Dynamic facial expressions of emotion transmit an evolving hierarchy of signals over time.

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Jack, Rachael E; Garrod, Oliver G B; Schyns, Philippe G

2014-01-20

Designed by biological and social evolutionary pressures, facial expressions of emotion comprise specific facial movements to support a near-optimal system of signaling and decoding. Although highly dynamical, little is known about the form and function of facial expression temporal dynamics. Do facial expressions transmit diagnostic signals simultaneously to optimize categorization of the six classic emotions, or sequentially to support a more complex communication system of successive categorizations over time? Our data support the latter. Using a combination of perceptual expectation modeling, information theory, and Bayesian classifiers, we show that dynamic facial expressions of emotion transmit an evolving hierarchy of "biologically basic to socially specific" information over time. Early in the signaling dynamics, facial expressions systematically transmit few, biologically rooted face signals supporting the categorization of fewer elementary categories (e.g., approach/avoidance). Later transmissions comprise more complex signals that support categorization of a larger number of socially specific categories (i.e., the six classic emotions). Here, we show that dynamic facial expressions of emotion provide a sophisticated signaling system, questioning the widely accepted notion that emotion communication is comprised of six basic (i.e., psychologically irreducible) categories, and instead suggesting four. Copyright © 2014 Elsevier Ltd. All rights reserved.

Reconstructing dynamic mental models of facial expressions in prosopagnosia reveals distinct representations for identity and expression.

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Richoz, Anne-Raphaëlle; Jack, Rachael E; Garrod, Oliver G B; Schyns, Philippe G; Caldara, Roberto

2015-04-01

The human face transmits a wealth of signals that readily provide crucial information for social interactions, such as facial identity and emotional expression. Yet, a fundamental question remains unresolved: does the face information for identity and emotional expression categorization tap into common or distinct representational systems? To address this question we tested PS, a pure case of acquired prosopagnosia with bilateral occipitotemporal lesions anatomically sparing the regions that are assumed to contribute to facial expression (de)coding (i.e., the amygdala, the insula and the posterior superior temporal sulcus--pSTS). We previously demonstrated that PS does not use information from the eye region to identify faces, but relies on the suboptimal mouth region. PS's abnormal information use for identity, coupled with her neural dissociation, provides a unique opportunity to probe the existence of a dichotomy in the face representational system. To reconstruct the mental models of the six basic facial expressions of emotion in PS and age-matched healthy observers, we used a novel reverse correlation technique tracking information use on dynamic faces. PS was comparable to controls, using all facial features to (de)code facial expressions with the exception of fear. PS's normal (de)coding of dynamic facial expressions suggests that the face system relies either on distinct representational systems for identity and expression, or dissociable cortical pathways to access them. Interestingly, PS showed a selective impairment for categorizing many static facial expressions, which could be accounted for by her lesion in the right inferior occipital gyrus. PS's advantage for dynamic facial expressions might instead relate to a functionally distinct and sufficient cortical pathway directly connecting the early visual cortex to the spared pSTS. Altogether, our data provide critical insights on the healthy and impaired face systems, question evidence of deficits

Representational momentum in dynamic facial expressions is modulated by the level of expressed pain: Amplitude and direction effects.

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Prigent, Elise; Amorim, Michel-Ange; de Oliveira, Armando Mónica

2018-01-01

Humans have developed a specific capacity to rapidly perceive and anticipate other people's facial expressions so as to get an immediate impression of their emotional state of mind. We carried out two experiments to examine the perceptual and memory dynamics of facial expressions of pain. In the first experiment, we investigated how people estimate other people's levels of pain based on the perception of various dynamic facial expressions; these differ both in terms of the amount and intensity of activated action units. A second experiment used a representational momentum (RM) paradigm to study the emotional anticipation (memory bias) elicited by the same facial expressions of pain studied in Experiment 1. Our results highlighted the relationship between the level of perceived pain (in Experiment 1) and the direction and magnitude of memory bias (in Experiment 2): When perceived pain increases, the memory bias tends to be reduced (if positive) and ultimately becomes negative. Dynamic facial expressions of pain may reenact an "immediate perceptual history" in the perceiver before leading to an emotional anticipation of the agent's upcoming state. Thus, a subtle facial expression of pain (i.e., a low contraction around the eyes) that leads to a significant positive anticipation can be considered an adaptive process-one through which we can swiftly and involuntarily detect other people's pain.

Direction of Amygdala-Neocortex Interaction During Dynamic Facial Expression Processing.

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Sato, Wataru; Kochiyama, Takanori; Uono, Shota; Yoshikawa, Sakiko; Toichi, Motomi

2017-03-01

Dynamic facial expressions of emotion strongly elicit multifaceted emotional, perceptual, cognitive, and motor responses. Neuroimaging studies revealed that some subcortical (e.g., amygdala) and neocortical (e.g., superior temporal sulcus and inferior frontal gyrus) brain regions and their functional interaction were involved in processing dynamic facial expressions. However, the direction of the functional interaction between the amygdala and the neocortex remains unknown. To investigate this issue, we re-analyzed functional magnetic resonance imaging (fMRI) data from 2 studies and magnetoencephalography (MEG) data from 1 study. First, a psychophysiological interaction analysis of the fMRI data confirmed the functional interaction between the amygdala and neocortical regions. Then, dynamic causal modeling analysis was used to compare models with forward, backward, or bidirectional effective connectivity between the amygdala and neocortical networks in the fMRI and MEG data. The results consistently supported the model of effective connectivity from the amygdala to the neocortex. Further increasing time-window analysis of the MEG demonstrated that this model was valid after 200 ms from the stimulus onset. These data suggest that emotional processing in the amygdala rapidly modulates some neocortical processing, such as perception, recognition, and motor mimicry, when observing dynamic facial expressions of emotion. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Do Dynamic Facial Expressions Convey Emotions to Children Better than Do Static Ones?

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Widen, Sherri C.; Russell, James A.

2015-01-01

Past research has shown that children recognize emotions from facial expressions poorly and improve only gradually with age, but the stimuli in such studies have been static faces. Because dynamic faces include more information, it may well be that children more readily recognize emotions from dynamic facial expressions. The current study of…

Thiol-linked alkylation of RNA to assess expression dynamics.

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Herzog, Veronika A; Reichholf, Brian; Neumann, Tobias; Rescheneder, Philipp; Bhat, Pooja; Burkard, Thomas R; Wlotzka, Wiebke; von Haeseler, Arndt; Zuber, Johannes; Ameres, Stefan L

2017-12-01

Gene expression profiling by high-throughput sequencing reveals qualitative and quantitative changes in RNA species at steady state but obscures the intracellular dynamics of RNA transcription, processing and decay. We developed thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM seq), an orthogonal-chemistry-based RNA sequencing technology that detects 4-thiouridine (s 4 U) incorporation in RNA species at single-nucleotide resolution. In combination with well-established metabolic RNA labeling protocols and coupled to standard, low-input, high-throughput RNA sequencing methods, SLAM seq enabled rapid access to RNA-polymerase-II-dependent gene expression dynamics in the context of total RNA. We validated the method in mouse embryonic stem cells by showing that the RNA-polymerase-II-dependent transcriptional output scaled with Oct4/Sox2/Nanog-defined enhancer activity, and we provide quantitative and mechanistic evidence for transcript-specific RNA turnover mediated by post-transcriptional gene regulatory pathways initiated by microRNAs and N 6 -methyladenosine. SLAM seq facilitates the dissection of fundamental mechanisms that control gene expression in an accessible, cost-effective and scalable manner.

Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy

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Oyang Yen-Jen

2010-10-01

Full Text Available Abstract Background Molecular networks represent the backbone of molecular activity within cells and provide opportunities for understanding the mechanism of diseases. While protein-protein interaction data constitute static network maps, integration of condition-specific co-expression information provides clues to the dynamic features of these networks. Dilated cardiomyopathy is a leading cause of heart failure. Although previous studies have identified putative biomarkers or therapeutic targets for heart failure, the underlying molecular mechanism of dilated cardiomyopathy remains unclear. Results We developed a network-based comparative analysis approach that integrates protein-protein interactions with gene expression profiles and biological function annotations to reveal dynamic functional modules under different biological states. We found that hub proteins in condition-specific co-expressed protein interaction networks tended to be differentially expressed between biological states. Applying this method to a cohort of heart failure patients, we identified two functional modules that significantly emerged from the interaction networks. The dynamics of these modules between normal and disease states further suggest a potential molecular model of dilated cardiomyopathy. Conclusions We propose a novel framework to analyze the interaction networks in different biological states. It successfully reveals network modules closely related to heart failure; more importantly, these network dynamics provide new insights into the cause of dilated cardiomyopathy. The revealed molecular modules might be used as potential drug targets and provide new directions for heart failure therapy.

Do Dynamic Compared to Static Facial Expressions of Happiness and Anger Reveal Enhanced Facial Mimicry?

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Krystyna Rymarczyk

Full Text Available Facial mimicry is the spontaneous response to others' facial expressions by mirroring or matching the interaction partner. Recent evidence suggested that mimicry may not be only an automatic reaction but could be dependent on many factors, including social context, type of task in which the participant is engaged, or stimulus properties (dynamic vs static presentation. In the present study, we investigated the impact of dynamic facial expression and sex differences on facial mimicry and judgment of emotional intensity. Electromyography recordings were recorded from the corrugator supercilii, zygomaticus major, and orbicularis oculi muscles during passive observation of static and dynamic images of happiness and anger. The ratings of the emotional intensity of facial expressions were also analysed. As predicted, dynamic expressions were rated as more intense than static ones. Compared to static images, dynamic displays of happiness also evoked stronger activity in the zygomaticus major and orbicularis oculi, suggesting that subjects experienced positive emotion. No muscles showed mimicry activity in response to angry faces. Moreover, we found that women exhibited greater zygomaticus major muscle activity in response to dynamic happiness stimuli than static stimuli. Our data support the hypothesis that people mimic positive emotions and confirm the importance of dynamic stimuli in some emotional processing.

Brief Report: Representational Momentum for Dynamic Facial Expressions in Pervasive Developmental Disorder

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Uono, Shota; Sato, Wataru; Toichi, Motomi

2010-01-01

Individuals with pervasive developmental disorder (PDD) have difficulty with social communication via emotional facial expressions, but behavioral studies involving static images have reported inconsistent findings about emotion recognition. We investigated whether dynamic presentation of facial expression would enhance subjective perception of…

Aging and emotional expressions: is there a positivity bias during dynamic emotion recognition?

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Alberto eDi Domenico

2015-08-01

Full Text Available In this study, we investigated whether age-related differences in emotion regulation priorities influence online dynamic emotional facial discrimination. A group of 40 younger and a group of 40 older adults were invited to recognize a positive or negative expression as soon as the expression slowly emerged and subsequently rate it in terms of intensity. Our findings show that older adults recognized happy expressions faster than angry ones, while the direction of emotional expression does not seem to affect younger adults’ performance. Furthermore, older adults rated both negative and positive emotional faces as more intense compared to younger controls. This study detects age-related differences with a dynamic online paradigm and suggests that different regulation strategies may shape emotional face recognition.

Expression dynamics of self-renewal factors for spermatogonial stem cells in the mouse testis.

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Sakai, Mizuki; Masaki, Kaito; Aiba, Shota; Tone, Masaaki; Takashima, Seiji

2018-04-16

Glial cell line-derived neurotrophic factor (GDNF) and fibroblast growth factor 2 (FGF2) are bona fide self-renewal factors for spermatogonial stem cells (SSCs). Although GDNF is indispensable for the maintenance of SSCs, the role of FGF2 in the testis remains to be elucidated. To clarify this, the expression dynamics and regulatory mechanisms of Fgf2 and Gdnf in the mouse testes were analyzed. It is well known that Sertoli cells express Gdnf, and its receptor is expressed in a subset of undifferentiated spermatogonia, including SSCs. However, we found that Fgf2 was mainly expressed in the germ cells and its receptors were expressed not only in the cultured spermatogonial cell line, but also in testicular somatic cells. Aging, hypophysectomy, retinoic acid treatment, and testicular injury induced distinct Fgf2 and Gdnf expression dynamics, suggesting a difference in the expression mechanism of Fgf2 and Gdnf in the testis. Such differences might cause a dynamic fluctuation of Gdnf/Fgf2 ratio depending on the intrinsic/extrinsic cues. Considering that FGF2-cultured spermatogonia exhibit more differentiated phenotype than those cultured with GDNF, FGF2 might play a role distinct from that of GDNF in the testis, despite the fact that both factors are self-renewal factor for SSC in vitro.

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

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

2013-01-01

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

The derivation of the analytic expressions of the dynamical ...

African Journals Online (AJOL)

... expressions of the dynamical susceptibility of the spin system, by setting up the equation of motion and solving it in a generalized HFA of the susceptibility tensor, Χ-+, and quoting the result for the first derivative of the Green's function. Journal of the Nigerian Association of Mathematical Physics Vol. 10 2006: pp. 579-582 ...

Early signatures of regime shifts in gene expression dynamics

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Pal, Mainak; Pal, Amit Kumar; Ghosh, Sayantari; Bose, Indrani

2013-06-01

Recently, a large number of studies have been carried out on the early signatures of sudden regime shifts in systems as diverse as ecosystems, financial markets, population biology and complex diseases. The signatures of regime shifts in gene expression dynamics are less systematically investigated. In this paper, we consider sudden regime shifts in the gene expression dynamics described by a fold-bifurcation model involving bistability and hysteresis. We consider two alternative models, models 1 and 2, of competence development in the bacterial population B. subtilis and determine some early signatures of the regime shifts between competence and noncompetence. We use both deterministic and stochastic formalisms for the purpose of our study. The early signatures studied include the critical slowing down as a transition point is approached, rising variance and the lag-1 autocorrelation function, skewness and a ratio of two mean first passage times. Some of the signatures could provide the experimental basis for distinguishing between bistability and excitability as the correct mechanism for the development of competence.

Early signatures of regime shifts in gene expression dynamics

International Nuclear Information System (INIS)

Pal, Mainak; Pal, Amit Kumar; Ghosh, Sayantari; Bose, Indrani

2013-01-01

Recently, a large number of studies have been carried out on the early signatures of sudden regime shifts in systems as diverse as ecosystems, financial markets, population biology and complex diseases. The signatures of regime shifts in gene expression dynamics are less systematically investigated. In this paper, we consider sudden regime shifts in the gene expression dynamics described by a fold-bifurcation model involving bistability and hysteresis. We consider two alternative models, models 1 and 2, of competence development in the bacterial population B. subtilis and determine some early signatures of the regime shifts between competence and noncompetence. We use both deterministic and stochastic formalisms for the purpose of our study. The early signatures studied include the critical slowing down as a transition point is approached, rising variance and the lag-1 autocorrelation function, skewness and a ratio of two mean first passage times. Some of the signatures could provide the experimental basis for distinguishing between bistability and excitability as the correct mechanism for the development of competence. (paper)

Dynamic modulation of thymidylate synthase gene expression and fluorouracil sensitivity in human colorectal cancer cells.

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Kentaro Wakasa

Full Text Available Biomarkers have revolutionized cancer chemotherapy. However, many biomarker candidates are still in debate. In addition to clinical studies, a priori experimental approaches are needed. Thymidylate synthase (TS expression is a long-standing candidate as a biomarker for 5-fluorouracil (5-FU treatment of cancer patients. Using the Tet-OFF system and a human colorectal cancer cell line, DLD-1, we first constructed an in vitro system in which TS expression is dynamically controllable. Quantitative assays have elucidated that TS expression in the transformant was widely modulated, and that the dynamic range covered 15-fold of the basal level. 5-FU sensitivity of the transformant cells significantly increased in response to downregulated TS expression, although being not examined in the full dynamic range because of the doxycycline toxicity. Intriguingly, our in vitro data suggest that there is a linear relationship between TS expression and the 5-FU sensitivity in cells. Data obtained in a mouse model using transformant xenografts were highly parallel to those obtained in vitro. Thus, our in vitro and in vivo observations suggest that TS expression is a determinant of 5-FU sensitivity in cells, at least in this specific genetic background, and, therefore, support the possibility of TS expression as a biomarker for 5-FU-based cancer chemotherapy.

When dynamic, the head and face alone can express pride.

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Nelson, Nicole L; Russell, James A

2011-08-01

Prior research suggested that pride is recognized only when a head and facial expression (e.g., tilted head with a slight smile) is combined with a postural expression (e.g., expanded body and arm gestures). However, these studies used static photographs. In the present research, participants labeled the emotion conveyed by four dynamic cues to pride, presented as video clips: head and face alone, body posture alone, voice alone, and an expression in which head and face, body posture, and voice were presented simultaneously. Participants attributed pride to the head and face alone, even when postural or vocal information was absent. Pride can be conveyed without body posture or voice. 2011 APA, all rights reserved

Automatic Emotional State Detection using Facial Expression Dynamic in Videos

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Hongying Meng

2014-11-01

Full Text Available In this paper, an automatic emotion detection system is built for a computer or machine to detect the emotional state from facial expressions in human computer communication. Firstly, dynamic motion features are extracted from facial expression videos and then advanced machine learning methods for classification and regression are used to predict the emotional states. The system is evaluated on two publicly available datasets, i.e. GEMEP_FERA and AVEC2013, and satisfied performances are achieved in comparison with the baseline results provided. With this emotional state detection capability, a machine can read the facial expression of its user automatically. This technique can be integrated into applications such as smart robots, interactive games and smart surveillance systems.

Influences of sex, type and intensity of emotion in the ecognition of static and dynamic facial expressions*

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Nelson Torro-Alves

2013-01-01

Full Text Available Ecological validity of static and intense facial expressions in emotional recognition has been questioned. Recent studies have recommended the use of facial stimuli more compatible to the natural conditions of social interaction, which involves motion and variations in emotional intensity. In this study, we compared the recognition of static and dynamic facial expressions of happiness, fear, anger and sadness, presented in four emotional intensities (25 %, 50 %, 75 % and 100 %. Twenty volunteers (9 women and 11 men, aged between 19 and 31 years, took part in the study. The experiment consisted of two sessions in which participants had to identify the emotion of static (photographs and dynamic (videos displays of facial expressions on the computer screen. The mean accuracy was submitted to an Anova for repeated measures of model: 2 sexes x [2 conditions x 4 expressions x 4 intensities]. We observed an advantage for the recognition of dynamic expressions of happiness and fear compared to the static stimuli (p < .05. Analysis of interactions showed that expressions with intensity of 25 % were better recognized in the dynamic condition (p < .05. The addition of motion contributes to improve recognition especially in male participants (p < .05. We concluded that the effect of the motion varies as a function of the type of emotion, intensity of the expression and sex of the participant. These results support the hypothesis that dynamic stimuli have more ecological validity and are more appropriate to the research with emotions.

Aging and emotional expressions: is there a positivity bias during dynamic emotion recognition?

OpenAIRE

Di Domenico, Alberto; Palumbo, Rocco; Mammarella, Nicola; Fairfield, Beth

2015-01-01

In this study, we investigated whether age-related differences in emotion regulation priorities influence online dynamic emotional facial discrimination. A group of 40 younger and a group of 40 older adults were invited to recognize a positive or negative expression as soon as the expression slowly emerged and subsequently rate it in terms of intensity. Our findings show that older adults recognized happy expressions faster than angry ones, while the direction of emotional expression does not...

Moving faces, looking places: validation of the Amsterdam Dynamic Facial Expression Set (ADFES)

NARCIS (Netherlands)

van der Schalk, J.; Hawk, S.T.; Fischer, A.H.; Doosje, B.

2011-01-01

We report two studies validating a new standardized set of filmed emotion expressions, the Amsterdam Dynamic Facial Expression Set (ADFES). The ADFES is distinct from existing datasets in that it includes a face-forward version and two different head-turning versions (faces turning toward and away

Understanding the Earth Systems: Expressions of Dynamic and Cyclic Thinking among University Students

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Batzri, Or; Ben Zvi Assaraf, Orit; Cohen, Carmit; Orion, Nir

2015-01-01

In this two-part study, we examine undergraduate university students' expression of two important system thinking characteristics--dynamic thinking and cyclic thinking--focusing particularly on students of geology. The study was conducted using an Earth systems questionnaire designed to elicit and reflect either dynamic or cyclic thinking. The…

Dynamic Displays Enhance the Ability to Discriminate Genuine and Posed Facial Expressions of Emotion

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Namba, Shushi; Kabir, Russell S.; Miyatani, Makoto; Nakao, Takashi

2018-01-01

Accurately gauging the emotional experience of another person is important for navigating interpersonal interactions. This study investigated whether perceivers are capable of distinguishing between unintentionally expressed (genuine) and intentionally manipulated (posed) facial expressions attributed to four major emotions: amusement, disgust, sadness, and surprise. Sensitivity to this discrimination was explored by comparing unstaged dynamic and static facial stimuli and analyzing the results with signal detection theory. Participants indicated whether facial stimuli presented on a screen depicted a person showing a given emotion and whether that person was feeling a given emotion. The results showed that genuine displays were evaluated more as felt expressions than posed displays for all target emotions presented. In addition, sensitivity to the perception of emotional experience, or discriminability, was enhanced in dynamic facial displays, but was less pronounced in the case of static displays. This finding indicates that dynamic information in facial displays contributes to the ability to accurately infer the emotional experiences of another person. PMID:29896135

Emotion unfolded by motion: a role for parietal lobe in decoding dynamic facial expressions.

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Sarkheil, Pegah; Goebel, Rainer; Schneider, Frank; Mathiak, Klaus

2013-12-01

Facial expressions convey important emotional and social information and are frequently applied in investigations of human affective processing. Dynamic faces may provide higher ecological validity to examine perceptual and cognitive processing of facial expressions. Higher order processing of emotional faces was addressed by varying the task and virtual face models systematically. Blood oxygenation level-dependent activation was assessed using functional magnetic resonance imaging in 20 healthy volunteers while viewing and evaluating either emotion or gender intensity of dynamic face stimuli. A general linear model analysis revealed that high valence activated a network of motion-responsive areas, indicating that visual motion areas support perceptual coding for the motion-based intensity of facial expressions. The comparison of emotion with gender discrimination task revealed increased activation of inferior parietal lobule, which highlights the involvement of parietal areas in processing of high level features of faces. Dynamic emotional stimuli may help to emphasize functions of the hypothesized 'extended' over the 'core' system for face processing.

Dynamic facial expressions evoke distinct activation in the face perception network: a connectivity analysis study.

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Foley, Elaine; Rippon, Gina; Thai, Ngoc Jade; Longe, Olivia; Senior, Carl

2012-02-01

Very little is known about the neural structures involved in the perception of realistic dynamic facial expressions. In the present study, a unique set of naturalistic dynamic facial emotional expressions was created. Through fMRI and connectivity analysis, a dynamic face perception network was identified, which is demonstrated to extend Haxby et al.'s [Haxby, J. V., Hoffman, E. A., & Gobbini, M. I. The distributed human neural system for face perception. Trends in Cognitive Science, 4, 223-233, 2000] distributed neural system for face perception. This network includes early visual regions, such as the inferior occipital gyrus, which is identified as insensitive to motion or affect but sensitive to the visual stimulus, the STS, identified as specifically sensitive to motion, and the amygdala, recruited to process affect. Measures of effective connectivity between these regions revealed that dynamic facial stimuli were associated with specific increases in connectivity between early visual regions, such as the inferior occipital gyrus and the STS, along with coupling between the STS and the amygdala, as well as the inferior frontal gyrus. These findings support the presence of a distributed network of cortical regions that mediate the perception of different dynamic facial expressions.

Dynamics of gene expression with positive feedback to histone modifications at bivalent domains

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Huang, Rongsheng; Lei, Jinzhi

2018-03-01

Experiments have shown that in embryonic stem cells, the promoters of many lineage-control genes contain “bivalent domains”, within which the nucleosomes possess both active (H3K4me3) and repressive (H3K27me3) marks. Such bivalent modifications play important roles in maintaining pluripotency in embryonic stem cells. Here, to investigate gene expression dynamics when there are regulations in bivalent histone modifications and random partition in cell divisions, we study how positive feedback to histone methylation/demethylation controls the transition dynamics of the histone modification patterns along with cell cycles. We constructed a computational model that includes dynamics of histone marks, three-stage chromatin state transitions, transcription and translation, feedbacks from protein product to enzymes to regulate the addition and removal of histone marks, and the inheritance of nucleosome state between cell cycles. The model reveals how dynamics of both nucleosome state transition and gene expression are dependent on the enzyme activities and feedback regulations. Results show that the combination of stochastic histone modification at each cell division and the deterministic feedback regulation work together to adjust the dynamics of chromatin state transition in stem cell regenerations.

A microcosm of musical expression: II. Quantitative analysis of pianists' dynamics in the initial measures of Chopin's Etude in E major.

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Repp, B H

1999-03-01

Patterns of expressive dynamics were measured in bars 1-5 of 115 commercially recorded performances of Chopin's Etude in E major, op. 10, No. 3. The grand average pattern (or dynamic profile) was representative of many performances and highly similar to the average dynamic profile of a group of advanced student performances, which suggests a widely shared central norm of expressive dynamics. The individual dynamic profiles were subjected to principal components analysis, which yielded Varimax-rotated components, each representing a different, nonstandard dynamic profile associated with a small subset of performances. Most performances had dynamic patterns resembling a mixture of several components, and no clustering of of performances into distinct groups was apparent. Some weak relationships of dynamic profiles with sociocultural variables were found, most notably a tendency of female pianists to exhibit a greater dynamic range in the melody. Within the melody, there were no significant relationships between expressive timing [Repp, J. Acoust. Soc. Am. 104, 1085-1100 (1998)] and expressive dynamics. These two important dimensions seemed to be controlled independently at this local level and thus offer the artist many degrees of freedom in giving a melody expressive shape.

Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression

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Verd, Berta; Crombach, Anton

2017-01-01

Pattern formation during development is a highly dynamic process. In spite of this, few experimental and modelling approaches take into account the explicit time-dependence of the rules governing regulatory systems. We address this problem by studying dynamic morphogen interpretation by the gap gene network in Drosophila melanogaster. Gap genes are involved in segment determination during early embryogenesis. They are activated by maternal morphogen gradients encoded by bicoid (bcd) and caudal (cad). These gradients decay at the same time-scale as the establishment of the antero-posterior gap gene pattern. We use a reverse-engineering approach, based on data-driven regulatory models called gene circuits, to isolate and characterise the explicitly time-dependent effects of changing morphogen concentrations on gap gene regulation. To achieve this, we simulate the system in the presence and absence of dynamic gradient decay. Comparison between these simulations reveals that maternal morphogen decay controls the timing and limits the rate of gap gene expression. In the anterior of the embyro, it affects peak expression and leads to the establishment of smooth spatial boundaries between gap domains. In the posterior of the embryo, it causes a progressive slow-down in the rate of gap domain shifts, which is necessary to correctly position domain boundaries and to stabilise the spatial gap gene expression pattern. We use a newly developed method for the analysis of transient dynamics in non-autonomous (time-variable) systems to understand the regulatory causes of these effects. By providing a rigorous mechanistic explanation for the role of maternal gradient decay in gap gene regulation, our study demonstrates that such analyses are feasible and reveal important aspects of dynamic gene regulation which would have been missed by a traditional steady-state approach. More generally, it highlights the importance of transient dynamics for understanding complex regulatory

Global Analysis of miRNA Gene Clusters and Gene Families Reveals Dynamic and Coordinated Expression

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Li Guo

2014-01-01

Full Text Available To further understand the potential expression relationships of miRNAs in miRNA gene clusters and gene families, a global analysis was performed in 4 paired tumor (breast cancer and adjacent normal tissue samples using deep sequencing datasets. The compositions of miRNA gene clusters and families are not random, and clustered and homologous miRNAs may have close relationships with overlapped miRNA species. Members in the miRNA group always had various expression levels, and even some showed larger expression divergence. Despite the dynamic expression as well as individual difference, these miRNAs always indicated consistent or similar deregulation patterns. The consistent deregulation expression may contribute to dynamic and coordinated interaction between different miRNAs in regulatory network. Further, we found that those clustered or homologous miRNAs that were also identified as sense and antisense miRNAs showed larger expression divergence. miRNA gene clusters and families indicated important biological roles, and the specific distribution and expression further enrich and ensure the flexible and robust regulatory network.

Community helping services: dynamic of formation and expressiveness of the cultural care.

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Landim, Fátima Luna Pinheiro

2006-01-01

Community helping services is an expression used by the social movements to designate families that live in shacks installed in a public area intended for building of own house at a community helping system. Studies in ethnonursing that aimed: in order to detail dynamic configuration in a community helping service. It took place in an community helping area located in the outskirts of Fortaleza, Ceará. The community members acting as general informants from the local culture, while eight (8) women heads-of-families, working as key informers. The data collect used the Observation-Participation-Reflection Model. The analyses were processing by the time that the dates were collected, considering the categories: inserting in the community helping culture to obtain their history; community helping is not a slum -describing the formation dynamic. Established that the formation dynamic of the community helping go on the own house representation as a symbol of " a better life". To assimilate such expression introducing in own cultural universe is a challenge for the nursing to assist a care culture congruent.

Nonlinear Dynamics in Gene Regulation Promote Robustness and Evolvability of Gene Expression Levels.

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Steinacher, Arno; Bates, Declan G; Akman, Ozgur E; Soyer, Orkun S

2016-01-01

Cellular phenotypes underpinned by regulatory networks need to respond to evolutionary pressures to allow adaptation, but at the same time be robust to perturbations. This creates a conflict in which mutations affecting regulatory networks must both generate variance but also be tolerated at the phenotype level. Here, we perform mathematical analyses and simulations of regulatory networks to better understand the potential trade-off between robustness and evolvability. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics, through the creation of regions presenting sudden changes in phenotype with small changes in genotype. For genotypes embedding low levels of nonlinearity, robustness and evolvability correlate negatively and almost perfectly. By contrast, genotypes embedding nonlinear dynamics allow expression levels to be robust to small perturbations, while generating high diversity (evolvability) under larger perturbations. Thus, nonlinearity breaks the robustness-evolvability trade-off in gene expression levels by allowing disparate responses to different mutations. Using analytical derivations of robustness and system sensitivity, we show that these findings extend to a large class of gene regulatory network architectures and also hold for experimentally observed parameter regimes. Further, the effect of nonlinearity on the robustness-evolvability trade-off is ensured as long as key parameters of the system display specific relations irrespective of their absolute values. We find that within this parameter regime genotypes display low and noisy expression levels. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics. Our results provide a possible solution to the robustness-evolvability trade-off, suggest an explanation for

Nonlinear Dynamics in Gene Regulation Promote Robustness and Evolvability of Gene Expression Levels.

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Arno Steinacher

Full Text Available Cellular phenotypes underpinned by regulatory networks need to respond to evolutionary pressures to allow adaptation, but at the same time be robust to perturbations. This creates a conflict in which mutations affecting regulatory networks must both generate variance but also be tolerated at the phenotype level. Here, we perform mathematical analyses and simulations of regulatory networks to better understand the potential trade-off between robustness and evolvability. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics, through the creation of regions presenting sudden changes in phenotype with small changes in genotype. For genotypes embedding low levels of nonlinearity, robustness and evolvability correlate negatively and almost perfectly. By contrast, genotypes embedding nonlinear dynamics allow expression levels to be robust to small perturbations, while generating high diversity (evolvability under larger perturbations. Thus, nonlinearity breaks the robustness-evolvability trade-off in gene expression levels by allowing disparate responses to different mutations. Using analytical derivations of robustness and system sensitivity, we show that these findings extend to a large class of gene regulatory network architectures and also hold for experimentally observed parameter regimes. Further, the effect of nonlinearity on the robustness-evolvability trade-off is ensured as long as key parameters of the system display specific relations irrespective of their absolute values. We find that within this parameter regime genotypes display low and noisy expression levels. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics. Our results provide a possible solution to the robustness-evolvability trade-off, suggest

Human amygdala response to dynamic facial expressions of positive and negative surprise.

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Vrticka, Pascal; Lordier, Lara; Bediou, Benoît; Sander, David

2014-02-01

Although brain imaging evidence accumulates to suggest that the amygdala plays a key role in the processing of novel stimuli, only little is known about its role in processing expressed novelty conveyed by surprised faces, and even less about possible interactive encoding of novelty and valence. Those investigations that have already probed human amygdala involvement in the processing of surprised facial expressions either used static pictures displaying negative surprise (as contained in fear) or "neutral" surprise, and manipulated valence by contextually priming or subjectively associating static surprise with either negative or positive information. Therefore, it still remains unresolved how the human amygdala differentially processes dynamic surprised facial expressions displaying either positive or negative surprise. Here, we created new artificial dynamic 3-dimensional facial expressions conveying surprise with an intrinsic positive (wonderment) or negative (fear) connotation, but also intrinsic positive (joy) or negative (anxiety) emotions not containing any surprise, in addition to neutral facial displays either containing ("typical surprise" expression) or not containing ("neutral") surprise. Results showed heightened amygdala activity to faces containing positive (vs. negative) surprise, which may either correspond to a specific wonderment effect as such, or to the computation of a negative expected value prediction error. Findings are discussed in the light of data obtained from a closely matched nonsocial lottery task, which revealed overlapping activity within the left amygdala to unexpected positive outcomes. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Dynamic association rules for gene expression data analysis.

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Chen, Shu-Chuan; Tsai, Tsung-Hsien; Chung, Cheng-Han; Li, Wen-Hsiung

2015-10-14

The purpose of gene expression analysis is to look for the association between regulation of gene expression levels and phenotypic variations. This association based on gene expression profile has been used to determine whether the induction/repression of genes correspond to phenotypic variations including cell regulations, clinical diagnoses and drug development. Statistical analyses on microarray data have been developed to resolve gene selection issue. However, these methods do not inform us of causality between genes and phenotypes. In this paper, we propose the dynamic association rule algorithm (DAR algorithm) which helps ones to efficiently select a subset of significant genes for subsequent analysis. The DAR algorithm is based on association rules from market basket analysis in marketing. We first propose a statistical way, based on constructing a one-sided confidence interval and hypothesis testing, to determine if an association rule is meaningful. Based on the proposed statistical method, we then developed the DAR algorithm for gene expression data analysis. The method was applied to analyze four microarray datasets and one Next Generation Sequencing (NGS) dataset: the Mice Apo A1 dataset, the whole genome expression dataset of mouse embryonic stem cells, expression profiling of the bone marrow of Leukemia patients, Microarray Quality Control (MAQC) data set and the RNA-seq dataset of a mouse genomic imprinting study. A comparison of the proposed method with the t-test on the expression profiling of the bone marrow of Leukemia patients was conducted. We developed a statistical way, based on the concept of confidence interval, to determine the minimum support and minimum confidence for mining association relationships among items. With the minimum support and minimum confidence, one can find significant rules in one single step. The DAR algorithm was then developed for gene expression data analysis. Four gene expression datasets showed that the proposed

Exposure to the self-face facilitates identification of dynamic facial expressions: influences on individual differences.

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Li, Yuan Hang; Tottenham, Nim

2013-04-01

A growing literature suggests that the self-face is involved in processing the facial expressions of others. The authors experimentally activated self-face representations to assess its effects on the recognition of dynamically emerging facial expressions of others. They exposed participants to videos of either their own faces (self-face prime) or faces of others (nonself-face prime) prior to a facial expression judgment task. Their results show that experimentally activating self-face representations results in earlier recognition of dynamically emerging facial expression. As a group, participants in the self-face prime condition recognized expressions earlier (when less affective perceptual information was available) compared to participants in the nonself-face prime condition. There were individual differences in performance, such that poorer expression identification was associated with higher autism traits (in this neurocognitively healthy sample). However, when randomized into the self-face prime condition, participants with high autism traits performed as well as those with low autism traits. Taken together, these data suggest that the ability to recognize facial expressions in others is linked with the internal representations of our own faces. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Mathematical model of flagella gene expression dynamics in Salmonella enterica serovar typhimurium

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Jain, Kirti; Pradhan, Amit; Mokashi, Chaitanya; Saini, Supreet

2015-01-01

Flagellar assembly in Salmonella is controlled by an intricate genetic and biochemical network. This network comprises of a number of inter-connected feedback loops, which control the assembly process dynamically. Critical among these are the FliA–FlgM feedback, FliZ-mediated positive feedback, and FliT-mediated negative feedback. In this work, we develop a mathematical model to track the dynamics of flagellar gene expression in Salmonella. Analysis of our model demonstrates that the network ...

The Development of Dynamic Facial Expression Recognition at Different Intensities in 4- to 18-Year-Olds

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Montirosso, Rosario; Peverelli, Milena; Frigerio, Elisa; Crespi, Monica; Borgatti, Renato

2010-01-01

The primary purpose of this study was to examine the effect of the intensity of emotion expression on children's developing ability to label emotion during a dynamic presentation of five facial expressions (anger, disgust, fear, happiness, and sadness). A computerized task (AFFECT--animated full facial expression comprehension test) was used to…

Visualization of the Dynamics of Gene Expression in the Living Mouse

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Amy Ryan

2004-01-01

Full Text Available Reporter genes can monitor the status and activity of recombinant genomes in a diverse array of organisms, from bacteria and yeast to plants and animals. We have combined luciferase reporter genes with a conditional gene expression system based on regulatory elements from the lac Operon of Escherichia coli to visualize the dynamics of gene expression in realtime in the living mouse. Using this technology, we have determined the rate of gene induction and repression, the level of target gene activity in response to different doses of inducer, and the schedule of induction during early embryogenesis of both the endogenous and the experimentally manipulated programs of mammalian gene expression associated with the HD/Hdh locus. The combination of in vivo imaging and lac regulation is a powerful tool for generating conditional transgenic mice that can be screened rapidly for optimal regulation and expression patterns, and for monitoring the induction and repression of regulated genes noninvasively in the living animal.

Emotional recognition from dynamic facial, vocal and musical expressions following traumatic brain injury.

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Drapeau, Joanie; Gosselin, Nathalie; Peretz, Isabelle; McKerral, Michelle

2017-01-01

To assess emotion recognition from dynamic facial, vocal and musical expressions in sub-groups of adults with traumatic brain injuries (TBI) of different severities and identify possible common underlying mechanisms across domains. Forty-one adults participated in this study: 10 with moderate-severe TBI, nine with complicated mild TBI, 11 with uncomplicated mild TBI and 11 healthy controls, who were administered experimental (emotional recognition, valence-arousal) and control tasks (emotional and structural discrimination) for each domain. Recognition of fearful faces was significantly impaired in moderate-severe and in complicated mild TBI sub-groups, as compared to those with uncomplicated mild TBI and controls. Effect sizes were medium-large. Participants with lower GCS scores performed more poorly when recognizing fearful dynamic facial expressions. Emotion recognition from auditory domains was preserved following TBI, irrespective of severity. All groups performed equally on control tasks, indicating no perceptual disorders. Although emotional recognition from vocal and musical expressions was preserved, no correlation was found across auditory domains. This preliminary study may contribute to improving comprehension of emotional recognition following TBI. Future studies of larger samples could usefully include measures of functional impacts of recognition deficits for fearful facial expressions. These could help refine interventions for emotional recognition following a brain injury.

Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts.

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Viñuelas, José; Kaneko, Gaël; Coulon, Antoine; Vallin, Elodie; Morin, Valérie; Mejia-Pous, Camila; Kupiec, Jean-Jacques; Beslon, Guillaume; Gandrillon, Olivier

2013-02-25

A number of studies have established that stochasticity in gene expression may play an important role in many biological phenomena. This therefore calls for further investigations to identify the molecular mechanisms at stake, in order to understand and manipulate cell-to-cell variability. In this work, we explored the role played by chromatin dynamics in the regulation of stochastic gene expression in higher eukaryotic cells. For this purpose, we generated isogenic chicken-cell populations expressing a fluorescent reporter integrated in one copy per clone. Although the clones differed only in the genetic locus at which the reporter was inserted, they showed markedly different fluorescence distributions, revealing different levels of stochastic gene expression. Use of chromatin-modifying agents showed that direct manipulation of chromatin dynamics had a marked effect on the extent of stochastic gene expression. To better understand the molecular mechanism involved in these phenomena, we fitted these data to a two-state model describing the opening/closing process of the chromatin. We found that the differences between clones seemed to be due mainly to the duration of the closed state, and that the agents we used mainly seem to act on the opening probability. In this study, we report biological experiments combined with computational modeling, highlighting the importance of chromatin dynamics in stochastic gene expression. This work sheds a new light on the mechanisms of gene expression in higher eukaryotic cells, and argues in favor of relatively slow dynamics with long (hours to days) periods of quiet state.

Dynamic Changes in Amygdala Psychophysiological Connectivity Reveal Distinct Neural Networks for Facial Expressions of Basic Emotions.

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Diano, Matteo; Tamietto, Marco; Celeghin, Alessia; Weiskrantz, Lawrence; Tatu, Mona-Karina; Bagnis, Arianna; Duca, Sergio; Geminiani, Giuliano; Cauda, Franco; Costa, Tommaso

2017-03-27

The quest to characterize the neural signature distinctive of different basic emotions has recently come under renewed scrutiny. Here we investigated whether facial expressions of different basic emotions modulate the functional connectivity of the amygdala with the rest of the brain. To this end, we presented seventeen healthy participants (8 females) with facial expressions of anger, disgust, fear, happiness, sadness and emotional neutrality and analyzed amygdala's psychophysiological interaction (PPI). In fact, PPI can reveal how inter-regional amygdala communications change dynamically depending on perception of various emotional expressions to recruit different brain networks, compared to the functional interactions it entertains during perception of neutral expressions. We found that for each emotion the amygdala recruited a distinctive and spatially distributed set of structures to interact with. These changes in amygdala connectional patters characterize the dynamic signature prototypical of individual emotion processing, and seemingly represent a neural mechanism that serves to implement the distinctive influence that each emotion exerts on perceptual, cognitive, and motor responses. Besides these differences, all emotions enhanced amygdala functional integration with premotor cortices compared to neutral faces. The present findings thus concur to reconceptualise the structure-function relation between brain-emotion from the traditional one-to-one mapping toward a network-based and dynamic perspective.

A novel method for prediction of dynamic smiling expressions after orthodontic treatment: a case report.

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Dai, Fanfan; Li, Yangjing; Chen, Gui; Chen, Si; Xu, Tianmin

2016-02-01

Smile esthetics has become increasingly important for orthodontic patients, thus prediction of post-treatment smile is necessary for a perfect treatment plan. In this study, with a combination of three-dimensional craniofacial data from the cone beam computed tomography and color-encoded structured light system, a novel method for smile prediction was proposed based on facial expression transfer, in which dynamic facial expression was interpreted as a matrix of facial depth changes. Data extracted from the pre-treatment smile expression record were applied to the post-treatment static model to realize expression transfer. Therefore smile esthetics of the patient after treatment could be evaluated in pre-treatment planning procedure. The positive and negative mean values of error for prediction accuracy were 0.9 and - 1.1 mm respectively, with the standard deviation of ± 1.5 mm, which is clinically acceptable. Further studies would be conducted to reduce the prediction error from both the static and dynamic sides as well as to explore automatically combined prediction from the two sides.

Reproducibility of the dynamics of facial expressions in unilateral facial palsy.

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Alagha, M A; Ju, X; Morley, S; Ayoub, A

2018-02-01

The aim of this study was to assess the reproducibility of non-verbal facial expressions in unilateral facial paralysis using dynamic four-dimensional (4D) imaging. The Di4D system was used to record five facial expressions of 20 adult patients. The system captured 60 three-dimensional (3D) images per second; each facial expression took 3-4seconds which was recorded in real time. Thus a set of 180 3D facial images was generated for each expression. The procedure was repeated after 30min to assess the reproducibility of the expressions. A mathematical facial mesh consisting of thousands of quasi-point 'vertices' was conformed to the face in order to determine the morphological characteristics in a comprehensive manner. The vertices were tracked throughout the sequence of the 180 images. Five key 3D facial frames from each sequence of images were analyzed. Comparisons were made between the first and second capture of each facial expression to assess the reproducibility of facial movements. Corresponding images were aligned using partial Procrustes analysis, and the root mean square distance between them was calculated and analyzed statistically (paired Student t-test, PFacial expressions of lip purse, cheek puff, and raising of eyebrows were reproducible. Facial expressions of maximum smile and forceful eye closure were not reproducible. The limited coordination of various groups of facial muscles contributed to the lack of reproducibility of these facial expressions. 4D imaging is a useful clinical tool for the assessment of facial expressions. Copyright © 2017 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Beyond face value: does involuntary emotional anticipation shape the perception of dynamic facial expressions?

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Letizia Palumbo

Full Text Available Emotional facial expressions are immediate indicators of the affective dispositions of others. Recently it has been shown that early stages of social perception can already be influenced by (implicit attributions made by the observer about the agent's mental state and intentions. In the current study possible mechanisms underpinning distortions in the perception of dynamic, ecologically-valid, facial expressions were explored. In four experiments we examined to what extent basic perceptual processes such as contrast/context effects, adaptation and representational momentum underpinned the perceptual distortions, and to what extent 'emotional anticipation', i.e. the involuntary anticipation of the other's emotional state of mind on the basis of the immediate perceptual history, might have played a role. Neutral facial expressions displayed at the end of short video-clips, in which an initial facial expression of joy or anger gradually morphed into a neutral expression, were misjudged as being slightly angry or slightly happy, respectively (Experiment 1. This response bias disappeared when the actor's identity changed in the final neutral expression (Experiment 2. Videos depicting neutral-to-joy-to-neutral and neutral-to-anger-to-neutral sequences again produced biases but in opposite direction (Experiment 3. The bias survived insertion of a 400 ms blank (Experiment 4. These results suggested that the perceptual distortions were not caused by any of the low-level perceptual mechanisms (adaptation, representational momentum and contrast effects. We speculate that especially when presented with dynamic, facial expressions, perceptual distortions occur that reflect 'emotional anticipation' (a low-level mindreading mechanism, which overrules low-level visual mechanisms. Underpinning neural mechanisms are discussed in relation to the current debate on action and emotion understanding.

Beyond face value: does involuntary emotional anticipation shape the perception of dynamic facial expressions?

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Palumbo, Letizia; Jellema, Tjeerd

2013-01-01

Emotional facial expressions are immediate indicators of the affective dispositions of others. Recently it has been shown that early stages of social perception can already be influenced by (implicit) attributions made by the observer about the agent's mental state and intentions. In the current study possible mechanisms underpinning distortions in the perception of dynamic, ecologically-valid, facial expressions were explored. In four experiments we examined to what extent basic perceptual processes such as contrast/context effects, adaptation and representational momentum underpinned the perceptual distortions, and to what extent 'emotional anticipation', i.e. the involuntary anticipation of the other's emotional state of mind on the basis of the immediate perceptual history, might have played a role. Neutral facial expressions displayed at the end of short video-clips, in which an initial facial expression of joy or anger gradually morphed into a neutral expression, were misjudged as being slightly angry or slightly happy, respectively (Experiment 1). This response bias disappeared when the actor's identity changed in the final neutral expression (Experiment 2). Videos depicting neutral-to-joy-to-neutral and neutral-to-anger-to-neutral sequences again produced biases but in opposite direction (Experiment 3). The bias survived insertion of a 400 ms blank (Experiment 4). These results suggested that the perceptual distortions were not caused by any of the low-level perceptual mechanisms (adaptation, representational momentum and contrast effects). We speculate that especially when presented with dynamic, facial expressions, perceptual distortions occur that reflect 'emotional anticipation' (a low-level mindreading mechanism), which overrules low-level visual mechanisms. Underpinning neural mechanisms are discussed in relation to the current debate on action and emotion understanding.

Dynamic iodide trapping by tumor cells expressing the thyroidal sodium iodide symporter

International Nuclear Information System (INIS)

Dingli, David; Bergert, Elizabeth R.; Bajzer, Zeljko; O'Connor, Michael K.; Russell, Stephen J.; Morris, John C.

2004-01-01

The thyroidal sodium iodide symporter (NIS) in combination with various radioactive isotopes has shown promise as a therapeutic gene in various tumor models. Therapy depends on adequate retention of the isotope in the tumor. We hypothesized that in the absence of iodide organification, isotope trapping is a dynamic process either due to slow efflux or re-uptake of the isotope by cells expressing NIS. Iodide efflux is slower in ARH-77 and K-562 cells expressing NIS compared to a thyroid cell line. Isotope retention half times varied linearly with the number of cells expressing NIS. With sufficient NIS expression, iodide efflux is a zero-order process. Efflux kinetics in the presence or absence of perchlorate also supports the hypothesis that iodide re-uptake occurs and contributes to the retention of the isotope in tumor cells. Iodide organification was insignificant. In vivo studies in tumors composed of mixed cell populations confirmed these observations

Amygdala and fusiform gyrus temporal dynamics: Responses to negative facial expressions

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Rauch Scott L

2008-05-01

Full Text Available Abstract Background The amygdala habituates in response to repeated human facial expressions; however, it is unclear whether this brain region habituates to schematic faces (i.e., simple line drawings or caricatures of faces. Using an fMRI block design, 16 healthy participants passively viewed repeated presentations of schematic and human neutral and negative facial expressions. Percent signal changes within anatomic regions-of-interest (amygdala and fusiform gyrus were calculated to examine the temporal dynamics of neural response and any response differences based on face type. Results The amygdala and fusiform gyrus had a within-run "U" response pattern of activity to facial expression blocks. The initial block within each run elicited the greatest activation (relative to baseline and the final block elicited greater activation than the preceding block. No significant differences between schematic and human faces were detected in the amygdala or fusiform gyrus. Conclusion The "U" pattern of response in the amygdala and fusiform gyrus to facial expressions suggests an initial orienting, habituation, and activation recovery in these regions. Furthermore, this study is the first to directly compare brain responses to schematic and human facial expressions, and the similarity in brain responses suggest that schematic faces may be useful in studying amygdala activation.

Dynamic changes in protein functional linkage networks revealed by integration with gene expression data.

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Shubhada R Hegde

2008-11-01

Full Text Available Response of cells to changing environmental conditions is governed by the dynamics of intricate biomolecular interactions. It may be reasonable to assume, proteins being the dominant macromolecules that carry out routine cellular functions, that understanding the dynamics of protein:protein interactions might yield useful insights into the cellular responses. The large-scale protein interaction data sets are, however, unable to capture the changes in the profile of protein:protein interactions. In order to understand how these interactions change dynamically, we have constructed conditional protein linkages for Escherichia coli by integrating functional linkages and gene expression information. As a case study, we have chosen to analyze UV exposure in wild-type and SOS deficient E. coli at 20 minutes post irradiation. The conditional networks exhibit similar topological properties. Although the global topological properties of the networks are similar, many subtle local changes are observed, which are suggestive of the cellular response to the perturbations. Some such changes correspond to differences in the path lengths among the nodes of carbohydrate metabolism correlating with its loss in efficiency in the UV treated cells. Similarly, expression of hubs under unique conditions reflects the importance of these genes. Various centrality measures applied to the networks indicate increased importance for replication, repair, and other stress proteins for the cells under UV treatment, as anticipated. We thus propose a novel approach for studying an organism at the systems level by integrating genome-wide functional linkages and the gene expression data.

Nogo-A expression dynamically varies after spinal cord injury

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Jian-wei Wang

2015-01-01

Full Text Available The mechanism involved in neural regeneration after spinal cord injury is unclear. The myelin-derived protein Nogo-A, which is specific to the central nervous system, has been identified to negatively affect the cytoskeleton and growth program of axotomized neurons. Studies have shown that Nogo-A exerts immediate and chronic inhibitory effects on neurite outgrowth. In vivo, inhibitors of Nogo-A have been shown to lead to a marked enhancement of regenerative axon extension. We established a spinal cord injury model in rats using a free-falling weight drop device to subsequently investigate Nogo-A expression. Nogo-A mRNA and protein expression and immunoreactivity were detected in spinal cord tissue using real-time quantitative PCR, immunohistochemistry and western blot analysis. At 24 hours after spinal cord injury, Nogo-A protein and mRNA expression was low in the injured group compared with control and sham-operated groups. The levels then continued to drop further and were at their lowest at 3 days, rapidly rose to a peak after 7 days, and then gradually declined again after 14 days. These changes were observed at both the mRNA and protein level. The transient decrease observed early after injury followed by high levels for a few days indicates Nogo-A expression is time dependent. This may contribute to the lack of regeneration in the central nervous system after spinal cord injury. The dynamic variation of Nogo-A should be taken into account in the treatment of spinal cord injury.

Self-expressive Dictionary Learning for Dynamic 3D Reconstruction.

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Zheng, Enliang; Ji, Dinghuang; Dunn, Enrique; Frahm, Jan-Michael

2017-08-22

We target the problem of sparse 3D reconstruction of dynamic objects observed by multiple unsynchronized video cameras with unknown temporal overlap. To this end, we develop a framework to recover the unknown structure without sequencing information across video sequences. Our proposed compressed sensing framework poses the estimation of 3D structure as the problem of dictionary learning, where the dictionary is defined as an aggregation of the temporally varying 3D structures. Given the smooth motion of dynamic objects, we observe any element in the dictionary can be well approximated by a sparse linear combination of other elements in the same dictionary (i.e. self-expression). Our formulation optimizes a biconvex cost function that leverages a compressed sensing formulation and enforces both structural dependency coherence across video streams, as well as motion smoothness across estimates from common video sources. We further analyze the reconstructability of our approach under different capture scenarios, and its comparison and relation to existing methods. Experimental results on large amounts of synthetic data as well as real imagery demonstrate the effectiveness of our approach.

The Temporal Dynamics of Arc Expression Regulate Cognitive Flexibility.

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

2018-05-24

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

Gene Expression Dynamics Accompanying the Sponge Thermal Stress Response.

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Guzman, Christine; Conaco, Cecilia

2016-01-01

Marine sponges are important members of coral reef ecosystems. Thus, their responses to changes in ocean chemistry and environmental conditions, particularly to higher seawater temperatures, will have potential impacts on the future of these reefs. To better understand the sponge thermal stress response, we investigated gene expression dynamics in the shallow water sponge, Haliclona tubifera (order Haplosclerida, class Demospongiae), subjected to elevated temperature. Using high-throughput transcriptome sequencing, we show that these conditions result in the activation of various processes that interact to maintain cellular homeostasis. Short-term thermal stress resulted in the induction of heat shock proteins, antioxidants, and genes involved in signal transduction and innate immunity pathways. Prolonged exposure to thermal stress affected the expression of genes involved in cellular damage repair, apoptosis, signaling and transcription. Interestingly, exposure to sublethal temperatures may improve the ability of the sponge to mitigate cellular damage under more extreme stress conditions. These insights into the potential mechanisms of adaptation and resilience of sponges contribute to a better understanding of sponge conservation status and the prediction of ecosystem trajectories under future climate conditions.

A multi-Poisson dynamic mixture model to cluster developmental patterns of gene expression by RNA-seq.

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Ye, Meixia; Wang, Zhong; Wang, Yaqun; Wu, Rongling

2015-03-01

Dynamic changes of gene expression reflect an intrinsic mechanism of how an organism responds to developmental and environmental signals. With the increasing availability of expression data across a time-space scale by RNA-seq, the classification of genes as per their biological function using RNA-seq data has become one of the most significant challenges in contemporary biology. Here we develop a clustering mixture model to discover distinct groups of genes expressed during a period of organ development. By integrating the density function of multivariate Poisson distribution, the model accommodates the discrete property of read counts characteristic of RNA-seq data. The temporal dependence of gene expression is modeled by the first-order autoregressive process. The model is implemented with the Expectation-Maximization algorithm and model selection to determine the optimal number of gene clusters and obtain the estimates of Poisson parameters that describe the pattern of time-dependent expression of genes from each cluster. The model has been demonstrated by analyzing a real data from an experiment aimed to link the pattern of gene expression to catkin development in white poplar. The usefulness of the model has been validated through computer simulation. The model provides a valuable tool for clustering RNA-seq data, facilitating our global view of expression dynamics and understanding of gene regulation mechanisms. © The Author 2014. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Dynamic changes in prefrontal cortex gene expression following lysergic acid diethylamide administration.

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Nichols, Charles D; Garcia, Efrain E; Sanders-Bush, Elaine

2003-03-17

Lysergic acid diethylamide (LSD) is a psychoactive drug that transiently alters human perception, behavior, and mood at extremely low doses. Certain aspects of the behavior elicited by acute doses of LSD closely resemble symptoms of mental disorders such as schizophrenia. Characterizing gene expression profiles after LSD will be important for understanding how it alters behavior, and will lead to novel insights into disorders, such as schizophrenia, whose behavioral symptoms resemble the temporary effects of hallucinogenic drugs. We previously identified a small collection of genes within the rat prefrontal cortex that respond to LSD. Many of the products of these genes are involved in the process of synaptic plasticity. In the current report, we present a detailed analysis of the expression of these genes within the brain using RNase protection analysis. We find that the gene response to LSD is quite dynamic. The expression of some genes increases rapidly and decreases rapidly, while other genes change more gradually. Dose-response studies show two classes of expression; gene expression maximally stimulated at lower doses, versus gene expression that continues to rise at the higher doses. The role of the 5-HT(1A) and 5-HT(2A) receptor in mediating the increases in gene expression was examined in a series of experiments using receptor specific antagonists. Most expression increases were due to activation of the 5-HT(2A) receptor, however expression of two genes had neither a 5-HT(1A) nor a 5-HT(2A) receptor component.

A big data pipeline: Identifying dynamic gene regulatory networks from time-course Gene Expression Omnibus data with applications to influenza infection.

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Carey, Michelle; Ramírez, Juan Camilo; Wu, Shuang; Wu, Hulin

2018-07-01

A biological host response to an external stimulus or intervention such as a disease or infection is a dynamic process, which is regulated by an intricate network of many genes and their products. Understanding the dynamics of this gene regulatory network allows us to infer the mechanisms involved in a host response to an external stimulus, and hence aids the discovery of biomarkers of phenotype and biological function. In this article, we propose a modeling/analysis pipeline for dynamic gene expression data, called Pipeline4DGEData, which consists of a series of statistical modeling techniques to construct dynamic gene regulatory networks from the large volumes of high-dimensional time-course gene expression data that are freely available in the Gene Expression Omnibus repository. This pipeline has a consistent and scalable structure that allows it to simultaneously analyze a large number of time-course gene expression data sets, and then integrate the results across different studies. We apply the proposed pipeline to influenza infection data from nine studies and demonstrate that interesting biological findings can be discovered with its implementation.

Gene expression dynamics in the oxidative stress response of fission yeast

DEFF Research Database (Denmark)

Papadakis, Emmanouil

Changes in the environment continuously challenge living organisms during their lifetime. A cell’s survival depends on its ability to coordinate a rapid and successful stress response when exposed to acute doses of damaging agents. Oxidative stress caused by an excess of reactive oxygen species......, especially using model organisms. The fission yeast Schizosaccharomyces pombe is a unicellular eukaryotic organism that possesses genome features and molecular pathways that are highly conserved in humans. Moreover, the limited redundancy of its genome make S. pombe well suited for phenotypic studies...... (HP, 0.5 mM). The applied experimental design allowed us to measure both the activation and recovery phases of the response at a sufficiently high time resolution to model transcription and translation dynamics. Absolute expression levels (copies per cell) and time-resolved expression profiles for 4...

Dynamic gene expression analysis in a H1N1 influenza virus mouse pneumonia model.

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Bao, Yanyan; Gao, Yingjie; Shi, Yujing; Cui, Xiaolan

2017-06-01

H1N1, a major pathogenic subtype of influenza A virus, causes a respiratory infection in humans and livestock that can range from a mild infection to more severe pneumonia associated with acute respiratory distress syndrome. Understanding the dynamic changes in the genome and the related functional changes induced by H1N1 influenza virus infection is essential to elucidating the pathogenesis of this virus and thereby determining strategies to prevent future outbreaks. In this study, we filtered the significantly expressed genes in mouse pneumonia using mRNA microarray analysis. Using STC analysis, seven significant gene clusters were revealed, and using STC-GO analysis, we explored the significant functions of these seven gene clusters. The results revealed GOs related to H1N1 virus-induced inflammatory and immune functions, including innate immune response, inflammatory response, specific immune response, and cellular response to interferon-beta. Furthermore, the dynamic regulation relationships of the key genes in mouse pneumonia were revealed by dynamic gene network analysis, and the most important genes were filtered, including Dhx58, Cxcl10, Cxcl11, Zbp1, Ifit1, Ifih1, Trim25, Mx2, Oas2, Cd274, Irgm1, and Irf7. These results suggested that during mouse pneumonia, changes in the expression of gene clusters and the complex interactions among genes lead to significant changes in function. Dynamic gene expression analysis revealed key genes that performed important functions. These results are a prelude to advancements in mouse H1N1 influenza virus infection biology, as well as the use of mice as a model organism for human H1N1 influenza virus infection studies.

Dynamic expression of the translational machinery during Bacillus subtilis life cycle at a single cell level.

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Alex Rosenberg

Full Text Available The ability of bacteria to responsively regulate the expression of translation components is crucial for rapid adaptation to fluctuating environments. Utilizing Bacillus subtilis (B. subtilis as a model organism, we followed the dynamics of the translational machinery at a single cell resolution during growth and differentiation. By comprehensive monitoring the activity of the major rrn promoters and ribosomal protein production, we revealed diverse dynamics between cells grown in rich and poor medium, with the most prominent dissimilarities exhibited during deep stationary phase. Further, the variability pattern of translational activity varied among the cells, being affected by nutrient availability. We have monitored for the first time translational dynamics during the developmental process of sporulation within the two distinct cellular compartments of forespore and mother-cell. Our study uncovers a transient forespore specific increase in expression of translational components. Finally, the contribution of each rrn promoter throughout the bacterium life cycle was found to be relatively constant, implying that differential expression is not the main purpose for the existence of multiple rrn genes. Instead, we propose that coordination of the rrn operons serves as a strategy to rapidly fine tune translational activities in a synchronized fashion to achieve an optimal translation level for a given condition.

Dynamic expression of leukocyte innate immune genes in whole blood from horses with lipopolysaccharide-induced acute systemic inflammation

DEFF Research Database (Denmark)

Vinther, Anne Mette L.; Skovgaard, Kerstin; Heegaard, Peter M. H.

2015-01-01

Background: In horses, insights into the innate immune processes in acute systemic inflammation are limited even though these processes may be highly important for future diagnostic and therapeutic advances in high-mortality disease conditions as the systemic inflammatory response syndrome (SIRS......) and sepsis. Therefore, the aim of this study was to investigate the expression of 31 selected blood leukocyte immune genes in an equine model of acute systemic inflammation to identify significantly regulated genes and to describe their expression dynamics during a 24-h experimental period. Systemic...... expressions in blood leukocytes during equine acute LPS-induced systemic inflammation thoroughly characterized a highly regulated and dynamic innate immune response. These results provide new insights into the molecular mechanisms of equine systemic inflammation....

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

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Sofia Fertuzinhos

2014-03-01

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

Dynamic gene expression response to altered gravity in human T cells.

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Thiel, Cora S; Hauschild, Swantje; Huge, Andreas; Tauber, Svantje; Lauber, Beatrice A; Polzer, Jennifer; Paulsen, Katrin; Lier, Hartwin; Engelmann, Frank; Schmitz, Burkhard; Schütte, Andreas; Layer, Liliana E; Ullrich, Oliver

2017-07-12

We investigated the dynamics of immediate and initial gene expression response to different gravitational environments in human Jurkat T lymphocytic cells and compared expression profiles to identify potential gravity-regulated genes and adaptation processes. We used the Affymetrix GeneChip® Human Transcriptome Array 2.0 containing 44,699 protein coding genes and 22,829 non-protein coding genes and performed the experiments during a parabolic flight and a suborbital ballistic rocket mission to cross-validate gravity-regulated gene expression through independent research platforms and different sets of control experiments to exclude other factors than alteration of gravity. We found that gene expression in human T cells rapidly responded to altered gravity in the time frame of 20 s and 5 min. The initial response to microgravity involved mostly regulatory RNAs. We identified three gravity-regulated genes which could be cross-validated in both completely independent experiment missions: ATP6V1A/D, a vacuolar H + -ATPase (V-ATPase) responsible for acidification during bone resorption, IGHD3-3/IGHD3-10, diversity genes of the immunoglobulin heavy-chain locus participating in V(D)J recombination, and LINC00837, a long intergenic non-protein coding RNA. Due to the extensive and rapid alteration of gene expression associated with regulatory RNAs, we conclude that human cells are equipped with a robust and efficient adaptation potential when challenged with altered gravitational environments.

Quantitative tissue-specific dynamics of in vivo GILZ mRNA expression and regulation by endogenous and exogenous glucocorticoids.

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Ayyar, Vivaswath S; Almon, Richard R; Jusko, William J; DuBois, Debra C

2015-06-01

Glucocorticoids (GC) are steroid hormones, which regulate metabolism and immune function. Synthetic GCs, or corticosteroids (CS), have appreciable clinical utility via their ability to suppress inflammation in immune-mediated diseases like asthma and rheumatoid arthritis. Recent work has provided insight to novel GC-induced genes that mediate their anti-inflammatory effects, including glucocorticoid-induced leucine zipper (GILZ). Since GILZ comprises an important part of GC action, its regulation by both drug and hormone will influence CS therapy. In addition, GILZ expression is often employed as a biomarker of GC action, which requires judicious selection of sampling time. Understanding the in vivo regulation of GILZ mRNA expression over time will provide insight into both the physiological regulation of GILZ by endogenous GC and the dynamics of its enhancement by CS. A highly quantitative qRT-PCR assay was developed for measuring GILZ mRNA expression in tissues obtained from normal and CS-treated rats. This assay was applied to measure GILZ mRNA expression in eight tissues; to determine its endogenous regulation over time; and to characterize its dynamics in adipose tissue, muscle, and liver following treatment with CS. We demonstrate that GILZ mRNA is expressed in several tissues. GILZ mRNA expression in adipose tissue displayed a robust circadian rhythm that was entrained with the circadian oscillation of endogenous corticosterone; and is strongly enhanced by acute and chronic dosing. Single dosing also enhanced GILZ mRNA in muscle and liver, but the dynamics varied. In conclusion, GILZ is widely expressed in the rat and highly regulated by endogenous and exogenous GCs. © 2015 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of the American Physiological Society and The Physiological Society.

Correlation between hedonic liking and facial expression measurement using dynamic affective response representation.

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Zhi, Ruicong; Wan, Jingwei; Zhang, Dezheng; Li, Weiping

2018-06-01

Emotional reactions towards products play an essential role in consumers' decision making, and are more important than rational evaluation of sensory attributes. It is crucial to understand consumers' emotion, and the relationship between sensory properties, human liking and choice. There are many inconsistencies between Asian and Western consumers in the usage of hedonic scale, as well as the intensity of facial reactions, due to different culture and consuming habits. However, very few studies discussed the facial responses characteristics of Asian consumers during food consumption. In this paper, explicit liking measurement (hedonic scale) and implicit emotional measurement (facial expressions) were evaluated to judge the consumers' emotions elicited by five types of juices. The contributions of this study included: (1) Constructed the relationship model between hedonic liking and facial expressions analyzed by face reading technology. Negative emotions "sadness", "anger", and "disgust" showed noticeable high negative correlation tendency to hedonic scores. The "liking" hedonic scores could be characterized by positive emotion "happiness". (2) Several emotional intensity based parameters, especially dynamic parameter, were extracted to describe the facial characteristic in sensory evaluation procedure. Both amplitude information and frequency information were involved in the dynamic parameters to remain more information of the emotional responses signals. From the comparison of four types of emotional descriptive parameters, the maximum parameter and dynamic parameter were suggested to be utilized for representing emotional state and intensities. Copyright © 2018 Elsevier Ltd. All rights reserved.

Precise regulation of gene expression dynamics favors complex promoter architectures.

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Dirk Müller

2009-01-01

Full Text Available Promoters process signals through recruitment of transcription factors and RNA polymerase, and dynamic changes in promoter activity constitute a major noise source in gene expression. However, it is barely understood how complex promoter architectures determine key features of promoter dynamics. Here, we employ prototypical promoters of yeast ribosomal protein genes as well as simplified versions thereof to analyze the relations among promoter design, complexity, and function. These promoters combine the action of a general regulatory factor with that of specific transcription factors, a common motif of many eukaryotic promoters. By comprehensively analyzing stationary and dynamic promoter properties, this model-based approach enables us to pinpoint the structural characteristics underlying the observed behavior. Functional tradeoffs impose constraints on the promoter architecture of ribosomal protein genes. We find that a stable scaffold in the natural design results in low transcriptional noise and strong co-regulation of target genes in the presence of gene silencing. This configuration also exhibits superior shut-off properties, and it can serve as a tunable switch in living cells. Model validation with independent experimental data suggests that the models are sufficiently realistic. When combined, our results offer a mechanistic explanation for why specific factors are associated with low protein noise in vivo. Many of these findings hold for a broad range of model parameters and likely apply to other eukaryotic promoters of similar structure.

Evolution-development congruence in pattern formation dynamics: Bifurcations in gene expression and regulation of networks structures.

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Kohsokabe, Takahiro; Kaneko, Kunihiko

2016-01-01

Search for possible relationships between phylogeny and ontogeny is important in evolutionary-developmental biology. Here we uncover such relationships by numerical evolution and unveil their origin in terms of dynamical systems theory. By representing developmental dynamics of spatially located cells with gene expression dynamics with cell-to-cell interaction under external morphogen gradient, gene regulation networks are evolved under mutation and selection with the fitness to approach a prescribed spatial pattern of expressed genes. For most numerical evolution experiments, evolution of pattern over generations and development of pattern by an evolved network exhibit remarkable congruence. Both in the evolution and development pattern changes consist of several epochs where stripes are formed in a short time, while for other temporal regimes, pattern hardly changes. In evolution, these quasi-stationary regimes are generations needed to hit relevant mutations, while in development, they are due to some gene expression that varies slowly and controls the pattern change. The morphogenesis is regulated by combinations of feedback or feedforward regulations, where the upstream feedforward network reads the external morphogen gradient, and generates a pattern used as a boundary condition for the later patterns. The ordering from up to downstream is common in evolution and development, while the successive epochal changes in development and evolution are represented as common bifurcations in dynamical-systems theory, which lead to the evolution-development congruence. Mechanism of exceptional violation of the congruence is also unveiled. Our results provide a new look on developmental stages, punctuated equilibrium, developmental bottlenecks, and evolutionary acquisition of novelty in morphogenesis. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution Published by Wiley Periodicals, Inc.

The dynamics of long-term transgene expression in engrafted neural stem cells.

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Lee, Jean-Pyo; Tsai, David J; In Park, Kook; Harvey, Alan R; Snyder, Evan Y

2009-07-01

To assess the dynamics and confounding variables that influence transgene expression in neural stem cells (NSCs), we generated distinct NSC clones from the same pool of cells, carrying the same reporter gene transcribed from the same promoter, transduced by the same retroviral vector, and transplanted similarly at the same differentiation state, at the same time and location, into the brains of newborn mouse littermates, and monitored in parallel for over a year in vivo (without immunosuppression). Therefore, the sole variables were transgene chromosomal insertion site and copy number. We then adapted and optimized a technique that tests, at the single cell level, persistence of stem cell-mediated transgene expression in vivo based on correlating the presence of the transgene in a given NSC's nucleus (by fluorescence in situ hybridization [FISH]) with the frequency of that transgene's product within the same cell (by combined immunohistochemistry [IHC]). Under the above-stated conditions, insertion site is likely the most contributory variable dictating transgene downregulation in an NSC after 3 months in vivo. We also observed that this obstacle could be effectively and safely counteracted by simple serial infections (as few as three) inserting redundant copies of the transgene into the prospective donor NSC. (The preservation of normal growth control mechanisms and an absence of tumorigenic potential can be readily screened and ensured ex vivo prior to transplantation.) The combined FISH/IHC strategy employed here for monitoring the dynamics of transgene expression at the single cell level in vivo may be used for other types of therapeutic and housekeeping genes in endogenous and exogenous stem cells of many organs and lineages. Copyright 2009 Wiley-Liss, Inc.

Chemical memory reactions induced bursting dynamics in gene expression.

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Tian, Tianhai

2013-01-01

Memory is a ubiquitous phenomenon in biological systems in which the present system state is not entirely determined by the current conditions but also depends on the time evolutionary path of the system. Specifically, many memorial phenomena are characterized by chemical memory reactions that may fire under particular system conditions. These conditional chemical reactions contradict to the extant stochastic approaches for modeling chemical kinetics and have increasingly posed significant challenges to mathematical modeling and computer simulation. To tackle the challenge, I proposed a novel theory consisting of the memory chemical master equations and memory stochastic simulation algorithm. A stochastic model for single-gene expression was proposed to illustrate the key function of memory reactions in inducing bursting dynamics of gene expression that has been observed in experiments recently. The importance of memory reactions has been further validated by the stochastic model of the p53-MDM2 core module. Simulations showed that memory reactions is a major mechanism for realizing both sustained oscillations of p53 protein numbers in single cells and damped oscillations over a population of cells. These successful applications of the memory modeling framework suggested that this innovative theory is an effective and powerful tool to study memory process and conditional chemical reactions in a wide range of complex biological systems.

Dynamic Web Expression for Near-real-time Sensor Networks

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Lindquist, K. G.; Newman, R. L.; Nayak, A.; Vernon, F. L.; Nelson, C.; Hansen, T. S.; Yuen-Wong, R.

2003-12-01

As near-real-time sensor grids become more widespread, and processing systems based on them become more powerful, summarizing the raw and derived information products and delivering them to the end user become increasingly important both for ongoing monitoring and as a platform for cross-disciplinary research. We have re-engineered the dbrecenteqs program, which was designed to express real-time earthquake databases into dynamic web pages, with several powerful new technologies. While the application is still most fully developed for seismic data, the infrastructure is extensible (and being extended) to create a real-time information architecture for numerous signal domains. This work provides a practical, lightweight approach suitable for individual seismic and sensor networks, which does not require a full 'web-services' implementation. Nevertheless, the technologies here are extensible to larger applications such as the Storage-Resource-Broker based VORB project. The technologies included in the new system blend real-time relational databases as a focus for processing and data handling; an XML->XSLT architecture as the core of the web mirroring; PHP extensions to Antelope (the environmental monitoring-system context adopted for RoadNET) in order to support complex, user-driven interactivity; and VRML output for expression of information as web-browsable three-dimensional worlds.

Dynamics of immune system gene expression upon bacterial challenge and wounding in a social insect (Bombus terrestris.

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Silvio Erler

2011-03-01

Full Text Available The innate immune system which helps individuals to combat pathogens comprises a set of genes representing four immune system pathways (Toll, Imd, JNK and JAK/STAT. There is a lack of immune genes in social insects (e.g. honeybees when compared to Diptera. Potentially, this might be compensated by an advanced system of social immunity (synergistic action of several individuals. The bumble bee, Bombus terrestris, is a primitively eusocial species with an annual life cycle and colonies headed by a single queen. We used this key pollinator to study the temporal dynamics of immune system gene expression in response to wounding and bacterial challenge.Antimicrobial peptides (AMP (abaecin, defensin 1, hymenoptaecin were strongly up-regulated by wounding and bacterial challenge, the latter showing a higher impact on the gene expression level. Sterile wounding down-regulated TEP A, an effector gene of the JAK/STAT pathway, and bacterial infection influenced genes of the Imd (relish and JNK pathway (basket. Relish was up-regulated within the first hour after bacterial challenge, but decreased strongly afterwards. AMP expression following wounding and bacterial challenge correlates with the expression pattern of relish whereas correlated expression with dorsal was absent. Although expression of AMPs was high, continuous bacterial growth was observed throughout the experiment.Here we demonstrate for the first time the temporal dynamics of immune system gene expression in a social insect. Wounding and bacterial challenge affected the innate immune system significantly. Induction of AMP expression due to wounding might comprise a pre-adaptation to accompanying bacterial infections. Compared with solitary species this social insect exhibits reduced immune system efficiency, as bacterial growth could not be inhibited. A negative feedback loop regulating the Imd-pathway is suggested. AMPs, the end product of the Imd-pathway, inhibited the up-regulation of the

Dynamic Compression Promotes the Matrix Synthesis of Nucleus Pulposus Cells Through Up-Regulating N-CDH Expression in a Perfusion Bioreactor Culture.

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Xu, Yichun; Yao, Hui; Li, Pei; Xu, Wenbin; Zhang, Junbin; Lv, Lulu; Teng, Haijun; Guo, Zhiliang; Zhao, Huiqing; Hou, Gang

2018-01-01

An adequate matrix production of nucleus pulposus (NP) cells is an important tissue engineering-based strategy to regenerate degenerative discs. Here, we mainly aimed to investigate the effects and mechanism of mechanical compression (i.e., static compression vs. dynamic compression) on the matrix synthesis of three-dimensional (3D) cultured NP cells in vitro. Rat NP cells seeded on small intestinal submucosa (SIS) cryogel scaffolds were cultured in the chambers of a self-developed, mechanically active bioreactor for 10 days. Meanwhile, the NP cells were subjected to compression (static compression or dynamic compression at a 10% scaffold deformation) for 6 hours once per day. Unloaded NP cells were used as controls. The cellular phenotype and matrix biosynthesis of NP cells were investigated by real-time PCR and Western blotting assays. Lentivirus-mediated N-cadherin (N-CDH) knockdown and an inhibitor, LY294002, were used to further investigate the role of N-CDH and the PI3K/Akt pathway in this process. Dynamic compression better maintained the expression of cell-specific markers (keratin-19, FOXF1 and PAX1) and matrix macromolecules (aggrecan and collagen II), as well as N-CDH expression and the activity of the PI3K/Akt pathway, in the 3D-cultured NP cells compared with those expression levels and activity in the cells grown under static compression. Further analysis showed that the N-CDH knockdown significantly down-regulated the expression of NP cell-specific markers and matrix macromolecules and inhibited the activation of the PI3K/Akt pathway under dynamic compression. However, inhibition of the PI3K/Akt pathway had no effects on N-CDH expression but down-regulated the expression of NP cell-specific markers and matrix macromolecules under dynamic compression. Dynamic compression increases the matrix synthesis of 3D-cultured NP cells compared with that of the cells under static compression, and the N-CDH-PI3K/Akt pathway is involved in this regulatory process

Emotion expression of an affective state space; a humanoid robot displaying a dynamic emotional state during a soccer game

NARCIS (Netherlands)

van der Mey, A.; Smit, F; Droog, K.J.; Visser, A.

2010-01-01

Following a soccer game is an example where clear emotions are displayed. This example is worked out for a humanoid robot which can express emotions with body language. The emotions expressed by the robot are not just stimuli-response, but are based on an affective state which shows dynamic behavior

Are facial expressions of emotion produced by categorical affect programs or dynamically driven by appraisal?

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Scherer, Klaus R; Ellgring, Heiner

2007-02-01

The different assumptions made by discrete and componential emotion theories about the nature of the facial expression of emotion and the underlying mechanisms are reviewed. Explicit and implicit predictions are derived from each model. It is argued that experimental expression-production paradigms rather than recognition studies are required to critically test these differential predictions. Data from a large-scale actor portrayal study are reported to demonstrate the utility of this approach. The frequencies with which 12 professional actors use major facial muscle actions individually and in combination to express 14 major emotions show little evidence for emotion-specific prototypical affect programs. Rather, the results encourage empirical investigation of componential emotion model predictions of dynamic configurations of appraisal-driven adaptive facial actions. (c) 2007 APA, all rights reserved.

Transcriptional dynamics of a conserved gene expression network associated with craniofacial divergence in Arctic charr.

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Ahi, Ehsan Pashay; Kapralova, Kalina Hristova; Pálsson, Arnar; Maier, Valerie Helene; Gudbrandsson, Jóhannes; Snorrason, Sigurdur S; Jónsson, Zophonías O; Franzdóttir, Sigrídur Rut

2014-01-01

Understanding the molecular basis of craniofacial variation can provide insights into key developmental mechanisms of adaptive changes and their role in trophic divergence and speciation. Arctic charr (Salvelinus alpinus) is a polymorphic fish species, and, in Lake Thingvallavatn in Iceland, four sympatric morphs have evolved distinct craniofacial structures. We conducted a gene expression study on candidates from a conserved gene coexpression network, focusing on the development of craniofacial elements in embryos of two contrasting Arctic charr morphotypes (benthic and limnetic). Four Arctic charr morphs were studied: one limnetic and two benthic morphs from Lake Thingvallavatn and a limnetic reference aquaculture morph. The presence of morphological differences at developmental stages before the onset of feeding was verified by morphometric analysis. Following up on our previous findings that Mmp2 and Sparc were differentially expressed between morphotypes, we identified a network of genes with conserved coexpression across diverse vertebrate species. A comparative expression study of candidates from this network in developing heads of the four Arctic charr morphs verified the coexpression relationship of these genes and revealed distinct transcriptional dynamics strongly correlated with contrasting craniofacial morphologies (benthic versus limnetic). A literature review and Gene Ontology analysis indicated that a significant proportion of the network genes play a role in extracellular matrix organization and skeletogenesis, and motif enrichment analysis of conserved noncoding regions of network candidates predicted a handful of transcription factors, including Ap1 and Ets2, as potential regulators of the gene network. The expression of Ets2 itself was also found to associate with network gene expression. Genes linked to glucocorticoid signalling were also studied, as both Mmp2 and Sparc are responsive to this pathway. Among those, several transcriptional

Attention and awareness influence amygdala activity for dynamic bodily expressions - A short review.

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Beatrice eDe Gelder

2012-08-01

Full Text Available The amygdala (AMG has long been viewed as the gateway to sensory processing of emotions and is also known to play an importanta role at the interface between cognition and emotion. However, the debate continues on whether AMG activation is independent of attentional demands. Recently, researchers started exploring AMG functions using dynamic stimuli rather than the traditional pictures of facial expressions. Our present goal is to review some recent studies using dynamic stimuli to investigate AMG activation and discuss the impact of different viewing conditions, including oddball detection, explicit or implicit recognition, variable cognitive task load, and non-conscious perception. In the second part we relate these different effects to a dynamic dual route model of affective processing and discuss its implications for AMG activity. We sketch a dynamic dual route perspective of affective perception and we argue that this allows for multiple AMG involvement in separate networks and at different times in the processing streams. Attention has a different impact on these separate but interacting networks. Route I is engaged in early emotion processing, is partly supported by AMG activity and is possibly independent of attention, whereas activity in the later emotion processing is influenced by attention. Route II is a cortical-based network that underlies body recognition and action representation. The end result of route I and II is reflexive and voluntary behavior respectively. We conclude that using dynamic emotion stimuli and a dynamic dual route model of affective perception can provide new insights into the varieties of AMG activation.

Profiling of REST-dependent microRNAs reveals dynamic modes of expression

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Zhengliang eGao

2012-05-01

Full Text Available Multipotent neural stem cells (NSCs possess the ability to self-renew and differentiate into both neurons and glia. However, the detailed mechanisms underlying NSC fate decisions are not well understood. Recent work suggest that the interaction between cell-type specific transcription factors and microRNAs (miRNAs is important as resident neural stem/progenitor cells give rise to functionally mature neurons. Recently, we demonstrated that the transcriptional repressor REST (RE1-silencing transcription factor is essential to prevent precocious neuronal differentiation and maintain NSC self-renewal in the adult hippocampus. Here we show that REST is required for orchestrating the expression of distinct subsets of miRNAs in primary mouse NSC cultures, a physiologically relevant cell type. Using miRNA array profiling, we identified known REST-regulated miRNA genes, as well as previously uncharacterized REST-dependent miRNAs. Interestingly, REST-regulated miRNAs undergo dynamic expression changes under differentiation conditions over time, but not under proliferation conditions. These results suggest that REST functions in a context-dependent manner through its target miRNAs for mediating neuronal production.

Processing of facial affect in social drinkers: a dose-response study of alcohol using dynamic emotion expressions.

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Kamboj, Sunjeev K; Joye, Alyssa; Bisby, James A; Das, Ravi K; Platt, Bradley; Curran, H Valerie

2013-05-01

Studies of affect recognition can inform our understanding of the interpersonal effects of alcohol and help develop a more complete neuropsychological profile of this drug. The objective of the study was to examine affect recognition in social drinkers using a novel dynamic affect-recognition task, sampling performance across a range of evolutionarily significant target emotions and neutral expressions. Participants received 0, 0.4 or 0.8 g/kg alcohol in a double-blind, independent groups design. Relatively naturalistic changes in facial expression-from neutral (mouth open) to increasing intensities of target emotions, as well as neutral (mouth closed)-were simulated using computer-generated dynamic morphs. Accuracy and reaction time were measured and a two-high-threshold model applied to hits and false-alarm data to determine sensitivity and response bias. While there was no effect on the principal emotion expressions (happiness, sadness, fear, anger and disgust), compared to those receiving 0.8 g/kg of alcohol and placebo, participants administered with 0.4 g/kg alcohol tended to show an enhanced response bias to neutral expressions. Exploration of this effect suggested an accompanying tendency to misattribute neutrality to sad expressions following the 0.4-g/kg dose. The 0.4-g/kg alcohol-but not 0.8 g/kg-produced a limited and specific modification in affect recognition evidenced by a neutral response bias and possibly an accompanying tendency to misclassify sad expressions as neutral. In light of previous findings on involuntary negative memory following the 0.4-g/kg dose, we suggest that moderate-but not high-doses of alcohol have a special relevance to emotional processing in social drinkers.

Dynamic modulation of phosphoprotein expression in ovarian cancer xenograft models

International Nuclear Information System (INIS)

Koussounadis, Antonis; Langdon, Simon P.; Um, Inhwa; Kay, Charlene; Francis, Kyle E.; Harrison, David J.; Smith, V. Anne

2016-01-01

The dynamic changes that occur in protein expression after treatment of a cancer in vivo are poorly described. In this study we measure the effect of chemotherapy over time on the expression of a panel of proteins in ovarian cancer xenograft models. The objective was to identify phosphoprotein and other protein changes indicative of pathway activation that might link with drug response. Two xenograft models, platinum-responsive OV1002 and platinum-unresponsive HOX424, were used. Treatments were carboplatin and carboplatin-paclitaxel. Expression of 49 proteins over 14 days post treatment was measured by quantitative immunofluorescence and analysed by AQUA. Carboplatin treatment in the platinum-sensitive OV1002 model triggered up-regulation of cell cycle, mTOR and DDR pathways, while at late time points WNT, invasion, EMT and MAPK pathways were modulated. Estrogen receptor-alpha (ESR1) and ERBB pathways were down-regulated early, within 24 h from treatment administration. Combined carboplatin-paclitaxel treatment triggered a more extensive response in the OV1002 model modulating expression of 23 of 49 proteins. Therefore the cell cycle and DDR pathways showed similar or more pronounced changes than with carboplatin alone. In addition to expression of pS6 and pERK increasing, components of the AKT pathway were modulated with pAKT increasing while its regulator PTEN was down-regulated early. WNT signaling, EMT and invasion markers were modulated at later time points. Additional pathways were also observed with the NFκB and JAK/STAT pathways being up-regulated. ESR1 was down-regulated as was HER4, while further protein members of the ERBB pathway were upregulated late. By contrast, in the carboplatin-unresponsive HOX 424 xenograft, carboplatin only modulated expression of MLH1 while carboplatin-paclitaxel treatment modulated ESR1 and pMET. Thirteen proteins were modulated by carboplatin and a more robust set of changes by carboplatin-paclitaxel. Early changes included

Expression of Critical Sulfur- and Iron-Oxidation Genes and the Community Dynamics During Bioleaching of Chalcopyrite Concentrate by Moderate Thermophiles.

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Zhou, Dan; Peng, Tangjian; Zhou, Hongbo; Liu, Xueduan; Gu, Guohua; Chen, Miao; Qiu, Guanzhou; Zeng, Weimin

2015-07-01

Sulfate adenylyltransferase gene and 4Fe-4S ferredoxin gene are the key genes related to sulfur and iron oxidations during bioleaching system, respectively. In order to better understand the bioleaching and microorganism synergistic mechanism in chalcopyrite bioleaching by mixed culture of moderate thermophiles, expressions of the two energy metabolism genes and community dynamics of free and attached microorganisms were investigated. Specific primers were designed for real-time quantitative PCR to study the expression of these genes. Real-time PCR results showed that sulfate adenylyltransferase gene was more highly expressed in Sulfobacillus thermosulfidooxidans than that in Acidithiobacillus caldus, and expression of 4Fe-4S ferredoxin gene was higher in Ferroplasma thermophilum than that in S. thermosulfidooxidans and Leptospirillum ferriphilum. The results indicated that in the bioleaching system of chalcopyrite concentrate, sulfur and iron oxidations were mainly performed by S. thermosulfidooxidans and F. thermophilum, respectively. The community dynamics results revealed that S. thermosulfidooxidans took up the largest proportion during the whole period, followed by F. thermophilum, A. caldus, and L. ferriphilum. The CCA analysis showed that 4Fe-4S ferredoxin gene expression was mainly affected (positively correlated) by high pH and elevated concentration of ferrous ion, while no factor was observed to prominently influence the expression of sulfate adenylyltransferase gene.

Human fatigue expression recognition through image-based dynamic multi-information and bimodal deep learning

Science.gov (United States)

Zhao, Lei; Wang, Zengcai; Wang, Xiaojin; Qi, Yazhou; Liu, Qing; Zhang, Guoxin

2016-09-01

Human fatigue is an important cause of traffic accidents. To improve the safety of transportation, we propose, in this paper, a framework for fatigue expression recognition using image-based facial dynamic multi-information and a bimodal deep neural network. First, the landmark of face region and the texture of eye region, which complement each other in fatigue expression recognition, are extracted from facial image sequences captured by a single camera. Then, two stacked autoencoder neural networks are trained for landmark and texture, respectively. Finally, the two trained neural networks are combined by learning a joint layer on top of them to construct a bimodal deep neural network. The model can be used to extract a unified representation that fuses landmark and texture modalities together and classify fatigue expressions accurately. The proposed system is tested on a human fatigue dataset obtained from an actual driving environment. The experimental results demonstrate that the proposed method performs stably and robustly, and that the average accuracy achieves 96.2%.

Facial Expression Aftereffect Revealed by Adaption to Emotion-Invisible Dynamic Bubbled Faces

Science.gov (United States)

Luo, Chengwen; Wang, Qingyun; Schyns, Philippe G.; Kingdom, Frederick A. A.; Xu, Hong

2015-01-01

Visual adaptation is a powerful tool to probe the short-term plasticity of the visual system. Adapting to local features such as the oriented lines can distort our judgment of subsequently presented lines, the tilt aftereffect. The tilt aftereffect is believed to be processed at the low-level of the visual cortex, such as V1. Adaptation to faces, on the other hand, can produce significant aftereffects in high-level traits such as identity, expression, and ethnicity. However, whether face adaptation necessitate awareness of face features is debatable. In the current study, we investigated whether facial expression aftereffects (FEAE) can be generated by partially visible faces. We first generated partially visible faces using the bubbles technique, in which the face was seen through randomly positioned circular apertures, and selected the bubbled faces for which the subjects were unable to identify happy or sad expressions. When the subjects adapted to static displays of these partial faces, no significant FEAE was found. However, when the subjects adapted to a dynamic video display of a series of different partial faces, a significant FEAE was observed. In both conditions, subjects could not identify facial expression in the individual adapting faces. These results suggest that our visual system is able to integrate unrecognizable partial faces over a short period of time and that the integrated percept affects our judgment on subsequently presented faces. We conclude that FEAE can be generated by partial face with little facial expression cues, implying that our cognitive system fills-in the missing parts during adaptation, or the subcortical structures are activated by the bubbled faces without conscious recognition of emotion during adaptation. PMID:26717572

Pgas, a Low-pH-Induced Promoter, as a Tool for Dynamic Control of Gene Expression for Metabolic Engineering of Aspergillus niger.

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Yin, Xian; Shin, Hyun-Dong; Li, Jianghua; Du, Guocheng; Liu, Long; Chen, Jian

2017-03-15

The dynamic control of gene expression is important for adjusting fluxes in order to obtain desired products and achieve appropriate cell growth, particularly when the synthesis of a desired product drains metabolites required for cell growth. For dynamic gene expression, a promoter responsive to a particular environmental stressor is vital. Here, we report a low-pH-inducible promoter, P gas , which promotes minimal gene expression at pH values above 5.0 but functions efficiently at low pHs, such as pH 2.0. First, we performed a transcriptional analysis of Aspergillus niger , an excellent platform for the production of organic acids, and we found that the promoter P gas may act efficiently at low pH. Then, a gene for synthetic green fluorescent protein ( sGFP ) was successfully expressed by P gas at pH 2.0, verifying the results of the transcriptional analysis. Next, P gas was used to express the cis -aconitate decarboxylase ( cad ) gene of Aspergillus terreus in A. niger , allowing the production of itaconic acid at a titer of 4.92 g/liter. Finally, we found that P gas strength was independent of acid type and acid ion concentration, showing dependence on pH only. IMPORTANCE The promoter P gas can be used for the dynamic control of gene expression in A. niger for metabolic engineering to produce organic acids. This promoter may also be a candidate tool for genetic engineering. Copyright © 2017 American Society for Microbiology.

AUTOCOUNTER, an ImageJ JavaScript to analyze LC3B-GFP expression dynamics in autophagy-induced astrocytoma cells.

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Fassina, L; Magenes, G; Inzaghi, A; Palumbo, S; Allavena, G; Miracco, C; Pirtoli, L; Biggiogera, M; Comincini, S

2012-10-11

An ImageJ JavaScript, AUTOCOUNTER, was specifically developed to monitor and measure LC3B-GFP expression in living human astrocytoma cells, namely T98G and U373-MG. Discrete intracellular GFP fluorescent spots derived from transduction of a Baculovirus replication-defective vector (BacMam LC3B-GFP), followed by microscope examinations at different times. After viral transgene expression, autophagy was induced by Rapamycin administration and assayed in ph-p70S6K/p70S6K and LC3B immunoblotting expression as well as by electron microscopy examinations. A mutated transgene, defective in LC3B lipidation, was employed as a negative control to further exclude fluorescent dots derived from protein intracellular aggregation. The ImageJ JavaScript was then employed to evaluate and score the dynamics changes of the number and area of LC3B-GFP puncta per cell in time course assays and in complex microscope examinations. In conclusion, AUTOCOUNTER enabled to quantify LC3B-GFP expression and to monitor dynamics changes in number and shapes of autophagosomal-like vesicles: it might therefore represent a suitable algorithmic tool for in vitro autophagy modulation studies.

Transcriptome dynamics along axolotl regenerative development are consistent with an extensive reduction in gene expression heterogeneity in dedifferentiated cells

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Carlos Díaz-Castillo

2017-11-01

Full Text Available Although in recent years the study of gene expression variation in the absence of genetic or environmental cues or gene expression heterogeneity has intensified considerably, many basic and applied biological fields still remain unaware of how useful the study of gene expression heterogeneity patterns might be for the characterization of biological systems and/or processes. Largely based on the modulator effect chromatin compaction has for gene expression heterogeneity and the extensive changes in chromatin compaction known to occur for specialized cells that are naturally or artificially induced to revert to less specialized states or dedifferentiate, I recently hypothesized that processes that concur with cell dedifferentiation would show an extensive reduction in gene expression heterogeneity. The confirmation of the existence of such trend could be of wide interest because of the biomedical and biotechnological relevance of cell dedifferentiation-based processes, i.e., regenerative development, cancer, human induced pluripotent stem cells, or plant somatic embryogenesis. Here, I report the first empirical evidence consistent with the existence of an extensive reduction in gene expression heterogeneity for processes that concur with cell dedifferentiation by analyzing transcriptome dynamics along forearm regenerative development in Ambystoma mexicanum or axolotl. Also, I briefly discuss on the utility of the study of gene expression heterogeneity dynamics might have for the characterization of cell dedifferentiation-based processes, and the engineering of tools that afforded better monitoring and modulating such processes. Finally, I reflect on how a transitional reduction in gene expression heterogeneity for dedifferentiated cells can promote a long-term increase in phenotypic heterogeneity following cell dedifferentiation with potential adverse effects for biomedical and biotechnological applications.

Transcriptome dynamics along axolotl regenerative development are consistent with an extensive reduction in gene expression heterogeneity in dedifferentiated cells

Science.gov (United States)

2017-01-01

Although in recent years the study of gene expression variation in the absence of genetic or environmental cues or gene expression heterogeneity has intensified considerably, many basic and applied biological fields still remain unaware of how useful the study of gene expression heterogeneity patterns might be for the characterization of biological systems and/or processes. Largely based on the modulator effect chromatin compaction has for gene expression heterogeneity and the extensive changes in chromatin compaction known to occur for specialized cells that are naturally or artificially induced to revert to less specialized states or dedifferentiate, I recently hypothesized that processes that concur with cell dedifferentiation would show an extensive reduction in gene expression heterogeneity. The confirmation of the existence of such trend could be of wide interest because of the biomedical and biotechnological relevance of cell dedifferentiation-based processes, i.e., regenerative development, cancer, human induced pluripotent stem cells, or plant somatic embryogenesis. Here, I report the first empirical evidence consistent with the existence of an extensive reduction in gene expression heterogeneity for processes that concur with cell dedifferentiation by analyzing transcriptome dynamics along forearm regenerative development in Ambystoma mexicanum or axolotl. Also, I briefly discuss on the utility of the study of gene expression heterogeneity dynamics might have for the characterization of cell dedifferentiation-based processes, and the engineering of tools that afforded better monitoring and modulating such processes. Finally, I reflect on how a transitional reduction in gene expression heterogeneity for dedifferentiated cells can promote a long-term increase in phenotypic heterogeneity following cell dedifferentiation with potential adverse effects for biomedical and biotechnological applications. PMID:29134148

Evolution‐development congruence in pattern formation dynamics: Bifurcations in gene expression and regulation of networks structures

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Kohsokabe, Takahiro

2016-01-01

ABSTRACT Search for possible relationships between phylogeny and ontogeny is important in evolutionary‐developmental biology. Here we uncover such relationships by numerical evolution and unveil their origin in terms of dynamical systems theory. By representing developmental dynamics of spatially located cells with gene expression dynamics with cell‐to‐cell interaction under external morphogen gradient, gene regulation networks are evolved under mutation and selection with the fitness to approach a prescribed spatial pattern of expressed genes. For most numerical evolution experiments, evolution of pattern over generations and development of pattern by an evolved network exhibit remarkable congruence. Both in the evolution and development pattern changes consist of several epochs where stripes are formed in a short time, while for other temporal regimes, pattern hardly changes. In evolution, these quasi‐stationary regimes are generations needed to hit relevant mutations, while in development, they are due to some gene expression that varies slowly and controls the pattern change. The morphogenesis is regulated by combinations of feedback or feedforward regulations, where the upstream feedforward network reads the external morphogen gradient, and generates a pattern used as a boundary condition for the later patterns. The ordering from up to downstream is common in evolution and development, while the successive epochal changes in development and evolution are represented as common bifurcations in dynamical‐systems theory, which lead to the evolution‐development congruence. Mechanism of exceptional violation of the congruence is also unveiled. Our results provide a new look on developmental stages, punctuated equilibrium, developmental bottlenecks, and evolutionary acquisition of novelty in morphogenesis. J. Exp. Zool. (Mol. Dev. Evol.) 326B:61–84, 2016. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Dynamic Wnt5a expression in murine hair follicle cycle and its inhibitory effects on follicular.

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Fang, De-Ren; Lv, Zhong-Fa; Qiao, Gang

2014-04-01

To analyze the dynamic expression of Wnt family member 5A (Wingless-type MMTV integration Wnt site family, member 5a) in murine hair cycle and its inhibitory effects on follicle in vivo. Situ hybridization in full-thickness skin was used to observe the change of mouse protein expression in different growth stages, and Ad-Wnt5a was injected after defeathering to observe the hair follicle growth in vivo. The Wnt5a mRNA was expressed at birth, and was firstly increased then decreased along with the progress of the hair cycle. It reached the peak in advanced stage of growth cycle (P<0.05). Rhoa and β-catenin expression levels were significantly decreased in three groups. Rac2 expression was significantly up-regulated, and the expression level of Wnt5a, Shh and Frizzled2 was increased, but less significantly than group 2. The expression of Wnt5a mRNA is consistent with change of murine follicle cycle, and has obvious inhibitory effects on the growth of hair follicle in vivo, indicating that it is antagonistic to Wnts pathway and interferes the growth of follicle together. Copyright © 2014 Hainan Medical College. Published by Elsevier B.V. All rights reserved.

GENE EXPRESSION DYNAMICS IN PATIENTS WITH SEVERE THERAPY-RESISTANT ASTHMA DURING TREATMENT PERIOD

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Ye. S. Kulikov

2014-01-01

Full Text Available Introduction: The leading mechanisms and causes of severe therapy resistant asthma are poorly understood. The aim of this study was to define global patterns of gene expression in adults with severe therapy-resistant asthma in dynamic during treatment period.Methods: Performed 24-week prospective interventional study in parallel groups. Severe asthma patients was aposterior divided at therapy sensitive and resistant patients according to ATS criteria. Global transcriptome profile was characterized using the Affymetrix HuGene ST1.0 chip. Cluster analysis was performed.Results and conclusion: According to our data several mechanisms of therapy resistance may be considered: increased levels of nitric oxide and beta2-agonists nitration, dysregulation of endogenous steroids secretion and involvement in the pathogenesis of Staphylococcus aureus. Absence of suppression of gene expression KEGG-pathway “asthma" may reflect the low efficiency or long period of anti-inflammatory therapy effect realization.

Validation of the Amsterdam Dynamic Facial Expression Set--Bath Intensity Variations (ADFES-BIV: A Set of Videos Expressing Low, Intermediate, and High Intensity Emotions.

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Tanja S H Wingenbach

Full Text Available Most of the existing sets of facial expressions of emotion contain static photographs. While increasing demand for stimuli with enhanced ecological validity in facial emotion recognition research has led to the development of video stimuli, these typically involve full-blown (apex expressions. However, variations of intensity in emotional facial expressions occur in real life social interactions, with low intensity expressions of emotions frequently occurring. The current study therefore developed and validated a set of video stimuli portraying three levels of intensity of emotional expressions, from low to high intensity. The videos were adapted from the Amsterdam Dynamic Facial Expression Set (ADFES and termed the Bath Intensity Variations (ADFES-BIV. A healthy sample of 92 people recruited from the University of Bath community (41 male, 51 female completed a facial emotion recognition task including expressions of 6 basic emotions (anger, happiness, disgust, fear, surprise, sadness and 3 complex emotions (contempt, embarrassment, pride that were expressed at three different intensities of expression and neutral. Accuracy scores (raw and unbiased (Hu hit rates were calculated, as well as response times. Accuracy rates above chance level of responding were found for all emotion categories, producing an overall raw hit rate of 69% for the ADFES-BIV. The three intensity levels were validated as distinct categories, with higher accuracies and faster responses to high intensity expressions than intermediate intensity expressions, which had higher accuracies and faster responses than low intensity expressions. To further validate the intensities, a second study with standardised display times was conducted replicating this pattern. The ADFES-BIV has greater ecological validity than many other emotion stimulus sets and allows for versatile applications in emotion research. It can be retrieved free of charge for research purposes from the

Validation of the Amsterdam Dynamic Facial Expression Set--Bath Intensity Variations (ADFES-BIV): A Set of Videos Expressing Low, Intermediate, and High Intensity Emotions.

Science.gov (United States)

Wingenbach, Tanja S H; Ashwin, Chris; Brosnan, Mark

2016-01-01

Most of the existing sets of facial expressions of emotion contain static photographs. While increasing demand for stimuli with enhanced ecological validity in facial emotion recognition research has led to the development of video stimuli, these typically involve full-blown (apex) expressions. However, variations of intensity in emotional facial expressions occur in real life social interactions, with low intensity expressions of emotions frequently occurring. The current study therefore developed and validated a set of video stimuli portraying three levels of intensity of emotional expressions, from low to high intensity. The videos were adapted from the Amsterdam Dynamic Facial Expression Set (ADFES) and termed the Bath Intensity Variations (ADFES-BIV). A healthy sample of 92 people recruited from the University of Bath community (41 male, 51 female) completed a facial emotion recognition task including expressions of 6 basic emotions (anger, happiness, disgust, fear, surprise, sadness) and 3 complex emotions (contempt, embarrassment, pride) that were expressed at three different intensities of expression and neutral. Accuracy scores (raw and unbiased (Hu) hit rates) were calculated, as well as response times. Accuracy rates above chance level of responding were found for all emotion categories, producing an overall raw hit rate of 69% for the ADFES-BIV. The three intensity levels were validated as distinct categories, with higher accuracies and faster responses to high intensity expressions than intermediate intensity expressions, which had higher accuracies and faster responses than low intensity expressions. To further validate the intensities, a second study with standardised display times was conducted replicating this pattern. The ADFES-BIV has greater ecological validity than many other emotion stimulus sets and allows for versatile applications in emotion research. It can be retrieved free of charge for research purposes from the corresponding author.

The neural dynamics underlying the interpersonal effects of emotional expression on decision making.

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Chen, Xuhai; Zheng, Tingting; Han, Lingzi; Chang, Yingchao; Luo, Yangmei

2017-04-20

Although numerous studies explore the effects of emotion on decision-making, the existing research has mainly focused on the influence of intrapersonal emotions, leaving the influence of one person's emotions on another's decisions underestimated. To specify how interpersonal emotions shape decision-making and delineate the underlying neural dynamics involved, the present study examined brain responses to utilitarian feedback combined with angry or happy faces in competitive and cooperative contexts. Behavioral results showed that participants responded slower following losses than wins when competitors express happiness but responded faster following losses than wins when cooperators express anger. Importantly, angry faces in competitive context reversed the differentiation pattern of feedback-related negativity (FRN) between losses and wins and diminished the difference between losses and wins on both P300 and theta power, but only diminished the difference on FRN between losses and wins in cooperative context. However, when partner displays happiness, losses versus wins elicited larger FRN and theta power in competitive context but smaller P300 in both contexts. These results suggest that interpersonal emotions shape decisions during both automatic motivational salience valuation (FRN) and conscious cognitive appraisal (P300) stages of processing, in which different emotional expressions exert interpersonal influence through different routes.

Expression and Dynamics of Podoplanin in Cultured Osteoblasts with Mechanostress and Mineralization Stimulus.

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Takenawa, Tomohiro; Kanai, Takenori; Kitamura, Tetsuya; Yoshimura, Yoshitaka; Sawa, Yoshihiko; Iida, Junichiro

2018-02-27

This study investigates the significance of the expression and dynamics of podoplanin in mechanostress and mineralization in cultured murine osteoblasts. Podoplanin increased in osteoblasts subjected to straining in non-mineralization medium, suggesting that the mechanostress alone is a podoplanin induction factor. In osteoblasts subjected to vertical elongation straining in the mineralization medium, the mRNA amounts of podoplanin, osteopontin, and osteocalcin were significantly larger than those in cells not subjected to straining, suggesting that mechanostress is the cause of a synergistic effect in the expression of these proteins. In osteoblasts in the mineralization medium, significant increases in osteocalcin mRNA occurred earlier in cells subjected to straining than in the cells not subjected to straining, suggesting that the mechanostress is a critical factor to enhance the expression of osteocalcin. Western blot and ELISA analysis showed increased podoplanin production in osteoblasts with longer durations of straining. There was significantly less mineralization product in osteoblasts with antibodies for podoplanin, osteopontin, and osteocalcin. There was also less osteopontin and osteocalcin produced in osteoblasts with anti-podoplanin. These findings suggest that mechanostress induces the production of podoplanin in osteoblasts and that podoplanin may play a role in mineralization in cooperation with bone-associated proteins.

Validation of the Amsterdam Dynamic Facial Expression Set – Bath Intensity Variations (ADFES-BIV): A Set of Videos Expressing Low, Intermediate, and High Intensity Emotions

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Wingenbach, Tanja S. H.

2016-01-01

Most of the existing sets of facial expressions of emotion contain static photographs. While increasing demand for stimuli with enhanced ecological validity in facial emotion recognition research has led to the development of video stimuli, these typically involve full-blown (apex) expressions. However, variations of intensity in emotional facial expressions occur in real life social interactions, with low intensity expressions of emotions frequently occurring. The current study therefore developed and validated a set of video stimuli portraying three levels of intensity of emotional expressions, from low to high intensity. The videos were adapted from the Amsterdam Dynamic Facial Expression Set (ADFES) and termed the Bath Intensity Variations (ADFES-BIV). A healthy sample of 92 people recruited from the University of Bath community (41 male, 51 female) completed a facial emotion recognition task including expressions of 6 basic emotions (anger, happiness, disgust, fear, surprise, sadness) and 3 complex emotions (contempt, embarrassment, pride) that were expressed at three different intensities of expression and neutral. Accuracy scores (raw and unbiased (Hu) hit rates) were calculated, as well as response times. Accuracy rates above chance level of responding were found for all emotion categories, producing an overall raw hit rate of 69% for the ADFES-BIV. The three intensity levels were validated as distinct categories, with higher accuracies and faster responses to high intensity expressions than intermediate intensity expressions, which had higher accuracies and faster responses than low intensity expressions. To further validate the intensities, a second study with standardised display times was conducted replicating this pattern. The ADFES-BIV has greater ecological validity than many other emotion stimulus sets and allows for versatile applications in emotion research. It can be retrieved free of charge for research purposes from the corresponding author

DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks

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Gerstein, Mark

2016-01-01

Gene expression is controlled by the combinatorial effects of regulatory factors from different biological subsystems such as general transcription factors (TFs), cellular growth factors and microRNAs. A subsystem’s gene expression may be controlled by its internal regulatory factors, exclusively, or by external subsystems, or by both. It is thus useful to distinguish the degree to which a subsystem is regulated internally or externally–e.g., how non-conserved, species-specific TFs affect the expression of conserved, cross-species genes during evolution. We developed a computational method (DREISS, dreiss.gerteinlab.org) for analyzing the Dynamics of gene expression driven by Regulatory networks, both External and Internal based on State Space models. Given a subsystem, the “state” and “control” in the model refer to its own (internal) and another subsystem’s (external) gene expression levels. The state at a given time is determined by the state and control at a previous time. Because typical time-series data do not have enough samples to fully estimate the model’s parameters, DREISS uses dimensionality reduction, and identifies canonical temporal expression trajectories (e.g., degradation, growth and oscillation) representing the regulatory effects emanating from various subsystems. To demonstrate capabilities of DREISS, we study the regulatory effects of evolutionarily conserved vs. divergent TFs across distant species. In particular, we applied DREISS to the time-series gene expression datasets of C. elegans and D. melanogaster during their embryonic development. We analyzed the expression dynamics of the conserved, orthologous genes (orthologs), seeing the degree to which these can be accounted for by orthologous (internal) versus species-specific (external) TFs. We found that between two species, the orthologs have matched, internally driven expression patterns but very different externally driven ones. This is particularly true for genes with

DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks.

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Daifeng Wang

2016-10-01

Full Text Available Gene expression is controlled by the combinatorial effects of regulatory factors from different biological subsystems such as general transcription factors (TFs, cellular growth factors and microRNAs. A subsystem's gene expression may be controlled by its internal regulatory factors, exclusively, or by external subsystems, or by both. It is thus useful to distinguish the degree to which a subsystem is regulated internally or externally-e.g., how non-conserved, species-specific TFs affect the expression of conserved, cross-species genes during evolution. We developed a computational method (DREISS, dreiss.gerteinlab.org for analyzing the Dynamics of gene expression driven by Regulatory networks, both External and Internal based on State Space models. Given a subsystem, the "state" and "control" in the model refer to its own (internal and another subsystem's (external gene expression levels. The state at a given time is determined by the state and control at a previous time. Because typical time-series data do not have enough samples to fully estimate the model's parameters, DREISS uses dimensionality reduction, and identifies canonical temporal expression trajectories (e.g., degradation, growth and oscillation representing the regulatory effects emanating from various subsystems. To demonstrate capabilities of DREISS, we study the regulatory effects of evolutionarily conserved vs. divergent TFs across distant species. In particular, we applied DREISS to the time-series gene expression datasets of C. elegans and D. melanogaster during their embryonic development. We analyzed the expression dynamics of the conserved, orthologous genes (orthologs, seeing the degree to which these can be accounted for by orthologous (internal versus species-specific (external TFs. We found that between two species, the orthologs have matched, internally driven expression patterns but very different externally driven ones. This is particularly true for genes with

dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data.

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Huynh-Thu, Vân Anh; Geurts, Pierre

2018-02-21

The elucidation of gene regulatory networks is one of the major challenges of systems biology. Measurements about genes that are exploited by network inference methods are typically available either in the form of steady-state expression vectors or time series expression data. In our previous work, we proposed the GENIE3 method that exploits variable importance scores derived from Random forests to identify the regulators of each target gene. This method provided state-of-the-art performance on several benchmark datasets, but it could however not specifically be applied to time series expression data. We propose here an adaptation of the GENIE3 method, called dynamical GENIE3 (dynGENIE3), for handling both time series and steady-state expression data. The proposed method is evaluated extensively on the artificial DREAM4 benchmarks and on three real time series expression datasets. Although dynGENIE3 does not systematically yield the best performance on each and every network, it is competitive with diverse methods from the literature, while preserving the main advantages of GENIE3 in terms of scalability.

Global transgenerational gene expression dynamics in two newly synthesized allohexaploid wheat (Triticum aestivum lines

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Qi Bao

2012-01-01

Full Text Available Abstract Background Alteration in gene expression resulting from allopolyploidization is a prominent feature in plants, but its spectrum and extent are not fully known. Common wheat (Triticum aestivum was formed via allohexaploidization about 10,000 years ago, and became the most important crop plant. To gain further insights into the genome-wide transcriptional dynamics associated with the onset of common wheat formation, we conducted microarray-based genome-wide gene expression analysis on two newly synthesized allohexaploid wheat lines with chromosomal stability and a genome constitution analogous to that of the present-day common wheat. Results Multi-color GISH (genomic in situ hybridization was used to identify individual plants from two nascent allohexaploid wheat lines between Triticum turgidum (2n = 4x = 28; genome BBAA and Aegilops tauschii (2n = 2x = 14; genome DD, which had a stable chromosomal constitution analogous to that of common wheat (2n = 6x = 42; genome BBAADD. Genome-wide analysis of gene expression was performed for these allohexaploid lines along with their parental plants from T. turgidum and Ae. tauschii, using the Affymetrix Gene Chip Wheat Genome-Array. Comparison with the parental plants coupled with inclusion of empirical mid-parent values (MPVs revealed that whereas the great majority of genes showed the expected parental additivity, two major patterns of alteration in gene expression in the allohexaploid lines were identified: parental dominance expression and non-additive expression. Genes involved in each of the two altered expression patterns could be classified into three distinct groups, stochastic, heritable and persistent, based on their transgenerational heritability and inter-line conservation. Strikingly, whereas both altered patterns of gene expression showed a propensity of inheritance, identity of the involved genes was highly stochastic, consistent with the involvement of diverse Gene Ontology (GO

Dynamic Blue Light-Inducible T7 RNA Polymerases (Opto-T7RNAPs) for Precise Spatiotemporal Gene Expression Control.

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Baumschlager, Armin; Aoki, Stephanie K; Khammash, Mustafa

2017-11-17

Light has emerged as a control input for biological systems due to its precise spatiotemporal resolution. The limited toolset for light control in bacteria motivated us to develop a light-inducible transcription system that is independent from cellular regulation through the use of an orthogonal RNA polymerase. Here, we present our engineered blue light-responsive T7 RNA polymerases (Opto-T7RNAPs) that show properties such as low leakiness of gene expression in the dark state, high expression strength when induced with blue light, and an inducible range of more than 300-fold. Following optimization of the system to reduce expression variability, we created a variant that returns to the inactive dark state within minutes once the blue light is turned off. This allows for precise dynamic control of gene expression, which is a key aspect for most applications using optogenetic regulation. The regulators, which only require blue light from ordinary light-emitting diodes for induction, were developed and tested in the bacterium Escherichia coli, which is a crucial cell factory for biotechnology due to its fast and inexpensive cultivation and well understood physiology and genetics. Opto-T7RNAP, with minor alterations, should be extendable to other bacterial species as well as eukaryotes such as mammalian cells and yeast in which the T7 RNA polymerase and the light-inducible Vivid regulator have been shown to be functional. We anticipate that our approach will expand the applicability of using light as an inducer for gene expression independent from cellular regulation and allow for a more reliable dynamic control of synthetic and natural gene networks.

Jumping for Joy: The Importance of the Body and of Dynamics in the Expression and Recognition of Positive Emotions

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Marcello Mortillaro

2018-05-01

Full Text Available The majority of research on emotion expression has focused on static facial prototypes of a few selected, mostly negative emotions. Implicitly, most researchers seem to have considered all positive emotions as sharing one common signal (namely, the smile, and consequently as being largely indistinguishable from each other in terms of expression. Recently, a new wave of studies has started to challenge the traditional assumption by considering the role of multiple modalities and the dynamics in the expression and recognition of positive emotions. Based on these recent studies, we suggest that positive emotions are better expressed and correctly perceived when (a they are communicated simultaneously through the face and body and (b perceivers have access to dynamic stimuli. Notably, we argue that this improvement is comparatively more important for positive emotions than for negative emotions. Our view is that the misperception of positive emotions has fewer immediate and potentially life-threatening consequences than the misperception of negative emotions; therefore, from an evolutionary perspective, there was only limited benefit in the development of clear, quick signals that allow observers to draw fine distinctions between them. Consequently, we suggest that the successful communication of positive emotions requires a stronger signal than that of negative emotions, and that this signal is provided by the use of the body and the way those movements unfold. We hope our contribution to this growing field provides a new direction and a theoretical grounding for the many lines of empirical research on the expression and recognition of positive emotions.

Dynamics of GATA1 binding and expression response in a GATA1-induced erythroid differentiation system

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Deepti Jain

2015-06-01

Full Text Available During the maturation phase of mammalian erythroid differentiation, highly proliferative cells committed to the erythroid lineage undergo dramatic changes in morphology and function to produce circulating, enucleated erythrocytes. These changes are caused by equally dramatic alterations in gene expression, which in turn are driven by changes in the abundance and binding patterns of transcription factors such as GATA1. We have studied the dynamics of GATA1 binding by ChIP-seq and the global expression responses by RNA-seq in a GATA1-dependent mouse cell line model for erythroid maturation, in both cases examining seven progressive stages during differentiation. Analyses of these data should provide insights both into mechanisms of regulation (early versus late targets and the consequences in cell physiology (e.g., distinctive categories of genes regulated at progressive stages of differentiation. The data are deposited in the Gene Expression Omnibus, series GSE36029, GSE40522, GSE49847, and GSE51338.

Replication-Competent Influenza A and B Viruses Expressing a Fluorescent Dynamic Timer Protein for In Vitro and In Vivo Studies.

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Michael Breen

Full Text Available Influenza A and B viruses (IAV and IBV, respectively cause annual seasonal human respiratory disease epidemics. In addition, IAVs have been implicated in occasional pandemics with inordinate health and economic consequences. Studying influenza viruses in vitro or in vivo requires the use of laborious secondary methodologies to identify infected cells. To circumvent this requirement, replication-competent infectious influenza viruses expressing an easily traceable fluorescent reporter protein can be used. Timer is a fluorescent protein that undergoes a time-dependent color emission conversion from green to red. The rate of spectral change is independent of Timer protein concentration and can be used to chronologically measure the duration of its expression. Here, we describe the generation of replication-competent IAV and IBV where the viral non-structural protein 1 (NS1 was fused to the fluorescent dynamic Timer protein. Timer-expressing IAV and IBV displayed similar plaque phenotypes and growth kinetics to wild-type viruses in tissue culture. Within infected cells, Timer's spectral shift can be used to measure the rate and cell-to-cell spread of infection using fluorescent microscopy, plate readers, or flow cytometry. The progression of Timer-expressing IAV infection was also evaluated in a mouse model, demonstrating the feasibility to characterize IAV cell-to-cell infections in vivo. By providing the ability to chronologically track viral spread, Timer-expressing influenza viruses are an excellent option to evaluate the in vitro and in vivo dynamics of viral infection.

Interplay of Noisy Gene Expression and Dynamics Explains Patterns of Bacterial Operon Organization

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Igoshin, Oleg

2011-03-01

Bacterial chromosomes are organized into operons -- sets of genes co-transcribed into polycistronic messenger RNA. Hypotheses explaining the emergence and maintenance of operons include proportional co-regulation, horizontal transfer of intact ``selfish'' operons, emergence via gene duplication, and co-production of physically interacting proteins to speed their association. We hypothesized an alternative: operons can reduce or increase intrinsic gene expression noise in a manner dependent on the post-translational interactions, thereby resulting in selection for or against operons in depending on the network architecture. We devised five classes of two-gene network modules and show that the effects of operons on intrinsic noise depend on class membership. Two classes exhibit decreased noise with co-transcription, two others reveal increased noise, and the remaining one does not show a significant difference. To test our modeling predictions we employed bioinformatic analysis to determine the relationship gene expression noise and operon organization. The results confirm the overrepresentation of noise-minimizing operon architectures and provide evidence against other hypotheses. Our results thereby suggest a central role for gene expression noise in selecting for or maintaining operons in bacterial chromosomes. This demonstrates how post-translational network dynamics may provide selective pressure for organizing bacterial chromosomes, and has practical consequences for designing synthetic gene networks. This work is supported by National Institutes of Health grant 1R01GM096189-01.

Rapid transcriptional pulsing dynamics of high expressing retroviral transgenes in embryonic stem cells.

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Mandy Y M Lo

Full Text Available Single cell imaging studies suggest that transcription is not continuous and occurs as discrete pulses of gene activity. To study mechanisms by which retroviral transgenes can transcribe to high levels, we used the MS2 system to visualize transcriptional dynamics of high expressing proviral integration sites in embryonic stem (ES cells. We established two ES cell lines each bearing a single copy, self-inactivating retroviral vector with a strong ubiquitous human EF1α gene promoter directing expression of mRFP fused to an MS2-stem-loop array. Transfection of MS2-EGFP generated EGFP focal dots bound to the mRFP-MS2 stem loop mRNA. These transcription foci colocalized with the transgene integration site detected by immunoFISH. Live tracking of single cells for 20 minutes detected EGFP focal dots that displayed frequent and rapid fluctuations in transcription over periods as short as 25 seconds. Similarly rapid fluctuations were detected from focal doublet signals that colocalized with replicated proviral integration sites by immunoFISH, consistent with transcriptional pulses from sister chromatids. We concluded that retroviral transgenes experience rapid transcriptional pulses in clonal ES cell lines that exhibit high level expression. These events are directed by a constitutive housekeeping gene promoter and may provide precedence for rapid transcriptional pulsing at endogenous genes in mammalian stem cells.

Are event-related potentials to dynamic facial expressions of emotion related to individual differences in the accuracy of processing facial expressions and identity?

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Recio, Guillermo; Wilhelm, Oliver; Sommer, Werner; Hildebrandt, Andrea

2017-04-01

Despite a wealth of knowledge about the neural mechanisms behind emotional facial expression processing, little is known about how they relate to individual differences in social cognition abilities. We studied individual differences in the event-related potentials (ERPs) elicited by dynamic facial expressions. First, we assessed the latent structure of the ERPs, reflecting structural face processing in the N170, and the allocation of processing resources and reflexive attention to emotionally salient stimuli, in the early posterior negativity (EPN) and the late positive complex (LPC). Then we estimated brain-behavior relationships between the ERP factors and behavioral indicators of facial identity and emotion-processing abilities. Structural models revealed that the participants who formed faster structural representations of neutral faces (i.e., shorter N170 latencies) performed better at face perception (r = -.51) and memory (r = -.42). The N170 amplitude was not related to individual differences in face cognition or emotion processing. The latent EPN factor correlated with emotion perception (r = .47) and memory (r = .32), and also with face perception abilities (r = .41). Interestingly, the latent factor representing the difference in EPN amplitudes between the two neutral control conditions (chewing and blinking movements) also correlated with emotion perception (r = .51), highlighting the importance of tracking facial changes in the perception of emotional facial expressions. The LPC factor for negative expressions correlated with the memory for emotional facial expressions. The links revealed between the latency and strength of activations of brain systems and individual differences in processing socio-emotional information provide new insights into the brain mechanisms involved in social communication.

Executives' speech expressiveness: analysis of perceptive and acoustic aspects of vocal dynamics.

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Marquezin, Daniela Maria Santos Serrano; Viola, Izabel; Ghirardi, Ana Carolina de Assis Moura; Madureira, Sandra; Ferreira, Léslie Piccolotto

2015-01-01

To analyze speech expressiveness in a group of executives based on perceptive and acoustic aspects of vocal dynamics. Four male subjects participated in the research study (S1, S2, S3, and S4). The assessments included the Kingdomality test to obtain the keywords of communicative attitudes; perceptive-auditory assessment to characterize vocal quality and dynamics, performed by three judges who are speech language pathologists; perceptiveauditory assessment to judge the chosen keywords; speech acoustics to assess prosodic elements (Praat software); and a statistical analysis. According to the perceptive-auditory analysis of vocal dynamics, S1, S2, S3, and S4 did not show vocal alterations and all of them were considered with lowered habitual pitch. S1: pointed out as insecure, nonobjective, nonempathetic, and unconvincing with inappropriate use of pauses that are mainly formed by hesitations; inadequate separation of prosodic groups with breaking of syntagmatic constituents. S2: regular use of pauses for respiratory reload, organization of sentences, and emphasis, which is considered secure, little objective, empathetic, and convincing. S3: pointed out as secure, objective, empathetic, and convincing with regular use of pauses for respiratory reload and organization of sentences and hesitations. S4: the most secure, objective, empathetic, and convincing, with proper use of pauses for respiratory reload, planning, and emphasis; prosodic groups agreed with the statement, without separating the syntagmatic constituents. The speech characteristics and communicative attitudes were highlighted in two subjects in a different manner, in such a way that the slow rate of speech and breaks of the prosodic groups transmitted insecurity, little objectivity, and nonpersuasion.

Valence Scaling of Dynamic Facial Expressions Is Altered in High-Functioning Subjects with Autism Spectrum Disorders: An FMRI Study

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Rahko, Jukka S.; Paakki, Jyri-Johan; Starck, Tuomo H.; Nikkinen, Juha; Pauls, David L.; Katsyri, Jari V.; Jansson-Verkasalo, Eira M.; Carter, Alice S.; Hurtig, Tuula M.; Mattila, Marja-Leena; Jussila, Katja K.; Remes, Jukka J.; Kuusikko-Gauffin, Sanna A.; Sams, Mikko E.; Bolte, Sven; Ebeling, Hanna E.; Moilanen, Irma K.; Tervonen, Osmo; Kiviniemi, Vesa

2012-01-01

FMRI was performed with the dynamic facial expressions fear and happiness. This was done to detect differences in valence processing between 25 subjects with autism spectrum disorders (ASDs) and 27 typically developing controls. Valence scaling was abnormal in ASDs. Positive valence induces lower deactivation and abnormally strong activity in ASD…

Dynamic changes in connexin expression following engraftment of neural stem cells to striatal tissue

International Nuclear Information System (INIS)

Jaederstad, Johan; Jaederstad, Linda Maria; Herlenius, Eric

2011-01-01

Gap-junctional intercellular communication between grafted neural stem cells (NSCs) and host cells seem to be essential for many of the beneficial effects associated with NSC engraftment. Utilizing murine NSCs (mNSCs) grafted into an organotypic ex vivo model system for striatal tissue we examined the prerequisites for formation of gap-junctional couplings between graft and host cells at different time points following implantation. We utilized flow cytometry (to quantify the proportion of connexin (Cx) 26 and 43 expressing cells), immunohistochemistry (for localization of the gap-junctional proteins in graft and host cells), dye-transfer studies with and without pharmacological gap-junctional blockers (assaying the functionality of the formed gap-junctional couplings), and proliferation assays (to estimate the role of gap junctions for NSC well-being) to this end. Immunohistochemical staining and dye-transfer studies revealed that the NSCs already form functional gap junctions prior to engraftment, thereby creating a substrate for subsequent graft and host communication. The expression of Cx43 by grafted NSCs was decreased by neurotrophin-3 overexpression in NSCs and culturing of grafted tissue in serum-free Neurobasal B27 medium. Cx43 expression in NSC-derived cells also changed significantly following engraftment. In host cells the expression of Cx43 peaked following traumatic stimulation and then declined within two weeks, suggesting a window of opportunity for successful host cell rescue by NSC engraftment. Further investigation of the dynamic changes in gap junction expression in graft and host cells and the associated variations in intercellular communication between implanted and endogenous cells might help to understand and control the early positive and negative effects evident following neural stem cell transplantation and thereby optimize the outcome of future clinical NSC transplantation therapies.

A Trigger or a Muffler? - Examining the Dynamics of Crosscutting Exposure and Political Expression in Online Social Media

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Soo Young Bae

2013-11-01

Full Text Available This study explores the potential of online social media to serve as a sphere for political discourse and investigates the extent to which everyday uses of online social networking sites can expose citizens to politically diverse viewpoints.  In addition, this study asks whether such crosscutting exposure in online social networks will act as a trigger or a muffler for political expression – that is, whether exposure political difference will stimulate or discourage political discussions.  With analyses of a sample of online social networking site users in the context of the 2012 presidential election in South Korea, this study explicates the link between crosscutting exposure and citizens’ political expressions in social media.  Results reveal that contrary to the predictions in previous literature, exposure to politically incongruent viewpoints in online social networking sites does not seem to undermine users’ expressive behaviors but instead positively contribute to political expression.  In addition, this study shows the significant role of citizens’ perceptions of candidate support in their own networks, and illustrates that the dynamics of political expression differ significantly depending on the users’ age.

Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection.

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Guthke, Reinhard; Möller, Ulrich; Hoffmann, Martin; Thies, Frank; Töpfer, Susanne

2005-04-15

The immune response to bacterial infection represents a complex network of dynamic gene and protein interactions. We present an optimized reverse engineering strategy aimed at a reconstruction of this kind of interaction networks. The proposed approach is based on both microarray data and available biological knowledge. The main kinetics of the immune response were identified by fuzzy clustering of gene expression profiles (time series). The number of clusters was optimized using various evaluation criteria. For each cluster a representative gene with a high fuzzy-membership was chosen in accordance with available physiological knowledge. Then hypothetical network structures were identified by seeking systems of ordinary differential equations, whose simulated kinetics could fit the gene expression profiles of the cluster-representative genes. For the construction of hypothetical network structures singular value decomposition (SVD) based methods and a newly introduced heuristic Network Generation Method here were compared. It turned out that the proposed novel method could find sparser networks and gave better fits to the experimental data. Reinhard.Guthke@hki-jena.de.

Pex11α in brown trout (Salmo trutta f. fario): Expression dynamics during the reproductive cycle reveals sex-specific seasonal patterns.

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Castro, L Filipe C; Lobo-da-Cunha, Alexandre; Rocha, Maria J; Urbatzka, Ralph; Rocha, Eduardo

2013-01-01

A negative correlation between female gonadal maturation kinetics and size variations of hepatic peroxisomes was earlier documented in brown trout, as a probable impact of serum estrogen changes during the reproductive cycle. Herein, we investigated whether the organelle volume/surface dynamics seen in female brown trout liver peroxisomes - without numerical changes within each hepatocyte - is followed by variations in the expression of the membrane peroxisome protein Pex11α gene. For comparison, we also studied males. We find in females a seasonal variation with the highest Pex11α expression in February, which was statistically different from all other tested periods. Overall, the expression of PEX11α had over a fivefold decrease from February to September. This period coincides with the reproductive transition between the earlier post-spawning gonadal remodeling and preparatory staging and the pre-spawning period. Males did not show changes. Our approach allowed the first characterization of a peroxin gene in a teleost, the Pex11α, while offering a correlation scenario were, as we hypothesized, the peroxisomal size kinetics is paralleled by membrane-related gene alterations (measured herein as proxy of Pex11α gene expression). Our data support and expand previous results on the regulation, function and morphology of peroxisome dynamics in brown trout, with a broader interest. Copyright © 2012 Elsevier Inc. All rights reserved.

Reduced Recognition of Dynamic Facial Emotional Expressions and Emotion-Specific Response Bias in Children with an Autism Spectrum Disorder

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Evers, Kris; Steyaert, Jean; Noens, Ilse; Wagemans, Johan

2015-01-01

Emotion labelling was evaluated in two matched samples of 6-14-year old children with and without an autism spectrum disorder (ASD; N = 45 and N = 50, resp.), using six dynamic facial expressions. The Emotion Recognition Task proved to be valuable demonstrating subtle emotion recognition difficulties in ASD, as we showed a general poorer emotion…

Dynamic expression of ancient and novel molluscan shell genes during ecological transitions

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Wörheide Gert

2007-09-01

Full Text Available Abstract Background The Mollusca constitute one of the most morphologically and ecologically diverse metazoan phyla, occupying a wide range of marine, terrestrial and freshwater habitats. The evolutionary success of the molluscs can in part be attributed to the evolvability of the external shell. Typically, the shell first forms during embryonic and larval development, changing dramatically in shape, colour and mineralogical composition as development and maturation proceeds. Major developmental transitions in shell morphology often correlate with ecological transitions (e.g. from a planktonic to benthic existence at metamorphosis. While the genes involved in molluscan biomineralisation are beginning to be identified, there is little understanding of how these are developmentally regulated, or if the same genes are operational at different stages of the mollusc's life. Results Here we relate the developmental expression of nine genes in the tissue responsible for shell production – the mantle – to ecological transitions that occur during the lifetime of the tropical abalone Haliotis asinina (Vetigastropoda. Four of these genes encode evolutionarily ancient proteins, while four others encode secreted proteins with little or no identity to known proteins. Another gene has been previously described from the mantle of another haliotid vetigastropod. All nine genes display dynamic spatial and temporal expression profiles within the larval shell field and juvenile mantle. Conclusion These expression data reflect the regulatory complexity that underlies molluscan shell construction from larval stages to adulthood, and serves to highlight the different ecological demands placed on each stage. The use of both ancient and novel genes in all stages of shell construction also suggest that a core set of shell-making genes was provided by a shared metazoan ancestor, which has been elaborated upon to produce the range of molluscan shell types we see today.

Neural Correlates of Facial Mimicry: Simultaneous Measurements of EMG and BOLD Responses during Perception of Dynamic Compared to Static Facial Expressions

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Rymarczyk, Krystyna; Żurawski, Łukasz; Jankowiak-Siuda, Kamila; Szatkowska, Iwona

2018-01-01

Facial mimicry (FM) is an automatic response to imitate the facial expressions of others. However, neural correlates of the phenomenon are as yet not well established. We investigated this issue using simultaneously recorded EMG and BOLD signals during perception of dynamic and static emotional facial expressions of happiness and anger. During display presentations, BOLD signals and zygomaticus major (ZM), corrugator supercilii (CS) and orbicularis oculi (OO) EMG responses were recorded simultaneously from 46 healthy individuals. Subjects reacted spontaneously to happy facial expressions with increased EMG activity in ZM and OO muscles and decreased CS activity, which was interpreted as FM. Facial muscle responses correlated with BOLD activity in regions associated with motor simulation of facial expressions [i.e., inferior frontal gyrus, a classical Mirror Neuron System (MNS)]. Further, we also found correlations for regions associated with emotional processing (i.e., insula, part of the extended MNS). It is concluded that FM involves both motor and emotional brain structures, especially during perception of natural emotional expressions. PMID:29467691

Space-by-time manifold representation of dynamic facial expressions for emotion categorization

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Delis, Ioannis; Chen, Chaona; Jack, Rachael E.; Garrod, Oliver G. B.; Panzeri, Stefano; Schyns, Philippe G.

2016-01-01

Visual categorization is the brain computation that reduces high-dimensional information in the visual environment into a smaller set of meaningful categories. An important problem in visual neuroscience is to identify the visual information that the brain must represent and then use to categorize visual inputs. Here we introduce a new mathematical formalism—termed space-by-time manifold decomposition—that describes this information as a low-dimensional manifold separable in space and time. We use this decomposition to characterize the representations used by observers to categorize the six classic facial expressions of emotion (happy, surprise, fear, disgust, anger, and sad). By means of a Generative Face Grammar, we presented random dynamic facial movements on each experimental trial and used subjective human perception to identify the facial movements that correlate with each emotion category. When the random movements projected onto the categorization manifold region corresponding to one of the emotion categories, observers categorized the stimulus accordingly; otherwise they selected “other.” Using this information, we determined both the Action Unit and temporal components whose linear combinations lead to reliable categorization of each emotion. In a validation experiment, we confirmed the psychological validity of the resulting space-by-time manifold representation. Finally, we demonstrated the importance of temporal sequencing for accurate emotion categorization and identified the temporal dynamics of Action Unit components that cause typical confusions between specific emotions (e.g., fear and surprise) as well as those resolving these confusions. PMID:27305521

Dynamic changes in Bach1 expression in the kidney of rhabdomyolysis-associated acute kidney injury.

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Masakazu Yamaoka

Full Text Available Free heme, a pro-oxidant released from myoglobin, is thought to contribute to the pathogenesis of rhabdomyolysis-associated acute kidney injury (RM-AKI, because renal overexpression of heme oxygenase-1 (HO-1, the rate-limiting enzyme in heme catabolism, confers protection against RM-AKI. BTB and CNC homology 1 (Bach1 is a heme-responsive transcription factor that represses HO-1. Here, we examined the changes with time in the gene expression of Bach1, HO-1, and δ-aminolevulinate synthase (ALAS1, a heme biosynthetic enzyme in the rat kidney using an RM-AKI model induced by the injection of 50% glycerol (10 mL/kg body weight into bilateral limbs. We also examined the protein expression of Bach1 in the nucleus and cytosol, and HO-1 in the rat kidney. Glycerol treatment induced significant elevation of serum creatinine kinase and aspartate aminotransferase levels followed by the marked elevation of serum blood urea nitrogen and creatinine levels, which caused serious damage to renal tubules. Following glycerol treatment, HO-1 mRNA and protein levels were significantly up-regulated, while ALAS1 mRNA expression was down-regulated, suggesting an increase in the free renal heme concentration. The Bach1 mRNA level was drastically increased 3 h after glycerol treatment, and the increased level was maintained for 12 h. Nuclear Bach1 protein levels were significantly decreased 3 h after treatment. Conversely, cytosolic Bach1 protein levels abruptly increased after 6 h. In conclusion, we demonstrate the dynamic changes in Bach1 expression in a rat model of RM-AKI. Our findings suggest that the increase in Bach1 mRNA and cytosolic Bach1 protein expression may reflect de novo Bach1 protein synthesis to compensate for the depletion of nuclear Bach1 protein caused by the induction of HO-1 by free heme.

The dynamics of connexin expression, degradation and localisation are regulated by gonadotropins during the early stages of in vitro maturation of swine oocytes.

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Nicolas Santiquet

Full Text Available Gap junctional communication (GJC plays a primordial role in oocyte maturation and meiotic resumption in mammals by directing the transfer of numerous molecules between cumulus cells and the oocyte. Gap junctions are made of connexins (Cx, proteins that regulate GJC in numerous ways. Understanding the dynamic regulation of connexin arrangements during in vitro maturation (IVM could provide a powerful tool for controlling meiotic resumption and consequently in vitro development of fully competent oocytes. However, physiological events happening during the early hours of IVM may still be elucidated. The present study reports the dynamic regulation of connexin expression, degradation and localization during this stage. Cx43, Cx45 and Cx60 were identified as the main connexins expressed in swine COC. Cx43 and Cx45 transcripts were judged too static to be a regulator of GJC, while Cx43 protein expression was highly responsive to gonadotropins, suggesting that it might be the principal regulator of GJC. In addition, the degradation of Cx43 expressed after 4.5 h of IVM in response to equine chorionic gonadotropin appeared to involve the proteasomal complex. Cx43 localisation appeared to be associated with GJC. Taken together, these results show for the first time that gonadotropins regulate Cx43 protein expression, degradation and localisation in porcine COC during the first several hours of IVM. Regulation of Cx43 may in turn, via GJC, participate in the development of fully competent oocytes.

Dynamics of processing invisible faces in the brain: automatic neural encoding of facial expression information.

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Jiang, Yi; Shannon, Robert W; Vizueta, Nathalie; Bernat, Edward M; Patrick, Christopher J; He, Sheng

2009-02-01

The fusiform face area (FFA) and the superior temporal sulcus (STS) are suggested to process facial identity and facial expression information respectively. We recently demonstrated a functional dissociation between the FFA and the STS as well as correlated sensitivity of the STS and the amygdala to facial expressions using an interocular suppression paradigm [Jiang, Y., He, S., 2006. Cortical responses to invisible faces: dissociating subsystems for facial-information processing. Curr. Biol. 16, 2023-2029.]. In the current event-related brain potential (ERP) study, we investigated the temporal dynamics of facial information processing. Observers viewed neutral, fearful, and scrambled face stimuli, either visibly or rendered invisible through interocular suppression. Relative to scrambled face stimuli, intact visible faces elicited larger positive P1 (110-130 ms) and larger negative N1 or N170 (160-180 ms) potentials at posterior occipital and bilateral occipito-temporal regions respectively, with the N170 amplitude significantly greater for fearful than neutral faces. Invisible intact faces generated a stronger signal than scrambled faces at 140-200 ms over posterior occipital areas whereas invisible fearful faces (compared to neutral and scrambled faces) elicited a significantly larger negative deflection starting at 220 ms along the STS. These results provide further evidence for cortical processing of facial information without awareness and elucidate the temporal sequence of automatic facial expression information extraction.

Steady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen

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Airoldi, Edoardo M.; Miller, Darach; Athanasiadou, Rodoniki; Brandt, Nathan; Abdul-Rahman, Farah; Neymotin, Benjamin; Hashimoto, Tatsu; Bahmani, Tayebeh; Gresham, David

2016-01-01

Cell growth rate is regulated in response to the abundance and molecular form of essential nutrients. In Saccharomyces cerevisiae (budding yeast), the molecular form of environmental nitrogen is a major determinant of cell growth rate, supporting growth rates that vary at least threefold. Transcriptional control of nitrogen use is mediated in large part by nitrogen catabolite repression (NCR), which results in the repression of specific transcripts in the presence of a preferred nitrogen source that supports a fast growth rate, such as glutamine, that are otherwise expressed in the presence of a nonpreferred nitrogen source, such as proline, which supports a slower growth rate. Differential expression of the NCR regulon and additional nitrogen-responsive genes results in >500 transcripts that are differentially expressed in cells growing in the presence of different nitrogen sources in batch cultures. Here we find that in growth rate–controlled cultures using nitrogen-limited chemostats, gene expression programs are strikingly similar regardless of nitrogen source. NCR expression is derepressed in all nitrogen-limiting chemostat conditions regardless of nitrogen source, and in these conditions, only 34 transcripts exhibit nitrogen source–specific differential gene expression. Addition of either the preferred nitrogen source, glutamine, or the nonpreferred nitrogen source, proline, to cells growing in nitrogen-limited chemostats results in rapid, dose-dependent repression of the NCR regulon. Using a novel means of computational normalization to compare global gene expression programs in steady-state and dynamic conditions, we find evidence that the addition of nitrogen to nitrogen-limited cells results in the transient overproduction of transcripts required for protein translation. Simultaneously, we find that that accelerated mRNA degradation underlies the rapid clearing of a subset of transcripts, which is most pronounced for the highly expressed NCR

A stochastic approach to multi-gene expression dynamics

International Nuclear Information System (INIS)

Ochiai, T.; Nacher, J.C.; Akutsu, T.

2005-01-01

In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of the cell functions. In this process, the correlation among genes is crucial to determine the specific functions of genes. Here, we propose a novel multi-dimensional stochastic approach to deal with the gene correlation phenomena. Interestingly, our stochastic framework suggests that the study of the gene correlation requires only one theoretical assumption-Markov property-and the experimental transition probability, which characterizes the gene correlation system. Finally, a gene expression experiment is proposed for future applications of the model

The Perception of Dynamic and Static Facial Expressions of Happiness and Disgust Investigated by ERPs and fMRI Constrained Source Analysis

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Trautmann-Lengsfeld, Sina Alexa; Domínguez-Borràs, Judith; Escera, Carles; Herrmann, Manfred; Fehr, Thorsten

2013-01-01

A recent functional magnetic resonance imaging (fMRI) study by our group demonstrated that dynamic emotional faces are more accurately recognized and evoked more widespread patterns of hemodynamic brain responses than static emotional faces. Based on this experimental design, the present study aimed at investigating the spatio-temporal processing of static and dynamic emotional facial expressions in 19 healthy women by means of multi-channel electroencephalography (EEG), event-related potentials (ERP) and fMRI-constrained regional source analyses. ERP analysis showed an increased amplitude of the LPP (late posterior positivity) over centro-parietal regions for static facial expressions of disgust compared to neutral faces. In addition, the LPP was more widespread and temporally prolonged for dynamic compared to static faces of disgust and happiness. fMRI constrained source analysis on static emotional face stimuli indicated the spatio-temporal modulation of predominantly posterior regional brain activation related to the visual processing stream for both emotional valences when compared to the neutral condition in the fusiform gyrus. The spatio-temporal processing of dynamic stimuli yielded enhanced source activity for emotional compared to neutral conditions in temporal (e.g., fusiform gyrus), and frontal regions (e.g., ventromedial prefrontal cortex, medial and inferior frontal cortex) in early and again in later time windows. The present data support the view that dynamic facial displays trigger more information reflected in complex neural networks, in particular because of their changing features potentially triggering sustained activation related to a continuing evaluation of those faces. A combined fMRI and EEG approach thus provides an advanced insight to the spatio-temporal characteristics of emotional face processing, by also revealing additional neural generators, not identifiable by the only use of an fMRI approach. PMID:23818974

Neural Substrates of Social Emotion Regulation: A fMRI Study on Imitation and Expressive Suppression to Dynamic Facial Signals

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Pascal eVrticka

2013-02-01

Full Text Available Emotion regulation is crucial for successfully engaging in social interactions. Yet, little is known about the neural mechanisms controlling behavioral responses to emotional expressions perceived in the face of other people, which constitute a key element of interpersonal communication. Here, we investigated brain systems involved in social emotion perception and regulation, using functional magnetic resonance imaging (fMRI in 20 healthy participants who saw dynamic facial expressions of either happiness or sadness, and were asked to either imitate the expression or to suppress any expression on their own face (in addition to a gender judgment control task. fMRI results revealed higher activity in regions associated with emotion (e.g., the insula, motor function (e.g., motor cortex, and theory of mind during imitation. Activity in dorsal cingulate cortex was also increased during imitation, possibly reflecting greater action monitoring or conflict with own feeling states. In addition, premotor regions were more strongly activated during both imitation and suppression, suggesting a recruitment of motor control for both the production and inhibition of emotion expressions. Expressive suppression produced increases in dorsolateral and lateral prefrontal cortex typically related to cognitive control. These results suggest that voluntary imitation and expressive suppression modulate brain responses to emotional signals perceived from faces, by up- and down-regulating activity in distributed subcortical and cortical networks that are particularly involved in emotion, action monitoring, and cognitive control.

Endogenous oxytocin levels are associated with the perception of emotion in dynamic body expressions in schizophrenia.

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Strauss, Gregory P; Keller, William R; Koenig, James I; Sullivan, Sara K; Gold, James M; Buchanan, Robert W

2015-03-01

Lower endogenous oxytocin levels have been associated with impaired social cognition in schizophrenia, particularly facial affect identification. Little is known about the relationship between oxytocin and other forms of emotion perception. In the current study, 41 individuals with schizophrenia (SZ) and 22 demographically matched healthy controls (CN) completed a forced-choice affective body expression classification task. Stimuli included dynamic videos of male and female actors portraying 4 discrete emotions: happiness, sadness, anger, and neutral. Plasma oxytocin levels were determined via radioimmunoassay. Results indicated that SZ had significantly higher plasma oxytocin concentrations than CN. SZ were also less accurate at identifying expressions of happiness and sadness; however, there were no group differences for anger or neutral stimuli. A group×sex interaction was also present, such that female CN were more accurate than male CN, whereas male SZ were more accurate than female SZ. Higher endogenous oxytocin levels were associated with better total recognition in both SZ and CN; this association was specific to females in SZ. Findings indicate that sex plays an important role in identifying emotional expressions in body gestures in SZ, and that individual differences in endogenous oxytocin predict emotion perception accuracy. Copyright © 2015 Elsevier B.V. All rights reserved.

Studying Dynamic Features in Myocardial Infarction Progression by Integrating miRNA-Transcription Factor Co-Regulatory Networks and Time-Series RNA Expression Data from Peripheral Blood Mononuclear Cells.

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Hongbo Shi

Full Text Available Myocardial infarction (MI is a serious heart disease and a leading cause of mortality and morbidity worldwide. Although some molecules (genes, miRNAs and transcription factors (TFs associated with MI have been studied in a specific pathological context, their dynamic characteristics in gene expressions, biological functions and regulatory interactions in MI progression have not been fully elucidated to date. In the current study, we analyzed time-series RNA expression data from peripheral blood mononuclear cells. We observed that significantly differentially expressed genes were sharply up- or down-regulated in the acute phase of MI, and then changed slowly until the chronic phase. Biological functions involved at each stage of MI were identified. Additionally, dynamic miRNA-TF co-regulatory networks were constructed based on the significantly differentially expressed genes and miRNA-TF co-regulatory motifs, and the dynamic interplay of miRNAs, TFs and target genes were investigated. Finally, a new panel of candidate diagnostic biomarkers (STAT3 and ICAM1 was identified to have discriminatory capability for patients with or without MI, especially the patients with or without recurrent events. The results of the present study not only shed new light on the understanding underlying regulatory mechanisms involved in MI progression, but also contribute to the discovery of true diagnostic biomarkers for MI.

Dynamic expression of leukocyte innate immune genes in whole blood from horses with lipopolysaccharide-induced acute systemic inflammation

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Vinther, Anne Mette L.; Skovgaard, Kerstin; Heegaard, Peter M. H.

2015-01-01

Background: In horses, insights into the innate immune processes in acute systemic inflammation are limited even though these processes may be highly important for future diagnostic and therapeutic advances in high-mortality disease conditions as the systemic inflammatory response syndrome (SIRS......) and sepsis. Therefore, the aim of this study was to investigate the expression of 31 selected blood leukocyte immune genes in an equine model of acute systemic inflammation to identify significantly regulated genes and to describe their expression dynamics during a 24-h experimental period. Systemic...... were compared with baseline levels. Results: Systemic inflammation was confirmed by the presence of clinical and hematological changes which were consistent with SIRS. The clinical response to LPS was transient and brief as all horses except one showed unaltered general demeanor after 24 h. Twenty...

An extended Kalman filtering approach to modeling nonlinear dynamic gene regulatory networks via short gene expression time series.

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Wang, Zidong; Liu, Xiaohui; Liu, Yurong; Liang, Jinling; Vinciotti, Veronica

2009-01-01

In this paper, the extended Kalman filter (EKF) algorithm is applied to model the gene regulatory network from gene time series data. The gene regulatory network is considered as a nonlinear dynamic stochastic model that consists of the gene measurement equation and the gene regulation equation. After specifying the model structure, we apply the EKF algorithm for identifying both the model parameters and the actual value of gene expression levels. It is shown that the EKF algorithm is an online estimation algorithm that can identify a large number of parameters (including parameters of nonlinear functions) through iterative procedure by using a small number of observations. Four real-world gene expression data sets are employed to demonstrate the effectiveness of the EKF algorithm, and the obtained models are evaluated from the viewpoint of bioinformatics.

The dynamics of gene expression changes in a mouse model of oral tumorigenesis may help refine prevention and treatment strategies in patients with oral cancer.

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Foy, Jean-Philippe; Tortereau, Antonin; Caulin, Carlos; Le Texier, Vincent; Lavergne, Emilie; Thomas, Emilie; Chabaud, Sylvie; Perol, David; Lachuer, Joël; Lang, Wenhua; Hong, Waun Ki; Goudot, Patrick; Lippman, Scott M; Bertolus, Chloé; Saintigny, Pierre

2016-06-14

A better understanding of the dynamics of molecular changes occurring during the early stages of oral tumorigenesis may help refine prevention and treatment strategies. We generated genome-wide expression profiles of microdissected normal mucosa, hyperplasia, dysplasia and tumors derived from the 4-NQO mouse model of oral tumorigenesis. Genes differentially expressed between tumor and normal mucosa defined the "tumor gene set" (TGS), including 4 non-overlapping gene subsets that characterize the dynamics of gene expression changes through different stages of disease progression. The majority of gene expression changes occurred early or progressively. The relevance of these mouse gene sets to human disease was tested in multiple datasets including the TCGA and the Genomics of Drug Sensitivity in Cancer project. The TGS was able to discriminate oral squamous cell carcinoma (OSCC) from normal oral mucosa in 3 independent datasets. The OSCC samples enriched in the mouse TGS displayed high frequency of CASP8 mutations, 11q13.3 amplifications and low frequency of PIK3CA mutations. Early changes observed in the 4-NQO model were associated with a trend toward a shorter oral cancer-free survival in patients with oral preneoplasia that was not seen in multivariate analysis. Progressive changes observed in the 4-NQO model were associated with an increased sensitivity to 4 different MEK inhibitors in a panel of 51 squamous cell carcinoma cell lines of the areodigestive tract. In conclusion, the dynamics of molecular changes in the 4-NQO model reveal that MEK inhibition may be relevant to prevention and treatment of a specific molecularly-defined subgroup of OSCC.

Perceiving and producing facial expressions of emotion : The role of dynamic expressions and culture

NARCIS (Netherlands)

Fang, X.

2018-01-01

We spend much of our waking lives interacting with other people, reading their facial expressions to figure out what they might be feeling, thinking, or intending to do next (Ekman 1994; Fridlund 1994). At the same time, we also express our own feelings, thoughts, and intentions through facial

Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge Sycon ciliatum.

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Bråte, Jon; Adamski, Marcin; Neumann, Ralf S; Shalchian-Tabrizi, Kamran; Adamska, Maja

2015-12-22

Long non-coding RNAs (lncRNAs) play important regulatory roles during animal development, and it has been hypothesized that an RNA-based gene regulation was important for the evolution of developmental complexity in animals. However, most studies of lncRNA gene regulation have been performed using model animal species, and very little is known about this type of gene regulation in non-bilaterians. We have therefore analysed RNA-Seq data derived from a comprehensive set of embryogenesis stages in the calcareous sponge Sycon ciliatum and identified hundreds of developmentally expressed intergenic lncRNAs (lincRNAs) in this species. In situ hybridization of selected lincRNAs revealed dynamic spatial and temporal expression during embryonic development. More than 600 lincRNAs constitute integral parts of differentially expressed gene modules, which also contain known developmental regulatory genes, e.g. transcription factors and signalling molecules. This study provides insights into the non-coding gene repertoire of one of the earliest evolved animal lineages, and suggests that RNA-based gene regulation was probably present in the last common ancestor of animals. © 2015 The Authors.

A glycogene mutation map for discovery of diseases of glycosylation

DEFF Research Database (Denmark)

Hansen, Lars; Lind-Thomsen, Allan; Joshi, Hiren J

2015-01-01

homologous families. However, Genome-Wide-Association Studies (GWAS) have identified such isoenzyme genes as candidates for different diseases, but validation is not straightforward without biomarkers. Large-scale whole exome sequencing (WES) provides access to mutations in e.g. glycosyltransferase genes...... in populations, which can be used to predict and/or analyze functional deleterious mutations. Here, we constructed a draft of a Functional Mutational Map of glycogenes, GlyMAP, from WES of a rather homogenous population of 2,000 Danes. We catalogued all missense mutations and used prediction algorithms, manual...... inspection, and in case of CAZy family GT27 experimental analysis of mutations to map deleterious mutations. GlyMAP provides a first global view of the genetic stability of the glycogenome and should serve as a tool for discovery of novel CDGs....

A Novel Dynamic Model Describing the Spread of the MERS-CoV and the Expression of Dipeptidyl Peptidase 4

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Siming Tang

2017-01-01

Full Text Available The Middle East respiratory syndrome (MERS coronavirus, a newly identified pathogen, causes severe pneumonia in humans. MERS is caused by a coronavirus known as MERS-CoV, which attacks the respiratory system. The recently defined receptor for MERS-CoV, dipeptidyl peptidase 4 (DPP4, is generally expressed in endothelial and epithelial cells and has been shown to be present on cultured human nonciliated bronchiolar epithelium cells. In this paper, a class of novel four-dimensional dynamic model describing the infection of MERS-CoV is given, and then global stability of the equilibria of the model is discussed. Our results show that the spread of MERS-CoV can also be controlled by decreasing the expression rate of DPP4.

Temporal expression-based analysis of metabolism.

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Sara B Collins

Full Text Available Metabolic flux is frequently rerouted through cellular metabolism in response to dynamic changes in the intra- and extra-cellular environment. Capturing the mechanisms underlying these metabolic transitions in quantitative and predictive models is a prominent challenge in systems biology. Progress in this regard has been made by integrating high-throughput gene expression data into genome-scale stoichiometric models of metabolism. Here, we extend previous approaches to perform a Temporal Expression-based Analysis of Metabolism (TEAM. We apply TEAM to understanding the complex metabolic dynamics of the respiratorily versatile bacterium Shewanella oneidensis grown under aerobic, lactate-limited conditions. TEAM predicts temporal metabolic flux distributions using time-series gene expression data. Increased predictive power is achieved by supplementing these data with a large reference compendium of gene expression, which allows us to take into account the unique character of the distribution of expression of each individual gene. We further propose a straightforward method for studying the sensitivity of TEAM to changes in its fundamental free threshold parameter θ, and reveal that discrete zones of distinct metabolic behavior arise as this parameter is changed. By comparing the qualitative characteristics of these zones to additional experimental data, we are able to constrain the range of θ to a small, well-defined interval. In parallel, the sensitivity analysis reveals the inherently difficult nature of dynamic metabolic flux modeling: small errors early in the simulation propagate to relatively large changes later in the simulation. We expect that handling such "history-dependent" sensitivities will be a major challenge in the future development of dynamic metabolic-modeling techniques.

Dynamics of hepatic gene expression and serum cytokine profiles in single and double-hit burn and sepsis animal models

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Rohit Rao

2015-06-01

Full Text Available We simulate the pathophysiology of severe burn trauma and burn-induced sepsis, using rat models of experimental burn injury and cecal ligation and puncture (CLP either individually (singe-hit model or in combination (double-hit model. The experimental burn injury simulates a systemic but sterile pro-inflammatory response, while the CLP simulates the effect of polymicrobial sepsis. Given the liver׳s central role in mediating the host immune response and onset of hypermetabolism after burn injury, elucidating the alterations in hepatic gene expression in response to injury can lead to a better understanding of the regulation of the inflammatory response, whereas circulating cytokine protein expression, reflects key systemic inflammatory mediators. In this article, we present both the hepatic gene expression and circulating cytokine/chemokine protein expression data for the above-mentioned experimental model to gain insights into the temporal dynamics of the inflammatory and hypermetabolic response following burn and septic injury. This data article supports results discussed in research articles (Yang et al., 2012 [1,4]; Mattick et al. 2012, 2013 [2,3]; Nguyen et al., 2014 [5]; Orman et al., 2011, 2012 [6–8].

A model of gene expression based on random dynamical systems reveals modularity properties of gene regulatory networks.

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Antoneli, Fernando; Ferreira, Renata C; Briones, Marcelo R S

2016-06-01

Here we propose a new approach to modeling gene expression based on the theory of random dynamical systems (RDS) that provides a general coupling prescription between the nodes of any given regulatory network given the dynamics of each node is modeled by a RDS. The main virtues of this approach are the following: (i) it provides a natural way to obtain arbitrarily large networks by coupling together simple basic pieces, thus revealing the modularity of regulatory networks; (ii) the assumptions about the stochastic processes used in the modeling are fairly general, in the sense that the only requirement is stationarity; (iii) there is a well developed mathematical theory, which is a blend of smooth dynamical systems theory, ergodic theory and stochastic analysis that allows one to extract relevant dynamical and statistical information without solving the system; (iv) one may obtain the classical rate equations form the corresponding stochastic version by averaging the dynamic random variables (small noise limit). It is important to emphasize that unlike the deterministic case, where coupling two equations is a trivial matter, coupling two RDS is non-trivial, specially in our case, where the coupling is performed between a state variable of one gene and the switching stochastic process of another gene and, hence, it is not a priori true that the resulting coupled system will satisfy the definition of a random dynamical system. We shall provide the necessary arguments that ensure that our coupling prescription does indeed furnish a coupled regulatory network of random dynamical systems. Finally, the fact that classical rate equations are the small noise limit of our stochastic model ensures that any validation or prediction made on the basis of the classical theory is also a validation or prediction of our model. We illustrate our framework with some simple examples of single-gene system and network motifs. Copyright © 2016 Elsevier Inc. All rights reserved.

Dynamic gene expression in fish muscle during recovery growth induced by a fasting-refeeding schedule

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Esquerré Diane

2007-11-01

Full Text Available Abstract Background Recovery growth is a phase of rapid growth that is triggered by adequate refeeding of animals following a period of weight loss caused by starvation. In this study, to obtain more information on the system-wide integration of recovery growth in muscle, we undertook a time-course analysis of transcript expression in trout subjected to a food deprivation-refeeding sequence. For this purpose complex targets produced from muscle of trout fasted for one month and from muscle of trout fasted for one month and then refed for 4, 7, 11 and 36 days were hybridized to cDNA microarrays containing 9023 clones. Results Significance analysis of microarrays (SAM and temporal expression profiling led to the segregation of differentially expressed genes into four major clusters. One cluster comprising 1020 genes with high expression in muscle from fasted animals included a large set of genes involved in protein catabolism. A second cluster that included approximately 550 genes with transient induction 4 to 11 days post-refeeding was dominated by genes involved in transcription, ribosomal biogenesis, translation, chaperone activity, mitochondrial production of ATP and cell division. A third cluster that contained 480 genes that were up-regulated 7 to 36 days post-refeeding was enriched with genes involved in reticulum and Golgi dynamics and with genes indicative of myofiber and muscle remodelling such as genes encoding sarcomeric proteins and matrix compounds. Finally, a fourth cluster of 200 genes overexpressed only in 36-day refed trout muscle contained genes with function in carbohydrate metabolism and lipid biosynthesis. Remarkably, among the genes induced were several transcriptional regulators which might be important for the gene-specific transcriptional adaptations that underlie muscle recovery. Conclusion Our study is the first demonstration of a coordinated expression of functionally related genes during muscle recovery growth

Gaze Dynamics in the Recognition of Facial Expressions of Emotion.

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Barabanschikov, Vladimir A

2015-01-01

We studied preferably fixated parts and features of human face in the process of recognition of facial expressions of emotion. Photographs of facial expressions were used. Participants were to categorize these as basic emotions; during this process, eye movements were registered. It was found that variation in the intensity of an expression is mirrored in accuracy of emotion recognition; it was also reflected by several indices of oculomotor function: duration of inspection of certain areas of the face, its upper and bottom or right parts, right and left sides; location, number and duration of fixations, viewing trajectory. In particular, for low-intensity expressions, right side of the face was found to be attended predominantly (right-side dominance); the right-side dominance effect, was, however, absent for expressions of high intensity. For both low- and high-intensity expressions, upper face part was predominantly fixated, though with greater fixation of high-intensity expressions. The majority of trials (70%), in line with findings in previous studies, revealed a V-shaped pattern of inspection trajectory. No relationship, between accuracy of recognition of emotional expressions, was found, though, with either location and duration of fixations or pattern of gaze directedness in the face. © The Author(s) 2015.

Exaggerated perception of facial expressions is increased in individuals with schizotypal traits.

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Uono, Shota; Sato, Wataru; Toichi, Motomi

2015-07-02

Emotional facial expressions are indispensable communicative tools, and social interactions involving facial expressions are impaired in some psychiatric disorders. Recent studies revealed that the perception of dynamic facial expressions was exaggerated in normal participants, and this exaggerated perception is weakened in autism spectrum disorder (ASD). Based on the notion that ASD and schizophrenia spectrum disorder are at two extremes of the continuum with respect to social impairment, we hypothesized that schizophrenic characteristics would strengthen the exaggerated perception of dynamic facial expressions. To test this hypothesis, we investigated the relationship between the perception of facial expressions and schizotypal traits in a normal population. We presented dynamic and static facial expressions, and asked participants to change an emotional face display to match the perceived final image. The presence of schizotypal traits was positively correlated with the degree of exaggeration for dynamic, as well as static, facial expressions. Among its subscales, the paranoia trait was positively correlated with the exaggerated perception of facial expressions. These results suggest that schizotypal traits, specifically the tendency to over-attribute mental states to others, exaggerate the perception of emotional facial expressions.

Dynamic pattern of endothelial cell adhesion molecule expression in muscle and perineural vessels from patients with classic polyarteritis nodosa.

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Coll-Vinent, B; Cebrián, M; Cid, M C; Font, C; Esparza, J; Juan, M; Yagüe, J; Urbano-Márquez, A; Grau, J M

1998-03-01

To investigate endothelial cell adhesion molecule expression in vessels from patients with classic polyarteritis nodosa (PAN). Frozen sections of 21 muscle and 16 nerve samples from 30 patients with biopsy-proven PAN and 12 histologically normal muscle and 2 histologically normal nerve samples from 12 controls were studied immunohistochemically, using specific monoclonal antibodies (MAb) that recognize adhesion molecules. Adhesion molecules identified were intercellular adhesion molecule 1 (ICAM-1), ICAM-2, ICAM-3, vascular cell adhesion molecule 1 (VCAM-1), platelet endothelial cell adhesion molecule 1 (PECAM-1), E-selectin, P-selectin, L-selectin, lymphocyte function-associated antigen 1 (LFA-1), and very late activation antigen 4 (VLA-4). Neutrophils were identified with a MAb recognizing neutrophil elastase. Endothelial cells were identified with the lectin ulex europaeus. In early lesions, expression of PECAM-1, ICAM-1, ICAM-2, and P-selectin was similar to that in control samples, and VCAM-1 and E-selectin were induced in vascular endothelium. In advanced lesions, immunostaining for adhesion molecules diminished or disappeared in luminal endothelium, whereas these molecules were clearly expressed in microvessels within and surrounding inflamed vessels. Staining in endothelia from vessels in a healing stage tended to be negative. A high proportion of infiltrating leukocytes expressed LFA-1 and VLA-4, and only a minority expressed L-selectin. No relationship between the expression pattern of adhesion molecules and clinical features, disease duration, or previous corticosteroid treatment was observed. Endothelial adhesion molecule expression in PAN is a dynamic process that varies according to the histopathologic stage of the vascular lesions. The preferential expression of constitutive and inducible adhesion molecules in microvessels suggests that angiogenesis contributes to the persistence of inflammatory infiltration in PAN.

P2-35: The KU Facial Expression Database: A Validated Database of Emotional and Conversational Expressions

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Haenah Lee

2012-10-01

Full Text Available Facial expressions are one of the most important means of nonverbal communication transporting both emotional and conversational content. For investigating this large space of expressions we recently developed a large database containing dynamic emotional and conversational expressions in Germany (MPI facial expression database. As facial expressions crucially depend on the cultural context, however, a similar resource is needed for studies outside of Germany. Here, we introduce and validate a new, extensive Korean facial expression database containing dynamic emotional and conversational information. Ten individuals performed 62 expressions following a method-acting protocol, in which each person was asked to imagine themselves in one of 62 corresponding everyday scenarios and to react accordingly. To validate this database, we conducted two experiments: 20 participants were asked to name the appropriate expression for each of the 62 everyday scenarios shown as text. Ten additional participants were asked to name each of the 62 expression videos from 10 actors in addition to rating its naturalness. All naming answers were then rated as valid or invalid. Scenario validation yielded 89% valid answers showing that the scenarios are effective in eliciting appropriate expressions. Video sequences were judged as natural with an average of 66% valid answers. This is an excellent result considering that videos were seen without any conversational context and that 62 expressions were to be recognized. These results validate our Korean database and, as they also parallel the German validation results, will enable detailed cross-cultural comparisons of the complex space of emotional and conversational expressions.

Calsyntenins Are Expressed in a Dynamic and Partially Overlapping Manner during Neural Development

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Gemma de Ramon Francàs

2017-08-01

Full Text Available Calsyntenins form a family of linker proteins between distinct populations of vesicles and kinesin motors for axonal transport. They were implicated in synapse formation and synaptic plasticity by findings in worms, mice and humans. These findings were in accordance with the postsynaptic localization of the Calsyntenins in the adult brain. However, they also affect the formation of neural circuits, as loss of Calsyntenin-1 (Clstn1 was shown to interfere with axonal branching and axon guidance. Despite the fact that Calsyntenins were discovered originally in embryonic chicken motoneurons, their distribution in the developing nervous system has not been analyzed in detail so far. Here, we summarize our analysis of the temporal and spatial expression patterns of the cargo-docking proteins Clstn1, Clstn2 and Clstn3 during neural development by comparing the dynamic distribution of their mRNAs by in situ hybridization in the spinal cord, the cerebellum, the retina and the tectum, as well as in the dorsal root ganglia (DRG.

Analysis of the dynamic co-expression network of heart regeneration in the zebrafish

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Rodius, Sophie; Androsova, Ganna; Götz, Lou; Liechti, Robin; Crespo, Isaac; Merz, Susanne; Nazarov, Petr V.; de Klein, Niek; Jeanty, Céline; González-Rosa, Juan M.; Muller, Arnaud; Bernardin, Francois; Niclou, Simone P.; Vallar, Laurent; Mercader, Nadia; Ibberson, Mark; Xenarios, Ioannis; Azuaje, Francisco

2016-05-01

The zebrafish has the capacity to regenerate its heart after severe injury. While the function of a few genes during this process has been studied, we are far from fully understanding how genes interact to coordinate heart regeneration. To enable systematic insights into this phenomenon, we generated and integrated a dynamic co-expression network of heart regeneration in the zebrafish and linked systems-level properties to the underlying molecular events. Across multiple post-injury time points, the network displays topological attributes of biological relevance. We show that regeneration steps are mediated by modules of transcriptionally coordinated genes, and by genes acting as network hubs. We also established direct associations between hubs and validated drivers of heart regeneration with murine and human orthologs. The resulting models and interactive analysis tools are available at http://infused.vital-it.ch. Using a worked example, we demonstrate the usefulness of this unique open resource for hypothesis generation and in silico screening for genes involved in heart regeneration.

Violent Media Consumption and the Recognition of Dynamic Facial Expressions

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Kirsh, Steven J.; Mounts, Jeffrey R. W.; Olczak, Paul V.

2006-01-01

This study assessed the speed of recognition of facial emotional expressions (happy and angry) as a function of violent media consumption. Color photos of calm facial expressions morphed to either an angry or a happy facial expression. Participants were asked to make a speeded identification of the emotion (happiness or anger) during the morph.…

Microarray Gene Expression Analysis of Murine Tumor Heterogeneity Defined by Dynamic Contrast-Enhanced MRI

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Nick G. Costouros

2002-07-01

Full Text Available Current methods of studying angiogenesis are limited in their ability to serially evaluate in vivo function throughout a target tissue. Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI and pharmacokinetic modeling provide a useful method for evaluating tissue vasculature based on contrast accumulation and washout. While it is often assumed that areas of high contrast enhancement and washout comprise areas of increased angiogenesis and tumor activity, the actual molecular pathways that are active in such areas are poorly understood. Using DCE-MRI in a murine subcutaneous tumor model, we were able to perform pharmacokinetic functional analysis of a tumor, coregistration of MRI images with histological cross-sections, immunohistochemistry, laser capture microdissection, and genetic profiling of tumor heterogeneity based on pharmacokinetic parameters. Using imaging as a template for biologic investigation, we have not found evidence of increased expression of proangiogenic modulators at the transcriptional level in either distinct pharmacokinetic region. Furthermore, these regions show no difference on histology and CD31 immunohistochemistry. However, the expression of ribosomal proteins was greatly increased in high enhancement and washout regions, implying increased protein translation and consequent increased cellular activity. Together, these findings point to the potential importance of posttranscriptional regulation in angiogenesis and the need for the development of angiogenesis-specific contrast agents to evaluate in vivo angiogenesis at a molecular level.

Dynamic CRM occupancy reflects a temporal map of developmental progression.

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Wilczyński, Bartek; Furlong, Eileen E M

2010-06-22

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

Modelling multimodal expression of emotion in a virtual agent.

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Pelachaud, Catherine

2009-12-12

Over the past few years we have been developing an expressive embodied conversational agent system. In particular, we have developed a model of multimodal behaviours that includes dynamism and complex facial expressions. The first feature refers to the qualitative execution of behaviours. Our model is based on perceptual studies and encompasses several parameters that modulate multimodal behaviours. The second feature, the model of complex expressions, follows a componential approach where a new expression is obtained by combining facial areas of other expressions. Lately we have been working on adding temporal dynamism to expressions. So far they have been designed statically, typically at their apex. Only full-blown expressions could be modelled. To overcome this limitation, we have defined a representation scheme that describes the temporal evolution of the expression of an emotion. It is no longer represented by a static definition but by a temporally ordered sequence of multimodal signals.

Gene Expression Commons: an open platform for absolute gene expression profiling.

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Jun Seita

Full Text Available Gene expression profiling using microarrays has been limited to comparisons of gene expression between small numbers of samples within individual experiments. However, the unknown and variable sensitivities of each probeset have rendered the absolute expression of any given gene nearly impossible to estimate. We have overcome this limitation by using a very large number (>10,000 of varied microarray data as a common reference, so that statistical attributes of each probeset, such as the dynamic range and threshold between low and high expression, can be reliably discovered through meta-analysis. This strategy is implemented in a web-based platform named "Gene Expression Commons" (https://gexc.stanford.edu/ which contains data of 39 distinct highly purified mouse hematopoietic stem/progenitor/differentiated cell populations covering almost the entire hematopoietic system. Since the Gene Expression Commons is designed as an open platform, investigators can explore the expression level of any gene, search by expression patterns of interest, submit their own microarray data, and design their own working models representing biological relationship among samples.

Person perception from changing emotional expressions: primacy, recency, or averaging effect?

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Fang, Xia; van Kleef, Gerben A; Sauter, Disa A

2018-02-01

Dynamic changes in emotional expressions are a valuable source of information in social interactions. As the expressive behaviour of a person changes, the inferences drawn from the behaviour may also change. Here, we test the possibility that dynamic changes in emotional expressions affect person perception in terms of stable trait attributions. Across three experiments, we examined perceivers' inferences about others' personality traits from changing emotional expressions. Expressions changed from one emotion ("start emotion") to another emotion ("end emotion"), allowing us to disentangle potential primacy, recency, and averaging effects. Drawing on three influential models of person perception, we examined perceptions of dominance and affiliation (Experiment 1a), competence and warmth (Experiment 1b), and dominance and trustworthiness (Experiment 2). A strong recency effect was consistently found across all trait judgments, that is, the end emotion of dynamic expressions had a strong impact on trait ratings. Evidence for a primacy effect was also observed (i.e. the information of start emotions was integrated), but less pronounced, and only for trait ratings relating to affiliation, warmth, and trustworthiness. Taken together, these findings suggest that, when making trait judgements about others, observers weigh the most recently displayed emotion in dynamic expressions more heavily than the preceding emotion.

Peri-dynamics

International Nuclear Information System (INIS)

Littlewood, D.

2015-01-01

Peri-dynamics, a nonlocal extension of continuum mechanics, is a natural framework for capturing constitutive response and modelling pervasive material failure and fracture. Unlike classical approaches incorporating partial derivatives, the peri-dynamic governing equations utilise integral expressions that remain valid in the presence of discontinuities such as cracks. The mathematical theory of peri-dynamics unifies the mechanics of continuous media, cracks, and discrete particles. The result is a consistent framework for capturing a wide range of constitutive responses, including inelasticity, in combination with robust material failure laws. Peri-dynamics has been implemented in a number of computational simulation codes, including the open source code Peridigm and the Sierra/SolidMechanics analysis code at Sandia National Laboratories. (author)

Spatial expression dynamics of Men-9 delineate the third floral whorl in male and female flowers of dioecious Silene latifolia.

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Robertson, S E; Li, Y; Scutt, C P; Willis, M E; Gilmartin, P M

1997-07-01

Sex determination in Silene latifolia is controlled by heteromorphic sex chromosomes. Female flowers have five fused carpels and ten arrested stamen primordia. The male-determining Y chromosome overrides female development to suppress carpel formation and promote stamen development. The isolation and characterization of two S. latifolia. Male enhanced cDNAs, Men-9a and Men-9b, which probably represent different alleles of a novel gene are reported here. Men-9a and Men-9b share 91.8% coding sequence nucleotide identity, yet only 85.4% amino acid identity. The Men-9 cDNAs are related to the previously reported MROS3 cDNA from S. latifolia. However, MROS3 is not present in the S. latifolia population used in these studies and the expression dynamics of Men-9a and Men-9b contrast dramatically with those reported for MROS3. Men-9 cDNAs are expressed primarily in anthers of young male flowers, with highest expression in 1-2 mm buds. Men-9 expression is also observed at a low level in female flowers. In situ hybridization analysis reveals two phases of Men-9 expression. The first phase is during a common stage of early stamen development in male and female flowers prior to stamen arrest in female flowers. The second phase of Men-9 expression is maximal in the epidermis and endothecium of Y chromosome- and Ustilago violacea-induced stamens; expression in male and female flowers extends to the epidermis of the staminal nectaries with strict boundaries at the second and fourth whorls, Men-9 gene expression therefore delineates the boundaries of the third floral whorl in S. latifolia flowers.

Dynamized Preparations in Cell Culture

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Ellanzhiyil Surendran Sunila

2009-01-01

Full Text Available Although reports on the efficacy of homeopathic medicines in animal models are limited, there are even fewer reports on the in vitro action of these dynamized preparations. We have evaluated the cytotoxic activity of 30C and 200C potencies of ten dynamized medicines against Dalton's Lymphoma Ascites, Ehrlich's Ascites Carcinoma, lung fibroblast (L929 and Chinese Hamster Ovary (CHO cell lines and compared activity with their mother tinctures during short-term and long-term cell culture. The effect of dynamized medicines to induce apoptosis was also evaluated and we studied how dynamized medicines affected genes expressed during apoptosis. Mother tinctures as well as some dynamized medicines showed significant cytotoxicity to cells during short and long-term incubation. Potentiated alcohol control did not produce any cytotoxicity at concentrations studied. The dynamized medicines were found to inhibit CHO cell colony formation and thymidine uptake in L929 cells and those of Thuja, Hydrastis and Carcinosinum were found to induce apoptosis in DLA cells. Moreover, dynamized Carcinosinum was found to induce the expression of p53 while dynamized Thuja produced characteristic laddering pattern in agarose gel electrophoresis of DNA. These results indicate that dynamized medicines possess cytotoxic as well as apoptosis-inducing properties.

Characterization of big bang, a novel gene encoding for PDZ domain-containing proteins that are dynamically expressed throughout Drosophila development.

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Kim, Sabrina Y; Renihan, Maia K; Boulianne, Gabrielle L

2006-06-01

PDZ (PSD-95, Discs-large, ZO-1) domain proteins often function as scaffolding proteins and have been shown to play important roles in diverse cellular processes such as the establishment and maintenance of cell polarity, and signal transduction. Here, we report the identification and cloning of a novel Drosophila melanogaster gene that is predicted to produce several different PDZ domain-containing proteins through alternative promoter usage and alternative splicing. This gene, that we have named big bang (bbg), was first identified as C96-GAL4, a GAL4 enhancer trap line that was generated in our lab. To further characterize bbg, its expression pattern was examined in ovaries, embryos, and late third instar larvae using UAS reporter gene constructs, in situ hybridization, or immunocytochemistry. In addition, the expression of alternatively spliced transcripts was examined in more detail using in situ hybridization. We find that during embryogenesis bbg is predominantly expressed in the developing gut, but it is also expressed in external sensory organs found in the epidermis. In the late third instar larva, bbg is expressed along the presumptive wing margin in the wing disc, broadly in the eye disc, and in other imaginal discs as well as in the brain. The expression patterns observed are dynamic and specific during development, suggesting that like other genes that encode for several different PDZ domain protein isoforms, bbg likely plays important roles in multiple developmental processes.

Dynamic stiffness of suction caissons

DEFF Research Database (Denmark)

Ibsen, Lars Bo; Liingaard, Morten; Andersen, Lars

The purpose of this report is to evaluate the dynamic soil-structure interaction of suction caissons for offshore wind turbines. The investigation is limited to a determination of the vertical dynamic stiffness of suction caissons. The soil surrounding the foundation is homogenous with linear...... viscoelastic properties. The dynamic stiffness of the suction caisson is expressed by dimensionless frequency-dependent dynamic stiffness coefficients corresponding to the vertical degree of freedom. The dynamic stiffness coefficients for the foundations are evaluated by means of a dynamic three...

Phage exposure causes dynamic shifts in the expression states of specific phase-variable genes of Campylobacter jejuni

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Aidley, Jack; Holst Sørensen, Martine C.; Bayliss, Christopher D.

2017-01-01

Phase variation (PV) creates phenotypic heterogeneity at high frequencies and in a reversible manner. This phenomenon allows bacteria to adapt to a variety of different environments and selective pressures. In Campylobacter jejuni this reversible adaptive process is mediated by mutations in homop......Phase variation (PV) creates phenotypic heterogeneity at high frequencies and in a reversible manner. This phenomenon allows bacteria to adapt to a variety of different environments and selective pressures. In Campylobacter jejuni this reversible adaptive process is mediated by mutations...... in homopolymeric G/C tracts. Many C. jejuni-specific phages are dependent on phase-variable surface structures for successful infection. We previously identified the capsular polysaccharide (CPS) moiety, MeOPN-GalfNAc, as a receptor for phage F336 and showed that phase-variable expression of the transferase...... for this CPS modification, cj1421, and two other phase-variable CPS genes generated phage resistance in C. jejuni. Here we investigate the population dynamics of C. jejuni NCTC11168 when exposed to phage F336 in vitro using a newly described method - the 28-locus-CJ11168 PV analysis. Dynamic switching...

Dynamics of Hippocampal Protein Expression During Long-term Spatial Memory Formation*

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Borovok, Natalia; Nesher, Elimelech; Levin, Yishai; Reichenstein, Michal; Pinhasov, Albert

2016-01-01

Spatial memory depends on the hippocampus, which is particularly vulnerable to aging. This vulnerability has implications for the impairment of navigation capacities in older people, who may show a marked drop in performance of spatial tasks with advancing age. Contemporary understanding of long-term memory formation relies on molecular mechanisms underlying long-term synaptic plasticity. With memory acquisition, activity-dependent changes occurring in synapses initiate multiple signal transduction pathways enhancing protein turnover. This enhancement facilitates de novo synthesis of plasticity related proteins, crucial factors for establishing persistent long-term synaptic plasticity and forming memory engrams. Extensive studies have been performed to elucidate molecular mechanisms of memory traces formation; however, the identity of plasticity related proteins is still evasive. In this study, we investigated protein turnover in mouse hippocampus during long-term spatial memory formation using the reference memory version of radial arm maze (RAM) paradigm. We identified 1592 proteins, which exhibited a complex picture of expression changes during spatial memory formation. Variable linear decomposition reduced significantly data dimensionality and enriched three principal factors responsible for variance of memory-related protein levels at (1) the initial phase of memory acquisition (165 proteins), (2) during the steep learning improvement (148 proteins), and (3) the final phase of the learning curve (123 proteins). Gene ontology and signaling pathways analysis revealed a clear correlation between memory improvement and learning phase-curbed expression profiles of proteins belonging to specific functional categories. We found differential enrichment of (1) neurotrophic factors signaling pathways, proteins regulating synaptic transmission, and actin microfilament during the first day of the learning curve; (2) transcription and translation machinery, protein

Dynamics of Hippocampal Protein Expression During Long-term Spatial Memory Formation.

Science.gov (United States)

Borovok, Natalia; Nesher, Elimelech; Levin, Yishai; Reichenstein, Michal; Pinhasov, Albert; Michaelevski, Izhak

2016-02-01

Spatial memory depends on the hippocampus, which is particularly vulnerable to aging. This vulnerability has implications for the impairment of navigation capacities in older people, who may show a marked drop in performance of spatial tasks with advancing age. Contemporary understanding of long-term memory formation relies on molecular mechanisms underlying long-term synaptic plasticity. With memory acquisition, activity-dependent changes occurring in synapses initiate multiple signal transduction pathways enhancing protein turnover. This enhancement facilitates de novo synthesis of plasticity related proteins, crucial factors for establishing persistent long-term synaptic plasticity and forming memory engrams. Extensive studies have been performed to elucidate molecular mechanisms of memory traces formation; however, the identity of plasticity related proteins is still evasive. In this study, we investigated protein turnover in mouse hippocampus during long-term spatial memory formation using the reference memory version of radial arm maze (RAM) paradigm. We identified 1592 proteins, which exhibited a complex picture of expression changes during spatial memory formation. Variable linear decomposition reduced significantly data dimensionality and enriched three principal factors responsible for variance of memory-related protein levels at (1) the initial phase of memory acquisition (165 proteins), (2) during the steep learning improvement (148 proteins), and (3) the final phase of the learning curve (123 proteins). Gene ontology and signaling pathways analysis revealed a clear correlation between memory improvement and learning phase-curbed expression profiles of proteins belonging to specific functional categories. We found differential enrichment of (1) neurotrophic factors signaling pathways, proteins regulating synaptic transmission, and actin microfilament during the first day of the learning curve; (2) transcription and translation machinery, protein

Diverse Soil Carbon Dynamics Expressed at the Molecular Level

Science.gov (United States)

van der Voort, T. S.; Zell, C. I.; Hagedorn, F.; Feng, X.; McIntyre, C. P.; Haghipour, N.; Graf Pannatier, E.; Eglinton, T. I.

2017-12-01

The stability and potential vulnerability of soil organic matter (SOM) to global change remain incompletely understood due to the complex processes involved in its formation and turnover. Here we combine compound-specific radiocarbon analysis with fraction-specific and bulk-level radiocarbon measurements in order to further elucidate controls on SOM dynamics in a temperate and subalpine forested ecosystem. Radiocarbon contents of individual organic compounds isolated from the same soil interval generally exhibit greater variation than those among corresponding operationally defined fractions. Notably, markedly older ages of long-chain plant leaf wax lipids (n-alkanoic acids) imply that they reflect a highly stable carbon pool. Furthermore, marked 14C variations among shorter- and longer-chain n-alkanoic acid homologues suggest that they track different SOM pools. Extremes in SOM dynamics thus manifest themselves within a single compound class. This exploratory study highlights the potential of compound-specific radiocarbon analysis for understanding SOM dynamics in ecosystems potentially vulnerable to global change.

Sequential dynamics of culturally moderated facial expressions of emotion.

Science.gov (United States)

Matsumoto, David; Willingham, Bob; Olide, Andres

2009-10-01

There is consensus that when emotions are aroused, the displays of those emotions are either universal or culture-specific. We investigated the idea that an individual's emotional displays in a given context can be both universal and culturally variable, as they change over time. We examined the emotional displays of Olympic athletes across time, classified their expressive styles, and tested the association between those styles and a number of characteristics associated with the countries the athletes represented. Athletes from relatively urban, individualistic cultures expressed their emotions more, whereas athletes from less urban, collectivistic cultures masked their emotions more. These culturally influenced expressions occurred within a few seconds after initial, immediate, and universal emotional displays. Thus, universal and culture-specific emotional displays can unfold across time in an individual in a single context.

Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in Paramecium tetraurelia.

Science.gov (United States)

Cheaib, Miriam; Dehghani Amirabad, Azim; Nordström, Karl J V; Schulz, Marcel H; Simon, Martin

2015-08-01

Phenotypic variation of a single genotype is achieved by alterations in gene expression patterns. Regulation of such alterations depends on their time scale, where short-time adaptations differ from permanently established gene expression patterns maintained by epigenetic mechanisms. In the ciliate Paramecium, serotypes were described for an epigenetically controlled gene expression pattern of an individual multigene family. Paradoxically, individual serotypes can be triggered in Paramecium by alternating environments but are then stabilized by epigenetic mechanisms, thus raising the question to which extend their expression follows environmental stimuli. To characterize environmental adaptation in the context of epigenetically controlled serotype expression, we used RNA-seq to characterize transcriptomes of serotype pure cultures. The resulting vegetative transcriptome resource is first analysed for genes involved in the adaptive response to the altered environment. Secondly, we identified groups of genes that do not follow the adaptive response but show co-regulation with the epigenetically controlled serotype system, suggesting that their gene expression pattern becomes manifested by similar mechanisms. In our experimental set-up, serotype expression and the entire group of co-regulated genes were stable among environmental changes and only heat-shock genes altered expression of these gene groups. The data suggest that the maintenance of these gene expression patterns in a lineage represents epigenetically controlled robustness counteracting short-time adaptation processes. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Facial Expressivity at 4 Months: A Context by Expression Analysis.

Science.gov (United States)

Bennett, David S; Bendersky, Margaret; Lewis, Michael

2002-01-01

The specificity predicted by differential emotions theory (DET) for early facial expressions in response to 5 different eliciting situations was studied in a sample of 4-month-old infants (n = 150). Infants were videotaped during tickle, sour taste, jack-in-the-box, arm restraint, and masked-stranger situations and their expressions were coded second by second. Infants showed a variety of facial expressions in each situation; however, more infants exhibited positive (joy and surprise) than negative expressions (anger, disgust, fear, and sadness) across all situations except sour taste. Consistent with DET-predicted specificity, joy expressions were the most common in response to tickling, and were less common in response to other situations. Surprise expressions were the most common in response to the jack-in-the-box, as predicted, but also were the most common in response to the arm restraint and masked-stranger situations, indicating a lack of specificity. No evidence of predicted specificity was found for anger, disgust, fear, and sadness expressions. Evidence of individual differences in expressivity within situations, as well as stability in the pattern across situations, underscores the need to examine both child and contextual factors in studying emotional development. The results provide little support for the DET postulate of situational specificity and suggest that a synthesis of differential emotions and dynamic systems theories of emotional expression should be considered.

Enabling dynamics in face analysis

NARCIS (Netherlands)

Dibeklioğlu, H.

2014-01-01

Most of the approaches in automatic face analysis rely solely on static appearance. However, temporal analysis of expressions reveals interesting patterns. For a better understanding of the human face, this thesis focuses on temporal changes in the face, and dynamic patterns of expressions. In

Polymer dynamics from synthetic polymers to proteins

Indian Academy of Sciences (India)

Keywords. Polymer dynamics; reptation; domain dynamics biomolecules. Abstract. Starting from the standard model of polymer motion - the Rouse model - we briefly present some key experimental results on the mesoscopic dynamics of polymer systems. We touch the role of topological confinement as expressed in the ...

Allele-dependent differences in quorum-sensing dynamics result in variant expression of virulence genes in Staphylococcus aureus.

Science.gov (United States)

Geisinger, Edward; Chen, John; Novick, Richard P

2012-06-01

Agr is an autoinducing, quorum-sensing system that functions in many Gram-positive species and is best characterized in the pathogen Staphylococcus aureus, in which it is a global regulator of virulence gene expression. Allelic variations in the agr genes have resulted in the emergence of four quorum-sensing specificity groups in S. aureus, which correlate with different strain pathotypes. The basis for these predilections is unclear but is hypothesized to involve the phenomenon of quorum-sensing interference between strains of different agr groups, which may drive S. aureus strain isolation and divergence. Whether properties intrinsic to each agr allele directly influence virulence phenotypes within S. aureus is unknown. In this study, we examined group-specific differences in agr autoinduction and virulence gene regulation by utilizing congenic strains, each harboring a unique S. aureus agr allele, enabling a dissection of agr locus-dependent versus genotype-dependent effects on quorum-sensing dynamics and virulence factor production. Employing a reporter fusion to the principal agr promoter, P3, we observed allele-dependent differences in the timing and magnitude of agr activation. These differences were mediated by polymorphisms within the agrBDCA genes and translated to significant variations in the expression of a key transcriptional regulator, Rot, and of several important exoproteins and surface factors involved in pathogenesis. This work uncovers the contribution of divergent quorum-sensing alleles to variant expression of virulence determinants within a bacterial species.

Dynamics of Na+,K+,2Cl- cotransporter and Na+,K+-ATPase expression in the branchial epithelium of brown trout (Salmo trutta) and Atlantic salmon (Salmo salar)

DEFF Research Database (Denmark)

Tipsmark, Christian Kølbæk; Madsen, Steffen; Seidelin, Michel

2002-01-01

The dynamics of branchial Na+,K+,2Cl- cotransporter (NKCC) and Na+,K+-ATPase (NKA) expression were investigated in brown trout and Atlantic salmon during salinity shifts and the parr-smolt transformation, respectively. In the brown trout, Western blotting revealed that NKCC and NKA abundance...

Dynamic heterogeneity and DNA methylation in embryonic stem cells.

KAUST Repository

Singer, Zakary S

2014-07-01

Cell populations can be strikingly heterogeneous, composed of multiple cellular states, each exhibiting stochastic noise in its gene expression. A major challenge is to disentangle these two types of variability and to understand the dynamic processes and mechanisms that control them. Embryonic stem cells (ESCs) provide an ideal model system to address this issue because they exhibit heterogeneous and dynamic expression of functionally important regulatory factors. We analyzed gene expression in individual ESCs using single-molecule RNA-FISH and quantitative time-lapse movies. These data discriminated stochastic switching between two coherent (correlated) gene expression states and burst-like transcriptional noise. We further showed that the "2i" signaling pathway inhibitors modulate both types of variation. Finally, we found that DNA methylation plays a key role in maintaining these metastable states. Together, these results show how ESC gene expression states and dynamics arise from a combination of intrinsic noise, coherent cellular states, and epigenetic regulation.

Serial Expression Analysis: a web tool for the analysis of serial gene expression data

Science.gov (United States)

Nueda, Maria José; Carbonell, José; Medina, Ignacio; Dopazo, Joaquín; Conesa, Ana

2010-01-01

Serial transcriptomics experiments investigate the dynamics of gene expression changes associated with a quantitative variable such as time or dosage. The statistical analysis of these data implies the study of global and gene-specific expression trends, the identification of significant serial changes, the comparison of expression profiles and the assessment of transcriptional changes in terms of cellular processes. We have created the SEA (Serial Expression Analysis) suite to provide a complete web-based resource for the analysis of serial transcriptomics data. SEA offers five different algorithms based on univariate, multivariate and functional profiling strategies framed within a user-friendly interface and a project-oriented architecture to facilitate the analysis of serial gene expression data sets from different perspectives. SEA is available at sea.bioinfo.cipf.es. PMID:20525784

The evolution of gene expression in primates

OpenAIRE

Tashakkori Ghanbarian, Avazeh

2015-01-01

The evolution of a gene’s expression profile is commonly assumed to be independent of its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between expression of neighboring genes in extant taxa. Indeed, in all eukaryotic genomes, genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their e...

Micro-Expression Recognition Using Color Spaces.

Science.gov (United States)

Wang, Su-Jing; Yan, Wen-Jing; Li, Xiaobai; Zhao, Guoying; Zhou, Chun-Guang; Fu, Xiaolan; Yang, Minghao; Tao, Jianhua

2015-12-01

Micro-expressions are brief involuntary facial expressions that reveal genuine emotions and, thus, help detect lies. Because of their many promising applications, they have attracted the attention of researchers from various fields. Recent research reveals that two perceptual color spaces (CIELab and CIELuv) provide useful information for expression recognition. This paper is an extended version of our International Conference on Pattern Recognition paper, in which we propose a novel color space model, tensor independent color space (TICS), to help recognize micro-expressions. In this paper, we further show that CIELab and CIELuv are also helpful in recognizing micro-expressions, and we indicate why these three color spaces achieve better performance. A micro-expression color video clip is treated as a fourth-order tensor, i.e., a four-dimension array. The first two dimensions are the spatial information, the third is the temporal information, and the fourth is the color information. We transform the fourth dimension from RGB into TICS, in which the color components are as independent as possible. The combination of dynamic texture and independent color components achieves a higher accuracy than does that of RGB. In addition, we define a set of regions of interests (ROIs) based on the facial action coding system and calculated the dynamic texture histograms for each ROI. Experiments are conducted on two micro-expression databases, CASME and CASME 2, and the results show that the performances for TICS, CIELab, and CIELuv are better than those for RGB or gray.

TLR Stimulation Dynamically Regulates Heme and Iron Export Gene Expression in Macrophages

Directory of Open Access Journals (Sweden)

Mary Philip

2016-01-01

Full Text Available Pathogenic bacteria have evolved multiple mechanisms to capture iron or iron-containing heme from host tissues or blood. In response, organisms have developed defense mechanisms to keep iron from pathogens. Very little of the body’s iron store is available as free heme; rather nearly all body iron is complexed with heme or other proteins. The feline leukemia virus, subgroup C (FeLV-C receptor, FLVCR, exports heme from cells. It was unknown whether FLVCR regulates heme-iron availability after infection, but given that other heme regulatory proteins are upregulated in macrophages in response to bacterial infection, we hypothesized that macrophages dynamically regulate FLVCR. We stimulated murine primary macrophages or macrophage cell lines with LPS and found that Flvcr is rapidly downregulated in a TLR4/MD2-dependent manner; TLR1/2 and TLR3 stimulation also decreased Flvcr expression. We identified several candidate TLR-activated transcription factors that can bind to the Flvcr promoter. Macrophages must balance the need to sequester iron from systemic circulating or intracellular pathogens with the macrophage requirement for heme and iron to produce reactive oxygen species. Our findings underscore the complexity of this regulation and point to a new role for FLVCR and heme export in macrophages responses to infection and inflammation.

A dynamic appearance descriptor approach to facial actions temporal modeling

NARCIS (Netherlands)

Jiang, Bihan; Valstar, Michel; Martinez, Brais; Pantic, Maja

Both the configuration and the dynamics of facial expressions are crucial for the interpretation of human facial behavior. Yet to date, the vast majority of reported efforts in the field either do not take the dynamics of facial expressions into account, or focus only on prototypic facial

Analysis Evacuation Route for KM Zahro Express on Fire Condition using Agent Based Modeling and Fire Dynamics Simulatior

Directory of Open Access Journals (Sweden)

Trika Pitana

2017-09-01

Full Text Available Safety is the thing that needs to be preferred by users of transport, passengers should also understand about safety procedures and evacuation procedures in the means of transport. There have been many accidents that happen in the world of transport, particularly in the shipping world, from 2010 to 2016 is no more than 50 accidents of ships in accordance with the cause recorded by KNKT (Komisi Nasional Keselamatan Transportasi. On this research was discussed the evacuation time on the ship KM Zahro express that occurred earlier in the year 2017 in the Kepulauan Seribu, DKI Jakarta. Almost all passenger dead caused by fire from power source in engine room. This thesis will explaine about evacuation time and dangers from fire that interfere the process of evacuation. The methods used are Agent Based Modeling and Simulation (ABMS and Fire Dynamics Simulator (FDS for modeling fire simulation. Agent-Based Modeling software (pathfinder and Fire Dynamics Simulator software (pyrosim are used to calculate time evacuation in normal condition and fire condition of KM Zahro Express. Agent-Based Modeling and Simulator (ABMS is a modeling method that aims to model complex problems based on real cases. Agent-Based Modeling and Simulator (ABMS is designed to model a place that has a seat, path, exit door, humans, and others. Pyrosim is a graphical user interface for the Fire Dynamics Simulator (FDS. FDS models can predict smoke, temperature, carbon monoxide, and other substances during fires.  In this case the existing models can be used to plan and prepare an emergency if unwanted things happen. As well as using basic rules which refer to the Safety Of Life At Sea (SOLAS and International Maritime Organization (IMO. Result of Evacuation simulation calculation on emergency conditions (two rear exit doors will be closed that match at actually condition is 29,783 minutes (respon is not taken in this simulation, calculation results obtained from simulation of

Dimensional Information-Theoretic Measurement of Facial Emotion Expressions in Schizophrenia

Directory of Open Access Journals (Sweden)

Jihun Hamm

2014-01-01

Full Text Available Altered facial expressions of emotions are characteristic impairments in schizophrenia. Ratings of affect have traditionally been limited to clinical rating scales and facial muscle movement analysis, which require extensive training and have limitations based on methodology and ecological validity. To improve reliable assessment of dynamic facial expression changes, we have developed automated measurements of facial emotion expressions based on information-theoretic measures of expressivity of ambiguity and distinctiveness of facial expressions. These measures were examined in matched groups of persons with schizophrenia (n=28 and healthy controls (n=26 who underwent video acquisition to assess expressivity of basic emotions (happiness, sadness, anger, fear, and disgust in evoked conditions. Persons with schizophrenia scored higher on ambiguity, the measure of conditional entropy within the expression of a single emotion, and they scored lower on distinctiveness, the measure of mutual information across expressions of different emotions. The automated measures compared favorably with observer-based ratings. This method can be applied for delineating dynamic emotional expressivity in healthy and clinical populations.

Multivariate Pattern Classification of Facial Expressions Based on Large-Scale Functional Connectivity.

Science.gov (United States)

Liang, Yin; Liu, Baolin; Li, Xianglin; Wang, Peiyuan

2018-01-01

It is an important question how human beings achieve efficient recognition of others' facial expressions in cognitive neuroscience, and it has been identified that specific cortical regions show preferential activation to facial expressions in previous studies. However, the potential contributions of the connectivity patterns in the processing of facial expressions remained unclear. The present functional magnetic resonance imaging (fMRI) study explored whether facial expressions could be decoded from the functional connectivity (FC) patterns using multivariate pattern analysis combined with machine learning algorithms (fcMVPA). We employed a block design experiment and collected neural activities while participants viewed facial expressions of six basic emotions (anger, disgust, fear, joy, sadness, and surprise). Both static and dynamic expression stimuli were included in our study. A behavioral experiment after scanning confirmed the validity of the facial stimuli presented during the fMRI experiment with classification accuracies and emotional intensities. We obtained whole-brain FC patterns for each facial expression and found that both static and dynamic facial expressions could be successfully decoded from the FC patterns. Moreover, we identified the expression-discriminative networks for the static and dynamic facial expressions, which span beyond the conventional face-selective areas. Overall, these results reveal that large-scale FC patterns may also contain rich expression information to accurately decode facial expressions, suggesting a novel mechanism, which includes general interactions between distributed brain regions, and that contributes to the human facial expression recognition.

Precise Analysis of String Expressions

DEFF Research Database (Denmark)

Christensen, Aske Simon; Møller, Anders; Schwartzbach, Michael Ignatieff

2003-01-01

We perform static analysis of Java programs to answer a simple question: which values may occur as results of string expressions? The answers are summarized for each expression by a regular language that is guaranteed to contain all possible values. We present several applications of this analysis...... are automatically produced. We present extensive benchmarks demonstrating that the analysis is efficient and produces results of useful precision......., including statically checking the syntax of dynamically generated expressions, such as SQL queries. Our analysis constructs flow graphs from class files and generates a context-free grammar with a nonterminal for each string expression. The language of this grammar is then widened into a regular language...

Cosmology with modified Newtonian dynamics (MOND)

NARCIS (Netherlands)

Sanders, R. H.

1998-01-01

It is well known that the application of Newtonian dynamics to an expanding spherical region leads to the correct relativistic expression (the Friedmann equation) for the evolution of the cosmic scalefactor. Here, the cosmological implications of Milgrom's modified Newtonian dynamics (MOND) are

Dynamic Magnification Factor in a Box-Shape Steel Girder

Science.gov (United States)

Rahbar-Ranji, A.

2014-01-01

The dynamic effect of moving loads on structures is treated as a dynamic magnification factor when resonant is not imminent. Studies have shown that the calculated magnification factors from field measurements could be higher than the values specified in design codes. It is the main aim of present paper to investigate the applicability and accuracy of a rule-based expression for calculation of dynamic magnification factor for lifting appliances used in marine industry. A steel box shape girder of a crane is considered and transient dynamic analysis using computer code ANSYS is implemented. Dynamic magnification factor is calculated for different loading conditions and compared with rule-based equation. The effects of lifting speeds, acceleration, damping ratio and position of cargo are examined. It is found that rule-based expression underestimate dynamic magnification factor.

The Effects of Tocotrienol and Lovastatin Co-Supplementation on Bone Dynamic Histomorphometry and Bone Morphogenetic Protein-2 Expression in Rats with Estrogen Deficiency

Directory of Open Access Journals (Sweden)

Kok-Yong Chin

2017-02-01

Full Text Available Both tocotrienol and statins are suppressors of the mevalonate pathway. Supplementation of tocotrienol among statin users could potentially protect them against osteoporosis. This study aimed to compare the effects of tocotrienol and lovastatin co-supplementation with individual treatments on bone dynamic histomorphometric indices and bone morphogenetic protein-2 (BMP-2 gene expression in ovariectomized rats. Forty-eight female Sprague-Dawley rats were randomized equally into six groups. The baseline was sacrificed upon receipt. All other groups were ovariectomized, except for the sham group. The ovariectomized groups were administered orally daily with (1 lovastatin 11 mg/kg/day alone; (2 tocotrienol derived from annatto bean (annatto tocotrienol 60 mg/kg/day alone; (3 lovastatin 11 mg/kg/day, and annatto tocotrienol 60 mg/kg/day. The sham and ovariectomized control groups were treated with equal volume of vehicle. After eight weeks of treatment, the rats were sacrificed. Their bones were harvested for bone dynamic histomorphometry and BMP-2 gene expression. Rats supplemented with annatto tocotrienol and lovastatin concurrently demonstrated significantly lower single-labeled surface, but increased double-labeled surface, mineralizing surface, mineral apposition rate and bone formation rate compared to individual treatments (p < 0.05. There was a parallel increase in BMP-2 gene expression in the rats receiving combined treatment (p < 0.05. The combination of annatto tocotrienol and lovastatin exerted either additively or synergistically on selected bone parameters. In conclusion, tocotrienol can augment the bone formation and mineralization in rats receiving low-dose statins. Supplementation of tocotrienol in statin users can potentially protect them from osteoporosis.

Dynamic gene and protein expression patterns of the autism-associated met receptor tyrosine kinase in the developing mouse forebrain.

Science.gov (United States)

Judson, Matthew C; Bergman, Mica Y; Campbell, Daniel B; Eagleson, Kathie L; Levitt, Pat

2009-04-10

The establishment of appropriate neural circuitry depends on the coordination of multiple developmental events across space and time. These events include proliferation, migration, differentiation, and survival-all of which can be mediated by hepatocyte growth factor (HGF) signaling through the Met receptor tyrosine kinase. We previously found a functional promoter variant of the MET gene to be associated with autism spectrum disorder, suggesting that forebrain circuits governing social and emotional function may be especially vulnerable to developmental disruptions in HGF/Met signaling. However, little is known about the spatiotemporal distribution of Met expression in the forebrain during the development of such circuits. To advance our understanding of the neurodevelopmental influences of Met activation, we employed complementary Western blotting, in situ hybridization, and immunohistochemistry to comprehensively map Met transcript and protein expression throughout perinatal and postnatal development of the mouse forebrain. Our studies reveal complex and dynamic spatiotemporal patterns of expression during this period. Spatially, Met transcript is localized primarily to specific populations of projection neurons within the neocortex and in structures of the limbic system, including the amygdala, hippocampus, and septum. Met protein appears to be principally located in axon tracts. Temporally, peak expression of transcript and protein occurs during the second postnatal week. This period is characterized by extensive neurite outgrowth and synaptogenesis, supporting a role for the receptor in these processes. Collectively, these data suggest that Met signaling may be necessary for the appropriate wiring of forebrain circuits, with particular relevance to the social and emotional dimensions of behavior. (c) 2009 Wiley-Liss, Inc.

Facial expression movement enhances the measurement of temporal dynamics of attentional bias in the dot-probe task.

Science.gov (United States)

Caudek, Corrado; Ceccarini, Francesco; Sica, Claudio

2017-08-01

The facial dot-probe task is one of the most common experimental paradigms used to assess attentional bias toward emotional information. In recent years, however, the psychometric properties of this paradigm have been questioned. In the present study, attentional bias to emotional face stimuli was measured with dynamic and static images of realistic human faces in 97 college students (63 women) who underwent either a positive or a negative mood-induction prior to the experiment. We controlled the bottom-up salience of the stimuli in order to dissociate the top-down orienting of attention from the effects of the bottom-up physical properties of the stimuli. A Bayesian analysis of our results indicates that 1) the traditional global attentional bias index shows a low reliability, 2) reliability increases dramatically when biased attention is analyzed by extracting a series of bias estimations from trial-to-trial (Zvielli, Bernstein, & Koster, 2015), 3) dynamic expression of emotions strengthens biased attention to emotional information, and 4) mood-congruency facilitates the measurement of biased attention to emotional stimuli. These results highlight the importance of using ecologically valid stimuli in attentional bias research, together with the importance of estimating biased attention at the trial level. Copyright © 2017 Elsevier Ltd. All rights reserved.

Trichostatin-A induces differential changes in histone protein dynamics and expression in HeLa cells

International Nuclear Information System (INIS)

Rao, Jyothsna; Bhattacharya, Dipanjan; Banerjee, Bidisha; Sarin, Apurva; Shivashankar, G.V.

2007-01-01

Trichostatin-A (TSA), a histone deacetylase (HDAC) inhibitor, results in enhanced acetylation of core histones thereby disrupting chromatin organization within living cells. We report on changes in chromatin organization and the resultant alteration in nuclear architecture following treatment with TSA using fluorescence imaging. TSA triggers an expected increase in the euchromatin fraction which is accompanied by a significant increase in nuclear volume and alterations in chromatin compaction mapped using fluorescence anisotropy imaging. We observe differential changes in the mobility of core and linker histones as measured by fluorescence recovery after photo-bleaching (FRAP) and fluorescence correlation spectroscopy (FCS) methods. Further TSA induces a differential increase in linker histone transcription and increased phosphorylation of linker histone proteins accompanying an expected increase in core histone acetylation patterns. Thus subtle feedback responses triggered by changes in chromatin configurations impinge selectively on linker histone mobility and its expression. These observations have implications for understanding the role of HDAC in the dynamic maintenance of chromatin organization

Bioinspired nanocomplex for spatiotemporal imaging of sequential mRNA expression in differentiating neural stem cells.

Science.gov (United States)

Wang, Zhe; Zhang, Ruili; Wang, Zhongliang; Wang, He-Fang; Wang, Yu; Zhao, Jun; Wang, Fu; Li, Weitao; Niu, Gang; Kiesewetter, Dale O; Chen, Xiaoyuan

2014-12-23

Messenger RNA plays a pivotal role in regulating cellular activities. The expression dynamics of specific mRNA contains substantial information on the intracellular milieu. Unlike the imaging of stationary mRNAs, real-time intracellular imaging of the dynamics of mRNA expression is of great value for investigating mRNA biology and exploring specific cellular cascades. In addition to advanced imaging methods, timely extracellular stimulation is another key factor in regulating the mRNA expression repertoire. The integration of effective stimulation and imaging into a single robust system would significantly improve stimulation efficiency and imaging accuracy, producing fewer unwanted artifacts. In this study, we developed a multifunctional nanocomplex to enable self-activating and spatiotemporal imaging of the dynamics of mRNA sequential expression during the neural stem cell differentiation process. This nanocomplex showed improved enzymatic stability, fast recognition kinetics, and high specificity. With a mechanism regulated by endogenous cell machinery, this nanocomplex realized the successive stimulating motif release and the dynamic imaging of chronological mRNA expression during neural stem cell differentiation without the use of transgenetic manipulation. The dynamic imaging montage of mRNA expression ultimately facilitated genetic heterogeneity analysis. In vivo lateral ventricle injection of this nanocomplex enabled endogenous neural stem cell activation and labeling at their specific differentiation stages. This nanocomplex is highly amenable as an alternative tool to explore the dynamics of intricate mRNA activities in various physiological and pathological conditions.

Gene expression from polynomial dynamics in the 2-adic information space

International Nuclear Information System (INIS)

Khrennikov, Andrei Yu.

2009-01-01

We perform geometrization of genetics by representing genetic information by points of the 4-adic information space. By well known theorem of number theory this space can also be represented as the 2-adic space. The process of DNA-reproduction is described by the action of a 4-adic (or equivalently 2-adic) dynamical system. As we know, the genes contain information for production of proteins. The genetic code is a degenerate map of codons to proteins. We model this map as functioning of a polynomial dynamical system. The purely mathematical problem under consideration is to find a dynamical system reproducing the degenerate structure of the genetic code. We present one of possible solutions of this problem.

Highly dynamic and sex-specific expression of microRNAs during early ES cell differentiation.

Directory of Open Access Journals (Sweden)

Constance Ciaudo

2009-08-01

Full Text Available Embryonic stem (ES cells are pluripotent cells derived from the inner cell mass of the mammalian blastocyst. Cellular differentiation entails loss of pluripotency and gain of lineage-specific characteristics. However, the molecular controls that govern the differentiation process remain poorly understood. We have characterized small RNA expression profiles in differentiating ES cells as a model for early mammalian development. High-throughput 454 pyro-sequencing was performed on 19-30 nt RNAs isolated from undifferentiated male and female ES cells, as well as day 2 and 5 differentiating derivatives. A discrete subset of microRNAs (miRNAs largely dominated the small RNA repertoire, and the dynamics of their accumulation could be readily used to discriminate pluripotency from early differentiation events. Unsupervised partitioning around meloids (PAM analysis revealed that differentiating ES cell miRNAs can be divided into three expression clusters with highly contrasted accumulation patterns. PAM analysis afforded an unprecedented level of definition in the temporal fluctuations of individual members of several miRNA genomic clusters. Notably, this unravelled highly complex post-transcriptional regulations of the key pluripotency miR-290 locus, and helped identify miR-293 as a clear outlier within this cluster. Accordingly, the miR-293 seed sequence and its predicted cellular targets differed drastically from those of the other abundant cluster members, suggesting that previous conclusions drawn from whole miR-290 over-expression need to be reconsidered. Our analysis in ES cells also uncovered a striking male-specific enrichment of the miR-302 family, which share the same seed sequence with most miR-290 family members. Accordingly, a miR-302 representative was strongly enriched in embryonic germ cells derived from primordial germ cells of male but not female mouse embryos. Identifying the chromatin remodelling and E2F-dependent transcription

Positive Bioluminescence Imaging of MicroRNA Expression in Small Animal Models Using an Engineered Genetic-Switch Expression System, RILES.

Science.gov (United States)

Baril, Patrick; Pichon, Chantal

2016-01-01

MicroRNAs (miRNAs) are a class of small, noncoding RNAs which regulate gene expression by directing their target mRNA for degradation or translational repression. Since their discovery in the early 1990s, miRNAs have emerged as key components in the posttranscriptional regulation of gene networks, shaping many biological processes from development, morphogenesis, differentiation, proliferation and apoptosis. Although understanding of the molecular basis of miRNA biology is improving, methods to monitor the dynamic and the spatiotemporal aspects of miRNA expression under physiopathological conditions are required. However, monitoring of miRNAs is difficult due to their small size, low abundance, high degree of sequence similarity, and their dynamic expression pattern which is subjected to tight transcriptional and post-transcriptional controls. Recently, we developed a miRNA monitoring system called RILES, standing for RNAi-inducible expression system, which relies on an engineered regulatable expression system, to switch on the expression of the luciferase gene when the targeted miRNA is expressed in cells. We demonstrated that RILES is a specific, sensitive, and robust method to determine the fine-tuning of miRNA expression during the development of an experimental pathological process in mice. Because RILES offers the possibility for longitudinal studies on individual subjects, sharper insights into miRNA regulation can be generated, with applications in physiology, pathophysiology and development of RNAi-based therapies. This chapter describes methods and protocols to monitor the expression of myomiR-206, -1, and -133 in the tibialis anterior muscle of mice. These protocols can be used and adapted to monitor the expression of other miRNAs in other biological processes.

Perceptual integration of kinematic components in the recognition of emotional facial expressions.

Science.gov (United States)

Chiovetto, Enrico; Curio, Cristóbal; Endres, Dominik; Giese, Martin

2018-04-01

According to a long-standing hypothesis in motor control, complex body motion is organized in terms of movement primitives, reducing massively the dimensionality of the underlying control problems. For body movements, this low-dimensional organization has been convincingly demonstrated by the learning of low-dimensional representations from kinematic and EMG data. In contrast, the effective dimensionality of dynamic facial expressions is unknown, and dominant analysis approaches have been based on heuristically defined facial "action units," which reflect contributions of individual face muscles. We determined the effective dimensionality of dynamic facial expressions by learning of a low-dimensional model from 11 facial expressions. We found an amazingly low dimensionality with only two movement primitives being sufficient to simulate these dynamic expressions with high accuracy. This low dimensionality is confirmed statistically, by Bayesian model comparison of models with different numbers of primitives, and by a psychophysical experiment that demonstrates that expressions, simulated with only two primitives, are indistinguishable from natural ones. In addition, we find statistically optimal integration of the emotion information specified by these primitives in visual perception. Taken together, our results indicate that facial expressions might be controlled by a very small number of independent control units, permitting very low-dimensional parametrization of the associated facial expression.

The Perception of Time While Perceiving Dynamic Emotional Faces

Directory of Open Access Journals (Sweden)

Wang On eLi

2015-08-01

Full Text Available Emotion plays an essential role in the perception of time such that time is perceived to fly when events are enjoyable, while unenjoyable moments are perceived to drag. Previous studies have reported a time-drag effect when participants are presented with emotional facial expressions, regardless of the emotion presented. This effect can hardly be explained by induced emotion given the heterogeneous nature of emotional expressions. We conducted two experiments (n=44 & n=39 to examine the cognitive mechanism underlying this effect by presenting dynamic sequences of emotional expressions to participants. Each sequence started with a particular expression, then morphed to another. The presentation of dynamic facial expressions allows a comparison between the time-drag effect of homogeneous pairs of emotional expressions sharing similar valence and arousal to heterogeneous pairs. Sequences of seven durations (400ms, 600ms, 800ms, 1,000ms, 1,200ms, 1,400ms, 1,600ms were presented to participants, who were asked to judge whether the sequences were closer to 400ms or 1,600ms in a two-alternative forced choice task. The data were then collated according to conditions and fit into cumulative Gaussian curves to estimate the point of subjective equivalence indicating the perceived duration of 1,000ms. Consistent with previous reports, a feeling of time dragging is induced regardless of the sequence presented, such that 1,000ms is perceived to be longer than 1,000ms. In addition, dynamic facial expressions exert a greater effect on perceived time drag than static expressions. The effect is most prominent when the dynamics involve an angry face or a change in valence. The significance of this sensitivity is discussed in terms of emotion perception and its evolutionary significance for our attention mechanism.

Random Dynamics

Science.gov (United States)

Bennett, D. L.; Brene, N.; Nielsen, H. B.

1987-01-01

The goal of random dynamics is the derivation of the laws of Nature as we know them (standard model) from inessential assumptions. The inessential assumptions made here are expressed as sets of general models at extremely high energies: gauge glass and spacetime foam. Both sets of models lead tentatively to the standard model.

Reconstructing Dynamic Promoter Activity Profiles from Reporter Gene Data

DEFF Research Database (Denmark)

Kannan, Soumya; Sams, Thomas; Maury, Jérôme

2018-01-01

activity despite the fact that the observed output may be dynamic and is a number of steps away from the transcription process. In fact, some promoters that are often thought of as constitutive can show changes in activity when growth conditions change. For these reasons, we have developed a system......Accurate characterization of promoter activity is important when designing expression systems for systems biology and metabolic engineering applications. Promoters that respond to changes in the environment enable the dynamic control of gene expression without the necessity of inducer compounds......, for example. However, the dynamic nature of these processes poses challenges for estimating promoter activity. Most experimental approaches utilize reporter gene expression to estimate promoter activity. Typically the reporter gene encodes a fluorescent protein that is used to infer a constant promoter...

Adolescent Mouse Takes on An Active Transcriptomic Expression During Postnatal Cerebral Development

KAUST Repository

Xu, Wei; Xin, Chengqi; Lin, Qiang; Ding, Feng; Gong, Wei; Zhou, Yuanyuan; Yu, Jun; Cui, Peng; Hu, Songnian

2014-01-01

has the most active gene expression, with expression of a large number of regulatory genes up-regulated and some crucial pathways activated. Transcription factor (TF) analysis suggested the similar dynamics as expression profiling, especially those TFs

Extracellular matrix influence in Streptococcus mutans gene expression in a cariogenic biofilm.

Science.gov (United States)

Florez Salamanca, E J; Klein, M I

2018-04-01

Caries etiology is biofilm-diet-dependent. Biofilms are highly dynamic and structured microbial communities enmeshed in a three-dimensional extracellular matrix. The study evaluated the expression dynamics of Streptococcus mutans genes associated with exopolysaccharides (EPS) (gtfBCD, gbpB, dexA), lipoteichoic acids (LTA) (dltABCD, SMU_775c) and extracellular DNA (eDNA) (lytST, lrgAB, ccpA) during matrix development within a mixed-species biofilm of S. mutans, Actinomyces naeslundii and Streptococcus gordonii. Mixed-species biofilms using S. mutans strains UA159 or ΔgtfB formed on saliva-coated hydroxyapatite discs were submitted to a nutritional challenge (providing an abundance of sucrose and starch). Biofilms were removed at eight developmental stages for gene expression analysis by quantitative polymerase chain reaction. The pH of spent culture media remained acidic throughout the experimental periods, being lower after sucrose and starch exposure. All genes were expressed at all biofilm developmental phases. EPS- and LTA-associated genes had a similar expression profile for both biofilms, presenting lower levels of expression at 67, 91 and 115 hours and a peak of expression at 55 hours, but having distinct expression magnitudes, with lower values for ΔgtfB (eg, fold-difference of ~382 for gtfC and ~16 for dltB at 43 hours). The eDNA-associated genes presented different dynamics of expression between both strains. In UA159 biofilms lrgA and lrgB genes were highly expressed at 29 hours (which were ~13 and ~5.4 times vs ΔgtfB, respectively), whereas in ΔgtfB biofilms an inverse relationship between lytS and lrgA and lrgB expression was detected. Therefore, the deletion of gtfB influences dynamics and magnitude of expression of genes associated with matrix main components. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Population dynamics of Sesamia inferens on transgenic rice expressing Cry1Ac and CpTI in southern China.

Science.gov (United States)

Han, Lanzhi; Liu, Peilei; Wu, Kongming; Peng, Yufa; Wang, Feng

2008-10-01

Genetically modified insect-resistant rice lines containing the cry1Ac gene from Bacillus thuringiensis (Bt) or the CpTI (cowpea trypsin inhibitor) gene developed for the management of lepidopterous pests are highly resistant to the major target pests, Chilo suppressalis (Walker), Cnaphalocrocis medinalis (Guenée), and Scirpophaga incertulas (Walker), in the main rice-growing areas of China. However, the effects of these transgenic lines on Sesamia inferens (Walker), an important lepidopterous rice pest, are currently unknown. Because different insect species have varying susceptibility to Bt insecticidal proteins that may affect population dynamics, research into the effects of these transgenic rice lines on the population dynamics of S. inferens was conducted in Fuzhou, southern China, in 2005 and 2006. The results of laboratory, field cage, and field plot experiments show that S. inferens has comparatively high susceptibility to the transgenic line during the early growing season, with significant differences observed in larval density and infestation levels between transgenic and control lines. Because of a decrease in Cry1Ac levels in the plant as it ages, the transgenic line provided only a low potential for population suppression late in the growing season. There is a correlation between the changing expression of Cry1Ac and the impact of transgenic rice on the population dynamics of S. inferens during the season. These results indicate that S. inferens may become a major pest in fields of prospective commercially released transgenic rice, and more attention should be paid to developing an effective alternative management strategy.

Parametric Linear Dynamic Logic

Directory of Open Access Journals (Sweden)

Peter Faymonville

2014-08-01

Full Text Available We introduce Parametric Linear Dynamic Logic (PLDL, which extends Linear Dynamic Logic (LDL by temporal operators equipped with parameters that bound their scope. LDL was proposed as an extension of Linear Temporal Logic (LTL that is able to express all ω-regular specifications while still maintaining many of LTL's desirable properties like an intuitive syntax and a translation into non-deterministic Büchi automata of exponential size. But LDL lacks capabilities to express timing constraints. By adding parameterized operators to LDL, we obtain a logic that is able to express all ω-regular properties and that subsumes parameterized extensions of LTL like Parametric LTL and PROMPT-LTL. Our main technical contribution is a translation of PLDL formulas into non-deterministic Büchi word automata of exponential size via alternating automata. This yields a PSPACE model checking algorithm and a realizability algorithm with doubly-exponential running time. Furthermore, we give tight upper and lower bounds on optimal parameter values for both problems. These results show that PLDL model checking and realizability are not harder than LTL model checking and realizability.

Dynamic methylation and expression of Oct4 in early neural stem cells.

Science.gov (United States)

Lee, Shih-Han; Jeyapalan, Jennie N; Appleby, Vanessa; Mohamed Noor, Dzul Azri; Sottile, Virginie; Scotting, Paul J

2010-09-01

Neural stem cells are a multipotent population of tissue-specific stem cells with a broad but limited differentiation potential. However, recent studies have shown that over-expression of the pluripotency gene, Oct4, alone is sufficient to initiate a process by which these can form 'induced pluripotent stem cells' (iPS cells) with the same broad potential as embryonic stem cells. This led us to examine the expression of Oct4 in endogenous neural stem cells, as data regarding its expression in neural stem cells in vivo are contradictory and incomplete. In this study we have therefore analysed the expression of Oct4 and other genes associated with pluripotency throughout development of the mouse CNS and in neural stem cells grown in vitro. We find that Oct4 is still expressed in the CNS by E8.5, but that this expression declines rapidly until it is undetectable by E15.5. This decline is coincident with the gradual methylation of the Oct4 promoter and proximal enhancer. Immunostaining suggests that the Oct4 protein is predominantly cytoplasmic in location. We also found that neural stem cells from all ages expressed the pluripotency associated genes, Sox2, c-Myc, Klf4 and Nanog. These data provide an explanation for the varying behaviour of cells from the early neuroepithelium at different stages of development. The expression of these genes also provides an indication of why Oct4 alone is sufficient to induce iPS formation in neural stem cells at later stages.

Modeling Dynamic Regulatory Processes in Stroke

Science.gov (United States)

McDermott, Jason E.; Jarman, Kenneth; Taylor, Ronald; Lancaster, Mary; Shankaran, Harish; Vartanian, Keri B.; Stevens, Susan L.; Stenzel-Poore, Mary P.; Sanfilippo, Antonio

2012-01-01

The ability to examine the behavior of biological systems in silico has the potential to greatly accelerate the pace of discovery in diseases, such as stroke, where in vivo analysis is time intensive and costly. In this paper we describe an approach for in silico examination of responses of the blood transcriptome to neuroprotective agents and subsequent stroke through the development of dynamic models of the regulatory processes observed in the experimental gene expression data. First, we identified functional gene clusters from these data. Next, we derived ordinary differential equations (ODEs) from the data relating these functional clusters to each other in terms of their regulatory influence on one another. Dynamic models were developed by coupling these ODEs into a model that simulates the expression of regulated functional clusters. By changing the magnitude of gene expression in the initial input state it was possible to assess the behavior of the networks through time under varying conditions since the dynamic model only requires an initial starting state, and does not require measurement of regulatory influences at each time point in order to make accurate predictions. We discuss the implications of our models on neuroprotection in stroke, explore the limitations of the approach, and report that an optimized dynamic model can provide accurate predictions of overall system behavior under several different neuroprotective paradigms. PMID:23071432

Random dynamics

International Nuclear Information System (INIS)

Bennett, D.L.

1987-01-01

The goal of random dynamics is the derivation of the laws of Nature as we know them (standard model) from inessential assumptions. The inessential assumptions made here are expressed as sets of general models at extremely high energies: Gauge glass and spacetime foam. Both sets of models lead tentatively to the standard model. (orig.)

Random dynamics

International Nuclear Information System (INIS)

Bennett, D.L.; Brene, N.; Nielsen, H.B.

1986-06-01

The goal of random dynamics is the derivation of the laws of Nature as we know them (standard model) from inessential assumptions. The inessential assumptions made here are expressed as sets of general models at extremely high energies: gauge glass and spacetime foam. Both sets of models lead tentatively to the standard model. (orig.)

Dynamic Change in p63 Protein Expression during Implantation of Urothelial Cancer Clusters

Directory of Open Access Journals (Sweden)

Takahiro Yoshida

2015-07-01

Full Text Available Although the dissemination of urothelial cancer cells is supposed to be a major cause of the multicentricity of urothelial tumors, the mechanism of implantation has not been well investigated. Here, we found that cancer cell clusters from the urine of patients with urothelial cancer retain the ability to survive, grow, and adhere. By using cell lines and primary cells collected from multiple patients, we demonstrate that △Np63α protein in cancer cell clusters was rapidly decreased through proteasomal degradation when clusters were attached to the matrix, leading to downregulation of E-cadherin and upregulation of N-cadherin. Decreased △Np63α protein level in urothelial cancer cell clusters was involved in the clearance of the urothelium. Our data provide the first evidence that clusters of urothelial cancer cells exhibit dynamic changes in △Np63α expression during attachment to the matrix, and decreased △Np63α protein plays a critical role in the interaction between cancer cell clusters and the urothelium. Thus, because △Np63α might be involved in the process of intraluminal dissemination of urothelial cancer cells, blocking the degradation of △Np63α could be a target of therapy to prevent the dissemination of urothelial cancer.

Measuring facial expression of emotion.

Science.gov (United States)

Wolf, Karsten

2015-12-01

Research into emotions has increased in recent decades, especially on the subject of recognition of emotions. However, studies of the facial expressions of emotion were compromised by technical problems with visible video analysis and electromyography in experimental settings. These have only recently been overcome. There have been new developments in the field of automated computerized facial recognition; allowing real-time identification of facial expression in social environments. This review addresses three approaches to measuring facial expression of emotion and describes their specific contributions to understanding emotion in the healthy population and in persons with mental illness. Despite recent progress, studies on human emotions have been hindered by the lack of consensus on an emotion theory suited to examining the dynamic aspects of emotion and its expression. Studying expression of emotion in patients with mental health conditions for diagnostic and therapeutic purposes will profit from theoretical and methodological progress.

A general treatment of dynamic integrity constraints

NARCIS (Netherlands)

de Brock, EO

This paper introduces a general, set-theoretic model for expressing dynamic integrity constraints, i.e., integrity constraints on the state changes that are allowed in a given state space. In a managerial context, such dynamic integrity constraints can be seen as representations of "real world"

Expression of Sox genes in tooth development.

Science.gov (United States)

Kawasaki, Katsushige; Kawasaki, Maiko; Watanabe, Momoko; Idrus, Erik; Nagai, Takahiro; Oommen, Shelly; Maeda, Takeyasu; Hagiwara, Nobuko; Que, Jianwen; Sharpe, Paul T; Ohazama, Atsushi

2015-01-01

Members of the Sox gene family play roles in many biological processes including organogenesis. We carried out comparative in situ hybridization analysis of seventeen sox genes (Sox1-14, 17, 18, 21) during murine odontogenesis from the epithelial thickening to the cytodifferentiation stages. Localized expression of five Sox genes (Sox6, 9, 13, 14 and 21) was observed in tooth bud epithelium. Sox13 showed restricted expression in the primary enamel knots. At the early bell stage, three Sox genes (Sox8, 11, 17 and 21) were expressed in pre-ameloblasts, whereas two others (Sox5 and 18) showed expression in odontoblasts. Sox genes thus showed a dynamic spatio-temporal expression during tooth development.

Analysis of musical expression in audio signals

Science.gov (United States)

Dixon, Simon

2003-01-01

In western art music, composers communicate their work to performers via a standard notation which specificies the musical pitches and relative timings of notes. This notation may also include some higher level information such as variations in the dynamics, tempo and timing. Famous performers are characterised by their expressive interpretation, the ability to convey structural and emotive information within the given framework. The majority of work on audio content analysis focusses on retrieving score-level information; this paper reports on the extraction of parameters describing the performance, a task which requires a much higher degree of accuracy. Two systems are presented: BeatRoot, an off-line beat tracking system which finds the times of musical beats and tracks changes in tempo throughout a performance, and the Performance Worm, a system which provides a real-time visualisation of the two most important expressive dimensions, tempo and dynamics. Both of these systems are being used to process data for a large-scale study of musical expression in classical and romantic piano performance, which uses artificial intelligence (machine learning) techniques to discover fundamental patterns or principles governing expressive performance.

Detecting subnetwork-level dynamic correlations.

Science.gov (United States)

Yan, Yan; Qiu, Shangzhao; Jin, Zhuxuan; Gong, Sihong; Bai, Yun; Lu, Jianwei; Yu, Tianwei

2017-01-15

The biological regulatory system is highly dynamic. The correlations between many functionally related genes change over different biological conditions. Finding dynamic relations on the existing biological network may reveal important regulatory mechanisms. Currently no method is available to detect subnetwork-level dynamic correlations systematically on the genome-scale network. Two major issues hampered the development. The first is gene expression profiling data usually do not contain time course measurements to facilitate the analysis of dynamic relations, which can be partially addressed by using certain genes as indicators of biological conditions. Secondly, it is unclear how to effectively delineate subnetworks, and define dynamic relations between them. Here we propose a new method named LANDD (Liquid Association for Network Dynamics Detection) to find subnetworks that show substantial dynamic correlations, as defined by subnetwork A is concentrated with Liquid Association scouting genes for subnetwork B. The method produces easily interpretable results because of its focus on subnetworks that tend to comprise functionally related genes. Also, the collective behaviour of genes in a subnetwork is a much more reliable indicator of underlying biological conditions compared to using single genes as indicators. We conducted extensive simulations to validate the method's ability to detect subnetwork-level dynamic correlations. Using a real gene expression dataset and the human protein-protein interaction network, we demonstrate the method links subnetworks of distinct biological processes, with both confirmed relations and plausible new functional implications. We also found signal transduction pathways tend to show extensive dynamic relations with other functional groups. The R package is available at https://cran.r-project.org/web/packages/LANDD CONTACTS: yunba@pcom.edu, jwlu33@hotmail.com or tianwei.yu@emory.eduSupplementary information: Supplementary data

Teaching nonlinear dynamics through elastic cords

International Nuclear Information System (INIS)

Chacon, R; Galan, C A; Sanchez-Bajo, F

2011-01-01

We experimentally studied the restoring force of a length of stretched elastic cord. A simple analytical expression for the restoring force was found to fit all the experimental results for different elastic materials. Remarkably, this analytical expression depends upon an elastic-cord characteristic parameter which exhibits two limiting values corresponding to two nonlinear springs with different Hooke's elastic constants. Additionally, the simplest model of elastic cord dynamics is capable of exhibiting a great diversity of nonlinear phenomena, including bifurcations and chaos, thus providing a suitable alternative model system for discussing the basic essentials of nonlinear dynamics in the context of intermediate physics courses at university level.

An accurate expression for radial distribution function of the Lennard-Jones fluid

International Nuclear Information System (INIS)

Morsali, Ali; Goharshadi, Elaheh K.; Ali Mansoori, G.; Abbaspour, Mohsen

2005-01-01

A simple and accurate expression for radial distribution function (RDF) of the Lennard-Jones fluid is presented. The expression explicitly states the RDF as a continuous function of reduced interparticle distance, temperature, and density. It satisfies the limiting conditions of zero density and infinite distance imposed by statistical thermodynamics. The distance dependence of this expression is expressed by an equation which contains 11 adjustable parameters. These parameters are fitted to 353 RDF data, obtained by molecular dynamics calculations, and then expressed as functions of reduced distance, temperature and density. This expression, having a total of 65 constants, reproduces the RDF data with an average root-mean-squared deviation of 0.0152 for the range of state variables of 0.5= * = * = * =ρσ 3 are reduced temperature and density, respectively). The expression predicts the pressure and the internal energy of the Lennard-Jones fluid with an uncertainty that is comparable to that obtained directly from the molecular dynamics simulations

DTFP-Growth: Dynamic Threshold-Based FP-Growth Rule Mining Algorithm Through Integrating Gene Expression, Methylation, and Protein-Protein Interaction Profiles.

Science.gov (United States)

Mallik, Saurav; Bhadra, Tapas; Mukherji, Ayan; Mallik, Saurav; Bhadra, Tapas; Mukherji, Ayan; Mallik, Saurav; Bhadra, Tapas; Mukherji, Ayan

2018-04-01

Association rule mining is an important technique for identifying interesting relationships between gene pairs in a biological data set. Earlier methods basically work for a single biological data set, and, in maximum cases, a single minimum support cutoff can be applied globally, i.e., across all genesets/itemsets. To overcome this limitation, in this paper, we propose dynamic threshold-based FP-growth rule mining algorithm that integrates gene expression, methylation and protein-protein interaction profiles based on weighted shortest distance to find the novel associations among different pairs of genes in multi-view data sets. For this purpose, we introduce three new thresholds, namely, Distance-based Variable/Dynamic Supports (DVS), Distance-based Variable Confidences (DVC), and Distance-based Variable Lifts (DVL) for each rule by integrating co-expression, co-methylation, and protein-protein interactions existed in the multi-omics data set. We develop the proposed algorithm utilizing these three novel multiple threshold measures. In the proposed algorithm, the values of , , and are computed for each rule separately, and subsequently it is verified whether the support, confidence, and lift of each evolved rule are greater than or equal to the corresponding individual , , and values, respectively, or not. If all these three conditions for a rule are found to be true, the rule is treated as a resultant rule. One of the major advantages of the proposed method compared with other related state-of-the-art methods is that it considers both the quantitative and interactive significance among all pairwise genes belonging to each rule. Moreover, the proposed method generates fewer rules, takes less running time, and provides greater biological significance for the resultant top-ranking rules compared to previous methods.

A Dynamic Logic for Learning Theory

DEFF Research Database (Denmark)

Baltag, Alexandru; Gierasimczuk, Nina; Özgün, Aybüke

2017-01-01

Building on previous work that bridged Formal Learning Theory and Dynamic Epistemic Logic in a topological setting, we introduce a Dynamic Logic for Learning Theory (DLLT), extending Subset Space Logics with dynamic observation modalities, as well as with a learning operator, which encodes the le...... the learner’s conjecture after observing a finite sequence of data. We completely axiomatise DLLT, study its expressivity and use it to characterise various notions of knowledge, belief, and learning. ...

Dynamic expression pattern of kinesin accessory protein in Drosophila

Indian Academy of Sciences (India)

Unknown

terization of the function of the DmKAP gene, we studied its expression pattern at different stages of development using the mRNA in .... region of the developing brain. ..... Kido M and Hirokawa N 1998 Randomization of left-right asymmetry ...

Predicting Expressive Dynamics in Piano Performances using Neural Networks

NARCIS (Netherlands)

van Herwaarden, Sam; Grachten, Maarten; de Haas, W. Bas

2014-01-01

This paper presents a model for predicting expressive accentuation in piano performances with neural networks. Using Restricted Boltzmann Machines (RBMs), features are learned from performance data, after which these features are used to predict performed loudness. During feature learning, data

Dynamic ductile fracture of a central crack

Science.gov (United States)

Tsai, Y. M.

1976-01-01

A central crack, symmetrically growing at a constant speed in a two dimensional ductile material subject to uniform tension at infinity, is investigated using the integral transform methods. The crack is assumed to be the Dugdale crack, and the finite stress condition at the crack tip is satisfied during the propagation of the crack. Exact expressions of solution are obtained for the finite stress condition at the crack tip, the crack shape, the crack opening displacement, and the energy release rate. All those expressions are written as the product of explicit dimensional quantities and a nondimensional dynamic correction function. The expressions reduce to the associated static results when the crack speed tends to zero, and the nondimensional dynamic correction functions were calculated for various values of the parameter involved.

Nonlinear dynamics and damage induced properties of soft matter with application in oncology

Science.gov (United States)

Naimark, O.

2017-09-01

Molecular-morphological signs of oncogenesis could be linked to multiscale collective effects in molecular, cell and tissue related to defects (damage) dynamics. It was shown that nonlinear behavior of biological systems can be linked to the existence of characteristic collective open state modes providing the coherent expression dynamics. New type of criticality in nonequilibrium systems with defects—structural-scaling transition allows the definition of the `driving force' for a biological soft matter related to consolidated open states. The set of collective open states (breathers, autosolitons and blow-up modes) in the molecular ensembles provides the collective expression dynamics to attract the entire system (cell, tissue) toward a few preferred global states. The co-existence of three types of collective modes determines the multifractal scenario of biological soft matter dynamics. The appearance of `globally convergent' dynamics corresponding to the coherent behavior of multiscale blow-up open states (blow-up gene expression) leads to anomalous localized softening (blow-up localized damage) and the subjection of the cells (or tissue) to monofractal dynamics. This dynamics can be associated with cancer progression.

Reconstructing Dynamic Promoter Activity Profiles from Reporter Gene Data.

Science.gov (United States)

Kannan, Soumya; Sams, Thomas; Maury, Jérôme; Workman, Christopher T

2018-03-16

Accurate characterization of promoter activity is important when designing expression systems for systems biology and metabolic engineering applications. Promoters that respond to changes in the environment enable the dynamic control of gene expression without the necessity of inducer compounds, for example. However, the dynamic nature of these processes poses challenges for estimating promoter activity. Most experimental approaches utilize reporter gene expression to estimate promoter activity. Typically the reporter gene encodes a fluorescent protein that is used to infer a constant promoter activity despite the fact that the observed output may be dynamic and is a number of steps away from the transcription process. In fact, some promoters that are often thought of as constitutive can show changes in activity when growth conditions change. For these reasons, we have developed a system of ordinary differential equations for estimating dynamic promoter activity for promoters that change their activity in response to the environment that is robust to noise and changes in growth rate. Our approach, inference of dynamic promoter activity (PromAct), improves on existing methods by more accurately inferring known promoter activity profiles. This method is also capable of estimating the correct scale of promoter activity and can be applied to quantitative data sets to estimate quantitative rates.

Correlative study of dynamic MRI and tumor angiogenesis in gastric carcinoma

International Nuclear Information System (INIS)

Tang Qunfeng; Shen Junkang; Feng Yizhong; Qian Minghui; Chai Yuhai

2004-01-01

Objective: To investigate the correlation between the dynamic MRI enhancement characteristics and tumor angiogenesis in gastric carcinoma. Methods: Histopathological slides of 30 patients underwent CD34 and vascular endothelial growth factor (VEGF) immunohistochemical staining. Microvessel density (MVD) and VEGF protein expression were analyzed with their relationship to pathological features. The dynamic MRI characteristics, including the maximum contrast enhancement ratio (CERmax), were correlatively studied with MVD and VEGF expression. Results: In 30 cases, MVD was 13.00 to 68.25 per vision field with an average of 42.95 ±14.79. The low expression rate of VEGF was 30% (9/30), while the high expression rate of VEGF was 70% (21/30). MVD and VEGF expression correlated with lymph node metastasis (P>0.05), but their relationships to the degree of differentiation and depth of invasion were not significant (P>0.05). MVD was related to TNM-staging of gastric carcinoma (P>0.05). The expression of VEGF between the stage I and IV had significant differences (P>0.05). MVD was higher in VEGF-high expression than in VEGF-low expression [(47.30 ± 14.16) per vision versus (32.81 ± 11.25) per vision]. CERmax was significantly correlated with MVD (r=0.556, P=0.0014). The distribution features and shape of microvessels within gastric carcinoma were related to the enhancement characteristics such as irregular enhancement and delaminated enhancement. The correlation between CERmax and expression of VEGF was not significant (t=-0.847, P=0.404). Conclusion: The manifestations on dynamic MR images can reflect the distribution features and shape of microvessels within gastric carcinoma. Dynamic MR imaging may prove to be a valuable means in estimating the MVD of gastric carcinoma noninvasively, and further predicting the biological behavior of gastric carcinoma and judging the prognosis. (authors)

Temporal protein expression pattern in intracellular signalling ...

Indian Academy of Sciences (India)

Supplementary figure 1. Protein expression dynamics observed in Experiment, Synchronous and. Asynchronous simulation. .... molecular basis for T cell suppression by IL-10: CD28-asso- ciated IL-10 receptor inhibits CD28 tyrosine ...

Dynamic expression of Lgr6 in the developing and mature mouse cochlea

Science.gov (United States)

Zhang, Yanping; Chen, Yan; Ni, Wenli; Guo, Luo; Lu, Xiaoling; Liu, Liman; Li, Wen; Sun, Shan; Wang, Lei; Li, Huawei

2015-01-01

The Wnt/β-catenin signaling pathway plays important roles in mammalian inner ear development. Lgr5, one of the downstream target genes of the Wnt/β-catenin signaling pathway, has been reported to be a marker for inner ear hair cell progenitors. Lgr6 shares approximately 50% sequence homology with Lgr5 and has been identified as a stem cell marker in several organs. However, the detailed expression profiles of Lgr6 have not yet been investigated in the mouse inner ear. Here, we first used Lgr6-EGFP-Ires-CreERT2 mice to examine the spatiotemporal expression of Lgr6 protein in the cochlear duct during embryonic and postnatal development. Lgr6-EGFP was first observed in one row of prosensory cells in the middle and basal turn at embryonic day 15.5 (E15.5). From E18.5 to postnatal day 3 (P3), the expression of Lgr6-EGFP was restricted to the inner pillar cells (IPCs). From P7 to P15, the Lgr6-EGFP expression level gradually decreased in the IPCs and gradually increased in the inner border cells (IBCs). At P20, Lgr6-EGFP was only expressed in the IBCs, and by P30 Lgr6-EGFP expression had completely disappeared. Next, we demonstrated that Wnt/β-catenin signaling is required to maintain the Lgr6-EGFP expression in vitro. Finally, we demonstrated that the Lgr6-EGFP-positive cells isolated by flow cytometry could differentiate into myosin 7a-positive hair cells after 10 days in-culture, and this suggests that the Lgr6-positive cells might serve as the hair cell progenitor cells in the cochlea. PMID:26029045

Dynamic Expression of Lgr6 in the Developing and Mature Mouse Cochlea

Directory of Open Access Journals (Sweden)

Yanping eZhang

2015-05-01

Full Text Available The Wnt/β-catenin signaling pathway plays important roles in mammalian inner ear development. Lgr5, one of the downstream target genes of the Wnt/β-catenin signaling pathway, has been reported to be a marker for inner ear hair cell progenitors. Lgr6 shares approximately 50% sequence homology with Lgr5 and has been identified as a stem cell marker in several organs. However, the detailed expression profiles of Lgr6 have not yet been investigated in the mouse inner ear. Here, we first used Lgr6-EGFP-Ires-CreERT2 mice to examine the spatiotemporal expression of Lgr6 protein in the cochlear duct during embryonic and postnatal development. Lgr6-EGFP was first observed in one row of prosensory cells in the middle and basal turn at embryonic day 15.5 (E15.5. From E18.5 to postnatal day 3 (P3, the expression of Lgr6-EGFP was restricted to the inner pillar cells (IPCs. From P7 to P15, the Lgr6-EGFP expression level gradually decreased in the IPCs and gradually increased in the inner border cells (IBCs. At P20, Lgr6-EGFP was only expressed in the IBCs, and by P30 Lgr6-EGFP expression had completely disappeared. Next, we demonstrated that Wnt/β-catenin signaling is required to maintain the Lgr6-EGFP expression in vitro. Finally, we demonstrated that the Lgr6-EGFP-positive cells isolated by flow cytometry could differentiate into myosin 7a-positive hair cells after 10 days in-culture, and this suggests that the Lgr6-positive cells might serve as the hair cell progenitor cells in the cochlea.

ANALYZING THE SPEECH EXPRESSIVENESS USING PROSODIC DYNAMIC CONTROL

Directory of Open Access Journals (Sweden)

Valentin Eugen Ghisa

2018-04-01

Full Text Available At the level of verbal communication, the prosodic support and emotional space is modelled as a nonlinear system described through some parameters extracted from the spectral model of vocal wave, respectively the outline of the fundamental frequency, the time and energy of sonorous segments, the duration of non-acoustic segments and breaks, the voice timbre etc. Through the discretised addressing of the spectral model, the aim is to optimise the prosodic characteristics extracted from local variations of the fundamental frequency, by a method of dynamic control.

ClC-3 Promotes Osteogenic Differentiation in MC3T3-E1 Cell After Dynamic Compression.

Science.gov (United States)

Wang, Dawei; Wang, Hao; Gao, Feng; Wang, Kun; Dong, Fusheng

2017-06-01

ClC-3 chloride channel has been proved to have a relationship with the expression of osteogenic markers during osteogenesis, persistent static compression can upregulate the expression of ClC-3 and regulate osteodifferentiation in osteoblasts. However, there was no study about the relationship between the expression of ClC-3 and osteodifferentiation after dynamic compression. In this study, we applied dynamic compression on MC3T3-E1 cells to detect the expression of ClC-3, runt-related transcription factor 2 (Runx2), bone morphogenic protein-2 (BMP-2), osteopontin (OPN), nuclear-associated antigen Ki67 (Ki67), and proliferating cell nuclear antigen (PCNA) in biopress system, then we investigated the expression of these genes after dynamic compression with Chlorotoxin (specific ClC-3 chloride channel inhibitor) added. Under transmission electron microscopy, there were more cell surface protrusions, rough surfaced endoplasmic reticulum, mitochondria, Golgi apparatus, abundant glycogen, and lysosomes scattered in the cytoplasm in MC3T3-E1 cells after dynamic compression. The nucleolus was more obvious. We found that ClC-3 was significantly up-regulated after dynamic compression. The compressive force also up-regulated Runx2, BMP-2, and OPN after dynamic compression for 2, 4 and 8 h. The proliferation gene Ki67 and PCNA did not show significantly change after dynamic compression for 8 h. Chlorotoxin did not change the expression of ClC-3 but reduced the expression of Runx2, BMP-2, and OPN after dynamic compression compared with the group without Cltx added. The data from the current study suggested that ClC-3 may promotes osteogenic differentiation in MC3T3-E1 cell after dynamic compression. J. Cell. Biochem. 118: 1606-1613, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Dynamic epigenetic regulation of gene expression during the life cycle of malaria parasite Plasmodium falciparum.

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Archna P Gupta

2013-02-01

Full Text Available Epigenetic mechanisms are emerging as one of the major factors of the dynamics of gene expression in the human malaria parasite, Plasmodium falciparum. To elucidate the role of chromatin remodeling in transcriptional regulation associated with the progression of the P. falciparum intraerythrocytic development cycle (IDC, we mapped the temporal pattern of chromosomal association with histone H3 and H4 modifications using ChIP-on-chip. Here, we have generated a broad integrative epigenomic map of twelve histone modifications during the P. falciparum IDC including H4K5ac, H4K8ac, H4K12ac, H4K16ac, H3K9ac, H3K14ac, H3K56ac, H4K20me1, H4K20me3, H3K4me3, H3K79me3 and H4R3me2. While some modifications were found to be associated with the vast majority of the genome and their occupancy was constant, others showed more specific and highly dynamic distribution. Importantly, eight modifications displaying tight correlations with transcript levels showed differential affinity to distinct genomic regions with H4K8ac occupying predominantly promoter regions while others occurred at the 5' ends of coding sequences. The promoter occupancy of H4K8ac remained unchanged when ectopically inserted at a different locus, indicating the presence of specific DNA elements that recruit histone modifying enzymes regardless of their broad chromatin environment. In addition, we showed the presence of multivalent domains on the genome carrying more than one histone mark, highlighting the importance of combinatorial effects on transcription. Overall, our work portrays a substantial association between chromosomal locations of various epigenetic markers, transcriptional activity and global stage-specific transitions in the epigenome.

Dynamic epigenetic regulation of gene expression during the life cycle of malaria parasite Plasmodium falciparum.

Science.gov (United States)

Gupta, Archna P; Chin, Wai Hoe; Zhu, Lei; Mok, Sachel; Luah, Yen-Hoon; Lim, Eng-How; Bozdech, Zbynek

2013-02-01

Epigenetic mechanisms are emerging as one of the major factors of the dynamics of gene expression in the human malaria parasite, Plasmodium falciparum. To elucidate the role of chromatin remodeling in transcriptional regulation associated with the progression of the P. falciparum intraerythrocytic development cycle (IDC), we mapped the temporal pattern of chromosomal association with histone H3 and H4 modifications using ChIP-on-chip. Here, we have generated a broad integrative epigenomic map of twelve histone modifications during the P. falciparum IDC including H4K5ac, H4K8ac, H4K12ac, H4K16ac, H3K9ac, H3K14ac, H3K56ac, H4K20me1, H4K20me3, H3K4me3, H3K79me3 and H4R3me2. While some modifications were found to be associated with the vast majority of the genome and their occupancy was constant, others showed more specific and highly dynamic distribution. Importantly, eight modifications displaying tight correlations with transcript levels showed differential affinity to distinct genomic regions with H4K8ac occupying predominantly promoter regions while others occurred at the 5' ends of coding sequences. The promoter occupancy of H4K8ac remained unchanged when ectopically inserted at a different locus, indicating the presence of specific DNA elements that recruit histone modifying enzymes regardless of their broad chromatin environment. In addition, we showed the presence of multivalent domains on the genome carrying more than one histone mark, highlighting the importance of combinatorial effects on transcription. Overall, our work portrays a substantial association between chromosomal locations of various epigenetic markers, transcriptional activity and global stage-specific transitions in the epigenome.

RNA-Seq reveals dynamic changes of gene expression in key stages of intestine regeneration in the sea cucumber Apostichopus japonicus. [corrected].

Directory of Open Access Journals (Sweden)

Lina Sun

Full Text Available BACKGROUND: Sea cucumbers (Holothuroidea; Echinodermata have the capacity to regenerate lost tissues and organs. Although the histological and cytological aspects of intestine regeneration have been extensively studied, little is known of the genetic mechanisms involved. There has, however, been a renewed effort to develop a database of Expressed Sequence Tags (ESTs in Apostichopus japonicus, an economically-important species that occurs in China. This is important for studies on genetic breeding, molecular markers and special physiological phenomena. We have also constructed a library of ESTs obtained from the regenerative body wall and intestine of A. japonicus. The database has increased to ~30000 ESTs. RESULTS: We used RNA-Seq to determine gene expression profiles associated with intestinal regeneration in A. japonicus at 3, 7, 14 and 21 days post evisceration (dpe. This was compared to profiles obtained from a normally-functioning intestine. Approximately 5 million (M reads were sequenced in every library. Over 2400 up-regulated genes (>10% and over 1000 down-regulated genes (~5% were observed at 3 and 7dpe (log2Ratio ≥ 1, FDR ≤ 0.001. Specific "Go terms" revealed that the DEGs (Differentially Expressed Genes performed an important function at every regeneration stage. Besides some expected pathways (for example, Ribosome and Spliceosome pathway term, the "Notch signaling pathway," the "ECM-receptor interaction" and the "Cytokine-cytokine receptor interaction" were significantly enriched. We also investigated the expression profiles of developmental genes, ECM-associated genes and Cytoskeletal genes. Twenty of the most important differentially expressed genes (DEGs were verified by Real-time PCR, which resulted in a trend concordance of almost 100% between the two techniques. CONCLUSION: Our studies demonstrated dynamic changes in global gene expression during intestine regeneration and presented a series of candidate genes and enriched

The MPI facial expression database--a validated database of emotional and conversational facial expressions.

Directory of Open Access Journals (Sweden)

Kathrin Kaulard

Full Text Available The ability to communicate is one of the core aspects of human life. For this, we use not only verbal but also nonverbal signals of remarkable complexity. Among the latter, facial expressions belong to the most important information channels. Despite the large variety of facial expressions we use in daily life, research on facial expressions has so far mostly focused on the emotional aspect. Consequently, most databases of facial expressions available to the research community also include only emotional expressions, neglecting the largely unexplored aspect of conversational expressions. To fill this gap, we present the MPI facial expression database, which contains a large variety of natural emotional and conversational expressions. The database contains 55 different facial expressions performed by 19 German participants. Expressions were elicited with the help of a method-acting protocol, which guarantees both well-defined and natural facial expressions. The method-acting protocol was based on every-day scenarios, which are used to define the necessary context information for each expression. All facial expressions are available in three repetitions, in two intensities, as well as from three different camera angles. A detailed frame annotation is provided, from which a dynamic and a static version of the database have been created. In addition to describing the database in detail, we also present the results of an experiment with two conditions that serve to validate the context scenarios as well as the naturalness and recognizability of the video sequences. Our results provide clear evidence that conversational expressions can be recognized surprisingly well from visual information alone. The MPI facial expression database will enable researchers from different research fields (including the perceptual and cognitive sciences, but also affective computing, as well as computer vision to investigate the processing of a wider range of natural

Microsoft Expression Web for dummies

CERN Document Server

Hefferman, Linda

2013-01-01

Expression Web is Microsoft's newest tool for creating and maintaining dynamic Web sites. This FrontPage replacement offers all the simple ""what-you-see-is-what-you-get"" tools for creating a Web site along with some pumped up new features for working with Cascading Style Sheets and other design options. Microsoft Expression Web For Dummies arrives in time for early adopters to get a feel for how to build an attractive Web site. Author Linda Hefferman teams up with longtime FrontPage For Dummies author Asha Dornfest to show the easy way for first-time Web designers, FrontPage ve

Expert Oracle Application Express Plug-Ins

CERN Document Server

D'Souza, Martin Giffy

2011-01-01

Expert Oracle Application Express Plugins is your "go to" book on the groundbreaking plugin architecture introduced in Oracle Application Express 4.0. Using the new APEX functionality, you can create well-packaged, documented, reusable components and reliably leverage your coding investments across many applications. Components you create can define new item and region types, specify validation processes, and present dynamic actions to client applications. You can design innovative and colorful ways to display information, such as displaying the temperature using an image of a thermometer, or

Protein-DNA binding dynamics predict transcriptional response to nutrients in archaea.

Science.gov (United States)

Todor, Horia; Sharma, Kriti; Pittman, Adrianne M C; Schmid, Amy K

2013-10-01

Organisms across all three domains of life use gene regulatory networks (GRNs) to integrate varied stimuli into coherent transcriptional responses to environmental pressures. However, inferring GRN topology and regulatory causality remains a central challenge in systems biology. Previous work characterized TrmB as a global metabolic transcription factor in archaeal extremophiles. However, it remains unclear how TrmB dynamically regulates its ∼100 metabolic enzyme-coding gene targets. Using a dynamic perturbation approach, we elucidate the topology of the TrmB metabolic GRN in the model archaeon Halobacterium salinarum. Clustering of dynamic gene expression patterns reveals that TrmB functions alone to regulate central metabolic enzyme-coding genes but cooperates with various regulators to control peripheral metabolic pathways. Using a dynamical model, we predict gene expression patterns for some TrmB-dependent promoters and infer secondary regulators for others. Our data suggest feed-forward gene regulatory topology for cobalamin biosynthesis. In contrast, purine biosynthesis appears to require TrmB-independent regulators. We conclude that TrmB is an important component for mediating metabolic modularity, integrating nutrient status and regulating gene expression dynamics alone and in concert with secondary regulators.

VEGFR-2 expression in HCC, dysplastic and regenerative liver nodules, and correlation with pre-biopsy Dynamic Contrast Enhanced CT

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Thaiss, W.M., E-mail: wolfgang.thaiss@med.uni-tuebingen.de [Eberhard Karls University, Department of Radiology, Diagnostic and Interventional Radiology, Hoppe-Seyler-Str. 3, D-72076 Tuebingen (Germany); Kaufmann, S., E-mail: sascha.kaufmann@med.uni-tuebingen.de [Eberhard Karls University, Department of Radiology, Diagnostic and Interventional Radiology, Hoppe-Seyler-Str. 3, D-72076 Tuebingen (Germany); Kloth, C., E-mail: christopher.kloth@med.uni-tuebingen.de [Eberhard Karls University, Department of Radiology, Diagnostic and Interventional Radiology, Hoppe-Seyler-Str. 3, D-72076 Tuebingen (Germany); Nikolaou, K., E-mail: konstantin.nikolaou@med.uni-tuebingen.de [Eberhard Karls University, Department of Radiology, Diagnostic and Interventional Radiology, Hoppe-Seyler-Str. 3, D-72076 Tuebingen (Germany); Bösmüller, H., E-mail: hans.boesmueller@med.uni-tuebingen.de [Eberhard Karls University, Department of Pathology, Liebermeisterstraße 8, D-72076 Tuebingen (Germany); Horger, M., E-mail: Marius.Horger@med.uni-tuebingen.de [Eberhard Karls University, Department of Radiology, Diagnostic and Interventional Radiology, Hoppe-Seyler-Str. 3, D-72076 Tuebingen (Germany)

2016-11-15

Highlights: • VEGFR-2-expression levels vary between HCC, dysplastic and regenerative liver nodules. • Perfusion parameters vary between these groups in blood flow, blood volume and HPI. • Strong correlations were observed between perfusion parameters and VEGFR-2-expression. • The results might influence diagnosis and therapy of anti-vascular therapeutic regimes. - Abstract: Purpose: To evaluate whether VEGFR-2-expression in hepatocellular carcinoma (HCC), dysplastic (DLN) and regenerative liver nodules (RLN) correlates with pre-histology, in vivo Dynamic Contrast Enhanced-Computed Tomography (DCE-CT) data as VEGFR-2-expression affects prognosis and therapeutic options. Materials and methods: 34 patients (63.6 ± 8.9 years, 7 females) underwent liver biopsy or surgery due to suspected HCC or dysplastic nodules after DCE-CT between 2009 and 2015 with no previous chemo- or interventional therapy. Immunohistochemistry staining for VEGFR-2 was performed using Immunoreactive-Remmele-Stegner-Score (IRS) for quantification. A 128-row CT-scanner was used for DCE-CT with assessment of perfusion parameters blood flow (BF), blood volume (BV), arterial liver perfusion (ALP), portal venous perfusion (PVP), and hepatic perfusion index (HPI). Results: Histology confirmed HCC (n = 10), DLN (n = 7) and RLN (n = 34). Mean IRS for VEGFR-2 in HCCs was 9.1 ± 3.0, 7.3 ± 1.6 for DLN and 5.2 ± 2.8 for RLN (p = 0.0004 for HCC vs. RLN). Perfusion values varied significantly between all three groups for BF and HPI (p < 0.001 and p < 0.0001) and for BV in HCC vs. RLN (p < 0.0001) and DLN vs. RLN (p = 0.0019). Strong correlations between VEGFR-2-IRS and perfusion parameters were observed for BF in HCC (r = 0.88, p < 0.01) and HPI in HCC and DLN (r = 0.85, p < 0.04; r = 0.9, p < 0.01). Conclusion: Immunostaining revealed different VEGFR-2-expression levels in HCC, dysplastic and regenerative liver nodules. Perfusion markers blood flow, blood volume and hepatic perfusion index

Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq.

Science.gov (United States)

Reinius, Björn; Mold, Jeff E; Ramsköld, Daniel; Deng, Qiaolin; Johnsson, Per; Michaëlsson, Jakob; Frisén, Jonas; Sandberg, Rickard

2016-11-01

Cellular heterogeneity can emerge from the expression of only one parental allele. However, it has remained controversial whether, or to what degree, random monoallelic expression of autosomal genes (aRME) is mitotically inherited (clonal) or stochastic (dynamic) in somatic cells, particularly in vivo. Here we used allele-sensitive single-cell RNA-seq on clonal primary mouse fibroblasts and freshly isolated human CD8 + T cells to dissect clonal and dynamic monoallelic expression patterns. Dynamic aRME affected a considerable portion of the cells' transcriptomes, with levels dependent on the cells' transcriptional activity. Notably, clonal aRME was detected, but it was surprisingly scarce (aRME occurs transiently within individual cells, and patterns of aRME are thus primarily scattered throughout somatic cell populations rather than, as previously hypothesized, confined to patches of clonally related cells.

Identification of highly synchronized subnetworks from gene expression data.

Science.gov (United States)

Gao, Shouguo; Wang, Xujing

2013-01-01

There has been a growing interest in identifying context-specific active protein-protein interaction (PPI) subnetworks through integration of PPI and time course gene expression data. However the interaction dynamics during the biological process under study has not been sufficiently considered previously. Here we propose a topology-phase locking (TopoPL) based scoring metric for identifying active PPI subnetworks from time series expression data. First the temporal coordination in gene expression changes is evaluated through phase locking analysis; The results are subsequently integrated with PPI to define an activity score for each PPI subnetwork, based on individual member expression, as well topological characteristics of the PPI network and of the expression temporal coordination network; Lastly, the subnetworks with the top scores in the whole PPI network are identified through simulated annealing search. Application of TopoPL to simulated data and to the yeast cell cycle data showed that it can more sensitively identify biologically meaningful subnetworks than the method that only utilizes the static PPI topology, or the additive scoring method. Using TopoPL we identified a core subnetwork with 49 genes important to yeast cell cycle. Interestingly, this core contains a protein complex known to be related to arrangement of ribosome subunits that exhibit extremely high gene expression synchronization. Inclusion of interaction dynamics is important to the identification of relevant gene networks.

Dynamic Open Inquiry Performances of High-School Biology Students

Science.gov (United States)

Zion, Michal; Sadeh, Irit

2010-01-01

In examining open inquiry projects among high-school biology students, we found dynamic inquiry performances expressed in two criteria: "changes occurring during inquiry" and "procedural understanding". Characterizing performances in a dynamic open inquiry project can shed light on both the procedural and epistemological…

The expression of VE-cadherin in breast cancer cells modulates cell dynamics as a function of tumor differentiation and promotes tumor-endothelial cell interactions.

Science.gov (United States)

Rezaei, Maryam; Cao, Jiahui; Friedrich, Katrin; Kemper, Björn; Brendel, Oliver; Grosser, Marianne; Adrian, Manuela; Baretton, Gustavo; Breier, Georg; Schnittler, Hans-Joachim

2018-01-01

The cadherin switch has profound consequences on cancer invasion and metastasis. The endothelial-specific vascular endothelial cadherin (VE-cadherin) has been demonstrated in diverse cancer types including breast cancer and is supposed to modulate tumor progression and metastasis, but underlying mechanisms need to be better understood. First, we evaluated VE-cadherin expression by tissue microarray in 392 cases of breast cancer tumors and found a diverse expression and distribution of VE-cadherin. Experimental expression of fluorescence-tagged VE-cadherin (VE-EGFP) in undifferentiated, fibroblastoid and E-cadherin-negative MDA-231 (MDA-VE-EGFP) as well as in differentiated E-cadherin-positive MCF-7 human breast cancer cell lines (MCF-VE-EGFP), respectively, displayed differentiation-dependent functional differences. VE-EGFP expression reversed the fibroblastoid MDA-231 cells to an epithelial-like phenotype accompanied by increased β-catenin expression, actin and vimentin remodeling, increased cell spreading and barrier function and a reduced migration ability due to formation of VE-cadherin-mediated cell junctions. The effects were largely absent in both MDA-VE-EGFP and in control MCF-EGFP cell lines. However, MCF-7 cells displayed a VE-cadherin-independent planar cell polarity and directed cell migration that both developed in MDA-231 only after VE-EGFP expression. Furthermore, VE-cadherin expression had no effect on tumor cell proliferation in monocultures while co-culturing with endothelial cells enhanced tumor cell proliferation due to integration of the tumor cells into monolayer where they form VE-cadherin-mediated cell contacts with the endothelium. We propose an interactive VE-cadherin-based crosstalk that might activate proliferation-promoting signals. Together, our study shows a VE-cadherin-mediated cell dynamics and an endothelial-dependent proliferation in a differentiation-dependent manner.

Developmental expression of Drosophila Wiskott-Aldrich Syndrome family proteins

Science.gov (United States)

Rodriguez-Mesa, Evelyn; Abreu-Blanco, Maria Teresa; Rosales-Nieves, Alicia E.; Parkhurst, Susan M.

2012-01-01

Background Wiskott-Aldrich Syndrome (WASP) family proteins participate in many cellular processes involving rearrangements of the actin cytoskeleton. To the date, four WASP subfamily members have been described in Drosophila: Wash, WASp, SCAR, and Whamy. Wash, WASp, and SCAR are essential during early Drosophila development where they function in orchestrating cytoplasmic events including membrane-cytoskeleton interactions. A mutant for Whamy has not yet been reported. Results We generated monoclonal antibodies that are specific to Drosophila Wash, WASp, SCAR, and Whamy, and use these to describe their spatial and temporal localization patterns. Consistent with the importance of WASP family proteins in flies, we find that Wash, WASp, SCAR, and Whamy are dynamically expressed throughout oogenesis and embryogenesis. For example, we find that Wash accumulates at the oocyte cortex. WASp is highly expressed in the PNS, while SCAR is the most abundantly expressed in the CNS. Whamy exhibits an asymmetric subcellular localization that overlaps with mitochondria and is highly expressed in muscle. Conclusion All four WASP family members show specific expression patterns, some of which reflect their previously known roles and others revealing new potential functions. The monoclonal antibodies developed offer valuable new tools to investigate how WASP family proteins regulate actin cytoskeleton dynamics. PMID:22275148

Interplay of Gene Expression Noise and Ultrasensitive Dynamics Affects Bacterial Operon Organization

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Ray, J. Christian J; Igoshin, Oleg A.

2012-01-01

Bacterial chromosomes are organized into polycistronic cotranscribed operons, but the evolutionary pressures maintaining them are unclear. We hypothesized that operons alter gene expression noise characteristics, resulting in selection for or against maintaining operons depending on network architecture. Mathematical models for 6 functional classes of network modules showed that three classes exhibited decreased noise and 3 exhibited increased noise with same-operon cotranscription of interacting proteins. Noise reduction was often associated with a decreased chance of reaching an ultrasensitive threshold. Stochastic simulations of the lac operon demonstrated that the predicted effects of transcriptional coupling hold for a complex network module. We employed bioinformatic analysis to find overrepresentation of noise-minimizing operon organization compared with randomized controls. Among constitutively expressed physically interacting protein pairs, higher coupling frequencies appeared at lower expression levels, where noise effects are expected to be dominant. Our results thereby suggest an important role for gene expression noise, in many cases interacting with an ultrasensitive switch, in maintaining or selecting for operons in bacterial chromosomes. PMID:22956903

Dynamic expression of viral and cellular microRNAs in infectious mononucleosis caused by primary Epstein-Barr virus infection in children.

Science.gov (United States)

Gao, Liwei; Ai, Junhong; Xie, Zhengde; Zhou, Chen; Liu, Chunyan; Zhang, Hui; Shen, Kunling

2015-12-03

Epstein-Barr virus (EBV) was the first virus identified to encode microRNAs (miRNAs). Both of viral and human cellular miRNAs are important in EBV infection. However, the dynamic expression profile of miRNAs during primary EBV infection was unknown. This study aimed to investigate the dynamic expression profile of viral and cellular miRNAs in infectious mononucleosis (IM) caused by primary EBV infection. The levels of viral and cellular miRNAs were measured in fifteen pediatric IM patients at three different time-points. Fifteen healthy children who were seropositive for EBV were enrolled in the control group. Relative expression levels of miRNAs were detected by quantitative real-time PCR (qPCR) assay. EBV-miR-BHRF1-1, 1-2-3P, miR-BART13-1, 19-3p, 11-3P, 12-1, and 16-1 in IM patients of early phase were significantly higher than in healthy children. Most cellular miRNAs of B cells, such as hsa-miR-155-5p, -34a-5p, -18b-5p, -181a-5p, and -142-5p were up-regulated; while most of cellular miRNAs of CD8 + T cells, such as hsa-miR-223, -29c-3p, -181a, -200a-3p, miR-155-5p, -146a, and -142-5p were down-regulated in IM patients. With disease progression, nearly all of EBV-miRNAs decreased, especially miR-BHRF1, but at a slower rate than EBV DNA loads. Most of the cellular miRNAs of B cells, including hsa-miR-134-5p, -18b-5p, -34a-5p, and -196a-5p increased with time. However, most of the cellular miRNAs of CD8 + T cells, including hsa-let-7a-5p, -142-3p, -142-5p, and -155-5p decreased with time. Additionally, hsa-miR-155-5p of B cells and hsa-miR-18b-5p of CD8+ T cells exhibited a positive correlation with miR-BHRF1-2-5P and miR-BART2-5P (0.96 ≤ r ≤ 0.99, P < 0.05). Finally, hsa-miR-181a-5p of B cells had positive correlation with miR-BART4-3p, 4-5P, 16-1, and 22 (0.97 ≤ r ≤ 0.99, P < 0.05). Our study is the first to describe the expression profile of viral and cellular miRNAs in IM caused by primary EBV infection. These results might be the basis of

The MPI Facial Expression Database — A Validated Database of Emotional and Conversational Facial Expressions

Science.gov (United States)

Kaulard, Kathrin; Cunningham, Douglas W.; Bülthoff, Heinrich H.; Wallraven, Christian

2012-01-01

The ability to communicate is one of the core aspects of human life. For this, we use not only verbal but also nonverbal signals of remarkable complexity. Among the latter, facial expressions belong to the most important information channels. Despite the large variety of facial expressions we use in daily life, research on facial expressions has so far mostly focused on the emotional aspect. Consequently, most databases of facial expressions available to the research community also include only emotional expressions, neglecting the largely unexplored aspect of conversational expressions. To fill this gap, we present the MPI facial expression database, which contains a large variety of natural emotional and conversational expressions. The database contains 55 different facial expressions performed by 19 German participants. Expressions were elicited with the help of a method-acting protocol, which guarantees both well-defined and natural facial expressions. The method-acting protocol was based on every-day scenarios, which are used to define the necessary context information for each expression. All facial expressions are available in three repetitions, in two intensities, as well as from three different camera angles. A detailed frame annotation is provided, from which a dynamic and a static version of the database have been created. In addition to describing the database in detail, we also present the results of an experiment with two conditions that serve to validate the context scenarios as well as the naturalness and recognizability of the video sequences. Our results provide clear evidence that conversational expressions can be recognized surprisingly well from visual information alone. The MPI facial expression database will enable researchers from different research fields (including the perceptual and cognitive sciences, but also affective computing, as well as computer vision) to investigate the processing of a wider range of natural facial expressions

The Effect of Fearful Expressions on Multiple Face Tracking

Directory of Open Access Journals (Sweden)

Hongjun Jin

2015-07-01

Full Text Available How does the visual system realize dynamic tracking? This topic has become popular within cognitive science in recent years. The classical theory argues that multiple object tracking is accomplished via pre-attention visual indexes as part of a cognitively impenetrable low-level visual system. The present research aimed to investigate whether and how tracking processes are influenced by facial expressions that convey abundant social information about one’s mental state and situated environment. The results showed that participants tracked fearful faces more effectively than neutral faces. However, this advantage was only present under the low-attentional load condition, and distractor face emotion did not impact tracking performance. These findings imply that visual tracking is not driven entirely by low-level vision and encapsulated by high-level representations; rather, that facial expressions, a kind of social information, are able to influence dynamic tracking. Furthermore, the effect of fearful expressions on multiple face tracking is mediated by the availability of attentional resources.

Dynamic stiffness of suction caissons

DEFF Research Database (Denmark)

Ibsen, Lars Bo; Liingaard, Morten; Andersen, Lars

This report concerns the dynamic soil-structure interaction of steel suction caissons applied as foundations for offshore wind turbines. An emphasis is put on torsional vibrations and coupled sliding/rocking motion, and the influence of the foundation geometry and the properties of the surrounding...... soil is examined. The soil is simplified as a homogenous linear viscoelastic material and the dynamic stiffness of the suction caisson is expressed in terms of dimensionless frequency-dependent coefficients corresponding to the different degrees of freedom. The dynamic stiffness coefficients...... for the skirted foundation are evaluated by means of a three-dimensional coupled boundary element/finite element model. Comparisons with known analytical and numerical solutions indicate that the static and dynamic behaviour of the foundation are predicted accurately with the applied model. The analysis has been...

Insights into the dynamics of hind leg development in honey bee (Apis mellifera L. queen and worker larvae - A morphology/differential gene expression analysis

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Carolina Gonçalves Santos

2015-09-01

Full Text Available Phenotypic plasticity is a hallmark of the caste systems of social insects, expressed in their life history and morphological traits. These are best studied in bees. In their co-evolution with angiosperm plants, the females of corbiculate bees have acquired a specialized structure on their hind legs for collecting pollen. In the highly eusocial bees (Apini and Meliponini, this structure is however only present in workers and absent in queens. By means of histological sections and cell proliferation analysis we followed the developmental dynamics of the hind legs of queens and workers in the fourth and fifth larval instars. In parallel, we generated subtractive cDNA libraries for hind leg discs of queen and worker larvae by means of a Representational Difference Analysis (RDA. From the total of 135 unique sequences we selected 19 for RT-qPCR analysis, where six of these were confirmed as differing significantly in their expression between the two castes in the larval spinning stage. The development of complex structures such as the bees’ hind legs, requires diverse patterning mechanisms and signaling modules, as indicated by the set of differentially expressed genes related with cell adhesion and signaling pathways.

Insights into the dynamics of hind leg development in honey bee (Apis mellifera L.) queen and worker larvae - A morphology/differential gene expression analysis

Science.gov (United States)

Santos, Carolina Gonçalves; Hartfelder, Klaus

2015-01-01

Phenotypic plasticity is a hallmark of the caste systems of social insects, expressed in their life history and morphological traits. These are best studied in bees. In their co-evolution with angiosperm plants, the females of corbiculate bees have acquired a specialized structure on their hind legs for collecting pollen. In the highly eusocial bees (Apini and Meliponini), this structure is however only present in workers and absent in queens. By means of histological sections and cell proliferation analysis we followed the developmental dynamics of the hind legs of queens and workers in the fourth and fifth larval instars. In parallel, we generated subtractive cDNA libraries for hind leg discs of queen and worker larvae by means of a Representational Difference Analysis (RDA). From the total of 135 unique sequences we selected 19 for RT-qPCR analysis, where six of these were confirmed as differing significantly in their expression between the two castes in the larval spinning stage. The development of complex structures such as the bees’ hind legs, requires diverse patterning mechanisms and signaling modules, as indicated by the set of differentially expressed genes related with cell adhesion and signaling pathways. PMID:26500430

Emotion regulation and the temporal dynamics of emotions: Effects of cognitive reappraisal and expressive suppression on emotional inertia.

Science.gov (United States)

Koval, Peter; Butler, Emily A; Hollenstein, Tom; Lanteigne, Dianna; Kuppens, Peter

2015-01-01

The tendency for emotions to be predictable over time, labelled emotional inertia, has been linked to low well-being and is thought to reflect impaired emotion regulation. However, almost no studies have examined how emotion regulation relates to emotional inertia. We examined the effects of cognitive reappraisal and expressive suppression on the inertia of behavioural, subjective and physiological measures of emotion. In Study 1 (N = 111), trait suppression was associated with higher inertia of negative behaviours. We replicated this finding experimentally in Study 2 (N = 186). Furthermore, in Study 2, instructed suppressors and reappraisers both showed higher inertia of positive behaviours, and reappraisers displayed higher inertia of heart rate. Neither suppression nor reappraisal were associated with the inertia of subjective feelings in either study. Thus, the effects of suppression and reappraisal on the temporal dynamics of emotions depend on the valence and emotional response component in question.

microRNA as a potential vector for the propagation of robustness in protein expression and oscillatory dynamics within a ceRNA network.

Directory of Open Access Journals (Sweden)

Claude Gérard

Full Text Available microRNAs (miRNAs are small noncoding RNAs that are important post-transcriptional regulators of gene expression. miRNAs can induce thresholds in protein synthesis. Such thresholds in protein output can be also achieved by oligomerization of transcription factors (TF for the control of gene expression. First, we propose a minimal model for protein expression regulated by miRNA and by oligomerization of TF. We show that miRNA and oligomerization of TF generate a buffer, which increases the robustness of protein output towards molecular noise as well as towards random variation of kinetics parameters. Next, we extend the model by considering that the same miRNA can bind to multiple messenger RNAs, which accounts for the dynamics of a minimal competing endogenous RNAs (ceRNAs network. The model shows that, through common miRNA regulation, TF can control the expression of all proteins formed by the ceRNA network, even if it drives the expression of only one gene in the network. The model further suggests that the threshold in protein synthesis mediated by the oligomerization of TF can be propagated to the other genes, which can increase the robustness of the expression of all genes in such ceRNA network. Furthermore, we show that a miRNA could increase the time delay of a "Goodwin-like" oscillator model, which may favor the occurrence of oscillations of large amplitude. This result predicts important roles of miRNAs in the control of the molecular mechanisms leading to the emergence of biological rhythms. Moreover, a model for the latter oscillator embedded in a ceRNA network indicates that the oscillatory behavior can be propagated, via the shared miRNA, to all proteins formed by such ceRNA network. Thus, by means of computational models, we show that miRNAs could act as vectors allowing the propagation of robustness in protein synthesis as well as oscillatory behaviors within ceRNA networks.

Cellular reprogramming dynamics follow a simple 1D reaction coordinate

Science.gov (United States)

Teja Pusuluri, Sai; Lang, Alex H.; Mehta, Pankaj; Castillo, Horacio E.

2018-01-01

Cellular reprogramming, the conversion of one cell type to another, induces global changes in gene expression involving thousands of genes, and understanding how cells globally alter their gene expression profile during reprogramming is an ongoing problem. Here we reanalyze time-course data on cellular reprogramming from differentiated cell types to induced pluripotent stem cells (iPSCs) and show that gene expression dynamics during reprogramming follow a simple 1D reaction coordinate. This reaction coordinate is independent of both the time it takes to reach the iPSC state as well as the details of the experimental protocol used. Using Monte-Carlo simulations, we show that such a reaction coordinate emerges from epigenetic landscape models where cellular reprogramming is viewed as a ‘barrier-crossing’ process between cell fates. Overall, our analysis and model suggest that gene expression dynamics during reprogramming follow a canonical trajectory consistent with the idea of an ‘optimal path’ in gene expression space for reprogramming.

Emotion attribution to basic parametric static and dynamic stimuli

NARCIS (Netherlands)

Visch, V.; Goudbeek, M.B.; Cohn, J.; Nijholt, A.; Pantic, P.

2009-01-01

The following research investigates the effect of basic visual stimuli on the attribution of basic emotions by the viewer. In an empirical study (N = 33) we used two groups of visually minimal expressive stimuli: dynamic and static. The dynamic stimuli consisted of an animated circle moving

Transformative Dynamics in Detailed Planning

DEFF Research Database (Denmark)

Quitzau, Maj-Britt; Poulsen, Naja; Gustavsson, Ted

Many of the ambitious sustainable strategies on how to integrate sustainable solutions expressed in urban development projects do not become materialized in the urban design. This paper aims to uncover the transformative dynamics involved in this translation process of materializing the formulate...

Mechanisms of gap gene expression canalization in the Drosophila blastoderm

Directory of Open Access Journals (Sweden)

Samsonova Maria G

2011-07-01

Full Text Available Abstract Background Extensive variation in early gap gene expression in the Drosophila blastoderm is reduced over time because of gap gene cross regulation. This phenomenon is a manifestation of canalization, the ability of an organism to produce a consistent phenotype despite variations in genotype or environment. The canalization of gap gene expression can be understood as arising from the actions of attractors in the gap gene dynamical system. Results In order to better understand the processes of developmental robustness and canalization in the early Drosophila embryo, we investigated the dynamical effects of varying spatial profiles of Bicoid protein concentration on the formation of the expression border of the gap gene hunchback. At several positions on the anterior-posterior axis of the embryo, we analyzed attractors and their basins of attraction in a dynamical model describing expression of four gap genes with the Bicoid concentration profile accounted as a given input in the model equations. This model was tested against a family of Bicoid gradients obtained from individual embryos. These gradients were normalized by two independent methods, which are based on distinct biological hypotheses and provide different magnitudes for Bicoid spatial variability. We showed how the border formation is dictated by the biological initial conditions (the concentration gradient of maternal Hunchback protein being attracted to specific attracting sets in a local vicinity of the border. Different types of these attracting sets (point attractors or one dimensional attracting manifolds define several possible mechanisms of border formation. The hunchback border formation is associated with intersection of the spatial gradient of the maternal Hunchback protein and a boundary between the attraction basins of two different point attractors. We demonstrated how the positional variability for hunchback is related to the corresponding variability of the

Notch-RBP-J signaling regulates the mobilization and function of endothelial progenitor cells by dynamic modulation of CXCR4 expression in mice.

Directory of Open Access Journals (Sweden)

Lin Wang

Full Text Available Bone marrow (BM-derived endothelial progenitor cells (EPC have therapeutic potentials in promoting tissue regeneration, but how these cells are modulated in vivo has been elusive. Here, we report that RBP-J, the critical transcription factor mediating Notch signaling, modulates EPC through CXCR4. In a mouse partial hepatectomy (PHx model, RBP-J deficient EPC showed attenuated capacities of homing and facilitating liver regeneration. In resting mice, the conditional deletion of RBP-J led to a decrease of BM EPC, with a concomitant increase of EPC in the peripheral blood. This was accompanied by a down-regulation of CXCR4 on EPC in BM, although CXCR4 expression on EPC in the circulation was up-regulated in the absence of RBP-J. PHx in RBP-J deficient mice induced stronger EPC mobilization. In vitro, RBP-J deficient EPC showed lowered capacities of adhering, migrating, and forming vessel-like structures in three-dimensional cultures. Over-expression of CXCR4 could at least rescue the defects in vessel formation by the RBP-J deficient EPC. These data suggested that the RBP-J-mediated Notch signaling regulated EPC mobilization and function, at least partially through dynamic modulation of CXCR4 expression. Our findings not only provide new insights into the regulation of EPC, but also have implications for clinical therapies using EPC in diseases.

Towards Dynamic Updates in Service Composition

Directory of Open Access Journals (Sweden)

Mario Bravetti

2015-12-01

Full Text Available We survey our results about verification of adaptable processes. We present adaptable processes as a way of overcoming the limitations that process calculi have for describing patterns of dynamic process evolution. Such patterns rely on direct ways of controlling the behavior and location of running processes, and so they are at the heart of the adaptation capabilities present in many modern concurrent systems. Adaptable processes have named scopes and are sensible to actions of dynamic update at runtime; this allows to express dynamic and static topologies of adaptable processes as well as different evolvability patterns for concurrent processes. We introduce a core calculus of adaptable processes and consider verification problems for them: first based on specific properties related to error occurrence, that we call bounded and eventual adaptation, and then by considering a simple yet expressive temporal logic over adaptable processes. We provide (undecidability results of such verification problems over adaptable processes considering the spectrum of topologies/evolvability patterns introduced. We then consider distributed adaptability, where a process can update part of a protocol by performing dynamic distributed updates over a set of protocol participants. Dynamic updates in this context are presented as an extension of our work on choreographies and behavioural contracts in multiparty interactions. We show how update mechanisms considered for adaptable processes can be used to extend the theory of choreography and orchestration/contracts, allowing them to be modified at run-time by internal (self-adaptation or external intervention.

Dynamic Musical Communication of Core Affect

Directory of Open Access Journals (Sweden)

Nicole eFlaig

2014-03-01

Full Text Available Is there something special about the way music communicates feelings? Theorists since Meyer (1956 have attempted to explain how music could stimulate varied and subtle affective experiences by violating learned expectancies, or by mimicking other forms of social interaction. Our proposal is that music speaks to the brain in its own language; it need not imitate any other form of communication. We review recent theoretical and empirical literature, which suggests that all conscious processes consist of dynamic neural events, produced by spatially dispersed processes in the physical brain. Intentional thought and affective experience arise as dynamical aspects of neural events taking place in multiple brain areas simultaneously. At any given moment, this content comprises a unified scene that is integrated into a dynamic core through synchrony of neuronal oscillations. We propose that 1 neurodynamic synchrony with musical stimuli gives rise to musical qualia including tonal and temporal expectancies, and that 2 music-synchronous responses couple into core neurodynamics, enabling music to directly modulate core affect. Expressive music performance, for example, may recruit rhythm-synchronous neural responses to support affective communication. We suggest that the dynamic relationship between musical expression and the experience of affect presents a unique opportunity for the study of emotional experience. This may help elucidate the neural mechanisms underlying arousal and valence, and offer a new approach to exploring the complex dynamics of the how and why of emotional experience.

The Influence of Gene Expression Time Delays on Gierer–Meinhardt Pattern Formation Systems

KAUST Repository

Seirin Lee, S.

2010-03-23

There are numerous examples of morphogen gradients controlling long range signalling in developmental and cellular systems. The prospect of two such interacting morphogens instigating long range self-organisation in biological systems via a Turing bifurcation has been explored, postulated, or implicated in the context of numerous developmental processes. However, modelling investigations of cellular systems typically neglect the influence of gene expression on such dynamics, even though transcription and translation are observed to be important in morphogenetic systems. In particular, the influence of gene expression on a large class of Turing bifurcation models, namely those with pure kinetics such as the Gierer-Meinhardt system, is unexplored. Our investigations demonstrate that the behaviour of the Gierer-Meinhardt model profoundly changes on the inclusion of gene expression dynamics and is sensitive to the sub-cellular details of gene expression. Features such as concentration blow up, morphogen oscillations and radical sensitivities to the duration of gene expression are observed and, at best, severely restrict the possible parameter spaces for feasible biological behaviour. These results also indicate that the behaviour of Turing pattern formation systems on the inclusion of gene expression time delays may provide a means of distinguishing between possible forms of interaction kinetics. Finally, this study also emphasises that sub-cellular and gene expression dynamics should not be simply neglected in models of long range biological pattern formation via morphogens. © 2010 Society for Mathematical Biology.

Decoding facial expressions based on face-selective and motion-sensitive areas.

Science.gov (United States)

Liang, Yin; Liu, Baolin; Xu, Junhai; Zhang, Gaoyan; Li, Xianglin; Wang, Peiyuan; Wang, Bin

2017-06-01

Humans can easily recognize others' facial expressions. Among the brain substrates that enable this ability, considerable attention has been paid to face-selective areas; in contrast, whether motion-sensitive areas, which clearly exhibit sensitivity to facial movements, are involved in facial expression recognition remained unclear. The present functional magnetic resonance imaging (fMRI) study used multi-voxel pattern analysis (MVPA) to explore facial expression decoding in both face-selective and motion-sensitive areas. In a block design experiment, participants viewed facial expressions of six basic emotions (anger, disgust, fear, joy, sadness, and surprise) in images, videos, and eyes-obscured videos. Due to the use of multiple stimulus types, the impacts of facial motion and eye-related information on facial expression decoding were also examined. It was found that motion-sensitive areas showed significant responses to emotional expressions and that dynamic expressions could be successfully decoded in both face-selective and motion-sensitive areas. Compared with static stimuli, dynamic expressions elicited consistently higher neural responses and decoding performance in all regions. A significant decrease in both activation and decoding accuracy due to the absence of eye-related information was also observed. Overall, the findings showed that emotional expressions are represented in motion-sensitive areas in addition to conventional face-selective areas, suggesting that motion-sensitive regions may also effectively contribute to facial expression recognition. The results also suggested that facial motion and eye-related information played important roles by carrying considerable expression information that could facilitate facial expression recognition. Hum Brain Mapp 38:3113-3125, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Dynamic T-lymphocyte chemokine receptor expression induced by interferon-beta therapy in multiple sclerosis

DEFF Research Database (Denmark)

Krakauer, M; Sorensen, P S; Khademi, M

2006-01-01

chemokine receptor (CXCR)3 was unaltered. Conversely, at 9-12 h after the most recent IFN-beta injection, CCR4, CCR5 and CCR7 expressions were unaltered, while CXCR3 expression was reduced. CD4(+) T-cell surface expression of CCR4 was significantly lower in untreated MS patients compared with healthy...

DMPD: LPS induction of gene expression in human monocytes. [Dynamic Macrophage Pathway CSML Database

Lifescience Database Archive (English)

Full Text Available 11257452 LPS induction of gene expression in human monocytes. Guha M, Mackman N. Ce...ll Signal. 2001 Feb;13(2):85-94. (.png) (.svg) (.html) (.csml) Show LPS induction of gene expression in human... monocytes. PubmedID 11257452 Title LPS induction of gene expression in human monocytes. Authors Guha M, Ma

Identify Dynamic Network Modules with Temporal and Spatial Constraints

Energy Technology Data Exchange (ETDEWEB)

Jin, R; McCallen, S; Liu, C; Almaas, E; Zhou, X J

2007-09-24

Despite the rapid accumulation of systems-level biological data, understanding the dynamic nature of cellular activity remains a difficult task. The reason is that most biological data are static, or only correspond to snapshots of cellular activity. In this study, we explicitly attempt to detangle the temporal complexity of biological networks by using compilations of time-series gene expression profiling data.We define a dynamic network module to be a set of proteins satisfying two conditions: (1) they form a connected component in the protein-protein interaction (PPI) network; and (2) their expression profiles form certain structures in the temporal domain. We develop the first efficient mining algorithm to discover dynamic modules in a temporal network, as well as frequently occurring dynamic modules across many temporal networks. Using yeast as a model system, we demonstrate that the majority of the identified dynamic modules are functionally homogeneous. Additionally, many of them provide insight into the sequential ordering of molecular events in cellular systems. We further demonstrate that identifying frequent dynamic network modules can significantly increase the signal to noise separation, despite the fact that most dynamic network modules are highly condition-specific. Finally, we note that the applicability of our algorithm is not limited to the study of PPI systems, instead it is generally applicable to the combination of any type of network and time-series data.

The BOLD signal in the amygdala does not differentiate between dynamic facial expressions

NARCIS (Netherlands)

van der Gaag, Christiaan; Minderaa, Ruud B.; Keysers, Christian

The amygdala has been considered to be essential for recognizing fear in other people's facial expressions. Recent studies shed doubt on this interpretation. Here we used movies of facial expressions instead of static photographs to investigate the putative fear selectivity of the amygdala using

The dynamical behaviour of SS 433

International Nuclear Information System (INIS)

Collins, G.W. II

1985-01-01

In this paper a dynamical formalism is developed for describing the motion of a distorted object moving under the influence of the gravitational fields present in a close binary system. The object is assumed to be centred about one of the components and to have a form or shape sustained by axial forces such as rotation in addition to tides generated by the companion. Although such a shape will not be temporally constant, the moments of inertia are expressible in terms of the canonical coordinates of the problem and vary in a periodic manner. The dynamical behaviour of this 'elastic' body can be expressed in terms of periodic motion analogous to that found in a rigid body. The details of the resultant motion in turn places constraints on the nature of the components of the system. (author)

Facial Expression Recognition Through Machine Learning

Directory of Open Access Journals (Sweden)

Nazia Perveen

2015-08-01

Full Text Available Facial expressions communicate non-verbal cues which play an important role in interpersonal relations. Automatic recognition of facial expressions can be an important element of normal human-machine interfaces it might likewise be utilized as a part of behavioral science and in clinical practice. In spite of the fact that people perceive facial expressions for all intents and purposes immediately solid expression recognition by machine is still a challenge. From the point of view of automatic recognition a facial expression can be considered to comprise of disfigurements of the facial parts and their spatial relations or changes in the faces pigmentation. Research into automatic recognition of the facial expressions addresses the issues encompassing the representation and arrangement of static or dynamic qualities of these distortions or face pigmentation. We get results by utilizing the CVIPtools. We have taken train data set of six facial expressions of three persons and for train data set purpose we have total border mask sample 90 and 30 border mask sample for test data set purpose and we use RST- Invariant features and texture features for feature analysis and then classified them by using k- Nearest Neighbor classification algorithm. The maximum accuracy is 90.

Common cues to emotion in the dynamic facial expressions of speech and song.

Science.gov (United States)

Livingstone, Steven R; Thompson, William F; Wanderley, Marcelo M; Palmer, Caroline

2015-01-01

Speech and song are universal forms of vocalization that may share aspects of emotional expression. Research has focused on parallels in acoustic features, overlooking facial cues to emotion. In three experiments, we compared moving facial expressions in speech and song. In Experiment 1, vocalists spoke and sang statements each with five emotions. Vocalists exhibited emotion-dependent movements of the eyebrows and lip corners that transcended speech-song differences. Vocalists' jaw movements were coupled to their acoustic intensity, exhibiting differences across emotion and speech-song. Vocalists' emotional movements extended beyond vocal sound to include large sustained expressions, suggesting a communicative function. In Experiment 2, viewers judged silent videos of vocalists' facial expressions prior to, during, and following vocalization. Emotional intentions were identified accurately for movements during and after vocalization, suggesting that these movements support the acoustic message. Experiment 3 compared emotional identification in voice-only, face-only, and face-and-voice recordings. Emotion judgements for voice-only singing were poorly identified, yet were accurate for all other conditions, confirming that facial expressions conveyed emotion more accurately than the voice in song, yet were equivalent in speech. Collectively, these findings highlight broad commonalities in the facial cues to emotion in speech and song, yet highlight differences in perception and acoustic-motor production.

Perfusion parameters of dynamic contrast-enhanced magnetic resonance imaging in patients with rectal cancer: Correlation with microvascular density and vascular endothelial growth factor expression

International Nuclear Information System (INIS)

Kim, Yeo Eun; Lim, Joon Seok; Kim, Myeong Jin; Kim, Ki Whang; Choi, Jun Jeong; Kim, Dae Hong; Myoung, Sung Min

2013-01-01

To determine whether quantitative perfusion parameters of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) correlate with immunohistochemical markers of angiogenesis in rectal cancer. Preoperative DCE-MRI was performed in 63 patients with rectal adenocarcinoma. Transendothelial volume transfer (K trans ) and fractional volume of the extravascular-extracellular space (Ve) were measured by Interactive Data Language software in rectal cancer. After surgery, microvessel density (MVD) and vascular endothelial growth factor (VEGF) expression scores were determined using immunohistochemical staining of rectal cancer specimens. Perfusion parameters (K trans , Ve) of DCE-MRI in rectal cancer were found to be correlated with MVD and VEGF expression scores by Spearman's rank coefficient analysis. T stage and N stage (negative or positive) were correlated with perfusion parameters and MVD. Significant correlation was not found between any DCE-MRI perfusion parameters and MVD (rs = -0.056 and p 0.662 for K trans ; rs = -0.103 and p = 0.416 for Ve), or between any DCE-MRI perfusion parameters and the VEGF expression score (rs = -0.042, p 0.741 for K trans ; r = 0.086, p = 0.497 for Ve) in rectal cancer. TN stage showed no significant correlation with perfusion parameters or MVD (p > 0.05 for all). DCE-MRI perfusion parameters, K trans and Ve, correlated poorly with MVD and VEGF expression scores in rectal cancer, suggesting that these parameters do not simply denote static histological vascular properties.

Dynamic epigenetic responses to muscle contraction

DEFF Research Database (Denmark)

Rasmussen, Morten; Zierath, Juleen R; Barrès, Romain

2014-01-01

Skeletal muscle is a malleable organ that responds to a single acute exercise bout by inducing the expression of genes involved in structural, metabolic and functional adaptations. Several epigenetic mechanisms including histone H4 deacetylation and loss of promoter methylation have been implicated...... in modifying exercise-responsive gene expression. These transient changes suggest that epigenetic mechanisms are not restricted to early stages of human development but are broad dynamic controllers of genomic plasticity in response to environmental factors....

On the Dynamics of the Furuta Pendulum

Directory of Open Access Journals (Sweden)

Benjamin Seth Cazzolato

2011-01-01

Full Text Available The Furuta pendulum, or rotational inverted pendulum, is a system found in many control labs. It provides a compact yet impressive platform for control demonstrations and draws the attention of the control community as a platform for the development of nonlinear control laws. Despite the popularity of the platform, there are very few papers which employ the correct dynamics and only one that derives the full system dynamics. In this paper, the full dynamics of the Furuta pendulum are derived using two methods: a Lagrangian formulation and an iterative Newton-Euler formulation. Approximations are made to the full dynamics which converge to the more commonly presented expressions. The system dynamics are then linearised using a Jacobian. To illustrate the influence the commonly neglected inertia terms have on the system dynamics, a brief example is offered.

Planar multibody dynamics formulation, programming and applications

CERN Document Server

Nikravesh, Parviz E

2007-01-01

Introduction Multibody Mechanical Systems Types of Analyses Methods of Formulation Computer Programming Application Examples Unit System Remarks Preliminaries Reference Axes Scalars and Vectors Matrices Vector, Array, and Matrix Differentiation Equations and Expressions Remarks Problems Fundamentals of Kinematics A Particle Kinematics of a Rigid Body Definitions Remarks Problems Fundamentals of Dynamics Newton's Laws of Motion Dynamics of a Body Force Elements Applied Forces Reaction Force Remarks Problems Point-Coordinates: Kinematics Multipoint

Violations of conservation laws in viscous liquid dynamics

DEFF Research Database (Denmark)

Dyre, Jeppe

2007-01-01

The laws expressing conservation of momentum and energy apply to any isolated system, but these laws are violated for highly viscous liquids under laboratory conditions because of the unavoidable interactions with the measuring equipment over the long times needed to study the dynamics. Moreover,......, although particle number conservation applies strictly for any liquid, the solidity of viscous liquids implies that even this conservation law is apparently violated in coarse-grained descriptions of density fluctuations.......The laws expressing conservation of momentum and energy apply to any isolated system, but these laws are violated for highly viscous liquids under laboratory conditions because of the unavoidable interactions with the measuring equipment over the long times needed to study the dynamics. Moreover...

Judgments of subtle facial expressions of emotion.

Science.gov (United States)

Matsumoto, David; Hwang, Hyisung C

2014-04-01

Most studies on judgments of facial expressions of emotion have primarily utilized prototypical, high-intensity expressions. This paper examines judgments of subtle facial expressions of emotion, including not only low-intensity versions of full-face prototypes but also variants of those prototypes. A dynamic paradigm was used in which observers were shown a neutral expression followed by the target expression to judge, and then the neutral expression again, allowing for a simulation of the emergence of the expression from and then return to a baseline. We also examined how signal and intensity clarities of the expressions (explained more fully in the Introduction) were associated with judgment agreement levels. Low-intensity, full-face prototypical expressions of emotion were judged as the intended emotion at rates significantly greater than chance. A number of the proposed variants were also judged as the intended emotions. Both signal and intensity clarities were individually associated with agreement rates; when their interrelationships were taken into account, signal clarity independently predicted agreement rates but intensity clarity did not. The presence or absence of specific muscles appeared to be more important to agreement rates than their intensity levels, with the exception of the intensity of zygomatic major, which was positively correlated with agreement rates for judgments of joy.

Physical exercise in aging human skeletal muscle increases mitochondrial calcium uniporter expression levels and affects mitochondria dynamics.

Science.gov (United States)

Zampieri, Sandra; Mammucari, Cristina; Romanello, Vanina; Barberi, Laura; Pietrangelo, Laura; Fusella, Aurora; Mosole, Simone; Gherardi, Gaia; Höfer, Christian; Löfler, Stefan; Sarabon, Nejc; Cvecka, Jan; Krenn, Matthias; Carraro, Ugo; Kern, Helmut; Protasi, Feliciano; Musarò, Antonio; Sandri, Marco; Rizzuto, Rosario

2016-12-01

Age-related sarcopenia is characterized by a progressive loss of muscle mass with decline in specific force, having dramatic consequences on mobility and quality of life in seniors. The etiology of sarcopenia is multifactorial and underlying mechanisms are currently not fully elucidated. Physical exercise is known to have beneficial effects on muscle trophism and force production. Alterations of mitochondrial Ca 2+ homeostasis regulated by mitochondrial calcium uniporter (MCU) have been recently shown to affect muscle trophism in vivo in mice. To understand the relevance of MCU-dependent mitochondrial Ca 2+ uptake in aging and to investigate the effect of physical exercise on MCU expression and mitochondria dynamics, we analyzed skeletal muscle biopsies from 70-year-old subjects 9 weeks trained with either neuromuscular electrical stimulation (ES) or leg press. Here, we demonstrate that improved muscle function and structure induced by both trainings are linked to increased protein levels of MCU Ultrastructural analyses by electron microscopy showed remodeling of mitochondrial apparatus in ES-trained muscles that is consistent with an adaptation to physical exercise, a response likely mediated by an increased expression of mitochondrial fusion protein OPA1. Altogether these results indicate that the ES-dependent physiological effects on skeletal muscle size and force are associated with changes in mitochondrial-related proteins involved in Ca 2+ homeostasis and mitochondrial shape. These original findings in aging human skeletal muscle confirm the data obtained in mice and propose MCU and mitochondria-related proteins as potential pharmacological targets to counteract age-related muscle loss. © 2016 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of The Physiological Society and the American Physiological Society.

DMPD: Iron regulation of hepatic macrophage TNFalpha expression. [Dynamic Macrophage Pathway CSML Database

Lifescience Database Archive (English)

Full Text Available 11841920 Iron regulation of hepatic macrophage TNFalpha expression. Tsukamoto H. Fr...ee Radic Biol Med. 2002 Feb 15;32(4):309-13. (.png) (.svg) (.html) (.csml) Show Iron regulation of hepatic macrophage... TNFalpha expression. PubmedID 11841920 Title Iron regulation of hepatic macrophage TNFalpha expres

A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums

Energy Technology Data Exchange (ETDEWEB)

Shakoor, N; Nair, R; Crasta, O; Morris, G; Feltus, A; Kresovich, S

2014-01-23

Background: Effective improvement in sorghum crop development necessitates a genomics-based approach to identify functional genes and QTLs. Sequenced in 2009, a comprehensive annotation of the sorghum genome and the development of functional genomics resources is key to enable the discovery and deployment of regulatory and metabolic genes and gene networks for crop improvement. Results: This study utilizes the first commercially available whole-transcriptome sorghum microarray (Sorgh-WTa520972F) to identify tissue and genotype-specific expression patterns for all identified Sorghum bicolor exons and UTRs. The genechip contains 1,026,373 probes covering 149,182 exons (27,577 genes) across the Sorghum bicolor nuclear, chloroplast, and mitochondrial genomes. Specific probesets were also included for putative non-coding RNAs that may play a role in gene regulation (e. g., microRNAs), and confirmed functional small RNAs in related species (maize and sugarcane) were also included in our array design. We generated expression data for 78 samples with a combination of four different tissue types (shoot, root, leaf and stem), two dissected stem tissues (pith and rind) and six diverse genotypes, which included 6 public sorghum lines (R159, Atlas, Fremont, PI152611, AR2400 and PI455230) representing grain, sweet, forage, and high biomass ideotypes. Conclusions: Here we present a summary of the microarray dataset, including analysis of tissue-specific gene expression profiles and associated expression profiles of relevant metabolic pathways. With an aim to enable identification and functional characterization of genes in sorghum, this expression atlas presents a new and valuable resource to the research community.

Dynamics of the surveying gyrocompass

Science.gov (United States)

Petrenko, V. E.; Zakharenko, S. A.; Ponomarenko, A. E.

The dynamics of the surveying gyrocompass is investigated analytically for the case of perturbations due to ball bearing imperfections. Approximate analytical expressions are obtained for calculating the natural frequencies of the compass in the presence of parametric perturbations of this kind. An example of natural frequency calculations is presented.

Prediction of dynamic expected time to system failure

Energy Technology Data Exchange (ETDEWEB)

Oh, Deog Yeon; Lee, Chong Chul [Korea Nuclear Fuel Co., Ltd., Taejon (Korea, Republic of)

1998-12-31

The mean time to failure (MTTF) expressing the mean value of the system life is a measure of system effectiveness. To estimate the remaining life of component and/or system, the dynamic mean time to failure concept is suggested. It is the time-dependent property depending on the status of components. The Kalman filter is used to estimate the reliability of components using the on-line information (directly measured sensor output or device-specific diagnostics in the intelligent sensor) in form of the numerical value (state factor). This factor considers the persistency of the fault condition and confidence level in measurement. If there is a complex system with many components, each calculated reliability`s of components are combined, which results in the dynamic MTTF of system. The illustrative examples are discussed. The results show that the dynamic MTTF can well express the component and system failure behaviour whether any kinds of failure are occurred or not. 9 refs., 6 figs. (Author)

Prediction of dynamic expected time to system failure

Energy Technology Data Exchange (ETDEWEB)

Oh, Deog Yeon; Lee, Chong Chul [Korea Nuclear Fuel Co., Ltd., Taejon (Korea, Republic of)

1997-12-31

The mean time to failure (MTTF) expressing the mean value of the system life is a measure of system effectiveness. To estimate the remaining life of component and/or system, the dynamic mean time to failure concept is suggested. It is the time-dependent property depending on the status of components. The Kalman filter is used to estimate the reliability of components using the on-line information (directly measured sensor output or device-specific diagnostics in the intelligent sensor) in form of the numerical value (state factor). This factor considers the persistency of the fault condition and confidence level in measurement. If there is a complex system with many components, each calculated reliability`s of components are combined, which results in the dynamic MTTF of system. The illustrative examples are discussed. The results show that the dynamic MTTF can well express the component and system failure behaviour whether any kinds of failure are occurred or not. 9 refs., 6 figs. (Author)

Neighboring Genes Show Correlated Evolution in Gene Expression

Science.gov (United States)

Ghanbarian, Avazeh T.; Hurst, Laurence D.

2015-01-01

When considering the evolution of a gene’s expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking. PMID:25743543

On the Expressive Power of Temporal Concurrent Constraint Programming Languages

DEFF Research Database (Denmark)

Nielsen, Mogens; Palamidessi, Catuscia; Valencia, Frank D.

2002-01-01

The tcc paradigm is a formalism for timed concurrent constraint programming. Several tcc languages differing in their way of expressing infinite behavior have been proposed in the literature. In this paper we study the expressive power of some of these languages. In particular, we show that: (1......) recursive procedures with parameters can be encoded into parameterless recursive procedures with dynamic scoping, and viceversa. (2) replication can be encoded into parameterless recursive procedures with static scoping, and viceversa. (3) the languages from (1) are strictly more expressive than...

The Influence of Gene Expression Time Delays on Gierer–Meinhardt Pattern Formation Systems

KAUST Repository

Seirin Lee, S.; Gaffney, E. A.; Monk, N. A. M.

2010-01-01

investigations demonstrate that the behaviour of the Gierer-Meinhardt model profoundly changes on the inclusion of gene expression dynamics and is sensitive to the sub-cellular details of gene expression. Features such as concentration blow up, morphogen

Consistent dynamical and statistical description of fission and comparison

Energy Technology Data Exchange (ETDEWEB)

Shunuan, Wang [Chinese Nuclear Data Center, Beijing, BJ (China)

1996-06-01

The research survey of consistent dynamical and statistical description of fission is briefly introduced. The channel theory of fission with diffusive dynamics based on Bohr channel theory of fission and Fokker-Planck equation and Kramers-modified Bohr-Wheeler expression according to Strutinsky method given by P.Frobrich et al. are compared and analyzed. (2 figs.).

Dynamic stiffness of suction caissons - vertical vibrations

Energy Technology Data Exchange (ETDEWEB)

Ibsen, Lars Bo; Liingaard, M.; Andersen, Lars

2006-12-15

The dynamic response of offshore wind turbines are affected by the properties of the foundation and the subsoil. The purpose of this report is to evaluate the dynamic soil-structure interaction of suction caissons for offshore wind turbines. The investigation is limited to a determination of the vertical dynamic stiffness of suction caissons. The soil surrounding the foundation is homogenous with linear viscoelastic properties. The dynamic stiffness of the suction caisson is expressed by dimensionless frequency-dependent dynamic stiffness coefficients corresponding to the vertical degree of freedom. The dynamic stiffness coefficients for the foundations are evaluated by means of a dynamic three-dimensional coupled Boundary Element/Finite Element model. Comparisons are made with known analytical and numerical solutions in order to evaluate the static and dynamic behaviour of the Boundary Element/Finite Element model. The vertical frequency dependent stiffness has been determined for different combinations of the skirt length, Poisson's ratio and the ratio between soil stiffness and skirt stiffness. Finally the dynamic behaviour at high frequencies is investigated. (au)

The role of emotion in dynamic audiovisual integration of faces and voices.

Science.gov (United States)

Kokinous, Jenny; Kotz, Sonja A; Tavano, Alessandro; Schröger, Erich

2015-05-01

We used human electroencephalogram to study early audiovisual integration of dynamic angry and neutral expressions. An auditory-only condition served as a baseline for the interpretation of integration effects. In the audiovisual conditions, the validity of visual information was manipulated using facial expressions that were either emotionally congruent or incongruent with the vocal expressions. First, we report an N1 suppression effect for angry compared with neutral vocalizations in the auditory-only condition. Second, we confirm early integration of congruent visual and auditory information as indexed by a suppression of the auditory N1 and P2 components in the audiovisual compared with the auditory-only condition. Third, audiovisual N1 suppression was modulated by audiovisual congruency in interaction with emotion: for neutral vocalizations, there was N1 suppression in both the congruent and the incongruent audiovisual conditions. For angry vocalizations, there was N1 suppression only in the congruent but not in the incongruent condition. Extending previous findings of dynamic audiovisual integration, the current results suggest that audiovisual N1 suppression is congruency- and emotion-specific and indicate that dynamic emotional expressions compared with non-emotional expressions are preferentially processed in early audiovisual integration. © The Author (2014). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Vector analysis as a fast and easy method to compare gene expression responses between different experimental backgrounds

NARCIS (Netherlands)

Breitling, R.; Armengaud, P.; Amtmann, A.

2005-01-01

Background Gene expression studies increasingly compare expression responses between different experimental backgrounds (genetic, physiological, or phylogenetic). By focusing on dynamic responses rather than a direct comparison of static expression levels, this type of study allows a finer

Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity in Drosophila ovarian cell cultures.

Science.gov (United States)

Sytnikova, Yuliya A; Rahman, Reazur; Chirn, Gung-Wei; Clark, Josef P; Lau, Nelson C

2014-12-01

Piwi proteins and Piwi-interacting RNAs (piRNAs) repress transposable elements (TEs) from mobilizing in gonadal cells. To determine the spectrum of piRNA-regulated targets that may extend beyond TEs, we conducted a genome-wide survey for transcripts associated with PIWI and for transcripts affected by PIWI knockdown in Drosophila ovarian somatic sheet (OSS) cells, a follicle cell line expressing the Piwi pathway. Despite the immense sequence diversity among OSS cell piRNAs, our analysis indicates that TE transcripts are the major transcripts associated with and directly regulated by PIWI. However, several coding genes were indirectly regulated by PIWI via an adjacent de novo TE insertion that generated a nascent TE transcript. Interestingly, we noticed that PIWI-regulated genes in OSS cells greatly differed from genes affected in a related follicle cell culture, ovarian somatic cells (OSCs). Therefore, we characterized the distinct genomic TE insertions across four OSS and OSC lines and discovered dynamic TE landscapes in gonadal cultures that were defined by a subset of active TEs. Particular de novo TEs appeared to stimulate the expression of novel candidate long noncoding RNAs (lncRNAs) in a cell lineage-specific manner, and some of these TE-associated lncRNAs were associated with PIWI and overlapped PIWI-regulated genes. Our analyses of OSCs and OSS cells demonstrate that despite having a Piwi pathway to suppress endogenous mobile elements, gonadal cell TE landscapes can still dramatically change and create transcriptome diversity. © 2014 Sytnikova et al.; Published by Cold Spring Harbor Laboratory Press.

Expression of parasite genetic variation changes over the course of infection: implications of within-host dynamics for the evolution of virulence.

Science.gov (United States)

Clerc, Melanie; Ebert, Dieter; Hall, Matthew D

2015-04-07

How infectious disease agents interact with their host changes during the course of infection and can alter the expression of disease-related traits. Yet by measuring parasite life-history traits at one or few moments during infection, studies have overlooked the impact of variable parasite growth trajectories on disease evolution. Here we show that infection-age-specific estimates of host and parasite fitness components can reveal new insight into the evolution of parasites. We do so by characterizing the within-host dynamics over an entire infection period for five genotypes of the castrating bacterial parasite Pasteuria ramosa infecting the crustacean Daphnia magna. Our results reveal that genetic variation for parasite-induced gigantism, host castration and parasite spore loads increases with the age of infection. Driving these patterns appears to be variation in how well the parasite maintains control of host reproduction late in the infection process. We discuss the evolutionary consequences of this finding with regard to natural selection acting on different ages of infection and the mechanism underlying the maintenance of castration efficiency. Our results highlight how elucidating within-host dynamics can shed light on the selective forces that shape infection strategies and the evolution of virulence. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Temperature dependent dynamics of DegP-trimer: A molecular dynamics study

Directory of Open Access Journals (Sweden)

Nivedita Rai

2015-01-01

Full Text Available DegP is a heat shock protein from high temperature requirement protease A family, which reacts to the environmental stress conditions in an ATP independent way. The objective of the present analysis emerged from the temperature dependent functional diversity of DegP between chaperonic and protease activities at temperatures below and above 28 °C, respectively. DegP is a multimeric protein and the minimal functional unit, DegP-trimer, is of great importance in understanding the DegP pathway. The structural aspects of DegP-trimer with respect to temperature variation have been studied using molecular dynamics simulations (for 100 ns and principal component analysis to highlight the temperature dependent dynamics facilitating its functional diversity. The DegP-trimer revealed a pronounced dynamics at both 280 and 320 K, when compared to the dynamics observed at 300 K. The LA loop is identified as the highly flexible region during dynamics and at extreme temperatures, the residues 46–80 of LA loop express a flip towards right (at 280 and left ( at 320 K with respect to the fixed β-sheet connecting the LA loop of protease for which Phe46 acts as one of the key residues. Such dynamics of LA loop facilitates inter-monomeric interaction with the PDZ1 domain of the neighbouring monomer and explains its active participation when DegP exists as trimer. Hence, the LA loop mediated dynamics of DegP-trimer is expected to provide further insight into the temperature dependent dynamics of DegP towards the understanding of its assembly and functional diversity in the presence of substrate.

Dynamic Modeling and Analysis of an Industrial Gas Suspension Absorber for Flue Gas Desulfurization

DEFF Research Database (Denmark)

Cignitti, Stefano; Mansouri, Seyed Soheil; Sales-Cruz, Mauricio

2016-01-01

parameters were fitted to operational data from a real cement plant. A detailed statistical analysis of the parameter estimation procedure was performed, and the confidence intervals for estimated kinetic parameters were calculated. The model and reaction rate expression prediction ability was tested using...... another plant data set. It was verified that in spite of the simplicity of the model, very good prediction of industrial behavior was obtained. Furthermore, the dynamic analysis of the system was performed by carrying out open-loop and closed-loop simulations to verify plant dynamics. Therefore, a simple...... dynamic model with a reaction rate expression that is simple and efficient to use to predict the dynamics of GSA process was proposed in this work....

Task-dependent enhancement of facial expression and identity representations in human cortex.

Science.gov (United States)

Dobs, Katharina; Schultz, Johannes; Bülthoff, Isabelle; Gardner, Justin L

2018-05-15

What cortical mechanisms allow humans to easily discern the expression or identity of a face? Subjects detected changes in expression or identity of a stream of dynamic faces while we measured BOLD responses from topographically and functionally defined areas throughout the visual hierarchy. Responses in dorsal areas increased during the expression task, whereas responses in ventral areas increased during the identity task, consistent with previous studies. Similar to ventral areas, early visual areas showed increased activity during the identity task. If visual responses are weighted by perceptual mechanisms according to their magnitude, these increased responses would lead to improved attentional selection of the task-appropriate facial aspect. Alternatively, increased responses could be a signature of a sensitivity enhancement mechanism that improves representations of the attended facial aspect. Consistent with the latter sensitivity enhancement mechanism, attending to expression led to enhanced decoding of exemplars of expression both in early visual and dorsal areas relative to attending identity. Similarly, decoding identity exemplars when attending to identity was improved in dorsal and ventral areas. We conclude that attending to expression or identity of dynamic faces is associated with increased selectivity in representations consistent with sensitivity enhancement. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

FTO is expressed in neurones throughout the brain and its expression is unaltered by fasting.

Science.gov (United States)

McTaggart, James S; Lee, Sheena; Iberl, Michaela; Church, Chris; Cox, Roger D; Ashcroft, Frances M

2011-01-01

Single-nucleotide polymorphisms in the first intron of the ubiquitously expressed FTO gene are associated with obesity. Although the physiological functions of FTO remain unclear, food intake is often altered when Fto expression levels are manipulated. Furthermore, deletion of FTO from neurones alone has a similar effect on food intake to deletion of FTO in all tissues. These results indicate that FTO expression in the brain is particularly important. Considerable focus has been placed on the dynamic regulation of Fto mRNA expression in the hypothalamus after short-term (16-48 hour) fasting, but results have been controversial. There are no studies that quantify FTO protein levels across the brain, and assess its alteration following short-term fasting. Using immunohistochemistry, we found that FTO protein is widely expressed in mouse brain, and present in the majority of neurones. Using quantitative Western blotting and RT-qPCR we show that FTO protein and mRNA levels in the hypothalamus, cerebellum and rostral brain are relatively uniform, and levels in the brain are higher than in skeletal muscles of the lower limbs. Fasting for 18 hours does not alter the expression pattern, or levels, of FTO protein and mRNA. We further show that the majority of POMC neurones, which are critically involved in food intake regulation, also express FTO, but that the percentage of FTO-positive POMC neurones is not altered by fasting. In summary, we find no evidence that Fto/FTO expression is regulated by short-term (18-hour) fasting. Thus, it is unlikely that the hunger and increased post-fasting food intake caused by such food deprivation is driven by alterations in Fto/FTO expression. The widespread expression of FTO in neurones also suggests that physiological studies of this protein should not be limited to the hypothalamus.

FTO is expressed in neurones throughout the brain and its expression is unaltered by fasting.

Directory of Open Access Journals (Sweden)

James S McTaggart

Full Text Available Single-nucleotide polymorphisms in the first intron of the ubiquitously expressed FTO gene are associated with obesity. Although the physiological functions of FTO remain unclear, food intake is often altered when Fto expression levels are manipulated. Furthermore, deletion of FTO from neurones alone has a similar effect on food intake to deletion of FTO in all tissues. These results indicate that FTO expression in the brain is particularly important. Considerable focus has been placed on the dynamic regulation of Fto mRNA expression in the hypothalamus after short-term (16-48 hour fasting, but results have been controversial. There are no studies that quantify FTO protein levels across the brain, and assess its alteration following short-term fasting. Using immunohistochemistry, we found that FTO protein is widely expressed in mouse brain, and present in the majority of neurones. Using quantitative Western blotting and RT-qPCR we show that FTO protein and mRNA levels in the hypothalamus, cerebellum and rostral brain are relatively uniform, and levels in the brain are higher than in skeletal muscles of the lower limbs. Fasting for 18 hours does not alter the expression pattern, or levels, of FTO protein and mRNA. We further show that the majority of POMC neurones, which are critically involved in food intake regulation, also express FTO, but that the percentage of FTO-positive POMC neurones is not altered by fasting. In summary, we find no evidence that Fto/FTO expression is regulated by short-term (18-hour fasting. Thus, it is unlikely that the hunger and increased post-fasting food intake caused by such food deprivation is driven by alterations in Fto/FTO expression. The widespread expression of FTO in neurones also suggests that physiological studies of this protein should not be limited to the hypothalamus.

Tracking neuronal marker expression inside living differentiating cells using molecular beacons

DEFF Research Database (Denmark)

Ilieva, Mirolyuba; Della Vedova, Paolo; Hansen, Ole

2013-01-01

and tyrosine hydroxylase mRNAs were expressed 2 and 3 days post induction of differentiation, respectively. Oct 4 was not detected with MB in these cells and signal was not increased over time suggesting that MB are generally stable inside the cells. The gene expression changes measured using MBs were...... confirmed using qRT-PCR. These results suggest that MBs are simple to use sensors inside living cell, and particularly useful for studying dynamic gene expression in heterogeneous cell populations....

Expression dynamics of HSP70 during chronic heat stress in Tharparkar cattle.

Science.gov (United States)

Bharati, Jaya; Dangi, S S; Chouhan, V S; Mishra, S R; Bharti, M K; Verma, V; Shankar, O; Yadav, V P; Das, K; Paul, A; Bag, S; Maurya, V P; Singh, G; Kumar, P; Sarkar, M

2017-06-01

Six male Tharparkar cattle aged 2-3 years were selected for the study. The animals were acclimatized in the psychrometric chamber at thermoneutral zone (TNZ) for 15 days and then exposed to 42 °C temperature up to 23 days followed by 12 days of recovery period. Physiological responses were estimated, and peripheral blood mononuclear cells (PBMCs) were isolated at TNZ on day 1, day 5, and day 12; after 6 h of heat stress exposure on day 16 to day 20, day 25, day 30, day 32, day 34, day 36, and day 38; and a recovery period on day 45 and day 50. The PBMCs were cultured to study the effect of thermal challenge on HSP70 messenger RNA (mRNA) expression pattern at different temperature-time combinations. The mRNA and protein expression of HSP70 in PBMCs along with serum extracellular HSP70 (eHSP70) was increased (P cattle and the biphasic expression pattern may be providing a second window of protection during chronic heat stress.

A microcosm of musical expression. III. Contributions of timing and dynamics to the aesthetic impression of pianists' performances of the initial measures of Chopin's Etude in E major.

Science.gov (United States)

Repp, B H

1999-07-01

Four judges repeatedly assessed the overall aesthetic quality of more than 100 recorded performances of the opening of Chopin's Etude in E major on a 10-point scale. The judgments, which exhibited reasonable reliability and modest intercorrelations, were entered into regression analyses with 16 independent variables derived from earlier objective analyses of the expressive timing and dynamics of the performances [Repp, J. Acoust. Soc. Am. 104, 1085-1100 (1998); 105, 1972-1988 (1999)]. Only between 9% and 18% of the variance in the judges' ratings was accounted for. By contrast, timing variables accounted for 53% of the variance in one judge's ratings of synthesized performances that varied in timing only and mimicked the timing patterns of the original performances. These results indicate, first, that the aesthetic impression of the original recordings rested primarily on aspects other than those measured (such as texture, tone, or aspects of timing and dynamics that eluded the earlier analyses) and, second, that very different patterns of timing and dynamics are aesthetically acceptable for the same music, provided that other, aesthetically more crucial performance aspects are present.

Gently does it: Humans outperform a software classifier in recognizing subtle, nonstereotypical facial expressions.

Science.gov (United States)

Yitzhak, Neta; Giladi, Nir; Gurevich, Tanya; Messinger, Daniel S; Prince, Emily B; Martin, Katherine; Aviezer, Hillel

2017-12-01

According to dominant theories of affect, humans innately and universally express a set of emotions using specific configurations of prototypical facial activity. Accordingly, thousands of studies have tested emotion recognition using sets of highly intense and stereotypical facial expressions, yet their incidence in real life is virtually unknown. In fact, a commonplace experience is that emotions are expressed in subtle and nonprototypical forms. Such facial expressions are at the focus of the current study. In Experiment 1, we present the development and validation of a novel stimulus set consisting of dynamic and subtle emotional facial displays conveyed without constraining expressers to using prototypical configurations. Although these subtle expressions were more challenging to recognize than prototypical dynamic expressions, they were still well recognized by human raters, and perhaps most importantly, they were rated as more ecological and naturalistic than the prototypical expressions. In Experiment 2, we examined the characteristics of subtle versus prototypical expressions by subjecting them to a software classifier, which used prototypical basic emotion criteria. Although the software was highly successful at classifying prototypical expressions, it performed very poorly at classifying the subtle expressions. Further validation was obtained from human expert face coders: Subtle stimuli did not contain many of the key facial movements present in prototypical expressions. Together, these findings suggest that emotions may be successfully conveyed to human viewers using subtle nonprototypical expressions. Although classic prototypical facial expressions are well recognized, they appear less naturalistic and may not capture the richness of everyday emotional communication. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Dual Selectivity Expressed in [2+2+1] Dynamic Clipping of Unsymmetrical [2]Catenanes

Energy Technology Data Exchange (ETDEWEB)

Liu, Yi

2010-06-11

A {pi}-templated dynamic [2+2+1] clipping protocol is established for the synthesis of [2]catenanes from two parts dialdehyde, two parts diamine and one part tetracationic cyclophane. It is further diversified for the selective formation of an unsymmetrical [2]catenane showing great translational selectivity by employing two different dialdehydes in a one-pot reaction. The dual selectivity and the dynamic nature are verified by {sup 1}H NMR spectroscopy, X-ray single crystal structural studies and exchange experiments.

The Viterbi Algorithm expressed in Constraint Handling Rules

DEFF Research Database (Denmark)

Christiansen, Henning; Have, Christian Theil; Lassen, Ole Torp

2010-01-01

The Viterbi algorithm is a classical example of a dynamic programming algorithm, in which pruning reduces the search space drastically, so that an otherwise exponential time complexity is reduced to linearity. The central steps of the algorithm, expansion and pruning, can be expressed in a concis...

A Rigorous, Compositional, and Extensible Framework for Dynamic Fault Tree Analysis

NARCIS (Netherlands)

Boudali, H.; Sandhu, R.; Crouzen, Pepijn; Stoelinga, Mariëlle Ida Antoinette

Fault trees (FT) are among the most prominent formalisms for reliability analysis of technical systems. Dynamic FTs extend FTs with support for expressing dynamic dependencies among components. The standard analysis vehicle for DFTs is state-based, and treats the model as a CTMC, a continuous-time

Dynamic Music and Immersion in the Action-Adventure

DEFF Research Database (Denmark)

Gasselseder, Hans-Peter

2014-01-01

in the context of dynamic and non-dynamic music. 60 subjects answered self-report questionnaires each time after playing a 3rd-person action-adventure in one of three conditions accounting for (1) dynamic music, (2) non-dynamic music/low arousal potential and (3) non-dynamic music/high arousal potential......Aiming to immerse players into a new realm of drama experience, a growing number of video games utilize interactive, ‘dynamic’ music that reacts adaptively to game events. Though little is known about the involved perceptual processes, the design rationale of enhanced immersive experiences is taken...... over by public discussion including scientific accounts, despite lacking empirical validation. The present paper intends to fill this gap by hypothesizing facilitatory effects of dynamic music on attention allocation in the matching of expected and incoming expressive characteristics of concurrent...

Dynamic statistical information theory

Institute of Scientific and Technical Information of China (English)

无

2006-01-01

In recent years we extended Shannon static statistical information theory to dynamic processes and established a Shannon dynamic statistical information theory, whose core is the evolution law of dynamic entropy and dynamic information. We also proposed a corresponding Boltzmman dynamic statistical information theory. Based on the fact that the state variable evolution equation of respective dynamic systems, i.e. Fokker-Planck equation and Liouville diffusion equation can be regarded as their information symbol evolution equation, we derived the nonlinear evolution equations of Shannon dynamic entropy density and dynamic information density and the nonlinear evolution equations of Boltzmann dynamic entropy density and dynamic information density, that describe respectively the evolution law of dynamic entropy and dynamic information. The evolution equations of these two kinds of dynamic entropies and dynamic informations show in unison that the time rate of change of dynamic entropy densities is caused by their drift, diffusion and production in state variable space inside the systems and coordinate space in the transmission processes; and that the time rate of change of dynamic information densities originates from their drift, diffusion and dissipation in state variable space inside the systems and coordinate space in the transmission processes. Entropy and information have been combined with the state and its law of motion of the systems. Furthermore we presented the formulas of two kinds of entropy production rates and information dissipation rates, the expressions of two kinds of drift information flows and diffusion information flows. We proved that two kinds of information dissipation rates (or the decrease rates of the total information) were equal to their corresponding entropy production rates (or the increase rates of the total entropy) in the same dynamic system. We obtained the formulas of two kinds of dynamic mutual informations and dynamic channel

Quantum dynamics without the wavefunction

International Nuclear Information System (INIS)

Sorkin, Rafael D

2007-01-01

When suitably generalized and interpreted, the path integral offers an alternative to the more familiar quantal formalism based on state vectors, self-adjoint operators and external observers. Mathematically one generalizes the path-integral-as-propagator to a quantal measure μ on the space Ω of all 'conceivable worlds', and this generalized measure expresses the dynamics or law of motion of the theory, much as Wiener measure expresses the dynamics of Brownian motion. Within such 'histories-based' schemes new and more 'realistic' possibilities open up for resolving the philosophical problems of the state-vector formalism. In particular, one can dispense with the need for external agents by locating the predictive content of μ in its sets of measure zero: such sets are to be 'precluded'. But unrestricted application of this rule engenders contradictions. One possible response would remove the contradictions by circumscribing the application of the preclusion concept. Another response, more in the tradition of 'quantum logic', would accommodate the contradictions by dualizing Ω to a space of 'co-events' and effectively identifying reality with an element of this dual space

An application of the ESD framework to the probabilistic risk assessment of dynamic systems

International Nuclear Information System (INIS)

Swaminathan, S.; Smidts, Carol

2000-01-01

Dynamic reliability is the probabilistic study of man-machine-software systems affected by an underlying physical process. The theory of probabilistic dynamics established that dynamic reliability methodologies are essentially semi-Markovian frameworks and can be expressed by an extension of the Chapman-Kolmogorov equation. The mathematical complexity associated with the assessment of dynamic systems' behaviour can be rather overwhelming for real life size systems. This is due to the fact that dynamic methodologies emphasize a component based representation rather than the sequence based representation used in the traditional Event Tree/Fault Tree framework or in the original Event Sequence Diagram (ESD) Framework. An extension of the ESD framework was proposed that facilitates capture of dynamic situations. The modeling framework is composed of events, gates, conditions, competitions and constraints which express many of the dynamic situations encountered in the evolution of accidents. The following paper illustrates an application of this extended ESD framework on a complex dynamic application. The problem at hand is an extension of a problem extensively studied in the validation of dynamic reliability algorithms, a simplified model of the fast reactor Europa. A discussion on how ESDs can help in guiding dynamic reliability simulations as well as aggregating and binning the numerous scenarios generated by dynamic reliability algorithms is provided.(author)

A Novel Gli3 Enhancer Controls the Gli3 Spatiotemporal Expression Pattern through a TALE Homeodomain Protein Binding Site ▿‡

OpenAIRE

Coy, Sarah; Caamaño, Jorge H.; Carvajal, Jaime; Cleary, Michael L.; Borycki, Anne-Gaëlle

2011-01-01

The zinc finger transcription factor Gli3 is an essential mediator of hedgehog signaling. Gli3 has a dynamic expression pattern during embryonic development. In the neural tube, Gli3 transcripts are patterned along the anteroposterior and dorsoventral axes such that the initial broad expression in the posterior neural tube becomes dorsally restricted as neurogenesis takes place. Little is known about the molecular mechanisms that regulate this dynamic expression. Here, we report on a phylogen...

Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening

Directory of Open Access Journals (Sweden)

Sansavini Silviero

2010-10-01

Full Text Available Abstract Background Fruit development, maturation and ripening consists of a complex series of biochemical and physiological changes that in climacteric fruits, including apple and tomato, are coordinated by the gaseous hormone ethylene. These changes lead to final fruit quality and understanding of the functional machinery underlying these processes is of both biological and practical importance. To date many reports have been made on the analysis of gene expression in apple. In this study we focused our investigation on the role of ethylene during apple maturation, specifically comparing transcriptomics of normal ripening with changes resulting from application of the hormone receptor competitor 1-Methylcyclopropene. Results To gain insight into the molecular process regulating ripening in apple, and to compare to tomato (model species for ripening studies, we utilized both homologous and heterologous (tomato microarray to profile transcriptome dynamics of genes involved in fruit development and ripening, emphasizing those which are ethylene regulated. The use of both types of microarrays facilitated transcriptome comparison between apple and tomato (for the later using data previously published and available at the TED: tomato expression database and highlighted genes conserved during ripening of both species, which in turn represent a foundation for further comparative genomic studies. The cross-species analysis had the secondary aim of examining the efficiency of heterologous (specifically tomato microarray hybridization for candidate gene identification as related to the ripening process. The resulting transcriptomics data revealed coordinated gene expression during fruit ripening of a subset of ripening-related and ethylene responsive genes, further facilitating the analysis of ethylene response during fruit maturation and ripening. Conclusion Our combined strategy based on microarray hybridization enabled transcriptome characterization

Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening.

Science.gov (United States)

Costa, Fabrizio; Alba, Rob; Schouten, Henk; Soglio, Valeria; Gianfranceschi, Luca; Serra, Sara; Musacchi, Stefano; Sansavini, Silviero; Costa, Guglielmo; Fei, Zhangjun; Giovannoni, James

2010-10-25

Fruit development, maturation and ripening consists of a complex series of biochemical and physiological changes that in climacteric fruits, including apple and tomato, are coordinated by the gaseous hormone ethylene. These changes lead to final fruit quality and understanding of the functional machinery underlying these processes is of both biological and practical importance. To date many reports have been made on the analysis of gene expression in apple. In this study we focused our investigation on the role of ethylene during apple maturation, specifically comparing transcriptomics of normal ripening with changes resulting from application of the hormone receptor competitor 1-methylcyclopropene. To gain insight into the molecular process regulating ripening in apple, and to compare to tomato (model species for ripening studies), we utilized both homologous and heterologous (tomato) microarray to profile transcriptome dynamics of genes involved in fruit development and ripening, emphasizing those which are ethylene regulated.The use of both types of microarrays facilitated transcriptome comparison between apple and tomato (for the later using data previously published and available at the TED: tomato expression database) and highlighted genes conserved during ripening of both species, which in turn represent a foundation for further comparative genomic studies. The cross-species analysis had the secondary aim of examining the efficiency of heterologous (specifically tomato) microarray hybridization for candidate gene identification as related to the ripening process. The resulting transcriptomics data revealed coordinated gene expression during fruit ripening of a subset of ripening-related and ethylene responsive genes, further facilitating the analysis of ethylene response during fruit maturation and ripening. Our combined strategy based on microarray hybridization enabled transcriptome characterization during normal climacteric apple ripening, as well as

Dynamic, mating-induced gene expression changes in female head and brain tissues of Drosophila melanogaster

Directory of Open Access Journals (Sweden)

Stirling Emma J

2010-10-01

Full Text Available Abstract Background Drosophila melanogaster females show changes in behavior and physiology after mating that are thought to maximize the number of progeny resulting from the most recent copulation. Sperm and seminal fluid proteins induce post-mating changes in females, however, very little is known about the resulting gene expression changes in female head and central nervous system tissues that contribute to the post-mating response. Results We determined the temporal gene expression changes in female head tissues 0-2, 24, 48 and 72 hours after mating. Females from each time point had a unique post-mating gene expression response, with 72 hours post-mating having the largest number of genes with significant changes in expression. At most time points, genes expressed in the head fat body that encode products involved in metabolism showed a marked change in expression. Additional analysis of gene expression changes in dissected brain tissues 24 hours post-mating revealed changes in transcript abundance of many genes, notably, the reduced transcript abundance of genes that encode ion channels. Conclusions Substantial changes occur in the regulation of many genes in female head tissues after mating, which might underlie aspects of the female post-mating response. These results provide new insights into the physiological and metabolic changes that accompany changes in female behaviors.

On the quantum dynamical foundations of collision terms

International Nuclear Information System (INIS)

Nemes, M.C.; Toledo Piza, A.F.R. de

1981-08-01

Collision terms are non-unitary corrections usually added to mean field descriptions in order to describe dissipative effects. Derivations of collision terms usually include assumptions which lack an explicit connection with a fully quantum dynamical description. Quantum dynamical foundations of collision terms are examined: they are shown to reflect the dynamics of quantum correlations. A careful study of the non-unitary aspects of the evolution of quantum correlations leads naturally to an unambiguous definition of a collision term. This collision term is shown to obey a non-linear pre-master equation, whose derivation is fully quantum-mechanical. Moreover, it is shown that quantum correlations also yield an unitary correction to the mean field description, which could be absorbed in a suitable redefinition of the mean field. Formal expressions for these corrections are derived and their connection with memory effects exhibited explicitely. The typical time of evaluation of quantum correlations allows for an analytical expression for the 'lifetime of mean field descriptions'. Finally, a quantum mechanical point of view for 'irreversibility' in deep inelastic is discussed. (Author) [pt

FABP4 dynamics in obesity: discrepancies in adipose tissue and liver expression regarding circulating plasma levels.

Directory of Open Access Journals (Sweden)

María Isabel Queipo-Ortuño

Full Text Available BACKGROUND: FABP4 is predominantly expressed in adipose tissue, and its circulating levels are linked with obesity and a poor atherogenic profile. OBJECTIVE: In patients with a wide BMI range, we analyze FABP4 expression in adipose and hepatic tissues in the settings of obesity and insulin resistance. Associations between FABP4 expression in adipose tissue and the FABP4 plasma level as well as the main adipogenic and lipolytic genes expressed in adipose tissue were also analyzed. METHODS: The expression of several lipogenic, lipolytic, PPAR family and FABP family genes was analyzed by real time PCR. FABP4 protein expression in total adipose tissues and its fractions were determined by western blot. RESULTS: In obesity FABP4 expression was down-regulated (at both mRNA and protein levels, with its levels mainly predicted by ATGL and inversely by the HOMA-IR index. The BMI appeared as the only determinant of the FABP4 variation in both adipose tissue depots. FABP4 plasma levels showed a significant progressive increase according to BMI but no association was detected between FABP4 circulating levels and SAT or VAT FABP4 gene expression. The gene expression of FABP1, FABP4 and FABP5 in hepatic tissue was significantly higher in tissue from the obese IR patients compared to the non-IR group. CONCLUSION: The inverse pattern in FABP4 expression between adipose and hepatic tissue observed in morbid obese patients, regarding the IR context, suggests that both tissues may act in a balanced manner. These differences may help us to understand the discrepancies between circulating plasma levels and adipose tissue expression in obesity.

Collective intelligence for control of distributed dynamical systems

Science.gov (United States)

Wolpert, D. H.; Wheeler, K. R.; Tumer, K.

2000-03-01

We consider the El Farol bar problem, also known as the minority game (W. B. Arthur, The American Economic Review, 84 (1994) 406; D. Challet and Y. C. Zhang, Physica A, 256 (1998) 514). We view it as an instance of the general problem of how to configure the nodal elements of a distributed dynamical system so that they do not "work at cross purposes", in that their collective dynamics avoids frustration and thereby achieves a provided global goal. We summarize a mathematical theory for such configuration applicable when (as in the bar problem) the global goal can be expressed as minimizing a global energy function and the nodes can be expressed as minimizers of local free energy functions. We show that a system designed with that theory performs nearly optimally for the bar problem.

Dynamic Inheritance and Static Analysis can be Reconciled

DEFF Research Database (Denmark)

Ernst, Erik

1998-01-01

the exibility and expressivity of staticlanguages while preserving the safety properties. It is an inheritancemechanism, with standard single inheritance as a special case. It al-lows both compile-time and run-time construction of new classes. More-over, it supports specialization of existing objects at run......-time. This helpsavoiding the combinatorial explosion in the number of classes associatedwith multiple inheritance, and it supports a better separation of con-cerns in large systems. Pre-methoding|inheritance applied to behavioraldescriptors|has been used for the construction of control structures formany years, in Beta....... With dynamic inheritance, pre-methoding becomesmore expressive, supporting control structures as rst class values whichmay be constructed and combined dynamically. Even though the conceptof pre-methoding is missing from most other languages, the basic ideacould be applied to any statically typed object...

Angiogenesis and dynamic contrast enhanced MRI of benign and malignant breast lesions: preliminary results

International Nuclear Information System (INIS)

Liu Peifang; Bao Runxian; Niu Yun; Yu Yong

2002-01-01

Objective: To determine whether dynamic contrast enhanced MRI features of early-phase enhancement rate, enhancement amplitude, and signal intensity (SI) time course are associated with the microvessel density (MVD) and vascular endothelial growth factor (VEGF) expression of malignant and benign breast lesions. Methods: Thirty-eight patients with histopathologically verified breast lesions underwent dynamic contrast enhanced MRI. SI changes during dynamic scanning were assessed quantitatively. Early-phase enhancement rate and enhancement amplitude were calculated. Time-SI curves of the lesions were obtained and classified according to their shapes as type I (which was steady enhancement to the end of the dynamic data acquisition at 7.5 min), type II (plateau of SI after avid initial contrast enhancement), or type III (washout of SI after avid initial contrast enhancement). the mean MVD and VEGF expression of the lesions were measured with immuno-histochemical staining method in all the histologic specimens by pathologists without the knowledge of the results of the MR examination. The relationships among dynamic contrast enhanced MRI features, MVD, and VEGF expression of benign and malignant breast lesions were analyzed. Results: Histology revealed 21 malignancies and 17 benign lesions. The mean MVD and VEGF expression for 21 malignant lesions were statistically higher than the mean MVD and VEGF expression for 17 benign lesions. High VEGF expression of benign and malignant breast lesions showed an association with increased MVD. Among all 38 lesions, greater (> 60%) MR early-phase enhancement rate and time-SI curve type II and III showed an association with increased MVD and higher VEGF expression level. All the differences mentioned above showed statistical significance except that the difference between VEGF expression and the distribution of curve types had no statistical significance. No significant relationships were observed between the mean of enhancement

Protein Expression Analyses at the Single Cell Level

Directory of Open Access Journals (Sweden)

Masae Ohno

2014-09-01

Full Text Available The central dogma of molecular biology explains how genetic information is converted into its end product, proteins, which are responsible for the phenotypic state of the cell. Along with the protein type, the phenotypic state depends on the protein copy number. Therefore, quantification of the protein expression in a single cell is critical for quantitative characterization of the phenotypic states. Protein expression is typically a dynamic and stochastic phenomenon that cannot be well described by standard experimental methods. As an alternative, fluorescence imaging is being explored for the study of protein expression, because of its high sensitivity and high throughput. Here we review key recent progresses in fluorescence imaging-based methods and discuss their application to proteome analysis at the single cell level.

Lattice dynamics and thermal diffuse scattering for molecular crystals

International Nuclear Information System (INIS)

Kroon, P.A.

1977-01-01

Thermal diffuse scattering (TDS) corrections on the observed reflection intensities in the accurate determination of crystal structures by X-ray diffraction are emphasized. A lattice-dynamical model and procedure for lattice-dynamical calculations are set up. Expression for first- and second-order TDS intensity distributions are derived. A comparison with other models is made. First-order TDS corrections for naphtalene at 100 K are presented

The evolution of gene expression levels in mammalian organs

DEFF Research Database (Denmark)

Brawand, David; Soumillon, Magali; Necsulea, Anamaria

2011-01-01

and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation. Although gene expression evolution in mammals was strongly shaped......Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across...... ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. We show that the rate of gene expression evolution varies among organs, lineages...

3D Protein Dynamics in the Cell Nucleus.

Science.gov (United States)

Singh, Anand P; Galland, Rémi; Finch-Edmondson, Megan L; Grenci, Gianluca; Sibarita, Jean-Baptiste; Studer, Vincent; Viasnoff, Virgile; Saunders, Timothy E

2017-01-10

The three-dimensional (3D) architecture of the cell nucleus plays an important role in protein dynamics and in regulating gene expression. However, protein dynamics within the 3D nucleus are poorly understood. Here, we present, to our knowledge, a novel combination of 1) single-objective based light-sheet microscopy, 2) photoconvertible proteins, and 3) fluorescence correlation microscopy, to quantitatively measure 3D protein dynamics in the nucleus. We are able to acquire >3400 autocorrelation functions at multiple spatial positions within a nucleus, without significant photobleaching, allowing us to make reliable estimates of diffusion dynamics. Using this tool, we demonstrate spatial heterogeneity in Polymerase II dynamics in live U2OS cells. Further, we provide detailed measurements of human-Yes-associated protein diffusion dynamics in a human gastric cancer epithelial cell line. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Static and dynamic 3D facial expression recognition: A comprehensive survey

NARCIS (Netherlands)

Sandbach, G.; Zafeiriou, S.; Pantic, Maja; Yin, Lijun

2012-01-01

Automatic facial expression recognition constitutes an active research field due to the latest advances in computing technology that make the user's experience a clear priority. The majority of work conducted in this area involves 2D imagery, despite the problems this presents due to inherent pose

Calreticulin expression in relation to exchangeable Ca(2+) level that changes dynamically during anthesis, progamic phase, and double fertilization in Petunia.

Science.gov (United States)

Lenartowski, Robert; Suwińska, Anna; Lenartowska, Marta

2015-01-01

Calcium (Ca(2+)) plays essential roles in plant sexual reproduction, but the sites and the mechanism of Ca(2+) mobile storage during pollen-pistil interactions have not been fully defined. Because the Ca(2+)-buffering protein calreticulin (CRT) is able to bind and sequester Ca(2+), it can serve as a mobile intracellular store of easily releasable Ca(2+) and control its local concentration within the cytoplasm. Our previous studies showed an enhanced expression of Petunia hybrida CRT gene (PhCRT) during pistil transmitting tract maturation, pollen germination and tube outgrowth on the stigma, gamete fusion, and early embryogenesis. Here, we demonstrate that elevated expression of CRT results in the accumulation of this protein in response to anthesis, pollination, sperm cells deposition within the receptive synergid and fertilization, when the level of exchangeable Ca(2+) changes dynamically. CRT localizes mainly to the endoplasmic reticulum and Golgi compartments in the pistil transmitting tract cells, germinated pollen/tubes, and sporophytic/gametophytic cells of the ovule and corresponds with loosely bound Ca(2+). Additionally, the immunogold research shows, for the first time, highly selective CRT distribution in specific nuclear sub-domains. On the basis of our results, we discuss the possible functions of CRT with respect to the critical role of Ca(2+) homeostasis during key events of the multi-step process of generative reproduction in angiosperms.

Tools for assessing mitochondrial dynamics in mouse tissues and neurodegenerative models

Science.gov (United States)

Pham, Anh H.

Mitochondria are dynamic organelles that undergo membrane fusion and fission and transport. The dynamic properties of mitochondria are important for regulating mitochondrial function. Defects in mitochondrial dynamics are linked neurodegenerative diseases and affect the development of many tissues. To investigate the role of mitochondrial dynamics in diseases, versatile tools are needed to explore the physiology of these dynamic organelles in multiple tissues. Current tools for monitoring mitochondrial dynamics have been limited to studies in cell culture, which may be inadequate model systems for exploring the network of tissues. Here, we have generated mouse models for monitoring mitochondrial dynamics in a broad spectrum of tissues and cell types. The Photo-Activatable Mitochondrial (PhAM floxed) line enables Cre-inducible expression of a mitochondrial targeted photoconvertible protein, Dendra2 (mito-Dendra2). In the PhAMexcised line, mito-Dendra2 is ubiquitously expressed to facilitate broad analysis of mitochondria at various developmental processes. We have utilized these models to study mitochondrial dynamics in the nigrostriatal circuit of Parkinson's disease (PD) and in the development of skeletal muscles. Increasing evidences implicate aberrant regulation of mitochondrial fusion and fission in models of PD. To assess the function of mitochondrial dynamics in the nigrostriatal circuit, we utilized transgenic techniques to abrogate mitochondrial fusion. We show that deletion of the Mfn2 leads to the degeneration of dopaminergic neurons and Parkinson's-like features in mice. To elucidate the dynamic properties of mitochondria during muscle development, we established a platform for examining mitochondrial compartmentalization in skeletal muscles. This model system may yield clues to the role of mitochondrial dynamics in mitochondrial myopathies.

DMPD: Signalling pathways mediating type I interferon gene expression. [Dynamic Macrophage Pathway CSML Database

Lifescience Database Archive (English)

Full Text Available 17904888 Signalling pathways mediating type I interferon gene expression. Edwards M...hways mediating type I interferon gene expression. PubmedID 17904888 Title Signalling pathways...R, Slater L, Johnston SL. Microbes Infect. 2007 Sep;9(11):1245-51. Epub 2007 Jul 1. (.png) (.svg) (.html) (.csml) Show Signalling pat

Static compression down-regulates N-cadherin expression and facilitates loss of cell phenotype of nucleus pulposus cells in a disc perfusion culture.

Science.gov (United States)

Zhou, Haibo; Shi, Jianmin; Zhang, Chao; Li, Pei

2018-02-28

Mechanical compression often induces degenerative changes of disc nucleus pulposus (NP) tissue. It has been indicated that N-cadherin (N-CDH)-mediated signaling helps to preserve the NP cell phenotype. However, N-CDH expression and the resulting NP-specific phenotype alteration under the static compression and dynamic compression remain unclear. To study the effects of static compression and dynamic compression on N-CDH expression and NP-specific phenotype in an in vitro disc organ culture. Porcine discs were organ cultured in a self-developed mechanically active bioreactor for 7 days and subjected to static or dynamic compression (0.4 MPa for 2 h once per day). The noncompressed discs were used as controls. Compared with the dynamic compression, static compression significantly down-regulated the expression of N-CDH and NP-specific markers (laminin, brachyury, and keratin 19); decreased the Alcian Blue staining intensity, glycosaminoglycan and hydroxyproline contents; and declined the matrix macromolecule (aggrecan and collagen II) expression. Compared with the dynamic compression, static compression causes N-CDH down-regulation, loss of NP-specific phenotype, and the resulting decrease in NP matrix synthesis. © 2018 The Author(s).

Dynamical duality of type- and token-computation as an abstract brain

Energy Technology Data Exchange (ETDEWEB)

Gunji, Yukio-Pegio [Department of Earth and Planetary Sciences, Faculty of Science, Kobe University (Japan); Graduate School of Science and Technology, Kobe University (Japan)] e-mail: yukio@kobe-u.ac.jp; Miyoshi, Hiroyuki [Department of Computer Sciences, Faculty of Science, Kyoto Sangyo University (Japan); Takahashi, Tatsuji [Graduate School of Science and Technology, Kobe University (Japan); Kamiura, Moto [Graduate School of Science and Technology, Kobe University (Japan)

2006-03-01

In brain science, there are few researches focusing on the theoretical relation between cognition (top-down processing) and perception (bottom-up processing). Philosophically they were regarded as the alternative leading to the dualism of mind and body, while it is an adequate problem for the endo-physics. Qualia are conjectured as the hard problem under those situations. To overcome such an impasse, we propose an abstract brain model featuring the dynamical duality of two parts of computations in a brain, in a term of endo-physics and internal measurement. Two parts of computations are expressed as binary relations, and the relationship between them is expressed as a pair of maps, called an infomorphism [Barwise J, Seligman J. Information flow, the logic of distributed systems. Cambridge University Press 1997]. Dynamical duality is implemented by the interaction between a binary relation and an infomorphism, and that leads to a dynamical change of a pair of binary relations. When a binary relation is expressed as a partial ordered set, one can check whether a part of computation is closed with respect to logical operations (i.e., a lattice) or not. By estimating a binary relation in terms of properties of lattice, we show that dynamical infomorphism robustly develops to a pair of logical computations corresponding to type cognition and non-logical one corresponding to qualia perception. It implies origin of differentiation and robust co-existence of type-cognition and qualia-perception. It is easy to see that dynamical infomorphism can also develop to a pair of singleton sets corresponding to savants' special cognitive style.

Dynamical duality of type- and token-computation as an abstract brain

International Nuclear Information System (INIS)

Gunji, Yukio-Pegio; Miyoshi, Hiroyuki; Takahashi, Tatsuji; Kamiura, Moto

2006-01-01

In brain science, there are few researches focusing on the theoretical relation between cognition (top-down processing) and perception (bottom-up processing). Philosophically they were regarded as the alternative leading to the dualism of mind and body, while it is an adequate problem for the endo-physics. Qualia are conjectured as the hard problem under those situations. To overcome such an impasse, we propose an abstract brain model featuring the dynamical duality of two parts of computations in a brain, in a term of endo-physics and internal measurement. Two parts of computations are expressed as binary relations, and the relationship between them is expressed as a pair of maps, called an infomorphism [Barwise J, Seligman J. Information flow, the logic of distributed systems. Cambridge University Press 1997]. Dynamical duality is implemented by the interaction between a binary relation and an infomorphism, and that leads to a dynamical change of a pair of binary relations. When a binary relation is expressed as a partial ordered set, one can check whether a part of computation is closed with respect to logical operations (i.e., a lattice) or not. By estimating a binary relation in terms of properties of lattice, we show that dynamical infomorphism robustly develops to a pair of logical computations corresponding to type cognition and non-logical one corresponding to qualia perception. It implies origin of differentiation and robust co-existence of type-cognition and qualia-perception. It is easy to see that dynamical infomorphism can also develop to a pair of singleton sets corresponding to savants' special cognitive style

Influence of forced respiration on nonlinear dynamics in heart rate variability

DEFF Research Database (Denmark)

Kanters, J K; Højgaard, M V; Agner, E

1997-01-01

Although it is doubtful whether the normal sinus rhythm can be described as low-dimensional chaos, there is evidence for inherent nonlinear dynamics and determinism in time series of consecutive R-R intervals. However, the physiological origin for these nonlinearities is unknown. The aim...... with a metronome set to 12 min(-1). Nonlinear dynamics were measured as the correlation dimension and the nonlinear prediction error. Complexity expressed as correlation dimension was unchanged from normal respiration, 9.1 +/- 0.5, compared with forced respiration, 9.3 +/- 0.6. Also, nonlinear determinism...... expressed as the nonlinear prediction error did not differ between spontaneous respiration, 32.3 +/- 3.4 ms, and forced respiration, 31.9 +/- 5.7. It is concluded that the origin of the nonlinear dynamics in heart rate variability is not a nonlinear input from the respiration into the cardiovascular...

“Can I wear this?” : blending clothing and digital expression by wearing dynamic fabric

NARCIS (Netherlands)

Mackey, A.M.; Wakkary, R.L.; Wensveen, S.A.G.; Tomico Plasencia, O

2017-01-01

We explore the future scenario of wearing garments with digital display capabilities, or dynamic fabric, in everyday life. Our study, called Greenscreen Dress, investigates the experience of wearing dynamic fabric and how this type of garment quality might alter our daily interactions with clothing

Gene expression in the tanoak-Phytophthora ramorum interaction

Science.gov (United States)

Katherine J. Hayden; Matteo Garbelotto; Hardeep Fai; Brian Knaus; Richard Cronn; Jessica W. Wright

2012-01-01

Disease processes are dynamic, involving a suite of gene expression changes in both the host and the pathogen, all within a single tissue. As such, they lend themselves well to transcriptomic analysis. Here we focus on a generalist invasive pathogen (Phytophthora ramorum) and its most susceptible California Floristic Province native host, tanoak (...

Mitochondrial Dynamics: Coupling Mitochondrial Fitness with Healthy Aging.

Science.gov (United States)

Sebastián, David; Palacín, Manuel; Zorzano, Antonio

2017-03-01

Aging is associated with a decline in mitochondrial function and the accumulation of abnormal mitochondria. However, the precise mechanisms by which aging promotes these mitochondrial alterations and the role of the latter in aging are still not fully understood. Mitochondrial dynamics is a key process regulating mitochondrial function and quality. Altered expression of some mitochondrial dynamics proteins has been recently associated with aging and with age-related alterations in yeast, Caenorhabditis elegans, mice, and humans. Here, we review the link between alterations in mitochondrial dynamics, aging, and age-related impairment. We propose that the dysregulation of mitochondrial dynamics leads to age-induced accumulation of unhealthy mitochondria and contributes to alterations linked to aging, such as diabetes and neurodegeneration. Copyright © 2017 Elsevier Ltd. All rights reserved.

DMPD: G-protein-coupled receptor expression, function, and signaling in macrophages. [Dynamic Macrophage Pathway CSML Database

Lifescience Database Archive (English)

Full Text Available 17456803 G-protein-coupled receptor expression, function, and signaling in macropha...2007 Apr 24. (.png) (.svg) (.html) (.csml) Show G-protein-coupled receptor expression, function, and signali...ng in macrophages. PubmedID 17456803 Title G-protein-coupled receptor expression, function

A longitudinal study of gene expression in healthy individuals

Directory of Open Access Journals (Sweden)

Tessier Michel

2009-06-01

Full Text Available Abstract Background The use of gene expression in venous blood either as a pharmacodynamic marker in clinical trials of drugs or as a diagnostic test requires knowledge of the variability in expression over time in healthy volunteers. Here we defined a normal range of gene expression over 6 months in the blood of four cohorts of healthy men and women who were stratified by age (22–55 years and > 55 years and gender. Methods Eleven immunomodulatory genes likely to play important roles in inflammatory conditions such as rheumatoid arthritis and infection in addition to four genes typically used as reference genes were examined by quantitative reverse transcription-polymerase chain reaction (qRT-PCR, as well as the full genome as represented by Affymetrix HG U133 Plus 2.0 microarrays. Results Gene expression levels as assessed by qRT-PCR and microarray were relatively stable over time with ~2% of genes as measured by microarray showing intra-subject differences over time periods longer than one month. Fifteen genes varied by gender. The eleven genes examined by qRT-PCR remained within a limited dynamic range for all individuals. Specifically, for the seven most stably expressed genes (CXCL1, HMOX1, IL1RN, IL1B, IL6R, PTGS2, and TNF, 95% of all samples profiled fell within 1.5–2.5 Ct, the equivalent of a 4- to 6-fold dynamic range. Two subjects who experienced severe adverse events of cancer and anemia, had microarray gene expression profiles that were distinct from normal while subjects who experienced an infection had only slightly elevated levels of inflammatory markers. Conclusion This study defines the range and variability of gene expression in healthy men and women over a six-month period. These parameters can be used to estimate the number of subjects needed to observe significant differences from normal gene expression in clinical studies. A set of genes that varied by gender was also identified as were a set of genes with elevated

Investigating the Role of TNF-α and IFN-γ Activation on the Dynamics of iNOS Gene Expression in LPS Stimulated Macrophages.

Directory of Open Access Journals (Sweden)

Taha Salim

Full Text Available Macrophage produced inducible nitric oxide synthase (iNOS is known to play a critical role in the proinflammatory response against intracellular pathogens by promoting the generation of bactericidal reactive nitrogen species. Robust and timely production of nitric oxide (NO by iNOS and analogous production of reactive oxygen species are critical components of an effective immune response. In addition to pathogen associated lipopolysaccharides (LPS, iNOS gene expression is dependent on numerous proinflammatory cytokines in the cellular microenvironment of the macrophage, two of which include interferon gamma (IFN-γ and tumor necrosis factor alpha (TNF-α. To understand the synergistic effect of IFN-γ and TNF-α activation, and LPS stimulation on iNOS expression dynamics and NO production, we developed a systems biology based mathematical model. Using our model, we investigated the impact of pre-infection cytokine exposure, or priming, on the system. We explored the essentiality of IFN-γ priming to the robustness of initial proinflammatory response with respect to the ability of macrophages to produce reactive species needed for pathogen clearance. Results from our theoretical studies indicated that IFN-γ and subsequent activation of IRF1 are essential in consequential production of iNOS upon LPS stimulation. We showed that IFN-γ priming at low concentrations greatly increases the effector response of macrophages against intracellular pathogens. Ultimately the model demonstrated that although TNF-α contributed towards a more rapid response time, measured as time to reach maximum iNOS production, IFN-γ stimulation was significantly more significant in terms of the maximum expression of iNOS and the concentration of NO produced.

Investigating the Role of TNF-α and IFN-γ Activation on the Dynamics of iNOS Gene Expression in LPS Stimulated Macrophages.

Science.gov (United States)

Salim, Taha; Sershen, Cheryl L; May, Elebeoba E

2016-01-01

Macrophage produced inducible nitric oxide synthase (iNOS) is known to play a critical role in the proinflammatory response against intracellular pathogens by promoting the generation of bactericidal reactive nitrogen species. Robust and timely production of nitric oxide (NO) by iNOS and analogous production of reactive oxygen species are critical components of an effective immune response. In addition to pathogen associated lipopolysaccharides (LPS), iNOS gene expression is dependent on numerous proinflammatory cytokines in the cellular microenvironment of the macrophage, two of which include interferon gamma (IFN-γ) and tumor necrosis factor alpha (TNF-α). To understand the synergistic effect of IFN-γ and TNF-α activation, and LPS stimulation on iNOS expression dynamics and NO production, we developed a systems biology based mathematical model. Using our model, we investigated the impact of pre-infection cytokine exposure, or priming, on the system. We explored the essentiality of IFN-γ priming to the robustness of initial proinflammatory response with respect to the ability of macrophages to produce reactive species needed for pathogen clearance. Results from our theoretical studies indicated that IFN-γ and subsequent activation of IRF1 are essential in consequential production of iNOS upon LPS stimulation. We showed that IFN-γ priming at low concentrations greatly increases the effector response of macrophages against intracellular pathogens. Ultimately the model demonstrated that although TNF-α contributed towards a more rapid response time, measured as time to reach maximum iNOS production, IFN-γ stimulation was significantly more significant in terms of the maximum expression of iNOS and the concentration of NO produced.

Characterization and Expression Patterns of microRNAs Involved in Rice Grain Filling

Science.gov (United States)

Du, Yanxiu; Zhang, Jing; Li, Junzhou; Liu, Yanxia; Zhao, Yafan; Zhao, Quanzhi

2013-01-01

MicroRNAs (miRNAs) are upstream gene regulators of plant development and hormone homeostasis through their directed cleavage or translational repression of the target mRNAs, which may play crucial roles in rice grain filling and determining the final grain weight and yield. In this study, high-throughput sequencing was performed to survey the dynamic expressions of miRNAs and their corresponding target genes at five distinct developmental stages of grain filling. In total, 445 known miRNAs and 45 novel miRNAs were detected with most of them expressed in a developmental stage dependent manner, and the majority of known miRNAs, which increased gradually with rice grain filling, showed negatively related to the grain filling rate. Detailed expressional comparisons revealed a clear negative correlation between most miRNAs and their target genes. It was found that specific miRNA cohorts are expressed in a developmental stage dependent manner during grain filling and the known functions of these miRNAs are involved in plant hormone homeostasis and starch accumulation, indicating that the expression dynamics of these miRNAs might play key roles in regulating rice grain filling. PMID:23365650

Ligand-selective activation of heterologously-expressed mammalian olfactory receptor.

Science.gov (United States)

Ukhanov, K; Bobkov, Y; Corey, E A; Ache, B W

2014-10-01

Mammalian olfactory receptors (ORs) appear to have the capacity to couple to multiple G protein-coupled signaling pathways in a ligand-dependent selective manner. To better understand the mechanisms and molecular range of such ligand selectivity, we expressed the mouse eugenol OR (mOR-EG) in HEK293T cells together with Gα15 to monitor activation of the phospholipase-C (PLC) signaling pathway and/or Gαolf to monitor activation of the adenylate cyclase (AC) signaling pathway, resulting in intracellular Ca(2+) release and/or Ca(2+) influx through a cyclic nucleotide-gated channel, respectively. PLC-dependent responses differed dynamically from AC-dependent responses, allowing them to be distinguished when Gα15 and Gαolf were co-expressed. The dynamic difference in readout was independent of the receptor, the heterologous expression system, and the ligand concentration. Of 17 reported mOR-EG ligands tested, including eugenol, its analogs, and structurally dissimilar compounds (mousse cristal, nootkatone, orivone), some equally activated both signaling pathways, some differentially activated both signaling pathways, and some had no noticeable effect even at 1-5mM. Our findings argue that mOR-EG, when heterologously expressed, can couple to two different signaling pathways in a ligand selective manner. The challenge now is to determine the potential of mOR-EG, and perhaps other ORs, to activate multiple signaling pathways in a ligand selective manner in native ORNs. Copyright © 2014 Elsevier Ltd. All rights reserved.

Theobroma cacao L. pathogenesis-related gene tandem array members show diverse expression dynamics in response to pathogen colonization.

Science.gov (United States)

Fister, Andrew S; Mejia, Luis C; Zhang, Yufan; Herre, Edward Allen; Maximova, Siela N; Guiltinan, Mark J

2016-05-17

The pathogenesis-related (PR) group of proteins are operationally defined as polypeptides that increase in concentration in plant tissues upon contact with a pathogen. To date, 17 classes of highly divergent proteins have been described that act through multiple mechanisms of pathogen resistance. Characterizing these families in cacao, an economically important tree crop, and comparing the families to those in other species, is an important step in understanding cacao's immune response. Using publically available resources, all members of the 17 recognized pathogenesis-related gene families in the genome of Theobroma cacao were identified and annotated resulting in a set of ~350 members in both published cacao genomes. Approximately 50 % of these genes are organized in tandem arrays scattered throughout the genome. This feature was observed in five additional plant taxa (three dicots and two monocots), suggesting that tandem duplication has played an important role in the evolution of the PR genes in higher plants. Expression profiling captured the dynamics and complexity of PR genes expression at basal levels and after induction by two cacao pathogens (the oomycete, Phytophthora palmivora, and the fungus, Colletotrichum theobromicola), identifying specific genes within families that are more responsive to pathogen challenge. Subsequent qRT-PCR validated the induction of several PR-1, PR-3, PR-4, and PR-10 family members, with greater than 1000 fold induction detected for specific genes. We describe candidate genes that are likely to be involved in cacao's defense against Phytophthora and Colletotrichum infection and could be potentially useful for marker-assisted selection for breeding of disease resistant cacao varieties. The data presented here, along with existing cacao-omics resources, will enable targeted functional genetic screening of defense genes likely to play critical functions in cacao's defense against its pathogens.

Surface and finite size effect on fluctuations dynamics in nanoparticles with long-range order

Science.gov (United States)

Morozovska, A. N.; Eliseev, E. A.

2010-02-01

The influence of surface and finite size on the dynamics of the order parameter fluctuations and critical phenomena in the three-dimensional (3D)-confined systems with long-range order was not considered theoretically. In this paper, we study the influence of surface and finite size on the dynamics of the order parameter fluctuations in the particles of arbitrary shape. We consider concrete examples of the spherical and cylindrical ferroic nanoparticles within Landau-Ginzburg-Devonshire phenomenological approach. Allowing for the strong surface energy contribution in micro and nanoparticles, the analytical expressions derived for the Ornstein-Zernike correlator of the long-range order parameter spatial-temporal fluctuations, dynamic generalized susceptibility, relaxation times, and correlation radii discrete spectra are different from those known for bulk systems. Obtained analytical expressions for the correlation function of the order parameter spatial-temporal fluctuations in micro and nanosized systems can be useful for the quantitative analysis of the dynamical structural factors determined from magnetic resonance diffraction and scattering spectra. Besides the practical importance of the correlation function for the analysis of the experimental data, derived expressions for the fluctuations strength determine the fundamental limits of phenomenological theories applicability for 3D-confined systems.

Perceptually Valid Facial Expressions for Character-Based Applications

Directory of Open Access Journals (Sweden)

Ali Arya

2009-01-01

Full Text Available This paper addresses the problem of creating facial expression of mixed emotions in a perceptually valid way. The research has been done in the context of a “game-like” health and education applications aimed at studying social competency and facial expression awareness in autistic children as well as native language learning, but the results can be applied to many other applications such as games with need for dynamic facial expressions or tools for automating the creation of facial animations. Most existing methods for creating facial expressions of mixed emotions use operations like averaging to create the combined effect of two universal emotions. Such methods may be mathematically justifiable but are not necessarily valid from a perceptual point of view. The research reported here starts by user experiments aiming at understanding how people combine facial actions to express mixed emotions, and how the viewers perceive a set of facial actions in terms of underlying emotions. Using the results of these experiments and a three-dimensional emotion model, we associate facial actions to dimensions and regions in the emotion space, and create a facial expression based on the location of the mixed emotion in the three-dimensional space. We call these regionalized facial actions “facial expression units.”

Dynamics and spatial distribution of beta-lactamase expression in Pseudomonas aeruginosa biofilms

DEFF Research Database (Denmark)

Bagge, N.; Hentzer, Morten; Andersen, Jens Bo

2004-01-01

of increased imipenem concentrations. Ceftazidime induced the monitor system of the biofilm bacteria as well, but only bacteria in the peripheries of the microcolonies were induced in the presence of even very high concentrations. The experiments illustrate for the first time the dynamic and spatial...

Volatile Gas Production by Methyl Halide Transferase: An In Situ Reporter Of Microbial Gene Expression In Soil.

Science.gov (United States)

Cheng, Hsiao-Ying; Masiello, Caroline A; Bennett, George N; Silberg, Jonathan J

2016-08-16

Traditional visual reporters of gene expression have only very limited use in soils because their outputs are challenging to detect through the soil matrix. This severely restricts our ability to study time-dependent microbial gene expression in one of the Earth's largest, most complex habitats. Here we describe an approach to report on dynamic gene expression within a microbial population in a soil under natural water levels (at and below water holding capacity) via production of methyl halides using a methyl halide transferase. As a proof-of-concept application, we couple the expression of this gas reporter to the conjugative transfer of a bacterial plasmid in a soil matrix and show that gas released from the matrix displays a strong correlation with the number of transconjugant bacteria that formed. Gas reporting of gene expression will make possible dynamic studies of natural and engineered microbes within many hard-to-image environmental matrices (soils, sediments, sludge, and biomass) at sample scales exceeding those used for traditional visual reporting.

Deciphering the Developmental Dynamics of the Mouse Liver Transcriptome.

Directory of Open Access Journals (Sweden)

Sumedha S Gunewardena

Full Text Available During development, liver undergoes a rapid transition from a hematopoietic organ to a major organ for drug metabolism and nutrient homeostasis. However, little is known on a transcriptome level of the genes and RNA-splicing variants that are differentially regulated with age, and which up-stream regulators orchestrate age-specific biological functions in liver. We used RNA-Seq to interrogate the developmental dynamics of the liver transcriptome in mice at 12 ages from late embryonic stage (2-days before birth to maturity (60-days after birth. Among 21,889 unique NCBI RefSeq-annotated genes, 9,641 were significantly expressed in at least one age, 7,289 were differently regulated with age, and 859 had multiple (> = 2 RNA splicing-variants. Factor analysis showed that the dynamics of hepatic genes fall into six distinct groups based on their temporal expression. The average expression of cytokines, ion channels, kinases, phosphatases, transcription regulators and translation regulators decreased with age, whereas the average expression of peptidases, enzymes and transmembrane receptors increased with age. The average expression of growth factors peak between Day-3 and Day-10, and decrease thereafter. We identified critical biological functions, upstream regulators, and putative transcription modules that seem to govern age-specific gene expression. We also observed differential ontogenic expression of known splicing variants of certain genes, and 1,455 novel splicing isoform candidates. In conclusion, the hepatic ontogeny of the transcriptome ontogeny has unveiled critical networks and up-stream regulators that orchestrate age-specific biological functions in liver, and suggest that age contributes to the complexity of the alternative splicing landscape of the hepatic transcriptome.

Younger and Older Users’ Recognition of Virtual Agent Facial Expressions

Science.gov (United States)

Beer, Jenay M.; Smarr, Cory-Ann; Fisk, Arthur D.; Rogers, Wendy A.

2015-01-01

As technology advances, robots and virtual agents will be introduced into the home and healthcare settings to assist individuals, both young and old, with everyday living tasks. Understanding how users recognize an agent’s social cues is therefore imperative, especially in social interactions. Facial expression, in particular, is one of the most common non-verbal cues used to display and communicate emotion in on-screen agents (Cassell, Sullivan, Prevost, & Churchill, 2000). Age is important to consider because age-related differences in emotion recognition of human facial expression have been supported (Ruffman et al., 2008), with older adults showing a deficit for recognition of negative facial expressions. Previous work has shown that younger adults can effectively recognize facial emotions displayed by agents (Bartneck & Reichenbach, 2005; Courgeon et al. 2009; 2011; Breazeal, 2003); however, little research has compared in-depth younger and older adults’ ability to label a virtual agent’s facial emotions, an import consideration because social agents will be required to interact with users of varying ages. If such age-related differences exist for recognition of virtual agent facial expressions, we aim to understand if those age-related differences are influenced by the intensity of the emotion, dynamic formation of emotion (i.e., a neutral expression developing into an expression of emotion through motion), or the type of virtual character differing by human-likeness. Study 1 investigated the relationship between age-related differences, the implication of dynamic formation of emotion, and the role of emotion intensity in emotion recognition of the facial expressions of a virtual agent (iCat). Study 2 examined age-related differences in recognition expressed by three types of virtual characters differing by human-likeness (non-humanoid iCat, synthetic human, and human). Study 2 also investigated the role of configural and featural processing as a

Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks.

Directory of Open Access Journals (Sweden)

Xiaoke Ma

2015-06-01

Full Text Available Development of heart diseases is driven by dynamic changes in both the activity and connectivity of gene pathways. Understanding these dynamic events is critical for understanding pathogenic mechanisms and development of effective treatment. Currently, there is a lack of computational methods that enable analysis of multiple gene networks, each of which exhibits differential activity compared to the network of the baseline/healthy condition. We describe the iMDM algorithm to identify both unique and shared gene modules across multiple differential co-expression networks, termed M-DMs (multiple differential modules. We applied iMDM to a time-course RNA-Seq dataset generated using a murine heart failure model generated on two genotypes. We showed that iMDM achieves higher accuracy in inferring gene modules compared to using single or multiple co-expression networks. We found that condition-specific M-DMs exhibit differential activities, mediate different biological processes, and are enriched for genes with known cardiovascular phenotypes. By analyzing M-DMs that are present in multiple conditions, we revealed dynamic changes in pathway activity and connectivity across heart failure conditions. We further showed that module dynamics were correlated with the dynamics of disease phenotypes during the development of heart failure. Thus, pathway dynamics is a powerful measure for understanding pathogenesis. iMDM provides a principled way to dissect the dynamics of gene pathways and its relationship to the dynamics of disease phenotype. With the exponential growth of omics data, our method can aid in generating systems-level insights into disease progression.

VESPUCCI: exploring patterns of gene expression in grapevine

Directory of Open Access Journals (Sweden)

Marco eMoretto

2016-05-01

Full Text Available Large-scale transcriptional studies aim to decipher the dynamic cellular responses to a stimulus, like different environmental conditions. In the era of high-throughput omics biology, the most used technologies for these purposes are microarray and RNA-Seq, whose data are usually required to be deposited in public repositories upon publication. Such repositories have the enormous potential to provide a comprehensive view of how different experimental conditions lead to expression changes, by comparing gene expression across all possible measured conditions. Unfortunately, this task is greatly impaired by differences among experimental platforms that make direct comparisons difficult.In this paper we present the Vitis Expression Studies Platform Using COLOMBOS Compendia Instances (VESPUCCI, a gene expression compendium for grapevine which was built by adapting an approach originally developed for bacteria, and show how it can be used to investigate complex gene expression patterns. We integrated nearly all publicly available microarray and RNA-Seq expression data: 1608 gene expression samples from 10 different technological platforms. Each sample has been manually annotated using a controlled vocabulary developed ad hoc to ensure both human readability and computational tractability. Expression data in the compendium can be visually explored using several tools provided by the web interface or can be programmatically accessed using the REST interface. VESPUCCI is freely accessible at http://vespucci.colombos.fmach.it.

Facial Expressions in Context: Contributions to Infant Emotion Theory.

Science.gov (United States)

Camras, Linda A.

To make the point that infant emotions are more dynamic than suggested by Differential Emotions Theory, which maintains that infants show the same prototypical facial expressions for emotions as adults do, this paper explores two questions: (1) when infants experience an emotion, do they always show the corresponding prototypical facial…

Noncoding transcription by alternative rna polymerases dynamically regulates an auxin-driven chromatin loop

KAUST Repository

Ariel, Federico D.; Jé gu, Teddy; Latrasse, David; Romero-Barrios, Natali; Christ, Auré lie; Benhamed, Moussa; Crespi, Martí n D.

2014-01-01

The eukaryotic epigenome is shaped by the genome topology in three-dimensional space. Dynamic reversible variations in this epigenome structure directly influence the transcriptional responses to developmental cues. Here, we show that the Arabidopsis long intergenic noncoding RNA (lincRNA) APOLO is transcribed by RNA polymerases II and V in response to auxin, a phytohormone controlling numerous facets of plant development. This dual APOLO transcription regulates the formation of a chromatin loop encompassing the promoter of its neighboring gene PID, a key regulator of polar auxin transport. Altering APOLO expression affects chromatin loop formation, whereas RNA-dependent DNA methylation, active DNA demethylation, and Polycomb complexes control loop dynamics. This dynamic chromatin topology determines PID expression patterns. Hence, the dual transcription of a lincRNA influences local chromatin topology and directs dynamic auxin-controlled developmental outputs on neighboring genes. This mechanism likely underscores the adaptive success of plants in diverse environments and may be widespread in eukaryotes. © 2014 Elsevier Inc.

Noncoding transcription by alternative rna polymerases dynamically regulates an auxin-driven chromatin loop

KAUST Repository

Ariel, Federico D.

2014-08-01

The eukaryotic epigenome is shaped by the genome topology in three-dimensional space. Dynamic reversible variations in this epigenome structure directly influence the transcriptional responses to developmental cues. Here, we show that the Arabidopsis long intergenic noncoding RNA (lincRNA) APOLO is transcribed by RNA polymerases II and V in response to auxin, a phytohormone controlling numerous facets of plant development. This dual APOLO transcription regulates the formation of a chromatin loop encompassing the promoter of its neighboring gene PID, a key regulator of polar auxin transport. Altering APOLO expression affects chromatin loop formation, whereas RNA-dependent DNA methylation, active DNA demethylation, and Polycomb complexes control loop dynamics. This dynamic chromatin topology determines PID expression patterns. Hence, the dual transcription of a lincRNA influences local chromatin topology and directs dynamic auxin-controlled developmental outputs on neighboring genes. This mechanism likely underscores the adaptive success of plants in diverse environments and may be widespread in eukaryotes. © 2014 Elsevier Inc.

Local Descriptors of Dynamic and Nondynamic Correlation.

Science.gov (United States)

Ramos-Cordoba, Eloy; Matito, Eduard

2017-06-13

Quantitatively accurate electronic structure calculations rely on the proper description of electron correlation. A judicious choice of the approximate quantum chemistry method depends upon the importance of dynamic and nondynamic correlation, which is usually assesed by scalar measures. Existing measures of electron correlation do not consider separately the regions of the Cartesian space where dynamic or nondynamic correlation are most important. We introduce real-space descriptors of dynamic and nondynamic electron correlation that admit orbital decomposition. Integration of the local descriptors yields global numbers that can be used to quantify dynamic and nondynamic correlation. Illustrative examples over different chemical systems with varying electron correlation regimes are used to demonstrate the capabilities of the local descriptors. Since the expressions only require orbitals and occupation numbers, they can be readily applied in the context of local correlation methods, hybrid methods, density matrix functional theory, and fractional-occupancy density functional theory.

Caudal regulates the spatiotemporal dynamics of pair-rule waves in Tribolium.

Directory of Open Access Journals (Sweden)

Ezzat El-Sherif

2014-10-01

Full Text Available In the short-germ beetle Tribolium castaneum, waves of pair-rule gene expression propagate from the posterior end of the embryo towards the anterior and eventually freeze into stable stripes, partitioning the anterior-posterior axis into segments. Similar waves in vertebrates are assumed to arise due to the modulation of a molecular clock by a posterior-to-anterior frequency gradient. However, neither a molecular candidate nor a functional role has been identified to date for such a frequency gradient, either in vertebrates or elsewhere. Here we provide evidence that the posterior gradient of Tc-caudal expression regulates the oscillation frequency of pair-rule gene expression in Tribolium. We show this by analyzing the spatiotemporal dynamics of Tc-even-skipped expression in strong and mild knockdown of Tc-caudal, and by correlating the extension, level and slope of the Tc-caudal expression gradient to the spatiotemporal dynamics of Tc-even-skipped expression in wild type as well as in different RNAi knockdowns of Tc-caudal regulators. Further, we show that besides its absolute importance for stripe generation in the static phase of the Tribolium blastoderm, a frequency gradient might serve as a buffer against noise during axis elongation phase in Tribolium as well as vertebrates. Our results highlight the role of frequency gradients in pattern formation.

Circadian control of mRNA polyadenylation dynamics regulates rhythmic protein expression

OpenAIRE

Kojima, Shihoko; Sher-Chen, Elaine L.; Green, Carla B.

2012-01-01

Green and colleagues perform a global analysis of circadian-controlled poly(A) tails and identify hundreds of mRNAs that display dynamic rhythmic polyadenylation states. They identify three distinct classes of mRNAs with rhythmic poly(A) tails. Interestingly, class III mRNAs are controlled not by transcription, but by rhythmic cytoplasmic polyadenylation, and are regulated by the components of the cytoplasmic polyadenylation machinery, CPEB2 in particular, which are themselves rhythmically ex...

A novel mutual information-based Boolean network inference method from time-series gene expression data.

Directory of Open Access Journals (Sweden)

Shohag Barman

Full Text Available Inferring a gene regulatory network from time-series gene expression data in systems biology is a challenging problem. Many methods have been suggested, most of which have a scalability limitation due to the combinatorial cost of searching a regulatory set of genes. In addition, they have focused on the accurate inference of a network structure only. Therefore, there is a pressing need to develop a network inference method to search regulatory genes efficiently and to predict the network dynamics accurately.In this study, we employed a Boolean network model with a restricted update rule scheme to capture coarse-grained dynamics, and propose a novel mutual information-based Boolean network inference (MIBNI method. Given time-series gene expression data as an input, the method first identifies a set of initial regulatory genes using mutual information-based feature selection, and then improves the dynamics prediction accuracy by iteratively swapping a pair of genes between sets of the selected regulatory genes and the other genes. Through extensive simulations with artificial datasets, MIBNI showed consistently better performance than six well-known existing methods, REVEAL, Best-Fit, RelNet, CST, CLR, and BIBN in terms of both structural and dynamics prediction accuracy. We further tested the proposed method with two real gene expression datasets for an Escherichia coli gene regulatory network and a fission yeast cell cycle network, and also observed better results using MIBNI compared to the six other methods.Taken together, MIBNI is a promising tool for predicting both the structure and the dynamics of a gene regulatory network.

Microscopic theory for coupled atomistic magnetization and lattice dynamics

Science.gov (United States)

Fransson, J.; Thonig, D.; Bessarab, P. F.; Bhattacharjee, S.; Hellsvik, J.; Nordström, L.

2017-12-01

A coupled atomistic spin and lattice dynamics approach is developed which merges the dynamics of these two degrees of freedom into a single set of coupled equations of motion. The underlying microscopic model comprises local exchange interactions between the electron spin and magnetic moment and the local couplings between the electronic charge and lattice displacements. An effective action for the spin and lattice variables is constructed in which the interactions among the spin and lattice components are determined by the underlying electronic structure. In this way, expressions are obtained for the electronically mediated couplings between the spin and lattice degrees of freedom, besides the well known interatomic force constants and spin-spin interactions. These former susceptibilities provide an atomistic ab initio description for the coupled spin and lattice dynamics. It is important to notice that this theory is strictly bilinear in the spin and lattice variables and provides a minimal model for the coupled dynamics of these subsystems and that the two subsystems are treated on the same footing. Questions concerning time-reversal and inversion symmetry are rigorously addressed and it is shown how these aspects are absorbed in the tensor structure of the interaction fields. By means of these results regarding the spin-lattice coupling, simple explanations of ionic dimerization in double-antiferromagnetic materials, as well as charge density waves induced by a nonuniform spin structure, are given. In the final parts, coupled equations of motion for the combined spin and lattice dynamics are constructed, which subsequently can be reduced to a form which is analogous to the Landau-Lifshitz-Gilbert equations for spin dynamics and a damped driven mechanical oscillator for the ionic motion. It is important to notice, however, that these equations comprise contributions that couple these descriptions into one unified formulation. Finally, Kubo-like expressions for

Dynamic energy release rate in couple-stress elasticity

International Nuclear Information System (INIS)

Morini, L; Piccolroaz, A; Mishuris, G

2013-01-01

This paper is concerned with energy release rate for dynamic steady state crack problems in elastic materials with microstructures. A Mode III semi-infinite crack subject to loading applied on the crack surfaces is considered. The micropolar behaviour of the material is described by the theory of couple-stress elasticity developed by Koiter. A general expression for the dynamic J-integral including both traslational and micro-rotational inertial contributions is derived, and the conservation of this integral on a path surrounding the crack tip is demonstrated

Adolescent Mouse Takes on An Active Transcriptomic Expression During Postnatal Cerebral Development

KAUST Repository

Xu, Wei

2014-06-01

Postnatal cerebral development is a complicated biological process precisely controlled by multiple genes. To understand the molecular mechanism of cerebral development, we compared dynamics of mouse cerebrum transcriptome through three developmental stages using high-throughput RNA-seq technique. Three libraries were generated from the mouse cerebrum at infancy, adolescence and adulthood, respectively. Consequently, 44,557,729 (infancy), 59,257,530 (adolescence) and 72,729,636 (adulthood) reads were produced, which were assembled into 15,344, 16,048 and 15,775 genes, respectively. We found that the overall gene expression level increased from infancy to adolescence and decreased later on upon reaching adulthood. The adolescence cerebrum has the most active gene expression, with expression of a large number of regulatory genes up-regulated and some crucial pathways activated. Transcription factor (TF) analysis suggested the similar dynamics as expression profiling, especially those TFs functioning in neurogenesis differentiation, oligodendrocyte lineage determination and circadian rhythm regulation. Moreover, our data revealed a drastic increase in myelin basic protein (MBP)-coding gene expression in adolescence and adulthood, suggesting that the brain myelin may be generated since mouse adolescence. In addition, differential gene expression analysis indicated the activation of rhythmic pathway, suggesting the function of rhythmic movement since adolescence; Furthermore, during infancy and adolescence periods, gene expression related to axon. repulsion and attraction showed the opposite trends, indicating that axon repulsion was activated after birth, while axon attraction might be activated at the embryonic stage and declined during the postnatal development. Our results from the present study may shed light on the molecular mechanism underlying the postnatal development of the mammalian cerebrum. © 2014 .

Dynamic assessment for life extension of nuclear power plants (NPPs) using system dynamics (SD) method

International Nuclear Information System (INIS)

Woo, Tae Ho

2012-01-01

It has been proposed to extend the life of nuclear power plants (NPPs) for the economic purpose. Especially, the primary systems in reactor are considered in the thermohydraulic and neutronic aspect, which is related to the safety system. The electric power and the lifespan of components are expressed as economic situation. In addition, political considerations are given by the presidential change and the nuclear non-proliferation characteristics. The dynamical investigation using system dynamics (SD) shows the effective time for the life extension of the NPPs by Monte-Carlo simulations. This non-linear algorithm is incorporated with the feedback loop of the event sequences. The expected event is related to the past event, which affects to the dynamical simulations of lifetime in the NPPs. In the conclusions, the safety guarantee as well as the economic profit in the re-use of long term operated power plants is presented, which is mentioned as the transient time between 2019 and 2021 in this paper. (orig.)

Dynamic assessment for life extension of nuclear power plants (NPPs) using system dynamics (SD) method

Energy Technology Data Exchange (ETDEWEB)

Woo, Tae Ho [Seoul National Univ. (Korea, Republic of). Dept. of Nuclear Engineering

2012-12-15

It has been proposed to extend the life of nuclear power plants (NPPs) for the economic purpose. Especially, the primary systems in reactor are considered in the thermohydraulic and neutronic aspect, which is related to the safety system. The electric power and the lifespan of components are expressed as economic situation. In addition, political considerations are given by the presidential change and the nuclear non-proliferation characteristics. The dynamical investigation using system dynamics (SD) shows the effective time for the life extension of the NPPs by Monte-Carlo simulations. This non-linear algorithm is incorporated with the feedback loop of the event sequences. The expected event is related to the past event, which affects to the dynamical simulations of lifetime in the NPPs. In the conclusions, the safety guarantee as well as the economic profit in the re-use of long term operated power plants is presented, which is mentioned as the transient time between 2019 and 2021 in this paper. (orig.)

The Financial Accounting Model from a System Dynamics' Perspective

OpenAIRE

Melse, Eric

2006-01-01

This paper explores the foundation of the financial accounting model. We examine the properties of the accounting equation as the principal algorithm for the design and the development of a System Dynamics model. Key to the perspective is the foundational requirement that resolves the temporal conflict that resides in a stock and flow model. Through formal analysis the accounting equation is redefined as a cybernetic model by expressing the temporal and dynamic properties of its terms. Articu...

Global sensitivity analysis of a dynamic model for gene expression in Drosophila embryos

Science.gov (United States)

McCarthy, Gregory D.; Drewell, Robert A.

2015-01-01

It is well known that gene regulation is a tightly controlled process in early organismal development. However, the roles of key processes involved in this regulation, such as transcription and translation, are less well understood, and mathematical modeling approaches in this field are still in their infancy. In recent studies, biologists have taken precise measurements of protein and mRNA abundance to determine the relative contributions of key factors involved in regulating protein levels in mammalian cells. We now approach this question from a mathematical modeling perspective. In this study, we use a simple dynamic mathematical model that incorporates terms representing transcription, translation, mRNA and protein decay, and diffusion in an early Drosophila embryo. We perform global sensitivity analyses on this model using various different initial conditions and spatial and temporal outputs. Our results indicate that transcription and translation are often the key parameters to determine protein abundance. This observation is in close agreement with the experimental results from mammalian cells for various initial conditions at particular time points, suggesting that a simple dynamic model can capture the qualitative behavior of a gene. Additionally, we find that parameter sensitivites are temporally dynamic, illustrating the importance of conducting a thorough global sensitivity analysis across multiple time points when analyzing mathematical models of gene regulation. PMID:26157608

Minority rights, freedom of expression and of the media: dynamics and dilemmas

NARCIS (Netherlands)

McGonagle, T.

2011-01-01

This book offers a rigorous, theory-based, and uniquely comprehensive, analysis of European and international legal standards shaping minorities’ right to freedom of expression. The analysis pays particular attention to the instrumental role played by traditional and new forms of media in ensuring

Affective Dynamics in Triadic Peer Interactions in Early Childhood

NARCIS (Netherlands)

Lavictoire, L.A.; Snyder, J.; Stoolmiller, M.; Hollenstein, T.P.

2012-01-01

In interpersonal interaction research, moving beyond dyadic to triadic dynamics can be analytically daunting. We explored the affective states expressed during triadic peer interactions to understand how patterns were associated with childhood psychopathology and sociometric status. High-risk

Time-Delay Effects on Constitutive Gene Expression*

International Nuclear Information System (INIS)

Feng Yan-Ling; Wang Dan; Tang Xu-Lei; Dong Jian-Min

2017-01-01

The dynamics of constitutive gene expression with delayed mRNA degradation is investigated, where the intrinsic noise caused by the small number of reactant molecules is introduced. It is found that the oscillatory behavior claimed in previous investigations does not appear in the approximation of small time delay, and the steady state distribution still follows the Poisson law. Furthermore, we introduce the extrinsic noise induced by surrounding environment to explore the effects of this noise and time delay on the Fano factor. Based on a delay Langevin equation and the corresponding Fokker–Planck equation, the distribution of mRNA copy-number is achieved analytically. The time delay and extrinsic noise play similar roles in the gene expression system, that is, they are able to result in the deviation of the Fano factor from 1 evidently. The measured Fano factor for constitutive gene expression is slightly larger than 1, which is perhaps attributed to the time-delay effect. (paper)

Dynamic evolution and biogenesis of small RNAs during sex reversal.

Science.gov (United States)

Liu, Jie; Luo, Majing; Sheng, Yue; Hong, Qiang; Cheng, Hanhua; Zhou, Rongjia

2015-05-06

Understanding origin, evolution and functions of small RNA (sRNA) genes has been a great challenge in the past decade. Molecular mechanisms underlying sexual reversal in vertebrates, particularly sRNAs involved in this process, are largely unknown. By deep-sequencing of small RNA transcriptomes in combination with genomic analysis, we identified a large amount of piRNAs and miRNAs including over 1,000 novel miRNAs, which were differentially expressed during gonad reversal from ovary to testis via ovotesis. Biogenesis and expressions of miRNAs were dynamically changed during the reversal. Notably, phylogenetic analysis revealed dynamic expansions of miRNAs in vertebrates and an evolutionary trajectory of conserved miR-17-92 cluster in the Eukarya. We showed that the miR-17-92 cluster in vertebrates was generated through multiple duplications from ancestor miR-92 in invertebrates Tetranychus urticae and Daphnia pulex from the Chelicerata around 580 Mya. Moreover, we identified the sexual regulator Dmrt1 as a direct target of the members miR-19a and -19b in the cluster. These data suggested dynamic biogenesis and expressions of small RNAs during sex reversal and revealed multiple expansions and evolutionary trajectory of miRNAs from invertebrates to vertebrates, which implicate small RNAs in sexual reversal and provide new insight into evolutionary and molecular mechanisms underlying sexual reversal.

FocusHeuristics - expression-data-driven network optimization and disease gene prediction.

Science.gov (United States)

Ernst, Mathias; Du, Yang; Warsow, Gregor; Hamed, Mohamed; Endlich, Nicole; Endlich, Karlhans; Murua Escobar, Hugo; Sklarz, Lisa-Madeleine; Sender, Sina; Junghanß, Christian; Möller, Steffen; Fuellen, Georg; Struckmann, Stephan

2017-02-16

To identify genes contributing to disease phenotypes remains a challenge for bioinformatics. Static knowledge on biological networks is often combined with the dynamics observed in gene expression levels over disease development, to find markers for diagnostics and therapy, and also putative disease-modulatory drug targets and drugs. The basis of current methods ranges from a focus on expression-levels (Limma) to concentrating on network characteristics (PageRank, HITS/Authority Score), and both (DeMAND, Local Radiality). We present an integrative approach (the FocusHeuristics) that is thoroughly evaluated based on public expression data and molecular disease characteristics provided by DisGeNet. The FocusHeuristics combines three scores, i.e. the log fold change and another two, based on the sum and difference of log fold changes of genes/proteins linked in a network. A gene is kept when one of the scores to which it contributes is above a threshold. Our FocusHeuristics is both, a predictor for gene-disease-association and a bioinformatics method to reduce biological networks to their disease-relevant parts, by highlighting the dynamics observed in expression data. The FocusHeuristics is slightly, but significantly better than other methods by its more successful identification of disease-associated genes measured by AUC, and it delivers mechanistic explanations for its choice of genes.

Tissue-specific RNA expression marks distant-acting developmental enhancers.

Directory of Open Access Journals (Sweden)

Han Wu

2014-09-01

Full Text Available Short non-coding transcripts can be transcribed from distant-acting transcriptional enhancer loci, but the prevalence of such enhancer RNAs (eRNAs within the transcriptome, and the association of eRNA expression with tissue-specific enhancer activity in vivo remain poorly understood. Here, we investigated the expression dynamics of tissue-specific non-coding RNAs in embryonic mouse tissues via deep RNA sequencing. Overall, approximately 80% of validated in vivo enhancers show tissue-specific RNA expression that correlates with tissue-specific enhancer activity. Globally, we identified thousands of tissue-specifically transcribed non-coding regions (TSTRs displaying various genomic hallmarks of bona fide enhancers. In transgenic mouse reporter assays, over half of tested TSTRs functioned as enhancers with reproducible activity in the predicted tissue. Together, our results demonstrate that tissue-specific eRNA expression is a common feature of in vivo enhancers, as well as a major source of extragenic transcription, and that eRNA expression signatures can be used to predict tissue-specific enhancers independent of known epigenomic enhancer marks.

Dynamical chiral symmetry breaking and pion decay constant

International Nuclear Information System (INIS)

Gogohia, V.Sh.; Kluge, Gy.

1991-08-01

Flavour non-singlet, chiral axial-vector Ward-Takahashi identity is investigated in the framework of dynamical chiral symmetry breaking. The use of the condition of stationarity for the bound-state amplitude is proposed in order to fully determine this quantity and the regular piece of the corresponding axial vertex. This makes it possible to express the pion decay constant in terms of the quark propagator variables only. An exact expression was found for the pion decay constant in current algebra and in Jackiw-Johnson representation as well. We also find a new expression for the pion decay constant in the Pagels-Stokar-Cornwall variables within the framework of Jackiw-Johnson representation. (author) 22 refs.; 2 figs

Introducing the Geneva Multimodal expression corpus for experimental research on emotion perception.

Science.gov (United States)

Bänziger, Tanja; Mortillaro, Marcello; Scherer, Klaus R

2012-10-01

Research on the perception of emotional expressions in faces and voices is exploding in psychology, the neurosciences, and affective computing. This article provides an overview of some of the major emotion expression (EE) corpora currently available for empirical research and introduces a new, dynamic, multimodal corpus of emotion expressions, the Geneva Multimodal Emotion Portrayals Core Set (GEMEP-CS). The design features of the corpus are outlined and justified, and detailed validation data for the core set selection are presented and discussed. Finally, an associated database with microcoded facial, vocal, and body action elements, as well as observer ratings, is introduced.

Concentration dynamics in lakes and reservoirs. Studies using radioactive tracers

International Nuclear Information System (INIS)

Gilath, Ch.

1983-01-01

The use of radioactive tracers for the investigation of concentration dynamics of inert soluble matter in lakes and reservoirs is reviewed. Shallow and deep stratified lakes are considered. The mechanism of mixing in lakes, flow pattern and input - output response are discussed. The methodology of the use of radioactive tracers for concentration dynamic studies is described. Examples of various investigations are reviewed. The dynamics of shallow lakes can be found and expressed in terms of transfer functions, axial dispersion models, residence time distributions and sometimes only semiquantitative information about the flow pattern. The dynamics of deep, stratified lakes is more complex and difficult to investigate with tracers. Flow pattern, horizontal and vertical eddy diffusivities, mass transfer between the hypolimnion and epilimnion are tools used for describing this dynamics. (author)

Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics

KAUST Repository

Roy, S.

2015-06-27

Classically or alternatively activated macrophages (M1 and M2, respectively) play distinct and important roles for microbiocidal activity, regulation of inflammation and tissue homeostasis. Despite this, their transcriptional regulatory dynamics are poorly understood. Using promoter-level expression profiling by non-biased deepCAGE we have studied the transcriptional dynamics of classically and alternatively activated macrophages. Transcription factor (TF) binding motif activity analysis revealed four motifs, NFKB1_REL_RELA, IRF1,2, IRF7 and TBP that are commonly activated but have distinct activity dynamics in M1 and M2 activation. We observe matching changes in the expression profiles of the corresponding TFs and show that only a restricted set of TFs change expression. There is an overall drastic and transient up-regulation in M1 and a weaker and more sustainable up-regulation in M2. Novel TFs, such as Thap6, Maff, (M1) and Hivep1, Nfil3, Prdm1, (M2) among others, were suggested to be involved in the activation processes. Additionally, 52 (M1) and 67 (M2) novel differentially expressed genes and, for the first time, several differentially expressed long non-coding RNA (lncRNA) transcriptome markers were identified. In conclusion, the finding of novel motifs, TFs and protein-coding and lncRNA genes is an important step forward to fully understand the transcriptional machinery of macrophage activation.

An overview of the dynamic calibration of piezoelectric pressure transducers

Science.gov (United States)

Theodoro, F. R. F.; Reis, M. L. C. C.; d’ Souto, C.

2018-03-01

Dynamic calibration is a research area that is still under development and is of great interest to aerospace and automotive industries. This study discusses some concepts regarding dynamic measurements of pressure quantities and presents an overview of dynamic calibration of pressure transducers. Studies conducted by the Institute of Aeronautics and Space focusing on research regarding piezoelectric pressure transducer calibration in shock tube are presented. We employed the Guide to the Expression of Uncertainty and a Monte Carlo Method in the methodology. The results show that both device and methodology employed are adequate to calibrate the piezoelectric sensor.

Testing Object-Oriented Programs using Dynamic Aspects and Non-Determinism

DEFF Research Database (Denmark)

Achenbach, Michael; Ostermann, Klaus

2010-01-01

decisions exposing private data. We present an approach that both improves the expressiveness of test cases using non-deterministic choice and reduces design modifications using dynamic aspect-oriented programming techniques. Non-deterministic choice facilitates local definitions of multiple executions...... without parameterization or generation of tests. It also eases modelling naturally non-deterministic program features like IO or multi-threading in integration tests. Dynamic AOP facilitates powerful design adaptations without exposing test features, keeping the scope of these adaptations local to each...... test. We also combine non-determinism and dynamic aspects in a new approach to testing multi-threaded programs using co-routines....

Seeing Mixed Emotions: The Specificity of Emotion Perception From Static and Dynamic Facial Expressions Across Cultures.

Science.gov (United States)

Fang, Xia; Sauter, Disa A; Van Kleef, Gerben A

2018-01-01

Although perceivers often agree about the primary emotion that is conveyed by a particular expression, observers may concurrently perceive several additional emotions from a given facial expression. In the present research, we compared the perception of two types of nonintended emotions in Chinese and Dutch observers viewing facial expressions: emotions which were morphologically similar to the intended emotion and emotions which were morphologically dissimilar to the intended emotion. Findings were consistent across two studies and showed that (a) morphologically similar emotions were endorsed to a greater extent than dissimilar emotions and (b) Chinese observers endorsed nonintended emotions more than did Dutch observers. Furthermore, the difference between Chinese and Dutch observers was more pronounced for the endorsement of morphologically similar emotions than of dissimilar emotions. We also obtained consistent evidence that Dutch observers endorsed nonintended emotions that were congruent with the preceding expressions to a greater degree. These findings suggest that culture and morphological similarity both influence the extent to which perceivers see several emotions in a facial expression.

Seeing Mixed Emotions: The Specificity of Emotion Perception From Static and Dynamic Facial Expressions Across Cultures

Science.gov (United States)

Fang, Xia; Sauter, Disa A.; Van Kleef, Gerben A.

2017-01-01

Although perceivers often agree about the primary emotion that is conveyed by a particular expression, observers may concurrently perceive several additional emotions from a given facial expression. In the present research, we compared the perception of two types of nonintended emotions in Chinese and Dutch observers viewing facial expressions: emotions which were morphologically similar to the intended emotion and emotions which were morphologically dissimilar to the intended emotion. Findings were consistent across two studies and showed that (a) morphologically similar emotions were endorsed to a greater extent than dissimilar emotions and (b) Chinese observers endorsed nonintended emotions more than did Dutch observers. Furthermore, the difference between Chinese and Dutch observers was more pronounced for the endorsement of morphologically similar emotions than of dissimilar emotions. We also obtained consistent evidence that Dutch observers endorsed nonintended emotions that were congruent with the preceding expressions to a greater degree. These findings suggest that culture and morphological similarity both influence the extent to which perceivers see several emotions in a facial expression. PMID:29386689

Bubble dynamics equations in Newton fluid

International Nuclear Information System (INIS)

Xiao, J

2008-01-01

For the high-speed flow of Newton fluid, bubble is produced and expanded when it moves toward the surface of fluid. Bubble dynamics is a very important research field to understand the intrinsic feature of bubble production and motion. This research formulates the bubble expansion by expansion-local rotation transformation, which can be calculated by the measured velocity field. Then, the related dynamic equations are established to describe the interaction between the fluid and the bubble. The research shows that the bubble production condition can be expressed by critical vortex value and fluid pressure; and the bubble expansion rate can be obtained by solving the non-linear dynamic equation of bubble motion. The results may help the related research as it shows a special kind of fluid motion in theoretic sense. As an application example, the nanofiber radium-voltage relation and threshold voltage-surface tension relation in electrospinning process are discussed

Differential expression pattern of UBX family genes in Caenorhabditis elegans

International Nuclear Information System (INIS)

Yamauchi, Seiji; Sasagawa, Yohei; Ogura, Teru; Yamanaka, Kunitoshi

2007-01-01

UBX (ubiquitin regulatory X)-containing proteins belong to an evolutionary conserved protein family and determine the specificity of p97/VCP/Cdc48p function by binding as its adaptors. Caenorhabditis elegans was found to possess six UBX-containing proteins, named UBXN-1 to -6. However, no general or specific function of them has been revealed. During the course of understanding not only their function but also specified function of p97, we investigated spatial and temporal expression patterns of six ubxn genes in this study. Transcript analyses showed that the expression pattern of each ubxn gene was different throughout worm's development and may show potential developmental dynamics in their function, especially ubxn-5 was expressed specifically in the spermatogenic germline, suggesting a crucial role in spermatogenesis. In addition, as ubxn-4 expression was induced by ER stress, it would function as an ERAD factor in C. elegans. In vivo expression analysis by using GFP translational fusion constructs revealed that six ubxn genes show distinct expression patterns. These results altogether demonstrate that the expression of all six ubxn genes of C. elegans is differently regulated

On whole Abelian model dynamics

Energy Technology Data Exchange (ETDEWEB)

Chauca, J.; Doria, R. [CBPF, Rio de Janeiro (Brazil); Aprendanet, Petropolis, 25600 (Brazil)

2012-09-24

Physics challenge is to determine the objects dynamics. However, there are two ways for deciphering the part. The first one is to search for the ultimate constituents; the second one is to understand its behaviour in whole terms. Therefore, the parts can be defined either from elementary constituents or as whole functions. Historically, science has been moving through the first aspect, however, quarks confinement and complexity are interrupting this usual approach. These relevant facts are supporting for a systemic vision be introduced. Our effort here is to study on the whole meaning through gauge theory. Consider a systemic dynamics oriented through the U(1) - systemic gauge parameter which function is to collect a fields set {l_brace}A{sub {mu}I}{r_brace}. Derive the corresponding whole gauge invariant Lagrangian, equations of motion, Bianchi identities, Noether relationships, charges and Ward-Takahashi equations. Whole Lorentz force and BRST symmetry are also studied. These expressions bring new interpretations further than the usual abelian model. They are generating a systemic system governed by 2N+ 10 classical equations plus Ward-Takahashi identities. A whole dynamics based on the notions of directive and circumstance is producing a set determinism where the parts dynamics are inserted in the whole evolution. A dynamics based on state, collective and individual equations with a systemic interdependence.

Stochastic fluctuations and distributed control of gene expression impact cellular memory.

Directory of Open Access Journals (Sweden)

Guillaume Corre

Full Text Available Despite the stochastic noise that characterizes all cellular processes the cells are able to maintain and transmit to their daughter cells the stable level of gene expression. In order to better understand this phenomenon, we investigated the temporal dynamics of gene expression variation using a double reporter gene model. We compared cell clones with transgenes coding for highly stable mRNA and fluorescent proteins with clones expressing destabilized mRNA-s and proteins. Both types of clones displayed strong heterogeneity of reporter gene expression levels. However, cells expressing stable gene products produced daughter cells with similar level of reporter proteins, while in cell clones with short mRNA and protein half-lives the epigenetic memory of the gene expression level was completely suppressed. Computer simulations also confirmed the role of mRNA and protein stability in the conservation of constant gene expression levels over several cell generations. These data indicate that the conservation of a stable phenotype in a cellular lineage may largely depend on the slow turnover of mRNA-s and proteins.

Transcriptome dynamics-based operon prediction in prokaryotes.

Science.gov (United States)

Fortino, Vittorio; Smolander, Olli-Pekka; Auvinen, Petri; Tagliaferri, Roberto; Greco, Dario

2014-05-16

Inferring operon maps is crucial to understanding the regulatory networks of prokaryotic genomes. Recently, RNA-seq based transcriptome studies revealed that in many bacterial species the operon structure vary with the change of environmental conditions. Therefore, new computational solutions that use both static and dynamic data are necessary to create condition specific operon predictions. In this work, we propose a novel classification method that integrates RNA-seq based transcriptome profiles with genomic sequence features to accurately identify the operons that are expressed under a measured condition. The classifiers are trained on a small set of confirmed operons and then used to classify the remaining gene pairs of the organism studied. Finally, by linking consecutive gene pairs classified as operons, our computational approach produces condition-dependent operon maps. We evaluated our approach on various RNA-seq expression profiles of the bacteria Haemophilus somni, Porphyromonas gingivalis, Escherichia coli and Salmonella enterica. Our results demonstrate that, using features depending on both transcriptome dynamics and genome sequence characteristics, we can identify operon pairs with high accuracy. Moreover, the combination of DNA sequence and expression data results in more accurate predictions than each one alone. We present a computational strategy for the comprehensive analysis of condition-dependent operon maps in prokaryotes. Our method can be used to generate condition specific operon maps of many bacterial organisms for which high-resolution transcriptome data is available.

Dynamics of polynomial Chaplygin gas warm inflation

Energy Technology Data Exchange (ETDEWEB)

Jawad, Abdul [COMSATS Institute of Information Technology, Department of Mathematics, Lahore (Pakistan); Chaudhary, Shahid [Sharif College of Engineering and Technology, Department of Mathematics, Lahore (Pakistan); Videla, Nelson [Pontificia Universidad Catolica de Valparaiso, Instituto de Fisica, Valparaiso (Chile)

2017-11-15

In the present work, we study the consequences of a recently proposed polynomial inflationary potential in the context of the generalized, modified, and generalized cosmic Chaplygin gas models. In addition, we consider dissipative effects by coupling the inflation field to radiation, i.e., the inflationary dynamics is studied in the warm inflation scenario. We take into account a general parametrization of the dissipative coefficient Γ for describing the decay of the inflaton field into radiation. By studying the background and perturbative dynamics in the weak and strong dissipative regimes of warm inflation separately for the positive and negative quadratic and quartic potentials, we obtain expressions for the most relevant inflationary observables as the scalar power spectrum, the scalar spectral, and the tensor-to-scalar ratio. We construct the trajectories in the n{sub s}-r plane for several expressions of the dissipative coefficient and compare with the two-dimensional marginalized contours for (n{sub s}, r) from the latest Planck data. We find that our results are in agreement with WMAP9 and Planck 2015 data. (orig.)

Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes.

Science.gov (United States)

Wang, Cheng; Dong, Da; Strong, P J; Zhu, Weijing; Ma, Zhuang; Qin, Yong; Wu, Weixiang

2017-08-16

Animal manure is a reservoir of antibiotic resistance genes (ARGs) that pose a potential health risk globally, especially for resistance to the antibiotics commonly used in livestock production (such as tetracycline, sulfonamide, and fluoroquinolone). Currently, the effects of biological treatment (composting) on the transcriptional response of manure ARGs and their microbial hosts are not well characterized. Composting is a dynamic process that consists of four distinct phases that are distinguished by the temperature resulting from microbial activity, namely the mesophilic, thermophilic, cooling, and maturing phases. In this study, changes of resistome expression were determined and related to active microbiome profiles during the dynamic composting process. This was achieved by integrating metagenomic and time series metatranscriptomic data for the evolving microbial community during composting. Composting noticeably reduced the aggregated expression level of the manure resistome, which primarily consisted of genes encoding for tetracycline, vancomycin, fluoroquinolone, beta-lactam, and aminoglycoside resistance, as well as efflux pumps. Furthermore, a varied transcriptional response of resistome to composting at the ARG levels was highlighted. The expression of tetracycline resistance genes (tetM-tetW-tetO-tetS) decreased during composting, where distinctive shifts in the four phases of composting were related to variations in antibiotic concentration. Composting had no effect on the expression of sulfonamide and fluoroquinolone resistance genes, which increased slightly during the thermophilic phase and then decreased to initial levels. As indigenous populations switched greatly throughout the dynamic composting, the core resistome persisted and their reservoir hosts' composition was significantly correlated with dynamic active microbial phylogenetic structure. Hosts for sulfonamide and fuoroquinolone resistance genes changed notably in phylognetic structure

Gene Expression in the Human Brain: The Current State of the Study of Specificity and Spatiotemporal Dynamics

Science.gov (United States)

Naumova, Oksana Yu.; Lee, Maria; Rychkov, Sergei Yu.; Vlasova, Natalia V.; Grigorenko, Elena L.

2013-01-01

Gene expression is one of the main molecular processes regulating the differentiation, development, and functioning of cells and tissues. In this review a handful of relevant terms and concepts are introduced and the most common techniques used in studies of gene expression/expression profiling (also referred to as studies of the transcriptome or…

Inferring time-varying network topologies from gene expression data.

Science.gov (United States)

Rao, Arvind; Hero, Alfred O; States, David J; Engel, James Douglas

2007-01-01

Most current methods for gene regulatory network identification lead to the inference of steady-state networks, that is, networks prevalent over all times, a hypothesis which has been challenged. There has been a need to infer and represent networks in a dynamic, that is, time-varying fashion, in order to account for different cellular states affecting the interactions amongst genes. In this work, we present an approach, regime-SSM, to understand gene regulatory networks within such a dynamic setting. The approach uses a clustering method based on these underlying dynamics, followed by system identification using a state-space model for each learnt cluster--to infer a network adjacency matrix. We finally indicate our results on the mouse embryonic kidney dataset as well as the T-cell activation-based expression dataset and demonstrate conformity with reported experimental evidence.

Unique functional properties of somatostatin-expressing GABAergic neurons in mouse barrel cortex.

NARCIS (Netherlands)

Gentet, L.J.; Kremer, Y.; Taniguchi, H.; Huang, Z.J.; Staiger, J.F.; Petersen, C.C.H.

2012-01-01

Neocortical GABAergic neurons have diverse molecular, structural and electrophysiological features, but the functional correlates of this diversity are largely unknown. We found unique membrane potential dynamics of somatostatin-expressing (SOM) neurons in layer 2/3 of the primary somatosensory

Transient dynamic and modeling parameter sensitivity analysis of 1D solid oxide fuel cell model

International Nuclear Information System (INIS)

Huangfu, Yigeng; Gao, Fei; Abbas-Turki, Abdeljalil; Bouquain, David; Miraoui, Abdellatif

2013-01-01

Highlights: • A multiphysics, 1D, dynamic SOFC model is developed. • The presented model is validated experimentally in eight different operating conditions. • Electrochemical and thermal dynamic transient time expressions are given in explicit forms. • Parameter sensitivity is discussed for different semi-empirical parameters in the model. - Abstract: In this paper, a multiphysics solid oxide fuel cell (SOFC) dynamic model is developed by using a one dimensional (1D) modeling approach. The dynamic effects of double layer capacitance on the electrochemical domain and the dynamic effect of thermal capacity on thermal domain are thoroughly considered. The 1D approach allows the model to predict the non-uniform distributions of current density, gas pressure and temperature in SOFC during its operation. The developed model has been experimentally validated, under different conditions of temperature and gas pressure. Based on the proposed model, the explicit time constant expressions for different dynamic phenomena in SOFC have been given and discussed in detail. A parameters sensitivity study has also been performed and discussed by using statistical Multi Parameter Sensitivity Analysis (MPSA) method, in order to investigate the impact of parameters on the modeling accuracy

Analytical and semi-analytical formalism for the voltage and the current sources of a superconducting cavity under dynamic detuning

CERN Document Server

Doleans, M

2003-01-01

Elliptical superconducting radio frequency (SRF) cavities are sensitive to frequency detuning because they have a high Q value in comparison with normal conducting cavities and weak mechanical properties. Radiation pressure on the cavity walls, microphonics, and tuning system are possible sources of dynamic detuning during SRF cavity-pulsed operation. A general analytic relation between the cavity voltage, the dynamic detuning function, and the RF control function is developed. This expression for the voltage envelope in a cavity under dynamic detuning and dynamic RF controls is analytically expressed through an integral formulation. A semi-analytical scheme is derived to calculate the voltage behavior in any practical case. Examples of voltage envelope behavior for different cases of dynamic detuning and RF control functions are shown. The RF control function for a cavity under dynamic detuning is also investigated and as an application various filling schemes are presented.

Facial Expression Recognition from Video Sequences Based on Spatial-Temporal Motion Local Binary Pattern and Gabor Multiorientation Fusion Histogram

Directory of Open Access Journals (Sweden)

Lei Zhao

2017-01-01

Full Text Available This paper proposes novel framework for facial expressions analysis using dynamic and static information in video sequences. First, based on incremental formulation, discriminative deformable face alignment method is adapted to locate facial points to correct in-plane head rotation and break up facial region from background. Then, spatial-temporal motion local binary pattern (LBP feature is extracted and integrated with Gabor multiorientation fusion histogram to give descriptors, which reflect static and dynamic texture information of facial expressions. Finally, a one-versus-one strategy based multiclass support vector machine (SVM classifier is applied to classify facial expressions. Experiments on Cohn-Kanade (CK + facial expression dataset illustrate that integrated framework outperforms methods using single descriptors. Compared with other state-of-the-art methods on CK+, MMI, and Oulu-CASIA VIS datasets, our proposed framework performs better.

Investigation of Seasonal and Latitudinal Effects on the Expression of Clock Genes in Drosophila

Science.gov (United States)

Hosseini, Seyede Sanaz; Nazarimehr, Fahimeh; Jafari, Sajad

The primary goal in this work is to develop a dynamical model capturing the influence of seasonal and latitudinal variations on the expression of Drosophila clock genes. To this end, we study a specific dynamical system with strange attractors that exhibit changes of Drosophila activity in a range of latitudes and across different seasons. Bifurcations of this system are analyzed to peruse the effect of season and latitude on the behavior of clock genes. Existing experimental data collected from the activity of Drosophila melanogaster corroborate the dynamical model.

Modeling qRT-PCR dynamics with application to cancer biomarker quantification.

Science.gov (United States)

Chervoneva, Inna; Freydin, Boris; Hyslop, Terry; Waldman, Scott A

2017-01-01

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is widely used for molecular diagnostics and evaluating prognosis in cancer. The utility of mRNA expression biomarkers relies heavily on the accuracy and precision of quantification, which is still challenging for low abundance transcripts. The critical step for quantification is accurate estimation of efficiency needed for computing a relative qRT-PCR expression. We propose a new approach to estimating qRT-PCR efficiency based on modeling dynamics of polymerase chain reaction amplification. In contrast, only models for fluorescence intensity as a function of polymerase chain reaction cycle have been used so far for quantification. The dynamics of qRT-PCR efficiency is modeled using an ordinary differential equation model, and the fitted ordinary differential equation model is used to obtain effective polymerase chain reaction efficiency estimates needed for efficiency-adjusted quantification. The proposed new qRT-PCR efficiency estimates were used to quantify GUCY2C (Guanylate Cyclase 2C) mRNA expression in the blood of colorectal cancer patients. Time to recurrence and GUCY2C expression ratios were analyzed in a joint model for survival and longitudinal outcomes. The joint model with GUCY2C quantified using the proposed polymerase chain reaction efficiency estimates provided clinically meaningful results for association between time to recurrence and longitudinal trends in GUCY2C expression.

A gene expression system offering multiple levels of regulation: the Dual Drug Control (DDC) system.

Science.gov (United States)

Sudomoina, Marina; Latypova, Ekaterina; Favorova, Olga O; Golemis, Erica A; Serebriiskii, Ilya G

2004-04-29

Whether for cell culture studies of protein function, construction of mouse models to enable in vivo analysis of disease epidemiology, or ultimately gene therapy of human diseases, a critical enabling step is the ability to achieve finely controlled regulation of gene expression. Previous efforts to achieve this goal have explored inducible drug regulation of gene expression, and construction of synthetic promoters based on two-hybrid paradigms, among others. In this report, we describe the combination of dimerizer-regulated two-hybrid and tetracycline regulatory elements in an ordered cascade, placing expression of endpoint reporters under the control of two distinct drugs. In this Dual Drug Control (DDC) system, a first plasmid expresses fusion proteins to DBD and AD, which interact only in the presence of a small molecule dimerizer; a second plasmid encodes a cassette transcriptionally responsive to the first DBD, directing expression of the Tet-OFF protein; and a third plasmid encodes a reporter gene transcriptionally responsive to binding by Tet-OFF. We evaluate the dynamic range and specificity of this system in comparison to other available systems. This study demonstrates the feasibility of combining two discrete drug-regulated expression systems in a temporally sequential cascade, without loss of dynamic range of signal induction. The efficient layering of control levels allowed by this combination of elements provides the potential for the generation of complex control circuitry that may advance ability to regulate gene expression in vivo.

A gene expression system offering multiple levels of regulation: the Dual Drug Control (DDC system

Directory of Open Access Journals (Sweden)

Golemis Erica A

2004-04-01

Full Text Available Abstract Background Whether for cell culture studies of protein function, construction of mouse models to enable in vivo analysis of disease epidemiology, or ultimately gene therapy of human diseases, a critical enabling step is the ability to achieve finely controlled regulation of gene expression. Previous efforts to achieve this goal have explored inducible drug regulation of gene expression, and construction of synthetic promoters based on two-hybrid paradigms, among others. Results In this report, we describe the combination of dimerizer-regulated two-hybrid and tetracycline regulatory elements in an ordered cascade, placing expression of endpoint reporters under the control of two distinct drugs. In this Dual Drug Control (DDC system, a first plasmid expresses fusion proteins to DBD and AD, which interact only in the presence of a small molecule dimerizer; a second plasmid encodes a cassette transcriptionally responsive to the first DBD, directing expression of the Tet-OFF protein; and a third plasmid encodes a reporter gene transcriptionally responsive to binding by Tet-OFF. We evaluate the dynamic range and specificity of this system in comparison to other available systems. Conclusion This study demonstrates the feasibility of combining two discrete drug-regulated expression systems in a temporally sequential cascade, without loss of dynamic range of signal induction. The efficient layering of control levels allowed by this combination of elements provides the potential for the generation of complex control circuitry that may advance ability to regulate gene expression in vivo.

Self-consistent description of local density dynamics in simple liquids. The case of molten lithium.

Science.gov (United States)

Mokshin, A V; Galimzyanov, B N

2018-02-28

The dynamic structure factor is the quantity, which can be measured by means of Brillouin light-scattering as well as by means of inelastic scattering of neutrons and x-rays. The spectral (or frequency) moments of the dynamic structure factor define directly the sum rules of the scattering law. The theoretical scheme formulated in this study allows one to describe the dynamics of local density fluctuations in simple liquids and to obtain the expression of the dynamic structure factor in terms of the spectral moments. The theory satisfies all the sum rules, and the obtained expression for the dynamic structure factor yields correct extrapolations into the hydrodynamic limit as well as into the free-particle dynamics limit. We discuss correspondence of this theory with the generalized hydrodynamics and with the viscoelastic models, which are commonly used to analyze the data of inelastic neutron and x-ray scattering in liquids. In particular, we reveal that the postulated condition of the viscoelastic model for the memory function can be directly obtained within the presented theory. The dynamic structure factor of liquid lithium is computed on the basis of the presented theory, and various features of the scattering spectra are evaluated. It is found that the theoretical results are in agreement with inelastic x-ray scattering data.

Self-consistent description of local density dynamics in simple liquids. The case of molten lithium

Science.gov (United States)

Mokshin, A. V.; Galimzyanov, B. N.

2018-02-01

The dynamic structure factor is the quantity, which can be measured by means of Brillouin light-scattering as well as by means of inelastic scattering of neutrons and x-rays. The spectral (or frequency) moments of the dynamic structure factor define directly the sum rules of the scattering law. The theoretical scheme formulated in this study allows one to describe the dynamics of local density fluctuations in simple liquids and to obtain the expression of the dynamic structure factor in terms of the spectral moments. The theory satisfies all the sum rules, and the obtained expression for the dynamic structure factor yields correct extrapolations into the hydrodynamic limit as well as into the free-particle dynamics limit. We discuss correspondence of this theory with the generalized hydrodynamics and with the viscoelastic models, which are commonly used to analyze the data of inelastic neutron and x-ray scattering in liquids. In particular, we reveal that the postulated condition of the viscoelastic model for the memory function can be directly obtained within the presented theory. The dynamic structure factor of liquid lithium is computed on the basis of the presented theory, and various features of the scattering spectra are evaluated. It is found that the theoretical results are in agreement with inelastic x-ray scattering data.

Direct visualization of membrane architecture of myelinating cells in transgenic mice expressing membrane-anchored EGFP.

Science.gov (United States)

Deng, Yaqi; Kim, BongWoo; He, Xuelian; Kim, Sunja; Lu, Changqing; Wang, Haibo; Cho, Ssang-Goo; Hou, Yiping; Li, Jianrong; Zhao, Xianghui; Lu, Q Richard

2014-04-01

Myelinogenesis is a complex process that involves substantial and dynamic changes in plasma membrane architecture and myelin interaction with axons. Highly ramified processes of oligodendrocytes in the central nervous system (CNS) make axonal contact and then extrapolate to wrap around axons and form multilayer compact myelin sheathes. Currently, the mechanisms governing myelin sheath assembly and axon selection by myelinating cells are not fully understood. Here, we generated a transgenic mouse line expressing the membrane-anchored green fluorescent protein (mEGFP) in myelinating cells, which allow live imaging of details of myelinogenesis and cellular behaviors in the nervous systems. mEGFP expression is driven by the promoter of 2'-3'-cyclic nucleotide 3'-phosphodiesterase (CNP) that is expressed in the myelinating cell lineage. Robust mEGFP signals appear in the membrane processes of oligodendrocytes in the CNS and Schwann cells in the peripheral nervous system (PNS), wherein mEGFP expression defines the inner layers of myelin sheaths and Schmidt-Lanterman incisures in adult sciatic nerves. In addition, mEGFP expression can be used to track the extent of remyelination after demyelinating injury in a toxin-induced demyelination animal model. Taken together, the membrane-anchored mEGFP expression in the new transgenic line would facilitate direct visualization of dynamic myelin membrane formation and assembly during development and process remodeling during remyelination after various demyelinating injuries.

The perception of emotion in body expressions.

Science.gov (United States)

de Gelder, B; de Borst, A W; Watson, R

2015-01-01

During communication, we perceive and express emotional information through many different channels, including facial expressions, prosody, body motion, and posture. Although historically the human body has been perceived primarily as a tool for actions, there is now increased understanding that the body is also an important medium for emotional expression. Indeed, research on emotional body language is rapidly emerging as a new field in cognitive and affective neuroscience. This article reviews how whole-body signals are processed and understood, at the behavioral and neural levels, with specific reference to their role in emotional communication. The first part of this review outlines brain regions and spectrotemporal dynamics underlying perception of isolated neutral and affective bodies, the second part details the contextual effects on body emotion recognition, and final part discusses body processing on a subconscious level. More specifically, research has shown that body expressions as compared with neutral bodies draw upon a larger network of regions responsible for action observation and preparation, emotion processing, body processing, and integrative processes. Results from neurotypical populations and masking paradigms suggest that subconscious processing of affective bodies relies on a specific subset of these regions. Moreover, recent evidence has shown that emotional information from the face, voice, and body all interact, with body motion and posture often highlighting and intensifying the emotion expressed in the face and voice. © 2014 John Wiley & Sons, Ltd.

Gaze Behavior of Children with ASD toward Pictures of Facial Expressions.

Science.gov (United States)

Matsuda, Soichiro; Minagawa, Yasuyo; Yamamoto, Junichi

2015-01-01

Atypical gaze behavior in response to a face has been well documented in individuals with autism spectrum disorders (ASDs). Children with ASD appear to differ from typically developing (TD) children in gaze behavior for spoken and dynamic face stimuli but not for nonspeaking, static face stimuli. Furthermore, children with ASD and TD children show a difference in their gaze behavior for certain expressions. However, few studies have examined the relationship between autism severity and gaze behavior toward certain facial expressions. The present study replicated and extended previous studies by examining gaze behavior towards pictures of facial expressions. We presented ASD and TD children with pictures of surprised, happy, neutral, angry, and sad facial expressions. Autism severity was assessed using the Childhood Autism Rating Scale (CARS). The results showed that there was no group difference in gaze behavior when looking at pictures of facial expressions. Conversely, the children with ASD who had more severe autistic symptomatology had a tendency to gaze at angry facial expressions for a shorter duration in comparison to other facial expressions. These findings suggest that autism severity should be considered when examining atypical responses to certain facial expressions.

Mining Gene Regulatory Networks by Neural Modeling of Expression Time-Series.

Science.gov (United States)

Rubiolo, Mariano; Milone, Diego H; Stegmayer, Georgina

2015-01-01

Discovering gene regulatory networks from data is one of the most studied topics in recent years. Neural networks can be successfully used to infer an underlying gene network by modeling expression profiles as times series. This work proposes a novel method based on a pool of neural networks for obtaining a gene regulatory network from a gene expression dataset. They are used for modeling each possible interaction between pairs of genes in the dataset, and a set of mining rules is applied to accurately detect the subjacent relations among genes. The results obtained on artificial and real datasets confirm the method effectiveness for discovering regulatory networks from a proper modeling of the temporal dynamics of gene expression profiles.

Exploring gene expression changes in the amphioxus gill after poly(I:C) challenge using digital expression profiling.

Science.gov (United States)

Zhang, Qi-Lin; Qiu, Han-Yue; Liang, Ming-Zhong; Luo, Bang; Wang, Xiu-Qiang; Chen, Jun-Yuan

2017-11-01

Amphioxus, a cephalochordate, is a key model animal for studying the evolution of vertebrate immunity. Recently, studies have revealed that microRNA (miRNA) expression profiles change significantly in the amphioxus gill after immune stimulation, but it remains largely unknown how gene expression responds to immune stress. Elucidating gene expression changes in the amphioxus gill will provide a deeper understanding of the evolution of gill immunity in vertebrates. Here, we used high-throughput RNA sequencing technology (RNA-seq) to conduct tag-based digital gene expression profiling (DGE) analyses of the gills of control Branchiostoma belcheri and of those exposed to the viral mimic, poly(I:C) (pIC). Six libraries were created for the control and treatment groups including three biological replicates per group. A total of 1999 differently expressed genes (DEGs) were obtained, with 571 and 1428 DEGs showing up- or down-regulation, respectively, in the treatment group. Enrichment analysis of gene ontology (GO) terms and pathways revealed that the DEGs were primarily related to immune and defense response, apoptosis, human disease, cancer, protein metabolism, enzyme activity, and regulatory processes. In addition, eight DEGs were randomly selected to validate the RNA-seq data using real-time quantitative PCR (qRT-PCR), and the results confirmed the accuracy of the RNA-seq approach. Next, we screened eight key responding genes to examine the dynamic changes in expression levels at different time points in more detail. The results indicated that expressions of TRADD, MARCH, RNF31, NF-κb, CYP450, TNFRSF6B, IFI and LECT1 were induced to participate in the antiviral response against pIC. This study provides a valuable resource for understanding the role of the amphioxus gill in antiviral immunity and the evolution of gill immunity in vertebrates. Copyright © 2017 Elsevier Ltd. All rights reserved.

Trichoderma virens β-glucosidase I (BGLI) gene; expression in Saccharomyces cerevisiae including docking and molecular dynamics studies.

Science.gov (United States)

Wickramasinghe, Gammadde Hewa Ishan Maduka; Rathnayake, Pilimathalawe Panditharathna Attanayake Mudiyanselage Samith Indika; Chandrasekharan, Naduviladath Vishvanath; Weerasinghe, Mahindagoda Siril Samantha; Wijesundera, Ravindra Lakshman Chundananda; Wijesundera, Wijepurage Sandhya Sulochana

2017-06-21

Cellulose, a linear polymer of β 1-4, linked glucose, is the most abundant renewable fraction of plant biomass (lignocellulose). It is synergistically converted to glucose by endoglucanase (EG) cellobiohydrolase (CBH) and β-glucosidase (BGL) of the cellulase complex. BGL plays a major role in the conversion of randomly cleaved cellooligosaccharides into glucose. As it is well known, Saccharomyces cerevisiae can efficiently convert glucose into ethanol under anaerobic conditions. Therefore, S.cerevisiae was genetically modified with the objective of heterologous extracellular expression of the BGLI gene of Trichoderma virens making it capable of utilizing cellobiose to produce ethanol. The cDNA and a genomic sequence of the BGLI gene of Trichoderma virens was cloned in the yeast expression vector pGAPZα and separately transformed to Saccharomyces cerevisiae. The size of the BGLI cDNA clone was 1363 bp and the genomic DNA clone contained an additional 76 bp single intron following the first exon. The gene was 90% similar to the DNA sequence and 99% similar to the deduced amino acid sequence of 1,4-β-D-glucosidase of T. atroviride (AC237343.1). The BGLI activity expressed by the recombinant genomic clone was 3.4 times greater (1.7 x 10 -3  IU ml -1 ) than that observed for the cDNA clone (5 x 10 -4  IU ml -1 ). Furthermore, the activity was similar to the activity of locally isolated Trichoderma virens (1.5 x 10 -3  IU ml -1 ). The estimated size of the protein was 52 kDA. In fermentation studies, the maximum ethanol production by the genomic and the cDNA clones were 0.36 g and 0.06 g /g of cellobiose respectively. Molecular docking results indicated that the bare protein and cellobiose-protein complex behave in a similar manner with considerable stability in aqueous medium. The deduced binding site and the binding affinity of the constructed homology model appeared to be reasonable. Moreover, it was identified that the five hydrogen bonds formed

On planar quantum dynamics of a magnetic dipole moment in the presence of electric and magnetic fields

Energy Technology Data Exchange (ETDEWEB)

Silva, Edilberto O. [Universidade Federal do Maranhao, Departamento de Fisica, Sao Luis, MA (Brazil)

2014-10-15

The planar quantum dynamics of a neutral particle with a magnetic dipole moment in the presence of electric and magnetic fields is considered. The criteria to establish the planar dynamics reveal that the resulting nonrelativistic Hamiltonian has a simplified expression without making approximations, and some terms have crucial importance for the system dynamics. (orig.)

Dynamics of defect-induced dark solitons in an exciton-polariton condensate

Science.gov (United States)

Opala, Andrzej; Pieczarka, Maciej; Bobrovska, Nataliya; Matuszewski, Michał

2018-04-01

We study theoretically the emission of dark solitons induced by a moving defect in a nonresonantly pumped exciton-polariton condensate. The number of created dark solitons per unit of time is found to be strongly dependent on the pump power. We relate the observed dynamics of this process to the oscillations of the drag force experienced by the condensate. We investigate the stability of the polariton quantum fluid and present various types of dynamics depending on the condensate and moving obstacle parameters. Furthermore, we provide analytical expressions for dark soliton dynamics using the variational method adapted to the nonequilibrium polariton system. The determined dynamical equations are found to be in excellent agreement with the results of numerical simulations.

Investigation, development, and application of optimal output feedback theory. Volume 3: The relationship between dynamic compensators and observers and Kalman filters

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Broussard, John R.

1987-01-01

Relationships between observers, Kalman Filters and dynamic compensators using feedforward control theory are investigated. In particular, the relationship, if any, between the dynamic compensator state and linear functions of a discrete plane state are investigated. It is shown that, in steady state, a dynamic compensator driven by the plant output can be expressed as the sum of two terms. The first term is a linear combination of the plant state. The second term depends on plant and measurement noise, and the plant control. Thus, the state of the dynamic compensator can be expressed as an estimator of the first term with additive error given by the second term. Conditions under which a dynamic compensator is a Kalman filter are presented, and reduced-order optimal estimaters are investigated.

Seeing mixed emotions: The specificity of emotion perception from static and dynamic facial expressions across cultures

NARCIS (Netherlands)

Fang, X.; Sauter, D.A.; van Kleef, G.A.

2018-01-01

Although perceivers often agree about the primary emotion that is conveyed by a particular expression, observers may concurrently perceive several additional emotions from a given facial expression. In the present research, we compared the perception of two types of nonintended emotions in Chinese

Perturbation analysis for patch occupancy dynamics

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Martin, Julien; Nichols, James D.; McIntyre, Carol L.; Ferraz, Goncalo; Hines, James E.

2009-01-01

Perturbation analysis is a powerful tool to study population and community dynamics. This article describes expressions for sensitivity metrics reflecting changes in equilibrium occupancy resulting from small changes in the vital rates of patch occupancy dynamics (i.e., probabilities of local patch colonization and extinction). We illustrate our approach with a case study of occupancy dynamics of Golden Eagle (Aquila chrysaetos) nesting territories. Examination of the hypothesis of system equilibrium suggests that the system satisfies equilibrium conditions. Estimates of vital rates obtained using patch occupancy models are used to estimate equilibrium patch occupancy of eagles. We then compute estimates of sensitivity metrics and discuss their implications for eagle population ecology and management. Finally, we discuss the intuition underlying our sensitivity metrics and then provide examples of ecological questions that can be addressed using perturbation analyses. For instance, the sensitivity metrics lead to predictions about the relative importance of local colonization and local extinction probabilities in influencing equilibrium occupancy for rare and common species.

Identifying protein complex by integrating characteristic of core-attachment into dynamic PPI network.

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Xianjun Shen

Full Text Available How to identify protein complex is an important and challenging task in proteomics. It would make great contribution to our knowledge of molecular mechanism in cell life activities. However, the inherent organization and dynamic characteristic of cell system have rarely been incorporated into the existing algorithms for detecting protein complexes because of the limitation of protein-protein interaction (PPI data produced by high throughput techniques. The availability of time course gene expression profile enables us to uncover the dynamics of molecular networks and improve the detection of protein complexes. In order to achieve this goal, this paper proposes a novel algorithm DCA (Dynamic Core-Attachment. It detects protein-complex core comprising of continually expressed and highly connected proteins in dynamic PPI network, and then the protein complex is formed by including the attachments with high adhesion into the core. The integration of core-attachment feature into the dynamic PPI network is responsible for the superiority of our algorithm. DCA has been applied on two different yeast dynamic PPI networks and the experimental results show that it performs significantly better than the state-of-the-art techniques in terms of prediction accuracy, hF-measure and statistical significance in biology. In addition, the identified complexes with strong biological significance provide potential candidate complexes for biologists to validate.

Four not six: Revealing culturally common facial expressions of emotion.

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Jack, Rachael E; Sun, Wei; Delis, Ioannis; Garrod, Oliver G B; Schyns, Philippe G

2016-06-01

As a highly social species, humans generate complex facial expressions to communicate a diverse range of emotions. Since Darwin's work, identifying among these complex patterns which are common across cultures and which are culture-specific has remained a central question in psychology, anthropology, philosophy, and more recently machine vision and social robotics. Classic approaches to addressing this question typically tested the cross-cultural recognition of theoretically motivated facial expressions representing 6 emotions, and reported universality. Yet, variable recognition accuracy across cultures suggests a narrower cross-cultural communication supported by sets of simpler expressive patterns embedded in more complex facial expressions. We explore this hypothesis by modeling the facial expressions of over 60 emotions across 2 cultures, and segregating out the latent expressive patterns. Using a multidisciplinary approach, we first map the conceptual organization of a broad spectrum of emotion words by building semantic networks in 2 cultures. For each emotion word in each culture, we then model and validate its corresponding dynamic facial expression, producing over 60 culturally valid facial expression models. We then apply to the pooled models a multivariate data reduction technique, revealing 4 latent and culturally common facial expression patterns that each communicates specific combinations of valence, arousal, and dominance. We then reveal the face movements that accentuate each latent expressive pattern to create complex facial expressions. Our data questions the widely held view that 6 facial expression patterns are universal, instead suggesting 4 latent expressive patterns with direct implications for emotion communication, social psychology, cognitive neuroscience, and social robotics. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Synthetic tetracycline-inducible regulatory networks: computer-aided design of dynamic phenotypes

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Kaznessis Yiannis N

2007-01-01

Full Text Available Abstract Background Tightly regulated gene networks, precisely controlling the expression of protein molecules, have received considerable interest by the biomedical community due to their promising applications. Among the most well studied inducible transcription systems are the tetracycline regulatory expression systems based on the tetracycline resistance operon of Escherichia coli, Tet-Off (tTA and Tet-On (rtTA. Despite their initial success and improved designs, limitations still persist, such as low inducer sensitivity. Instead of looking at these networks statically, and simply changing or mutating the promoter and operator regions with trial and error, a systematic investigation of the dynamic behavior of the network can result in rational design of regulatory gene expression systems. Sophisticated algorithms can accurately capture the dynamical behavior of gene networks. With computer aided design, we aim to improve the synthesis of regulatory networks and propose new designs that enable tighter control of expression. Results In this paper we engineer novel networks by recombining existing genes or part of genes. We synthesize four novel regulatory networks based on the Tet-Off and Tet-On systems. We model all the known individual biomolecular interactions involved in transcription, translation, regulation and induction. With multiple time-scale stochastic-discrete and stochastic-continuous models we accurately capture the transient and steady state dynamics of these networks. Important biomolecular interactions are identified and the strength of the interactions engineered to satisfy design criteria. A set of clear design rules is developed and appropriate mutants of regulatory proteins and operator sites are proposed. Conclusion The complexity of biomolecular interactions is accurately captured through computer simulations. Computer simulations allow us to look into the molecular level, portray the dynamic behavior of gene regulatory

Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B-cell programming.

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Li, Rui; Cauchy, Pierre; Ramamoorthy, Senthilkumar; Boller, Sören; Chavez, Lukas; Grosschedl, Rudolf

2018-01-15

B-cell fate determination requires the action of transcription factors that operate in a regulatory network to activate B-lineage genes and repress lineage-inappropriate genes. However, the dynamics and hierarchy of events in B-cell programming remain obscure. To uncouple the dynamics of transcription factor expression from functional consequences, we generated induction systems in developmentally arrested Ebf1 -/- pre-pro-B cells to allow precise experimental control of EBF1 expression in the genomic context of progenitor cells. Consistent with the described role of EBF1 as a pioneer transcription factor, we show in a time-resolved analysis that EBF1 occupancy coincides with EBF1 expression and precedes the formation of chromatin accessibility. We observed dynamic patterns of EBF1 target gene expression and sequential up-regulation of transcription factors that expand the regulatory network at the pro-B-cell stage. A continuous EBF1 function was found to be required for Cd79a promoter activity and for the maintenance of an accessible chromatin domain that is permissive for binding of other transcription factors. Notably, transient EBF1 occupancy was detected at lineage-inappropriate genes prior to their silencing in pro-B cells. Thus, persistent and transient functions of EBF1 allow for an ordered sequence of epigenetic and transcriptional events in B-cell programming. © 2018 Li et al.; Published by Cold Spring Harbor Laboratory Press.

An Examination of Dynamic Gene Expression Changes in the Mouse Brain During Pregnancy and the Postpartum Period

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Surjyendu Ray

2016-01-01

Full Text Available The developmental transition to motherhood requires gene expression changes that alter the brain to drive the female to perform maternal behaviors. We broadly examined the global transcriptional response in the mouse maternal brain, by examining four brain regions: hypothalamus, hippocampus, neocortex, and cerebellum, in virgin females, two pregnancy time points, and three postpartum time points. We find that overall there are hundreds of differentially expressed genes, but each brain region and time point shows a unique molecular signature, with only 49 genes differentially expressed in all four regions. Interestingly, a set of “early-response genes” is repressed in all brain regions during pregnancy and postpartum stages. Several genes previously implicated in underlying postpartum depression change expression. This study serves as an atlas of gene expression changes in the maternal brain, with the results demonstrating that pregnancy, parturition, and postpartum maternal experience substantially impact diverse brain regions.

Do Valenced Odors and Trait Body Odor Disgust Affect Evaluation of Emotion in Dynamic Faces?

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Syrjänen, Elmeri; Liuzza, Marco Tullio; Fischer, Håkan; Olofsson, Jonas K

2017-12-01

Disgust is a core emotion evolved to detect and avoid the ingestion of poisonous food as well as the contact with pathogens and other harmful agents. Previous research has shown that multisensory presentation of olfactory and visual information may strengthen the processing of disgust-relevant information. However, it is not known whether these findings extend to dynamic facial stimuli that changes from neutral to emotionally expressive, or if individual differences in trait body odor disgust may influence the processing of disgust-related information. In this preregistered study, we tested whether a classification of dynamic facial expressions as happy or disgusted, and an emotional evaluation of these facial expressions, would be affected by individual differences in body odor disgust sensitivity, and by exposure to a sweat-like, negatively valenced odor (valeric acid), as compared with a soap-like, positively valenced odor (lilac essence) or a no-odor control. Using Bayesian hypothesis testing, we found evidence that odors do not affect recognition of emotion in dynamic faces even when body odor disgust sensitivity was used as moderator. However, an exploratory analysis suggested that an unpleasant odor context may cause faster RTs for faces, independent of their emotional expression. Our results further our understanding of the scope and limits of odor effects on facial perception affect and suggest further studies should focus on reproducibility, specifying experimental circumstances where odor effects on facial expressions may be present versus absent.

Dynamic neuroanatomy at subcellular resolution in the zebrafish.

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Faucherre, Adèle; López-Schier, Hernán

2014-01-01

Genetic means to visualize and manipulate neuronal circuits in the intact animal have revolutionized neurobiology. "Dynamic neuroanatomy" defines a range of approaches aimed at quantifying the architecture or subcellular organization of neurons over time during their development, regeneration, or degeneration. A general feature of these approaches is their reliance on the optical isolation of defined neurons in toto by genetically expressing markers in one or few cells. Here we use the afferent neurons of the lateral line as an example to describe a simple method for the dynamic neuroanatomical study of axon terminals in the zebrafish by laser-scanning confocal microscopy.

Short-term exposure to a synthetic estrogen disrupts mating dynamics in a pipefish.

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Partridge, Charlyn; Boettcher, Anne; Jones, Adam G

2010-11-01

Sexual selection is responsible for the evolution of some of the most elaborate traits occurring in nature, many of which play a vital role in competition over access to mates and individual reproductive fitness. Because expression of these traits is typically regulated by sex-steroids there is a significant potential for their expression to be affected by the presence of certain pollutants, such as endocrine disrupting compounds. Endocrine disruptors have been shown to alter primary sexual traits and impact reproduction, but few studies have investigated how these compounds affect secondary sexual trait expression and how that may, in turn, impact mating dynamics. In this study we examine how short-term exposure to a synthetic estrogen impacts secondary sexual trait expression and mating dynamics in the Gulf pipefish, a species displaying sex-role reversal. Our results show that only 10days of exposure to 17α-ethinylestradiol results in adult male pipefish developing female-like secondary sexual traits. While these males are capable of reproduction, females discriminate against exposed males in mate choice trials. In natural populations, this type of discrimination would reduce male mating opportunities, thus potentially reducing their long-term reproductive success. Importantly, the effects of these compounds on mating dynamics and mating opportunity would not be observed using the current standard methods of assessing environmental contamination. However, disrupting these processes could have profound effects on the viability of exposed populations. Copyright © 2010 Elsevier Inc. All rights reserved.

Kondo dynamics of quasiparticle tunneling in a two-reservoir Anderson model.

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Hong, Jongbae

2011-07-13

We study the Kondo dynamics in a two-reservoir Anderson impurity model in which quasiparticle tunneling occurs between two reservoirs. We show that singlet hopping is an essential component of Kondo dynamics in the quasiparticle tunneling. We prove that two resonant tunneling levels exist in the two-reservoir Anderson impurity model and the quasiparticle tunnels through one of these levels when a bias is applied. The Kondo dynamics is explained by obtaining the retarded Green's function. We obtain the analytic expressions of the spectral weights of coherent peaks by analyzing the Green's function at the atomic limit.

Kondo dynamics of quasiparticle tunneling in a two-reservoir Anderson model

International Nuclear Information System (INIS)

Hong, Jongbae

2011-01-01

We study the Kondo dynamics in a two-reservoir Anderson impurity model in which quasiparticle tunneling occurs between two reservoirs. We show that singlet hopping is an essential component of Kondo dynamics in the quasiparticle tunneling. We prove that two resonant tunneling levels exist in the two-reservoir Anderson impurity model and the quasiparticle tunnels through one of these levels when a bias is applied. The Kondo dynamics is explained by obtaining the retarded Green's function. We obtain the analytic expressions of the spectral weights of coherent peaks by analyzing the Green's function at the atomic limit.

Gauge-invariant cosmic structures---A dynamic systems approach

International Nuclear Information System (INIS)

Woszczyna, A.

1992-01-01

Gravitational instability is expressed in terms of the dynamic systems theory. The gauge-invariant Ellis-Bruni equation and Bardeen's equation are discussed in detail. It is shown that in an open universe filled with matter of constant sound velocity the Jeans criterion does not adequately define the length scale of the gravitational structure

Comparative gene expression analysis throughout the life cycle of Leishmania braziliensis: diversity of expression profiles among clinical isolates.

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Vanessa Adaui

Full Text Available BACKGROUND: Most of the Leishmania genome is reported to be constitutively expressed during the life cycle of the parasite, with a few regulated genes. Inter-species comparative transcriptomics evidenced a low number of species-specific differences related to differentially distributed genes or the differential regulation of conserved genes. It is of uppermost importance to ensure that the observed differences are indeed species-specific and not simply specific of the strains selected for representing the species. The relevance of this concern is illustrated by current study. METHODOLOGY/PRINCIPAL FINDINGS: We selected 5 clinical isolates of L. braziliensis characterized by their diversity of clinical and in vitro phenotypes. Real-time quantitative PCR was performed on promastigote and amastigote life stages to assess gene expression profiles at seven time points covering the whole life cycle. We tested 12 genes encoding proteins with roles in transport, thiol-based redox metabolism, cellular reduction, RNA poly(A-tail metabolism, cytoskeleton function and ribosomal function. The general trend of expression profiles showed that regulation of gene expression essentially occurs around the stationary phase of promastigotes. However, the genes involved in this phenomenon appeared to vary significantly among the isolates considered. CONCLUSION/SIGNIFICANCE: Our results clearly illustrate the unique character of each isolate in terms of gene expression dynamics. Results obtained on an individual strain are not necessarily representative of a given species. Therefore, extreme care should be taken when comparing the profiles of different species and extrapolating functional differences between them.

Impaired Overt Facial Mimicry in Response to Dynamic Facial Expressions in High-Functioning Autism Spectrum Disorders

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Yoshimura, Sayaka; Sato, Wataru; Uono, Shota; Toichi, Motomi

2015-01-01

Previous electromyographic studies have reported that individuals with autism spectrum disorders (ASD) exhibited atypical patterns of facial muscle activity in response to facial expression stimuli. However, whether such activity is expressed in visible facial mimicry remains unknown. To investigate this issue, we videotaped facial responses in…

An Examination of Dynamic Gene Expression Changes in the Mouse Brain During Pregnancy and the Postpartum Period.

Science.gov (United States)

Ray, Surjyendu; Tzeng, Ruei-Ying; DiCarlo, Lisa M; Bundy, Joseph L; Vied, Cynthia; Tyson, Gary; Nowakowski, Richard; Arbeitman, Michelle N

2015-11-23

The developmental transition to motherhood requires gene expression changes that alter the brain to drive the female to perform maternal behaviors. We broadly examined the global transcriptional response in the mouse maternal brain, by examining four brain regions: hypothalamus, hippocampus, neocortex, and cerebellum, in virgin females, two pregnancy time points, and three postpartum time points. We find that overall there are hundreds of differentially expressed genes, but each brain region and time point shows a unique molecular signature, with only 49 genes differentially expressed in all four regions. Interestingly, a set of "early-response genes" is repressed in all brain regions during pregnancy and postpartum stages. Several genes previously implicated in underlying postpartum depression change expression. This study serves as an atlas of gene expression changes in the maternal brain, with the results demonstrating that pregnancy, parturition, and postpartum maternal experience substantially impact diverse brain regions. Copyright © 2016 Ray et al.

Large N dynamics in QED in a magnetic field

International Nuclear Information System (INIS)

Gusynin, V.P.; Miransky, V.A.; Shovkovy, I.A.

2003-01-01

The expression for the dynamical mass of fermions in QED in a magnetic field is obtained for a large number of the fermion flavor N in the framework of 1/N expansion. The existence of a threshold value N thr , dividing the theories with essentially different dynamics, is established. For the number of flavors N thr , the dynamical mass is very sensitive to the value of the coupling constant α b , related to the magnetic scale μ=√(vertical bar eB vertical bar). For N of the order of N thr or larger, a dynamics similar to that in the Nambu-Jona-Lasinio model with a cutoff of the order of √(vertical bar eB vertical bar) and the dimensional coupling constant G∼1/(N vertical bar eB vertical bar) takes place. In this case, the value of the dynamical mass is essentially α b independent (the dynamics with an infrared stable fixed point). The value of N thr separates a weak coupling dynamics (with α-tilde b ≡Nα b b > or approx. 1) and is of the order of 1/α b

Identifying a Superfluid Reynolds Number via Dynamical Similarity.

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Reeves, M T; Billam, T P; Anderson, B P; Bradley, A S

2015-04-17

The Reynolds number provides a characterization of the transition to turbulent flow, with wide application in classical fluid dynamics. Identifying such a parameter in superfluid systems is challenging due to their fundamentally inviscid nature. Performing a systematic study of superfluid cylinder wakes in two dimensions, we observe dynamical similarity of the frequency of vortex shedding by a cylindrical obstacle. The universality of the turbulent wake dynamics is revealed by expressing shedding frequencies in terms of an appropriately defined superfluid Reynolds number, Re(s), that accounts for the breakdown of superfluid flow through quantum vortex shedding. For large obstacles, the dimensionless shedding frequency exhibits a universal form that is well-fitted by a classical empirical relation. In this regime the transition to turbulence occurs at Re(s)≈0.7, irrespective of obstacle width.

Topological constraints and their breakdown in dynamical evolution

International Nuclear Information System (INIS)

Goldstein, Raymond E; Moffatt, H Keith; Pesci, Adriana I

2012-01-01

A variety of physical and biological systems exhibit dynamical behaviour that has some explicit or implicit topological features. Here, the term ‘topological’ is meant to convey the idea of structures, e.g. physical knots, links or braids, that have some measure of invariance under continuous deformation. Dynamical evolution is then subject to the topological constraints that express this invariance. The simplest problem arising in these systems is the determination of minimum-energy structures (and routes towards these structures) permitted by such constraints, and elucidation of mechanisms by which the constraints may be broken. In more complex nonequilibrium cases there can be recurring singularities associated with topological rearrangements driven by continuous injection of energy. In this brief overview, motivated by an upcoming program on ‘Topological Dynamics in the Physical and Biological Sciences’ at the Isaac Newton Institute for Mathematical Sciences, we present a summary of this class of dynamical systems and discuss examples of important open problems. (invited articles)

Natural Poisson structures of nonlinear plasma dynamics

International Nuclear Information System (INIS)