteins that have a proven interaction with a TF, but are not considered TcoFs are also included. Our database contains 157 high-confidence TcoFs and additionally 379 hypothetical TcoFs. These have been identified and classified according to the type of available evidence for their involvement in transcriptional regulation and their presence in the cell nucleus. We have divided TcoFs into four groups, one of which contains high-confidence TcoFs and three others contain TcoFs which are hypothetical to different extents. We have developed the Dragon Database for Human Transcription Co-Factors and Transcription Factor Interacting Proteins (TcoF-DB). A web-based interface for this resource can be freely accessed at http://cbrc.kaust.edu.sa/tcof/ and http://apps.sanbi.ac.za/tcof/. © The Author(s) 2010.

  2. The loose evolutionary relationships between transcription factors and other gene products across prokaryotes

    OpenAIRE

    del Grande, Marc; Moreno-Hagelsieb, Gabriel

    2014-01-01

    Background Tests for the evolutionary conservation of associations between genes coding for transcription factors (TFs) and other genes have been limited to a few model organisms due to the lack of experimental information of functional associations in other organisms. We aimed at surmounting this limitation by using the most co-occurring gene pairs as proxies for the most conserved functional interactions available for each gene in a genome. We then used genes predicted to code for TFs to co...

  3. Comparative Analysis of Transcription Factors Families across Fungal Tree of Life

    Energy Technology Data Exchange (ETDEWEB)

    Salamov, Asaf; Grigoriev, Igor

    2015-03-19

    Transcription factors (TFs) are proteins that regulate the transcription of genes, by binding to specific DNA sequences. Based on literature (Shelest, 2008; Weirauch and Hughes,2011) collected and manually curated list of DBD Pfam domains (in total 62 DBD domains) We looked for distribution of TFs in 395 fungal genomes plus additionally in plant genomes (Phytozome), prokaryotes(IMG), some animals/metazoans and protists genomes

  4. GmPHR1, a Novel Homolog of the AtPHR1 Transcription Factor, Plays a Role in Plant Tolerance to Phosphate Starvation

    Institute of Scientific and Technical Information of China (English)

    LI Xi-huan; WANG Yun-jie; WU Bing; KONG You-bin; LI Wen-long; CHANG Wen-suo; ZHANG Cai-ying

    2014-01-01

    GmPHR1 from soybean (Glycine max) was isolated and characterized. This novel homolog of the AtPHR1 transcription factor confers tolerance to inorganic phosphate (Pi)-starvation. The gene is 2 751 bp long, with an 819-bp open reading frame and ifve introns. Analysis of transcription activity in yeast revealed that the full-length GmPHR1 and its C-terminal activate the reporter genes for His, Ade and Ura, suggesting that the C-terminal peptide functions as a transcriptional activator. Quantitative real-time PCR indicated that patterns of GmPHR1 expression differed. For example, under low-Pi stress, this gene was quickly induced in the tolerant JD11 after 0.5 h, with expression then decreasing slowly before peaking at 12-24 h. By contrast, induction in the sensitive Niumaohuang (NMH) was slow, peaking at 6 h before decreasing quickly at 9 h. GmPHR1 showed sub-cellular localization in the nuclei of onion epidermal cells and Arabidopsis roots. Growth parameters in wild-type (WT) Arabidopsis plants as well as in overexpression (OE) transgenic lines were examined. Under low-Pi conditions, values for shoot, root and whole-plant dry weights, root to shoot ratios, and lengths of primary roots were signiifcantly greater in OE lines than in the WT. These data demonstrate that GmPHR1 has an important role in conferring tolerance to phosphate starvation.

  5. Major Factors Affecting Incidence of Childhood Thyroid Cancer in Belarus after the Chernobyl Accident: Do Nitrates in Drinking Water Play a Role?

    Science.gov (United States)

    Drozd, Valentina M; Saenko, Vladimir A; Brenner, Alina V; Drozdovitch, Vladimir; Pashkevich, Vasilii I; Kudelsky, Anatoliy V; Demidchik, Yuri E; Branovan, Igor; Shiglik, Nikolay; Rogounovitch, Tatiana I; Yamashita, Shunichi; Biko, Johannes; Reiners, Christoph

    2015-01-01

    One of the major health consequences of the Chernobyl Nuclear Power Plant accident in 1986 was a dramatic increase in incidence of thyroid cancer among those who were aged less than 18 years at the time of the accident. This increase has been directly linked in several analytic epidemiological studies to iodine-131 (131I) thyroid doses received from the accident. However, there remains limited understanding of factors that modify the 131I-related risk. Focusing on post-Chernobyl pediatric thyroid cancer in Belarus, we reviewed evidence of the effects of radiation, thyroid screening, and iodine deficiency on regional differences in incidence rates of thyroid cancer. We also reviewed current evidence on content of nitrate in groundwater and thyroid cancer risk drawing attention to high levels of nitrates in open well water in several contaminated regions of Belarus, i.e. Gomel and Brest, related to the usage of nitrogen fertilizers. In this hypothesis generating study, based on ecological data and biological plausibility, we suggest that nitrate pollution may modify the radiation-related risk of thyroid cancer contributing to regional differences in rates of pediatric thyroid cancer in Belarus. Analytic epidemiological studies designed to evaluate joint effect of nitrate content in groundwater and radiation present a promising avenue of research and may provide useful insights into etiology of thyroid cancer.

  6. Major Factors Affecting Incidence of Childhood Thyroid Cancer in Belarus after the Chernobyl Accident: Do Nitrates in Drinking Water Play a Role?

    Directory of Open Access Journals (Sweden)

    Valentina M Drozd

    Full Text Available One of the major health consequences of the Chernobyl Nuclear Power Plant accident in 1986 was a dramatic increase in incidence of thyroid cancer among those who were aged less than 18 years at the time of the accident. This increase has been directly linked in several analytic epidemiological studies to iodine-131 (131I thyroid doses received from the accident. However, there remains limited understanding of factors that modify the 131I-related risk. Focusing on post-Chernobyl pediatric thyroid cancer in Belarus, we reviewed evidence of the effects of radiation, thyroid screening, and iodine deficiency on regional differences in incidence rates of thyroid cancer. We also reviewed current evidence on content of nitrate in groundwater and thyroid cancer risk drawing attention to high levels of nitrates in open well water in several contaminated regions of Belarus, i.e. Gomel and Brest, related to the usage of nitrogen fertilizers. In this hypothesis generating study, based on ecological data and biological plausibility, we suggest that nitrate pollution may modify the radiation-related risk of thyroid cancer contributing to regional differences in rates of pediatric thyroid cancer in Belarus. Analytic epidemiological studies designed to evaluate joint effect of nitrate content in groundwater and radiation present a promising avenue of research and may provide useful insights into etiology of thyroid cancer.

  7. A stress-associated NAC transcription factor (SlNAC35) from tomato plays a positive role in biotic and abiotic stresses.

    Science.gov (United States)

    Wang, Guodong; Zhang, Song; Ma, Xiaocui; Wang, Yong; Kong, Fanying; Meng, Qingwei

    2016-09-01

    The NAC transcription factor family participates in responses to various kinds of environmental stimuli in plants. Responses of NAC genes to abiotic stresses have been widely studied, but their functions in response to biotic stress are little reported in plants, especially in crops. In the present study, we examined the functions of a novel tomato (Solanum lycopersicum) NAC protein (SlNAC35) in abiotic and biotic stress resistance by using transgenic tobacco. Expression analysis found that SlNAC35 expression was induced by drought stress, salt stress, bacterial pathogen, and signaling molecules, suggesting its involvement in plant responses to biotic and abiotic stimuli. Moreover, transgenic lines exhibited a greater number of lateral roots and longer root length compared with Vec lines (empty vector lines) after drought and salt treatment. These results indicate that overexpression of SlNAC35 promoted root growth and development under drought and salt stresses. Higher expressions of NtARF1, NtARF2 and NtARF8 were observed under drought and salt stresses in transgenic lines, suggesting that overexpression of SlNAC35 promoted growth and development of roots in transgenic lines possibly by involving auxin signaling and by regulating NtARF expression. In addition, SlNAC35 overexpression improved resistance to bacterial pathogen in transgenic tobacco, and reactive oxygen species may be in the upstream of salicylic acid (SA) signaling in transgenic tobacco during defense response.

  8. Inflammatory cascades driven by tumor necrosis factor-alpha play a major role in the progression of acute liver failure and its neurological complications.

    Directory of Open Access Journals (Sweden)

    Anne Chastre

    Full Text Available BACKGROUND/AIMS: Acute liver failure (ALF due to ischemic or toxic liver injury is a clinical condition that results from massive loss of hepatocytes and may lead to hepatic encephalopathy (HE, a serious neuropsychiatric complication. Although increased expression of tumor necrosis factor-alpha (TNF-α in liver, plasma and brain has been observed, conflicting results exist concerning its roles in drug-induced liver injury and on the progression of HE. The present study aimed to investigate the therapeutic value of etanercept, a TNF-α neutralizing molecule, on the progression of liver injury and HE in mice with ALF resulting from azoxymethane (AOM hepatotoxicity. METHODS/PRINCIPAL FINDINGS: Mice were administered saline or etanercept (10 mg/kg; i.p. 30 minutes prior to, or up to 6 h after AOM. Etanercept-treated ALF mice were sacrificed in parallel with vehicle-treated comatose ALF mice and controls. AOM induced severe hepatic necrosis, leading to HE, and etanercept administered prior or up to 3 h after AOM significantly delayed the onset of coma stages of HE. Etanercept pretreatment attenuated AOM-induced liver injury, as assessed by histological examination, plasma ammonia and transaminase levels, and by hepatic glutathione content. Peripheral inflammation was significantly reduced by etanercept as shown by decreased plasma IL-6 (4.1-fold; p<0.001 and CD40L levels (3.7-fold; p<0.001 compared to saline-treated ALF mice. Etanercept also decreased IL-6 levels in brain (1.2-fold; p<0.05, attenuated microglial activation (assessed by OX-42 immunoreactivity, and increased brain glutathione concentrations. CONCLUSIONS: These results indicate that systemic sequestration of TNF-α attenuates both peripheral and cerebral inflammation leading to delayed progression of liver disease and HE in mice with ALF due to toxic liver injury. These results suggest that etanercept may provide a novel therapeutic approach for the management of ALF patients awaiting

  9. The Arabidopsis homologs of CCR4-associated factor 1 show mRNA deadenylation activity and play a role in plant defence responses

    Institute of Scientific and Technical Information of China (English)

    Wenxing Liang; Changbao Li; Fang Liu; Hongling Jiang; Shuyu Li; Jiaqiang Sun; Xiaoyan Wu; Chuanyou Li

    2009-01-01

    Messenger RNA (mRNA) turnover in eukaryotic cells begins with shortening of the poly (A) tail at the 3' end, a process called deadenylation. In yeast, the deadenylation reaction is predominantly mediated by CCR4 and CCR4-associated factor 1 (CAF1), two components of the well-characterised protein complex named CCR4-NOT. We re-port here that AtCAFla and AtCAFlb, putative Arabidopsis homologs of the yeast CAFI gene, partially complement the growth defect of the yeast cafl mutant in the presence of caffeine or at high temperatures. The expression of At-CAFla and AtCAFlb is induced by multiple stress-related hormones and stimuli. Both AtCAFIa and AtCAFIb show deadenylation activity in vitro and point mutations in the predicted active sites disrupt this activity. T-DNA inser-tion mutants disrupting the expression of AtCAFla and/or AtCAFlb are defective in deadenylation of stress-related mRNAs, indicating that the two AtCAFI proteins are involved in regulated mRNA deadenylation in vivo. Interest-ingly, the single and double mutants of AtCAFla and AtCAFlb show reduced expression of pathogenesis-related (PR) genes PR1 and PR2 and are more susceptible to Pseudomonas syringae pv tomato DC3000 (Pst DC3000) infection, whereas transgenic plants over-expressing AtCAFla show elevated expression of PR1 and PR2 and increased resis-tance to the same pathogen. Our results suggest roles of the AtCAF1 proteins in regulated mRNA deadenylation and defence responses to pathogen infections.

  10. Transforming growth factorplays divergent roles in modulating vascular remodeling, inflammation, and pulmonary fibrosis in a murine model of scleroderma.

    Science.gov (United States)

    Tsujino, Kazuyuki; Reed, Nilgun Isik; Atakilit, Amha; Ren, Xin; Sheppard, Dean

    2017-01-01

    The efficacy and feasibility of targeting transforming growth factor-β (TGFβ) in pulmonary fibrosis and lung vascular remodeling in systemic sclerosis (SSc) have not been well elucidated. In this study we analyzed how blocking TGFβ signaling affects pulmonary abnormalities in Fos-related antigen 2 (Fra-2) transgenic (Tg) mice, a murine model that manifests three important lung pathological features of SSc: fibrosis, inflammation, and vascular remodeling. To interrupt TGFβ signaling in the Fra-2 Tg mice, we used a pan-TGFβ-blocking antibody, 1D11, and Tg mice in which TGFβ receptor type 2 (Tgfbr2) is deleted from smooth muscle cells and myofibroblasts (α-SMA-Cre(ER);Tgfbr2(flox/flox)). Global inhibition of TGFβ by 1D11 did not ameliorate lung fibrosis histologically or biochemically, whereas it resulted in a significant increase in the number of immune cells infiltrating the lungs. In contrast, 1D11 treatment ameliorated the severity of pulmonary vascular remodeling in Fra-2 Tg mice. Similarly, genetic deletion of Tgfbr2 from smooth muscle cells resulted in improvement of pulmonary vascular remodeling in the Fra-2 Tg mice, as well as a decrease in the number of Ki67-positive vascular smooth muscle cells, suggesting that TGFβ signaling contributes to development of pulmonary vascular remodeling by promoting the proliferation of vascular smooth muscle cells. Deletion of Tgfbr2 from α-smooth muscle actin-expressing cells had no effect on fibrosis or inflammation in this model. These results suggest that efforts to target TGFβ in SSc will likely require more precision than simply global inhibition of TGFβ function. Copyright © 2017 the American Physiological Society.

  11. Late Modern Play Culture

    DEFF Research Database (Denmark)

    Skovbjerg-Karoff, Helle

    2008-01-01

    Children's play and culture have changed over the recent years, and it is possible to understand the changes as a result of a more general change in society. We witness a large degree of changes connected to demographical aspects of children's lives. First of all it is a fact that large groups....... They are changing play arenas in order to find the identity, which suits them. In order to play children must know and be conscious of the cultural heritage, which contains knowledge of the way to organize in the playing session, the aesthetics, the techniques of playing, and this is something that is handed down...... from one generation to the next. Because older children are no longer present as younger children grow up, the traditional "cultural leaders" are gone. They have taken with them much of the inspiration for play as well as important knowledge about how to organise a game. In that sense we can say...

  12. Play, dreams, and creativity.

    Science.gov (United States)

    Oremland, J D

    1998-01-01

    Viewed ontogenetically, creating, dreaming, and playing are a variant of object relatedness. It is suggested that in recapitulating the ontogenetic sequence, creating, dreaming, and playing each as a process initiates by de-differentiation to primal union, evolves into transitional functioning, and consummates in tertiary cognitive discourse. The products of the triad--the created object, the dream, and play--are viewed as synergistic psychodynamic composites of topical, personal, and arche-typical imperatives. Creating, dreaming, and playing are easily overburdened by events, becoming stereotypical and repetitious. Nowhere is this more clearly seen than in the play of chronically ill, hospitalized children. It is suggested that with development generally, playing is replaced by formalized games; only dreaming continues as the vestige of early creative abilities.

  13. The Plant Heat Stress Transcription Factors (HSFs): Structure, Regulation, and Function in Response to Abiotic Stresses.

    Science.gov (United States)

    Guo, Meng; Liu, Jin-Hong; Ma, Xiao; Luo, De-Xu; Gong, Zhen-Hui; Lu, Ming-Hui

    2016-01-01

    Abiotic stresses such as high temperature, salinity, and drought adversely affect the survival, growth, and reproduction of plants. Plants respond to such unfavorable changes through developmental, physiological, and biochemical ways, and these responses require expression of stress-responsive genes, which are regulated by a network of transcription factors (TFs), including heat stress transcription factors (HSFs). HSFs play a crucial role in plants response to several abiotic stresses by regulating the expression of stress-responsive genes, such as heat shock proteins (Hsps). In this review, we describe the conserved structure of plant HSFs, the identification of HSF gene families from various plant species, their expression profiling under abiotic stress conditions, regulation at different levels and function in abiotic stresses. Despite plant HSFs share highly conserved structure, their remarkable diversification across plants reflects their numerous functions as well as their integration into the complex stress signaling and response networks, which can be employed in crop improvement strategies via biotechnological intervention.

  14. The plant heat stress transcription factors (HSFs: structure, regulation and function in response to abiotic stresses

    Directory of Open Access Journals (Sweden)

    Meng eGuo

    2016-02-01

    Full Text Available Abiotic stresses such as high temperature, salinity and drought adversely affect the survival, growth and reproduction of plants. Plants respond to such unfavorable changes through developmental, physiological and biochemical ways, and these responses require expression of stress-responsive genes, which are regulated by a network of transcription factors (TFs, including heat stress transcription factors (HSFs. HSFs play a crucial role in plants response to several abiotic stresses by regulating the expression of stress-responsive genes, such as heat shock proteins (Hsps. In this review, we describe the conserved structure of plant HSFs, the identification of HSF gene families from various plant species, their expression profiling under abiotic stress conditions, regulation at different levels and function in abiotic stresses. Despite plant HSFs share highly conserved structure, their remarkable diversification across plants reflects their numerous functions as well as their integration into the complex stress signaling and response networks, which can be employed in crop improvement strategies via biotechnological intervention.

  15. Play and virtuality

    Directory of Open Access Journals (Sweden)

    Svein Sando

    2010-07-01

    Full Text Available The similarities between virtuality and play are obvious, beginning with, for instance, the ubiquitous character of both. This paper deals with how insights from research on play can be used to enlighten our understanding of the ethical dimensions of activities in cyberspace, and vice versa. In particular, a central claim that play is beyond vice and virtue is debated and contested.http://dx.doi.org/10.5324/eip.v4i2.1762

  16. Why do Dolphins Play?

    Directory of Open Access Journals (Sweden)

    Stan A. Kuczaj

    2014-05-01

    Full Text Available Play is an important aspect of dolphin life, perhaps even an essential one. Play provides opportunities for dolphin calves to practice and perfect locomotor skills, including those involved in foraging and mating strategies and behaviors. Play also allows dolphin calves to learn important social skills and acquire information about the characteristics and predispositions of members of their social group, particularly their peers. In addition to helping dolphin calves learn how to behave, play also provides valuable opportunities for them to learn how to think. The ability to create and control play contexts enables dolphins to create novel experiences for themselves and their playmates under relatively safe conditions. The behavioral variability and individual creativity that characterize dolphin play yield ample opportunities for individual cognitive development as well as social learning, and sometimes result in innovations that are reproduced by other members of the group. Although adults sometimes produce innovative play, calves are the primary source of such innovations. Calves are also more likely to imitate novel play behaviors than are adults, and so calves contribute significantly to both the creation and transmission of novel play behaviors within a group. Not unexpectedly, then, the complexity of dolphin play increases with the involvement of peers. As a result, the opportunity to observe and/or interact with other dolphin calves enhances the effects of play on the acquisition and maintenance of flexible problem solving skills, the emergence and strengthening of social and communicative competencies, and the establishment of social relationships. It seems that play may have evolved to help young dolphins learn to adapt to novel situations in both their physical and social worlds, the beneficial result being a set of abilities that increases the likelihood that an individual survives and reproduces.

  17. PlayBook三人行

    Institute of Scientific and Technical Information of China (English)

    黑莓时光

    2011-01-01

    PlayBook,来自非苹果的另外一个水果——黑莓,它不是iPad,却也是平板。PBer,这个并不完美的平板——PlayBook的用户,他们开朗、认真、执着。热爱PlayBook的三人,拥有各自的人生轨迹,却挂着同样的嘴角上扬。

  18. Phylogenetic Analyses Suggest that Factors Other Than the Capsid Protein Play a Role in the Epidemic Potential of GII.2 Norovirus

    Science.gov (United States)

    Tohma, Kentaro; Lepore, Cara J.; Ford-Siltz, Lauren A.

    2017-01-01

    variants. Over the last three seasons, minor genotypes have displaced the GII.4 viruses as the predominant strains. One of these genotypes, GII.2, reemerged as predominant during 2016 to 2017. Here we show that factors such as minor changes in the polymerase may have driven the reemergence of GII.2 during the last season. A better understanding of norovirus diversity is important for the development of effective treatments against noroviruses. PMID:28529975

  19. Characterization of three Arabidopsis AP2/EREBP family transcription factors involved in ABA sensitivity,freeze and salt tolerance

    Institute of Scientific and Technical Information of China (English)

    MEI WenQian; LEI Juan; Xu Yu; WEI Gang; ZHU YuXian

    2007-01-01

    AP2/EREBP transcription factors (TFs) play very important roles in plant development,hormonal regulation and stress response. Upon genome-wide cDNA cloning,phylogenetic and expression pattern analyses of this plant specific TF family,we found that three of the members including At1g71450,At1g50680 and At5g13910,were likely involved in responses to ABA,cold and salt. Complementary DNAs containing putative full-length ORFs of these three TFs were obtained and fused individually to the GAL4 DNA-binding domains. All the 3 genes functioned effectively as trans-activators using yeast one-hybrid assays. RT-PCR experiments showed that the At1g71450 gene was induced by ABA and low temperature; the At1g50680 gene was responsive to quite a few stress conditions,but especially to freezing temperature; and the At5g13910 gene was induced by high salt treatment,drought and ethylene. By searching the ABRC T-DNA insertion mutant stocks,we obtained knockout lines for these TFs. Homozygous ko1 (At1g71450) plants showed a hypersensitive response to ABA during seed germination and also in stomata movement. Homozygous ko2 (At1g50680) plants showed a significant reduction in plant freezing tolerance compared to the wild type after chilling treatment. Homozygous ko3 (At5g13910) were less tolerant to high salinity than wild type plants. Our data suggest that At1g71450 is a negative regulator in ABA signaling,while At1g50680 and At5g13910 are positive regulators in cold and salt stress responses,respectively.

  20. Play your part

    CERN Document Server

    Ramsey, Gaynor

    1978-01-01

    Play your part is a collection of then situations in which students have to take on the roles of particular people and express their opinions, feelings or arguments about the situation. Play your part is intended for use with advanced students of English.

  1. Role Playing and Skits

    Science.gov (United States)

    Letwin, Robert, Ed.

    1975-01-01

    Explores non-scripted role playing, dialogue role playing, sociodrama, and skits as variations of simulation techniques. Provides step-by-step guidelines for conducting such sessions. Successful Meetings, Bill Communications, Inc., 1422 Chestnut Street, Philadelphia, Pa. 19102. Subscription Rates: yearly (US, Canada, Mexico) $14.00; elsewhere,…

  2. The Play's the Thing

    Science.gov (United States)

    Bateman, Barbara

    2005-01-01

    The modern special education theater in the United States has hosted many plays, none with a larger or more diverse cast than the learning disabilities (LD) play. During the prologue, the children with LD were waiting in the wings, not yet identified as LD but there, nonetheless. With the advent of compulsory education in this country, awareness…

  3. Playfulness and Openness

    DEFF Research Database (Denmark)

    Marchetti, Emanuela; Petersson, Eva

    2011-01-01

    What does it mean to design a playful learning tool? What is needed for a learning tool to be perceived by potential users as playful? These questions emerged reflecting on a Participatory Design process aimed at enhancing museum-learning practice from the perspective of primary school children. ...

  4. Play as Experience

    Science.gov (United States)

    Henricks, Thomas S.

    2015-01-01

    The author investigates what he believes one of the more important aspects of play--the experience it generates in its participants. He considers the quality of this experience in relation to five ways of viewing play--as action, interaction, activity, disposition, and within a context. He treats broadly the different forms of affect, including…

  5. Art of Play

    DEFF Research Database (Denmark)

    Froes, Isabel Cristina G.; Walker, Kevin

    2011-01-01

    Play is a key element in cultural development, according to the Dutch historian Johan Huizinga. Nowadays many of us interact with other people in online games and social networks, through multiple digital devices. But harnessing playful activities for museum learning is mostly undeveloped. In thi...

  6. Family Play Therapy.

    Science.gov (United States)

    Ariel, Shlomo

    This paper examines a case study of family play therapy in Israel. The unique contributions of play therapy are evaluated including the therapy's accessibility to young children, its richness and flexibility, its exposure of covert patterns, its wealth of therapeutic means, and its therapeutic economy. The systematization of the therapy attempts…

  7. Return to Play

    Science.gov (United States)

    Mangan, Marianne

    2013-01-01

    Call it physical activity, call it games, or call it play. Whatever its name, it's a place we all need to return to. In the physical education, recreation, and dance professions, we need to redesign programs to address the need for and want of play that is inherent in all of us.

  8. Playful Collaboration (Or Not)

    DEFF Research Database (Denmark)

    Bogers, Marcel; Sproedt, Henrik

    2012-01-01

    This article explores how playing games can be used to teach intangible social interaction across boundaries, in particular within open collaborative innovation. We present an exploratory case study of how students learned from playing a board game in a graduate course of the international...... imply several opportunities and challenges within education and beyond....

  9. Art of Play

    DEFF Research Database (Denmark)

    Froes, Isabel Cristina G.; Walker, Kevin

    2011-01-01

    Play is a key element in cultural development, according to the Dutch historian Johan Huizinga. Nowadays many of us interact with other people in online games and social networks, through multiple digital devices. But harnessing playful activities for museum learning is mostly undeveloped. In thi...

  10. Play framework cookbook

    CERN Document Server

    Reelsen, Alexander

    2015-01-01

    This book is aimed at advanced developers who are looking to harness the power of Play 2.x. This book will also be useful for professionals looking to dive deeper into web development. Play 2 .x is an excellent framework to accelerate your learning of advanced topics.

  11. Let's Just Play

    Science.gov (United States)

    Schmidt, Janet

    2003-01-01

    Children have a right to play. The idea is so simple it seems self-evident. But a stroll through any toy superstore, or any half-hour of so-called "children's" programming on commercial TV, makes it clear that violence, not play, dominates what's being sold. In this article, the author discusses how teachers and parents share the responsibility in…

  12. Identification of Post-Transcriptional Modulators of Breast Cancer Transcription Factor Activity Using MINDy

    Science.gov (United States)

    Campbell, Thomas M.; Castro, Mauro A. A.; Ponder, Bruce A. J.

    2016-01-01

    We have recently identified transcription factors (TFs) that are key drivers of breast cancer risk. To better understand the pathways or sub-networks in which these TFs mediate their function we sought to identify upstream modulators of their activity. We applied the MINDy (Modulator Inference by Network Dynamics) algorithm to four TFs (ESR1, FOXA1, GATA3 and SPDEF) that are key drivers of estrogen receptor-positive (ER+) breast cancer risk, as well as cancer progression. Our computational analysis identified over 500 potential modulators. We assayed 189 of these and identified 55 genes with functional characteristics that were consistent with a role as TF modulators. In the future, the identified modulators may be tested as potential therapeutic targets, able to alter the activity of TFs that are critical in the development of breast cancer. PMID:27997592

  13. Systematic repression of transcription factors reveals limited patterns of gene expression changes in ES cells

    Science.gov (United States)

    Nishiyama, Akira; Sharov, Alexei A.; Piao, Yulan; Amano, Misa; Amano, Tomokazu; Hoang, Hien G.; Binder, Bernard Y.; Tapnio, Richard; Bassey, Uwem; Malinou, Justin N.; Correa-Cerro, Lina S.; Yu, Hong; Xin, Li; Meyers, Emily; Zalzman, Michal; Nakatake, Yuhki; Stagg, Carole; Sharova, Lioudmila; Qian, Yong; Dudekula, Dawood; Sheer, Sarah; Cadet, Jean S.; Hirata, Tetsuya; Yang, Hsih-Te; Goldberg, Ilya; Evans, Michele K.; Longo, Dan L.; Schlessinger, David; Ko, Minoru S. H.

    2013-01-01

    Networks of transcription factors (TFs) are thought to determine and maintain the identity of cells. Here we systematically repressed each of 100 TFs with shRNA and carried out global gene expression profiling in mouse embryonic stem (ES) cells. Unexpectedly, only the repression of a handful of TFs significantly affected transcriptomes, which changed in two directions/trajectories: one trajectory by the repression of either Pou5f1 or Sox2; the other trajectory by the repression of either Esrrb, Sall4, Nanog, or Tcfap4. The data suggest that the trajectories of gene expression change are already preconfigured by the gene regulatory network and roughly correspond to extraembryonic and embryonic fates of cell differentiation, respectively. These data also indicate the robustness of the pluripotency gene network, as the transient repression of most TFs did not alter the transcriptomes. PMID:23462645

  14. Protein intrinsic disorder in Arabidopsis NAC transcription factors: transcriptional activation by ANAC013 and ANAC046 and their interactions with RCD1.

    Science.gov (United States)

    O'Shea, Charlotte; Kryger, Mikael; Stender, Emil G P; Kragelund, Birthe B; Willemoës, Martin; Skriver, Karen

    2015-01-15

    Protein ID (intrinsic disorder) plays a significant, yet relatively unexplored role in transcription factors (TFs). In the present paper, analysis of the transcription regulatory domains (TRDs) of six phylogenetically representative, plant-specific NAC [no apical meristem, ATAF (Arabidopsis transcription activation factor), cup-shaped cotyledon] TFs shows that the domains are present in similar average pre-molten or molten globule-like states, but have different patterns of order/disorder and MoRFs (molecular recognition features). ANAC046 (Arabidopsis NAC 046) was selected for further studies because of its simple MoRF pattern and its ability to interact with RCD1 (radical-induced cell death 1). Experiments in yeast and thermodynamic characterization suggest that its single MoRF region is sufficient for both transcriptional activation and interaction with RCD1. The remainder of the large regulatory domain is unlikely to contribute to the interaction, since the domain and truncations thereof have similar affinities for RCD1, which are also similar for ANAC013-RCD1 interactions. However, different enthalpic and entropic contributions to binding were revealed for ANAC046 and ANAC013, suggestive of differences in binding mechanisms. Although substitution of both hydrophobic and acidic residues of the ANAC046 MoRF region abolished binding, substitution of other residues, even with α-helix-breaking proline, was less disruptive. Together, the biophysical analyses suggest that RCD1-ANAC046 complex formation does not involve folding-upon-binding, but rather fuzziness or an unknown structure in ANAC046. We suggest that the ANAC046 regulatory domain functions as an entropic chain with a terminal hot spot interacting with RCD1. RCD1, a cellular hub, may be able to interact with many different TFs by exploiting their ID-based flexibility, as demonstrated for its interactions with ANAC046 and ANAC013.

  15. Play vs. Procedures

    DEFF Research Database (Denmark)

    Hammar, Emil

    Through the theories of play by Gadamer (2004) and Henricks (2006), I will show how the relationship between play and game can be understood as dialectic and disruptive, thus challenging understandings of how the procedures of games determine player activity and vice versa. As such, I posit some...... analytical consequences for understandings of digital games as procedurally fixed (Boghost, 2006; Flannagan, 2009; Bathwaite & Sharp, 2010). That is, if digital games are argued to be procedurally fixed and if play is an appropriative and dialectic activity, then it could be argued that the latter affects...

  16. Factors at Play in Tertiary Curriculum Gamification

    Science.gov (United States)

    de Byl, Penny

    2013-01-01

    The compulsion to include games and game related mechanism in education is great among educators who want to engage and motivate today's students and the latest buzzword in this domain is gamification. However, without a thorough understanding of what a gamified curriculum looks like, how it can best be applied and why it might engross students,…

  17. Factors at Play in Tertiary Curriculum Gamification

    Science.gov (United States)

    de Byl, Penny

    2013-01-01

    The compulsion to include games and game related mechanism in education is great among educators who want to engage and motivate today's students and the latest buzzword in this domain is gamification. However, without a thorough understanding of what a gamified curriculum looks like, how it can best be applied and why it might engross students,…

  18. 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 p

  19. Play and Power

    DEFF Research Database (Denmark)

    The power of play, so central to psychoanalytic theory and practice, is conjoined to the social psychological or socio-politically coloured concept of power, giving rise to many fruitful discussions of how these concepts manifest themselves in clinical work with children, groups and adults....... The inspiration for this book was the 3-section EFPP conference in Copenhagen in May 2007 with the main theme "Play and Power". At the conference and in the book, this theme is presented both inside and outside the therapeutic space. It is amply illustrated in clinical cases from individual psychotherapies....... Play and power are also explored in the broader context of the community, however. In relation to society at large, psychoanalytic psychotherapy has important contributions to offer society, and we need playful creativity and power to bring forward our knowledge about it....

  20. Systematic Discovery of Archaeal Transcription Factor Functions in Regulatory Networks through Quantitative Phenotyping Analysis.

    Science.gov (United States)

    Darnell, Cynthia L; Tonner, Peter D; Gulli, Jordan G; Schmidler, Scott C; Schmid, Amy K

    2017-01-01

    Gene regulatory networks (GRNs) are critical for dynamic transcriptional responses to environmental stress. However, the mechanisms by which GRN regulation adjusts physiology to enable stress survival remain unclear. Here we investigate the functions of transcription factors (TFs) within the global GRN of the stress-tolerant archaeal microorganism Halobacterium salinarum. We measured growth phenotypes of a panel of TF deletion mutants in high temporal resolution under heat shock, oxidative stress, and low-salinity conditions. To quantitate the noncanonical functional forms of the growth trajectories observed for these mutants, we developed a novel modeling framework based on Gaussian process regression and functional analysis of variance (FANOVA). We employ unique statistical tests to determine the significance of differential growth relative to the growth of the control strain. This analysis recapitulated known TF functions, revealed novel functions, and identified surprising secondary functions for characterized TFs. Strikingly, we observed that the majority of the TFs studied were required for growth under multiple stress conditions, pinpointing regulatory connections between the conditions tested. Correlations between quantitative phenotype trajectories of mutants are predictive of TF-TF connections within the GRN. These phenotypes are strongly concordant with predictions from statistical GRN models inferred from gene expression data alone. With genome-wide and targeted data sets, we provide detailed functional validation of novel TFs required for extreme oxidative stress and heat shock survival. Together, results presented in this study suggest that many TFs function under multiple conditions, thereby revealing high interconnectivity within the GRN and identifying the specific TFs required for communication between networks responding to disparate stressors. IMPORTANCE To ensure survival in the face of stress, microorganisms employ inducible damage repair

  1. Network based transcription factor analysis of regenerating axolotl limbs

    Directory of Open Access Journals (Sweden)

    Cameron Jo Ann

    2011-03-01

    Full Text Available Abstract Background Studies on amphibian limb regeneration began in the early 1700's but we still do not completely understand the cellular and molecular events of this unique process. Understanding a complex biological process such as limb regeneration is more complicated than the knowledge of the individual genes or proteins involved. Here we followed a systems biology approach in an effort to construct the networks and pathways of protein interactions involved in formation of the accumulation blastema in regenerating axolotl limbs. Results We used the human orthologs of proteins previously identified by our research team as bait to identify the transcription factor (TF pathways and networks that regulate blastema formation in amputated axolotl limbs. The five most connected factors, c-Myc, SP1, HNF4A, ESR1 and p53 regulate ~50% of the proteins in our data. Among these, c-Myc and SP1 regulate 36.2% of the proteins. c-Myc was the most highly connected TF (71 targets. Network analysis showed that TGF-β1 and fibronectin (FN lead to the activation of these TFs. We found that other TFs known to be involved in epigenetic reprogramming, such as Klf4, Oct4, and Lin28 are also connected to c-Myc and SP1. Conclusions Our study provides a systems biology approach to how different molecular entities inter-connect with each other during the formation of an accumulation blastema in regenerating axolotl limbs. This approach provides an in silico methodology to identify proteins that are not detected by experimental methods such as proteomics but are potentially important to blastema formation. We found that the TFs, c-Myc and SP1 and their target genes could potentially play a central role in limb regeneration. Systems biology has the potential to map out numerous other pathways that are crucial to blastema formation in regeneration-competent limbs, to compare these to the pathways that characterize regeneration-deficient limbs and finally, to identify stem

  2. Evidence that levels of the dimeric cellular transcription factor CP2 play little role in the activation of the HIV-1 long terminal repeat in vivo or following superinfection with herpes simplex virus type 1.

    Science.gov (United States)

    Zhong, F; Swendeman, S L; Popik, W; Pitha, P M; Sheffery, M

    1994-08-19

    The dimeric transcription factor CP2 binds a sequence element found near the transcription start site of the human immunodeficiency virus (HIV-1) long terminal repeat. Several groups have suggested that cellular factors binding this element might play a role in modulating HIV-1 promoter activity in vivo. For example, induction of latent HIV-1 gene expression in response to superinfection by herpes simplex virus type 1 (HSV-1) or cytomegalovirus is thought to be mediated, in part, by factors binding the CP2 site. In this report we began to examine directly the relationship between CP2 and expression of the HIV-1 promoter. First, we tested what effect HSV-1 infection of T cells had on the cellular levels of CP2. The results showed that HSV-1 infection led to a significant reduction in the level of CP2 DNA binding activity and protein within 20 h. Next, we tested the effect of overexpressing either the wild-type factor or a dominant negative variant of CP2 on HIV-1 promoter activity in vivo. The results showed that CP2 had little effect or slightly repressed HIV-1 promoter activity in vivo. In addition, these expression constructs had little effect on the induction of HIV-1 promoter activity elicited by HSV-1 infection.

  3. Data in support of FSH induction of IRS-2 in human granulosa cells: Mapping the transcription factor binding sites in human IRS-2 promoter

    Directory of Open Access Journals (Sweden)

    Surleen Kaur

    2016-03-01

    Full Text Available Insulin receptor substrate-2 (IRS-2 plays critical role in the regulation of various metabolic processes by insulin and IGF-1. The defects in its expression and/or function are linked to diseases like polycystic ovary syndrome (PCOS, insulin resistance and cancer. To predict the transcription factors (TFs responsible for the regulation of human IRS-2 gene expression, the transcription factor binding sites (TFBS and the corresponding TFs were investigated by analysis of IRS-2 promoter sequence using MatInspector Genomatix software (Cartharius et al., 2005 [1]. The ibid data is part of author׳s publication (Anjali et al., 2015 [2] that explains Follicle stimulating hormone (FSH mediated IRS-2 promoter activation in human granulosa cells and its importance in the pathophysiology of PCOS. Further analysis was carried out for binary interactions of TF regulatory genes in IRS-2 network using Cytoscape software tool and R-code. In this manuscript, we describe the methodology used for the identification of TFBSs in human IRS-2 promoter region and provide details on experimental procedures, analysis method, validation of data and also the raw files. The purpose of this article is to provide the data on all TFBSs in the promoter region of human IRS-2 gene as it has the potential for prediction of the regulation of IRS-2 gene in normal or diseased cells from patients with metabolic disorders and cancer.

  4. Identifying Cell Type-Specific Transcription Factors by Integrating ChIP-seq and eQTL Data-Application to Monocyte Gene Regulation.

    Science.gov (United States)

    Choudhury, Mudra; Ramsey, Stephen A

    2016-01-01

    We describe a novel computational approach to identify transcription factors (TFs) that are candidate regulators in a human cell type of interest. Our approach involves integrating cell type-specific expression quantitative trait locus (eQTL) data and TF data from chromatin immunoprecipitation-to-tag-sequencing (ChIP-seq) experiments in cell lines. To test the method, we used eQTL data from human monocytes in order to screen for TFs. Using a list of known monocyte-regulating TFs, we tested the hypothesis that the binding sites of cell type-specific TF regulators would be concentrated in the vicinity of monocyte eQTLs. For each of 397 ChIP-seq data sets, we obtained an enrichment ratio for the number of ChIP-seq peaks that are located within monocyte eQTLs. We ranked ChIP-seq data sets according to their statistical significances for eQTL overlap, and from this ranking, we observed that monocyte-regulating TFs are more highly ranked than would be expected by chance. We identified 27 TFs that had significant monocyte enrichment scores and mapped them into a protein interaction network. Our analysis uncovered two novel candidate monocyte-regulating TFs, BCLAF1 and SIN3A. Our approach is an efficient method to identify candidate TFs that can be used for any cell/tissue type for which eQTL data are available.

  5. MicroRNA and transcription factor mediated regulatory network analysis reveals critical regulators and regulatory modules in myocardial infarction.

    Directory of Open Access Journals (Sweden)

    Guangde Zhang

    Full Text Available Myocardial infarction (MI is a severe coronary artery disease and a leading cause of mortality and morbidity worldwide. However, the molecular mechanisms of MI have yet to be fully elucidated. In this study, we compiled MI-related genes, MI-related microRNAs (miRNAs and known human transcription factors (TFs, and we then identified 1,232 feed-forward loops (FFLs among these miRNAs, TFs and their co-regulated target genes through integrating target prediction. By merging these FFLs, the first miRNA and TF mediated regulatory network for MI was constructed, from which four regulators (SP1, ESR1, miR-21-5p and miR-155-5p and three regulatory modules that might play crucial roles in MI were then identified. Furthermore, based on the miRNA and TF mediated regulatory network and literature survey, we proposed a pathway model for miR-21-5p, the miR-29 family and SP1 to demonstrate their potential co-regulatory mechanisms in cardiac fibrosis, apoptosis and angiogenesis. The majority of the regulatory relations in the model were confirmed by previous studies, which demonstrated the reliability and validity of this miRNA and TF mediated regulatory network. Our study will aid in deciphering the complex regulatory mechanisms involved in MI and provide putative therapeutic targets for MI.

  6. Can play be defined?

    DEFF Research Database (Denmark)

    Eichberg, Henning

    2015-01-01

    Can play be defined? There is reason to raise critical questions about the established academic demand that at phenomenon – also in humanist studies – should first of all be defined, i.e. de-lineated and by neat lines limited to a “little box” that can be handled. The following chapter develops t....... Human beings can very well understand play – or whatever phenomenon in human life – without defining it........ The academic imperative of definition seems to be linked to the positivistic attempts – and produces sometimes monstrous definitions. Have they any philosophical value for our knowledge of what play is? Definition is not a universal instrument of knowledge-building, but a culturally specific construction...

  7. Playing and gaming

    DEFF Research Database (Denmark)

    Karoff, Helle Skovbjerg; Ejsing-Duun, Stine; Hanghøj, Thorkild

    2013-01-01

    The paper develops an approach of playing and gaming activities through the perspective of both activities as mood activities . The point of departure is that a game - is a tool with which we, through our practices, achieve different moods. This based on an empirical study of children's everyday...... lives, where the differences emerge through actual practices, i.e. through the creation of meaning in the specific situations. The overall argument is that it is not that important whether it is a playing or a gaming activity - it is however crucial to be aware of how moods occur and what their optimal...... dimensions: practices and moods. Practice is the concept of all the doing in the activities. Moods are the particular concept of sense and feeling of being, which is what we are drawn to when we are playing or gaming....

  8. Playing and gaming

    DEFF Research Database (Denmark)

    Karoff, Helle Skovbjerg; Ejsing-Duun, Stine; Hanghøj, Thorkild

    2013-01-01

    The paper develops an approach of playing and gaming activities through the perspective of both activities as mood activities . The point of departure is that a game - is a tool with which we, through our practices, achieve different moods. This based on an empirical study of children's everyday...... lives, where the differences emerge through actual practices, i.e. through the creation of meaning in the specific situations. The overall argument is that it is not that important whether it is a playing or a gaming activity - it is however crucial to be aware of how moods occur and what their optimal...... dimensions: practices and moods. Practice is the concept of all the doing in the activities. Moods are the particular concept of sense and feeling of being, which is what we are drawn to when we are playing or gaming....

  9. General game playing

    CERN Document Server

    Genesereth, Michael

    2014-01-01

    General game players are computer systems able to play strategy games based solely on formal game descriptions supplied at ""runtime"" (n other words, they don't know the rules until the game starts). Unlike specialized game players, such as Deep Blue, general game players cannot rely on algorithms designed in advance for specific games; they must discover such algorithms themselves. General game playing expertise depends on intelligence on the part of the game player and not just intelligence of the programmer of the game player.GGP is an interesting application in its own right. It is intell

  10. Playful Collaboration (or Not)

    DEFF Research Database (Denmark)

    Bogers, Marcel; Sproedt, Henrik

    2011-01-01

    also be conducive to deep learning. As such, a game can engage different dimensions of learning and embed elements of active, collaborative, cooperative and problem-based learning. Building on this logic, we present an exploratory case study of the use of a particular board game in a class of a course......This paper explores how games and play, which are deeply rooted in human beings as a way to learn and interact, can be used to teach certain concepts and practices related to open collaborative innovation. We discuss how playing games can be a source of creativity, imagination and fun, while it can...

  11. Five recent play dates

    DEFF Research Database (Denmark)

    Abildgaard, Mette Simonsen; Birkbak, Andreas; Jensen, Torben Elgaard

    2017-01-01

    An advantage of the playground metaphor is that it comes with the activity of going out on ‘play dates’ and developing friendships. In such playful relationships, there is always something at stake, but the interaction is also fun and inherently exploratory. In the following, we take a tour of five...... recent collaborative projects that the TANTlab has participated in. The projects differ widely and testify to different experiences with collaboration and intervention – from a data print on obesity with other researchers to a Facebook-driven intervention in Aalborg municipality’s primary school reform...

  12. Expression analysis of transcription factors from the interaction between cacao and Moniliophthora perniciosa (Tricholomataceae).

    Science.gov (United States)

    Lopes, M A; Hora, B T; Dias, C V; Santos, G C; Gramacho, K P; Cascardo, J C M; Gesteira, A S; Micheli, F

    2010-07-06

    Cacao (Theobroma cacao) is one of the most important tropical crops; however, production is threatened by numerous pathogens, including the hemibiotrophic fungus Moniliophthora perniciosa, which causes witches' broom disease. To understand the mechanisms that lead to the development of this disease in cacao, we focused our attention on cacao transcription factors (TFs), which act as master regulators of cellular processes and are important for the fine-tuning of plant defense responses. We developed a macroarray with 88 TF cDNA from previously obtained cacao-M. perniciosa interaction libraries. Seventy-two TFs were found differentially expressed between the susceptible (Catongo) and resistant (TSH1188) genotypes and/or during the disease time course--from 24 h to 30 days after infection. Most of the differentially expressed TFs belonged to the bZIP, MYB and WRKY families and presented opposite expression patterns in susceptible and resistant cacao-M. perniciosa interactions (i.e., up-regulated in Catongo and down-regulated in TSH1188). The results of the macroarray were confirmed for bZIP and WRKY TFs by real-time PCR. These differentially expressed TFs are good candidates for subsequent functional analysis as well as for plant engineering. Some of these TFs could also be localized on the cacao reference map related to witches' broom resistance, facilitating the breeding and selection of resistant cacao trees.

  13. Generation and gene expression profiling of 48 transcription-factor-inducible mouse embryonic stem cell lines

    Science.gov (United States)

    Yamamizu, Kohei; Sharov, Alexei A.; Piao, Yulan; Amano, Misa; Yu, Hong; Nishiyama, Akira; Dudekula, Dawood B.; Schlessinger, David; Ko, Minoru S. H.

    2016-01-01

    Mouse embryonic stem cells (ESCs) can differentiate into a wide range – and possibly all cell types in vitro, and thus provide an ideal platform to study systematically the action of transcription factors (TFs) in cell differentiation. Previously, we have generated and analyzed 137 TF-inducible mouse ESC lines. As an extension of this “NIA Mouse ESC Bank,” we generated and characterized 48 additional mouse ESC lines, in which single TFs in each line could be induced in a doxycycline-controllable manner. Together, with the previous ESC lines, the bank now comprises 185 TF-manipulable ESC lines (>10% of all mouse TFs). Global gene expression (transcriptome) profiling revealed that the induction of individual TFs in mouse ESCs for 48 hours shifts their transcriptomes toward specific differentiation fates (e.g., neural lineages by Myt1 Isl1, and St18; mesodermal lineages by Pitx1, Pitx2, Barhl2, and Lmx1a; white blood cells by Myb, Etv2, and Tbx6, and ovary by Pitx1, Pitx2, and Dmrtc2). These data also provide and lists of inferred target genes of each TF and possible functions of these TFs. The results demonstrate the utility of mouse ESC lines and their transcriptome data for understanding the mechanism of cell differentiation and the function of TFs. PMID:27150017

  14. Systematic dissection of genomic features determining transcription factor binding and enhancer function

    Science.gov (United States)

    Grossman, Sharon R.; Zhang, Xiaolan; Wang, Li; Engreitz, Jesse; Melnikov, Alexandre; Rogov, Peter; Tewhey, Ryan; Isakova, Alina; Deplancke, Bart; Bernstein, Bradley E.; Mikkelsen, Tarjei S.; Lander, Eric S.

    2017-01-01

    Enhancers regulate gene expression through the binding of sequence-specific transcription factors (TFs) to cognate motifs. Various features influence TF binding and enhancer function—including the chromatin state of the genomic locus, the affinities of the binding site, the activity of the bound TFs, and interactions among TFs. However, the precise nature and relative contributions of these features remain unclear. Here, we used massively parallel reporter assays (MPRAs) involving 32,115 natural and synthetic enhancers, together with high-throughput in vivo binding assays, to systematically dissect the contribution of each of these features to the binding and activity of genomic regulatory elements that contain motifs for PPARγ, a TF that serves as a key regulator of adipogenesis. We show that distinct sets of features govern PPARγ binding vs. enhancer activity. PPARγ binding is largely governed by the affinity of the specific motif site and higher-order features of the larger genomic locus, such as chromatin accessibility. In contrast, the enhancer activity of PPARγ binding sites depends on varying contributions from dozens of TFs in the immediate vicinity, including interactions between combinations of these TFs. Different pairs of motifs follow different interaction rules, including subadditive, additive, and superadditive interactions among specific classes of TFs, with both spatially constrained and flexible grammars. Our results provide a paradigm for the systematic characterization of the genomic features underlying regulatory elements, applicable to the design of synthetic regulatory elements or the interpretation of human genetic variation. PMID:28137873

  15. The Activity of Play

    DEFF Research Database (Denmark)

    Pichlmair, Martin

    2016-01-01

    This paper presents Activity Theory as a framework for understanding the action of playing games with the intention of building a foundation for the creation of new game design tools and methods. Activity Theory, an epistemological framework rooted in Soviet psychology of the first half of the 20...

  16. Playing the Role

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    The G20 London summit made history. While applauding the summit’s productive communique, Ni Xiaoling, senior financial observer with Xinhua News Agency, warns of the gap between the greater responsibilities the International Monetary Fund shoulders and its limited capabilities to play the role of coordinator in economic globalization.

  17. Abstraction through Game Play

    Science.gov (United States)

    Avraamidou, Antri; Monaghan, John; Walker, Aisha

    2012-01-01

    This paper examines the computer game play of an 11-year-old boy. In the course of building a virtual house he developed and used, without assistance, an artefact and an accompanying strategy to ensure that his house was symmetric. We argue that the creation and use of this artefact-strategy is a mathematical abstraction. The discussion…

  18. Mobilities at Play

    DEFF Research Database (Denmark)

    Ungruhe, Christian

    2017-01-01

    -level perspective there is still an analytical gap between the ambitions and experiences of migrating players and economic power relations at play on the one hand and the socio-cultural embedding of the transnational connections in football migration on the other. In order to understand why and how football...

  19. Play's Importance in School

    Science.gov (United States)

    Sandberg, Anette; Heden, Rebecca

    2011-01-01

    The purpose of this study is to contribute knowledge on and gain an understanding of elementary school teachers' perspectives on the function of play in children's learning processes. The study is qualitative with a hermeneutical approach and has George Herbert Mead as a theoretical frame of reference. Interviews have been carried out with seven…

  20. Play framework essentials

    CERN Document Server

    Richard-Foy, Julien

    2014-01-01

    This book targets Java and Scala developers who already have some experience in web development and who want to master Play framework quickly and efficiently. This book assumes you have a good level of knowledge and understanding of efficient Java and Scala code.

  1. A Significant Play

    Institute of Scientific and Technical Information of China (English)

    梁海光; 陈明

    2002-01-01

    Yesterday evening, I went to see a play. It was really significant. It was about Zheng Xiaoyue, a very clever and diligent middle school student. Unfortunately, her mother died when she and her brother were very young. Her father was out of work and,

  2. Play or science?

    DEFF Research Database (Denmark)

    Lieberoth, Andreas; Pedersen, Mads Kock; Sherson, Jacob

    2015-01-01

    Crowdscience games may hold unique potentials as learning opportunities compared to games made for fun or education. They are part of an actual science problem solving process: By playing, players help scientists, and thereby interact with real continuous research processes. This mixes the two...... worlds of play and science in new ways. During usability testing we discovered that users of the crowdscience game Quantum Dreams tended to answer questions in game terms, even when directed explicitly to give science explanations. We then examined these competing frames of understanding though a mixed...... correlational and grounded theory analysis. This essay presents the core ideas of crowdscience games as learning opportunities, and reports how a group of players used “game”, “science” and “conceptual” frames to interpret their experience. Our results suggest that oscillating between the frames instead...

  3. Understanding Games as Played

    DEFF Research Database (Denmark)

    Leino, Olli Tapio

    2009-01-01

    Researchers interested in player’s experience would assumedly, across disciplines, agree that the goal behind enquiries into player’s experience is to understand the how games’ features end up affecting the player’s experience. Much of the contemporary interdisciplinary research into player......’s experience leans toward the empirical-scientific, in the forms (neuro)psychology, sociology and cognitive science, to name a few. In such approaches, for example demonstrating correlation between physiological symptoms and an in-game event may amount to ‘understanding’. However, the experience of computer...... game play is a viable topic also for computer game studies within the general tradition of humanities. In such context, the idea of ‘understanding an experience’ invites an approach focusing on the experienced significance of events and objects within computer game play. This focus, in turn, suggests...

  4. Ravens at Play

    Directory of Open Access Journals (Sweden)

    Deborah Bird Rose

    2011-09-01

    Full Text Available ‘We were driving through Death Valley, an American-Australian and two Aussies, taking the scenic route from Las Vegas to Santa Cruz.’ This multi-voiced account of multispecies encounters along a highway takes up the challenge of playful and humorous writing that is as well deeply serious and theoretically provocative. Our travels brought us into what Donna Haraway calls the contact zone: a region of recognition and response. The contact zone is a place of significant questions: ‘Who are you, and so who are we? Here we are, and so what are we to become?’ Events were everything in this ecology of play, in which the movements of all the actors involved the material field in its entirety. We were brought into dances of approach and withdrawal, dances emerging directly, to paraphrase Brian Massumi, from the dynamic relation between a myriad of charged particles.

  5. Public Computation & Boundary Play

    CERN Document Server

    Sengupta, Pratim

    2016-01-01

    In this paper, we introduce 'public computation' as a genre of learning environments that can be used to radically broaden public participation in authentic, computation-enabled STEM disciplinary practices. Our paradigmatic approach utilizes open source software designed for professional scientists, engineers and digital artists, and situates them in an undiluted form, alongside live and archived expert support, in a public space. We present a case study of DigiPlay, a prototypical public computation space we designed at the University of Calgary, where users can interact directly with scientific simulations as well as the underlying open source code using an array of massive multi- touch screens. We argue that in such a space, public interactions with the code can be thought of as boundary work and play, through which public participation becomes legitimate scientific act, as the public engages in scientific creation through truly open-ended explorations with the code.

  6. Play. Learn. Innovate

    DEFF Research Database (Denmark)

    Sproedt, Henrik

    evidence that play and games could be interesting perspectives to take in order to understand complex social interaction. I come to the conclusion that – in innovation settings – the social dynamics that affect the process are essentially about transformation of knowledge across boundaries. I propose......„Play. Learn. Innovate. – Grasping the Social Dynamics of Participatory Innovation“ the title of this thesis describes how the complex interplay of unexpected events led to some burning questions and eventually to this thesis, which one could call an innovation*1*. During several years...... study were to better understand the theoretical foundations and practical implications of complex social interaction in organizational innovation settings. As I did not find any existing models or hypotheses that I was interested in testing I set out to discover how I could grasp complex social...

  7. "Playing" with our users

    DEFF Research Database (Denmark)

    Brooks, Anthony Lewis

    2014-01-01

    was from the amazing Dr Anthony Lewis Brooks (aka Tony) who has conceived the concepts GameAbilitation, ArtAbilitation, and Ludic Engagement Designs for All. While presenting some of his work on GameAbilitation and ArtAbilitation he brought up the subject of conducting research with users with disabilities......, about what happens to our users when research is over, funds are gone and the curtain of experiments has fallen. Dr Brooks presented the case of a young user who while unable to move and communicate had to part with the test device that provided him with interactive playful experience. We’ve all been...... confined in a house. For researchers that work with people with disabilities and in my case with playful interactions and positive immersive experience, we might have to think harder when we write project proposals or sketch our methodology. Devices, software and experience should be available to the users...

  8. Creativity and Playfulness

    DEFF Research Database (Denmark)

    Ejsing-Duun, Stine; Skovbjerg, Helle Marie

    2015-01-01

    Abstract: This article explores how student behavior and interactions change when teachers use “producing games” as a primary pedagogical strategy (Papert, 1980; Ejsing-Duun and Karoff, 2014). Based on student and teacher actions and responses, as well as on students' production—observed during f...... fieldwork—this paper emphasizes the importance of understanding how students explore creativity and playfulness while producing in learning situations....

  9. Creativity and Playfulness

    DEFF Research Database (Denmark)

    Ejsing-Duun, Stine; Skovbjerg, Helle Marie

    2015-01-01

    Abstract: This article explores how student behavior and interactions change when teachers use “producing games” as a primary pedagogical strategy (Papert, 1980; Ejsing-Duun and Karoff, 2014). Based on student and teacher actions and responses, as well as on students' production—observed during f...... fieldwork—this paper emphasizes the importance of understanding how students explore creativity and playfulness while producing in learning situations....

  10. Solar Power at Play

    Science.gov (United States)

    2007-03-01

    For the very first time, astronomers have witnessed the speeding up of an asteroid's rotation, and have shown that it is due to a theoretical effect predicted but never seen before. The international team of scientists used an armada of telescopes to discover that the asteroid's rotation period currently decreases by 1 millisecond every year, as a consequence of the heating of the asteroid's surface by the Sun. Eventually it may spin faster than any known asteroid in the solar system and even break apart. ESO PR Photo 11a/07 ESO PR Photo 11a/07 Asteroid 2000 PH5 "The Yarkovsky-O'Keefe-Radzievskii-Paddack (YORP) effect is believed to alter the way small bodies in the Solar System rotate," said Stephen Lowry (Queens University Belfast, UK), lead-author of one of the two companion papers in which this work is reported [1, 2]. "The warming caused by sunlight hitting the surfaces of asteroids and meteoroids leads to a gentle recoil effect as the heat is released," he added. "By analogy, if one were to shine light on a propeller over a long enough period, it would start spinning." Although this is an almost immeasurably weak force, its effect over millions of years is far from negligible. Astronomers believe the YORP effect may be responsible for spinning some asteroids up so fast that they break apart, perhaps leading to the formation of double asteroids. Others may be slowed down so that they take many days to complete a full turn. The YORP effect also plays an important role in changing the orbits of asteroids between Mars and Jupiter, including their delivery to planet-crossing orbits, such as those of near-Earth asteroids. Despite its importance, the effect has never been seen acting on a solar system body, until now. Using extensive optical and radar imaging from powerful Earth-based observatories, astronomers have directly observed the YORP effect in action on a small near-Earth asteroid, known as (54509) 2000 PH5. Shortly after its discovery in 2000, it was

  11. Time perspective as a predictor of massive multiplayer online role-playing game playing.

    Science.gov (United States)

    Lukavska, Katerina

    2012-01-01

    This article focuses on the relationship between the time perspective (TP) personality trait and massive multiplayer online role-playing game (MMORPG) playing. We investigate the question of frequency of playing. The TP was measured with Zimbardo's TP Inventory (ZTPI), which includes five factors-past negative, past positive, present hedonistic, present fatalistic, and future. The study used data from 154 MMORPG players. We demonstrated that TP partially explained differences within a group of players with respect to the frequency of playing. Significant positive correlations were found between present factors and the amount of time spent playing MMORPGs, and significant negative correlation was found between the future factor and the time spent playing MMORPGs. Our study also revealed the influence of future-present balance on playing time. Players who scored lower in future-present balance variables (their present score was relatively high compared with their future score) reported higher values in playing time. In contrast to referential studies on TP and drug abuse and gambling, present fatalistic TP was demonstrated to be a stronger predictor of extensive playing than present hedonistic TP, which opened the question of motivation for playing. The advantage of our study compared with other personality-based studies lies in the fact that TP is a stable but malleable personality trait with a direct link to playing behavior. Therefore, TP is a promising conceptual resource for excessive playing therapy.

  12. Autophagosomal IκBα Degradation Plays a Role in the Long Term Control of Tumor Necrosis Factor-α-induced Nuclear Factor-κB (NF-κB) Activity*

    Science.gov (United States)

    Colleran, Amy; Ryan, Aideen; O'Gorman, Angela; Mureau, Coralie; Liptrot, Catherine; Dockery, Peter; Fearnhead, Howard; Egan, Laurence J.

    2011-01-01

    Transcription factor NF-κB is persistently activated in many chronic inflammatory diseases and cancers. The short term regulation of NF-κB is well understood, but little is known about the mechanisms of its long term activation. We studied the effect of a single application of TNF-α on NF-κB activity for up to 48 h in intestinal epithelial cells. Results show that NF-κB remained persistently activated up to 48 h after TNF-α and that the long term activation of NF-κB was accompanied by a biphasic degradation of IκBα. The first phase of IκBα degradation was proteasome-dependent, but the second was not. Further investigation showed that TNF-α stimulated formation of autophagosomes in intestinal epithelial cells and that IκBα co-localized with autophagosomal vesicles. Pharmacological or genetic blockade of autophagosome formation or the inhibition of lysosomal proteases decreased TNF-α-induced degradation of IκBα and lowered NF-κB target gene expression. Together, these findings indicate a role of autophagy in the control of long term NF-κB activity. Because abnormalities in autophagy have been linked to ineffective innate immunity, we propose that alterations in NF-κB may mediate this effect. PMID:21454695

  13. Autophagosomal IkappaB alpha degradation plays a role in the long term control of tumor necrosis factor-alpha-induced nuclear factor-kappaB (NF-kappaB) activity.

    Science.gov (United States)

    Colleran, Amy; Ryan, Aideen; O'Gorman, Angela; Mureau, Coralie; Liptrot, Catherine; Dockery, Peter; Fearnhead, Howard; Egan, Laurence J

    2011-07-01

    Transcription factor NF-κB is persistently activated in many chronic inflammatory diseases and cancers. The short term regulation of NF-κB is well understood, but little is known about the mechanisms of its long term activation. We studied the effect of a single application of TNF-α on NF-κB activity for up to 48 h in intestinal epithelial cells. Results show that NF-κB remained persistently activated up to 48 h after TNF-α and that the long term activation of NF-κB was accompanied by a biphasic degradation of IκBα. The first phase of IκBα degradation was proteasome-dependent, but the second was not. Further investigation showed that TNF-α stimulated formation of autophagosomes in intestinal epithelial cells and that IκBα co-localized with autophagosomal vesicles. Pharmacological or genetic blockade of autophagosome formation or the inhibition of lysosomal proteases decreased TNF-α-induced degradation of IκBα and lowered NF-κB target gene expression. Together, these findings indicate a role of autophagy in the control of long term NF-κB activity. Because abnormalities in autophagy have been linked to ineffective innate immunity, we propose that alterations in NF-κB may mediate this effect.

  14. Celadon Figurines Play Instruments

    Institute of Scientific and Technical Information of China (English)

    1995-01-01

    This group of figurines, each 0.15m tall, were unearthed from a Tang Dynasty tomb in Changsha in 1977. Music was very developed in the Tang Dynasty. Colorful musical instruments and dances were popular both among the people and in the palace. These vivid-looking figurines wear pleated skirts with small sleeves and open chest, a style influenced by the non-Han nationalities living in the north and west of China. Some of the musical instruments were brought from the Western Regions. The figurines are playing the xiao (a vertical bamboo flute), the konghou (an

  15. Motivation, Creativity, Play & Learning

    DEFF Research Database (Denmark)

    Petersson, Eva

    2005-01-01

    implementation of robotic physical movement synchronously manipulated from sourced data movement information of a human. SoundScapes is a concept based on non-verbal communication and stimulation through interactive play with sounds and images, which is being realised in the production of a non-wearable sensor...... groups of children, including children with severe physical/multi disabilities. The sourced capture of the human data is from enhanced virtual interactive space created from sensors. The data is constituted of the situated multimodal communication and forms of expression. The ‘VIS’ is considered...

  16. Motivation, Creativity, Play & Learning

    DEFF Research Database (Denmark)

    Petersson, Eva

    2005-01-01

    implementation of robotic physical movement synchronously manipulated from sourced data movement information of a human. SoundScapes is a concept based on non-verbal communication and stimulation through interactive play with sounds and images, which is being realised in the production of a non-wearable sensor...... groups of children, including children with severe physical/multi disabilities. The sourced capture of the human data is from enhanced virtual interactive space created from sensors. The data is constituted of the situated multimodal communication and forms of expression. The ‘VIS’ is considered...

  17. "Playing" with our users

    DEFF Research Database (Denmark)

    Brooks, Anthony Lewis

    2014-01-01

    . Unfortunately if donated in the school they are rarely being used by the students. In the case of virtual reality or artistic installations it is extremely difficult to provide such equipment to users. Last but not least we are not sure how the software will be used and if the experience will continue...... after the conduct of the research. If not due to restrictions, user should at least continue to be part of the research’s debrief and next steps. While I was in Nottingham I realised that sometimes our research, our playful educational experience, our DIY VR helmet, our beta, glitchy, research-only game...

  18. Turning training into play

    DEFF Research Database (Denmark)

    Aarhus, Rikke; Grönvall, Erik; Larsen, Simon Bo;

    2011-01-01

    Embodied gaming has been adopted and gained credibility in the field of physical rehabilitation. In this paper, we report on findings from a six-month-long study of three groups of senior citizens, and their use of Nintendo Wii Fit in a supervised physical training context. We argue that the study...... participants generally found physical training both fun and socially engaging, and experienced improved fitness. We also argue that embodied gaming motivates seniors to do more than they think themselves capable of, and allows seniors with different mental and physical capabilities to play together. However...

  19. Play and playfulness, basic features of early childhood education

    NARCIS (Netherlands)

    Singer, E.

    2013-01-01

    This article argues that play and playfulness are basic features in early childhood education, but that play curricula can have serious drawbacks. The starting point is the play theory of the Dutch historian Johan Huizinga, a radical critic of the focus on the educational benefits of play. According

  20. Play and playfulness, basic features of early childhood education

    NARCIS (Netherlands)

    Singer, E.

    2013-01-01

    This article argues that play and playfulness are basic features in early childhood education, but that play curricula can have serious drawbacks. The starting point is the play theory of the Dutch historian Johan Huizinga, a radical critic of the focus on the educational benefits of play. According

  1. Evaluation of methods for modeling transcription-factor sequence specificity

    Science.gov (United States)

    Weirauch, Matthew T.; Cote, Atina; Norel, Raquel; Annala, Matti; Zhao, Yue; Riley, Todd R.; Saez-Rodriguez, Julio; Cokelaer, Thomas; Vedenko, Anastasia; Talukder, Shaheynoor; Bussemaker, Harmen J.; Morris, Quaid D.; Bulyk, Martha L.; Stolovitzky, Gustavo

    2013-01-01

    Genomic analyses often involve scanning for potential transcription-factor (TF) binding sites using models of the sequence specificity of DNA binding proteins. Many approaches have been developed to model and learn a protein’s binding specificity, but these methods have not been systematically compared. Here we applied 26 such approaches to in vitro protein binding microarray data for 66 mouse TFs belonging to various families. For 9 TFs, we also scored the resulting motif models on in vivo data, and found that the best in vitro–derived motifs performed similarly to motifs derived from in vivo data. Our results indicate that simple models based on mononucleotide position weight matrices learned by the best methods perform similarly to more complex models for most TFs examined, but fall short in specific cases (<10%). In addition, the best-performing motifs typically have relatively low information content, consistent with widespread degeneracy in eukaryotic TF sequence preferences. PMID:23354101

  2. BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors

    Directory of Open Access Journals (Sweden)

    Morigen

    2009-10-01

    Full Text Available Abstract Background We have incorporated Bayesian model regularization with biophysical modeling of protein-DNA interactions, and of genome-wide nucleosome positioning to study protein-DNA interactions, using a high-throughput dataset. The newly developed method (BayesPI includes the estimation of a transcription factor (TF binding energy matrices, the computation of binding affinity of a TF target site and the corresponding chemical potential. Results The method was successfully tested on synthetic ChIP-chip datasets, real yeast ChIP-chip experiments. Subsequently, it was used to estimate condition-specific and species-specific protein-DNA interaction for several yeast TFs. Conclusion The results revealed that the modification of the protein binding parameters and the variation of the individual nucleotide affinity in either recognition or flanking sequences occurred under different stresses and in different species. The findings suggest that such modifications may be adaptive and play roles in the formation of the environment-specific binding patterns of yeast TFs and in the divergence of TF binding sites across the related yeast species.

  3. Playing The Lobby

    DEFF Research Database (Denmark)

    2014-01-01

    Playing a game can be defined as, in a fun way, to reach a goal by means of helpers and challenged by obstacles and opponents. In this workshop we will gain a new understanding of the lobby by making it into a game. The lobby of the museum can be understood as a game in which the players (the....... The object is surprisingly not to play the games, but to design them. Through the design process we are forced to discuss: What are the challenges of a particular lobby (e.g. ticketing, queueing, other visitors, guards, getting lost)? Which properties do the players have (e.g. patience, expectations, need...... of a toilet)? what boosters may they obtain in the lobby (e.g. coffee, help, souvenirs, signs)? And how can we make this an enjoyable experience? The object of the games is to understand the lobby in a new way to identify problems, and think of ways to improve the functions, flow, and services of the lobby....

  4. A High-Throughput Screening System for Arabidopsis Transcription Factors and Its Application to Med25-Dependent Transcriptional Regulation

    Institute of Scientific and Technical Information of China (English)

    Bin Ou; Minami Matsui; Hong-Ya Gu; Li-Jia Qu; Kang-Quan Yin; Sai-Nan Liu; Yan Yang; Tren Gu; Jennifer Man Wing Hui; Li Zhang; Jin Miao; Youichi Kondou

    2011-01-01

    T The activities of transcription factors (TFs) require interactions with specific DNA sequences and other regulatory proteins. To detect such interactions in Arabidopsis, we developed a high-throughput screening system with a Gateway-compatible Gal4-AD-TF library of 1589 Arabidopsis TFs, which can be easily screened by mating-based yeast-one-hybrid (Y1H) and yeast-two-hybrid (Y2H) methods. The efficiency of the system was validated by examining two well-characterized TF-DNA and TF-protein interactions: the CHE-CCA1 promoter interaction by Y1H and NPR1-TGAs interactions by Y2H. We used this system to identify eight TFs that interact with a Mediator subunit, Med25, a key regulator in JA signaling. We identified five TFs that interacted with the GCC-box cis-element in the promoter of PDF1.2, a downstream gene of Med25. We found that three of these TFs, all from the AP2-EREBP family, interact directly both with Med25 and the GCC-box of PDF1.2, suggesting that Med25 regulates PDF1.2 expression through these three TFs.These results demonstrate that this high-throughput Y1H/Y2H screening system is an efficient tool for studying transcriptional regulation networks in Arabidopsis. This system will be available for other Arabidopsis researchers, and thus it provides a vital resource for the Arabidopsis community.

  5. 高校心理委员发挥作用的动力源探究%A Study of College Psychological Members Playing a Role in the Power Source Factors

    Institute of Scientific and Technical Information of China (English)

    吴华丽

    2012-01-01

    Psychological members of colleges and universities to carry out the students" daily education and management and the launch of the new force of crisis intervention,is an important part of the university mental health education network,"suecess psychology" internal source of power factor and achievement goals"and" task difficulty "," external incentives "and" atmosphere "of these four factors together in an external power source, the members of the university mental are able to last and play a role effectively. Through a combination of basic quality and expertise training,the implementation of standardized psychological counseling,scientific and rational position duties, to provide an appropriate degree of external rewards and to build a learning organization culture and other initiatives to help enhance the team play a role in the power source.%心理委员是高校开展学生日常教育与管理工作及开展危机干预工作的新生力量,是高校心理健康教育网络的重要组成部分,在“成功心理”这一内部动力源因素和“成就目标”、“任务难度”、“外部奖励”以及“环境氛围”这四个外部动力源因素的共同作用下,高校心理委员的作用才得以持久有效地发挥。通过基本素质与专业知识相结合的培训.实施规范的心理辅导.科学合理地定位工作职责.提供适度的外部奖励以及构建学习型组织文化等举措有助于增强这支队伍发挥作用的动力源。

  6. Playing it Real

    DEFF Research Database (Denmark)

    Grubert, Jens; Morrison, Ann; Munz, Helmut

    2012-01-01

    Magic lens and static peephole interfaces are used in numerous consumer mobile phone applications such as Augmented Reality browsers, games or digital map applications in a variety of contexts including public spaces. Interface performance has been evaluated for various interaction tasks involving...... spatial relationships in a scene. However, interface usage outside laboratory conditions has not been considered in depth in the evaluation of these interfaces. We present findings about the usage of magic lens and static peephole interfaces for playing a find-and-select game in a public space and report...... on the reactions of the public audience to participants’ interactions. Contrary to our expectations participants favored the magic lens over a static peephole interface despite tracking errors, fatigue and potentially conspicuous gestures. Most passersby did not pay attention to the participants and vice versa...

  7. Still playing the game?

    DEFF Research Database (Denmark)

    Neergaard, Helle; Krueger, Norris

    2005-01-01

    of organizational and leadership practices are influenced by one important type of human capital: namely socialization from being trained to compete in sports involving such factors as physical strength, speed, endurance, a competitive mind, strategizing and team spirit; all ingredients necessary in building a new...

  8. Systematic identification of yeast cell cycle transcription factors using multiple data sources

    Directory of Open Access Journals (Sweden)

    Li Wen-Hsiung

    2008-12-01

    Full Text Available Abstract Background Eukaryotic cell cycle is a complex process and is precisely regulated at many levels. Many genes specific to the cell cycle are regulated transcriptionally and are expressed just before they are needed. To understand the cell cycle process, it is important to identify the cell cycle transcription factors (TFs that regulate the expression of cell cycle-regulated genes. Results We developed a method to identify cell cycle TFs in yeast by integrating current ChIP-chip, mutant, transcription factor binding site (TFBS, and cell cycle gene expression data. We identified 17 cell cycle TFs, 12 of which are known cell cycle TFs, while the remaining five (Ash1, Rlm1, Ste12, Stp1, Tec1 are putative novel cell cycle TFs. For each cell cycle TF, we assigned specific cell cycle phases in which the TF functions and identified the time lag for the TF to exert regulatory effects on its target genes. We also identified 178 novel cell cycle-regulated genes, among which 59 have unknown functions, but they may now be annotated as cell cycle-regulated genes. Most of our predictions are supported by previous experimental or computational studies. Furthermore, a high confidence TF-gene regulatory matrix is derived as a byproduct of our method. Each TF-gene regulatory relationship in this matrix is supported by at least three data sources: gene expression, TFBS, and ChIP-chip or/and mutant data. We show that our method performs better than four existing methods for identifying yeast cell cycle TFs. Finally, an application of our method to different cell cycle gene expression datasets suggests that our method is robust. Conclusion Our method is effective for identifying yeast cell cycle TFs and cell cycle-regulated genes. Many of our predictions are validated by the literature. Our study shows that integrating multiple data sources is a powerful approach to studying complex biological systems.

  9. Regulatory Factor X (RFX)-mediated transcriptional rewiring of ciliary genes in animals.

    Science.gov (United States)

    Piasecki, Brian P; Burghoorn, Jan; Swoboda, Peter

    2010-07-20

    Cilia were present in the last eukaryotic common ancestor (LECA) and were retained by most organisms spanning all extant eukaryotic lineages, including organisms in the Unikonta (Amoebozoa, fungi, choanoflagellates, and animals), Archaeplastida, Excavata, Chromalveolata, and Rhizaria. In certain animals, including humans, ciliary gene regulation is mediated by Regulatory Factor X (RFX) transcription factors (TFs). RFX TFs bind X-box promoter motifs and thereby positively regulate >50 ciliary genes. Though RFX-mediated ciliary gene regulation has been studied in several bilaterian animals, little is known about the evolutionary conservation of ciliary gene regulation. Here, we explore the evolutionary relationships between RFX TFs and cilia. By sampling the genome sequences of >120 eukaryotic organisms, we show that RFX TFs are exclusively found in unikont organisms (whether ciliated or not), but are completely absent from the genome sequences of all nonunikont organisms (again, whether ciliated or not). Sampling the promoter sequences of 12 highly conserved ciliary genes from 23 diverse unikont and nonunikont organisms further revealed that phylogenetic footprints of X-box promoter motif sequences are found exclusively in ciliary genes of certain animals. Thus, there is no correlation between cilia/ciliary genes and the presence or absence of RFX TFs and X-box promoter motifs in nonanimal unikont and in nonunikont organisms. These data suggest that RFX TFs originated early in the unikont lineage, distinctly after cilia evolved. The evolutionary model that best explains these observations indicates that the transcriptional rewiring of many ciliary genes by RFX TFs occurred early in the animal lineage.

  10. Selective alterations of transcription factors in MPP+-induced neurotoxicity in PC12 cells.

    Science.gov (United States)

    Xu, Z; Cawthon, D; McCastlain, K A; Duhart, H M; Newport, G D; Fang, H; Patterson, T A; Slikker, W; Ali, S F

    2005-08-01

    MPP(+) (1-methyl-4-phenylpyridinium; the active metabolite of the neurotoxin MPTP (1-methyl-4-phenyl-1,2,5,6-tetrahydropyridine)) depletes dopamine (DA) content and elicits cell death in PC12 cells. However, the mechanism of MPP(+)-induced neurotoxicity is still unclear. In this study, the dose response and time-course of MPP(+)-induced DA depletion and decreased cell viability were determined in nerve growth factor (NGF)-differentiated PC12 cells. The alteration of transcription factors (TFs) induced by MPP(+) from a selected dose level and time point was then evaluated using protein/DNA-binding arrays. K-means clustering analysis identified four patterns of protein/DNA-binding changes. Three of the 28 TFs identified in PC12 cells increased by 100% (p53, PRE, Smad SBE) and 2 decreased by 50% (HSE, RXR(DR1)) of control with MPP(+) treatment. In addition, three TFs decreased within the range of 33-50% (TFIID, E2F1, CREB) and two TFs increased within the range of 50-100% (PAX-5, Stat4). An electrophoretic mobility shift assay (EMSA) was used to confirm the changes of p53 and HSE. The observed changes in TFs correlated with the alterations of DA and cell viability. The data indicates that selective transcription factors are involved in MPP(+)-induced neurotoxicity and it provides mechanistic information that may be applicable to animal studies with MPTP and clinical studies of Parkinson's disease.

  11. Combinatorial analysis of lupulin gland transcription factors from R2R3Myb, bHLH and WDR families indicates a complex regulation of chs_H1 genes essential for prenylflavonoid biosynthesis in hop (Humulus Lupulus L.

    Directory of Open Access Journals (Sweden)

    Matoušek Jaroslav

    2012-02-01

    Full Text Available Abstract Background Lupulin glands of hop produce a specific metabolome including hop bitter acids valuable for the brewing process and prenylflavonoids with promising health-beneficial activities. The detailed analysis of the transcription factor (TF-mediated regulation of the oligofamily of one of the key enzymes, i.e., chalcone synthase CHS_H1 that efficiently catalyzes the production of naringenin chalcone, a direct precursor of prenylflavonoids in hop, constitutes an important part of the dissection of the biosynthetic pathways leading to the accumulation of these compounds. Results Homologues of flavonoid-regulating TFs HlMyb2 (M2, HlbHLH2 (B2 and HlWDR1 (W1 from hop were cloned using a lupulin gland-specific cDNA library from the hop variety Osvald's 72. Using a "combinatorial" transient GUS expression system it was shown that these unique lupulin-gland-associated TFs significantly activated the promoter (P of chs_H1 in ternary combinations of B2, W1 and either M2 or the previously characterized HlMyb3 (M3. The promoter activation was strongly dependent on the Myb-P binding box TCCTACC having a core sequence CCWACC positioned on its 5' end region and it seems that the complexity of the promoter plays an important role. M2B2W1-mediated activation significantly exceeded the strength of expression of native chs_H1 gene driven by the 35S promoter of CaMV, while M3B2W1 resulted in 30% of the 35S:chs_H1 expression level, as quantified by real-time PCR. Another newly cloned hop TF, HlMyb7, containing a transcriptional repressor-like motif pdLNLD/ELxiG/S (PDLNLELRIS, was identified as an efficient inhibitor of chs_H1-activating TFs. Comparative analyses of hop and A. thaliana TFs revealed a complex activation of Pchs_H1 and Pchs4 in combinatorial or independent manners. Conclusions This study on the sequences and functions of various lupulin gland-specific transcription factors provides insight into the complex character of the regulation of the

  12. Playful Learning and Montessori Education

    National Research Council Canada - National Science Library

    Angeline S Lillard

    2013-01-01

      Although Montessori education is often considered a form of playful learning, Maria Montessori herself spoke negatively about a major component of playful learning-pretend play, or fantasy-for young children...

  13. Current status and related factors of community nurses' playing duty role function%社区护士发挥角色功能现况及影响因素调查

    Institute of Scientific and Technical Information of China (English)

    李富君

    2012-01-01

    Objectives: To explore the main working content of community nurses, the various duty roles and related factors, and to provide scientific references for community health care managers to set position for community nurses, to make the duty clear, to provide targeted training for community nurse and to give full play for community nurse role function. Methods: We investigated 195 community nurses in 7 community health service centers by questionnaires. Results: Among 195 nurses, 72.82% nurses mainly did therapeutic work and 32.31% nurses mainly did preventive health care work. The factors restricting community nurse to play duty role function were manpower shortage, deficiency of related knowledge and skills, inadequate comprehensive ability, position limitation, insufficient leader supports and lack of service consciousness. Conclusion: Community nurses' ideas has changed, but they do not fully perform their due role function in community health care. Community health care managers should pay more attention to take effective measures to improve community nurses' comprehensive quality and to give full play for community nurses' role function.%目的:了解目前社区护士的主要工作内容,各种角色职责的履行情况及其相关因素,为社区卫生服务管理者更好地设置社区护士岗位,明确职责,有针对性地对社区护士进行培训,充分发挥社区护士的角色功能提供科学依据.方法:使用问卷方式对北京市7所社区卫生服务中心(站)195名社区护士进行调查.结果:被调查的195名护士中,72.82%主要从事治疗性工作,32.31%从事预防保健工作.制约社区护士履行角色功能的主要因素依次为:人力不足,缺乏相关知识技能,自身综合能力不足,岗位限制,领导支持力度不够,缺乏服务意识等.结论:社区护士的观念已经发生改变,但社区护士在社区卫生服务中没有充分履行其应有的角色职责,应引起社区卫生服务管理者

  14. Cell Growth Defect Factor1/CHAPERONE-LIKE PROTEIN OF POR1 Plays a Role in Stabilization of Light-Dependent Protochlorophyllide Oxidoreductase in Nicotiana benthamiana and Arabidopsis[C][W

    Science.gov (United States)

    Lee, Jae-Yong; Lee, Ho-Seok; Song, Ji-Young; Jung, Young Jun; Reinbothe, Steffen; Park, Youn-Il; Lee, Sang Yeol; Pai, Hyun-Sook

    2013-01-01

    Angiosperms require light for chlorophyll biosynthesis because one reaction in the pathway, the reduction of protochlorophyllide (Pchlide) to chlorophyllide, is catalyzed by the light-dependent protochlorophyllide oxidoreductase (POR). Here, we report that Cell growth defect factor1 (Cdf1), renamed here as CHAPERONE-LIKE PROTEIN OF POR1 (CPP1), an essential protein for chloroplast development, plays a role in the regulation of POR stability and function. Cdf1/CPP1 contains a J-like domain and three transmembrane domains, is localized in the thylakoid and envelope membranes, and interacts with POR isoforms in chloroplasts. CPP1 can stabilize POR proteins with its holdase chaperone activity. CPP1 deficiency results in diminished POR protein accumulation and defective chlorophyll synthesis, leading to photobleaching and growth inhibition of plants under light conditions. CPP1 depletion also causes reduced POR accumulation in etioplasts of dark-grown plants and as a result impairs the formation of prolamellar bodies, which subsequently affects chloroplast biogenesis upon illumination. Furthermore, in cyanobacteria, the CPP1 homolog critically regulates POR accumulation and chlorophyll synthesis under high-light conditions, in which the dark-operative Pchlide oxidoreductase is repressed by its oxygen sensitivity. These findings and the ubiquitous presence of CPP1 in oxygenic photosynthetic organisms suggest the conserved nature of CPP1 function in the regulation of POR. PMID:24151298

  15. Transcription Factors Synergistically Activated at the Crossing of the Restriction Point between G1 and S Cell Cycle Phases. Pathologic Gate Opening during Multi-Hit Malignant Transformation

    Directory of Open Access Journals (Sweden)

    Nicoletta Castagnino

    2016-12-01

    Full Text Available Transcription factors (TFs represent key regulators of gene-expression patterns controlling cell behavior. TFs are active at nuclear – chromatin levels. TFs do not act in isolation; small sets of TFs cooperate toward the transcription of sets of mRNAs and consequently the translation of new proteins (the molecular phenotypes of a cell. Most TFs are activated through a cascade of biochemical reactions mediated by receptors expressed on the target cell surface. Nuclear Receptors (NRs are transcription factors activated instead by small hydrophobic molecules capable of crossing the plasma membrane. The convergence of different pathways on TFs and their posttranslational modifications ensure that the external stimuli generate appropriate and integrated responses. The reconstruction of the molecular anatomy of these pathways through Molecular Interactions Maps (MIMs can depict these intricate interactions. A mathematical modeling approach simulates/mimics their mechanism of action in normal and pathological conditions. We can simulate the effect of virtual hits in neoplastic transformation as mutations/alterations in these pathways. We can also simulate the effect of targeted inhibitors on these deregulated pathways. This strategy can help to guide an appropriate combination of targeted drugs in the treatment of a cancer patient, a major innovative perspective of incoming years.

  16. Imagination, Playfulness, and Creativity in Children's Play with Different Toys

    Science.gov (United States)

    Mo????ller, Signe?? Juhl?

    2015-01-01

    Based on a four-month experimental study of preschool children's play with creative-construction and social-fantasy toys, the author examines the in?uence of both types of toys on the play of preschool children. Her comparative analysis considers the impact of transformative play on the development of imagination during play activities and…

  17. LASAGNA: A novel algorithm for transcription factor binding site alignment

    Science.gov (United States)

    2013-01-01

    Background Scientists routinely scan DNA sequences for transcription factor (TF) binding sites (TFBSs). Most of the available tools rely on position-specific scoring matrices (PSSMs) constructed from aligned binding sites. Because of the resolutions of assays used to obtain TFBSs, databases such as TRANSFAC, ORegAnno and PAZAR store unaligned variable-length DNA segments containing binding sites of a TF. These DNA segments need to be aligned to build a PSSM. While the TRANSFAC database provides scoring matrices for TFs, nearly 78% of the TFs in the public release do not have matrices available. As work on TFBS alignment algorithms has been limited, it is highly desirable to have an alignment algorithm tailored to TFBSs. Results We designed a novel algorithm named LASAGNA, which is aware of the lengths of input TFBSs and utilizes position dependence. Results on 189 TFs of 5 species in the TRANSFAC database showed that our method significantly outperformed ClustalW2 and MEME. We further compared a PSSM method dependent on LASAGNA to an alignment-free TFBS search method. Results on 89 TFs whose binding sites can be located in genomes showed that our method is significantly more precise at fixed recall rates. Finally, we described LASAGNA-ChIP, a more sophisticated version for ChIP (Chromatin immunoprecipitation) experiments. Under the one-per-sequence model, it showed comparable performance with MEME in discovering motifs in ChIP-seq peak sequences. Conclusions We conclude that the LASAGNA algorithm is simple and effective in aligning variable-length binding sites. It has been integrated into a user-friendly webtool for TFBS search and visualization called LASAGNA-Search. The tool currently stores precomputed PSSM models for 189 TFs and 133 TFs built from TFBSs in the TRANSFAC Public database (release 7.0) and the ORegAnno database (08Nov10 dump), respectively. The webtool is available at http://biogrid.engr.uconn.edu/lasagna_search/. PMID:23522376

  18. Playful Learning and Montessori Education

    Science.gov (United States)

    Lillard, Angeline S.

    2013-01-01

    Although Montessori education is often considered a form of playful learning, Maria Montessori herself spoke negatively about a major component of playful learning--pretend play, or fantasy--for young children. In this essay, the author discusses this apparent contradiction: how and why Montessori education includes elements of playful learning…

  19. TFpredict and SABINE: sequence-based prediction of structural and functional characteristics of transcription factors.

    Directory of Open Access Journals (Sweden)

    Johannes Eichner

    Full Text Available One of the key mechanisms of transcriptional control are the specific connections between transcription factors (TF and cis-regulatory elements in gene promoters. The elucidation of these specific protein-DNA interactions is crucial to gain insights into the complex regulatory mechanisms and networks underlying the adaptation of organisms to dynamically changing environmental conditions. As experimental techniques for determining TF binding sites are expensive and mostly performed for selected TFs only, accurate computational approaches are needed to analyze transcriptional regulation in eukaryotes on a genome-wide level. We implemented a four-step classification workflow which for a given protein sequence (1 discriminates TFs from other proteins, (2 determines the structural superclass of TFs, (3 identifies the DNA-binding domains of TFs and (4 predicts their cis-acting DNA motif. While existing tools were extended and adapted for performing the latter two prediction steps, the first two steps are based on a novel numeric sequence representation which allows for combining existing knowledge from a BLAST scan with robust machine learning-based classification. By evaluation on a set of experimentally confirmed TFs and non-TFs, we demonstrate that our new protein sequence representation facilitates more reliable identification and structural classification of TFs than previously proposed sequence-derived features. The algorithms underlying our proposed methodology are implemented in the two complementary tools TFpredict and SABINE. The online and stand-alone versions of TFpredict and SABINE are freely available to academics at http://www.cogsys.cs.uni-tuebingen.de/software/TFpredict/ and http://www.cogsys.cs.uni-tuebingen.de/software/SABINE/.

  20. Play and playfulness in early childhood education and care.

    Directory of Open Access Journals (Sweden)

    Singer E.

    2015-06-01

    Full Text Available Play and playfulness are basic features in early childhood education. The elements of play are pleasure, a sense of freedom, and the co-construction of shared meaning through the use of rules or rhythms. Play and learning are closely related in early childhood. But when the focus on the educational benefits of play becomes too strong, the most essential feature of play is lost: children’s pleasure. Young children in group settings often have to adapt to the teachers’ demands related to security, hygiene, and social norms and values. But the playfulness of the teachers helps to overcome differences in power in the caregiver-child relationship and prevents young children from becoming overburdened with strict rules and group discipline. Play and playfulness are a resource of shared pleasure and creativity in learning processes.

  1. Ouroboros - Playing A Biochemical

    Directory of Open Access Journals (Sweden)

    D. T. Rodrigues

    2014-08-01

    Full Text Available Ouroboros: Playing A Biochemical RODRIGUES,D.T.1,2;GAYER, M.C.1,2; ESCOTO, D.F.1; DENARDIN, E.L.G.2, ROEHRS, R.1,2 1Interdisciplinary Research Group on Teaching Practice, Graduate Program in Biochemistry, Unipampa, RS, Brazil 2Laboratory of Physicochemical Studies and Natural Products, Post Graduate Program in Biochemistry, Unipampa, RS, Brazil Introduction: Currently, teachers seek different alternatives to enhance the teaching-learning process. Innovative teaching methodologies are increasingly common tools in educational routine. The use of games, electronic or conventional, is an effective tool to assist in learning and also to raise the social interaction between students. Objective: In this sense our work aims to evaluate the card game and "Ouroboros" board as a teaching and learning tool in biochemistry for a graduating class in Natural Sciences. Materials and methods: The class gathered 22 students of BSc in Natural Sciences. Each letter contained a question across the board that was drawn to a group to answer within the allotted time. The questions related concepts of metabolism, organic and inorganic chemical reactions, bioenergetics, etc.. Before the game application, students underwent a pre-test with four issues involving the content that was being developed. Soon after, the game was applied. Then again questions were asked. Data analysis was performed from the ratio of the number of correct pre-test and post-test answers. Results and discussion: In the pre-test 18.1% of the students knew all issues, 18.1% got 3 correct answers, 40.9% answered only 2 questions correctly and 22.7% did not hit any. In post-test 45.4% answered all the questions right, 31.8% got 3 questions and 22.7% got 2 correct answers. The results show a significant improvement of the students about the field of content taught through the game. Conclusion: Generally, traditional approaches of chemistry and biochemistry are abstract and complex. Thus, through games

  2. Emerging Functions of Transcription Factors in Malaria Parasite

    Directory of Open Access Journals (Sweden)

    Renu Tuteja

    2011-01-01

    Full Text Available Transcription is a process by which the genetic information stored in DNA is converted into mRNA by enzymes known as RNA polymerase. Bacteria use only one RNA polymerase to transcribe all of its genes while eukaryotes contain three RNA polymerases to transcribe the variety of eukaryotic genes. RNA polymerase also requires other factors/proteins to produce the transcript. These factors generally termed as transcription factors (TFs are either associated directly with RNA polymerase or add in building the actual transcription apparatus. TFs are the most common tools that our cells use to control gene expression. Plasmodium falciparum is responsible for causing the most lethal form of malaria in humans. It shows most of its characteristics common to eukaryotic transcription but it is assumed that mechanisms of transcriptional control in P. falciparum somehow differ from those of other eukaryotes. In this article we describe the studies on the main TFs such as myb protein, high mobility group protein and ApiA2 family proteins from malaria parasite. These studies show that these TFs are slowly emerging to have defined roles in the regulation of gene expression in the parasite.

  3. Hypoxia-inducible factor-1α plays roles in Epstein-Barr virus's natural life cycle and tumorigenesis by inducing lytic infection through direct binding to the immediate-early BZLF1 gene promoter.

    Science.gov (United States)

    Kraus, Richard J; Yu, Xianming; Cordes, Blue-Leaf A; Sathiamoorthi, Saraniya; Iempridee, Tawin; Nawandar, Dhananjay M; Ma, Shidong; Romero-Masters, James C; McChesney, Kyle G; Lin, Zhen; Makielski, Kathleen R; Lee, Denis L; Lambert, Paul F; Johannsen, Eric C; Kenney, Shannon C; Mertz, Janet E

    2017-06-01

    When confronted with poor oxygenation, cells adapt by activating survival signaling pathways, including the oxygen-sensitive transcriptional regulators called hypoxia-inducible factor alphas (HIF-αs). We report here that HIF-1α also regulates the life cycle of Epstein-Barr virus (EBV). Incubation of EBV-positive gastric carcinoma AGS-Akata and SNU-719 and Burkitt lymphoma Sal and KemIII cell lines with a prolyl hydroxylase inhibitor, L-mimosine or deferoxamine, or the NEDDylation inhibitor MLN4924 promoted rapid and sustained accumulation of both HIF-1α and lytic EBV antigens. ShRNA knockdown of HIF-1α significantly reduced deferoxamine-mediated lytic reactivation. HIF-1α directly bound the promoter of the EBV primary latent-lytic switch BZLF1 gene, Zp, activating transcription via a consensus hypoxia-response element (HRE) located at nt -83 through -76 relative to the transcription initiation site. HIF-1α did not activate transcription from the other EBV immediate-early gene, BRLF1. Importantly, expression of HIF-1α induced EBV lytic-gene expression in cells harboring wild-type EBV, but not in cells infected with variants containing base-pair substitution mutations within this HRE. Human oral keratinocyte (NOK) and gingival epithelial (hGET) cells induced to differentiate by incubation with either methyl cellulose or growth in organotypic culture accumulated both HIF-1α and Blimp-1α, another cellular factor implicated in lytic reactivation. HIF-1α activity also accumulated along with Blimp-1α during B-cell differentiation into plasma cells. Furthermore, most BZLF1-expressing cells observed in lymphomas induced by EBV in NSG mice with a humanized immune system were located distal to blood vessels in hypoxic regions of the tumors. Thus, we conclude that HIF-1α plays central roles in both EBV's natural life cycle and EBV-associated tumorigenesis. We propose that drugs that induce HIF-1α protein accumulation are good candidates for development of a lytic

  4. 第30届奥运会男篮比赛的核心致胜因素分析%An analysis of core factors for winning men’s basketball games played in the 30th Olympic Games

    Institute of Scientific and Technical Information of China (English)

    郭永波; 吴泽泰

    2014-01-01

    The authors applied Spearman’s two column rank correlation analysis method to calculate the correla-tions between rankings listed for and techniques used in men’s basketball games played in the 30th London Olympic Games, used top 12 indexes arranged in the order of such correlation coefficients to compare the differences be-tween strong, medium and weak teams in order to verify various factors for winning, and therefore drew the fol-lowing conclusions:rankings were closely related to assists, 2-pointers, average points per game, misses and defen-sive rebounds;it can be known from index differences that ordinary factors for strong teams to win weak teams in group games were stronger individual offense ability, teamwork ability, defense aggressiveness and 3-point shooting ability;important factors for strong teams to win in elimination games were defense ability stronger than their op-ponents, stronger contest ability during offense, capability to make their opponents foul more and strong un-der-basket offense ability; competitions between strong teams were competitions of 3-pointers, rebounds, penalty shots and assists;core factors for strong teams to win were steady long shot technique, super strong individual of-fense ability, rebound snatching ability and inside scoring ability.%运用Spearman(斯皮尔曼)二列等级相关分析法计算第30届伦敦奥运会男篮比赛名次与技术相关关系,以此相关系数排序较高12项指标比较奥运会比赛强、中、弱3种水平队的差幅,求证获胜各种因素。因而得出,名次与助攻、2分球命中率次数及场均得分、失误、防守篮板有密切的关系。从指标差幅中可知,小组赛中强队胜弱队的一般制胜因素是较强的个人攻击能力、配合能力、防守攻击性和3分球远投能力。复赛中获胜强队的重要制胜因素是防守能力强于对手,进攻中对抗能力强,能更多地造成对方犯规和篮下攻击能力

  5. Computational identification of conserved transcription factor binding sites upstream of genes induced in rat brain by transient focal ischemic stroke.

    Science.gov (United States)

    Pulliam, John V K; Xu, Zhenfeng; Ford, Gregory D; Liu, Cuimei; Li, Yonggang; Stovall, Kyndra C; Cannon, Virginetta S; Tewolde, Teclemichael; Moreno, Carlos S; Ford, Byron D

    2013-02-07

    Microarray analysis has been used to understand how gene regulation plays a critical role in neuronal injury, survival and repair following ischemic stroke. To identify the transcriptional regulatory elements responsible for ischemia-induced gene expression, we examined gene expression profiles of rat brains following focal ischemia and performed computational analysis of consensus transcription factor binding sites (TFBS) in the genes of the dataset. In this study, rats were sacrificed 24 h after middle cerebral artery occlusion (MCAO) stroke and gene transcription in brain tissues following ischemia/reperfusion was examined using Affymetrix GeneChip technology. The CONserved transcription FACtor binding site (CONFAC) software package was used to identify over-represented TFBS in the upstream promoter regions of ischemia-induced genes compared to control datasets. CONFAC identified 12 TFBS that were statistically over-represented from our dataset of ischemia-induced genes, including three members of the Ets-1 family of transcription factors (TFs). Microarray results showed that mRNA for Ets-1 was increased following tMCAO but not pMCAO. Immunohistochemical analysis of Ets-1 protein in rat brains following MCAO showed that Ets-1 was highly expressed in neurons in the brain of sham control animals. Ets-1 protein expression was virtually abolished in injured neurons of the ischemic brain but was unchanged in peri-infarct brain areas. These data indicate that TFs, including Ets-1, may influence neuronal injury following ischemia. These findings could provide important insights into the mechanisms that lead to brain injury and could provide avenues for the development of novel therapies. Copyright © 2012 Elsevier B.V. All rights reserved.

  6. The school in play

    Directory of Open Access Journals (Sweden)

    Nicolás Viñes

    2013-05-01

    Full Text Available La extensión universitaria es entendida en el sistema universitario argentino como uno de los tres pilares fundamentales que lo componen, junto con la enseñanza y la investigación. En este marco, las prácticas de extensión son experiencias de intervención social, que ponen a prueba los saberes adquiridos en la formación de grado, saberes que se deconstruyen y reconstruyen a partir en una constante interacción entre los diversos actores sociales. El proyecto de extensión que describimos en el siguiente artículo surgió a partir de algunas observaciones focalizadas en la comunidad y la escuela de inserción. En ese diagnóstico inicial descubrimos que las prácticas lúdicas en niños y adolescentes del barrio en cuestión, se encontraban condicionadas por dos factores importantes: uno de índole social y el otro por la falta de disponibilidad de espacios para jugar. Por tal motivo creíamos relevante la recuperación de la práctica de algunos juegos desde la escuela, entendiéndola como un “territorio” socialmente legitimado, pero además como un lugar posible para generar políticas educativas hacia la transformación, entendiendo que tal como estaban las cosas era necesaria una reapropiación del juego como derecho y necesidad.

  7. Play technique in psychodynamic psychotherapy.

    Science.gov (United States)

    Yanof, Judith A

    2013-04-01

    Imaginary play is often a child's best way of communicating affects, fantasies, and internal states. In play children are freer to express their forbidden and conflicted thoughts. Consequently, one of the best ways for the therapist to enter the child's world is to do so from within the displacement of the play process. For children who cannot play, the therapist's goal is to teach the child to use play as a means of communication and to create meaning. This article present clinical examples to illustrate how the author uses play in the clinical situation.

  8. Learning, Play, and Your Newborn

    Science.gov (United States)

    ... Old Feeding Your 1- to 2-Year-Old Learning, Play, and Your Newborn KidsHealth > For Parents > Learning, ... juega su recién nacido What Is My Newborn Learning? Play is the chief way that infants learn ...

  9. Problematic Game Play: The Diagnostic Value of Playing Motives, Passion, and Playing Time in Men

    Directory of Open Access Journals (Sweden)

    Julia Kneer

    2015-04-01

    Full Text Available Internet gaming disorder is currently listed in the DSM—not in order to diagnose such a disorder but to encourage research to investigate this phenomenon. Even whether it is still questionable if Internet Gaming Disorder exists and can be judged as a form of addiction, problematic game play is already very well researched to cause problems in daily life. Approaches trying to predict problematic tendencies in digital game play have mainly focused on playing time as a diagnostic criterion. However, motives to engage in digital game play and obsessive passion for game play have also been found to predict problematic game play but have not yet been investigated together. The present study aims at (1 analyzing if obsessive passion can be distinguished from problematic game play as separate concepts, and (2 testing motives of game play, passion, and playing time for their predictive values for problematic tendencies. We found (N = 99 males, Age: M = 22.80, SD = 3.81 that obsessive passion can be conceptually separated from problematic game play. In addition, the results suggest that compared to solely playing time immersion as playing motive and obsessive passion have added predictive value for problematic game play. The implications focus on broadening the criteria in order to diagnose problematic playing.

  10. Two highly similar DEAD box proteins, OsRH2 and OsRH34, homologous to eukaryotic initiation factor 4AIII, play roles of the exon junction complex in regulating growth and development in rice.

    Science.gov (United States)

    Huang, Chun-Kai; Sie, Yi-Syuan; Chen, Yu-Fu; Huang, Tian-Sheng; Lu, Chung-An

    2016-04-12

    The exon junction complex (EJC), which contains four core components, eukaryotic initiation factor 4AIII (eIF4AIII), MAGO/NASHI (MAGO), Y14/Tsunagi/RNA-binding protein 8A, and Barentsz/Metastatic lymph node 51, is formed in both nucleus and cytoplasm, and plays important roles in gene expression. Genes encoding core EJC components have been found in plants, including rice. Currently, the functional characterizations of MAGO and Y14 homologs have been demonstrated in rice. However, it is still unknown whether eIF4AIII is essential for the functional EJC in rice. This study investigated two DEAD box RNA helicases, OsRH2 and OsRH34, which are homologous to eIF4AIII, in rice. Amino acid sequence analysis indicated that OsRH2 and OsRH34 had 99 % identity and 100 % similarity, and their gene expression patterns were similar in various rice tissues, but the level of OsRH2 mRNA was about 58-fold higher than that of OsRH34 mRNA in seedlings. From bimolecular fluorescence complementation results, OsRH2 and OsRH34 interacted physically with OsMAGO1 and OsY14b, respectively, which indicated that both of OsRH2 and OsRH34 were core components of the EJC in rice. To study the biological roles of OsRH2 and OsRH34 in rice, transgenic rice plants were generated by RNA interference. The phenotypes of three independent OsRH2 and OsRH34 double-knockdown transgenic lines included dwarfism, a short internode distance, reproductive delay, defective embryonic development, and a low seed setting rate. These phenotypes resembled those of mutants with gibberellin-related developmental defects. In addition, the OsRH2 and OsRH34 double-knockdown transgenic lines exhibited the accumulation of unspliced rice UNDEVELOPED TAPETUM 1 mRNA. Rice contains two eIF4AIII paralogous genes, OsRH2 and OsRH34. The abundance of OsRH2 mRNA was about 58-fold higher than that of OsRH34 mRNA in seedlings, suggesting that the OsRH2 is major eIF4AIII in rice. Both OsRH2 and OsRH34 are core components of the EJC

  11. The loose evolutionary relationships between transcription factors and other gene products across prokaryotes.

    Science.gov (United States)

    del Grande, Marc; Moreno-Hagelsieb, Gabriel

    2014-12-17

    Tests for the evolutionary conservation of associations between genes coding for transcription factors (TFs) and other genes have been limited to a few model organisms due to the lack of experimental information of functional associations in other organisms. We aimed at surmounting this limitation by using the most co-occurring gene pairs as proxies for the most conserved functional interactions available for each gene in a genome. We then used genes predicted to code for TFs to compare their most conserved interactions against the most conserved interactions for the rest of the genes within each prokaryotic genome available. We plotted profiles of phylogenetic profiles, p-cubic, to compare the maximally scoring interactions of TFs against those of other genes. In most prokaryotes, genes coding for TFs showed lower co-occurrences when compared to other genes. We also show that genes coding for TFs tend to have lower Codon Adaptation Indexes compared to other genes. The co-occurrence tests suggest that transcriptional regulation evolves quickly in most, if not all, prokaryotes. The Codon Adaptation Index analyses suggest quick gene exchange and rewiring of transcriptional regulation across prokaryotes.

  12. Selective influence of Sox2 on POU transcription factor binding in embryonic and neural stem cells.

    Science.gov (United States)

    Mistri, Tapan Kumar; Devasia, Arun George; Chu, Lee Thean; Ng, Wei Ping; Halbritter, Florian; Colby, Douglas; Martynoga, Ben; Tomlinson, Simon R; Chambers, Ian; Robson, Paul; Wohland, Thorsten

    2015-09-01

    Embryonic stem cell (ESC) identity is orchestrated by co-operativity between the transcription factors (TFs) Sox2 and the class V POU-TF Oct4 at composite Sox/Oct motifs. Neural stem cells (NSCs) lack Oct4 but express Sox2 and class III POU-TFs Oct6, Brn1 and Brn2. This raises the question of how Sox2 interacts with POU-TFs to transcriptionally specify ESCs versus NSCs. Here, we show that Oct4 alone binds the Sox/Oct motif and the octamer-containing palindromic MORE equally well. Sox2 binding selectively increases the affinity of Oct4 for the Sox/Oct motif. In contrast, Oct6 binds preferentially to MORE and is unaffected by Sox2. ChIP-Seq in NSCs shows the MORE to be the most enriched motif for class III POU-TFs, including MORE subtypes, and that the Sox/Oct motif is not enriched. These results suggest that in NSCs, co-operativity between Sox2 and class III POU-TFs may not occur and that POU-TF-driven transcription uses predominantly the MORE cis architecture. Thus, distinct interactions between Sox2 and POU-TF subclasses distinguish pluripotent ESCs from multipotent NSCs, providing molecular insight into how Oct4 alone can convert NSCs to pluripotency.

  13. DBD--taxonomically broad transcription factor predictions: new content and functionality.

    Science.gov (United States)

    Wilson, Derek; Charoensawan, Varodom; Kummerfeld, Sarah K; Teichmann, Sarah A

    2008-01-01

    DNA-binding domain (DBD) is a database of predicted sequence-specific DNA-binding transcription factors (TFs) for all publicly available proteomes. The proteomes have increased from 150 in the initial version of DBD to over 700 in the current version. All predicted TFs must contain a significant match to a hidden Markov model representing a sequence-specific DNA-binding domain family. Access to TF predictions is provided through http://transcriptionfactor.org, where new search options are now provided such as searching by gene names in model organisms, searching for all proteins in a particular DBD family and specific organism. We illustrate the application of this type of search facility by contrasting trends of DBD family occurrence throughout the tree of life, highlighting the clear partition between eukaryotic and prokaryotic DBD expansions. The website content has been expanded to include dedicated pages for each TF containing domain assignment details, gene names, links to external databases and links to TFs with similar domain arrangements. We compare the increase in number of predicted TFs with proteome size in eukaryotes and prokaryotes. Eukaryotes follow a slower rate of increase in TFs than prokaryotes, which could be due to the presence of splice variants or an increase in combinatorial control.

  14. Discovery and validation of information theory-based transcription factor and cofactor binding site motifs.

    Science.gov (United States)

    Lu, Ruipeng; Mucaki, Eliseos J; Rogan, Peter K

    2016-11-28

    Data from ChIP-seq experiments can derive the genome-wide binding specificities of transcription factors (TFs) and other regulatory proteins. We analyzed 765 ENCODE ChIP-seq peak datasets of 207 human TFs with a novel motif discovery pipeline based on recursive, thresholded entropy minimization. This approach, while obviating the need to compensate for skewed nucleotide composition, distinguishes true binding motifs from noise, quantifies the strengths of individual binding sites based on computed affinity and detects adjacent cofactor binding sites that coordinate with the targets of primary, immunoprecipitated TFs. We obtained contiguous and bipartite information theory-based position weight matrices (iPWMs) for 93 sequence-specific TFs, discovered 23 cofactor motifs for 127 TFs and revealed six high-confidence novel motifs. The reliability and accuracy of these iPWMs were determined via four independent validation methods, including the detection of experimentally proven binding sites, explanation of effects of characterized SNPs, comparison with previously published motifs and statistical analyses. We also predict previously unreported TF coregulatory interactions (e.g. TF complexes). These iPWMs constitute a powerful tool for predicting the effects of sequence variants in known binding sites, performing mutation analysis on regulatory SNPs and predicting previously unrecognized binding sites and target genes.

  15. Uncovering early response of gene regulatory networks in ES cells by systematic induction of transcription factors

    Science.gov (United States)

    Nishiyama, Akira; Xin, Li; Sharov, Alexei A.; Thomas, Marshall; Mowrer, Gregory; Meyers, Emily; Piao, Yulan; Mehta, Samir; Yee, Sarah; Nakatake, Yuhki; Stagg, Carole; Sharova, Lioudmila; Correa-Cerro, Lina S.; Bassey, Uwem; Hoang, Hien; Kim, Eugene; Tapnio, Richard; Qian, Yong; Dudekula, Dawood; Zalzman, Michal; Li, Manxiang; Falco, Geppino; Yang, Hsih-Te; Lee, Sung-Lim; Monti, Manuela; Stanghellini, Ilaria; Islam, Md. Nurul; Nagaraja, Ramaiah; Goldberg, Ilya; Wang, Weidong; Longo, Dan L.; Schlessinger, David; Ko, Minoru S. H.

    2009-01-01

    SUMMARY To examine transcription factor (TF) network(s), we created mouse ES cell lines, in each of which one of 50 TFs tagged with a FLAG moiety is inserted into a ubiquitously controllable tetracycline-repressible locus. Of the 50 TFs, Cdx2 provoked the most extensive transcriptome perturbation in ES cells, followed by Esx1, Sox9, Tcf3, Klf4, and Gata3. ChIP-Seq revealed that CDX2 binds to promoters of up-regulated target genes. By contrast, genes down-regulated by CDX2 did not show CDX2 binding, but were enriched with binding sites for POU5F1, SOX2, and NANOG. Genes with binding sites for these core TFs were also down-regulated by the induction of at least 15 other TFs, suggesting a common initial step for ES cell differentiation mediated by interference with the binding of core TFs to their target genes. These ES cell lines provide a fundamental resource to study biological networks in ES cells and mice. PMID:19796622

  16. Elicitor-induced transcription factors for metabolic reprogramming of secondary metabolism in Medicago truncatula

    Directory of Open Access Journals (Sweden)

    Dixon Richard A

    2008-12-01

    Full Text Available Abstract Background Exposure of Medicago truncatula cell suspension cultures to pathogen or wound signals leads to accumulation of various classes of flavonoid and/or triterpene defense molecules, orchestrated via a complex signalling network in which transcription factors (TFs are essential components. Results In this study, we analyzed TFs responding to yeast elicitor (YE or methyl jasmonate (MJ. From 502 differentially expressed TFs, WRKY and AP2/EREBP gene families were over-represented among YE-induced genes whereas Basic Helix-Loop-Helix (bHLH family members were more over-represented among the MJ-induced genes. Jasmonate ZIM-domain (JAZ transcriptional regulators were highly induced by MJ treatment. To investigate potential involvement of WRKY TFs in signalling, we expressed four Medicago WRKY genes in tobacco. Levels of soluble and wall bound phenolic compounds and lignin were increased in all cases. WRKY W109669 also induced tobacco endo-1,3-β-glucanase (NtPR2 and enhanced the systemic defense response to tobacco mosaic virus in transgenic tobacco plants. Conclusion These results confirm that Medicago WRKY TFs have broad roles in orchestrating metabolic responses to biotic stress, and that they also represent potentially valuable reagents for engineering metabolic changes that impact pathogen resistance.

  17. The Importance of Being Playful.

    Science.gov (United States)

    Bodrova, Elena; Leong, Deborah J.

    2003-01-01

    Recent research provides evidence of the strong connections between quality of play in preschool years and children's readiness for school instruction. Mature play, characterized by imaginary situations, multiple roles, clearly defined rules, flexible themes, language development, length of play, helps students' cognitive development. (Contains 12…

  18. Play in Evolution and Development

    Science.gov (United States)

    Pellegrini, Anthony D.; Dupuis, Danielle; Smith, Peter K.

    2007-01-01

    In this paper we examine the role of play in human ontogeny and phylogeny, following Surplus Resource Theory. We consider how juveniles use play to sample their environment in order to develop adaptive behaviors. We speculate about how innovative behaviors developed in play in response to environmental novelty may influence subsequent evolutionary…

  19. Pretend Play and Creative Processes

    Science.gov (United States)

    Russ, Sandra W.; Wallace, Claire E.

    2013-01-01

    The authors contend that many cognitive abilities and affective processes important in creativity also occur in pretend play and that pretend play in childhood affects the development of creativity in adulthood. They discuss a variety of theories and observations that attempt to explain the importance of pretend play to creativity. They argue that…

  20. P2TF: a comprehensive resource for analysis of prokaryotic transcription factors.

    Science.gov (United States)

    Ortet, Philippe; De Luca, Gilles; Whitworth, David E; Barakat, Mohamed

    2012-11-15

    Transcription factors (TFs) are DNA-binding proteins that regulate gene expression by activating or repressing transcription. Some have housekeeping roles, while others regulate the expression of specific genes in response to environmental change. The majority of TFs are multi-domain proteins, and they can be divided into families according to their domain organisation. There is a need for user-friendly, rigorous and consistent databases to allow researchers to overcome the inherent variability in annotation between genome sequences. P2TF (Predicted Prokaryotic Transcription Factors) is an integrated and comprehensive database relating to transcription factor proteins. The current version of the database contains 372,877 TFs from 1,987 completely sequenced prokaryotic genomes and 43 metagenomes. The database provides annotation, classification and visualisation of TF genes and their genetic context, providing researchers with a one-stop shop in which to investigate TFs. The P2TF database analyses TFs in both predicted proteomes and reconstituted ORFeomes, recovering approximately 3% more TF proteins than just screening predicted proteomes. Users are able to search the database with sequence or domain architecture queries, and resulting hits can be aligned to investigate evolutionary relationships and conservation of residues. To increase utility, all searches can be filtered by taxonomy, TF genes can be added to the P2TF cart, and gene lists can be exported for external analysis in a variety of formats. P2TF is an open resource for biologists, allowing exploration of all TFs within prokaryotic genomes and metagenomes. The database enables a variety of analyses, and results are presented for user exploration as an interactive web interface, which provides different ways to access and download the data. The database is freely available at http://www.p2tf.org/.

  1. Non-Digital Game Playing by Older Adults.

    Science.gov (United States)

    Mortenson, W Ben; Sixsmith, Andrew; Kaufman, David

    2017-09-01

    Research on video games' effect on cognition and behaviour has been extensive, yet little research has explored non-digital forms of game playing, especially among older adults. As part of a larger survey on game playing, 886 respondents (≥ age 55) filled out questionnaires about non-digital game play. The study aims were to determine perceived benefits of non-digital game play and to determine socio-demographic factors that might predict perceived benefits. Survey results indicate that non-digital game playing is social in nature and common (73% of respondents) among older adults. Older adults play for fun, but also to help maintain their cognition. Regression analyses indicated various socio-demographic factors - age, education, gender, and race - were independently associated with perceived benefits from game playing. The results thus emphasize the importance of non-digital game playing in this population and suggest that efforts to facilitate game playing may improve social interactions and quality of life.

  2. Identification and positional distribution analysis of transcription factor binding sites for genes from the wheat fl-cDNA sequences.

    Science.gov (United States)

    Chen, Zhen-Yong; Guo, Xiao-Jiang; Chen, Zhong-Xu; Chen, Wei-Ying; Wang, Ji-Rui

    2017-06-01

    The binding sites of transcription factors (TFs) in upstream DNA regions are called transcription factor binding sites (TFBSs). TFBSs are important elements for regulating gene expression. To date, there have been few studies on the profiles of TFBSs in plants. In total, 4,873 sequences with 5' upstream regions from 8530 wheat fl-cDNA sequences were used to predict TFBSs. We found 4572 TFBSs for the MADS TF family, which was twice as many as for bHLH (1951), B3 (1951), HB superfamily (1914), ERF (1820), and AP2/ERF (1725) TFs, and was approximately four times higher than the remaining TFBS types. The percentage of TFBSs and TF members showed a distinct distribution in different tissues. Overall, the distribution of TFBSs in the upstream regions of wheat fl-cDNA sequences had significant difference. Meanwhile, high frequencies of some types of TFBSs were found in specific regions in the upstream sequences. Both TFs and fl-cDNA with TFBSs predicted in the same tissues exhibited specific distribution preferences for regulating gene expression. The tissue-specific analysis of TFs and fl-cDNA with TFBSs provides useful information for functional research, and can be used to identify relationships between tissue-specific TFs and fl-cDNA with TFBSs. Moreover, the positional distribution of TFBSs indicates that some types of wheat TFBS have different positional distribution preferences in the upstream regions of genes.

  3. Genome-wide organization and expression profiling of the NAC transcription factor family in potato (Solanum tuberosum L.).

    Science.gov (United States)

    Singh, Anil Kumar; Sharma, Vishal; Pal, Awadhesh Kumar; Acharya, Vishal; Ahuja, Paramvir Singh

    2013-08-01

    NAC [no apical meristem (NAM), Arabidopsis thaliana transcription activation factor [ATAF1/2] and cup-shaped cotyledon (CUC2)] proteins belong to one of the largest plant-specific transcription factor (TF) families and play important roles in plant development processes, response to biotic and abiotic cues and hormone signalling. Our genome-wide analysis identified 110 StNAC genes in potato encoding for 136 proteins, including 14 membrane-bound TFs. The physical map positions of StNAC genes on 12 potato chromosomes were non-random, and 40 genes were found to be distributed in 16 clusters. The StNAC proteins were phylogenetically clustered into 12 subgroups. Phylogenetic analysis of StNACs along with their Arabidopsis and rice counterparts divided these proteins into 18 subgroups. Our comparative analysis has also identified 36 putative TNAC proteins, which appear to be restricted to Solanaceae family. In silico expression analysis, using Illumina RNA-seq transcriptome data, revealed tissue-specific, biotic, abiotic stress and hormone-responsive expression profile of StNAC genes. Several StNAC genes, including StNAC072 and StNAC101that are orthologs of known stress-responsive Arabidopsis RESPONSIVE TO DEHYDRATION 26 (RD26) were identified as highly abiotic stress responsive. Quantitative real-time polymerase chain reaction analysis largely corroborated the expression profile of StNAC genes as revealed by the RNA-seq data. Taken together, this analysis indicates towards putative functions of several StNAC TFs, which will provide blue-print for their functional characterization and utilization in potato improvement.

  4. Members of WRKY Group III transcription factors are important in TYLCV defense signaling pathway in tomato (Solanum lycopersicum).

    Science.gov (United States)

    Huang, Ying; Li, Meng-Yao; Wu, Peng; Xu, Zhi-Sheng; Que, Feng; Wang, Feng; Xiong, Ai-Sheng

    2016-10-07

    Transmitted by the whitefly Bemisia tabaci, tomato yellow leaf curly virus (TYLCV) has posed serious threats to plant growth and development. Plant innate immune systems against various threats involve WRKY Group III transcription factors (TFs). This group participates as a major component of biological processes in plants. In this study, 6 WRKY Group III TFs (SolyWRKY41, SolyWRKY42, SolyWRKY53, SolyWRKY54, SolyWRKY80, and SolyWRKY81) were identified, and these TFs responded to TYLCV infection. Subcellular localization analysis indicated that SolyWRKY41 and SolyWRKY54 were nuclear proteins in vivo. Many elements, including W-box, were found in the promoter region of Group III TFs. Interaction network analysis revealed that Group III TFs could interact with other proteins, such as mitogen-activated protein kinase 5 (MAPK) and isochorismate synthase (ICS), to respond to biotic and abiotic stresses. Positive and negative expression patterns showed that WRKY Group III genes could also respond to TYLCV infection in tomato. The DNA content of TYLCV resistant lines after SolyWRKY41 and SolyWRKY54 were subjected to virus-induced gene silencing (VIGS) was lower than that of the control lines. In the present study, 6 WRKY Group III TFs in tomato were identified to respond to TYLCV infection. Quantitative real-time-polymerase chain reaction (RT-qPCR) and VIGS analyses demonstrated that Group III genes served as positive and negative regulators in tomato-TYLCV interaction. WRKY Group III TFs could interact with other proteins by binding to cis elements existing in the promoter regions of other genes to regulate pathogen-related gene expression.

  5. Engineering zinc finger protein transcription factors to downregulate the epithelial glycoprotein-2 promoter as a novel anti-cancer treatment.

    Science.gov (United States)

    Gommans, Willemijn M; McLaughlin, Pamela M J; Lindhout, Beatrice I; Segal, David J; Wiegman, D J; Haisma, Hidde J; van der Zaal, Bert J; Rots, Marianne G

    2007-05-01

    Zinc finger protein transcription factors (ZFP-TFs) are emerging as powerful novel tools for the treatment of many different diseases. ZFPs are DNA-binding motifs and consist of modular zinc finger domains. Each domain can be engineered to recognize a specific DNA triplet, and stitching six domains together results in the recognition of a gene-specific sequence. Inhibition of gene expression can be achieved by fusing a repressor domain to these DNA-binding motifs. In this study, we engineered ZFP-TFs to downregulate the activity of the epithelial glycoprotein-2 (EGP-2) promoter. The protein EGP-2 is overexpressed in a wide variety of cancer types and EGP-2 downregulation has been shown to result in a decreased oncogenic potential of tumor cells. Therefore, downregulation of EGP-2 expression by ZFP-TFs provides a novel anti-cancer therapeutic. Using a straightforward strategy, we engineered a 3-ZFP that could bind a 9 bp sequence within the EGP-2 promoter. After the addition of a repressor domain, this 3-ZFP-TF could efficiently downregulate EGP-2 promoter activity by 60%. To demonstrate the flexibility of this technology, we coupled an activation domain to the engineered ZFP, resulting in a nearly 200% increase in EGP-2 promoter activity. To inhibit the endogenous EGP-2 promoter, we engineered 6-ZFP-TFs. Although none of the constructed ZFP-TFs could convincingly modulate the endogenous promoter, efficient and specific inhibition of the exogenous promoter was observed. Overall, ZFP-TFs are versatile bi-directional modulators of gene expression and downregulation of EGP-2 promoter activity using ZFP-TFs can ultimately result in a novel anti-cancer treatment.

  6. Motivations for play in computer role-playing games

    DEFF Research Database (Denmark)

    Tychsen, Anders; Hitchens, Michael; Brolund, Thea

    2008-01-01

    In this paper the motivations for play in the context of single-and multi-player digital Role-Playing Games (RPGs) are examined. Survey data were drawn from respondents online and participants in a related experimental study. The results indicate that motivations for play are not simple constructs......, but rather composed of multiple motivational drivers that are heavily interrelated and act in concert. Character uniqueness and Discovery & Immersion were the highest ranked motivational categories. Different levels of detail in motivations for playing single-/multi- Player RPGs were located...

  7. Cooperativity and rapid evolution of cobound transcription factors in closely related mammals.

    Science.gov (United States)

    Stefflova, Klara; Thybert, David; Wilson, Michael D; Streeter, Ian; Aleksic, Jelena; Karagianni, Panagiota; Brazma, Alvis; Adams, David J; Talianidis, Iannis; Marioni, John C; Flicek, Paul; Odom, Duncan T

    2013-08-01

    To mechanistically characterize the microevolutionary processes active in altering transcription factor (TF) binding among closely related mammals, we compared the genome-wide binding of three tissue-specific TFs that control liver gene expression in six rodents. Despite an overall fast turnover of TF binding locations between species, we identified thousands of TF regions of highly constrained TF binding intensity. Although individual mutations in bound sequence motifs can influence TF binding, most binding differences occur in the absence of nearby sequence variations. Instead, combinatorial binding was found to be significant for genetic and evolutionary stability; cobound TFs tend to disappear in concert and were sensitive to genetic knockout of partner TFs. The large, qualitative differences in genomic regions bound between closely related mammals, when contrasted with the smaller, quantitative TF binding differences among Drosophila species, illustrate how genome structure and population genetics together shape regulatory evolution.

  8. An Efficient Method to Identify Conditionally Activated Transcription Factors and their Corresponding Signal Transduction Pathway Segments

    Directory of Open Access Journals (Sweden)

    Haiyan Hu

    2009-11-01

    Full Text Available A signal transduction pathway (STP is a cascade composed of a series of signal transferring steps, which often activate one or more transcription factors (TFs to control the transcription of target genes. Understanding signaling pathways is important to our understanding of the molecular mechanisms of disease. Many condition-annotated pathways have been deposited in public databases. However, condition-annotated pathways are far from complete, considering the large number of possible conditions. Computational methods to assist in the identification of conditionally activated pathways are greatly needed. In this paper, we propose an efficient method to identify conditionally activated pathway segments starting from the identification of conditionally activated TFs, by incorporating protein-DNA binding data, gene expression data and protein interaction data. Applying our methods on several microarray datasets, we have discovered many significantly activated TFs and their corresponding pathway segments, which are supported by evidence in the literature.

  9. Controllability analysis of transcriptional regulatory networks reveals circular control patterns among transcription factors

    DEFF Research Database (Denmark)

    Österlund, Tobias; Bordel, Sergio; Nielsen, Jens

    2015-01-01

    Transcriptional regulation is the most committed type of regulation in living cells where transcription factors (TFs) control the expression of their target genes and TF expression is controlled by other TFs forming complex transcriptional regulatory networks that can be highly interconnected. Here...... we analyze the topology and organization of nine transcriptional regulatory networks for E. coli, yeast, mouse and human, and we evaluate how the structure of these networks influences two of their key properties, namely controllability and stability. We calculate the controllability for each network...... as a measure of the organization and interconnectivity of the network. We find that the number of driver nodes n(D) needed to control the whole network is 64% of the TFs in the E. coli transcriptional regulatory network in contrast to only 17% for the yeast network, 4% for the mouse network and 8...

  10. Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape.

    Science.gov (United States)

    Sherwood, Richard I; Hashimoto, Tatsunori; O'Donnell, Charles W; Lewis, Sophia; Barkal, Amira A; van Hoff, John Peter; Karun, Vivek; Jaakkola, Tommi; Gifford, David K

    2014-02-01

    We describe protein interaction quantitation (PIQ), a computational method for modeling the magnitude and shape of genome-wide DNase I hypersensitivity profiles to identify transcription factor (TF) binding sites. Through the use of machine-learning techniques, PIQ identified binding sites for >700 TFs from one DNase I hypersensitivity analysis followed by sequencing (DNase-seq) experiment with accuracy comparable to that of chromatin immunoprecipitation followed by sequencing (ChIP-seq). We applied PIQ to analyze DNase-seq data from mouse embryonic stem cells differentiating into prepancreatic and intestinal endoderm. We identified 120 and experimentally validated eight 'pioneer' TF families that dynamically open chromatin. Four pioneer TF families only opened chromatin in one direction from their motifs. Furthermore, we identified 'settler' TFs whose genomic binding is principally governed by proximity to open chromatin. Our results support a model of hierarchical TF binding in which directional and nondirectional pioneer activity shapes the chromatin landscape for population by settler TFs.

  11. Regulatory Network of Transcription Factors in Response to Drought in Arabidopsis and Crops

    Institute of Scientific and Technical Information of China (English)

    Chen Li-miao; Li Wen-bin; Zhou Xin-an

    2012-01-01

    Drought is one of the most important environmental constraints limiting plant growth, development and crop yield. Many drought-inducible genes have been identified by molecular and genomic analyses in Arabidopsis, rice and other crops. To better understand reaction mechanism of plant to drought tolerance, we mainly focused on introducing the research of transcription factors (TFs) in signal transduction and regulatory network of gene expression conferring drought. A TF could bind multiple target genes to increase one or more kinds of stress tolerance. Sometimes, several TFs might act together with a target gene. So drought-tolerance genes or TFs might respond to high-salinity, cold or other stresses. The crosstalk of multiple stresses signal pathways is a crucial aspect of understanding stress signaling.

  12. Identifying cooperative transcription factors by combining ChIP-chip data and knockout data

    Institute of Scientific and Technical Information of China (English)

    Yi Yang; Zili Zhang; Yixue Li; Xin-Guang Zhu; Qi Liu

    2010-01-01

    @@ Dear Editor, Eukaryotic transcriptional regulation networks are extremely complex.Usually,multiple transcription factors(TFs)bind to the promoter region of a gene and cooperate to control gene expression precisely.Identifying cooperative TFs remains a major challenge in modern biological research.Various types of data,including genomic sequences,expression profiles,ChiP-chip data and protein-protein interactions,have been used to identify mechanisms of cooperative transcriptional regulation.However,because of the noise inherent in these data and the fact that each data source only provides partial information about regulation,combining multiple types of data to improve their ability to infer cooperative TFs is advantageous[1-3].

  13. Behavioral approaches to promoting play.

    Science.gov (United States)

    Stahmer, Aubyn C; Ingersoll, Brooke; Carter, Cynthia

    2003-12-01

    A variety of techniques grounded in behavioral psychology, and more specifically in applied behavior analysis, have been established to increase and improve play skills in children with autistic spectrum disorders. This article introduces a set of efficacious methods, which range from highly structured techniques to more naturalistic strategies. It focuses on object play as other authors in the issue discuss social play in greater depth. Behavioral techniques that are reviewed include: discrete trial training, use of stereotyped behaviors to increase play skills, pivotal response training, reciprocal imitation training, differential reinforcement of appropriate behavior, in vivo modeling and play scripts, and video modeling. A discussion of expanding behavior techniques to teach more complex play as well as training in varied environments is also presented. References are provided to allow the reader to obtain more in-depth information about each technique.

  14. Playing with the Multiple Intelligences: How Play Helps Them Grow

    Science.gov (United States)

    Eberle, Scott G.

    2011-01-01

    Howard Gardner first posited a list of "multiple intelligences" as a liberating alternative to the assumptions underlying traditional IQ testing in his widely read study "Frames of Mind" (1983). Play has appeared only in passing in Gardner's thinking about intelligence, however, even though play instructs and trains the verbal, interpersonal,…

  15. Let's Play: Teaching Play Skills to Young Children with Autism

    Science.gov (United States)

    Boutot, E. Amanda; Guenther, Tracee; Crozier, Shannon

    2005-01-01

    Watch any young child and you will likely see him or her engaged in some form of play. Play is an integral part of early childhood development in which typically developing children learn social and language skills, as well as appropriate behaviors, problem solving, and a variety of other cognitive skills. By its very definition, autism is a…

  16. PlayFit: Designing playful activity interventions for teenagers

    NARCIS (Netherlands)

    M. M. Deen; Rob Tieben; Dr. Tilde Bekker; Dr. Janienke Sturm; B.A.M. Ben Schouten

    2011-01-01

    Young people spend a large part of their day sedentary, both at school and at home. The aim of the PlayFit project is to persuade teenagers to lead a more active lifestyle by using digital as well as non-digital games and play. In this position paper, we describe in detail the three key principles o

  17. The Temporal Focus Scale: Factor Structure and Association with Alcohol Use in a Sample of Northern Irish School Children

    Science.gov (United States)

    McKay, Michael T.; Percy, Andrew; Goudie, Andrew J.; Sumnall, Harry R.; Cole, Jon C.

    2012-01-01

    The Temporal Focus Scale (TFS) is a 12-item self-report measure of cognitive engagement with the temporal domains of past, present and future. Developed in college student samples, a three-factor structure with adequate reliability and validity was documented in a series of independent studies. We tested the factor structure of the scale in a…

  18. Children's active play: self-reported motivators, barriers and facilitators

    Directory of Open Access Journals (Sweden)

    Rowan Brockman

    2011-06-01

    Full Text Available Physical activity has important benefits for children's physical health and mental wellbeing, but many children do not meet recommended levels. Research suggests that active play has the potential to make a valuable contribution to children's overall physical activity, whilst providing additional cognitive, social and emotional benefits. However, relatively little is known about the determinants of UK children's active play. Understanding these factors provides the critical first step in developing interventions to increase children's active play, and therefore overall physical activity. Eleven focus groups were conducted with 77, 10-11 year old children from four primary schools in Bristol, UK. Focus groups examined: (i factors which motivate children to take part in active play; (ii factors which limit children's active play and (iii factors which facilitate children's active play. All focus groups were audio-taped and transcribed verbatim. Data were analysed using a thematic approach. Children were motivated to engage in active play because they perceived it to be enjoyable, to prevent boredom, to have physical and mental health benefits and to provide freedom from adult control, rules and structure. However, children's active play was constrained by a number of factors, including rainy weather and fear of groups of teenagers in their play spaces. Some features of the physical environment facilitated children's active play, including the presence of green spaces and cul-de-sacs in the neighbourhood. Additionally, children's use of mobile phones when playing away from home was reported to help to alleviate parents' safety fears, and therefore assist children's active play. Children express a range of motivational and environmental factors that constrain and facilitate their active play. Consideration of these factors should improve effectiveness of interventions designed to increase active play.

  19. "Reluctant Participants" in Role Play Simulations: Stage Fright or Bewilderment?

    Science.gov (United States)

    Saunders, Danny

    1985-01-01

    Discusses factors contributing to participant reluctance in role playing--isolation of role play from the curriculum; lack of interest because of perceived irrelevance to social psychological themes; and acting anxiety. A two-step design which involves gradual role play introduction and observation by reluctant participants is suggested as a…

  20. The Internet of Playful Things

    DEFF Research Database (Denmark)

    Wyeth, Peta; Brereton, Margot; Roe, Paul;

    2015-01-01

    This one-day workshop brings together researchers and practitioners to share knowledge and practices on how people can connect and interact with the Internet of Things in a playful way. Open to participants with a diverse range of interests and expertise, and by exploring novel ways to playfully...... will be a road map to support the development of a Model of Playful Connectedness, focusing on how best to design and make playful networks of things, identifying the challenges that need to be addressed in order to do so....

  1. Symbolic play and language development.

    Science.gov (United States)

    Orr, Edna; Geva, Ronny

    2015-02-01

    Symbolic play and language are known to be highly interrelated, but the developmental process involved in this relationship is not clear. Three hypothetical paths were postulated to explore how play and language drive each other: (1) direct paths, whereby initiation of basic forms in symbolic action or babbling, will be directly related to all later emerging language and motor outputs; (2) an indirect interactive path, whereby basic forms in symbolic action will be associated with more complex forms in symbolic play, as well as with babbling, and babbling mediates the relationship between symbolic play and speech; and (3) a dual path, whereby basic forms in symbolic play will be associated with basic forms of language, and complex forms of symbolic play will be associated with complex forms of language. We micro-coded 288 symbolic vignettes gathered during a yearlong prospective bi-weekly examination (N=14; from 6 to 18 months of age). Results showed that the age of initiation of single-object symbolic play correlates strongly with the age of initiation of later-emerging symbolic and vocal outputs; its frequency at initiation is correlated with frequency at initiation of babbling, later-emerging speech, and multi-object play in initiation. Results support the notion that a single-object play relates to the development of other symbolic forms via a direct relationship and an indirect relationship, rather than a dual-path hypothesis.

  2. Multispecies methods, technologies for play

    DEFF Research Database (Denmark)

    Jørgensen, Ida Kathrine Hammeleff; Wirman, Hanna

    2016-01-01

    reveals limitations of designers’ knowledge of prospected users. The article explores how to approach participants who cannot express themselves verbally and how to recognise play that may not look familiar to the designer. The article finally presents a participatory design method that allows for non......-human contributions in design. This method applies play as an interspecies co-creative act and can be used as a starting point for addressing questions of difference in play and designing games that allow for ambiguous play....

  3. Transcription factor-based biosensors enlightened by the analyte.

    Directory of Open Access Journals (Sweden)

    Raul eFernandez-Lopez

    2015-07-01

    Full Text Available Whole cell biosensors (WCBs have multiple applications for environmental monitoring, detecting a wide range of pollutants. WCBs depend critically on the sensitivity and specificity of the transcription factor (TF used to detect the analyte. We describe the mechanism of regulation and the structural and biochemical properties of TF families that are used, or could be used, for the development of environmental WCBs. Focusing on the chemical nature of the analyte, we review TFs that respond to aromatic compounds (XylS-AraC, XylR-NtrC and LysR, metal ions (MerR, ArsR, DtxR, Fur and NikR or antibiotics (TetR and MarR. Analyzing the structural domains involved in DNA recognition, we highlight the similitudes in the DNA binding domains (DBDs of these TF families. Opposite to DBDs, the wide range of analytes detected by TFs results in a diversity of structures at the effector binding domain (EBD. The modular architecture of TFs opens the possibility of engineering TFs with hybrid DNA and effector specificities. Yet, the lack of a crisp correlation between structural domains and specific functions makes this a challenging task.

  4. AP2/ERF Transcription Factors Involved in Response to Tomato Yellow Leaf Curly Virus in Tomato

    Directory of Open Access Journals (Sweden)

    Ying Huang

    2016-07-01

    Full Text Available Tomato yellow leaf curly virus (TYLCV, transmitted by the whitefly (, causes leaf curling and yellowing, plant dwarfism, and growth inhibition in tomato ( L.. The APETALA2 (AP2 and ethylene response factor (ERF transcription factor (TF family, the largest plant-specific TF family, was identified to function in plant development and pathogen defense. Our study aimed to analyze the mechanism underlying the function of ERF (SlERF TFs in response to TYLCV infection and improve useful information to increase the resistance to TYLCV in tomato. A total of 22 tomato AP2/ERF TFs in response to TYLCV were identified according to transcriptome database. Five ERF-B3 TFs were identified in cultivars Hongbeibei (highly resistant, Zheza-301, Zhefen-702 (both resistant, Jinpeng-1, and Xianke-6 (both susceptible. Interaction network indicated that SlERF TFs could interact with mitogen-activated protein kinase (MAPK. Expression profiles of five ERF-B3 genes (, , , , and were detected by quantitative real-time–polymerase chain reaction (qRT-PCR after TYLCV infection in five tomato cultivars. expression was upregulated in five tomato cultivars. The expressions of three genes (, , and were upregulated in Zheza-301 and Zhefen-702. and expressions were downregulated in Hongbeibei and Xianke-6, respectively. Yeast one-hybrid showed that the GCC-box binding ability of ERF-B3 TFs differed in resistant and susceptible tomato cultivars. Expression profiles were related to the GCC-box binding ability of SlERF TFs in resistant and susceptible tomato cultivars. The defense mechanism underlying the tomato’s response to TYLCV involved a complicated network, which provided important information for us in breeding and genetic analysis.

  5. The Influence of Play Context and Adult Attitudes on Young Children's Physical Risk-Taking during Outdoor Play

    Science.gov (United States)

    Little, Helen; Wyver, Shirley; Gibson, Frances

    2011-01-01

    Many children naturally seek challenging physically active play which may involve injury-risk. Prior studies have attempted to describe the characteristics of risky play but to date none have considered factors that impact on opportunities for risky play or the likely resultant outcomes. Using semi-structured interviews and naturalistic…

  6. The Influence of Play Context and Adult Attitudes on Young Children's Physical Risk-Taking during Outdoor Play

    Science.gov (United States)

    Little, Helen; Wyver, Shirley; Gibson, Frances

    2011-01-01

    Many children naturally seek challenging physically active play which may involve injury-risk. Prior studies have attempted to describe the characteristics of risky play but to date none have considered factors that impact on opportunities for risky play or the likely resultant outcomes. Using semi-structured interviews and naturalistic…

  7. Seductive play in digital games

    DEFF Research Database (Denmark)

    Jørgensen, Ida Kathrine Hammeleff

    2015-01-01

    seduction is meaningless because it is nothing but appearances – a sign without reference. In his conceptualization of seduction Baudrillard draws heavily upon Huizinga’s (1950) and Callois’ (1961) theory of play. To Baudrillard play is the mode of the seductive. But in contrast to both Callois and Huizinga...

  8. Making Play Work for Education

    Science.gov (United States)

    Weisberg, Deena Skolnick; Kittredge, Audrey K.; Hirsh-Pasek, Kathy; Golinkoff, Roberta Michnick; Klahr, David

    2015-01-01

    Children, especially in the preschool years, learn a tremendous amount through play. Research on guided play demonstrates how schools can couple a curriculum-centered preschool program with a developmentally appropriate pedagogical approach to classroom teaching. However, to fully test this claim, we need a clear definition of the term…

  9. Transmedia Play: Literacy across Media

    Science.gov (United States)

    Alper, Meryl; Herr-Stephenson, Rebecca

    2013-01-01

    Transmedia play is a new way to understand how children develop critical media literacy and new media literacies through their interactions with contemporary media that links stories and structures across platforms. This essay highlights five characteristics of transmedia play that make it particularly useful for learning:…

  10. Sand and Water Table Play

    Science.gov (United States)

    Wallace, Ann H.; White, Mary J.; Stone, Ryan

    2010-01-01

    The authors observed preschoolers engaged at the sand and water table to determine if math could be found within their play. Wanting to understand how children interact with provided materials and what kinds of math ideas they explore during these interactions, the authors offer practical examples of how such play can promote mathematical…

  11. Playful Interfaces: Introduction and History

    NARCIS (Netherlands)

    Nijholt, Anton; Nijholt, Anton

    2014-01-01

    In this short survey we have some historical notes about human-computer interface development with an emphasis on interface technology that has allowed us to design playful interactions with applications. The applications do not necessarily have to be entertainment applications. We can have playful

  12. Young Children and War Play.

    Science.gov (United States)

    Carlsson-Paige, Nancy; Levin, Diane E.

    1988-01-01

    In a recent survey of parents and early childhood professionals the prevalence of war play among children and an increase in the amount of violence in children's play was noted. Outlines how the deregulation of children's television during the Reagan administration has affected children's exposure to violence in children's television programming.…

  13. Sand and Water Table Play

    Science.gov (United States)

    Wallace, Ann H.; White, Mary J.; Stone, Ryan

    2010-01-01

    The authors observed preschoolers engaged at the sand and water table to determine if math could be found within their play. Wanting to understand how children interact with provided materials and what kinds of math ideas they explore during these interactions, the authors offer practical examples of how such play can promote mathematical…

  14. The Fractal Self at Play

    Science.gov (United States)

    Marks-Tarlow, Terry

    2010-01-01

    In this article, the author draws on contemporary science to illuminate the relationship between early play experiences, processes of self-development, and the later emergence of the fractal self. She argues that orientation within social space is a primary function of early play and developmentally a two-step process. With other people and with…

  15. The Play of Socratic Dialogue

    Science.gov (United States)

    Smith, Richard

    2011-01-01

    Proponents of philosophy for children generally see themselves as heirs to the "Socratic" tradition. They often claim too that children's aptitude for play leads them naturally to play with abstract, philosophical ideas. However in Plato's dialogues we find in the mouth of "Socrates" many warnings against philosophising with the young. Those…

  16. Empowering Groups that Enable Play

    Science.gov (United States)

    Wilson, David Sloan; Marshall, Danielle; Iserhott, Hindi

    2011-01-01

    Creating play environments for children usually requires groups of adults working together. An extensive scientific literature describes how groups function to achieve shared goals in general terms, and groups attempting to empower play may find this literature useful. Design principles for managing natural resources, identified by Elinor Ostrom…

  17. Let's Play Three on Three!

    Science.gov (United States)

    Kern, Jack; Calleja, Paul

    2008-01-01

    Over the course of nine years as a supervisor of intern teachers, the first author collected observations of game play during lessons taught by intern teachers or their mentors. In general, the observations indicated that the majority of students got limited practice opportunities during game play. A close look at the data revealed an interesting…

  18. TF-Cluster: A pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM

    Directory of Open Access Journals (Sweden)

    Thomson James A

    2011-04-01

    Full Text Available Abstract Background Identifying the key transcription factors (TFs controlling a biological process is the first step toward a better understanding of underpinning regulatory mechanisms. However, due to the involvement of a large number of genes and complex interactions in gene regulatory networks, identifying TFs involved in a biological process remains particularly difficult. The challenges include: (1 Most eukaryotic genomes encode thousands of TFs, which are organized in gene families of various sizes and in many cases with poor sequence conservation, making it difficult to recognize TFs for a biological process; (2 Transcription usually involves several hundred genes that generate a combination of intrinsic noise from upstream signaling networks and lead to fluctuations in transcription; (3 A TF can function in different cell types or developmental stages. Currently, the methods available for identifying TFs involved in biological processes are still very scarce, and the development of novel, more powerful methods is desperately needed. Results We developed a computational pipeline called TF-Cluster for identifying functionally coordinated TFs in two steps: (1 Construction of a shared coexpression connectivity matrix (SCCM, in which each entry represents the number of shared coexpressed genes between two TFs. This sparse and symmetric matrix embodies a new concept of coexpression networks in which genes are associated in the context of other shared coexpressed genes; (2 Decomposition of the SCCM using a novel heuristic algorithm termed "Triple-Link", which searches the highest connectivity in the SCCM, and then uses two connected TF as a primer for growing a TF cluster with a number of linking criteria. We applied TF-Cluster to microarray data from human stem cells and Arabidopsis roots, and then demonstrated that many of the resulting TF clusters contain functionally coordinated TFs that, based on existing literature, accurately represent

  19. Statistical Reconstruction of Transcription Factor Activity Using Michaelis–Menten Kinetics

    NARCIS (Netherlands)

    Khanin, R.; Vinciotti, V.; Mersinias, V.; Smith, C.P.; Wit, Ernst

    The basic building block of a gene regulatory network consists of a gene encoding a transcription factor (TF) and the gene(s) it regulates. Considerable efforts have been directed recently at devising experiments and algorithms to determine TFs and their corresponding target genes using gene

  20. CRITERIA FOR AN UPDATED CLASSIFICATION OF HUMAN TRANSCRIPTION FACTOR DNA-BINDING DOMAINS

    NARCIS (Netherlands)

    Wingender, Edgar

    2013-01-01

    By binding to cis-regulatory elements in a sequence-specific manner, transcription factors regulate the activity of nearby genes. Here, we discuss the criteria for a comprehensive classification of human TFs based on their DNA-binding domains. In particular, classification of basic leucine zipper (b

  1. CRITERIA FOR AN UPDATED CLASSIFICATION OF HUMAN TRANSCRIPTION FACTOR DNA-BINDING DOMAINS

    NARCIS (Netherlands)

    Wingender, Edgar

    By binding to cis-regulatory elements in a sequence-specific manner, transcription factors regulate the activity of nearby genes. Here, we discuss the criteria for a comprehensive classification of human TFs based on their DNA-binding domains. In particular, classification of basic leucine zipper

  2. Orphan nuclear receptor TR4 and fibroblast growth factor 1 in metabolism

    NARCIS (Netherlands)

    Liu, Weilin

    2016-01-01

    Metabolic homeostasis is achieved, in part, through the coordinated activities of members of the Nuclear Receptor (NR) family, a superfamily of ligand-modulated transcription factors (TFs) that mediate responses to a wide range of lipophilic signaling molecules including lipids, steroids, retinoids,

  3. Statistical Reconstruction of Transcription Factor Activity Using Michaelis–Menten Kinetics

    NARCIS (Netherlands)

    Khanin, R.; Vinciotti, V.; Mersinias, V.; Smith, C.P.; Wit, Ernst

    2007-01-01

    The basic building block of a gene regulatory network consists of a gene encoding a transcription factor (TF) and the gene(s) it regulates. Considerable efforts have been directed recently at devising experiments and algorithms to determine TFs and their corresponding target genes using gene express

  4. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

    DEFF Research Database (Denmark)

    Portales-Casamar, Elodie; Thongjuea, Supat; Kwon, Andrew T

    2009-01-01

    JASPAR (http://jaspar.genereg.net) is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. Its fourth major release is the largest expansion of the core database...

  5. An expression analysis of 57 transcription factors derived from ESTs of developing seeds in Maize (Zea mays).

    Science.gov (United States)

    Wang, Guifeng; Wang, Hui; Zhu, Jia; Zhang, Jing; Zhang, Xiaowei; Wang, Fei; Tang, Yuanping; Mei, Bing; Xu, Zhengkai; Song, Rentao

    2010-06-01

    Maize seeds are an important source of food, animal feed, and industrial raw materials. To understand global gene expression and regulation during maize seed development, a normalized cDNA library, covering most of the developmental stages of maize seeds, was constructed. Sequencing analysis of 10,848 randomly selected clones identified 6,630 unique ESTs. Among them, 57 putative transcription factors (TFs) were identified. The TFs belong to seven different super-families, specifically 17 Zinc-finger, 13 bZIP, 8 bHLH, 6 MADS, 7 MYB, 3 Homedomain, and 3 AP2/EREBP. The spatial and temporal expression of the TFs was analyzed by semi-quantitative RT-PCR with representative tissue types and seeds at different developmental stages, revealing their diverse expression patterns and expression levels. One-third (19) of the maize TFs was found their putative orthologs in Arabidopsis. Similar expression patterns were observed in both maize and Arabidopsis for the majority of orthologous pairs (15 out of 19), suggesting their conserved functions during seed development. In conclusion, the systematic analysis of maize seed TFs has provided valuable insight into transcriptional regulation during maize seed development.

  6. A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data.

    Science.gov (United States)

    Orenstein, Yaron; Shamir, Ron

    2014-04-01

    Understanding gene regulation is a key challenge in today's biology. The new technologies of protein-binding microarrays (PBMs) and high-throughput SELEX (HT-SELEX) allow measurement of the binding intensities of one transcription factor (TF) to numerous synthetic double-stranded DNA sequences in a single experiment. Recently, Jolma et al. reported the results of 547 HT-SELEX experiments covering human and mouse TFs. Because 162 of these TFs were also covered by PBM technology, for the first time, a large-scale comparison between implementations of these two in vitro technologies is possible. Here we assessed the similarities and differences between binding models, represented as position weight matrices, inferred from PBM and HT-SELEX, and also measured how well these models predict in vivo binding. Our results show that HT-SELEX- and PBM-derived models agree for most TFs. For some TFs, the HT-SELEX-derived models are longer versions of the PBM-derived models, whereas for other TFs, the HT-SELEX models match the secondary PBM-derived models. Remarkably, PBM-based 8-mer ranking is more accurate than that of HT-SELEX, but models derived from HT-SELEX predict in vivo binding better. In addition, we reveal several biases in HT-SELEX data including nucleotide frequency bias, enrichment of C-rich k-mers and oligos and underrepresentation of palindromes.

  7. On the Fair Play Spirit%论Fair Play

    Institute of Scientific and Technical Information of China (English)

    张维; 林琳

    2011-01-01

    采用文献资料法,历史分析了"Fair Play"精神的起源,并结合Fair Play精神面临的时代压力,探讨现代体育生命力延续的议题,提出"人"才是体育及其"Fair Play"精神继续生存或走向毁灭的主宰者.

  8. Playful biometrics: controversial technology through the lens of play.

    Science.gov (United States)

    Ellerbrok, Ariane

    2011-01-01

    This article considers the role of play in the context of technological emergence and expansion, particularly as it relates to recently emerging surveillance technologies. As a case study, I consider the trajectory of automated face recognition—a biometric technology of numerous applications, from its more controversial manifestations under the rubric of national security to a clearly emerging orientation toward play. This shift toward “playful” biometrics—or from a technology traditionally coded as “hard” to one now increasingly coded as “soft”—is critical insofar as it renders problematic the traditional modes of critique that have, up until this point, challenged the expansion of biometric systems into increasingly ubiquitous realms of everyday life. In response to this dynamic, I propose theorizing the expansion of face recognition specifically in relation to “play,” a step that allows us to broaden the critical space around newly emerging playful biometrics, as well as playful surveillance more generally. In addition, play may also have relevance for theorizing other forms of controversial technology, particularly given its potential role in processes of obfuscation, normalization, and marginalization.

  9. Global analysis of WRKY transcription factor superfamily in Setaria identifies potential candidates involved in abiotic stress signalling

    Directory of Open Access Journals (Sweden)

    Mehanathan eMuthamilarasan

    2015-10-01

    Full Text Available Transcription factors (TFs are major players in stress signalling and constitute an integral part of signalling networks. Among the major TFs, WRKY proteins play pivotal roles in regulation of transcriptional reprogramming associated with stress responses. In view of this, genome- and transcriptome-wide identification of WRKY TF family was performed in the C4 model plants, Setaria italica (SiWRKY and S. viridis (SvWRKY, respectively. The study identified 105 SiWRKY and 44 SvWRKY proteins that were computationally analysed for their physicochemical properties. Sequence alignment and phylogenetic analysis classified these proteins into three major groups, namely I, II and III with majority of WRKY proteins belonging to group II (53 SiWRKY and 23 SvWRKY, followed by group III (39 SiWRKY and 11 SvWRKY and group I (10 SiWRKY and 6 SvWRKY. Group II proteins were further classified into 5 subgroups (IIa to IIe based on their phylogeny. Domain analysis showed the presence of WRKY motif and zinc finger-like structures in these proteins along with additional domains in a few proteins. All SiWRKY genes were physically mapped on the S. italica genome and their duplication analysis revealed that 10 and 8 gene pairs underwent tandem and segmental duplications, respectively. Comparative mapping of SiWRKY and SvWRKY genes in related C4 panicoid genomes demonstrated the orthologous relationships between these genomes. In silico expression analysis of SiWRKY and SvWRKY genes showed their differential expression patterns in different tissues and stress conditions. Expression profiling of candidate SiWRKY genes in response to stress (dehydration and salinity and hormone treatments (abscisic acid, salicylic acid and methyl jasmonate suggested the putative involvement of SiWRKY066 and SiWRKY082 in stress and hormone signalling. These genes could be potential candidates for further characterization to delineate their functional roles in abiotic stress signalling.

  10. Identification and expression of the WRKY transcription factors of Carica papaya in response to abiotic and biotic stresses.

    Science.gov (United States)

    Pan, Lin-Jie; Jiang, Ling

    2014-03-01

    The WRKY transcription factor (TF) plays a very important role in the response of plants to various abiotic and biotic stresses. A local papaya database was built according to the GenBank expressed sequence tag database using the BioEdit software. Fifty-two coding sequences of Carica papaya WRKY TFs were predicted using the tBLASTn tool. The phylogenetic tree of the WRKY proteins was classified. The expression profiles of 13 selected C. papaya WRKY TF genes under stress induction were constructed by quantitative real-time polymerase chain reaction. The expression levels of these WRKY genes in response to 3 abiotic and 2 biotic stresses were evaluated. TF807.3 and TF72.14 are upregulated by low temperature; TF807.3, TF43.76, TF12.199 and TF12.62 are involved in the response to drought stress; TF9.35, TF18.51, TF72.14 and TF12.199 is involved in response to wound; TF12.199, TF807.3, TF21.156 and TF18.51 was induced by PRSV pathogen; TF72.14 and TF43.76 are upregulated by SA. The regulated expression levels of above eight genes normalized against housekeeping gene actin were significant at probability of 0.01 levels. These WRKY TFs could be related to corresponding stress resistance and selected as the candidate genes, especially, the two genes TF807.3 and TF12.199, which were regulated notably by four stresses respectively. This study may provide useful information and candidate genes for the development of transgenic stress tolerant papaya varieties.

  11. Mutations in transcription factor Mrr2p contribute to fluconazole resistance in clinical isolates of Candida albicans.

    Science.gov (United States)

    Wang, Ying; Liu, Jin-Yan; Shi, Ce; Li, Wen-Jing; Zhao, Yue; Yan, Lan; Xiang, Ming-Jie

    2015-11-01

    The Candida albicans zinc cluster proteins are a family of transcription factors (TFs) that play essential roles in the development of antifungal drug resistance. Gain-of-function mutations in several TFs, such as Tac1p, Mrr1p and Upc2p, have been previously well documented in azole-resistant clinical C. albicans isolates. Mrr2p (multidrug resistance regulator 2) is a novel TF controlling expression of the ABC transporter gene CDR1 and mediating fluconazole resistance. In this study, the relationship between naturally occurring mutations in MRR2 and fluconazole resistance in clinical C. albicans isolates was investigated. Among a group of 20 fluconazole-resistant clinical C. albicans and 10 fluconazole-susceptible C. albicans, 12 fluconazole-resistant isolates overexpressed CDR1 by at least two-fold compared with the fluconazole-susceptible isolates. Of these 12 resistant isolates, three (C7, C9, C15) contained 11 identical missense mutations, 6 of which occurred only in the azole-resistant isolates. The contribution of these mutations to CDR1 overexpression and therefore to fluconazole resistance was further verified by generating recombinant strains containing the mutated MRR2 gene. The mutated MRR2 alleles from isolate C9 contributed to an almost six-fold increase in CDR1 expression and an eight-fold increase in fluconazole resistance; the missense mutations S466L and T470N resulted in an increase in CDR1 expression of more than two-fold and a four-fold increase in fluconazole resistance. In contrast, the other four missense mutations conferred only two- to four-fold increases in fluconazole resistance, with no significant increase in CDR1 expression. These findings provide some insight into the mechanism by which MRR2 regulates C. albicans multidrug resistance.

  12. Generation of Wheat Transcription Factor FOX Rice Lines and Systematic Screening for Salt and Osmotic Stress Tolerance.

    Directory of Open Access Journals (Sweden)

    Jinxia Wu

    Full Text Available Transcription factors (TFs play important roles in plant growth, development, and responses to environmental stress. In this study, we collected 1,455 full-length (FL cDNAs of TFs, representing 45 families, from wheat and its relatives Triticum urartu, Aegilops speltoides, Aegilops tauschii, Triticum carthlicum, and Triticum aestivum. More than 15,000 T0 TF FOX (Full-length cDNA Over-eXpressing rice lines were generated; of these, 10,496 lines set seeds. About 14.88% of the T0 plants showed obvious phenotypic changes. T1 lines (5,232 lines were screened for salt and osmotic stress tolerance using 150 mM NaCl and 20% (v/v PEG-4000, respectively. Among them, five lines (591, 746, 1647, 1812, and J4065 showed enhanced salt stress tolerance, five lines (591, 746, 898, 1078, and 1647 showed enhanced osmotic stress tolerance, and three lines (591, 746, and 1647 showed both salt and osmotic stress tolerance. Further analysis of the T-DNA flanking sequences showed that line 746 over-expressed TaEREB1, line 898 over-expressed TabZIPD, and lines 1812 and J4065 over-expressed TaOBF1a and TaOBF1b, respectively. The enhanced salt and osmotic stress tolerance of lines 898 and 1812 was confirmed by retransformation of the respective genes. Our results demonstrate that a heterologous FOX system may be used as an alternative genetic resource for the systematic functional analysis of the wheat genome.

  13. Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs

    Directory of Open Access Journals (Sweden)

    Croft Larry

    2012-07-01

    Full Text Available Abstract Background Transcription factors (TFs have long been known to be principally activators of transcription in eukaryotes and prokaryotes. The growing awareness of the ubiquity of microRNAs (miRNAs as suppressive regulators in eukaryotes, suggests the possibility of a mutual, preferential, self-regulatory connectivity between miRNAs and TFs. Here we investigate the connectivity from TFs and miRNAs to other genes and each other using text mining, TF promoter binding site and 6 different miRNA binding site prediction methods. Results In the first approach text mining of PubMed abstracts reveal statistically significant associations between miRNAs and both TFs and signal transduction gene classes. Secondly, prediction of miRNA targets in human and mouse 3’UTRs show enrichment only for TFs but not consistently across prediction methods for signal transduction or other gene classes. Furthermore, a random sample of 986 TarBase entries was scored for experimental evidence by manual inspection of the original papers, and enrichment for TFs was observed to increase with score. Low-scoring TarBase entries, where experimental evidence is anticorrelated miRNA:mRNA expression with predicted miRNA targets, appear not to select for real miRNA targets to any degree. Our manually validated text-mining results also suggests that miRNAs may be activated by more TFs than other classes of genes, as 7% of miRNA:TF co-occurrences in the literature were TFs activating miRNAs. This was confirmed when thirdly, we found enrichment for predicted, conserved TF binding sites in miRNA and TF genes compared to other gene classes. Conclusions We see enrichment of connections between miRNAs and TFs using several independent methods, suggestive of a network of mutual activating and suppressive regulation. We have also built regulatory networks (containing 2- and 3-loop motifs for mouse and human using predicted miRNA and TF binding sites and we have developed a web server

  14. Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data

    Directory of Open Access Journals (Sweden)

    de los Reyes Benildo G

    2008-04-01

    Full Text Available Abstract Background Integrating data from multiple global assays and curated databases is essential to understand the spatio-temporal interactions within cells. Different experiments measure cellular processes at various widths and depths, while databases contain biological information based on established facts or published data. Integrating these complementary datasets helps infer a mutually consistent transcriptional regulatory network (TRN with strong similarity to the structure of the underlying genetic regulatory modules. Decomposing the TRN into a small set of recurring regulatory patterns, called network motifs (NM, facilitates the inference. Identifying NMs defined by specific transcription factors (TF establishes the framework structure of a TRN and allows the inference of TF-target gene relationship. This paper introduces a computational framework for utilizing data from multiple sources to infer TF-target gene relationships on the basis of NMs. The data include time course gene expression profiles, genome-wide location analysis data, binding sequence data, and gene ontology (GO information. Results The proposed computational framework was tested using gene expression data associated with cell cycle progression in yeast. Among 800 cell cycle related genes, 85 were identified as candidate TFs and classified into four previously defined NMs. The NMs for a subset of TFs are obtained from literature. Support vector machine (SVM classifiers were used to estimate NMs for the remaining TFs. The potential downstream target genes for the TFs were clustered into 34 biologically significant groups. The relationships between TFs and potential target gene clusters were examined by training recurrent neural networks whose topologies mimic the NMs to which the TFs are classified. The identified relationships between TFs and gene clusters were evaluated using the following biological validation and statistical analyses: (1 Gene set enrichment

  15. A multiverse play divides opinion

    Science.gov (United States)

    Crease, Robert P.

    2015-03-01

    The stage lights rise. A man and woman meet in a cute way - "Do you know why it's impossible to lick the tips of your elbows?" she asks - they chat momentarily, and separate. The play is Constellations by Nick Payne.

  16. Play the Blood Typing Game

    Science.gov (United States)

    ... Nobel's Life and Work Teachers' Questionnaire The Blood Typing Game What happens if you get a blood ... learn about human blood types! Play the Blood Typing Game About this game Embed the Blood Typing ...

  17. Discussion of "interpretation and play".

    Science.gov (United States)

    Pick, Irma Brenman

    2011-01-01

    This discussion addresses the conflict in technique between play versus interpretation. It further considers how the nature of the interpretation may be affected by a consideration of what is being projected into the analyst.

  18. Delayed Accumulation of H3K27me3 on Nascent DNA Is Essential for Recruitment of Transcription Factors at Early Stages of Stem Cell Differentiation.

    Science.gov (United States)

    Petruk, Svetlana; Cai, Jingli; Sussman, Robyn; Sun, Guizhi; Kovermann, Sina K; Mariani, Samanta A; Calabretta, Bruno; McMahon, Steven B; Brock, Hugh W; Iacovitti, Lorraine; Mazo, Alexander

    2017-04-20

    Recruitment of transcription factors (TFs) to repressed genes in euchromatin is essential to activate new transcriptional programs during cell differentiation. However, recruitment of all TFs, including pioneer factors, is impeded by condensed H3K27me3-containing chromatin. Single-cell and gene-specific analyses revealed that, during the first hours of induction of differentiation of mammalian embryonic stem cells (ESCs), accumulation of the repressive histone mark H3K27me3 is delayed after DNA replication, indicative of a decondensed chromatin structure in all regions of the replicating genome. This delay provides a critical "window of opportunity" for recruitment of lineage-specific TFs to DNA. Increasing the levels of post-replicative H3K27me3 or preventing S phase entry inhibited recruitment of new TFs to DNA and significantly blocked cell differentiation. These findings suggest that recruitment of lineage-specifying TFs occurs soon after replication and is facilitated by a decondensed chromatin structure. This insight may explain the developmental plasticity of stem cells and facilitate their exploitation for therapeutic purposes. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. THE VALUE OF ROLE PLAY

    Institute of Scientific and Technical Information of China (English)

    1996-01-01

    IntroductionIn China,the English as a foreign language (EFL) class for non-English majors at college levelprovides little opportunity for oral interaction among students.One solution to this problem is toadopt a series of communicative teaching techniques.Role play is one such technique.This paperattempts to assess the value of role play by analysing our experience of using it as a communicationactivity.

  20. Digital Play: A New Classification

    Science.gov (United States)

    Marsh, Jackie; Plowman, Lydia; Yamada-Rice, Dylan; Bishop, Julia; Scott, Fiona

    2016-01-01

    This paper draws on an ESRC-funded study of play and creativity in preschool-aged children's use of apps in the UK. The main objectives of the study were to collect information about access to and use of apps in the home, establish the most popular apps and identify the features of those apps that are successful in promoting play and creativity. A…

  1. An ethnomathematical study of play in minecraft

    DEFF Research Database (Denmark)

    Kørhsen, Kim Louis; Misfeldt, Morten

    2014-01-01

    This paper explores how children engaged in playing Minecraft in an afterschool program develop mathematical approaches in their in-game activities. The investigation is framed as ethnomathematical in the sense that, rather than searching for specific curricular concepts, it explores the problem...... between the children and the afterschool program’s attitude towards children’s collaborative gaming are crucial factors in the way Minecraft supports the development of mathematical thinking....

  2. Play and Space - Towards a Formal Definition of Play

    DEFF Research Database (Denmark)

    Larsen, Lasse Juel

    2015-01-01

    The aim of this article is to present a formal definition of the aspect of play generally known as ‘make-believe’. ‘Make-believe’ is defined in relation to theory of place and Dasein’s being- in-the-world as presented by Martin Heidegger in Being and time. From this point of view ‘make-believe’ can...... be defined as a uniform and situational spatial dyad where being is doubled, characterized by the presence of the physically absent. I will apply this definition after a survey of central and influential aspects of the history of the theory of play to demonstrate its relevance for a formal definition of play....

  3. Why Play Outside? Problematising Outdoor Play as a Biopedagogical Task

    Science.gov (United States)

    Robinson, Daniel B.; Barrett, Joe

    2017-01-01

    Although outdoor play has been widely recognised for the many benefits it affords children, some have rationalised the need for it based on goals related to physical health. More specifically, these instrumental goals have been closely related to obesity, overweight, and/or physical (in)activity. Adhering to obesity discourses and the notion of a…

  4. Parent-Child Play across Cultures: Advancing Play Research

    Science.gov (United States)

    Roopnarine, Jaipaul L.; Davidson, Kimberly L.

    2015-01-01

    In this article, the authors argue for a greater understanding of children's play across cultures through better integration of scientific thinking about the developed and developing societies, through consideration of socialization beliefs and goals, and, finally, through the use of more complex models in research investigations. They draw on…

  5. Modular robotics for playful physiotherapy

    DEFF Research Database (Denmark)

    Lund, Henrik Hautop

    2009-01-01

    We developed modular robotic tiles to be used for playful physiotherapy, which is supposed to motivate patients to engage in and perform physical rehabilitation exercises. We tested the modular robotic tiles for an extensive period of time (3 years) in daily use in a hospital rehabilitation unit e.......g. for cardiac patients. Also, the tiles were tested for performing physical rehabilitation of stroke patients in their private home. In all pilot test cases qualitative feedback indicate that the patients find the playful use of modular robotic tiles engaging and motivating for them to perform...... the rehabilitation. Also, initial pilot test data suggest that some playful exercises on the tiles demand an average heart rate of 75% and 86% of the maximum heart rate....

  6. Rapport. Play and Learn Innovation

    DEFF Research Database (Denmark)

    Larsen, Maria Neumann; Søgaard, Karoline

    Erfaringer og anbefalinger fra innovationsprojektet Play and Learn, hvor pædagoger har arbejdet med sprogstimulering af børn fra 3-9 år. Legende læring i daglige rutiner og pædagogiske aktiviteter har været fokuspunktet.......Erfaringer og anbefalinger fra innovationsprojektet Play and Learn, hvor pædagoger har arbejdet med sprogstimulering af børn fra 3-9 år. Legende læring i daglige rutiner og pædagogiske aktiviteter har været fokuspunktet....

  7. HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

    KAUST Repository

    Kulakovskiy, Ivan V.

    2015-11-19

    Models of transcription factor (TF) binding sites provide a basis for a wide spectrum of studies in regulatory genomics, from reconstruction of regulatory networks to functional annotation of transcripts and sequence variants. While TFs may recognize different sequence patterns in different conditions, it is pragmatic to have a single generic model for each particular TF as a baseline for practical applications. Here we present the expanded and enhanced version of HOCOMOCO (http://hocomoco.autosome.ru and http://www.cbrc.kaust.edu.sa/hocomoco10), the collection of models of DNA patterns, recognized by transcription factors. HOCOMOCO now provides position weight matrix (PWM) models for binding sites of 601 human TFs and, in addition, PWMs for 396 mouse TFs. Furthermore, we introduce the largest up to date collection of dinucleotide PWM models for 86 (52) human (mouse) TFs. The update is based on the analysis of massive ChIP-Seq and HT-SELEX datasets, with the validation of the resulting models on in vivo data. To facilitate a practical application, all HOCOMOCO models are linked to gene and protein databases (Entrez Gene, HGNC, UniProt) and accompanied by precomputed score thresholds. Finally, we provide command-line tools for PWM and diPWM threshold estimation and motif finding in nucleotide sequences.

  8. Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data.

    Science.gov (United States)

    Wu, Wei-Sheng; Chen, Bor-Sen

    2009-11-24

    Unicellular organisms such as yeasts have evolved to survive environmental stresses by rapidly reorganizing the genomic expression program to meet the challenges of harsh environments. The complex adaptation mechanisms to stress remain to be elucidated. In this study, we developed Stress Transcription Factor Identification Algorithm (STFIA), which integrates gene expression and TF-gene association data to identify the stress transcription factors (TFs) of six kinds of stresses. We identified some general stress TFs that are in response to various stresses, and some specific stress TFs that are in response to one specific stress. The biological significance of our findings is validated by the literature. We found that a small number of TFs may be sufficient to control a wide variety of expression patterns in yeast under different stresses. Two implications can be inferred from this observation. First, the adaptation mechanisms to different stresses may have a bow-tie structure. Second, there may exist extensive regulatory cross-talk among different stress responses. In conclusion, this study proposes a network of the regulators of stress responses and their mechanism of action.

  9. In silico identification of transcription factors in Medicago sativa using available transcriptomic resources.

    Science.gov (United States)

    Postnikova, Olga A; Shao, Jonathan; Nemchinov, Lev G

    2014-06-01

    Transcription factors (TFs) are proteins that govern organismal development and response to the environment by regulating gene expression. Information on the amount and diversity of TFs within individual plant species is critical for understanding of their biological roles and evolutionary history across the plant kingdom. Currently, only scattered information on separate TFs is available for alfalfa, the most extensively cultivated forage legume in the world. In the meantime, several large transcriptomic resources that can be used to identify and characterize alfalfa TF genes are freely accessible online. In this study, we have performed an in silico analysis of transcriptome data generated in our laboratory and publicly acquirable from other sources to reveal and systematize alfalfa transcription factors. Transcriptome-wide mining enabled prediction of 983 TFs along with their sequence features and putative phylogenies of the largest families. All data were assembled into a simple open-access database named AlfalfaTFDB ( http://plantpathology.ba.ars.usda.gov/alfalfatfdb.html ). Transcriptomic analysis used in this work represents an effective approach for the identification of TF genes in plants with incomplete genomes, such as alfalfa. Integrated TF repertoires of Medicago sativa will provide an important tool for studying regulation of gene expression in other complex non-model species of agricultural significance.

  10. Uncovering Transcriptional Regulatory Networks by Sparse Bayesian Factor Model

    Science.gov (United States)

    Meng, Jia; Zhang, Jianqiu(Michelle); Qi, Yuan(Alan); Chen, Yidong; Huang, Yufei

    2010-12-01

    The problem of uncovering transcriptional regulation by transcription factors (TFs) based on microarray data is considered. A novel Bayesian sparse correlated rectified factor model (BSCRFM) is proposed that models the unknown TF protein level activity, the correlated regulations between TFs, and the sparse nature of TF-regulated genes. The model admits prior knowledge from existing database regarding TF-regulated target genes based on a sparse prior and through a developed Gibbs sampling algorithm, a context-specific transcriptional regulatory network specific to the experimental condition of the microarray data can be obtained. The proposed model and the Gibbs sampling algorithm were evaluated on the simulated systems, and results demonstrated the validity and effectiveness of the proposed approach. The proposed model was then applied to the breast cancer microarray data of patients with Estrogen Receptor positive ([InlineEquation not available: see fulltext.]) status and Estrogen Receptor negative ([InlineEquation not available: see fulltext.]) status, respectively.

  11. Uncovering Transcriptional Regulatory Networks by Sparse Bayesian Factor Model

    Directory of Open Access Journals (Sweden)

    Qi Yuan(Alan

    2010-01-01

    Full Text Available Abstract The problem of uncovering transcriptional regulation by transcription factors (TFs based on microarray data is considered. A novel Bayesian sparse correlated rectified factor model (BSCRFM is proposed that models the unknown TF protein level activity, the correlated regulations between TFs, and the sparse nature of TF-regulated genes. The model admits prior knowledge from existing database regarding TF-regulated target genes based on a sparse prior and through a developed Gibbs sampling algorithm, a context-specific transcriptional regulatory network specific to the experimental condition of the microarray data can be obtained. The proposed model and the Gibbs sampling algorithm were evaluated on the simulated systems, and results demonstrated the validity and effectiveness of the proposed approach. The proposed model was then applied to the breast cancer microarray data of patients with Estrogen Receptor positive ( status and Estrogen Receptor negative ( status, respectively.

  12. Let's 'play' with molecular pharmacology.

    Science.gov (United States)

    Choudhury, Supriyo; Pradhan, Richeek; Sengupta, Gairik; Das, Manisha; Chatterjee, Manojit; Roy, Ranendra Kumar; Chatterjee, Suparna

    2015-01-01

    Understanding concepts of molecular mechanisms of drug action involves sequential visualization of physiological processes and drug effects, a task that can be difficult at an undergraduate level. Role-play is a teaching-learning methodology whereby active participation of students as well as clear visualization of the phenomenon is used to convey complex physiological concepts. However, its use in teaching drug action, a process that demands understanding of a second level of complexity over the physiological process, has not been investigated. We hypothesized that role-play can be an effective and well accepted method for teaching molecular pharmacology. In an observational study, students were guided to perform a role-play on a selected topic involving drug activity. Students' gain in knowledge was assessed comparing validated pre- and post-test questionnaires as well as class average normalized gain. The acceptance of role-play among undergraduate medical students was evaluated by Likert scale analysis and thematic analysis of their open-ended written responses. Significant improvement in knowledge (P pharmacology in undergraduate medical curricula.

  13. Playing with Protons CREATIONS Demonstrator

    CERN Document Server

    Alexopoulos, Angelos

    2017-01-01

    This document describes Playing with Protons, a CMS education initiative that seeks to enhance teachers’ pedagogical practice with creative, hands-on methodologies through which 10-12 year old students can, in turn, get engaged effectively with science, technology and innovation.

  14. For the Phenomenology of Play

    Directory of Open Access Journals (Sweden)

    Roberto Farné

    2016-10-01

    Full Text Available The success of phenomenology in contemporary culture is due above all to the new approach to knowledge that has been proposed, breaking with the traditional objectivism of scientific knowledge and placing the “phenomenon” at the centre of the relationship between the subject and the world. Everyday reality, the language of concrete things, have become fully-fledged targets of philosophical thought. While Eugen Fink, student of Husserl, elects the phenomenon of play as the “symbol of the world”, the original interpretation of man’s relation to the world, in Italy Piero Bertolini redefines the scientific basis of pedagogy according to phenomenological categories and places play among the fundamental fields of experience of education. On one hand overcoming the traditional educational instrumentalisation of play, on the other its sterile reduction to a consumer experience, Bertolini brings play back to its authentic dimension in which risk, error, adventure are constituent parts, the “active ingredients” of his pedagogy.

  15. Electronic Instruments -- Played or Used?

    Science.gov (United States)

    Ulveland, Randall Dana

    1998-01-01

    Compares the experience of playing an acoustic instrument to an electronic instrument by analyzing the constant structures and relationships between the experiences. Concludes that students' understanding of the physical experience of making music increases when experiences with acoustic instruments precede their exposure to electronic…

  16. Moral Education through Play Therapy

    Science.gov (United States)

    Mahalle, Salwa; Zakaria, Gamal Abdul Nasir; Nawi, Aliff

    2014-01-01

    This paper will discuss on how sand therapy (as one type of play therapies) can be applied as an additional technique or approach in counseling. The research questions for this study are to see what are the development, challenges faced by the therapist during the sessions given and how sand therapy can aid to the progress of the client. It is a…

  17. Obama Plays Cheerleader for STEM

    Science.gov (United States)

    Robelen, Erik W.

    2010-01-01

    Amid a struggling economy, a raft of foreign-policy headaches, and the tail end of a heated campaign season, President Barack Obama carved out time in his schedule last month to watch students in the State Dining Room demonstrate a solar-powered model car, a water-purification system, and a soccer-playing robot. The science fair was the fifth…

  18. Playing with a digital swing

    DEFF Research Database (Denmark)

    Skovbjerg, Helle Marie

    2017-01-01

    Based on a field study in a kindergarten among children in Denmark, this paper explores playing activities on a digital swing, the SON-X Octavia (SON-X) and its Applause application. SON-X is an interactive sound unit that can be attached to any swing chain. Here, I explore the relationship betwe...

  19. Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs

    DEFF Research Database (Denmark)

    Croft, Laurence J; Szklarczyk, Damian; Jensen, Lars J

    2012-01-01

    ABSTRACT: BACKGROUND: Transcription factors (TFs) have long been known to be principally activators of transcription in eukaryotes and prokaryotes. The growing awareness of the ubiquity of microRNAs (miRNAs) as suppressive regulators in eukaryotes, suggests the possibility of a mutual, preferential...

  20. Play for learning and learning for play: Children’s play in a toddler group

    Directory of Open Access Journals (Sweden)

    Anne Greve

    2013-10-01

    Full Text Available There is a concern that children’s right to play is restricted as a result of the governments’ narrow focus on school preparatory activities and learning. Play and learning are rights embodied in the United Nations convention on the rights of the child. This article discusses how play and learning are organized in the everyday life of a Norwegian toddler group. Critical voices claim that there is not enough structure and that there should be more teaching and mapping to facilitate early intervention in Norwegian kindergartens. The article suggests that the critics’ claim can be countered by asking if there are too few teachers with adequate education and too large groups of children.

  1. MAJOR PLAYS IN UTAH AND VICINITY

    Energy Technology Data Exchange (ETDEWEB)

    Craig D. Morgan; Thomas C. Chidsey

    2003-11-01

    Utah oil fields have produced over 1.2 billion barrels (191 million m{sup 3}). However, the 13.7 million barrels (2.2 million m{sup 3}) of production in 2002 was the lowest level in over 40 years and continued the steady decline that began in the mid-1980s. The Utah Geological Survey believes this trend can be reversed by providing play portfolios for the major oil-producing provinces (Paradox Basin, Uinta Basin, and thrust belt) in Utah and adjacent areas in Colorado and Wyoming. Oil plays are geographic areas with petroleum potential caused by favorable combinations of source rock, migration paths, reservoir rock characteristics, and other factors. The play portfolios will include: descriptions and maps of the major oil plays by reservoir; production and reservoir data; case-study field evaluations; summaries of the state-of-the-art drilling, completion, and secondary/tertiary techniques for each play; locations of major oil pipelines; descriptions of reservoir outcrop analogs; and identification and discussion of land-use constraints. All play maps, reports, databases, and so forth, produced for the project will be published in interactive, menu-driven digital (web-based and compact disc) and hard-copy formats. This report covers research activities for the first quarter of the second project year (July 1 through September 30, 2003). This work included (1) describing the Conventional Southern Uinta Basin Play, subplays, and outcrop reservoir analogs of the Uinta Green River Conventional Oil and Gas Assessment Unit (Eocene Green River Formation), and (2) technology transfer activities. The Conventional Oil and Gas Assessment Unit can be divided into plays having a dominantly southern sediment source (Conventional Southern Uinta Basin Play) and plays having a dominantly northern sediment source (Conventional Northern Uinta Basin Play). The Conventional Southern Uinta Basin Play is divided into six subplays: (1) conventional Uteland Butte interval, (2) conventional

  2. The role of preschool teacher in child structured and unstructured play

    OpenAIRE

    Bajde, Karmen

    2016-01-01

    The thesis entitled The Role of Preschool Teacher in Child Structured and Unstructured Play focuses on play, play materials and the role of preschool teacher in the preschool period. The theoretical part focuses on the meaning of child’s play and play materials as well as the role of the preschool professionals. Various types, factors and characteristics of child’s play were presented and play materials were defined. Toy quality criteria are also briefly described. The chapter dealing with th...

  3. Functional characterization of the Arabidopsis eukaryotic translation initiation factor 5A-2 that plays a crucial role in plant growth and development by regulating cell division, cell growth, and cell death.

    Science.gov (United States)

    Feng, Haizhong; Chen, Qingguo; Feng, Jian; Zhang, Jian; Yang, Xiaohui; Zuo, Jianru

    2007-07-01

    The eukaryotic translation initiation factor 5A (eIF-5A) is a highly conserved protein found in all eukaryotic organisms. Although originally identified as a translation initiation factor, recent studies in mammalian and yeast (Saccharomyces cerevisiae) cells suggest that eIF-5A is mainly involved in RNA metabolism and trafficking, thereby regulating cell proliferation, cell growth, and programmed cell death. In higher plants, the physiological function of eIF-5A remains largely unknown. Here, we report the identification and characterization of an Arabidopsis (Arabidopsis thaliana) mutant fumonisin B(1)-resistant12 (fbr12). The fbr12 mutant shows an antiapoptotic phenotype and has reduced dark-induced leaf senescence. Moreover, fbr12 displays severe defects in plant growth and development. The fbr12 mutant plant is extreme dwarf with substantially reduced size and number of all adult organs. During reproductive development, fbr12 causes abnormal development of floral organs and defective sporogenesis, leading to the abortion of both female and male germline cells. Microscopic studies revealed that these developmental defects are associated with abnormal cell division and cell growth. Genetic and molecular analyses indicated that FBR12 encodes a putative eIF-5A-2 protein. When expressed in a yeast mutant strain carrying a mutation in the eIF-5A gene, FBR12 cDNA is able to rescue the lethal phenotype of the yeast mutant, indicating that FBR12 is a functional eIF-5A. We propose that FBR12/eIF-5A-2 is fundamental for plant growth and development by regulating cell division, cell growth, and cell death.

  4. Reconstruction and analysis of transcription factor-miRNA co-regulatory feed-forward loops in human cancers using filter-wrapper feature selection.

    Directory of Open Access Journals (Sweden)

    Chen Peng

    Full Text Available BACKGROUND: As one of the most common types of co-regulatory motifs, feed-forward loops (FFLs control many cell functions and play an important role in human cancers. Therefore, it is crucial to reconstruct and analyze cancer-related FFLs that are controlled by transcription factor (TF and microRNA (miRNA simultaneously, in order to find out how miRNAs and TFs cooperate with each other in cancer cells and how they contribute to carcinogenesis. Current FFL studies rely on predicted regulation information and therefore suffer the false positive issue in prediction results. More critically, FFLs generated by existing approaches cannot represent the dynamic and conditional regulation relationship under different experimental conditions. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we proposed a novel filter-wrapper feature selection method to accurately identify co-regulatory mechanism by incorporating prior information from predicted regulatory interactions with parallel miRNA/mRNA expression datasets. By applying this method, we reconstructed 208 and 110 TF-miRNA co-regulatory FFLs from human pan-cancer and prostate datasets, respectively. Further analysis of these cancer-related FFLs showed that the top-ranking TF STAT3 and miRNA hsa-let-7e are key regulators implicated in human cancers, which have regulated targets significantly enriched in cellular process regulations and signaling pathways that are involved in carcinogenesis. CONCLUSIONS/SIGNIFICANCE: In this study, we introduced an efficient computational approach to reconstruct co-regulatory FFLs by accurately identifying gene co-regulatory interactions. The strength of the proposed feature selection method lies in the fact it can precisely filter out false positives in predicted regulatory interactions by quantitatively modeling the complex co-regulation of target genes mediated by TFs and miRNAs simultaneously. Moreover, the proposed feature selection method can be generally applied to

  5. [All signs of metabolic syndrome in the hypertensive ISIAH rats are associated with increased activity of transcription factors PPAR, LXR, PXR, and CAR in the liver].

    Science.gov (United States)

    Pivovarova, E N; Dushkin, M I; Perepechaeva, M L; Kobzev, V F; Trufakin, V A; Markel', A L

    2011-01-01

    It is known that the metabolic syndrome (MS), which includes hypertension, dislipidemia, glucose intolerance, and obesity leads to cardiovascular diseases. The MS risk is growing catastrophically. Molecular mechanisms allowing to understand the reason of integrated dysfunctions, taking place at MS cases, have remained almost unstudied. The chronical stress plays a crucial role in MS development; therefore in the present work a hypertensive rat strain with Inherited Stress-Induced Arterial Hypertension (ISIAH) was used as a model. It was shown that ISIAH rat strain as compared with the control WAG rat strain is characterized by increased content of triglyceride, VLDL and LDL cholesterols, a decreased content of HDL cholesterol, a high level of apolipoprotein B-100, and decreased level of apolipoprotein A-I. The ISIAH rats body weight was higher as compared with WAG rats; ISIAH rats blood glucose content was higher too. Thus, strain hypertension for ISIAH rat is accompanied by dislipidemia, increased glucose content, and increased body weight, representing a whole set of MS signs. Since at MS cases the systemic abnormalities in lipid and carbohydrate metabolism take place, the functional activity of transcription factors (TFs) participating in integral regulation of lipid and carbohydrate metabolism genes in liver was measured. PPAR, LXR, PXR, CAR DNA-binding activity was increased in ISIAH rats, suggesting involvement of these TFs in MS development. Integrated investigation of PPAR, LXR, PXR, CAR regulatory mechanisms, signal transduction and transcriptional targets will provide insights into the pathogenesis of MS and offer valuable information for designing of drugs for MS treatment.

  6. Agents Play Mix-game

    CERN Document Server

    Gou, C

    2005-01-01

    In mix-game which is an extension of minority game, there are two groups of agents; group1 plays the majority game, but the group2 plays the minority game. This paper studies the change of the average winnings of agents and volatilities vs. the change of mixture of agents in mix-game model. It finds that the correlations between the average winnings of agents and the mean of local volatilities are different with different combinations of agent memory length when the proportion of agents in group 1 increases. This study result suggests that memory length of agents in group1 be smaller than that of agent in group2 when mix-game model is used to simulate the financial markets.

  7. Effects of food ecology on social play: a laboratory simulation.

    Science.gov (United States)

    Baldwin, J D; Baldwin, J I

    1976-01-01

    A laboratory group of 8 squirrel monkeys was exposed to two experimental conditions in which food was made moderately and extremely difficult to obtain, compared with the free access conditions of baseline. Both experiments produced sharp decreased in the frequency of social play within 4 to 6 days. The stronger manipulation produced the more dramatic effect, reducing play to 1% of the baseline level (P less than .001). Neither experiment produced a total absence of play as was observed in a previous field study in southwestern Panama (Baldwin and Baldwin 1973, 1974) which suggests that the field study sampled conditions of even more severe and/or prolonged food deprivation. No pathological or dysfunctional consequences were observed in any of the circumstances where play was reduced to zero or near zero. The question is raised whether certain theories of play have overstated the case for the necessity of play experience in producing normal socialization in primates. Alternative hypotheses are presented concerning the factors that determine the frequency of play and the consequences of play versus no-play for socialization. After both experiments, the frequency of play rose to a level 50% higher than the average baseline levels of play. This "rebound" reached a peak 5 to 6 days after the termination of each experiment; and during the subsequent days the frequency of play declined to more normal levels. A reinforcement theory is presented as a possible explanation of the rebound effect.

  8. Playing Business "Ball" with Cuba

    Institute of Scientific and Technical Information of China (English)

    Yang Wei; Gong Liming

    2007-01-01

    @@ If you were lucky enough to have seen the World Volleyball Tournament,you must have seen the Cuban Women's volleyball team take on China in the championship game,a game of which Cuba has become the world champion for 10 times.The great determination and strong tenacity of these young Cuban girls' has been an encouragement to everyone that watches them play.

  9. Play Context, Commitment, and Dating Violence: A Structural Equation Model

    Science.gov (United States)

    Gonzalez-Mendez, Rosaura; Hernandez-Cabrera, Juan Andres

    2009-01-01

    This study develops a structural equation model to describe the effect of two groups of factors (type of commitment and play context) on the violence experienced during intimate partner conflict. After contrasting the model in adolescents and university students, we have confirmed that aggressive play and the simulation of jealousy and anger…

  10. Playing Moderately Hard to Get

    Directory of Open Access Journals (Sweden)

    Stephen Reysen

    2013-12-01

    Full Text Available In two studies, we examined the effect of different degrees of attraction reciprocation on ratings of attraction toward a potential romantic partner. Undergraduate college student participants imagined a potential romantic partner who reciprocated a low (reciprocating attraction one day a week, moderate (reciprocating attraction three days a week, high (reciprocating attraction five days a week, or unspecified degree of attraction (no mention of reciprocation. Participants then rated their degree of attraction toward the potential partner. The results of Study 1 provided only partial support for Brehm’s emotion intensity theory. However, after revising the high reciprocation condition vignette in Study 2, supporting Brehm’s emotion intensity theory, results show that a potential partners’ display of reciprocation of attraction acted as a deterrent to participants’ intensity of experienced attraction to the potential partner. The results support the notion that playing moderately hard to get elicits more intense feelings of attraction from potential suitors than playing too easy or too hard to get. Discussion of previous research examining playing hard to get is also re-examined through an emotion intensity theory theoretical lens.

  11. Ethylene response factor 6 is a regulator of reactive oxygen species signaling in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Nasser Sewelam

    Full Text Available Reactive oxygen species (ROS are produced in plant cells in response to diverse biotic and abiotic stresses as well as during normal growth and development. Although a large number of transcription factor (TF genes are up- or down-regulated by ROS, currently very little is known about the functions of these TFs during oxidative stress. In this work, we examined the role of ERF6 (ETHYLENE RESPONSE FACTOR6, an AP2/ERF domain-containing TF, during oxidative stress responses in Arabidopsis. Mutant analyses showed that NADPH oxidase (RbohD and calcium signaling are required for ROS-responsive expression of ERF6. erf6 insertion mutant plants showed reduced growth and increased H2O2 and anthocyanin levels. Expression analyses of selected ROS-responsive genes during oxidative stress identified several differentially expressed genes in the erf6 mutant. In particular, a number of ROS responsive genes, such as ZAT12, HSFs, WRKYs, MAPKs, RBOHs, DHAR1, APX4, and CAT1 were more strongly induced by H2O2 in erf6 plants than in wild-type. In contrast, MDAR3, CAT3, VTC2 and EX1 showed reduced expression levels in the erf6 mutant. Taken together, our results indicate that ERF6 plays an important role as a positive antioxidant regulator during plant growth and in response to biotic and abiotic stresses.

  12. Genome-Wide Dissection of the Heat Shock Transcription Factor Family Genes in Arachis.

    Science.gov (United States)

    Wang, Pengfei; Song, Hui; Li, Changsheng; Li, Pengcheng; Li, Aiqin; Guan, Hongshan; Hou, Lei; Wang, Xingjun

    2017-01-01

    Heat shock transcription factors (Hsfs) are important transcription factors (TFs) in protecting plants from damages caused by various stresses. The released whole genome sequences of wild peanuts make it possible for genome-wide analysis of Hsfs in peanut. In this study, a total of 16 and 17 Hsf genes were identified from Arachis duranensis and A. ipaensis, respectively. We identified 16 orthologous Hsf gene pairs in both peanut species; however HsfXs was only identified from A. ipaensis. Orthologous pairs between two wild peanut species were highly syntenic. Based on phylogenetic relationship, peanut Hsfs were divided into groups A, B, and C. Selection pressure analysis showed that group B Hsf genes mainly underwent positive selection and group A Hsfs were affected by purifying selection. Small scale segmental and tandem duplication may play important roles in the evolution of these genes. Cis-elements, such as ABRE, DRE, and HSE, were found in the promoters of most Arachis Hsf genes. Five AdHsfs and two AiHsfs contained fungal elicitor responsive elements suggesting their involvement in response to fungi infection. These genes were differentially expressed in cultivated peanut under abiotic stress and Aspergillus flavus infection. AhHsf2 and AhHsf14 were significantly up-regulated after inoculation with A. flavus suggesting their possible role in fungal resistance.

  13. 转录因子GGS1参与赤霉素和糖信号调控%Transcription Factor GGS1 Plays Roles in GA and Sugar Signaling Pathways

    Institute of Scientific and Technical Information of China (English)

    邹明学; 申宇欢; 陈艳红

    2012-01-01

    redundancy with GGSl. Second, we obtained the GGSl over expression transgenic line ( O/E) to study the expression level change of important genes concerning GA and glucose signaling. Q-PCR results demonstrated that the transcripts abundance of two GA-anabolism enzymes(GA30X1 and GA200X2) were increased while two GA-catabolism enzymes ( GA20X1 and GA2OX2) were reduced respectively in O/E lines. Three photosynthesis genes were also greatly up regulated in O/E lines. These results reveal that GGSl gene played critical roles in GA and sugar signaling pathways.

  14. Dendritic cell-derived VEGF-A plays a role in inflammatory angiogenesis of human secondary lymphoid organs and is driven by the coordinated activation of multiple transcription factors

    Science.gov (United States)

    Salvi, Valentina; Vermi, William; Gianello, Veronica; Lonardi, Silvia; Gagliostro, Vincenzo; Naldini, Antonella

    2016-01-01

    Lymph node expansion during inflammation is essential to establish immune responses and relies on the development of blood and lymph vessels. Previous work in mice has shown that this process depends on the presence of VEGF-A produced by B cells, macrophages and stromal cells. In humans, however, the cell types and the mechanisms regulating the intranodal production of VEGF-A remain elusive. Here we show that CD11c+ cells represent the main VEGF-A-producing cell population in human reactive secondary lymphoid organs. In addition we find that three transcription factors, namely CREB, HIF-1α and STAT3, regulate the expression of VEGF-A in inflamed DCs. Both HIF-1α and STAT3 are activated by inflammatory agonists. Conversely, CREB phosphorylation represents the critical contribution of endogenous or exogenous PGE2. Taken together, these results propose a crucial role for DCs in lymph node inflammatory angiogenesis and identify novel potential cellular and molecular targets to limit inflammation in chronic diseases and tumors. PMID:27256980

  15. Dendritic cell-derived VEGF-A plays a role in inflammatory angiogenesis of human secondary lymphoid organs and is driven by the coordinated activation of multiple transcription factors.

    Science.gov (United States)

    Salvi, Valentina; Vermi, William; Gianello, Veronica; Lonardi, Silvia; Gagliostro, Vincenzo; Naldini, Antonella; Sozzani, Silvano; Bosisio, Daniela

    2016-06-28

    Lymph node expansion during inflammation is essential to establish immune responses and relies on the development of blood and lymph vessels. Previous work in mice has shown that this process depends on the presence of VEGF-A produced by B cells, macrophages and stromal cells. In humans, however, the cell types and the mechanisms regulating the intranodal production of VEGF-A remain elusive. Here we show that CD11c+ cells represent the main VEGF-A-producing cell population in human reactive secondary lymphoid organs. In addition we find that three transcription factors, namely CREB, HIF-1α and STAT3, regulate the expression of VEGF-A in inflamed DCs. Both HIF-1α and STAT3 are activated by inflammatory agonists. Conversely, CREB phosphorylation represents the critical contribution of endogenous or exogenous PGE2. Taken together, these results propose a crucial role for DCs in lymph node inflammatory angiogenesis and identify novel potential cellular and molecular targets to limit inflammation in chronic diseases and tumors.

  16. Family play-learning through informal education: Make and play activities with traditional Thai toy activities at a science museum

    OpenAIRE

    Kanhadilok, Peeranut

    2013-01-01

    This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University This thesis charts the outcomes of family play-learning through make-and-play activities with traditional Thai toys activities (TTTA). Family learning is a component of inter-generational learning, and the research explores this through ‘edutainment’ activities within the informal educational system of a science museum. The thesis also identifies key factors that influence family play-learning...

  17. Jakob Kelemina on Shakespeare's plays

    Directory of Open Access Journals (Sweden)

    Mirko Jurak

    2007-12-01

    Full Text Available Among Slovene scholars in English and German studies Jakob Kelemina (19 July 1882- 14 May 1957 has a very important  place. Janez Stanonik justly places him among the founding fathers of the University of Ljubljana (Stanonik 1966: 332. From 1920 Kelemina was professor of Germanic philology and between 1920 and 1957 he was also the Chair of the Deparment ofGermanic Languages and Literatures at the Faculty of Arts of this university. The major part of Kelemina's research was devoted to German and Austrian literatures,  German  philology, German-Slovene cultural relations, and literary theory; his work in these fields has already been discussed  by severa! Slovene scholars. However, in the first two decades of the twentieth century Kelemina also wrote severa! book reviews of Slovene and Croatian translations of Shakespeare's plays as well as three introductory essays to Slovene translations  of Shakespeare's plays. They are considered  as the first serious studies on Shakespeare in Slovenia (Moravec 1974: 437, and have not been analysed yet. Therefore this topic presents the core of my study, together with an evaluation  of Kelemina's contribution  to Slovene translations  of Shakespeare's plays done by Oton Župančič (1878-1949 during the first half of the twentieth century. Župančič's translations  became the criterion  for all further translations  of Shakespeare's dramatic works in Slovene. Župančič is stili one of our most important  poets and translators of this time and Kelemina's advice and criticism undoubtedly  also helped him to achieve such a high standard in his translations. In the central part of my study I also include some new material (e.g. Kelernina's letters, which is relevant for our understanding  of his co-operation with Oton Župančič  and other Slovene authors and critics. In order to put Kelemina's work into a historical perspective I present at the beginning of my study a brief survey of the

  18. 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...... targeting specific cis-acting elements in genes, and by the significant lack of fixed tertiary structure in their extensive intrinsically disordered regions. Recent research in protein intrinsic disorder (ID) has changed our understanding of transcriptional activation domains from 'negative noodles' to ID...... them to participate in large interactomes, how they use only a few hydrophobic residues, short sequence motifs, prestructured motifs, and coupled folding and binding for their interactions with co-activators, and how their accessibility to post-translational modification affects their interactions...

  19. GRiP: a computational tool to simulate transcription factor binding in prokaryotes.

    Science.gov (United States)

    Zabet, Nicolae Radu; Adryan, Boris

    2012-05-01

    Transcription factors (TFs) are proteins that regulate gene activity by binding to specific sites on the DNA. Understanding the way these molecules locate their target site is of great importance in understanding gene regulation. We developed a comprehensive computational model of this process and estimated the model parameters in (N.R.Zabet and B.Adryan, submitted for publication). GRiP (gene regulation in prokaryotes) is a highly versatile implementation of this model and simulates the search process in a computationally efficient way. This program aims to provide researchers in the field with a flexible and highly customizable simulation framework. Its features include representation of DNA sequence, TFs and the interaction between TFs and the DNA (facilitated diffusion mechanism), or between various TFs (cooperative behaviour). The software will record both information on the dynamics associated with the search process (locations of molecules) and also steady-state results (affinity landscape, occupancy-bias and collision hotspots). http://logic.sysbiol.cam.ac.uk/grip, program and source code

  20. Engineering Synthetic cis-Regulatory Elements for Simultaneous Recognition of Three Transcriptional Factors in Bacteria.

    Science.gov (United States)

    Amores, Gerardo Ruiz; Guazzaroni, María-Eugenia; Silva-Rocha, Rafael

    2015-12-18

    Recognition of cis-regulatory elements by transcription factors (TF) at target promoters is crucial to gene regulation in bacteria. In this process, binding of TFs to their cognate sequences depends on a set of physical interactions between these proteins and specific nucleotides in the operator region. Previously, we showed that in silico optimization algorithms are able to generate short sequences that are recognized by two different TFs of Escherichia coli, namely, CRP and IHF, thus generating an AND logic gate. Here, we expanded this approach in order to engineer DNA sequences that can be simultaneously recognized by three unrelated TFs (CRP, IHF, and Fis). Using in silico optimization and experimental validation strategies, we were able to obtain a candidate promoter (Plac-CFI1) regulated by only two TFs with an AND logic, thus demonstrating a limitation in the design. Subsequently, we modified the algorithm to allow the optimization of extended sequences, and were able to design two synthetic promoters (PCFI20-1 and PCFI22-5) that were functional in vivo. Expression assays in E. coli mutant strains for each TF revealed that while CRP positively regulates the promoter activities, IHF and Fis are strong repressors of both the promoter variants. Taken together, our results demonstrate the potential of in silico strategies in bacterial synthetic promoter engineering. Furthermore, the study also shows how small modifications in cis-regulatory elements can drastically affect the final logic of the resulting promoter.

  1. Regulation of a transcription factor network by Cdk1 coordinates late cell cycle gene expression.

    Science.gov (United States)

    Landry, Benjamin D; Mapa, Claudine E; Arsenault, Heather E; Poti, Kristin E; Benanti, Jennifer A

    2014-05-02

    To maintain genome stability, regulators of chromosome segregation must be expressed in coordination with mitotic events. Expression of these late cell cycle genes is regulated by cyclin-dependent kinase (Cdk1), which phosphorylates a network of conserved transcription factors (TFs). However, the effects of Cdk1 phosphorylation on many key TFs are not known. We find that elimination of Cdk1-mediated phosphorylation of four S-phase TFs decreases expression of many late cell cycle genes, delays mitotic progression, and reduces fitness in budding yeast. Blocking phosphorylation impairs degradation of all four TFs. Consequently, phosphorylation-deficient mutants of the repressors Yox1 and Yhp1 exhibit increased promoter occupancy and decreased expression of their target genes. Interestingly, although phosphorylation of the transcriptional activator Hcm1 on its N-terminus promotes its degradation, phosphorylation on its C-terminus is required for its activity, indicating that Cdk1 both activates and inhibits a single TF. We conclude that Cdk1 promotes gene expression by both activating transcriptional activators and inactivating transcriptional repressors. Furthermore, our data suggest that coordinated regulation of the TF network by Cdk1 is necessary for faithful cell division.

  2. In Silico discovery of transcription factors as potential diagnostic biomarkers of ovarian cancer

    KAUST Repository

    Kaur, Mandeep

    2011-09-19

    Background: Our study focuses on identifying potential biomarkers for diagnosis and early detection of ovarian cancer (OC) through the study of transcription regulation of genes affected by estrogen hormone.Results: The results are based on a set of 323 experimentally validated OC-associated genes compiled from several databases, and their subset controlled by estrogen. For these two gene sets we computationally determined transcription factors (TFs) that putatively regulate transcription initiation. We ranked these TFs based on the number of genes they are likely to control. In this way, we selected 17 top-ranked TFs as potential key regulators and thus possible biomarkers for a set of 323 OC-associated genes. For 77 estrogen controlled genes from this set we identified three unique TFs as potential biomarkers.Conclusions: We introduced a new methodology to identify potential diagnostic biomarkers for OC. This report is the first bioinformatics study that explores multiple transcriptional regulators of OC-associated genes as potential diagnostic biomarkers in connection with estrogen responsiveness. We show that 64% of TF biomarkers identified in our study are validated based on real-time data from microarray expression studies. As an illustration, our method could identify CP2 that in combination with CA125 has been reported to be sensitive in diagnosing ovarian tumors. 2011 Kaur et al; licensee BioMed Central Ltd.

  3. Orthologous transcription factors in bacteria have different functions and regulate different genes.

    Directory of Open Access Journals (Sweden)

    Morgan N Price

    2007-09-01

    Full Text Available Transcription factors (TFs form large paralogous gene families and have complex evolutionary histories. Here, we ask whether putative orthologs of TFs, from bidirectional best BLAST hits (BBHs, are evolutionary orthologs with conserved functions. We show that BBHs of TFs from distantly related bacteria are usually not evolutionary orthologs. Furthermore, the false orthologs usually respond to different signals and regulate distinct pathways, while the few BBHs that are evolutionary orthologs do have conserved functions. To test the conservation of regulatory interactions, we analyze expression patterns. We find that regulatory relationships between TFs and their regulated genes are usually not conserved for BBHs in Escherichia coli K12 and Bacillus subtilis. Even in the much more closely related bacteria Vibrio cholerae and Shewanella oneidensis MR-1, predicting regulation from E. coli BBHs has high error rates. Using gene-regulon correlations, we identify genes whose expression pattern differs between E. coli and S. oneidensis. Using literature searches and sequence analysis, we show that these changes in expression patterns reflect changes in gene regulation, even for evolutionary orthologs. We conclude that the evolution of bacterial regulation should be analyzed with phylogenetic trees, rather than BBHs, and that bacterial regulatory networks evolve more rapidly than previously thought.

  4. Transfer factors of radioiodine from volcanic-ash soil (Andosol) to crops

    Energy Technology Data Exchange (ETDEWEB)

    Ban-Nai, Tadaaki; Muramatsu, Yasuyuki [National Inst. of Radiological Sciences, Chiba (Japan). Environmental and Toxicological Sciences Research Group

    2003-03-01

    In order to obtain soil-to-plant transfer factors (TFs) of radioiodine from volcanic-ash soil to agricultural crops, we carried out radiotracer experiments. The mean values of TFs (on a wet weight basis) of radioiodine from Andosol to edible parts of crops were as follows: water dropwort, 0.24; lettuce, 0.00098; onion, 0.0011; radish, 0.0044; turnip, 0.0013 and eggplant, 0.00010. The mean value of the TFs of radioiodine for edible parts of wheat (on a dry weight basis) was 0.00015. We also studied the distributions of iodine in crops. There was a tendency for the TFs of leaves to be higher than those of tubers, fruits and grains. A very high TF was found for water dropwort, because this plant was cultivated under a waterlogged condition, in which iodine desorbed from soil into soil solution with a drop in the Eh value. The data obtained in this study should be helpful to assess the long-lived {sup 129}I (half life: 1.57 x l0{sup 7} yr) pathway related to the fuel cycle. (author)

  5. Recent advances in utilizing transcription factors to improve plant abiotic stress tolerance by transgenic technology

    Directory of Open Access Journals (Sweden)

    Hongyan eWang

    2016-02-01

    Full Text Available Agricultural production and quality are adversely affected by various abiotic stresses worldwide and this will be exacerbated by the deterioration of global climate. To feed a growing world population, it is very urgent to breed stress-tolerant crops with higher yields and improved qualities against multiple environmental stresses. Since conventional breeding approaches had marginal success due to the complexity of stress tolerance traits, the transgenic approach is now being popularly used to breed stress-tolerant crops. So identifying and characterizing the the critical genes involved in plant stress responses is an essential prerequisite for engineering stress-tolerant crops. Far beyond the manipulation of single functional gene, engineering certain regulatory genes has emerged as an effective strategy now for controlling the expression of many stress-responsive genes. Transcription factors (TFs are good candidates for genetic engineering to breed stress-tolerant crop because of their role as master regulators of many stress-responsive genes. Many TFs belonging to families AP2/EREBP, MYB, WRKY, NAC, bZIP have been found to be involved in various abiotic stresses and some TF genes have also been engineered to improve stress tolerance in model and crop plants. In this review, we take five large families of TFs as examples and review the recent progress of TFs involved in plant abiotic stress responses and their potential utilization to improve multiple stress tolerance of crops in the field conditions.

  6. In Silico discovery of transcription factors as potential diagnostic biomarkers of ovarian cancer

    Directory of Open Access Journals (Sweden)

    Choolani Mahesh

    2011-09-01

    Full Text Available Abstract Background Our study focuses on identifying potential biomarkers for diagnosis and early detection of ovarian cancer (OC through the study of transcription regulation of genes affected by estrogen hormone. Results The results are based on a set of 323 experimentally validated OC-associated genes compiled from several databases, and their subset controlled by estrogen. For these two gene sets we computationally determined transcription factors (TFs that putatively regulate transcription initiation. We ranked these TFs based on the number of genes they are likely to control. In this way, we selected 17 top-ranked TFs as potential key regulators and thus possible biomarkers for a set of 323 OC-associated genes. For 77 estrogen controlled genes from this set we identified three unique TFs as potential biomarkers. Conclusions We introduced a new methodology to identify potential diagnostic biomarkers for OC. This report is the first bioinformatics study that explores multiple transcriptional regulators of OC-associated genes as potential diagnostic biomarkers in connection with estrogen responsiveness. We show that 64% of TF biomarkers identified in our study are validated based on real-time data from microarray expression studies. As an illustration, our method could identify CP2 that in combination with CA125 has been reported to be sensitive in diagnosing ovarian tumors.

  7. Role of transcription factor-mediated nucleosome disassembly in PHO5 gene expression

    Science.gov (United States)

    Kharerin, Hungyo; Bhat, Paike J.; Marko, John F.; Padinhateeri, Ranjith

    2016-02-01

    Studying nucleosome dynamics in promoter regions is crucial for understanding gene regulation. Nucleosomes regulate gene expression by sterically occluding transcription factors (TFs) and other non–histone proteins accessing genomic DNA. How the binding competition between nucleosomes and TFs leads to transcriptionally compatible promoter states is an open question. Here, we present a computational study of the nucleosome dynamics and organization in the promoter region of PHO5 gene in Saccharomyces cerevisiae. Introducing a model for nucleosome kinetics that takes into account ATP-dependent remodeling activity, DNA sequence effects, and kinetics of TFs (Pho4p), we compute the probability of obtaining different “promoter states” having different nucleosome configurations. Comparing our results with experimental data, we argue that the presence of local remodeling activity (LRA) as opposed to basal remodeling activity (BRA) is crucial in determining transcriptionally active promoter states. By modulating the LRA and Pho4p binding rate, we obtain different mRNA distributions—Poisson, bimodal, and long-tail. Through this work we explain many features of the PHO5 promoter such as sequence-dependent TF accessibility and the role of correlated dynamics between nucleosomes and TFs in opening/coverage of the TATA box. We also obtain possible ranges for TF binding rates and the magnitude of LRA.

  8. Spatial distribution of predicted transcription factor binding sites in Drosophila ChIP peaks.

    Science.gov (United States)

    Pettie, Kade P; Dresch, Jacqueline M; Drewell, Robert A

    2016-08-01

    In the development of the Drosophila embryo, gene expression is directed by the sequence-specific interactions of a large network of protein transcription factors (TFs) and DNA cis-regulatory binding sites. Once the identity of the typically 8-10bp binding sites for any given TF has been determined by one of several experimental procedures, the sequences can be represented in a position weight matrix (PWM) and used to predict the location of additional TF binding sites elsewhere in the genome. Often, alignments of large (>200bp) genomic fragments that have been experimentally determined to bind the TF of interest in Chromatin Immunoprecipitation (ChIP) studies are trimmed under the assumption that the majority of the binding sites are located near the center of all the aligned fragments. In this study, ChIP/chip datasets are analyzed using the corresponding PWMs for the well-studied TFs; CAUDAL, HUNCHBACK, KNIRPS and KRUPPEL, to determine the distribution of predicted binding sites. All four TFs are critical regulators of gene expression along the anterio-posterior axis in early Drosophila development. For all four TFs, the ChIP peaks contain multiple binding sites that are broadly distributed across the genomic region represented by the peak, regardless of the prediction stringency criteria used. This result suggests that ChIP peak trimming may exclude functional binding sites from subsequent analyses.

  9. Turbidite plays` immaturity means big potential remains

    Energy Technology Data Exchange (ETDEWEB)

    Pettingill, H.S. [Repsol Exploracion SA, Madrid (Spain)

    1998-10-05

    The international exploration and production industry is increasingly focusing on deepwater plays. Turbidites are not the only reservoir type that occurs in deepwater frontiers, but they are the primary reservoir type of those plays. A worldwide data base assembled from published information on 925 fields and discoveries with deepwater clastic reservoirs (turbidites sensu lato) has been employed to investigate the large-scale exploration and production trends. Coverage of the Former Soviet Union, China, and the Indian subcontinent has been minor, but with the large data base of fields and discoveries from the rest of the world, the broad conclusions should remain valid. This article describes the global turbidite play in terms of: (1) basins of the world where turbidite fields have been discovered; (2) the five largest basins in terms of total discovered resources; and (3) a summary of trap type, which is a critical geological factor in turbidite fields. The second article will summarize a population of the world`s 43 largest turbidite fields and discoveries.

  10. Playing Children Adorn Ancient Porcelain

    Institute of Scientific and Technical Information of China (English)

    1995-01-01

    Porcelain is one of China’s greatest achievernents. It appeared during the Eastern Han Dynasty (25-220) and developed into three types of blue porcelain, white porcelain and colored porcelain between the Tang and Song dynasties. From the time of the Ming Dynasty (1368-1644), porcelain-making evolved, glazes and colors improved and porcelain was sold overseas. The quaint shapes and colorfully deslgned porcelain of the Ming Dynasty showed the appeal of folklife, but it was mainly used in the palace. Shown here are some pieces decorated with children at play. From these artifacts we can get an idea of the hairstyles, dress and architecture of that time.

  11. How to play Reverse Hex

    DEFF Research Database (Denmark)

    Toft, Bjarne; Hayward, Ryan B.; Henderson, Philip

    2012-01-01

    We present new results on how to play Reverse Hex, also known as Rex, or Misère Hex, on n × n boards. We give new proofs – and strengthened versions – of Lagarias and Sleator’s theorem (for n × n boards, each player can prolong the game until the board is full, so the first/second player can always......, we find second-player winning replies. Finally, in response to comments by Martin Gardner, for each n ≤ 5, we give a simple winning strategy for the n × n board....

  12. Supervising the uncanny: the play within the play.

    Science.gov (United States)

    Leader, Carol

    2015-11-01

    The writer offers a combined experience in analysis and the performing arts to explore uncanny aspects of the unconscious subtext of the patient's inner drama; subtext which can remain hidden from view in supervision. Freud and Jung's understanding of uncanny experience is considered together with a painting from medieval alchemy and Matte Blanco's conceptions concerning the symmetrical nature of unconscious process. Theatre and the work of the theatre director and actor in approaching the multidimensional aspects of a play are then introduced. Finally clinical case material from group supervision demonstrates how the 'theatre of therapy' and the work of the supervisory couple and group promote the emergence of a more authentic conscious asymmetrical response to the patient's 'script' that can break the 'spell' of the transference/countertransference relationship. This in turn brings meaning to the underlying and implicit 'stage directions' that the patient has been unconsciously communicating. © 2015, The Society of Analytical Psychology.

  13. Identification of key transcription factors in caerulein-induced pancreatitis through expression profiling data.

    Science.gov (United States)

    Qi, Dachuan; Wu, Bo; Tong, Danian; Pan, Ye; Chen, Wei

    2015-08-01

    The current study aimed to isolate key transcription factors (TFs) in caerulein-induced pancreatitis, and to identify the difference between wild type and Mist1 knockout (KO) mice, in order to elucidate the contribution of Mist1 to pancreatitis. The gene profile of GSE3644 was downloaded from the Gene Expression Omnibus database then analyzed using the t-test. The isolated differentially expressed genes (DEGs) were mapped into a transcriptional regulatory network derived from the Integrated Transcription Factor Platform database and in the network, the interaction pairs involving at least one DEG were screened. Fisher's exact test was used to analyze the functional enrichment of the target genes. A total of 1,555 and 3,057 DEGs were identified in the wild type and Mist1KO mice treated with caerulein, respectively. DEGs screened in Mist1KO mice were predominantly enriched in apoptosis, mitogen-activated protein kinase signaling and other cancer-associated pathways. A total of 188 and 51 TFs associated with pathopoiesis were isolated in Mist1KO and wild type mice, respectively. Out of the top 10 TFs (ranked by P-value), 7 TFs, including S-phase kinase-associated protein 2 (Skp2); minichromosome maintenance complex component 3 (Mcm3); cell division cycle 6 (Cdc6); cyclin B1 (Ccnb1); mutS homolog 6 (Msh6); cyclin A2 (Ccna2); and cyclin B2 (Ccnb2), were expressed in the two types of mouse. These TFs were predominantly involved in phosphorylation, DNA replication, cell division and DNA mismatch repair. In addition, specific TFs, including minichromosome maintenance complex component 7 (Mcm7); lymphoid-specific helicase (Hells); and minichromosome maintenance complex component 6 (Mcm6), that function in the unwinding of DNA were identified to participate in Mist1KO pancreatitis. The DEGs, including Cdc6, Mcm6, Msh6 and Wdr1 are closely associated with the regulation of caerulein-induced pancreatitis. Furthermore, other identified TFs were also involved in this type of

  14. Playing Games with Quantum Mechanics

    CERN Document Server

    Phoenix, Simon J D

    2012-01-01

    We present a perspective on quantum games that focuses on the physical aspects of the quantities that are used to implement a game. If a game is to be played, it has to be played with objects and actions that have some physical existence. We call such games playable. By focusing on the notion of playability for games we can more clearly see the distinction between classical and quantum games and tackle the thorny issue of what it means to quantize a game. The approach we take can more properly be thought of as gaming the quantum rather than quantizing a game and we find that in this perspective we can think of a complete quantum game, for a given set of preferences, as representing a single family of quantum games with many different playable versions. The versions of Quantum Prisoners Dilemma presented in the literature can therefore be thought of specific instances of the single family of Quantum Prisoner's Dilemma with respect to a particular measurement. The conditions for equilibrium are given for playab...

  15. MAJOR OIL PLAYS IN UTAH AND VICINITY

    Energy Technology Data Exchange (ETDEWEB)

    Thomas C. Chidsey Jr; Craig D. Morgan; Roger L. Bon

    2003-07-01

    Utah oil fields have produced over 1.2 billion barrels (191 million m{sup 3}). However, the 13.7 million barrels (2.2 million m{sup 3}) of production in 2002 was the lowest level in over 40 years and continued the steady decline that began in the mid-1980s. The Utah Geological Survey believes this trend can be reversed by providing play portfolios for the major oil producing provinces (Paradox Basin, Uinta Basin, and thrust belt) in Utah and adjacent areas in Colorado and Wyoming. Oil plays are geographic areas with petroleum potential caused by favorable combinations of source rock, migration paths, reservoir rock characteristics, and other factors. The play portfolios will include: descriptions and maps of the major oil plays by reservoir; production and reservoir data; case-study field evaluations; summaries of the state-of-the-art drilling, completion, and secondary/tertiary techniques for each play; locations of major oil pipelines; descriptions of reservoir outcrop analogs; and identification and discussion of land use constraints. All play maps, reports, databases, and so forth, produced for the project will be published in interactive, menu-driven digital (web-based and compact disc) and hard-copy formats. This report covers research activities for the third quarter of the first project year (January 1 through March 31, 2003). This work included gathering field data and analyzing best practices in the eastern Uinta Basin, Utah, and the Colorado portion of the Paradox Basin. Best practices used in oil fields of the eastern Uinta Basin consist of conversion of all geophysical well logs into digital form, running small fracture treatments, fingerprinting oil samples from each producing zone, running spinner surveys biannually, mapping each producing zone, and drilling on 80-acre (32 ha) spacing. These practices ensure that induced fractures do not extend vertically out of the intended zone, determine the percentage each zone contributes to the overall

  16. Dynamic regulation of transcription factors by nucleosome remodeling.

    Science.gov (United States)

    Li, Ming; Hada, Arjan; Sen, Payel; Olufemi, Lola; Hall, Michael A; Smith, Benjamin Y; Forth, Scott; McKnight, Jeffrey N; Patel, Ashok; Bowman, Gregory D; Bartholomew, Blaine; Wang, Michelle D

    2015-06-05

    The chromatin landscape and promoter architecture are dominated by the interplay of nucleosome and transcription factor (TF) binding to crucial DNA sequence elements. However, it remains unclear whether nucleosomes mobilized by chromatin remodelers can influence TFs that are already present on the DNA template. In this study, we investigated the interplay between nucleosome remodeling, by either yeast ISW1a or SWI/SNF, and a bound TF. We found that a TF serves as a major barrier to ISW1a remodeling, and acts as a boundary for nucleosome repositioning. In contrast, SWI/SNF was able to slide a nucleosome past a TF, with concurrent eviction of the TF from the DNA, and the TF did not significantly impact the nucleosome positioning. Our results provide direct evidence for a novel mechanism for both nucleosome positioning regulation by bound TFs and TF regulation via dynamic repositioning of nucleosomes.

  17. Tunable signal processing through modular control of transcription factor translocation

    Science.gov (United States)

    Hao, Nan; Budnik, Bogdan A.; Gunawardena, Jeremy; O’Shea, Erin K.

    2013-01-01

    Signaling pathways can induce different dynamics of transcription factor (TF) activation. We explored how TFs process signaling inputs to generate diverse dynamic responses. The budding yeast general stress responsive TF Msn2 acted as a tunable signal processor that could track, filter, or integrate signals in an input dependent manner. This tunable signal processing appears to originate from dual regulation of both nuclear import and export by phosphorylation, as mutants with one form of regulation sustained only one signal processing function. Versatile signal processing by Msn2 is crucial for generating distinct dynamic responses to different natural stresses. Our findings reveal how complex signal processing functions are integrated into a single molecule and provide a guide for the design of TFs with “programmable” signal processing functions. PMID:23349292

  18. Tunable signal processing through modular control of transcription factor translocation.

    Science.gov (United States)

    Hao, Nan; Budnik, Bogdan A; Gunawardena, Jeremy; O'Shea, Erin K

    2013-01-25

    Signaling pathways can induce different dynamics of transcription factor (TF) activation. We explored how TFs process signaling inputs to generate diverse dynamic responses. The budding yeast general stress-responsive TF Msn2 acted as a tunable signal processor that could track, filter, or integrate signals in an input-dependent manner. This tunable signal processing appears to originate from dual regulation of both nuclear import and export by phosphorylation, as mutants with one form of regulation sustained only one signal-processing function. Versatile signal processing by Msn2 is crucial for generating distinct dynamic responses to different natural stresses. Our findings reveal how complex signal-processing functions are integrated into a single molecule and provide a guide for the design of TFs with "programmable" signal-processing functions.

  19. Inter- and intra-combinatorial regulation by transcription factors and microRNAs

    Directory of Open Access Journals (Sweden)

    Chang Joseph T

    2007-10-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are a novel class of non-coding small RNAs. In mammalian cells, miRNAs repress the translation of messenger RNAs (mRNAs or degrade mRNAs. miRNAs play important roles in development and differentiation, and they are also implicated in aging, and oncogenesis. Predictions of targets of miRNAs suggest that they may regulate more than one-third of all genes. The overall functions of mammalian miRNAs remain unclear. Combinatorial regulation by transcription factors alone or miRNAs alone offers a wide range of regulatory programs. However, joining transcriptional and post-transcriptional regulatory mechanisms enables higher complexity regulatory programs that in turn could give cells evolutionary advantages. Investigating coordinated regulation of genes by miRNAs and transcription factors (TFs from a statistical standpoint is a first step that may elucidate some of their roles in various biological processes. Results Here, we studied the nature and scope of coordination among regulators from the transcriptional and miRNA regulatory layers in the human genome. Our findings are based on genome wide statistical assessment of regulatory associations ("interactions" among the sets of predicted targets of miRNAs and sets of putative targets of transcription factors. We found that combinatorial regulation by transcription factor pairs and miRNA pairs is much more abundant than the combinatorial regulation by TF-miRNA pairs. In addition, many of the strongly interacting TF-miRNA pairs involve a subset of master TF regulators that co-regulate genes in coordination with almost any miRNA. Application of standard measures for evaluating the degree of interaction between pairs of regulators show that strongly interacting TF-miRNA, TF-TF or miRNA-miRNA pairs tend to include TFs or miRNAs that regulate very large numbers of genes. To correct for this potential bias we introduced an additional Bayesian measure that incorporates

  20. Unbiased identification of signal-activated transcription factors by barcoded synthetic tandem repeat promoter screening (BC-STAR-PROM).

    Science.gov (United States)

    Gosselin, Pauline; Rando, Gianpaolo; Fleury-Olela, Fabienne; Schibler, Ueli

    2016-08-15

    The discovery of transcription factors (TFs) controlling pathways in health and disease is of paramount interest. We designed a widely applicable method, dubbed barcorded synthetic tandem repeat promoter screening (BC-STAR-PROM), to identify signal-activated TFs without any a priori knowledge about their properties. The BC-STAR-PROM library consists of ∼3000 luciferase expression vectors, each harboring a promoter (composed of six tandem repeats of synthetic random DNA) and an associated barcode of 20 base pairs (bp) within the 3' untranslated mRNA region. Together, the promoter sequences encompass >400,000 bp of random DNA, a sequence complexity sufficient to capture most TFs. Cells transfected with the library are exposed to a signal, and the mRNAs that it encodes are counted by next-generation sequencing of the barcodes. This allows the simultaneous activity tracking of each of the ∼3000 synthetic promoters in a single experiment. Here we establish proof of concept for BC-STAR-PROM by applying it to the identification of TFs induced by drugs affecting actin and tubulin cytoskeleton dynamics. BC-STAR-PROM revealed that serum response factor (SRF) is the only immediate early TF induced by both actin polymerization and microtubule depolymerization. Such changes in cytoskeleton dynamics are known to occur during the cell division cycle, and real-time bioluminescence microscopy indeed revealed cell-autonomous SRF-myocardin-related TF (MRTF) activity bouts in proliferating cells.

  1. Novel disease susceptibility factors for fungal necrotrophic pathogens in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Albor Dobón

    2015-04-01

    Full Text Available Host cells use an intricate signaling system to respond to invasions by pathogenic microorganisms. Although several signaling components of disease resistance against necrotrophic fungal pathogens have been identified, our understanding for how molecular components and host processes contribute to plant disease susceptibility is rather sparse. Here, we identified four transcription factors (TFs from Arabidopsis that limit pathogen spread. Arabidopsis mutants defective in any of these TFs displayed increased disease susceptibility to Botrytis cinerea and Plectosphaerella cucumerina, and a general activation of non-immune host processes that contribute to plant disease susceptibility. Transcriptome analyses revealed that the mutants share a common transcriptional signature of 77 up-regulated genes. We characterized several of the up-regulated genes that encode peptides with a secretion signal, which we named PROVIR (for provirulence factors. Forward and reverse genetic analyses revealed that many of the PROVIRs are important for disease susceptibility of the host to fungal necrotrophs. The TFs and PROVIRs identified in our work thus represent novel genetic determinants for plant disease susceptibility to necrotrophic fungal pathogens.

  2. microProtein Prediction Program (miP3) : A Software for Predicting microProteins and Their Target Transcription Factors

    NARCIS (Netherlands)

    de Klein, Niek; Magnani, Enrico; Banf, Michael; Rhee, Seung Yon

    2015-01-01

    An emerging concept in transcriptional regulation is that a class of truncated transcription factors (TFs), called microProteins (miPs), engages in protein-protein interactions with TF complexes and provides feedback controls. A handful of miP examples have been described in the literature but the e

  3. iTAK: A program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators and protein kinases

    Science.gov (United States)

    Transcription factors (TFs) are proteins that regulate the expression of target genes by binding to specific elements in their regulatory regions. Transcriptional regulators (TRs) also regulate the expression of target genes; however, they operate indirectly via interaction with the basal transcript...

  4. Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)

    NARCIS (Netherlands)

    Kaufmann, K.; Muiño, J.M.; Østerås, M.; Farinelli, L.; Krajewski, P.; Angenent, G.C.

    2010-01-01

    Chromatin immunoprecipitation (ChIP) is a powerful technique to study interactions between transcription factors (TFs) and DNA in vivo. For genome-wide de novo discovery of TF-binding sites, the DNA that is obtained in ChIP experiments needs to be processed for sequence identification. The sequences

  5. Play behaviours and play object preferences of young children with autistic disorder in a clinical play environment.

    Science.gov (United States)

    Dominguez, Anna; Ziviani, Jenny; Rodger, Sylvia

    2006-01-01

    Play is the primary occupation of childhood and provides a potentially powerful means of assessing and treating children with autistic disorder. This study utilized a cross-sectional comparison design to investigate the nature of play engagement in children with AD (n = 24), relative to typically developing children (n = 34) matched for chronological age. Play behaviours were recorded in a clinical play environment. Videotapes comprising 15 minutes of the children's spontaneous play behaviour were analysed using time-interval analysis. The particular play behaviours observed and play objects used were coded. Differences in play behaviours (p motivation.

  6. Hand kinematics of piano playing.

    Science.gov (United States)

    Furuya, Shinichi; Flanders, Martha; Soechting, John F

    2011-12-01

    Dexterous use of the hand represents a sophisticated sensorimotor function. In behaviors such as playing the piano, it can involve strong temporal and spatial constraints. The purpose of this study was to determine fundamental patterns of covariation of motion across joints and digits of the human hand. Joint motion was recorded while 5 expert pianists played 30 excerpts from musical pieces, which featured ∼50 different tone sequences and fingering. Principal component analysis and cluster analysis using an expectation-maximization algorithm revealed that joint velocities could be categorized into several patterns, which help to simplify the description of the movements of the multiple degrees of freedom of the hand. For the thumb keystroke, two distinct patterns of joint movement covariation emerged and they depended on the spatiotemporal patterns of the task. For example, the thumb-under maneuver was clearly separated into two clusters based on the direction of hand translation along the keyboard. While the pattern of the thumb joint velocities differed between these clusters, the motions at the metacarpo-phalangeal and proximal-phalangeal joints of the four fingers were more consistent. For a keystroke executed with one of the fingers, there were three distinct patterns of joint rotations, across which motion at the striking finger was fairly consistent, but motion of the other fingers was more variable. Furthermore, the amount of movement spillover of the striking finger to the adjacent fingers was small irrespective of the finger used for the keystroke. These findings describe an unparalleled amount of independent motion of the fingers.

  7. Regulatory coordination of clustered microRNAs based on microRNA-transcription factor regulatory network

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    Wang Jin

    2011-12-01

    Full Text Available Abstract Background MicroRNA (miRNA is a class of small RNAs of ~22nt which play essential roles in many crucial biological processes and numerous human diseases at post-transcriptional level of gene expression. It has been revealed that miRNA genes tend to be clustered, and the miRNAs organized into one cluster are usually transcribed coordinately. This implies a coordinated regulation mode exerted by clustered miRNAs. However, how the clustered miRNAs coordinate their regulations on large scale gene expression is still unclear. Results We constructed the miRNA-transcription factor regulatory network that contains the interactions between transcription factors (TFs, miRNAs and non-TF protein-coding genes, and made a genome-wide study on the regulatory coordination of clustered miRNAs. We found that there are two types of miRNA clusters, i.e. homo-clusters that contain miRNAs of the same family and hetero-clusters that contain miRNAs of various families. In general, the homo-clustered as well as the hetero-clustered miRNAs both exhibit coordinated regulation since the miRNAs belonging to one cluster tend to be involved in the same network module, which performs a relatively isolated biological function. However, the homo-clustered miRNAs show a direct regulatory coordination that is realized by one-step regulation (i.e. the direct regulation of the coordinated targets, whereas the hetero-clustered miRNAs show an indirect regulatory coordination that is realized by a regulation comprising at least three steps (e.g. the regulation on the coordinated targets by a miRNA through a sequential action of two TFs. The direct and indirect regulation target different categories of genes, the former predominantly regulating genes involved in emergent responses, the latter targeting genes that imply long-term effects. Conclusion The genomic clustering of miRNAs is closely related to the coordinated regulation in the gene regulatory network. The pattern of

  8. Evaluating Transcription Factor Activity Changes by Scoring Unexplained Target Genes in Expression Data

    Science.gov (United States)

    Berchtold, Evi; Csaba, Gergely; Zimmer, Ralf

    2016-01-01

    Several methods predict activity changes of transcription factors (TFs) from a given regulatory network and measured expression data. But available gene regulatory networks are incomplete and contain many condition-dependent regulations that are not relevant for the specific expression measurement. It is not known which combination of active TFs is needed to cause a change in the expression of a target gene. A method to systematically evaluate the inferred activity changes is missing. We present such an evaluation strategy that indicates for how many target genes the observed expression changes can be explained by a given set of active TFs. To overcome the problem that the exact combination of active TFs needed to activate a gene is typically not known, we assume a gene to be explained if there exists any combination for which the predicted active TFs can possibly explain the observed change of the gene. We introduce the i-score (inconsistency score), which quantifies how many genes could not be explained by the set of activity changes of TFs. We observe that, even for these minimal requirements, published methods yield many unexplained target genes, i.e. large i-scores. This holds for all methods and all expression datasets we evaluated. We provide new optimization methods to calculate the best possible (minimal) i-score given the network and measured expression data. The evaluation of this optimized i-score on a large data compendium yields many unexplained target genes for almost every case. This indicates that currently available regulatory networks are still far from being complete. Both the presented Act-SAT and Act-A* methods produce optimal sets of TF activity changes, which can be used to investigate the difficult interplay of expression and network data. A web server and a command line tool to calculate our i-score and to find the active TFs associated with the minimal i-score is available from https://services.bio.ifi.lmu.de/i-score. PMID:27723775

  9. The Wade Factor: Marketing? A Team Sport Worth Playing

    Science.gov (United States)

    Perna, Mark C.

    2005-01-01

    Customer service people are the first line of marketing, sales and revenue growth. Give them the proper training and understanding to enthusiastically lead all potential students or customers through the information-gathering and sign-up process. It does not matter how many calls schools receives through a well-planned marketing campaign if the…

  10. Playing the game: psychological factors in surviving cancer.

    Science.gov (United States)

    Rom, Stephen A; Miller, Laurence; Peluso, Jennifer

    2009-01-01

    Cancer is a threat that can rob a person of their physical and mental wellbeing. While cancer awareness has ventured to the forefront of social consciousness, led by surges from Lance Armstrong and other celebrities affected by cancer, the medical world continually remains foiled in terms of regulating the many confounding variables that spawn cancer: toxins, pollutants, poor diet, etc. Yet there is a hope: one variable thought to affect cancer prognosis may be distinctly tractable: positive mental attitude (PMA). Principles of PMA that are readily utilized in the science of sports psychology to spur athletes to victory may be productively applied to the hospital arena. The parallels between sports and medicine are abundant, and can be utilized by the cancer patient to help secure victory. This paper describes the steps to victory, along with stratagems and concepts on how to keep the "opponent"--cancer--from gaining any further advantage.

  11. Transcription factor assisted loading and enhancer dynamics dictate the hepatic fasting response

    Science.gov (United States)

    Goldstein, Ido; Baek, Songjoon; Presman, Diego M.; Paakinaho, Ville; Swinstead, Erin E.; Hager, Gordon L.

    2017-01-01

    Fasting elicits transcriptional programs in hepatocytes leading to glucose and ketone production. This transcriptional program is regulated by many transcription factors (TFs). To understand how this complex network regulates the metabolic response to fasting, we aimed at isolating the enhancers and TFs dictating it. Measuring chromatin accessibility revealed that fasting massively reorganizes liver chromatin, exposing numerous fasting-induced enhancers. By utilizing computational methods in combination with dissecting enhancer features and TF cistromes, we implicated four key TFs regulating the fasting response: glucocorticoid receptor (GR), cAMP responsive element binding protein 1 (CREB1), peroxisome proliferator activated receptor alpha (PPARA), and CCAAT/enhancer binding protein beta (CEBPB). These TFs regulate fuel production by two distinctly operating modules, each controlling a separate metabolic pathway. The gluconeogenic module operates through assisted loading, whereby GR doubles the number of sites occupied by CREB1 as well as enhances CREB1 binding intensity and increases accessibility of CREB1 binding sites. Importantly, this GR-assisted CREB1 binding was enhancer-selective and did not affect all CREB1-bound enhancers. Single-molecule tracking revealed that GR increases the number and DNA residence time of a portion of chromatin-bound CREB1 molecules. These events collectively result in rapid synergistic gene expression and higher hepatic glucose production. Conversely, the ketogenic module operates via a GR-induced TF cascade, whereby PPARA levels are increased following GR activation, facilitating gradual enhancer maturation next to PPARA target genes and delayed ketogenic gene expression. Our findings reveal a complex network of enhancers and TFs that dynamically cooperate to restore homeostasis upon fasting. PMID:28031249

  12. MAJOR OIL PLAYS IN UTAH AND VICINITY

    Energy Technology Data Exchange (ETDEWEB)

    Thomas C. Chidsey, Jr.

    2003-01-01

    Utah oil fields have produced a total of 1.2 billion barrels (191 million m{sup 3}). However, the 15 million barrels (2.4 million m{sup 3}) of production in 2000 was the lowest level in over 40 years and continued the steady decline that began in the mid-1980s. The Utah Geological Survey believes this trend can be reversed by providing play portfolios for the major oil producing provinces (Paradox Basin, Uinta Basin, and thrust belt) in Utah and adjacent areas in Colorado and Wyoming. Oil plays are geographic areas with petroleum potential caused by favorable combinations of source rock, migration paths, reservoir rock characteristics, and other factors. The play portfolios will include: descriptions and maps of the major oil plays by reservoir; production and reservoir data; case-study field evaluations; summaries of the state-of-the-art drilling, completion, and secondary/tertiary techniques for each play; locations of major oil pipelines; descriptions of reservoir outcrop analogs; and identification and discussion of land use constraints. All play maps, reports, databases, and so forth, produced for the project will be published in interactive, menu-driven digital (web-based and compact disc) and hard-copy formats. This report covers research activities for the first quarter of the first project year (July 1 through September 30, 2002). This work included producing general descriptions of Utah's major petroleum provinces, gathering field data, and analyzing best practices in the Utah Wyoming thrust belt. Major Utah oil reservoirs and/or source rocks are found in Devonian through Permian, Jurassic, Cretaceous, and Tertiary rocks. Stratigraphic traps include carbonate buildups and fluvial-deltaic pinchouts, and structural traps include basement-involved and detached faulted anticlines. Best practices used in Utah's oil fields consist of waterflood, carbon-dioxide flood, gas-injection, and horizontal drilling programs. Nitrogen injection and horizontal

  13. A comprehensive resource of interacting protein regions for refining human transcription factor networks.

    Directory of Open Access Journals (Sweden)

    Etsuko Miyamoto-Sato

    Full Text Available Large-scale data sets of protein-protein interactions (PPIs are a valuable resource for mapping and analysis of the topological and dynamic features of interactome networks. The currently available large-scale PPI data sets only contain information on interaction partners. The data presented in this study also include the sequences involved in the interactions (i.e., the interacting regions, IRs suggested to correspond to functional and structural domains. Here we present the first large-scale IR data set obtained using mRNA display for 50 human transcription factors (TFs, including 12 transcription-related proteins. The core data set (966 IRs; 943 PPIs displays a verification rate of 70%. Analysis of the IR data set revealed the existence of IRs that interact with multiple partners. Furthermore, these IRs were preferentially associated with intrinsic disorder. This finding supports the hypothesis that intrinsically disordered regions play a major role in the dynamics and diversity of TF networks through their ability to structurally adapt to and bind with multiple partners. Accordingly, this domain-based interaction resource represents an important step in refining protein interactions and networks at the domain level and in associating network analysis with biological structure and function.

  14. Transcription factor-based biosensors in biotechnology: current state and future prospects.

    Science.gov (United States)

    Mahr, Regina; Frunzke, Julia

    2016-01-01

    Living organisms have evolved a plethora of sensing systems for the intra- and extracellular detection of small molecules, ions or physical parameters. Several recent studies have demonstrated that these principles can be exploited to devise synthetic regulatory circuits for metabolic engineering strategies. In this context, transcription factors (TFs) controlling microbial physiology at the level of transcription play a major role in biosensor design, since they can be implemented in synthetic circuits controlling gene expression in dependency of, for example, small molecule production. Here, we review recent progress on the utilization of TF-based biosensors in microbial biotechnology highlighting different areas of application. Recent advances in metabolic engineering reveal TF-based sensors to be versatile tools for strain and enzyme development using high-throughput (HT) screening strategies and adaptive laboratory evolution, the optimization of heterologous pathways via the implementation of dynamic control circuits and for the monitoring of single-cell productivity in live cell imaging studies. These examples underline the immense potential of TF-based biosensor circuits but also identify limitations and room for further optimization.

  15. Playing life away: Videogames and personality structure.

    Directory of Open Access Journals (Sweden)

    Leones do Couto G.

    2014-09-01

    Full Text Available This study aims to fill a gap in the current research on the personality organization of frequent videogame users. The scientific literature in this area refers only to the existence of risk factors that increase the likelihood of abusing videogames and their negative consequences on the mental health of users (Gentile et al., 2011; Lemmens, Valkenburg, & Peter, 2011; Rehbein & Baier, 2013. In this study, a sample of patients who reported spending an excessive amount of their time playing videogames were recruited from Instituto Quintino Aires–Lisbon/Oporto and took the Rorschach Personality Test (Exner, 1993, 1995. Two other samples—one consisting of patients who reported not playing videogames, and the other of patients who were discharged from the institution after psychotherapy—also took part in the study. The patients in the first sample revealed less exposure to the relational sources of stress that are necessary for socioemotional development and less interest in others than did patients in the other samples. Other results regarding the personality structure of the subjects in the three samples are compared and discussed in light of cultural-historical psychology.

  16. TEACHING SPEAKING BY ROLE-PLAY ACTIVITY

    Directory of Open Access Journals (Sweden)

    Fadilah Fadilah

    2016-11-01

    Full Text Available The students often find some problems in practising English speaking. The problem frequently found is that their native language causes them difficult to use the foreign language. Other reason is because of motivation lack to practice the second language in daily conversation. They are also too shy and afraid to take part in the conversation. Many factors can cause the problem of the students’ speaking skills namely the students’ interest, the material, and the media among others including the technique in teaching English. There are many ways that can be done by the students to develop their ability in speaking English. The appropriate technique used by the English teacher also supports their interested in practising their speaking. One of the techniques that can be applied is role play.

  17. Play and Community in the Classroom.

    Science.gov (United States)

    King, Nechie R.

    1997-01-01

    Children recognize two kinds of classroom play: instrumental play organized by teachers for academic purposes; and illicit play stressing surreptitious, unsanctioned activities like whispering and clowning around. Each is associated with a particular form of classroom community. This article considers how the nature of classroom play influences…

  18. Teatro! Hispanic Plays for Young People.

    Science.gov (United States)

    Vigil, Angel

    This collection of 14 folk drama scripts is drawn from the Hispanic culture and traditions of the American Southwest and designed for use in educational settings. The plays are short, simple, and easy to produce. A single play can fill a class period, while several plays grouped together would make a school assembly. Six plays, intended for grades…

  19. The development of early sociodramatic play

    NARCIS (Netherlands)

    Deunk, M.I.; Berenst, J.; de Glopper, C.M.

    2008-01-01

    In this article we study the beginnings of sociodramatic play. We examine the pretend play interactions of a Dutch girl, Peggy, and focus on her transition into sociodramatic play. Initially, Peggy interprets only some elements of her play interactions at the pretend level. At age 2;9, Peggy shows s

  20. Teatro! Hispanic Plays for Young People.

    Science.gov (United States)

    Vigil, Angel

    This collection of 14 folk drama scripts is drawn from the Hispanic culture and traditions of the American Southwest and designed for use in educational settings. The plays are short, simple, and easy to produce. A single play can fill a class period, while several plays grouped together would make a school assembly. Six plays, intended for grades…

  1. Evaluative Intervention Research in Child's Play.

    Science.gov (United States)

    Yawkey, Thomas Daniels; Fox, Franklin Daniel

    1981-01-01

    Evaluative intervention research studies in pretend play are investigations that examine the potential of imaginative play in young children to demonstrate a relationship between play and cognitive, social, and emotional growth. A review of the research indicates that children who engage in imaginative play yield higher test scores than those in…

  2. Superman Comes to Preschool: Superhero TV Play.

    Science.gov (United States)

    Ritchie, Kathleen E.; Johnson, Zita M.

    Systematic efforts at the Arizona State Child Study Laboratory were successful in replacing children's undesirable superhero play with other types of sociodramatic play. Teachers found superhero play undesirable because it was aggressive and noisy and was accompanied by an increase in random activity. Observations indicated that superhero play had…

  3. Conceptualizing the Play Policies in Preschool Curriculums

    Science.gov (United States)

    Sener, Tulin

    2013-01-01

    This research attempted to describe the play policies in preschool institutions in Ankara, Turkey. The aim of this study is to determine the approaches of the preschools to the children's play. "Play Policy Questionnaire" administered to all directors and teachers of 20 public preschools and 20 private preschools. Play policy of…

  4. Introduction to Plays, English: 5112.44.

    Science.gov (United States)

    Ozan, Ruth S.

    Several plays are studied to introduce students to theatrical terms and to the elements of a play in this quinmester course for Dade County High Schools. Several approaches to the study of the play are suggested such as individual and a large group production of a play, the use of a unified theme such as Youth vs. Tradition, or the line of…

  5. Strategies for Family Facilitation of Play Dates

    Science.gov (United States)

    Chambers, Cynthia R.; Horn, Eva M.

    2010-01-01

    Play dates can serve several functions for young children, including children with social difficulties, such as developmental delays, behavioral disorders, autism spectrum disorders, and shyness. Play dates provide children with additional opportunities to be around peers and to practice skills associated with peer play interactions. Play dates…

  6. Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes.

    Science.gov (United States)

    Pujato, Mario; Kieken, Fabien; Skiles, Amanda A; Tapinos, Nikos; Fiser, Andras

    2014-12-16

    Proper cell functioning depends on the precise spatio-temporal expression of its genetic material. Gene expression is controlled to a great extent by sequence-specific transcription factors (TFs). Our current knowledge on where and how TFs bind and associate to regulate gene expression is incomplete. A structure-based computational algorithm (TF2DNA) is developed to identify binding specificities of TFs. The method constructs homology models of TFs bound to DNA and assesses the relative binding affinity for all possible DNA sequences using a knowledge-based potential, after optimization in a molecular mechanics force field. TF2DNA predictions were benchmarked against experimentally determined binding motifs. Success rates range from 45% to 81% and primarily depend on the sequence identity of aligned target sequences and template structures, TF2DNA was used to predict 1321 motifs for 1825 putative human TF proteins, facilitating the reconstruction of most of the human gene regulatory network. As an illustration, the predicted DNA binding site for the poorly characterized T-cell leukemia homeobox 3 (TLX3) TF was confirmed with gel shift assay experiments. TLX3 motif searches in human promoter regions identified a group of genes enriched in functions relating to hematopoiesis, tissue morphology, endocrine system and connective tissue development and function. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines.

    KAUST Repository

    Foley, Joseph W

    2013-10-20

    BACKGROUND: High-occupancy target (HOT) regions are compact genome loci occupied by many different transcription factors (TFs). HOT regions were initially defined in invertebrate model organisms, and we here show that they are a ubiquitous feature of the human gene-regulation landscape. RESULTS: We identified HOT regions by a comprehensive analysis of ChIP-seq data from 96 DNA-associated proteins in 5 human cell lines. Most HOT regions co-localize with RNA polymerase II binding sites, but many are not near the promoters of annotated genes. At HOT promoters, TF occupancy is strongly predictive of transcription preinitiation complex recruitment and moderately predictive of initiating Pol II recruitment, but only weakly predictive of elongating Pol II and RNA transcript abundance. TF occupancy varies quantitatively within human HOT regions; we used this variation to discover novel associations between TFs. The sequence motif associated with any given TF\\'s direct DNA binding is somewhat predictive of its empirical occupancy, but a great deal of occupancy occurs at sites without the TF\\'s motif, implying indirect recruitment by another TF whose motif is present. CONCLUSIONS: Mammalian HOT regions are regulatory hubs that integrate the signals from diverse regulatory pathways to quantitatively tune the promoter for RNA polymerase II recruitment.

  8. Identification of drought, cadmium and root-lesion nematode infection stress-responsive transcription factors in ramie

    Directory of Open Access Journals (Sweden)

    Zheng Xia

    2016-01-01

    Full Text Available Drought, cadmium (Cd stress, and root lesion nematode (RLN infection are three of the most important stresses affecting ramie growth and development; therefore, ramie breeding programs focus on their management more than on any other abiotic or biotic stresses. The fact that only a small number of stress-responsive transcription factors (TFs have been identified so far is a major obstacle in the elucidation of mechanisms regulating the response to these three stresses in ramie. In this study, in order to uncover more stress-responsive TFs, a total of 179 nonredundant genes with full-length open reading frames from the MYB, AP2/ERF, bZIP, HD-ZIP, and COL families were obtained by searching for against the ramie transcriptome. Expression pattern analysis demonstrated that most of these genes showed relatively higher expression in the stem xylem and bast than in other tissues. Among these genes, 96 genes were found to be involved in responses to drought, Cd exposure, or RLN-infection. The expression of 54 of these genes was regulated by at least two stresses. These stress-responsive TFs probably have roles in the regulation of stress tolerance. The discovery of these stress-responsive TFs will be helpful for furthering our understanding of the mechanisms that regulate stress responses in ramie.

  9. Automated discovery of tissue-targeting enhancers and transcription factors from binding motif and gene function data.

    Directory of Open Access Journals (Sweden)

    Geetu Tuteja

    2014-01-01

    Full Text Available Identifying enhancers regulating gene expression remains an important and challenging task. While recent sequencing-based methods provide epigenomic characteristics that correlate well with enhancer activity, it remains onerous to comprehensively identify all enhancers across development. Here we introduce a computational framework to identify tissue-specific enhancers evolving under purifying selection. First, we incorporate high-confidence binding site predictions with target gene functional enrichment analysis to identify transcription factors (TFs likely functioning in a particular context. We then search the genome for clusters of binding sites for these TFs, overcoming previous constraints associated with biased manual curation of TFs or enhancers. Applying our method to the placenta, we find 33 known and implicate 17 novel TFs in placental function, and discover 2,216 putative placenta enhancers. Using luciferase reporter assays, 31/36 (86% tested candidates drive activity in placental cells. Our predictions agree well with recent epigenomic data in human and mouse, yet over half our loci, including 7/8 (87% tested regions, are novel. Finally, we establish that our method is generalizable by applying it to 5 additional tissues: heart, pancreas, blood vessel, bone marrow, and liver.

  10. Effects of cytosine methylation on transcription factor binding sites

    KAUST Repository

    Medvedeva, Yulia A

    2014-03-26

    Background: DNA methylation in promoters is closely linked to downstream gene repression. However, whether DNA methylation is a cause or a consequence of gene repression remains an open question. If it is a cause, then DNA methylation may affect the affinity of transcription factors (TFs) for their binding sites (TFBSs). If it is a consequence, then gene repression caused by chromatin modification may be stabilized by DNA methylation. Until now, these two possibilities have been supported only by non-systematic evidence and they have not been tested on a wide range of TFs. An average promoter methylation is usually used in studies, whereas recent results suggested that methylation of individual cytosines can also be important.Results: We found that the methylation profiles of 16.6% of cytosines and the expression profiles of neighboring transcriptional start sites (TSSs) were significantly negatively correlated. We called the CpGs corresponding to such cytosines " traffic lights" We observed a strong selection against CpG " traffic lights" within TFBSs. The negative selection was stronger for transcriptional repressors as compared with transcriptional activators or multifunctional TFs as well as for core TFBS positions as compared with flanking TFBS positions.Conclusions: Our results indicate that direct and selective methylation of certain TFBS that prevents TF binding is restricted to special cases and cannot be considered as a general regulatory mechanism of transcription. 2013 Medvedeva et al.; licensee BioMed Central Ltd.

  11. The effects of cytosine methylation on general transcription factors

    Science.gov (United States)

    Jin, Jianshi; Lian, Tengfei; Gu, Chan; Yu, Kai; Gao, Yi Qin; Su, Xiao-Dong

    2016-07-01

    DNA methylation on CpG sites is the most common epigenetic modification. Recently, methylation in a non-CpG context was found to occur widely on genomic DNA. Moreover, methylation of non-CpG sites is a highly controlled process, and its level may vary during cellular development. To study non-CpG methylation effects on DNA/protein interactions, we have chosen three human transcription factors (TFs): glucocorticoid receptor (GR), brain and muscle ARNT-like 1 (BMAL1) - circadian locomotor output cycles kaput (CLOCK) and estrogen receptor (ER) with methylated or unmethylated DNA binding sequences, using single-molecule and isothermal titration calorimetry assays. The results demonstrated that these TFs interact with methylated DNA with different effects compared with their cognate DNA sequences. The effects of non-CpG methylation on transcriptional regulation were validated by cell-based luciferase assay at protein level. The mechanisms of non-CpG methylation influencing DNA-protein interactions were investigated by crystallographic analyses and molecular dynamics simulation. With BisChIP-seq assays in HEK-293T cells, we found that GR can recognize highly methylated sites within chromatin in cells. Therefore, we conclude that non-CpG methylation of DNA can provide a mechanism for regulating gene expression through directly affecting the binding of TFs.

  12. Psychiatrists' Perceptions of Role-Playing Games.

    Science.gov (United States)

    Lis, Eric; Chiniara, Carl; Biskin, Robert; Montoro, Richard

    2015-09-01

    The literature has seen a surge in research on the mental health impacts of technologies such as Facebook, video games, and massively-multiplayer online role-playing games such as World of Warcraft, but little is known regarding the mental health impact of non-video role-playing games, such as Dungeons & Dragons. The present study examines how psychiatrists' perceive role-playing games and whether they play them. Psychiatrists at a tertiary care centre in Canada completed a questionnaire assessing history of playing role-playing games and whether they associate them with psychopathology. Forty-eight psychiatrists responded. Twenty-three percent have played a role-playing game over their lifetimes. Twenty-two percent believed there was an association between psychopathology and role-playing games. A majority of psychiatrists who responded do not associate role-playing games with psychopathology. Implications for clinical practice and future research are discussed.

  13. Finger Forces in Clarinet Playing

    Directory of Open Access Journals (Sweden)

    Alex Hofmann

    2016-08-01

    Full Text Available Clarinettists close and open multiple tone holes to alter the pitch of the tones. Their fingering technique must be fast, precise, and coordinated with the tongue articulation. In this empirical study, finger force profiles and tongue techniques of clarinet students (N = 17 and professional clarinettists (N = 6 were investigated under controlled performance conditions. First, in an expressive-performance task, eight selected excerpts from the first Weber Concerto were performed. These excerpts were chosen to fit in a 2 x 2 x 2 design (register: low--high; tempo: slow--fast, dynamics: soft--loud. There was an additional condition controlled by the experimenter, which determined the expression levels (low--high of the performers. Second, a technical-exercise task, an isochronous 23-tone melody was designed that required different effectors to produce the sequence (finger-only, tongue-only, combined tongue-finger actions. The melody was performed in three tempo conditions (slow, medium, fast in a synchronization-continuation paradigm. Participants played on a sensor-equipped Viennese clarinet, which tracked finger forces and reed oscillations simultaneously. From the data, average finger force (Fmean and peak force (Fmax were calculated. The overall finger forces were low (Fmean = 1.17 N, Fmax = 3.05 N compared to those on other musical instruments (e.g. guitar. Participants applied the largest finger forces during the high expression level performance conditions (Fmean = 1.21 N.For the technical exercise task, timing and articulation information were extracted from the reed signal. Here, the timing precision of the fingers deteriorated the timing precision of the tongue for combined tongue-finger actions, especially for faster tempi. Although individual finger force profiles were overlapping, the group of professional players applied less finger force overall (Fmean = 0.54 N. Such sensor instruments provide useful insights into player

  14. Finger Forces in Clarinet Playing.

    Science.gov (United States)

    Hofmann, Alex; Goebl, Werner

    2016-01-01

    Clarinettists close and open multiple tone holes to alter the pitch of the tones. Their fingering technique must be fast, precise, and coordinated with the tongue articulation. In this empirical study, finger force profiles and tongue techniques of clarinet students (N = 17) and professional clarinettists (N = 6) were investigated under controlled performance conditions. First, in an expressive-performance task, eight selected excerpts from the first Weber Concerto were performed. These excerpts were chosen to fit in a 2 × 2 × 2 design (register: low-high; tempo: slow-fast, dynamics: soft-loud). There was an additional condition controlled by the experimenter, which determined the expression levels (low-high) of the performers. Second, a technical-exercise task, an isochronous 23-tone melody was designed that required different effectors to produce the sequence (finger-only, tongue-only, combined tongue-finger actions). The melody was performed in three tempo conditions (slow, medium, fast) in a synchronization-continuation paradigm. Participants played on a sensor-equipped Viennese clarinet, which tracked finger forces and reed oscillations simultaneously. From the data, average finger force (F mean ) and peak force (F max ) were calculated. The overall finger forces were low (F mean = 1.17 N, F max = 3.05 N) compared to those on other musical instruments (e.g., guitar). Participants applied the largest finger forces during the high expression level performance conditions (F mean = 1.21 N). For the technical exercise task, timing and articulation information were extracted from the reed signal. Here, the timing precision of the fingers deteriorated the timing precision of the tongue for combined tongue-finger actions, especially for faster tempi. Although individual finger force profiles were overlapping, the group of professional players applied less finger force overall (F mean = 0.54 N). Such sensor instruments provide useful insights into player

  15. Play in adulthood. A developmental consideration.

    Science.gov (United States)

    Colarusso, C A

    1993-01-01

    This paper is about normal development, addressing the basic characteristics and evolution of play throughout life, with particular emphasis on the nature of play in adulthood. Although the psychoanalytic literature on play in childhood is extensive, undoubtedly because of its relevance to child analysis, very little has been written on the subject of adult play or on the relationship between adult play and its childhood antecedents.

  16. Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers.

    Directory of Open Access Journals (Sweden)

    Evgeniy A Ozonov

    Full Text Available Because DNA packaging in nucleosomes modulates its accessibility to transcription factors (TFs, unraveling the causal determinants of nucleosome positioning is of great importance to understanding gene regulation. Although there is evidence that intrinsic sequence specificity contributes to nucleosome positioning, the extent to which other factors contribute to nucleosome positioning is currently highly debated. Here we obtained both in vivo and in vitro reference maps of positions that are either consistently covered or free of nucleosomes across multiple experimental data-sets in Saccharomyces cerevisiae. We then systematically quantified the contribution of TF binding to nucleosome positioning using a rigorous statistical mechanics model in which TFs compete with nucleosomes for binding DNA. Our results reconcile previous seemingly conflicting results on the determinants of nucleosome positioning and provide a quantitative explanation for the difference between in vivo and in vitro positioning. On a genome-wide scale, nucleosome positioning is dominated by the phasing of nucleosome arrays over gene bodies, and their positioning is mainly determined by the intrinsic sequence preferences of nucleosomes. In contrast, larger nucleosome free regions in promoters, which likely have a much more significant impact on gene expression, are determined mainly by TF binding. Interestingly, of the 158 yeast TFs included in our modeling, we find that only 10-20 significantly contribute to inducing nucleosome-free regions, and these TFs are highly enriched for having direct interactions with chromatin remodelers. Together our results imply that nucleosome free regions in yeast promoters results from the binding of a specific class of TFs that recruit chromatin remodelers.

  17. Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers.

    Science.gov (United States)

    Ozonov, Evgeniy A; van Nimwegen, Erik

    2013-01-01

    Because DNA packaging in nucleosomes modulates its accessibility to transcription factors (TFs), unraveling the causal determinants of nucleosome positioning is of great importance to understanding gene regulation. Although there is evidence that intrinsic sequence specificity contributes to nucleosome positioning, the extent to which other factors contribute to nucleosome positioning is currently highly debated. Here we obtained both in vivo and in vitro reference maps of positions that are either consistently covered or free of nucleosomes across multiple experimental data-sets in Saccharomyces cerevisiae. We then systematically quantified the contribution of TF binding to nucleosome positioning using a rigorous statistical mechanics model in which TFs compete with nucleosomes for binding DNA. Our results reconcile previous seemingly conflicting results on the determinants of nucleosome positioning and provide a quantitative explanation for the difference between in vivo and in vitro positioning. On a genome-wide scale, nucleosome positioning is dominated by the phasing of nucleosome arrays over gene bodies, and their positioning is mainly determined by the intrinsic sequence preferences of nucleosomes. In contrast, larger nucleosome free regions in promoters, which likely have a much more significant impact on gene expression, are determined mainly by TF binding. Interestingly, of the 158 yeast TFs included in our modeling, we find that only 10-20 significantly contribute to inducing nucleosome-free regions, and these TFs are highly enriched for having direct interactions with chromatin remodelers. Together our results imply that nucleosome free regions in yeast promoters results from the binding of a specific class of TFs that recruit chromatin remodelers.

  18. Genetic basis for developmental homeostasis of germline stem cell niche number: a network of Tramtrack-Group nuclear BTB factors.

    Directory of Open Access Journals (Sweden)

    Mathieu Bartoletti

    Full Text Available The potential to produce new cells during adult life depends on the number of stem cell niches and the capacity of stem cells to divide, and is therefore under the control of programs ensuring developmental homeostasis. However, it remains generally unknown how the number of stem cell niches is controlled. In the insect ovary, each germline stem cell (GSC niche is embedded in a functional unit called an ovariole. The number of ovarioles, and thus the number of GSC niches, varies widely among species. In Drosophila, morphogenesis of ovarioles starts in larvae with the formation of terminal filaments (TFs, each made of 8-10 cells that pile up and sort in stacks. TFs constitute organizers of individual germline stem cell niches during larval and early pupal development. In the Drosophila melanogaster subgroup, the number of ovarioles varies interspecifically from 8 to 20. Here we show that pipsqueak, Trithorax-like, batman and the bric-à-brac (bab locus, all encoding nuclear BTB/POZ factors of the Tramtrack Group, are involved in limiting the number of ovarioles in D. melanogaster. At least two different processes are differentially perturbed by reducing the function of these genes. We found that when the bab dose is reduced, sorting of TF cells into TFs was affected such that each TF contains fewer cells and more TFs are formed. In contrast, psq mutants exhibited a greater number of TF cells per ovary, with a normal number of cells per TF, thereby leading to formation of more TFs per ovary than in the wild type. Our results indicate that two parallel genetic pathways under the control of a network of nuclear BTB factors are combined in order to negatively control the number of germline stem cell niches.

  19. Genetic basis for developmental homeostasis of germline stem cell niche number: a network of Tramtrack-Group nuclear BTB factors.

    Science.gov (United States)

    Bartoletti, Mathieu; Rubin, Thomas; Chalvet, Fabienne; Netter, Sophie; Dos Santos, Nicolas; Poisot, Emilie; Paces-Fessy, Mélanie; Cumenal, Delphine; Peronnet, Frédérique; Pret, Anne-Marie; Théodore, Laurent

    2012-01-01

    The potential to produce new cells during adult life depends on the number of stem cell niches and the capacity of stem cells to divide, and is therefore under the control of programs ensuring developmental homeostasis. However, it remains generally unknown how the number of stem cell niches is controlled. In the insect ovary, each germline stem cell (GSC) niche is embedded in a functional unit called an ovariole. The number of ovarioles, and thus the number of GSC niches, varies widely among species. In Drosophila, morphogenesis of ovarioles starts in larvae with the formation of terminal filaments (TFs), each made of 8-10 cells that pile up and sort in stacks. TFs constitute organizers of individual germline stem cell niches during larval and early pupal development. In the Drosophila melanogaster subgroup, the number of ovarioles varies interspecifically from 8 to 20. Here we show that pipsqueak, Trithorax-like, batman and the bric-à-brac (bab) locus, all encoding nuclear BTB/POZ factors of the Tramtrack Group, are involved in limiting the number of ovarioles in D. melanogaster. At least two different processes are differentially perturbed by reducing the function of these genes. We found that when the bab dose is reduced, sorting of TF cells into TFs was affected such that each TF contains fewer cells and more TFs are formed. In contrast, psq mutants exhibited a greater number of TF cells per ovary, with a normal number of cells per TF, thereby leading to formation of more TFs per ovary than in the wild type. Our results indicate that two parallel genetic pathways under the control of a network of nuclear BTB factors are combined in order to negatively control the number of germline stem cell niches.

  20. PERSONALITY AND CHARACTER PREFERENCE IN ROLE-PLAYING GAMES

    Directory of Open Access Journals (Sweden)

    Pedro José Ramos-Villagrasa

    2010-11-01

    Full Text Available In role-playing games players perform participative and episodic stories. Personality is a psychological construct associated with decision processes in many aspects of life. In this study, we analyzed if Big Five Personality Factors were related to game character preferences in the role-playing game “Dungeons & Dragons”. Results show that Personality is related only in the decision of character’s class. We also study the relationship between Personality and plots in role-playing games (action, intrigue, mystery, and personal relationships. Finally, recommendations to further investigation were given.

  1. MAJOR OIL PLAYS IN UTAH AND VICINITY

    Energy Technology Data Exchange (ETDEWEB)

    Thomas C. Chidsey; Craig D. Morgan; Kevin McClure; Grant C. Willis

    2003-09-01

    Utah oil fields have produced over 1.2 billion barrels (191 million m{sup 3}). However, the 13.7 million barrels (2.2 million m{sup 3}) of production in 2002 was the lowest level in over 40 years and continued the steady decline that began in the mid-1980s. The Utah Geological Survey believes this trend can be reversed by providing play portfolios for the major oil-producing provinces (Paradox Basin, Uinta Basin, and thrust belt) in Utah and adjacent areas in Colorado and Wyoming. Oil plays are geographic areas with petroleum potential caused by favorable combinations of source rock, migration paths, reservoir rock characteristics, and other factors. The play portfolios will include: descriptions and maps of the major oil plays by reservoir; production and reservoir data; case-study field evaluations; summaries of the state-of-the-art drilling, completion, and secondary/tertiary techniques for each play; locations of major oil pipelines; descriptions of reservoir outcrop analogs; and identification and discussion of land use constraints. All play maps, reports, databases, and so forth, produced for the project will be published in interactive, menu-driven digital (web-based and compact disc) and hard-copy formats. This report covers research activities for the fourth quarter of the first project year (April 1 through June 30, 2003). This work included describing outcrop analogs to the Jurassic Nugget Sandstone and Pennsylvanian Paradox Formation, the major oil producers in the thrust belt and Paradox Basin, respectively. Production-scale outcrop analogs provide an excellent view, often in three dimensions, of reservoir-facies characteristics and boundaries contributing to the overall heterogeneity of reservoir rocks. They can be used as a ''template'' for evaluation of data from conventional core, geophysical and petrophysical logs, and seismic surveys. The Nugget Sandstone was deposited in an extensive dune field that extended from Wyoming to

  2. RNA Sequencing Analysis Reveals Transcriptomic Variations in Tobacco (Nicotiana tabacum Leaves Affected by Climate, Soil, and Tillage Factors

    Directory of Open Access Journals (Sweden)

    Bo Lei

    2014-04-01

    Full Text Available The growth and development of plants are sensitive to their surroundings. Although numerous studies have analyzed plant transcriptomic variation, few have quantified the effect of combinations of factors or identified factor-specific effects. In this study, we performed RNA sequencing (RNA-seq analysis on tobacco leaves derived from 10 treatment combinations of three groups of ecological factors, i.e., climate factors (CFs, soil factors (SFs, and tillage factors (TFs. We detected 4980, 2916, and 1605 differentially expressed genes (DEGs that were affected by CFs, SFs, and TFs, which included 2703, 768, and 507 specific and 703 common DEGs (simultaneously regulated by CFs, SFs, and TFs, respectively. GO and KEGG enrichment analyses showed that genes involved in abiotic stress responses and secondary metabolic pathways were overrepresented in the common and CF-specific DEGs. In addition, we noted enrichment in CF-specific DEGs related to the circadian rhythm, SF-specific DEGs involved in mineral nutrient absorption and transport, and SF- and TF-specific DEGs associated with photosynthesis. Based on these results, we propose a model that explains how plants adapt to various ecological factors at the transcriptomic level. Additionally, the identified DEGs lay the foundation for future investigations of stress resistance, circadian rhythm and photosynthesis in tobacco.

  3. Gender differences in preschool children's play

    OpenAIRE

    Tarman Starc, Ana

    2015-01-01

    The goal of the final thesis is to shed some light on gender-based differences which can be observed in the way preschool children (aged 3 to 6) play, focusing on differences in the type of play, the size of play groups of boys and girls as well as differences in their playing behaviour with special focus on prosocial and aggressive behaviour. Moreover, the educators' attitude towards play is examined, i.e. how they intervene in the play of boy and girls. In the theoretical part the key c...

  4. Play as production – production as game?

    DEFF Research Database (Denmark)

    Eichberg, Henning

    2015-01-01

    “play” and “game” are, and of their social as well as political significance. At the municipal level, the city of Odense – “city of Hans Christian Andersen” – is branding itself as “city of play”. On the international level, Danish play-related products have expanded on the world market. In the field....... In contrast to the established understanding of play as per definition being “unproductive”, play also shows a productive power. Modernity has dissociated play and production, defining play as unproductive, and work as not-playful, and giving competitive sport priority as the ritual of industrial modernity...

  5. Major Oil Plays In Utah And Vicinity

    Energy Technology Data Exchange (ETDEWEB)

    Thomas Chidsey

    2007-12-31

    Utah oil fields have produced over 1.33 billion barrels (211 million m{sup 3}) of oil and hold 256 million barrels (40.7 million m{sup 3}) of proved reserves. The 13.7 million barrels (2.2 million m3) of production in 2002 was the lowest level in over 40 years and continued the steady decline that began in the mid-1980s. However, in late 2005 oil production increased, due, in part, to the discovery of Covenant field in the central Utah Navajo Sandstone thrust belt ('Hingeline') play, and to increased development drilling in the central Uinta Basin, reversing the decline that began in the mid-1980s. The Utah Geological Survey believes providing play portfolios for the major oil-producing provinces (Paradox Basin, Uinta Basin, and thrust belt) in Utah and adjacent areas in Colorado and Wyoming can continue this new upward production trend. Oil plays are geographic areas with petroleum potential caused by favorable combinations of source rock, migration paths, reservoir rock characteristics, and other factors. The play portfolios include descriptions and maps of the major oil plays by reservoir; production and reservoir data; case-study field evaluations; locations of major oil pipelines; identification and discussion of land-use constraints; descriptions of reservoir outcrop analogs; and summaries of the state-of-the-art drilling, completion, and secondary/tertiary recovery techniques for each play. The most prolific oil reservoir in the Utah/Wyoming thrust belt province is the eolian, Jurassic Nugget Sandstone, having produced over 288 million barrels (46 million m{sup 3}) of oil and 5.1 trillion cubic feet (145 billion m{sup 3}) of gas. Traps form on discrete subsidiary closures along major ramp anticlines where the depositionally heterogeneous Nugget is also extensively fractured. Hydrocarbons in Nugget reservoirs were generated from subthrust Cretaceous source rocks. The seals for the producing horizons are overlying argillaceous and gypsiferous beds in

  6. Major Oil Plays In Utah And Vicinity

    Energy Technology Data Exchange (ETDEWEB)

    Thomas Chidsey

    2007-12-31

    Utah oil fields have produced over 1.33 billion barrels (211 million m{sup 3}) of oil and hold 256 million barrels (40.7 million m{sup 3}) of proved reserves. The 13.7 million barrels (2.2 million m3) of production in 2002 was the lowest level in over 40 years and continued the steady decline that began in the mid-1980s. However, in late 2005 oil production increased, due, in part, to the discovery of Covenant field in the central Utah Navajo Sandstone thrust belt ('Hingeline') play, and to increased development drilling in the central Uinta Basin, reversing the decline that began in the mid-1980s. The Utah Geological Survey believes providing play portfolios for the major oil-producing provinces (Paradox Basin, Uinta Basin, and thrust belt) in Utah and adjacent areas in Colorado and Wyoming can continue this new upward production trend. Oil plays are geographic areas with petroleum potential caused by favorable combinations of source rock, migration paths, reservoir rock characteristics, and other factors. The play portfolios include descriptions and maps of the major oil plays by reservoir; production and reservoir data; case-study field evaluations; locations of major oil pipelines; identification and discussion of land-use constraints; descriptions of reservoir outcrop analogs; and summaries of the state-of-the-art drilling, completion, and secondary/tertiary recovery techniques for each play. The most prolific oil reservoir in the Utah/Wyoming thrust belt province is the eolian, Jurassic Nugget Sandstone, having produced over 288 million barrels (46 million m{sup 3}) of oil and 5.1 trillion cubic feet (145 billion m{sup 3}) of gas. Traps form on discrete subsidiary closures along major ramp anticlines where the depositionally heterogeneous Nugget is also extensively fractured. Hydrocarbons in Nugget reservoirs were generated from subthrust Cretaceous source rocks. The seals for the producing horizons are overlying argillaceous and gypsiferous beds in

  7. Forms of vitality play in infancy.

    Science.gov (United States)

    Español, Silvia; Martínez, Mauricio; Bordoni, Mariana; Camarasa, Rosario; Carretero, Soledad

    2014-12-01

    In this paper we report a qualitative study based on the constant comparative method to initiate the systematic study of forms of vitality play. This is an unnoticed non-figurative play frame linked to early social play and temporal arts in which child and adult elaborate the dynamics of their own movements and sounds in a repetition-variation form. In the introduction we present the theoretical underpinnings and the sporadic observations we have done in previous studies. Then, by the iterative observations of the recorded material of a longitudinal case study on play during the third year of life, we generated the general category of forms of vitality play and four subcategories of display modes of forms of vitality play (improvised forms of vitality play, ritualized forms of vitality play, forms of vitality play combined with pretend play, and forms of vitality play combined with role playing) which are illustrated with descriptive narratives. We discuss the properties of the developed categories, the limits of the present study, and the need to continue systematizing the research on this playful activity.

  8. Is Heading in Youth Soccer Dangerous Play?

    Science.gov (United States)

    O'Kane, John W

    2016-01-01

    Soccer is among the most popular youth sports with over 3 million youth players registered in the U.S. Soccer is unique in that players intentionally use their head to strike the ball, leading to concerns that heading could cause acute or chronic brain injury, especially in the immature brains of children. Pub Med search without date restriction was conducted in November 2014 and August 2015 using the terms soccer and concussion, heading and concussion, and youth soccer and concussion. 310 articles were identified and reviewed for applicable content specifically relating to youth athletes, heading, and/or acute or chronic brain injury from soccer. Soccer is a low-risk sport for catastrophic head injury, but concussions are relatively common and heading often plays a role. At all levels of play, concussions are more likely to occur in the act of heading than with other facets of the game. While concussion from heading the ball without other contact to the head appears rare in adult players, some data suggests children are more susceptible to concussion from heading primarily in game situations. Contributing factors include biomechanical forces, less developed technique, and the immature brain's susceptibility to injury. There is no evidence that heading in youth soccer causes any permanent brain injury and there is limited evidence that heading in youth soccer can cause concussion. A reasonable approach based on U.S. Youth Soccer recommendations is to teach heading after age 10 in controlled settings, and heading in games should be delayed until skill acquisition and physical maturity allow the youth player to head correctly with confidence.

  9. Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals

    OpenAIRE

    Stefflova, Klara,; Thybert, David; Wilson, Michael D.; Streeter, Ian; Aleksic, Jelena; Karagianni, Panagiota; Brazma, Alvis; Adams, David J.; Talianidis, Iannis; Marioni, John C.; Flicek, Paul; Odom, Duncan T.

    2013-01-01

    Summary To mechanistically characterize the microevolutionary processes active in altering transcription factor (TF) binding among closely related mammals, we compared the genome-wide binding of three tissue-specific TFs that control liver gene expression in six rodents. Despite an overall fast turnover of TF binding locations between species, we identified thousands of TF regions of highly constrained TF binding intensity. Although individual mutations in bound sequence motifs can influence ...

  10. Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

    Science.gov (United States)

    Jolma, Arttu; Kivioja, Teemu; Toivonen, Jarkko; Cheng, Lu; Wei, Gonghong; Enge, Martin; Taipale, Mikko; Vaquerizas, Juan M.; Yan, Jian; Sillanpää, Mikko J.; Bonke, Martin; Palin, Kimmo; Talukder, Shaheynoor; Hughes, Timothy R.; Luscombe, Nicholas M.; Ukkonen, Esko; Taipale, Jussi

    2010-01-01

    The genetic code—the binding specificity of all transfer-RNAs—defines how protein primary structure is determined by DNA sequence. DNA also dictates when and where proteins are expressed, and this information is encoded in a pattern of specific sequence motifs that are recognized by transcription factors. However, the DNA-binding specificity is only known for a small fraction of the ∼1400 human transcription factors (TFs). We describe here a high-throughput method for analyzing transcription factor binding specificity that is based on systematic evolution of ligands by exponential enrichment (SELEX) and massively parallel sequencing. The method is optimized for analysis of large numbers of TFs in parallel through the use of affinity-tagged proteins, barcoded selection oligonucleotides, and multiplexed sequencing. Data are analyzed by a new bioinformatic platform that uses the hundreds of thousands of sequencing reads obtained to control the quality of the experiments and to generate binding motifs for the TFs. The described technology allows higher throughput and identification of much longer binding profiles than current microarray-based methods. In addition, as our method is based on proteins expressed in mammalian cells, it can also be used to characterize DNA-binding preferences of full-length proteins or proteins requiring post-translational modifications. We validate the method by determining binding specificities of 14 different classes of TFs and by confirming the specificities for NFATC1 and RFX3 using ChIP-seq. Our results reveal unexpected dimeric modes of binding for several factors that were thought to preferentially bind DNA as monomers. PMID:20378718

  11. Happy Festivus! Parody as playful consumer resistance

    DEFF Research Database (Denmark)

    Mikkonen, Ilona; Bajde, Domen

    2013-01-01

    Drawing upon literary theory, play and consumer resistance literature, we conceptualize consumer parodic resistance – a resistant form of play that critically refunctions dominant consumption discourses and marketplace ideologies. We explore parodic resistance empirically by analyzing Festivus...

  12. Sports Fair Play and Critical Perspective

    Institute of Scientific and Technical Information of China (English)

    许晓峰

    2014-01-01

    Here, this paper suggests that CIFP tamp the ideal of fair play, re-establish the fair play value system, and conduct effective reform of organization and cause correspondingly instead of becoming agent of European centralism and American hegemonism.

  13. Play the Immune System Defender Game

    Science.gov (United States)

    ... Questionnaire The Immune System Play the Immune System Game About the game Granulocytes, macrophages and dendritic cells are immune cells ... last will in Paris. Play the Blood Typing Game Try to save some patients and learn about ...

  14. DigiFys : The interactive play landscape

    OpenAIRE

    Waern, Annika; Back, Jon; Sallnäs Pysander, Eva-Lotta; Heefer, Jasper; Rau, Andreas; Paget, Susan; Petterson, Linda

    2015-01-01

    The DigiFys project explores the design of interactive landscapes for children's outdoor play. The project combines landscape architecture with design of interactive technology, working towards designs that support children in their everyday play activity, close to home. In the creative lab session, we want to co-design the play landscape together with local children. The focus is on acquiring a perspective on similarities and differences between the children’s play culture in Sweden where th...

  15. Creative interactive play for disabled children

    DEFF Research Database (Denmark)

    Marti, Patrizia; Pollini, Alessandro; Rullo, Alessia

    2009-01-01

    The workshop addresses the emerging field of research on robotics, assistive technologies and interaction design promoting play for physically, visually, and hearing impaired children and for emotionally and mentally handicapped children. Interactive devices including toys, pets and educational...... tools as well as interactive collaborative environments may represent a unique opportunity for disable children to full engage in play and have fun. The Creative Interactive Play workshop presents a collection of innovative interactive technologies and case studies for inclusive play and discusses...

  16. Large Acrobatic Play Pilgrimage to the West

    Institute of Scientific and Technical Information of China (English)

    马洁

    2006-01-01

    Hosted by Ministry of Culture and Guangzhou Municipal People's Government,Guangzhou Bureau of Culture organized a list of first-class singing and dancing and acrobatic plays in Guangzhou in September 2006. Among these plays, large original acrobatic play Pilgrimage to the West of Guangzhou Acrobatic Troupe went on the stage during October 12th and November 5th.

  17. Pretend Play of Children with Cerebral Palsy

    Science.gov (United States)

    Pfeifer, Luzia Iara; Pacciulio, Amanda Mota; dos Santos, Camila Abrao; dos Santos, Jair Licio; Stagnitti, Karen Ellen

    2011-01-01

    Background and Purpose: Evaluate self-initiated pretend play of children with cerebral palsy. Method: Twenty preschool children participated in the study. Pretend play ability was measured by using the child-initiated pretend play assessment culturally adapted to Brazil. Results: There were significant negative correlations between the children's…

  18. Game Playing: Negotiating Rules and Identities

    Science.gov (United States)

    Winther-Lindqvist, Ditte

    2009-01-01

    Beginning with Lev Vygotsky's long-established assertion that the play of children always involves both imaginary play and rules of behavior, this article argues for a theoretical framework that connects such play with the construction of social identities in kindergarten peer groups. It begins with a discussion of Ivy Schousboe's model of the…

  19. Content Analysis of Block Play Literature.

    Science.gov (United States)

    Conrad, Annabel

    This study examined research on children's block play, using content analysis to review 75 documents that focused on such play. Each document was coded by type (empirical study or nonempirical article) and by 15 topics and 76 subtopics grouped into 4 broad categories: (1) environment/ecology; (2) block play and the school curriculum; (3) block…

  20. Curious Play: Children's Exploration of Nature

    Science.gov (United States)

    Gurholt, Kirsti Pedersen; Sanderud, Jostein Rønning

    2016-01-01

    This article explores the concept of "curious play" as a theoretical framework to understand and communicate children's experiences of free play in nature. The concept emerged interactively from three sources of inspiration: an ethnographically inspired study of children playing in nature; as a critique of the concept of "risky…