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Sample records for genes influencing temporal

  1. Monitoring the Temporal Expression of Genes Involved in Ochratoxin A Production of Aspergillus carbonarius under the Influence of Temperature and Water Activity

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    Iliada K. Lappa

    2017-09-01

    Full Text Available The objective of this study was to investigate the effect of environmental factors, namely temperature and water activity, on genes involved in the regulation of ochratoxin A (OTA production over time. For this purpose, the previously characterized toxigenic Aspergillus carbonarius Ac29 isolate from Greek vineyards and the A. carbonarius ITEM 5010 reference strain were subjected to combined temperature and water activity (aw treatments to study OTA production and relative gene expression. The fungal isolates were grown on a synthetic grape juice liquid medium (SGM under different temperature (20 °C, 25 °C and 30 °C and aw (0.94 and 0.98 regimes. The expression of the AcOTApks, AcOTAnrps, and laeA OTA related genes was investigated using real time PCR. Gene expression was monitored at the same time points, along with fungal biomass and OTA accumulation at three, six and nine days of incubation. In gene expression analysis, stimulation of the biosynthetic genes was observed a few days before any toxin could be detected. This fact may underline a possible early indicator of potential toxin contamination of grapes. However, the transcript levels varied with respect to the different combinations of ecophysiological conditions and time, highlighting a complex regulation of OTA related gene expression of A. carbonarius in the specific medium.

  2. Gene length as a biological timer to establish temporal transcriptional regulation.

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    Kirkconnell, Killeen S; Magnuson, Brian; Paulsen, Michelle T; Lu, Brian; Bedi, Karan; Ljungman, Mats

    2017-02-01

    Transcriptional timing is inherently influenced by gene length, thus providing a mechanism for temporal regulation of gene expression. While gene size has been shown to be important for the expression timing of specific genes during early development, whether it plays a role in the timing of other global gene expression programs has not been extensively explored. Here, we investigate the role of gene length during the early transcriptional response of human fibroblasts to serum stimulation. Using the nascent sequencing techniques Bru-seq and BruUV-seq, we identified immediate genome-wide transcriptional changes following serum stimulation that were linked to rapid activation of enhancer elements. We identified 873 significantly induced and 209 significantly repressed genes. Variations in gene size allowed for a large group of genes to be simultaneously activated but produce full-length RNAs at different times. The median length of the group of serum-induced genes was significantly larger than the median length of all expressed genes, housekeeping genes, and serum-repressed genes. These gene length relationships were also observed in corresponding mouse orthologs, suggesting that relative gene size is evolutionarily conserved. The sizes of transcription factor and microRNA genes immediately induced after serum stimulation varied dramatically, setting up a cascade mechanism for temporal expression arising from a single activation event. The retention and expansion of large intronic sequences during evolution have likely played important roles in fine-tuning the temporal expression of target genes in various cellular response programs.

  3. Genes That Influence Blood Pressure

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    ... Influence Blood Pressure Gene Linked to Optimism and Self-Esteem Designing New Diabetes Drugs Connect with Us Subscribe to get NIH Research Matters by email RSS Feed Facebook Email us Mailing Address: NIH Research Matters Bldg. ...

  4. Influence of a tone's tonal function on temporal change detection.

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    Lebrun-Guillaud, Géraldine; Tillmann, Barbara

    2007-11-01

    Music cognition research has provided evidence that the tonal function of a musical event influences perception and memory. Our study investigated whether tonal function influences a basic temporal judgment, notably the detection of a temporal change disrupting a sequence's regularity. The sequences consisted of six musical events presented in isochrony (or with the fifth event occurring earlier or later): Three chords (instilling a tonal context) were followed by a tone (repeated three times). The tones fulfilled one of two tonal functions in the tonal context. Participants had to detect whether the sequence contained a temporal change and were not informed about tonal manipulations. Discrimination performance (as measured by d') showed an influence of tonal function on temporal change detection: Performance was better for the tonic tone (having the most important tonal function in the key) than for the unstable leading tone, the less stable mediant tone, and even than the stable dominant tone. The outcome shows the influence of listeners' tonal knowledge on a perceptual time judgment and suggests that processing of tonal and temporal structures interact at some stage of processing.

  5. Enterotypes influence temporal changes in gut microbiota

    DEFF Research Database (Denmark)

    Roager, Henrik Munch; Licht, Tine Rask; Kellebjerg Poulsen, Sanne

    The human gut microbiota plays an important role for the health of the host. The question is whether we can modulate the gut microbiota by changing diet. During a 6-month, randomised, controlled dietary intervention, the effect of a moderate diet shift from Average Danish Diet to New Nordic Diet...... on the gut microbiota in humans (n=62) was investigated. Quantitative PCR analysis showed that the microbiota did not change significantly by the intervention. Nevertheless, by stratifying subjects into two enterotypes, distinguished by the Prevotella/Bacteroides ratio (P/B), we were able to detect...... significant changes in the gut microbiota composition resulting from the interventions. Subjects with a high-P/B experienced more pronounced changes in the gut microbiota composition than subjects with a low-P/B. The study is the first to indicate that enterotypes influence microbiota response to a dietary...

  6. Influence of Temporal Expectations on Response Priming by Subliminal Faces

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    Guex, Raphael; Vuilleumier, Patrik

    2016-01-01

    Unconscious processes are often assumed immune from attention influence. Recent behavioral studies suggest however that the processing of subliminal information can be influenced by temporal attention. To examine the neural mechanisms underlying these effects, we used a stringent masking paradigm together with fMRI to investigate how temporal attention modulates the processing of unseen (masked) faces. Participants performed a gender decision task on a visible neutral target face, preceded by a masked prime face that could vary in gender (same or different than target) and emotion expression (neutral or fearful). We manipulated temporal attention by instructing participants to expect targets to appear either early or late during the stimulus sequence. Orienting temporal attention to subliminal primes influenced response priming by masked faces, even when gender was incongruent. In addition, gender-congruent primes facilitated responses regardless of attention while gender-incongruent primes reduced accuracy when attended. Emotion produced no differential effects. At the neural level, incongruent and temporally unexpected primes increased brain response in regions of the fronto-parietal attention network, reflecting greater recruitment of executive control and reorienting processes. Congruent and expected primes produced higher activations in fusiform cortex, presumably reflecting facilitation of perceptual processing. These results indicate that temporal attention can influence subliminal processing of face features, and thus facilitate information integration according to task-relevance regardless of conscious awareness. They also suggest that task-congruent information between prime and target may facilitate response priming even when temporal attention is not selectively oriented to the prime onset time. PMID:27764124

  7. Relating Perturbation Magnitude to Temporal Gene Expression in Biological Systems

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    Callister, Stephen J.; Parnell, John J.; Pfrender, Michael E.; Hashsham, Syed

    2009-03-19

    A method to quantitatively relate stress to response at the level of gene expression is described using Saccharomyces cerevisiae as a model organism. Stress was defined as the magnitude of perturbation and strain was defined as the magnitude of cumulative response in terms of gene expression. Expression patterns of sixty genes previously reported to be significantly impacted by osmotic shock or belonging to the high-osmotic glycerol, glycerolipid metabolism, and glycolysis pathways were determined following perturbations of increasing sodium chloride concentrations (0, 0.5, 0.7, 1.0, 1.5, and 1.4 M). Expression of these genes was quantified temporally using reverse transcriptase real time polymerase chain reaction. The magnitude of cumulative response was obtained by calculating the total moment of area of the temporal response envelope for all the 60 genes, either together or for the set of genes related to each pathway. A non-linear relationship between stress and response was observed for the range of stress studied. This study examines a quantitative approach to quantify the strain at the level of gene expression to relate stress to strain in biological systems. The approach should be generally applicable to quantitatively evaluate the response of organisms to environmental change.

  8. Relating perturbation magnitude to temporal gene expression in biological systems

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    Pfrender Michael E

    2009-03-01

    Full Text Available Abstract Background Most transcriptional activity is a result of environmental variability. This cause (environment and effect (gene expression relationship is essential to survival in any changing environment. The specific relationship between environmental perturbation and gene expression – and stability of the response – has yet to be measured in detail. We describe a method to quantitatively relate perturbation magnitude to response at the level of gene expression. We test our method using Saccharomyces cerevisiae as a model organism and osmotic stress as an environmental stress. Results Patterns of gene expression were measured in response to increasing sodium chloride concentrations (0, 0.5, 0.7, 1.0, and 1.2 M for sixty genes impacted by osmotic shock. Expression of these genes was quantified over five time points using reverse transcriptase real-time polymerase chain reaction. Magnitudes of cumulative response for specific pathways, and the set of all genes, were obtained by combining the temporal response envelopes for genes exhibiting significant changes in expression with time. A linear relationship between perturbation magnitude and response was observed for the range of concentrations studied. Conclusion This study develops a quantitative approach to describe the stability of gene response and pathways to environmental perturbation and illustrates the utility of this approach. The approach should be applicable to quantitatively evaluate the response of organisms via the magnitude of response and stability of the transcriptome to environmental change.

  9. Odor identity influences tracking of temporally patterned plumes in Drosophila

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    Frye Mark A

    2011-06-01

    Full Text Available Abstract Background Turbulent fluid landscapes impose temporal patterning upon chemical signals, and the dynamical neuronal responses to patterned input vary across the olfactory receptor repertoire in flies, moths, and locusts. Sensory transformations exhibit low pass filtering that ultimately results in perceptual fusion of temporally transient sensory signals. For example, humans perceive a sufficiently fast flickering light as continuous, but the frequency threshold at which this fusion occurs varies with wavelength. Although the summed frequency sensitivity of the fly antenna has been examined to a considerable extent, it is unknown how intermittent odor signals are integrated to influence plume tracking behavior independent of wind cues, and whether temporal fusion for behavioral tracking might vary according to the odor encountered. Results Here we have adopted a virtual reality flight simulator to study the dynamics of plume tracking under different experimental conditions. Flies tethered in a magnetic field actively track continuous (non-intermittent plumes of vinegar, banana, or ethyl butyrate with equal precision. However, pulsing these plumes at varying frequency reveals that the threshold rate, above which flies track the plume as if it were continuous, is unique for each odorant tested. Thus, the capability of a fly to navigate an intermittent plume depends on the particular odorant being tracked during flight. Finally, we measured antennal field potential responses to an intermittent plume, found that receptor dynamics track the temporal pattern of the odor stimulus and therefore do not limit the observed behavioral temporal fusion limits. Conclusions This study explores the flies' ability to track odor plumes that are temporally intermittent. We were surprised to find that the perceptual critical fusion limit, determined behaviorally, is strongly dependent on odor identity. Antennal field potential recordings indicate that

  10. Considering spatial and temporal scale in landscape-genetic studies of gene flow.

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    Anderson, Corey Devin; Epperson, Bryan K; Fortin, Marie-Josée; Holderegger, Rolf; James, Patrick M A; Rosenberg, Michael S; Scribner, Kim T; Spear, Stephen

    2010-09-01

    Landscape features exist at multiple spatial and temporal scales, and these naturally affect spatial genetic structure and our ability to make inferences about gene flow. This article discusses how decisions about sampling of genotypes (including choices about analytical methods and genetic markers) should be driven by the scale of spatial genetic structure, the time frame that landscape features have existed in their current state, and all aspects of a species' life history. Researchers should use caution when making inferences about gene flow, especially when the spatial extent of the study area is limited. The scale of sampling of the landscape introduces different features that may affect gene flow. Sampling grain should be smaller than the average home-range size or dispersal distance of the study organism and, for raster data, existing research suggests that simplifying the thematic resolution into discrete classes may result in low power to detect effects on gene flow. Therefore, the methods used to characterize the landscape between sampling sites may be a primary determinant for the spatial scale at which analytical results are applicable, and the use of only one sampling scale for a particular statistical method may lead researchers to overlook important factors affecting gene flow. The particular analytical technique used to correlate landscape data and genetic data may also influence results; common landscape-genetic methods may not be suitable for all study systems, particularly when the rate of landscape change is faster than can be resolved by common molecular markers.

  11. Discovery of time-delayed gene regulatory networks based on temporal gene expression profiling

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    Guo Zheng

    2006-01-01

    Full Text Available Abstract Background It is one of the ultimate goals for modern biological research to fully elucidate the intricate interplays and the regulations of the molecular determinants that propel and characterize the progression of versatile life phenomena, to name a few, cell cycling, developmental biology, aging, and the progressive and recurrent pathogenesis of complex diseases. The vast amount of large-scale and genome-wide time-resolved data is becoming increasing available, which provides the golden opportunity to unravel the challenging reverse-engineering problem of time-delayed gene regulatory networks. Results In particular, this methodological paper aims to reconstruct regulatory networks from temporal gene expression data by using delayed correlations between genes, i.e., pairwise overlaps of expression levels shifted in time relative each other. We have thus developed a novel model-free computational toolbox termed TdGRN (Time-delayed Gene Regulatory Network to address the underlying regulations of genes that can span any unit(s of time intervals. This bioinformatics toolbox has provided a unified approach to uncovering time trends of gene regulations through decision analysis of the newly designed time-delayed gene expression matrix. We have applied the proposed method to yeast cell cycling and human HeLa cell cycling and have discovered most of the underlying time-delayed regulations that are supported by multiple lines of experimental evidence and that are remarkably consistent with the current knowledge on phase characteristics for the cell cyclings. Conclusion We established a usable and powerful model-free approach to dissecting high-order dynamic trends of gene-gene interactions. We have carefully validated the proposed algorithm by applying it to two publicly available cell cycling datasets. In addition to uncovering the time trends of gene regulations for cell cycling, this unified approach can also be used to study the complex

  12. Influence of Temporal Context on Value in the Multiple-Chains and Successive-Encounters Procedures

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    O'Daly, Matthew; Angulo, Samuel; Gipson, Cassandra; Fantino, Edmund

    2006-01-01

    This set of studies explored the influence of temporal context across multiple-chain and multiple-successive-encounters procedures. Following training with different temporal contexts, the value of stimuli sharing similar reinforcement schedules was assessed by presenting these stimuli in concurrent probes. The results for the multiple-chain…

  13. Association between serotonin transporter gene polymorphisms and non-lesional temporal lobe epilepsy in a Chinese Han population

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    Fengyuan Che; Youyi Wei; Xueyuan Heng; Qingxi Fu; Jianzhang Jiang

    2010-01-01

    Serotonin(5-hydroxytryptamine,5-HT)influences the cortical and subcortical excitatory/inhibitory balance and participates in the pathophysiological processes of epilepsy.The serotonin transporter(5-HTT)is the most important factor in serotonin inactivation.We tested whether 5-HTT polymorphisms are involved in the pathogenesis of epilepsy in Chinese Han population.We did not find a significant difference in the frequencies of genotypes and alleles in the 5-HTT gene-linked polymorphic region(5-HTTLPR)in patients with non-lesional temporal lobe epilepsy and normal controls(P > 0.05).Frequencies of the 5-HTT intren 2 variable number tandem repeat(5-HTTVNTR)12/12 genotype and allele 12 were higher in the patients with non-lesional temporal lobe epilepsy than normal controls(P < 0.01).The odds ratio of affecting non-lesional temporal lobe epilepsy was1.435(95% Cl,1.096 1.880)in patients carrying allele 12(P < 0.05).Although the 5-HTFLPR may not be a genetic locus of non-lesional temporal lobe epilepsy in Chinese Han population,allele 12 in the 5-HTFVNTR may correlate with non-lesional temporal lobe epilepsy.The Stin2.12 allele and12/12 genotype could be predisposing to non-lesional temporal lobe epilepsy.

  14. Minimum redundancy maximum relevance feature selection approach for temporal gene expression data.

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    Radovic, Milos; Ghalwash, Mohamed; Filipovic, Nenad; Obradovic, Zoran

    2017-01-03

    Feature selection, aiming to identify a subset of features among a possibly large set of features that are relevant for predicting a response, is an important preprocessing step in machine learning. In gene expression studies this is not a trivial task for several reasons, including potential temporal character of data. However, most feature selection approaches developed for microarray data cannot handle multivariate temporal data without previous data flattening, which results in loss of temporal information. We propose a temporal minimum redundancy - maximum relevance (TMRMR) feature selection approach, which is able to handle multivariate temporal data without previous data flattening. In the proposed approach we compute relevance of a gene by averaging F-statistic values calculated across individual time steps, and we compute redundancy between genes by using a dynamical time warping approach. The proposed method is evaluated on three temporal gene expression datasets from human viral challenge studies. Obtained results show that the proposed method outperforms alternatives widely used in gene expression studies. In particular, the proposed method achieved improvement in accuracy in 34 out of 54 experiments, while the other methods outperformed it in no more than 4 experiments. We developed a filter-based feature selection method for temporal gene expression data based on maximum relevance and minimum redundancy criteria. The proposed method incorporates temporal information by combining relevance, which is calculated as an average F-statistic value across different time steps, with redundancy, which is calculated by employing dynamical time warping approach. As evident in our experiments, incorporating the temporal information into the feature selection process leads to selection of more discriminative features.

  15. Involuntary Eye Movement during Fixation is Influenced by Spatio-Temporal Frequency of Visual Stimuli

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    Masae Yokota

    2011-05-01

    Full Text Available Involuntary eye movement during fixation is essential for visual information acquisition. Previous studies have suggested that such eye movement depends on the attributes of visual stimuli (e.g. Yokota, APCV2010. In this study, we focus on spatio-temporal frequency, as an attribute of visual stimuli in order to understand spatio-temporal frequency property in the pathway of human vision. We measured eye movement during fixation for three subjects when 16 random-dot dynamic textures that have various frequency bands in spatially and temporally, are presented to the subjects as visual stimuli. The result shows that eye movement depends on the spatio-temporal frequency of visual stimuli. The eye movement includes higher frequency components, in other words, higher velocity components, when visual stimulus has higher spatial frequency and/or higher temporal frequency. Future detailed experiments will show that involuntary eye movement during fixation might be influenced by spatio-temporal frequency sensitivity in vision.

  16. Temporal attending and prediction influence the perception of metrical rhythm: evidence from reaction times and ERPs

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    Fleur Leonie Bouwer

    2015-07-01

    Full Text Available The processing of rhythmic events in music is influenced by the induced metrical structure. Two mechanisms underlying this may be temporal attending and temporal prediction. Temporal fluctuations in attentional resources may influence the processing of rhythmic events by heightening sensitivity at metrically strong positions. Temporal predictions may attenuate responses to events that are highly expected within a metrical structure. In the current study we aimed to disentangle these two mechanisms by examining responses to unexpected sounds, using intensity increments and decrements as deviants. Temporal attending was hypothesized to lead to better detection of deviants in metrically strong (on the beat than weak (offbeat positions due to heightened sensitivity on the beat. Temporal prediction was hypothesized to lead to best detection of increments in offbeat positions and decrements on the beat, as they would be most unexpected in these positions. We used a speeded detection task to measure detectability of the deviants under attended conditions (Experiment 1. Under unattended conditions (Experiment 2, we used EEG to measure the mismatch negativity (MMN, an ERP component known to index the detectability of unexpected auditory events. Furthermore, we examined the amplitude of the auditory evoked P1 and N1 responses, which are known to be sensitive to both attention and prediction. We found better detection of small increments in offbeat positions than on the beat, consistent with the influence of temporal prediction (Experiment 1. In addition, we found faster detection of large increments on the beat as opposed to offbeat (Experiment 1, and larger amplitude P1 responses on the beat as compared to offbeat, both in support of temporal attending (Experiment 2. As such, we showed that both temporal attending and temporal prediction shape our processing of metrical rhythm.

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

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

    2009-01-01

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

  18. Analysis of spatial-temporal gene expression patterns reveals dynamics and regionalization in developing mouse brain.

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    Chou, Shen-Ju; Wang, Chindi; Sintupisut, Nardnisa; Niou, Zhen-Xian; Lin, Chih-Hsu; Li, Ker-Chau; Yeang, Chen-Hsiang

    2016-01-20

    Allen Brain Atlas (ABA) provides a valuable resource of spatial/temporal gene expressions in mammalian brains. Despite rich information extracted from this database, current analyses suffer from several limitations. First, most studies are either gene-centric or region-centric, thus are inadequate to capture the superposition of multiple spatial-temporal patterns. Second, standard tools of expression analysis such as matrix factorization can capture those patterns but do not explicitly incorporate spatial dependency. To overcome those limitations, we proposed a computational method to detect recurrent patterns in the spatial-temporal gene expression data of developing mouse brains. We demonstrated that regional distinction in brain development could be revealed by localized gene expression patterns. The patterns expressed in the forebrain, medullary and pontomedullary, and basal ganglia are enriched with genes involved in forebrain development, locomotory behavior, and dopamine metabolism respectively. In addition, the timing of global gene expression patterns reflects the general trends of molecular events in mouse brain development. Furthermore, we validated functional implications of the inferred patterns by showing genes sharing similar spatial-temporal expression patterns with Lhx2 exhibited differential expression in the embryonic forebrains of Lhx2 mutant mice. These analysis outcomes confirm the utility of recurrent expression patterns in studying brain development.

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

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    2009-03-01

    Full Text Available Gene expression time course data can be used not only to detect differentially expressed genes but also to find temporal associations among genes. The problem of reconstructing generalized logical networks to account for temporal dependencies among genes and environmental stimuli from transcriptomic data is addressed. A network reconstruction algorithm was developed that uses statistical significance as a criterion for network selection to avoid false-positive interactions arising from pure chance. The multinomial hypothesis testing-based network reconstruction allows for explicit specification of the false-positive rate, unique from all extant network inference algorithms. The method is superior to dynamic Bayesian network modeling in a simulation study. Temporal gene expression data from the brains of alcohol-treated mice in an analysis of the molecular response to alcohol are used for modeling. Genes from major neuronal pathways are identified as putative components of the alcohol response mechanism. Nine of these genes have associations with alcohol reported in literature. Several other potentially relevant genes, compatible with independent results from literature mining, may play a role in the response to alcohol. Additional, previously unknown gene interactions were discovered that, subject to biological verification, may offer new clues in the search for the elusive molecular mechanisms of alcoholism.

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

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    Lodowski Kerrie H

    2009-01-01

    Full Text Available Gene expression time course data can be used not only to detect differentially expressed genes but also to find temporal associations among genes. The problem of reconstructing generalized logical networks to account for temporal dependencies among genes and environmental stimuli from transcriptomic data is addressed. A network reconstruction algorithm was developed that uses statistical significance as a criterion for network selection to avoid false-positive interactions arising from pure chance. The multinomial hypothesis testing-based network reconstruction allows for explicit specification of the false-positive rate, unique from all extant network inference algorithms. The method is superior to dynamic Bayesian network modeling in a simulation study. Temporal gene expression data from the brains of alcohol-treated mice in an analysis of the molecular response to alcohol are used for modeling. Genes from major neuronal pathways are identified as putative components of the alcohol response mechanism. Nine of these genes have associations with alcohol reported in literature. Several other potentially relevant genes, compatible with independent results from literature mining, may play a role in the response to alcohol. Additional, previously unknown gene interactions were discovered that, subject to biological verification, may offer new clues in the search for the elusive molecular mechanisms of alcoholism.

  1. Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization.

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    Senturk, Serif; Shirole, Nitin H; Nowak, Dawid G; Corbo, Vincenzo; Pal, Debjani; Vaughan, Alexander; Tuveson, David A; Trotman, Lloyd C; Kinney, Justin B; Sordella, Raffaella

    2017-02-22

    The CRISPR/Cas9 system is a powerful tool for studying gene function. Here, we describe a method that allows temporal control of CRISPR/Cas9 activity based on conditional Cas9 destabilization. We demonstrate that fusing an FKBP12-derived destabilizing domain to Cas9 (DD-Cas9) enables conditional Cas9 expression and temporal control of gene editing in the presence of an FKBP12 synthetic ligand. This system can be easily adapted to co-express, from the same promoter, DD-Cas9 with any other gene of interest without co-modulation of the latter. In particular, when co-expressed with inducible Cre-ER(T2), our system enables parallel, independent manipulation of alleles targeted by Cas9 and traditional recombinase with single-cell specificity. We anticipate this platform will be used for the systematic characterization and identification of essential genes, as well as the investigation of the interactions between functional genes.

  2. Temporal dynamics of gene expression in the lung in a baboon model of E. coli sepsis

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    Zhu Hua

    2007-02-01

    Full Text Available Abstract Background Bacterial invasion during sepsis induces disregulated systemic responses that could lead to fatal lung failure. The purpose of this study was to relate the temporal dynamics of gene expression to the pathophysiological changes in the lung during the first and second stages of E. coli sepsis in baboons. Results Using human oligonucleotide microarrays, we have explored the temporal changes of gene expression in the lung of baboons challenged with sublethal doses of E. coli. Temporal expression pattern and biological significance of the differentially expressed genes were explored using clustering and pathway analysis software. Expression of selected genes was validated by real-time PCR. Cytokine levels in tissue and plasma were assayed by multiplex ELISA. Changes in lung ultrastructure were visualized by electron microscopy. We found that genes involved in primary inflammation, innate immune response, and apoptosis peaked at 2 hrs. Inflammatory and immune response genes that function in the stimulation of monocytes, natural killer and T-cells, and in the modulation of cell adhesion peaked at 8 hrs, while genes involved in wound healing and functional recovery were upregulated at 24 hrs. Conclusion The analysis of gene expression modulation in response to sepsis provides the baseline information that is crucial for the understanding of the pathophysiology of systemic inflammation and may facilitate the development of future approaches for sepsis therapy.

  3. Personality influences temporal discounting preferences: behavioral and brain evidence.

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    Manning, Joshua; Hedden, Trey; Wickens, Nina; Whitfield-Gabrieli, Susan; Prelec, Drazen; Gabrieli, John D E

    2014-09-01

    Personality traits are stable predictors of many life outcomes that are associated with important decisions that involve tradeoffs over time. Therefore, a fundamental question is how tradeoffs over time vary from person to person in relation to stable personality traits. We investigated the influence of personality, as measured by the Five-Factor Model, on time preferences and on neural activity engaged by intertemporal choice. During functional magnetic resonance imaging (fMRI), participants made choices between smaller-sooner and larger-later monetary rewards. For each participant, we estimated a constant-sensitivity discount function that dissociates impatience (devaluation of future consequences) from time sensitivity (consistency with rational, exponential discounting). Overall, higher neuroticism was associated with a relatively greater preference for immediate rewards and higher conscientiousness with a relatively greater preference for delayed rewards. Specifically, higher conscientiousness correlated positively with lower short-term impatience and more exponential time preferences, whereas higher neuroticism (lower emotional stability) correlated positively with higher short-term impatience and less exponential time preferences. Cognitive-control and reward brain regions were more activated when higher conscientiousness participants selected a smaller-sooner reward and, conversely, when higher neuroticism participants selected a larger-later reward. The greater activations that occurred when choosing rewards that contradicted personality predispositions may reflect the greater recruitment of mental resources needed to override those predispositions. These findings reveal that stable personality traits fundamentally influence how rewards are chosen over time. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Discovery and Replication of Gene Influences on Brain Structure Using LASSO Regression.

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    Kohannim, Omid; Hibar, Derrek P; Stein, Jason L; Jahanshad, Neda; Hua, Xue; Rajagopalan, Priya; Toga, Arthur W; Jack, Clifford R; Weiner, Michael W; de Zubicaray, Greig I; McMahon, Katie L; Hansell, Narelle K; Martin, Nicholas G; Wright, Margaret J; Thompson, Paul M

    2012-01-01

    We implemented least absolute shrinkage and selection operator (LASSO) regression to evaluate gene effects in genome-wide association studies (GWAS) of brain images, using an MRI-derived temporal lobe volume measure from 729 subjects scanned as part of the Alzheimer's Disease Neuroimaging Initiative (ADNI). Sparse groups of SNPs in individual genes were selected by LASSO, which identifies efficient sets of variants influencing the data. These SNPs were considered jointly when assessing their association with neuroimaging measures. We discovered 22 genes that passed genome-wide significance for influencing temporal lobe volume. This was a substantially greater number of significant genes compared to those found with standard, univariate GWAS. These top genes are all expressed in the brain and include genes previously related to brain function or neuropsychiatric disorders such as MACROD2, SORCS2, GRIN2B, MAGI2, NPAS3, CLSTN2, GABRG3, NRXN3, PRKAG2, GAS7, RBFOX1, ADARB2, CHD4, and CDH13. The top genes we identified with this method also displayed significant and widespread post hoc effects on voxelwise, tensor-based morphometry (TBM) maps of the temporal lobes. The most significantly associated gene was an autism susceptibility gene known as MACROD2. We were able to successfully replicate the effect of the MACROD2 gene in an independent cohort of 564 young, Australian healthy adult twins and siblings scanned with MRI (mean age: 23.8 ± 2.2 SD years). Our approach powerfully complements univariate techniques in detecting influences of genes on the living brain.

  5. Temporal, spatial, and environmental influences on the demographics of grizzly bears in the Greater Yellowstone Ecosystem

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    Schwartz, Charles C.; Haroldson, Mark A.; White, Gary C.; Harris, Richard B.; Cherry, Steve; Keating, Kim A.; Moody, Dave; Servheen, Christopher

    2006-01-01

    During the past 2 decades, the grizzly bear (Ursus arctos) population in the Greater Yellowstone Ecosystem (GYE) has increased in numbers and expanded in range. Understanding temporal, environmental, and spatial variables responsible for this change is useful in evaluating what likely influenced grizzly bear demographics in the GYE and where future management efforts might benefit conservation and management. We used recent data from radio-marked bears to estimate reproduction (1983–2002) and survival (1983–2001); these we combined into models to evaluate demographic vigor (lambda [λ]). We explored the influence of an array of individual, temporal, and spatial covariates on demographic vigor.

  6. Temporal gene expression profiling during rat femoral marrow ablation-induced intramembranous bone regeneration.

    Directory of Open Access Journals (Sweden)

    Joel K Wise

    Full Text Available Enhanced understanding of differential gene expression and biological pathways associated with distinct phases of intramembranous bone regeneration following femoral marrow ablation surgery will improve future advancements regarding osseointegration of joint replacement implants, biomaterials design, and bone tissue engineering. A rat femoral marrow ablation model was performed and genome-wide microarray data were obtained from samples at 1, 3, 5, 7, 10, 14, 28, and 56 days post-ablation, with intact bones serving as controls at Day 0. Bayesian model-based clustering produced eight distinct groups amongst 9,062 significant gene probe sets based on similar temporal expression profiles, which were further categorized into three major temporal classes of increased, variable, and decreased expression. Osteoblastic- and osteoclastic-associated genes were found to be significantly expressed within the increased expression groups. Chondrogenesis was not detected histologically. Adipogenic marker genes were found within variable/decreased expression groups, emphasizing that adipogenesis was inhibited during osteogenesis. Differential biological processes and pathways associated with each major temporal group were identified, and significantly expressed genes involved were visually represented by heat maps. It was determined that the increased expression group exclusively contains genes involved in pathways for matrix metalloproteinases (MMPs, Wnt signaling, TGF-β signaling, and inflammatory pathways. Only the variable expression group contains genes associated with glycolysis and gluconeogenesis, the notch signaling pathway, natural killer cell mediated cytotoxicity, and the B cell receptor signaling pathway. The decreased group exclusively consists of genes involved in heme biosynthesis, the p53 signaling pathway, and the hematopoietic cell lineage. Significant biological pathways and transcription factors expressed at each time point post

  7. Influence of temporally variable groundwater flow conditions on point measurements and contaminant mass flux estimations

    DEFF Research Database (Denmark)

    Rein, Arno; Bauer, S; Dietrich, P

    2009-01-01

    is present, the concentration variability due to a fluctuating groundwater flow direction varies significantly within the control plane and between the different realizations. Determination of contaminant mass fluxes is also influenced by the temporal variability of the concentration measurement, especially......Monitoring of contaminant concentrations, e.g., for the estimation of mass discharge or contaminant degradation rates. often is based on point measurements at observation wells. In addition to the problem, that point measurements may not be spatially representative. a further complication may arise...... due to the temporal dynamics of groundwater flow, which may cause a concentration measurement to be not temporally representative. This paper presents results from a numerical modeling study focusing on temporal variations of the groundwater flow direction. "Measurements" are obtained from point...

  8. Temporal characteristics of the influence of punishment on perceptual decision making in the human brain

    OpenAIRE

    Blank, H.; Guido, B.; Heekeren, H.R.; Philiastides, M.G.

    2013-01-01

    Perceptual decision making is the process by which information from sensory systems is combined and used to influence our behavior. In addition to the sensory input, this process can be affected by other factors, such as reward and punishment for correct and incorrect responses. To investigate the temporal dynamics of how monetary punishment influences perceptual decision making in humans, we collected electroencephalography (EEG) data during a perceptual categorization task whereby the punis...

  9. Continuous carryover of temporal context dissociates response bias from perceptual influence for duration.

    Directory of Open Access Journals (Sweden)

    Martin Wiener

    Full Text Available Recent experimental evidence suggests that the perception of temporal intervals is influenced by the temporal context in which they are presented. A longstanding example is the time-order-error, wherein the perception of two intervals relative to one another is influenced by the order in which they are presented. Here, we test whether the perception of temporal intervals in an absolute judgment task is influenced by the preceding temporal context. Human subjects participated in a temporal bisection task with no anchor durations (partition method. Intervals were demarcated by a Gaussian blob (visual condition or burst of white noise (auditory condition that persisted for one of seven logarithmically spaced sub-second intervals. Crucially, the order in which stimuli were presented was first-order counterbalanced, allowing us to measure the carryover effect of every successive combination of intervals. The results demonstrated a number of distinct findings. First, the perception of each interval was biased by the prior response, such that each interval was judged similarly to the preceding trial. Second, the perception of each interval was also influenced by the prior interval, such that perceived duration shifted away from the preceding interval. Additionally, the effect of decision bias was larger for visual intervals, whereas auditory intervals engendered greater perceptual carryover. We quantified these effects by designing a biologically-inspired computational model that measures noisy representations of time against an adaptive memory prior while simultaneously accounting for uncertainty, consistent with a Bayesian heuristic. We found that our model could account for all of the effects observed in human data. Additionally, our model could only accommodate both carryover effects when uncertainty and memory were calculated separately, suggesting separate neural representations for each. These findings demonstrate that time is susceptible to

  10. Academic motivation mediates the influence of temporal discounting on academic achievement during adolescence

    NARCIS (Netherlands)

    Lee, Nikki; Krabbendam, Lydia; Dekker, Sanne; Boschloo, Annemarie; De Groot, Renate; Jolles, Jelle

    2012-01-01

    Lee, N. C., Krabbendam, L., Dekker, S. J., Boschloo, A. M., De Groot, R. H. M., & Jolles, J. (2012). Academic motivation mediates the influence of temporal discounting on academic achievement during adolescence. Trends in Neuroscience and Education, 1(1), 43-48.

  11. Prestimulus Alpha Power Influences Tactile Temporal Perceptual Discrimination and Confidence in Decisions.

    Science.gov (United States)

    Baumgarten, Thomas J; Schnitzler, Alfons; Lange, Joachim

    2016-03-01

    Recent studies have demonstrated that prestimulus alpha-band activity substantially influences perception of near-threshold stimuli. Here, we studied the influence of prestimulus alpha power fluctuations on temporal perceptual discrimination of suprathreshold tactile stimuli and subjects' confidence regarding their perceptual decisions. We investigated how prestimulus alpha-band power influences poststimulus decision-making variables. We presented electrical stimuli with different stimulus onset asynchronies (SOAs) to human subjects, and determined the SOA for which temporal perceptual discrimination varied on a trial-by-trial basis between perceiving 1 or 2 stimuli, prior to recording brain activity with magnetoencephalography. We found that low prestimulus alpha power in contralateral somatosensory and occipital areas predicts the veridical temporal perceptual discrimination of 2 stimuli. Additionally, prestimulus alpha power was negatively correlated with confidence ratings in correctly perceived trials, but positively correlated for incorrectly perceived trials. Finally, poststimulus event-related fields (ERFs) were modulated by prestimulus alpha power and reflect the result of a decisional process rather than physical stimulus parameters around ∼150 ms. These findings provide new insights into the link between spontaneous prestimulus alpha power fluctuations, temporal perceptual discrimination, decision making, and decisional confidence. The results suggest that prestimulus alpha power modulates perception and decisions on a continuous scale, as reflected in confidence ratings.

  12. Moving events in time: Time-referent hand–arm movements influence perceived temporal distance to past events

    OpenAIRE

    Semin, Gün Refik; Blom, Stephanie S. A. H.

    2013-01-01

    We examine and find support for the hypothesis that time-referent hand-arm movements influence temporal judgments. In line with the concept of ""left is associated with earlier times, and right is associated with later times,"" we show that performing left (right) hand-arm movements while thinking about a past event increases (decreases) the perceived temporal distance to the event. These findings show for the first time that hand-arm movements can influence the perceived temporal distance to...

  13. Spatial and temporal analysis of gene expression during growth and fusion of the mouse facial prominences.

    Science.gov (United States)

    Feng, Weiguo; Leach, Sonia M; Tipney, Hannah; Phang, Tzulip; Geraci, Mark; Spritz, Richard A; Hunter, Lawrence E; Williams, Trevor

    2009-12-16

    Orofacial malformations resulting from genetic and/or environmental causes are frequent human birth defects yet their etiology is often unclear because of insufficient information concerning the molecular, cellular and morphogenetic processes responsible for normal facial development. We have, therefore, derived a comprehensive expression dataset for mouse orofacial development, interrogating three distinct regions - the mandibular, maxillary and frontonasal prominences. To capture the dynamic changes in the transcriptome during face formation, we sampled five time points between E10.5-E12.5, spanning the developmental period from establishment of the prominences to their fusion to form the mature facial platform. Seven independent biological replicates were used for each sample ensuring robustness and quality of the dataset. Here, we provide a general overview of the dataset, characterizing aspects of gene expression changes at both the spatial and temporal level. Considerable coordinate regulation occurs across the three prominences during this period of facial growth and morphogenesis, with a switch from expression of genes involved in cell proliferation to those associated with differentiation. An accompanying shift in the expression of polycomb and trithorax genes presumably maintains appropriate patterns of gene expression in precursor or differentiated cells, respectively. Superimposed on the many coordinated changes are prominence-specific differences in the expression of genes encoding transcription factors, extracellular matrix components, and signaling molecules. Thus, the elaboration of each prominence will be driven by particular combinations of transcription factors coupled with specific cell:cell and cell:matrix interactions. The dataset also reveals several prominence-specific genes not previously associated with orofacial development, a subset of which we externally validate. Several of these latter genes are components of bidirectional

  14. Spatial and temporal analysis of gene expression during growth and fusion of the mouse facial prominences.

    Directory of Open Access Journals (Sweden)

    Weiguo Feng

    Full Text Available Orofacial malformations resulting from genetic and/or environmental causes are frequent human birth defects yet their etiology is often unclear because of insufficient information concerning the molecular, cellular and morphogenetic processes responsible for normal facial development. We have, therefore, derived a comprehensive expression dataset for mouse orofacial development, interrogating three distinct regions - the mandibular, maxillary and frontonasal prominences. To capture the dynamic changes in the transcriptome during face formation, we sampled five time points between E10.5-E12.5, spanning the developmental period from establishment of the prominences to their fusion to form the mature facial platform. Seven independent biological replicates were used for each sample ensuring robustness and quality of the dataset. Here, we provide a general overview of the dataset, characterizing aspects of gene expression changes at both the spatial and temporal level. Considerable coordinate regulation occurs across the three prominences during this period of facial growth and morphogenesis, with a switch from expression of genes involved in cell proliferation to those associated with differentiation. An accompanying shift in the expression of polycomb and trithorax genes presumably maintains appropriate patterns of gene expression in precursor or differentiated cells, respectively. Superimposed on the many coordinated changes are prominence-specific differences in the expression of genes encoding transcription factors, extracellular matrix components, and signaling molecules. Thus, the elaboration of each prominence will be driven by particular combinations of transcription factors coupled with specific cell:cell and cell:matrix interactions. The dataset also reveals several prominence-specific genes not previously associated with orofacial development, a subset of which we externally validate. Several of these latter genes are components of

  15. Factors influencing temporal variation of a Sargassum filipendula (Phaeophyta: Fucales) bed in a subtropical shore

    OpenAIRE

    Jacobucci, GB; Tanaka, MO; Leite, FPP.

    2009-01-01

    In the present study, we evaluate the influence of biotic and abiotic factors on temporal fluctuations of Sargassum filipendula in a subtropical shore. Monthly algal samples, abiotic components, amphipod grazer density, and epiphyte biomass were obtained from a Sargassum bed in south-eastern Brazil. Density of S. filipendula fronds decreased during the sampling period, whereas dry mass was more constant, although with a noticeable reduction in the warmer months. Hypnea musciformis was the mos...

  16. Fast or Smart? How the Use of Scrum Can Influence the Temporal Environment in a Project

    DEFF Research Database (Denmark)

    Scheller, Vibeke Kristine; Hvid, Helge Søndergaard; Pries-Heje, Jan

    2015-01-01

    A recent survey shows that 40% of all projects use, or have used, agile methods. The most commonly used agile method is Scrum, one reason being that Scrum provides mechanisms for building a healthy temporal environment for the project participants. Through a case study carried out in a Danish...... municipality we demkonstrate how the tgemporal environment in a project is influenced - enhanced as well as challenged - by the use of Scrum....

  17. Differences in human cortical gene expression match the temporal properties of large-scale functional networks.

    Directory of Open Access Journals (Sweden)

    Claudia Cioli

    Full Text Available We explore the relationships between the cortex functional organization and genetic expression (as provided by the Allen Human Brain Atlas. Previous work suggests that functional cortical networks (resting state and task based are organized as two large networks (differentiated by their preferred information processing mode shaped like two rings. The first ring--Visual-Sensorimotor-Auditory (VSA--comprises visual, auditory, somatosensory, and motor cortices that process real time world interactions. The second ring--Parieto-Temporo-Frontal (PTF--comprises parietal, temporal, and frontal regions with networks dedicated to cognitive functions, emotions, biological needs, and internally driven rhythms. We found--with correspondence analysis--that the patterns of expression of the 938 genes most differentially expressed across the cortex organized the cortex into two sets of regions that match the two rings. We confirmed this result using discriminant correspondence analysis by showing that the genetic profiles of cortical regions can reliably predict to what ring these regions belong. We found that several of the proteins--coded by genes that most differentiate the rings--were involved in neuronal information processing such as ionic channels and neurotransmitter release. The systematic study of families of genes revealed specific proteins within families preferentially expressed in each ring. The results showed strong congruence between the preferential expression of subsets of genes, temporal properties of the proteins they code, and the preferred processing modes of the rings. Ionic channels and release-related proteins more expressed in the VSA ring favor temporal precision of fast evoked neural transmission (Sodium channels SCNA1, SCNB1 potassium channel KCNA1, calcium channel CACNA2D2, Synaptotagmin SYT2, Complexin CPLX1, Synaptobrevin VAMP1. Conversely, genes expressed in the PTF ring favor slower, sustained, or rhythmic activation (Sodium

  18. Influence of fluvial environments on sediment archiving processes and temporal pollutant dynamics (Upper Loire River, France).

    Science.gov (United States)

    Dhivert, E; Grosbois, C; Rodrigues, S; Desmet, M

    2015-02-01

    Floodplains are often cored to build long-term pollutant trends at the basin scale. To highlight the influences of depositional environments on archiving processes, aggradation rates, archived trace element signals and vertical redistribution processes, two floodplain cores were sampled near in two different environments of the Upper Loire River (France): (i) a river bank ridge and (ii) a paleochannel connected by its downstream end. The base of the river bank core is composed of sandy sediments from the end of the Little Ice Age (late 18th century). This composition corresponds to a proximal floodplain aggradation (aggradation rate depends on the topography and connection degree to the river channel. The temporal dynamics of anthropogenic trace element enrichments recorded in the distal floodplain are initially synchronous and present similar levels. Although the river bank core shows general temporal trends, the paleochannel core has a better resolution for short-time variations of trace element signals. After local water depth regulation began in the early 1930s, differences of connection degree were enhanced between the two cores. Therefore, large trace element signal divergences are recorded across the floodplain. The paleochannel core shows important temporal variations of enrichment levels from the 1930s to the coring date. However, the river bank core has no significant temporal variations of trace element enrichments and lower contamination levels because of a lower deposition of contaminated sediments and a pedogenetic trace elements redistribution.

  19. ASPECTUAL INFLUENCE ON TEMPORAL RELATIONS: A CASE STUDY OF THE EXPERIENTIAL GUO IN MANDARINE

    Directory of Open Access Journals (Sweden)

    Jiun-Shiung Wu

    2009-12-01

    Full Text Available This paper examines how the temporal relation between a clause containing the experiential guo and an adjacent clause is determined. Mandarin is a language not morphologically marked for tenses (e.g., Lin 2006, and therefore, tenses cannot help in determining temporal relations in Mandarin. However, Mandarin has a rich aspectual system. This paper argues that the experiential guo indirectly influences temporal relations via rhetorical relations by either specifying a default rhetorical relation, or by constraining the circumstances under which a certain rhetorical relation can connect a clause with guo to an adjacent clause. This paper also argues that the default rhetorical relation and the constraints are determined by the aspectual properties of the experiential marker. Other information, such as discourse connectors, lexical information, etc., can override the default rhetorical relation indicated by guo and specifies a rhetorical relation. Therefore, this paper concludes that in Mandarin aspect markers can indirectly affect temporal relations by means of rhetorical relations, a result consistent with Wu’s (2005b paper on the perfective marker le in Mandarin, and Wu’s (2007b, 2004 work on the progressive marker zai and the durative marker zhe.

  20. The good, the bad, and the timely: how temporal order and moral judgment influence causal selection.

    Science.gov (United States)

    Reuter, Kevin; Kirfel, Lara; van Riel, Raphael; Barlassina, Luca

    2014-01-01

    Causal selection is the cognitive process through which one or more elements in a complex causal structure are singled out as actual causes of a certain effect. In this paper, we report on an experiment in which we investigated the role of moral and temporal factors in causal selection. Our results are as follows. First, when presented with a temporal chain in which two human agents perform the same action one after the other, subjects tend to judge the later agent to be the actual cause. Second, the impact of temporal location on causal selection is almost canceled out if the later agent did not violate a norm while the former did. We argue that this is due to the impact that judgments of norm violation have on causal selection-even if the violated norm has nothing to do with the obtaining effect. Third, moral judgments about the effect influence causal selection even in the case in which agents could not have foreseen the effect and did not intend to bring it about. We discuss our findings in connection to recent theories of the role of moral judgment in causal reasoning, on the one hand, and to probabilistic models of temporal location, on the other.

  1. Temporal occurrence of two morpho butterflies (Lepidoptera: Nymphalidae): influence of weather and food resources.

    Science.gov (United States)

    Freire, Geraldo; Nascimento, André Rangel; Malinov, Ivan Konstantinov; Diniz, Ivone R

    2014-04-01

    The seasonality of fruit-feeding butterflies is very well known. However, few studies have analyzed the influence of climatic variables and resource availability on the temporal distributions of butterflies. Morpho helenor achillides (C. Felder and R. Felder 1867) and Morpho menelaus coeruleus (Perry 1810) (Nymphalidae) were used as models to investigate the influences of climatic factors and food resources on the temporal distribution of these Morphinae butterflies. These butterflies were collected weekly from January 2005 to December 2006 in the Parque Nacional de Brasília (PNB). In total, 408 individuals were collected, including 274 of M. helenor and 134 of M. menelaus. The relative abundance of the two species was similar in 2005 (n = 220) and 2006 (n = 188). Of the variables considered, only the relative humidity and resource availability measured in terms of phenology of zoochorous fruits of herbaceous plants explained a large proportion of the variation in the abundance of these butterflies. Both of the explanatory variables were positively associated with the total abundance of individuals and with the abundances of M. helenor and M. menelaus considered separately. The phenology of anemochorous fruits was negatively associated with butterfly abundance. The temporal distribution of the butterflies was better predicted by the phenology of the zoochorous fruits of herbaceous plants than by the climatic predictors.

  2. Melatonin-Induced Temporal Up-Regulation of Gene Expression Related to Ubiquitin/Proteasome System (UPS in the Human Malaria Parasite Plasmodium falciparum

    Directory of Open Access Journals (Sweden)

    Fernanda C. Koyama

    2014-12-01

    Full Text Available There is an increasing understanding that melatonin and the ubiquitin/ proteasome system (UPS interact to regulate multiple cellular functions. Post-translational modifications such as ubiquitination are important modulators of signaling processes, cell cycle and many other cellular functions. Previously, we reported a melatonin-induced upregulation of gene expression related to ubiquitin/proteasome system (UPS in Plasmodium falciparum, the human malaria parasite, and that P. falciparum protein kinase 7 influences this process. This implies a role of melatonin, an indolamine, in modulating intraerythrocytic development of the parasite. In this report we demonstrate by qPCR analysis, that melatonin induces gene upregulation in nine out of fourteen genes of the UPS, consisting of the same set of genes previously reported, between 4 to 5 h after melatonin treatment. We demonstrate that melatonin causes a temporally controlled gene expression of UPS members.

  3. Muscle wasting and the temporal gene expression pattern in a novel rat intensive care unit model

    Directory of Open Access Journals (Sweden)

    Llano-Diez Monica

    2011-12-01

    Full Text Available Abstract Background Acute quadriplegic myopathy (AQM or critical illness myopathy (CIM is frequently observed in intensive care unit (ICU patients. To elucidate duration-dependent effects of the ICU intervention on molecular and functional networks that control the muscle wasting and weakness associated with AQM, a gene expression profile was analyzed at time points varying from 6 hours to 14 days in a unique experimental rat model mimicking ICU conditions, i.e., post-synaptically paralyzed, mechanically ventilated and extensively monitored animals. Results During the observation period, 1583 genes were significantly up- or down-regulated by factors of two or greater. A significant temporal gene expression pattern was constructed at short (6 h-4 days, intermediate (5-8 days and long (9-14 days durations. A striking early and maintained up-regulation (6 h-14d of muscle atrogenes (muscle ring-finger 1/tripartite motif-containing 63 and F-box protein 32/atrogin-1 was observed, followed by an up-regulation of the proteolytic systems at intermediate and long durations (5-14d. Oxidative stress response genes and genes that take part in amino acid catabolism, cell cycle arrest, apoptosis, muscle development, and protein synthesis together with myogenic factors were significantly up-regulated from 5 to 14 days. At 9-14 d, genes involved in immune response and the caspase cascade were up-regulated. At 5-14d, genes related to contractile (myosin heavy chain and myosin binding protein C, regulatory (troponin, tropomyosin, developmental, caveolin-3, extracellular matrix, glycolysis/gluconeogenesis, cytoskeleton/sarcomere regulation and mitochondrial proteins were down-regulated. An activation of genes related to muscle growth and new muscle fiber formation (increase of myogenic factors and JunB and down-regulation of myostatin and up-regulation of genes that code protein synthesis and translation factors were found from 5 to 14 days. Conclusions Novel

  4. Genome-Wide Temporal Expression Profiling in Caenorhabditis elegans Identifies a Core Gene Set Related to Long-Term Memory.

    Science.gov (United States)

    Freytag, Virginie; Probst, Sabine; Hadziselimovic, Nils; Boglari, Csaba; Hauser, Yannick; Peter, Fabian; Gabor Fenyves, Bank; Milnik, Annette; Demougin, Philippe; Vukojevic, Vanja; de Quervain, Dominique J-F; Papassotiropoulos, Andreas; Stetak, Attila

    2017-07-12

    The identification of genes related to encoding, storage, and retrieval of memories is a major interest in neuroscience. In the current study, we analyzed the temporal gene expression changes in a neuronal mRNA pool during an olfactory long-term associative memory (LTAM) in Caenorhabditis elegans hermaphrodites. Here, we identified a core set of 712 (538 upregulated and 174 downregulated) genes that follows three distinct temporal peaks demonstrating multiple gene regulation waves in LTAM. Compared with the previously published positive LTAM gene set (Lakhina et al., 2015), 50% of the identified upregulated genes here overlap with the previous dataset, possibly representing stimulus-independent memory-related genes. On the other hand, the remaining genes were not previously identified in positive associative memory and may specifically regulate aversive LTAM. Our results suggest a multistep gene activation process during the formation and retrieval of long-term memory and define general memory-implicated genes as well as conditioning-type-dependent gene sets.SIGNIFICANCE STATEMENT The identification of genes regulating different steps of memory is of major interest in neuroscience. Identification of common memory genes across different learning paradigms and the temporal activation of the genes are poorly studied. Here, we investigated the temporal aspects of Caenorhabditis elegans gene expression changes using aversive olfactory associative long-term memory (LTAM) and identified three major gene activation waves. Like in previous studies, aversive LTAM is also CREB dependent, and CREB activity is necessary immediately after training. Finally, we define a list of memory paradigm-independent core gene sets as well as conditioning-dependent genes. Copyright © 2017 the authors 0270-6474/17/376661-12$15.00/0.

  5. Fast or Smart? How the Use of Scrum Can Influence the Temporal Environment in a Project

    DEFF Research Database (Denmark)

    Scheller, Vibeke Kristine; Hvid, Helge Søndergaard; Pries-Heje, Jan

    2015-01-01

    A recent survey shows that 40% of all projects use, or have used, agile methods. The most commonly used agile method is Scrum, one reason being that Scrum provides mechanisms for building a healthy temporal environment for the project participants. Through a case study carried out in a Danish mun...... municipality we demkonstrate how the tgemporal environment in a project is influenced - enhanced as well as challenged - by the use of Scrum.......A recent survey shows that 40% of all projects use, or have used, agile methods. The most commonly used agile method is Scrum, one reason being that Scrum provides mechanisms for building a healthy temporal environment for the project participants. Through a case study carried out in a Danish...

  6. Comparing the influence of spectro-temporal integration in computational speech segregation

    DEFF Research Database (Denmark)

    Bentsen, Thomas; May, Tobias; Kressner, Abigail Anne

    2016-01-01

    The goal of computational speech segregation systems is to automatically segregate a target speaker from interfering maskers. Typically, these systems include a feature extraction stage in the front-end and a classification stage in the back-end. A spectrotemporal integration strategy can...... be applied in either the frontend, using the so-called delta features, or in the back-end, using a second classifier that exploits the posterior probability of speech from the first classifier across a spectro-temporal window. This study systematically analyzes the influence of such stages on segregation...... performance, the error distributions and intelligibility predictions. Results indicated that it could be problematic to exploit context in the back-end, even though such a spectro-temporal integration stage improves the segregation performance. Also, the results emphasized the potential need of a single...

  7. Comparing the influence of spectro-temporal integration in computational speech segregation

    DEFF Research Database (Denmark)

    Bentsen, Thomas; May, Tobias; Kressner, Abigail Anne;

    2016-01-01

    The goal of computational speech segregation systems is to automatically segregate a target speaker from interfering maskers. Typically, these systems include a feature extraction stage in the front-end and a classification stage in the back-end. A spectrotemporal integration strategy can...... be applied in either the frontend, using the so-called delta features, or in the back-end, using a second classifier that exploits the posterior probability of speech from the first classifier across a spectro-temporal window. This study systematically analyzes the influence of such stages on segregation...... metric that comprehensively predicts computational segregation performance and correlates well with intelligibility. The outcome of this study could help to identify the most effective spectro-temporal integration strategy for computational segregation systems....

  8. Genes encoding novel secreted and transmembrane proteins are temporally and spatially regulated during Drosophila melanogaster embryogenesis

    Directory of Open Access Journals (Sweden)

    González Mauricio

    2009-09-01

    Full Text Available Abstract Background Morphogenetic events that shape the Drosophila melanogaster embryo are tightly controlled by a genetic program in which specific sets of genes are up-regulated. We used a suppressive subtractive hybridization procedure to identify a group of developmentally regulated genes during early stages of D. melanogaster embryogenesis. We studied the spatiotemporal activity of these genes in five different intervals covering 12 stages of embryogenesis. Results Microarrays were constructed to confirm induction of expression and to determine the temporal profile of isolated subtracted cDNAs during embryo development. We identified a set of 118 genes whose expression levels increased significantly in at least one developmental interval compared with a reference interval. Of these genes, 53% had a phenotype and/or molecular function reported in the literature, whereas 47% were essentially uncharacterized. Clustering analysis revealed demarcated transcript groups with maximum gene activity at distinct developmental intervals. In situ hybridization assays were carried out on 23 uncharacterized genes, 15 of which proved to have spatiotemporally restricted expression patterns. Among these 15 uncharacterized genes, 13 were found to encode putative secreted and transmembrane proteins. For three of them we validated our protein sequence predictions by expressing their cDNAs in Drosophila S2R+ cells and analyzed the subcellular distribution of recombinant proteins. We then focused on the functional characterization of the gene CG6234. Inhibition of CG6234 by RNA interference resulted in morphological defects in embryos, suggesting the involvement of this gene in germ band retraction. Conclusion Our data have yielded a list of developmentally regulated D. melanogaster genes and their expression profiles during embryogenesis and provide new information on the spatiotemporal expression patterns of several uncharacterized genes. In particular, we

  9. Differential DNA methylation profiles of coding and non-coding genes define hippocampal sclerosis in human temporal lobe epilepsy.

    Science.gov (United States)

    Miller-Delaney, Suzanne F C; Bryan, Kenneth; Das, Sudipto; McKiernan, Ross C; Bray, Isabella M; Reynolds, James P; Gwinn, Ryder; Stallings, Raymond L; Henshall, David C

    2015-03-01

    Temporal lobe epilepsy is associated with large-scale, wide-ranging changes in gene expression in the hippocampus. Epigenetic changes to DNA are attractive mechanisms to explain the sustained hyperexcitability of chronic epilepsy. Here, through methylation analysis of all annotated C-phosphate-G islands and promoter regions in the human genome, we report a pilot study of the methylation profiles of temporal lobe epilepsy with or without hippocampal sclerosis. Furthermore, by comparative analysis of expression and promoter methylation, we identify methylation sensitive non-coding RNA in human temporal lobe epilepsy. A total of 146 protein-coding genes exhibited altered DNA methylation in temporal lobe epilepsy hippocampus (n = 9) when compared to control (n = 5), with 81.5% of the promoters of these genes displaying hypermethylation. Unique methylation profiles were evident in temporal lobe epilepsy with or without hippocampal sclerosis, in addition to a common methylation profile regardless of pathology grade. Gene ontology terms associated with development, neuron remodelling and neuron maturation were over-represented in the methylation profile of Watson Grade 1 samples (mild hippocampal sclerosis). In addition to genes associated with neuronal, neurotransmitter/synaptic transmission and cell death functions, differential hypermethylation of genes associated with transcriptional regulation was evident in temporal lobe epilepsy, but overall few genes previously associated with epilepsy were among the differentially methylated. Finally, a panel of 13, methylation-sensitive microRNA were identified in temporal lobe epilepsy including MIR27A, miR-193a-5p (MIR193A) and miR-876-3p (MIR876), and the differential methylation of long non-coding RNA documented for the first time. The present study therefore reports select, genome-wide DNA methylation changes in human temporal lobe epilepsy that may contribute to the molecular architecture of the epileptic brain.

  10. Differential DNA methylation profiles of coding and non-coding genes define hippocampal sclerosis in human temporal lobe epilepsy

    Science.gov (United States)

    Miller-Delaney, Suzanne F.C.; Bryan, Kenneth; Das, Sudipto; McKiernan, Ross C.; Bray, Isabella M.; Reynolds, James P.; Gwinn, Ryder; Stallings, Raymond L.

    2015-01-01

    Temporal lobe epilepsy is associated with large-scale, wide-ranging changes in gene expression in the hippocampus. Epigenetic changes to DNA are attractive mechanisms to explain the sustained hyperexcitability of chronic epilepsy. Here, through methylation analysis of all annotated C-phosphate-G islands and promoter regions in the human genome, we report a pilot study of the methylation profiles of temporal lobe epilepsy with or without hippocampal sclerosis. Furthermore, by comparative analysis of expression and promoter methylation, we identify methylation sensitive non-coding RNA in human temporal lobe epilepsy. A total of 146 protein-coding genes exhibited altered DNA methylation in temporal lobe epilepsy hippocampus (n = 9) when compared to control (n = 5), with 81.5% of the promoters of these genes displaying hypermethylation. Unique methylation profiles were evident in temporal lobe epilepsy with or without hippocampal sclerosis, in addition to a common methylation profile regardless of pathology grade. Gene ontology terms associated with development, neuron remodelling and neuron maturation were over-represented in the methylation profile of Watson Grade 1 samples (mild hippocampal sclerosis). In addition to genes associated with neuronal, neurotransmitter/synaptic transmission and cell death functions, differential hypermethylation of genes associated with transcriptional regulation was evident in temporal lobe epilepsy, but overall few genes previously associated with epilepsy were among the differentially methylated. Finally, a panel of 13, methylation-sensitive microRNA were identified in temporal lobe epilepsy including MIR27A, miR-193a-5p (MIR193A) and miR-876-3p (MIR876), and the differential methylation of long non-coding RNA documented for the first time. The present study therefore reports select, genome-wide DNA methylation changes in human temporal lobe epilepsy that may contribute to the molecular architecture of the epileptic brain. PMID

  11. MulteeSum: a tool for comparative spatial and temporal gene expression data.

    Science.gov (United States)

    Meyer, Miriah; Munzner, Tamara; DePace, Angela; Pfister, Hanspeter

    2010-01-01

    Cells in an organism share the same genetic information in their DNA, but have very different forms and behavior because of the selective expression of subsets of their genes. The widely used approach of measuring gene expression over time from a tissue sample using techniques such as microarrays or sequencing do not provide information about the spatial position within the tissue where these genes are expressed. In contrast, we are working with biologists who use techniques that measure gene expression in every individual cell of entire fruitfly embryos over an hour of their development, and do so for multiple closely-related subspecies of Drosophila. These scientists are faced with the challenge of integrating temporal gene expression data with the spatial location of cells and, moreover, comparing this data across multiple related species. We have worked with these biologists over the past two years to develop MulteeSum, a visualization system that supports inspection and curation of data sets showing gene expression over time, in conjunction with the spatial location of the cells where the genes are expressed--it is the first tool to support comparisons across multiple such data sets. MulteeSum is part of a general and flexible framework we developed with our collaborators that is built around multiple summaries for each cell, allowing the biologists to explore the results of computations that mix spatial information, gene expression measurements over time, and data from multiple related species or organisms. We justify our design decisions based on specific descriptions of the analysis needs of our collaborators, and provide anecdotal evidence of the efficacy of MulteeSum through a series of case studies.

  12. Lack of influence of muscular performance parameters on spatio-temporal adaptations with increased running velocity.

    Science.gov (United States)

    Roche-Seruendo, Luis E; García-Pinillos, Felipe; Haicaguerre, Joana; Bataller-Cervero, Ana V; Soto-Hermoso, Víctor M; Latorre-Román, Pedro Á

    2017-02-08

    This study aimed to analyse the influence of muscular performance parameters on spatio-temporal gait characteristics during running when gradually increasing speed. 51 recreationally trained male endurance runners (age: 28 ± 8 years) voluntarily participated in this study. Subjects performed a battery of jumping tests (squat jump, countermovement jump, and 20 cm drop jump), and after that, the subjects performed an incremental running test (10 to 20 km/h) on a motorized treadmill. Spatio-temporal parameters were measured using the OptoGait system. Cluster k-means analysis grouped subjects according to the jumping test performance, by obtaining a group of good jumpers (GJ, n = 19) and a group of bad jumpers (BJ, n = 32). With increased running velocity, contact time was shorter, flight time and step length longer, whereas cadence and stride angle were greater (p adaptations between those runners with good jumping ability and those with poor jumping ability. Based on that, it seems that muscular performance parameters do not play a key role in spatio-temporal adaptations experienced by recreational endurance runners with increased velocity. However, taken into consideration the well-known relationship between running performance and neuromuscular performance, the authors suggest that muscular performance parameters would be much more determinant in the presence of fatigue (exhausted condition), or in the case of considering other variables such as running economy or kinetic.

  13. Transcriptional analysis of temporal gene expression in germinating Clostridium difficile 630 endospores.

    Directory of Open Access Journals (Sweden)

    Marcin Dembek

    Full Text Available Clostridium difficile is the leading cause of hospital acquired diarrhoea in industrialised countries. Under conditions that are not favourable for growth, the pathogen produces metabolically dormant endospores via asymmetric cell division. These are extremely resistant to both chemical and physical stress and provide the mechanism by which C. difficile can evade the potentially fatal consequences of exposure to heat, oxygen, alcohol, and certain disinfectants. Spores are the primary infective agent and must germinate to allow for vegetative cell growth and toxin production. While spore germination in Bacillus is well understood, little is known about C. difficile germination and outgrowth. Here we use genome-wide transcriptional analysis to elucidate the temporal gene expression patterns in C. difficile 630 endospore germination. We have optimized methods for large scale production and purification of spores. The germination characteristics of purified spores have been characterized and RNA extraction protocols have been optimized. Gene expression was highly dynamic during germination and outgrowth, and was found to involve a large number of genes. Using this genome-wide, microarray approach we have identified 511 genes that are significantly up- or down-regulated during C. difficile germination (p≤0.01. A number of functional groups of genes appeared to be co-regulated. These included transport, protein synthesis and secretion, motility and chemotaxis as well as cell wall biogenesis. These data give insight into how C. difficile re-establishes its metabolism, re-builds the basic structures of the vegetative cell and resumes growth.

  14. Nitrogen and phosphorus concentrations from agricultural catchments—influence of spatial and temporal variables

    Science.gov (United States)

    Arheimer, B.; Lidén, R.

    2000-01-01

    The eutrophication problem has drawn attention to nutrient leaching from arable land in southern Sweden, and further understanding of spatial and temporal variability is needed in order to develop decision-making tools. Thus, the influence of spatial and temporal variables was analysed statistically using empirical time series of different nutrient species from 35 well-documented catchments (2-35 km 2), which have been monitored for an average of 5 years. In the spatial analysis several significant correlations between winter median concentrations and catchment characteristics were found. The strongest correlation was found between inorganic nitrogen and land use, while concentrations of different phosphorus species were highly correlated to soil texture. Multiple linear regression models gave satisfactory results for prediction of median winter concentrations in unmeasured catchments, especially for inorganic nitrogen and phosphate. In the analysis of temporal variability within catchments, internal variables from a dynamic hydrological model (HBV) were linked to concentration fluxes. It was found that phosphorus and inorganic nitrogen concentrations were elevated during flow increase at low-flow conditions, while they were diluted as the wetness in the catchment increased. During unmonitored periods regression models were successful in predicting temporal variability of total phosphorus, phosphate and inorganic nitrogen, while organic nitrogen and particulate phosphorus could not be predicted with this approach. Dividing the data into different flow categories did not improve the prediction of nutrient concentration dynamics. The results and literature review presented, confirm parts of the present HBV-N model approach and will be useful for further development of nutrient routines linked to dynamic hydrological models.

  15. A scalable algorithm for structure identification of complex gene regulatory network from temporal expression data.

    Science.gov (United States)

    Gui, Shupeng; Rice, Andrew P; Chen, Rui; Wu, Liang; Liu, Ji; Miao, Hongyu

    2017-01-31

    Gene regulatory interactions are of fundamental importance to various biological functions and processes. However, only a few previous computational studies have claimed success in revealing genome-wide regulatory landscapes from temporal gene expression data, especially for complex eukaryotes like human. Moreover, recent work suggests that these methods still suffer from the curse of dimensionality if a network size increases to 100 or higher. Here we present a novel scalable algorithm for identifying genome-wide gene regulatory network (GRN) structures, and we have verified the algorithm performances by extensive simulation studies based on the DREAM challenge benchmark data. The highlight of our method is that its superior performance does not degenerate even for a network size on the order of 10(4), and is thus readily applicable to large-scale complex networks. Such a breakthrough is achieved by considering both prior biological knowledge and multiple topological properties (i.e., sparsity and hub gene structure) of complex networks in the regularized formulation. We also validate and illustrate the application of our algorithm in practice using the time-course gene expression data from a study on human respiratory epithelial cells in response to influenza A virus (IAV) infection, as well as the CHIP-seq data from ENCODE on transcription factor (TF) and target gene interactions. An interesting finding, owing to the proposed algorithm, is that the biggest hub structures (e.g., top ten) in the GRN all center at some transcription factors in the context of epithelial cell infection by IAV. The proposed algorithm is the first scalable method for large complex network structure identification. The GRN structure identified by our algorithm could reveal possible biological links and help researchers to choose which gene functions to investigate in a biological event. The algorithm described in this article is implemented in MATLAB (Ⓡ) , and the source code is

  16. Transposable element influences on gene expression in plants.

    Science.gov (United States)

    Hirsch, Cory D; Springer, Nathan M

    2017-01-01

    Transposable elements (TEs) comprise a major portion of many plant genomes and bursts of TE movements cause novel genomic variation within species. In order to maintain proper gene function, plant genomes have evolved a variety of mechanisms to tolerate the presence of TEs within or near genes. Here, we review our understanding of the interactions between TEs and gene expression in plants by assessing three ways that transposons can influence gene expression. First, there is growing evidence that TE insertions within introns or untranslated regions of genes are often tolerated and have minimal impact on expression level or splicing. However, there are examples in which TE insertions within genes can result in aberrant or novel transcripts. Second, TEs can provide novel alternative promoters, which can lead to new expression patterns or original coding potential of an alternate transcript. Third, TE insertions near genes can influence regulation of gene expression through a variety of mechanisms. For example, TEs may provide novel cis-acting regulatory sites behaving as enhancers or insert within existing enhancers to influence transcript production. Alternatively, TEs may change chromatin modifications in regions near genes, which in turn can influence gene expression levels. Together, the interactions of genes and TEs provide abundant evidence for the role of TEs in changing basic functions within plant genomes beyond acting as latent genomic elements or as simple insertional mutagens. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Bayesian state space models for inferring and predicting temporal gene expression profiles.

    Science.gov (United States)

    Liang, Yulan; Kelemen, Arpad

    2007-12-01

    Prediction of gene dynamic behavior is a challenging and important problem in genomic research while estimating the temporal correlations and non-stationarity are the keys in this process. Unfortunately, most existing techniques used for the inclusion of the temporal correlations treat the time course as evenly distributed time intervals and use stationary models with time-invariant settings. This is an assumption that is often violated in microarray time course data since the time course expression data are at unequal time points, where the difference in sampling times varies from minutes to days. Furthermore, the unevenly spaced short time courses with sudden changes make the prediction of genetic dynamics difficult. In this paper, we develop two types of Bayesian state space models to tackle this challenge for inferring and predicting the gene expression profiles associated with diseases. In the univariate time-varying Bayesian state space models we treat both the stochastic transition matrix and the observation matrix time-variant with linear setting and point out that this can easily be extended to nonlinear setting. In the multivariate Bayesian state space model we include temporal correlation structures in the covariance matrix estimations. In both models, the unevenly spaced short time courses with unseen time points are treated as hidden state variables. Bayesian approaches with various prior and hyper-prior models with MCMC algorithms are used to estimate the model parameters and hidden variables. We apply our models to multiple tissue polygenetic affymetrix data sets. Results show that the predictions of the genomic dynamic behavior can be well captured by the proposed models. (c) 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

  18. Identification and influence of spatio-temporal outliers in urban air quality measurements.

    Science.gov (United States)

    O'Leary, Brendan; Reiners, John J; Xu, Xiaohong; Lemke, Lawrence D

    2016-12-15

    Forty eight potential outliers in air pollution measurements taken simultaneously in Detroit, Michigan, USA and Windsor, Ontario, Canada in 2008 and 2009 were identified using four independent methods: box plots, variogram clouds, difference maps, and the Local Moran's I statistic. These methods were subsequently used in combination to reduce and select a final set of 13 outliers for nitrogen dioxide (NO2), volatile organic compounds (VOCs), total benzene, toluene, ethyl benzene, and xylene (BTEX), and particulate matter in two size fractions (PM2.5 and PM10). The selected outliers were excluded from the measurement datasets and used to revise air pollution models. In addition, a set of temporally-scaled air pollution models was generated using time series measurements from community air quality monitors, with and without the selected outliers. The influence of outlier exclusion on associations with asthma exacerbation rates aggregated at a postal zone scale in both cities was evaluated. Results demonstrate that the inclusion or exclusion of outliers influences the strength of observed associations between intraurban air quality and asthma exacerbation in both cities. The box plot, variogram cloud, and difference map methods largely determined the final list of outliers, due to the high degree of conformity among their results. The Moran's I approach was not useful for outlier identification in the datasets studied. Removing outliers changed the spatial distribution of modeled concentration values and derivative exposure estimates averaged over postal zones. Overall, associations between air pollution and acute asthma exacerbation rates were weaker with outliers removed, but improved with the addition of temporal information. Decreases in statistically significant associations between air pollution and asthma resulted, in part, from smaller pollutant concentration ranges used for linear regression. Nevertheless, the practice of identifying outliers through

  19. Influence of Game Evolution and the Phase of Competition on Temporal Game Structure in High-Level Table Tennis Tournaments.

    Science.gov (United States)

    Leite, Jorge Vieira de Mello; Barbieri, Fabio Augusto; Miyagi, Willian; Malta, Elvis de Souza; Zagatto, Alessandro Moura

    2017-01-01

    The aims of this study were: a) to investigate the game temporal structure in high-level table tennis competitions; b) to verify the influence of game evolution in international competitions from 2009 to 2012 (World Table Tennis Championships and the Olympic Games) on game temporal structure; c) to compare game temporal structure according to the phase of competition. Comparisons between the three international tournaments demonstrated that rally duration decreased significantly (p game evolution and the competition phase influenced the game temporal structure of table tennis, considering longer rest periods adopted by elite athletes in relation to non-elite athletes, the reduction in rally duration and an increase in rest time over the 2009-2012 period and through the competition phases (quarterfinals to finals).

  20. Temporal-spatial variation and the influence factors of precipitation in Sichuan Province, China

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Precipitation is a key factor in the water cycle.At the same time,precipitation is the focus of study in meteorology and climatology,ecological environmental assessment,non-point source pollution and so on.Understanding the temporal-spatial variation and the corresponding factors of precipitation has become the object of hydrology and environmentology.Based on the annual precipitation data,we analyzed the spatial distribution of precipitation in Sichuan Province in China as well as the temporal-spatial variation and the corresponding influence factors involved.The results show that the amount of precipitation was abundant,but the spatial distribution was not consistent with it and the amount of precipitation gradually declined from the south-east to the north-west in Sichuan Province,China.Moreover,the spatial distribution was different throughout the years.The result of correlation analysis indicated that elevation,temperature and air pressure were three key factors affecting the amount and distribution of precipitation,and the correlation coefficients were -0.56,0.38 and 0.45 respectively.Notably,the relationship between the slope of topography and precipitation were significantly negative and the average correlation coefficient was -0.28.

  1. Influence of spatial and temporal coherences on atomic resolution high angle annular dark field imaging.

    Science.gov (United States)

    Beyer, Andreas; Belz, Jürgen; Knaub, Nikolai; Jandieri, Kakhaber; Volz, Kerstin

    2016-10-01

    Aberration-corrected (scanning) transmission electron microscopy ((S)TEM) has become a widely used technique when information on the chemical composition is sought on an atomic scale. To extract the desired information, complementary simulations of the scattering process are inevitable. Often the partial spatial and temporal coherences are neglected in the simulations, although they can have a huge influence on the high resolution images. With the example of binary gallium phosphide (GaP) we elucidate the influence of the source size and shape as well as the chromatic aberration on the high angle annular dark field (HAADF) intensity. We achieve a very good quantitative agreement between the frozen phonon simulation and experiment for different sample thicknesses when a Lorentzian source distribution is assumed and the effect of the chromatic aberration is considered. Additionally the influence of amorphous layers introduced by the preparation of the TEM samples is discussed. Taking into account these parameters, the intensity in the whole unit cell of GaP, i.e. at the positions of the different atomic columns and in the region between them, is described correctly. With the knowledge of the decisive parameters, the determination of the chemical composition of more complex, multinary materials becomes feasible.

  2. Influence of bubble size on effervescent atomization. Part 2: unsteady spatial and temporal features

    Science.gov (United States)

    Shepard, Thomas; Forliti, David; Lewis, Taylor

    2016-11-01

    In this work, high-speed images of the near-nozzle exit of an effervescent atomizer operating at low gas to liquid ratios are examined using proper orthogonal decomposition and digital image analyses. These techniques allow for the extraction of coherent spatial and temporal patterns present in the high-speed image sets. The effervescent atomizer was operated in the bubbly regime and the experimental facility allowed independent control over bubble size. The impact of varying the mean bubble size on the atomizer near exit field is presented at multiple gas to liquid flow rate ratios. The results demonstrate an influence of mean bubble diameter on peak instability frequency, instability amplitude, axial convection velocities and dominant mode structure.

  3. Influence of spatial and temporal variability of subsurface soil moisture and temperature on vapour intrusion

    Science.gov (United States)

    Bekele, Dawit N.; Naidu, Ravi; Chadalavada, Sreenivasulu

    2014-05-01

    A comprehensive field study was conducted at a site contaminated with chlorinated solvents, mainly trichloroethylene (TCE), to investigate the influence of subsurface soil moisture and temperature on vapour intrusion (VI) into built structures. Existing approaches to predict the risk of VI intrusion into buildings assume homogeneous or discrete layers in the vadose zone through which TCE migrates from an underlying source zone. In reality, the subsurface of the majority of contaminated sites will be subject to significant variations in moisture and temperature. Detailed site-specific data were measured contemporaneously to evaluate the impact of spatial and temporal variability of subsurface soil properties on VI exposure assessment. The results revealed that indoor air vapour concentrations would be affected by spatial and temporal variability of subsurface soil moisture and temperature. The monthly monitoring of soil-gas concentrations over a period of one year at a depth of 3 m across the study site demonstrated significant variation in TCE vapour concentrations, which ranged from 480 to 629,308 μg/m3. Soil-gas wells at 1 m depth exhibited high seasonal variability in TCE vapour concentrations with a coefficient of variation 1.02 in comparison with values of 0.88 and 0.74 in 2 m and 3 m wells, respectively. Contour plots of the soil-gas TCE plume during wet and dry seasons showed that the plume moved across the site, hence locations of soil-gas monitoring wells for human risk assessment is a site specific decision. Subsurface soil-gas vapour plume characterisation at the study site demonstrates that assessment for VI is greatly influenced by subsurface soil properties such as temperature and moisture that fluctuate with the seasons of the year.

  4. Single-Cell Resolution of Temporal Gene Expression during Heart Development.

    Science.gov (United States)

    DeLaughter, Daniel M; Bick, Alexander G; Wakimoto, Hiroko; McKean, David; Gorham, Joshua M; Kathiriya, Irfan S; Hinson, John T; Homsy, Jason; Gray, Jesse; Pu, William; Bruneau, Benoit G; Seidman, J G; Seidman, Christine E

    2016-11-21

    Activation of complex molecular programs in specific cell lineages governs mammalian heart development, from a primordial linear tube to a four-chamber organ. To characterize lineage-specific, spatiotemporal developmental programs, we performed single-cell RNA sequencing of >1,200 murine cells isolated at seven time points spanning embryonic day 9.5 (primordial heart tube) to postnatal day 21 (mature heart). Using unbiased transcriptional data, we classified cardiomyocytes, endothelial cells, and fibroblast-enriched cells, thus identifying markers for temporal and chamber-specific developmental programs. By harnessing these datasets, we defined developmental ages of human and mouse pluripotent stem-cell-derived cardiomyocytes and characterized lineage-specific maturation defects in hearts of mice with heterozygous mutations in Nkx2.5 that cause human heart malformations. This spatiotemporal transcriptome analysis of heart development reveals lineage-specific gene programs underlying normal cardiac development and congenital heart disease. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Spatial-Temporal Yield Trend of Oil Palm as Influenced by Nitrogen Fertilizer Management

    Directory of Open Access Journals (Sweden)

    Abdul R. Anuar

    2008-01-01

    Full Text Available One of the major challenges in oil palm (Elaeis guineensis Jacq. plantations today is proper interpretation of yield maps for site-specific management and identification and understanding of the causal factors influencing the variability of oil palm yields. A study was conducted to examine the structural yield variation in order to assess the spatial and temporal yield trends so as to interpret multi-year yield maps of oil palm as influenced by the long-term N fertilizer applications in the palm circle in fertilizer response trial in Sabah, Malaysia. Two clusters of palms were selected for the study; with and without N fertilizer applications for the past 10 years. Fresh fruit bunch (ffb yields were recorded and summarized on an annual basis. Geostatistical analysis was used to characterize the spatial structure of the semivariogram while point kriging was used to interpolate the ffb yields at unsampled locations. A classified management zone map was developed based on the spatial and temporal stability yield maps from 1992-1999. Semivariance analysis revealed that the yield variations between plots and within plots could be distinguished from the structural semivariogram. The variability between plots was relatively higher compared with within plots. The maximum range of the semivariance of both fertilizer treatments was about 6-palm distance which corresponded well to the experimental plot size of 30 (5×6 palms. It was also observed that the structure of the semivariogram was governed by the sampling pattern and the experimental plot size. The annual yield maps suggested that the application of N could sustain ffb yields above 30 t ha-1 year-1 whereas its removal could result in a drastic decline in ffb yields after 1992. Long-term N fertilizer applications reduced the annual ffb yield fluctuations to between 35 and 45% based on the coefficient of variations between years obtained from individual palms. The results further demonstrate the

  6. Multiple enhancers contribute to spatial but not temporal complexity in the expression of the proneural gene, amos

    Directory of Open Access Journals (Sweden)

    zur Lage Petra I

    2006-11-01

    Full Text Available Abstract Background The regulation of proneural gene expression is an important aspect of neurogenesis. In the study of the Drosophila proneural genes, scute and atonal, several themes have emerged that contribute to our understanding of the mechanism of neurogenesis. First, spatial complexity in proneural expression results from regulation by arrays of enhancer elements. Secondly, regulation of proneural gene expression occurs in distinct temporal phases, which tend to be under the control of separate enhancers. Thirdly, the later phase of proneural expression often relies on positive autoregulation. The control of these phases and the transition between them appear to be central to the mechanism of neurogenesis. We present the first investigation of the regulation of the proneural gene, amos. Results Amos protein expression has a complex pattern and shows temporally distinct phases, in common with previously characterised proneural genes. GFP reporter gene constructs were used to demonstrate that amos has an array of enhancer elements up- and downstream of the gene, which are required for different locations of amos expression. However, unlike other proneural genes, there is no evidence for separable enhancers for the different temporal phases of amos expression. Using mutant analysis and site-directed mutagenesis of potential Amos binding sites, we find no evidence for positive autoregulation as an important part of amos control during neurogenesis. Conclusion For amos, as for other proneural genes, a complex expression pattern results from the sum of a number of simpler sub-patterns driven by specific enhancers. There is, however, no apparent separation of enhancers for distinct temporal phases of expression, and this correlates with a lack of positive autoregulation. For scute and atonal, both these features are thought to be important in the mechanism of neurogenesis. Despite similarities in function and expression between the Drosophila

  7. When meaning matters: The temporal dynamics of semantic influences on visual attention.

    Science.gov (United States)

    de Groot, Floor; Huettig, Falk; Olivers, Christian N L

    2016-02-01

    An important question is, to what extent is visual attention driven by the semantics of individual objects, rather than by their visual appearance? This study investigates the hypothesis that timing is a crucial factor in the occurrence and strength of semantic influences on visual orienting. To assess the dynamics of such influences, the authors presented the target instruction either before or after visual stimulus onset, while eye movements were continuously recorded throughout the search. The results show a substantial but delayed bias in orienting toward semantically related objects compared with visually related objects when target instruction is presented before visual stimulus onset. However, this delay can be completely undone by presenting the visual information before the target instruction (Experiment 1). Moreover, the absence or presence of visual competition does not change the temporal dynamics of the semantic bias (Experiment 2). Visual orienting is thus driven by priority settings that dynamically shift between visual and semantic representations, with each of these types of bias operating largely independently. The findings bridge the divide between the visual attention and the psycholinguistic literature. (PsycINFO Database Record

  8. Abiotic factors influencing the spatial and temporal variability of juvenile fish in Pamlico Sound, North Carolina

    Energy Technology Data Exchange (ETDEWEB)

    Pietrafesa, L.J.; Janowitz, G.S.; Miller, J.M.; Noble, E.B.; Ross, S.W.; Epperly, S.P.

    1985-07-01

    A 3-D, time dependent model of the circulation in Pamlico Sound, NC, is used to relate the direction and magnitude of winds to the number of juvenile fish sampled at specified estuarine nursery locations. NC marine sport fishes are known to be spawned in NC continental waters, and then make transit to an through barrier island inlets, into Pamlico Sound. The juveniles then move 40-70 kilometers across the Sound to the nurseries. It is hypothesized that wind driven, pressure gradient induced and topographically steered currents, all abiotic factors, provide the transport mechanisms, during the recruitment period February-April, necessary for the transect. Moreover, the inherent variability in the atmospherically derived physical factors and the influence of topographic irregularities such as a large shoal which laterally bisects the Sound and bifurcates the bottom currents are seen as sources of the temporal and spatial variation observed in the distribution of juvenile fish, while the influence of biological processes is viewed as providing fine-tuned structuring.

  9. Temporal characteristics of the influence of punishment on perceptual decision making in the human brain.

    Science.gov (United States)

    Blank, Helen; Biele, Guido; Heekeren, Hauke R; Philiastides, Marios G

    2013-02-27

    Perceptual decision making is the process by which information from sensory systems is combined and used to influence our behavior. In addition to the sensory input, this process can be affected by other factors, such as reward and punishment for correct and incorrect responses. To investigate the temporal dynamics of how monetary punishment influences perceptual decision making in humans, we collected electroencephalography (EEG) data during a perceptual categorization task whereby the punishment level for incorrect responses was parametrically manipulated across blocks of trials. Behaviorally, we observed improved accuracy for high relative to low punishment levels. Using multivariate linear discriminant analysis of the EEG, we identified multiple punishment-induced discriminating components with spatially distinct scalp topographies. Compared with components related to sensory evidence, components discriminating punishment levels appeared later in the trial, suggesting that punishment affects primarily late postsensory, decision-related processing. Crucially, the amplitude of these punishment components across participants was predictive of the size of the behavioral improvements induced by punishment. Finally, trial-by-trial changes in prestimulus oscillatory activity in the alpha and gamma bands were good predictors of the amplitude of these components. We discuss these findings in the context of increased motivation/attention, resulting from increases in punishment, which in turn yields improved decision-related processing.

  10. A hybrid dynamic Bayesian network approach for modelling temporal associations of gene expressions for hypertension diagnosis.

    Science.gov (United States)

    Akutekwe, Arinze; Seker, Huseyin

    2014-01-01

    Computational and machine learning techniques have been applied in identifying biomarkers and constructing predictive models for diagnosis of hypertension. Strategies such as improved classification rules based on decision trees have been proposed. Other techniques such as Fuzzy Expert Systems (FES) and Neuro-Fuzzy Systems (NFS) have recently been applied. However, these methods lack the ability to detect temporal relationships among biomarker genes that will aid better understanding of the mechanism of hypertension disease. In this paper we apply a proposed two-stage bio-network construction approach that combines the power and computational efficiency of classification methods with the well-established predictive ability of Dynamic Bayesian Network. We demonstrate our method using the analysis of male young-onset hypertension microarray dataset. Four key genes were identified by the Least Angle Shrinkage and Selection Operator (LASSO) and three Support Vector Machine Recursive Feature Elimination (SVM-RFE) methods. Results show that cell regulation FOXQ1 may inhibit the expression of focusyltransferase-6 (FUT6) and that ABCG1 ATP-binding cassette sub-family G may also play inhibitory role against NR2E3 nuclear receptor sub-family 2 and CGB2 Chromatin Gonadotrophin.

  11. Temporal changes in rat liver gene expression after acute cadmium and chromium exposure.

    Directory of Open Access Journals (Sweden)

    Michael S Madejczyk

    Full Text Available U.S. Service Members and civilians are at risk of exposure to a variety of environmental health hazards throughout their normal duty activities and in industrial occupations. Metals are widely used in large quantities in a number of industrial processes and are a common environmental toxicant, which increases the possibility of being exposed at toxic levels. While metal toxicity has been widely studied, the exact mechanisms of toxicity remain unclear. In order to further elucidate these mechanisms and identify candidate biomarkers, rats were exposed via a single intraperitoneal injection to three concentrations of CdCl2 and Na(2Cr(2O(7, with livers harvested at 1, 3, or 7 days after exposure. Cd and Cr accumulated in the liver at 1 day post exposure. Cd levels remained elevated over the length of the experiment, while Cr levels declined. Metal exposures induced ROS, including hydroxyl radical (•OH, resulting in DNA strand breaks and lipid peroxidation. Interestingly, ROS and cellular damage appeared to increase with time post-exposure in both metals, despite declines in Cr levels. Differentially expressed genes were identified via microarray analysis. Both metals perturbed gene expression in pathways related to oxidative stress, metabolism, DNA damage, cell cycle, and inflammatory response. This work provides insight into the temporal effects and mechanistic pathways involved in acute metal intoxication, leading to the identification of candidate biomarkers.

  12. Temporal Changes in Rat Liver Gene Expression after Acute Cadmium and Chromium Exposure

    Science.gov (United States)

    Madejczyk, Michael S.; Baer, Christine E.; Dennis, William E.; Minarchick, Valerie C.; Leonard, Stephen S.; Jackson, David A.; Stallings, Jonathan D.; Lewis, John A.

    2015-01-01

    U.S. Service Members and civilians are at risk of exposure to a variety of environmental health hazards throughout their normal duty activities and in industrial occupations. Metals are widely used in large quantities in a number of industrial processes and are a common environmental toxicant, which increases the possibility of being exposed at toxic levels. While metal toxicity has been widely studied, the exact mechanisms of toxicity remain unclear. In order to further elucidate these mechanisms and identify candidate biomarkers, rats were exposed via a single intraperitoneal injection to three concentrations of CdCl2 and Na2Cr2O7, with livers harvested at 1, 3, or 7 days after exposure. Cd and Cr accumulated in the liver at 1 day post exposure. Cd levels remained elevated over the length of the experiment, while Cr levels declined. Metal exposures induced ROS, including hydroxyl radical (•OH), resulting in DNA strand breaks and lipid peroxidation. Interestingly, ROS and cellular damage appeared to increase with time post-exposure in both metals, despite declines in Cr levels. Differentially expressed genes were identified via microarray analysis. Both metals perturbed gene expression in pathways related to oxidative stress, metabolism, DNA damage, cell cycle, and inflammatory response. This work provides insight into the temporal effects and mechanistic pathways involved in acute metal intoxication, leading to the identification of candidate biomarkers. PMID:25993096

  13. Temporal and spatial Bean pod mottle virus-induced gene silencing in soybean.

    Science.gov (United States)

    Juvale, Parijat S; Hewezi, Tarek; Zhang, Chunquan; Kandoth, Pramod Kaitheri; Mitchum, Melissa G; Hill, John H; Whitham, Steven A; Baum, Thomas J

    2012-12-01

    Virus-induced gene silencing (VIGS) is a powerful reverse genetics tool in plant science. In this study, we investigated the temporal and spatial silencing patterns achieved by Bean pod mottle virus (BPMV)-based VIGS in soybean using virus constructs targeting green fluorescence protein (GFP). Silencing GFP enabled an in-depth analysis of silencing in soybean tissues over time in a transgenic line constitutively expressing GFP. We discovered evidence for variable GFP silencing based on insert orientation and targeted region in the coding sequence. A 3' sequence in reverse orientation produced the strongest silencing phenotypes. Furthermore, we documented that BPMV VIGS can achieve widespread silencing in a broad range of tissues, including leaves, stems, flowers and roots. Near-complete silencing was attained in leaves and flowers. Although weaker than in shoots, the observed gene silencing in soybean roots will also allow reverse genetics studies in this tissue. When GFP fluorescence was assayed in cross-sections of stems and leaf petioles, near-complete and uniform silencing was observed in all cell types. Silencing was observed from as early as 2 weeks post-virus inoculation in leaves to 7 weeks post-virus inoculation in flowers, suggesting that this system can induce and maintain silencing for significant durations.

  14. The influence of seizure frequency on anterograde and remote memory in mesial temporal lobe epilepsy.

    Science.gov (United States)

    Voltzenlogel, Virginie; Vignal, Jean-Pierre; Hirsch, Edouard; Manning, Liliann

    2014-10-01

    Seizure frequency, although considered as an important factor in memory impairment in mesial temporal epilepsy (mTLE), is mostly confounded with other clinical variables, making it unclear to what extent recurrent seizures actually interfere with memory. The present study focuses on the influence of seizure frequency, studied as a main variable, on anterograde and remote memory. Seventy-one patients with unilateral mTLE were divided into two subgroups, as a function of their seizure frequency (monthly versus weekly seizures). Other seizure-related variables were controlled, namely, lateralisation and type of lesion, age at onset, years of ongoing seizures, etiologic factors, and number of AED. A comprehensive neuropsychological examination, including anterograde memory (verbal and non verbal recognition memory and free recall) tasks together with a large range of tests exploring different domains of remote memory, was carried out. Despite similar results on IQ, executive functions and attention, the low seizure-frequency group performed significantly better than the high seizure-frequency group on anterograde memory tests. Loss of autobiographical episodes and public-events memory, concomitant with spared personal semantic knowledge, was observed in both patient groups compared with healthy subjects. A worsening effect of high seizure frequency was recorded for autobiographical incidents and news-events memory, but unexpectedly, not for memory for famous people. The study of seizure frequency as the main variable leads us to suggest that high seizure frequency, itself, potentiates the effects of mesial temporal lobe damage on episodic memory deficits. Copyright © 2014 British Epilepsy Association. Published by Elsevier Ltd. All rights reserved.

  15. Toward the influence of temporal attention on the selection of targets in a visual search task: An ERP study.

    Science.gov (United States)

    Rolke, Bettina; Festl, Freya; Seibold, Verena C

    2016-11-01

    We used ERPs to investigate whether temporal attention interacts with spatial attention and feature-based attention to enhance visual processing. We presented a visual search display containing one singleton stimulus among a set of homogenous distractors. Participants were asked to respond only to target singletons of a particular color and shape that were presented in an attended spatial position. We manipulated temporal attention by presenting a warning signal before each search display and varying the foreperiod (FP) between the warning signal and the search display in a blocked manner. We observed distinctive ERP effects of both spatial and temporal attention. The amplitudes for the N2pc, SPCN, and P3 were enhanced by spatial attention indicating a processing benefit of relevant stimulus features at the attended side. Temporal attention accelerated stimulus processing; this was indexed by an earlier onset of the N2pc component and a reduction in reaction times to targets. Most importantly, temporal attention did not interact with spatial attention or stimulus features to influence visual processing. Taken together, the results suggest that temporal attention fosters visual perceptual processing in a visual search task independently from spatial attention and feature-based attention; this provides support for the nonspecific enhancement hypothesis of temporal attention.

  16. Spatio-temporal expression patterns of Arabidopsis thaliana and Medicago truncatula defensin-like genes.

    Directory of Open Access Journals (Sweden)

    Mesfin Tesfaye

    Full Text Available Plant genomes contain several hundred defensin-like (DEFL genes that encode short cysteine-rich proteins resembling defensins, which are well known antimicrobial polypeptides. Little is known about the expression patterns or functions of many DEFLs because most were discovered recently and hence are not well represented on standard microarrays. We designed a custom Affymetrix chip consisting of probe sets for 317 and 684 DEFLs from Arabidopsis thaliana and Medicago truncatula, respectively for cataloging DEFL expression in a variety of plant organs at different developmental stages and during symbiotic and pathogenic associations. The microarray analysis provided evidence for the transcription of 71% and 90% of the DEFLs identified in Arabidopsis and Medicago, respectively, including many of the recently annotated DEFL genes that previously lacked expression information. Both model plants contain a subset of DEFLs specifically expressed in seeds or fruits. A few DEFLs, including some plant defensins, were significantly up-regulated in Arabidopsis leaves inoculated with Alternaria brassicicola or Pseudomonas syringae pathogens. Among these, some were dependent on jasmonic acid signaling or were associated with specific types of immune responses. There were notable differences in DEFL gene expression patterns between Arabidopsis and Medicago, as the majority of Arabidopsis DEFLs were expressed in inflorescences, while only a few exhibited root-enhanced expression. By contrast, Medicago DEFLs were most prominently expressed in nitrogen-fixing root nodules. Thus, our data document salient differences in DEFL temporal and spatial expression between Arabidopsis and Medicago, suggesting distinct signaling routes and distinct roles for these proteins in the two plant species.

  17. Spatio-temporal expression patterns of Arabidopsis thaliana and Medicago truncatula defensin-like genes.

    Science.gov (United States)

    Tesfaye, Mesfin; Silverstein, Kevin At; Nallu, Sumitha; Wang, Lin; Botanga, Christopher J; Gomez, S Karen; Costa, Liliana M; Harrison, Maria J; Samac, Deborah A; Glazebrook, Jane; Katagiri, Fumiaki; Gutierrez-Marcos, Jose F; Vandenbosch, Kathryn A

    2013-01-01

    Plant genomes contain several hundred defensin-like (DEFL) genes that encode short cysteine-rich proteins resembling defensins, which are well known antimicrobial polypeptides. Little is known about the expression patterns or functions of many DEFLs because most were discovered recently and hence are not well represented on standard microarrays. We designed a custom Affymetrix chip consisting of probe sets for 317 and 684 DEFLs from Arabidopsis thaliana and Medicago truncatula, respectively for cataloging DEFL expression in a variety of plant organs at different developmental stages and during symbiotic and pathogenic associations. The microarray analysis provided evidence for the transcription of 71% and 90% of the DEFLs identified in Arabidopsis and Medicago, respectively, including many of the recently annotated DEFL genes that previously lacked expression information. Both model plants contain a subset of DEFLs specifically expressed in seeds or fruits. A few DEFLs, including some plant defensins, were significantly up-regulated in Arabidopsis leaves inoculated with Alternaria brassicicola or Pseudomonas syringae pathogens. Among these, some were dependent on jasmonic acid signaling or were associated with specific types of immune responses. There were notable differences in DEFL gene expression patterns between Arabidopsis and Medicago, as the majority of Arabidopsis DEFLs were expressed in inflorescences, while only a few exhibited root-enhanced expression. By contrast, Medicago DEFLs were most prominently expressed in nitrogen-fixing root nodules. Thus, our data document salient differences in DEFL temporal and spatial expression between Arabidopsis and Medicago, suggesting distinct signaling routes and distinct roles for these proteins in the two plant species.

  18. Moving Events in Time: Time-Referent Hand-Arm Movements Influence Perceived Temporal Distance to Past Events

    Science.gov (United States)

    Blom, Stephanie S. A. H.; Semin, Gun R.

    2013-01-01

    We examine and find support for the hypothesis that time-referent hand-arm movements influence temporal judgments. In line with the concept of "left is associated with earlier times, and right is associated with later times," we show that performing left (right) hand-arm movements while thinking about a past event increases (decreases) the…

  19. Influence of Temporal Distance on the Perceived Importance of Career-Related Self-Efficacy and Outcome Expectations

    Science.gov (United States)

    Lee, Seungcheol Austin; Park, Hee Sun

    2012-01-01

    Because all career choices are about future actions, time is an important contextual variable in social cognitive career choice (Hesketh, 2000). However, there is a dearth of research examining the effect of time. The authors examined how temporal distance to career entry influences the perceived importance of self-efficacy and outcome…

  20. Temporal dynamics of Arc gene induction in hippocampus: relationship to context memory formation.

    Science.gov (United States)

    Pevzner, Aleksandr; Miyashita, Teiko; Schiffman, Aaron J; Guzowski, John F

    2012-03-01

    Past studies have proposed a role for the hippocampus in the rapid encoding of context memories. Despite this, there is little data regarding the molecular processes underlying the stable formation of a context representation that occurs in the time window established through such behavioral studies. One task that is useful for investigating the rapid encoding of context is contextual fear conditioning (CFC). Behavioral studies demonstrate that animals require approximately 30 s of exploration prior to a footshock to form a contextual representation supporting CFC. Thus, any potential molecular process required for the stabilization of the cellular representation for context must be activated within this narrow and behaviorally defined time window. Detection of the immediate-early gene Arc presents an ideal method to assess the activation of specific neuronal ensembles, given past studies showing the context specific expression of Arc in CA3 and CA1 subfields and the role of Arc in hippocampal long-term synaptic plasticity. Therefore, we examined the temporal dynamics of Arc induction within the hippocampus after brief context exposure to determine whether experience-dependent Arc expression could be involved in the rapid encoding of incidental context memories. We found that the duration of context exposure differentially activated Arc expression in hippocampal subfields, with CA3 showing rapid engagement within as little as 3 s of exposure. By contrast, Arc induction in CA1 required 30 s of context exposure to reach maximal levels. A parallel behavioral experiment revealed that 30 s, but not 3 s, exposure to a context resulted in strong conditioned freezing 24 h later, consistent with past studies from other laboratories. The current study is the first to examine the rapid temporal dynamics of Arc induction in hippocampus in a well-defined context memory paradigm. These studies demonstrate within 30 s of context exposure Arc is fully activated in CA3 and CA1

  1. Temporal Control of Cre Recombinase-mediated in Vitro DNA Recombination by Tet-on Gene Expression System

    Institute of Scientific and Technical Information of China (English)

    Zhong-Min GUO; Kang XU; Ying YUE; Bing HUANG; Xin-Yan DENG; Nü-Qi ZHONG; Xun HONG; Xi-Gu CHEN; Dong XIAO

    2005-01-01

    Conditional gene expression and gene deletion are important experimental approaches for examining the functions of particular gene products in mouse models. These strategies exploiting Cre-mediated site-specific DNA recombination have been incorporated into transgenic and gene-targeting procedures to allow in vivo manipulation of DNA in embryonic stem cells (ES cells) or living animals. The Cre/lox P system has become widely used in conditional gene targeting, conditional gene repair and activation, inducible chromosome translocation, and chromosome engineering. In this project, we have employed the universal transgenic system and the liver-specific promoter system for tightly temporal and liver-specific control of Cre gene expression in mice that (1) integrates the advantages of the Tet-on gene expression system and Cre/lox P site-mediated gene activation, and (2) simplifies the scheme of animal crosses through a combination of two control elements in a single transgene. A liver-specific apoE promoter was inserted into the promoter cloning site upstream of the rtTA cassette of pCore construct to generate the transgene construct pApoErtTAtetO-Cre, followed by demonstrating stringent regulation of doxycycline (Dox)-induced Cre-mediated recombination in the lox P-flanked transcription STOP cassette-modified BEL-7402 cells. That is to say, in the absence of Dox, the Cre gene is not expressed and will not induce site-specific recombination between two lox P sites, whereas on exposure to Dox, the Cre gene will be expressed and the recombination will occur.Together, these data indicate that the Tet-on gene expression system is able to successfully and stringently control Cre expression in vitro, which lays a solid foundation for efficient and spatio-temporal Cre gene activation in transgenic mice.

  2. A hormone receptor-based transactivator bridges different binary systems to precisely control spatial-temporal gene expression in Drosophila.

    Directory of Open Access Journals (Sweden)

    Shu-Yun Kuo

    Full Text Available The GAL4/UAS gene expression system is a precise means of targeted gene expression employed to study biological phenomena in Drosophila. A modified GAL4/UAS system can be conditionally regulated using a temporal and regional gene expression targeting (TARGET system that responds to heat shock induction. However heat shock-related temperature shifts sometimes cause unexpected physiological responses that confound behavioral analyses. We describe here the construction of a drug-inducible version of this system that takes advantage of tissue-specific GAL4 driver lines to yield either RU486-activated LexA-progesterone receptor chimeras (LexPR or β-estradiol-activated LexA-estrogen receptor chimeras (XVE. Upon induction, these chimeras bind to a LexA operator (LexAop and activate transgene expression. Using GFP expression as a marker for induction in fly brain cells, both approaches are capable of tightly and precisely modulating transgene expression in a temporal and dosage-dependent manner. Additionally, tissue-specific GAL4 drivers resulted in target gene expression that was restricted to those specific tissues. Constitutive expression of the active PKA catalytic subunit using these systems altered the sleep pattern of flies, demonstrating that both systems can regulate transgene expression that precisely mimics regulation that was previously engineered using the GeneSwitch/UAS system. Unlike the limited number of GeneSwitch drivers, this approach allows for the usage of the multitudinous, tissue-specific GAL4 lines for studying temporal gene regulation and tissue-specific gene expression. Together, these new inducible systems provide additional, highly valuable tools available to study gene function in Drosophila.

  3. The influence of pre-melting in laser drilling with temporally modulated pulse

    Science.gov (United States)

    Duan, Wenqiang; Wang, Kedian; Dong, Xia; Mei, Xuesong; Wang, Wenjun; Fan, Zhengjie; Lv, Jing

    2016-05-01

    Laser drilling by temporally modulated pulse is a promising technique and has many advantages compared with normal pulse drilling. In this work, the effect of modulated pulse comprising pre-heating front and sharp trail was mainly studied. The function of the former was to pre-melt the radiated material, and the latter was to expel the liquid melt from the molten pool, thus to form a blind hole. While the trail subpulse was kept constant, the difference in the pre-heating subpulse parameter could cause a considerable influence on the hole quality and drilling efficiency. The depth and volume of the molten pool were proportional to the pre-heating energy, and inversely proportional to the pre-heating duration. With pre-heating subpulses of proper parameters, the sharp trail subpulse was very effective in expelling the melt liquid, leaving only a small quantity of melt to re-solidify as the recast layer, which was observably thinner compared with the holes drilled using the normal pulse mode. In the pre-melting process, the directional melt flow and heat conduction were found to be the reasons why the deep melting phenomenon had occurred.

  4. Temporal expression of wound healing-related genes in skin burn injury.

    Science.gov (United States)

    Kubo, Hidemichi; Hayashi, Takahito; Ago, Kazutoshi; Ago, Mihoko; Kanekura, Takuro; Ogata, Mamoru

    2014-01-01

    Determination of the age of burns, as well as of wounds induced mechanically, is essential in forensic practice, particularly in cases of suspected child abuse. Here, we investigated temporal changes in the expression of 13 genes during wound healing after a burn. The expression of cytokines (IL-1β, IL-6, IL-10, TNF-α, and IFN-γ), chemokines (KC, MCP-1), proliferative factors (TGF-β, VEGF), proteases (MMP-2, 9, 13) and type I collagen in murine skin was examined by real-time PCR at 3, 6, 9, and 12 h and 1, 2, 3, 5, 7, and 14 days after a burn. Based on macroscopic and histological appearance, the healing process of a burn consists of 3 phases: inflammatory (from 3 h to 1 day after the burn), proliferative (from 1 to 7 days), and maturation (from 7 to 14 days). Expression of IL-1β, IL-6, TNF-α, IFN-γ and KC increased significantly in a biphasic pattern from 3 or 6 h to 12 h or 1 day and from 3 or 5 days to 7 days. Expression of MCP-1 increased significantly from 6 h to 5 days. Expression of both IL-10 and TGF-β increased significantly from 12 h to 7 days. Expression of VEGF, MMP-2, MMP-13 and type I collagen increased significantly from 3 days to 7 or 14 days. Expression of MMP-9 increased significantly from 6 h to 14 days. Our results suggest that evaluating the expression of a combination of these genes would enable the exact estimation of the age of a burn.

  5. Network Analysis of Human Genes Influencing Susceptibility to Mycobacterial Infections.

    Directory of Open Access Journals (Sweden)

    Ettie M Lipner

    Full Text Available Tuberculosis and nontuberculous mycobacterial infections constitute a high burden of pulmonary disease in humans, resulting in over 1.5 million deaths per year. Building on the premise that genetic factors influence the instance, progression, and defense of infectious disease, we undertook a systems biology approach to investigate relationships among genetic factors that may play a role in increased susceptibility or control of mycobacterial infections. We combined literature and database mining with network analysis and pathway enrichment analysis to examine genes, pathways, and networks, involved in the human response to Mycobacterium tuberculosis and nontuberculous mycobacterial infections. This approach allowed us to examine functional relationships among reported genes, and to identify novel genes and enriched pathways that may play a role in mycobacterial susceptibility or control. Our findings suggest that the primary pathways and genes influencing mycobacterial infection control involve an interplay between innate and adaptive immune proteins and pathways. Signaling pathways involved in autoimmune disease were significantly enriched as revealed in our networks. Mycobacterial disease susceptibility networks were also examined within the context of gene-chemical relationships, in order to identify putative drugs and nutrients with potential beneficial immunomodulatory or anti-mycobacterial effects.

  6. The Caenorhabditis elegans PcG-like gene sop-2 regulates the temporal and sexual specificities of cell fates.

    Science.gov (United States)

    Cai, Qingchun; Sun, Yinyan; Huang, Xinxin; Guo, Cong; Zhang, Yuxia; Zhu, Zuoyan; Zhang, Hong

    2008-03-01

    How spatial, temporal, and sexual specific cues are integrated to specify distinct cell fates during multicellular organism development is largely unknown. Here we demonstrate that the Caenorhabditis elegans PcG-like gene sop-2 determines the temporal and sexual specificities of a row of hypodermal seam cells, in addition to specifying their positional identities. Loss-of-function of sop-2 causes premature expression of adult fates at larval stages. sop-2 acts upstream of lin-29 in the heterochronic pathway and genetically interacts with other heterochronic genes in specifying the temporal fates of seam cells at different larval stages. We show that the number of ALG-1-containing P bodies is increased in seam cells in sop-2 mutants. Furthermore, the microRNA-mediated repression of a heterochronic gene reporter is enhanced in sop-2 mutants. Mutations in sop-2 also cause partial hermaphrodite-to-male sexual transformations. The homeotic transformations, heterochronic defects, and sexual transformations can occur concomitantly in sop-2 mutants. In summary, our studies reveal that sop-2 integrates spatial, temporal, and sexual cues during C. elegans development.

  7. Genes implicated in stem cell identity and temporal programme are directly targeted by Notch in neuroblast tumours.

    Science.gov (United States)

    Zacharioudaki, Evanthia; Housden, Benjamin E; Garinis, George; Stojnic, Robert; Delidakis, Christos; Bray, Sarah J

    2016-01-15

    Notch signalling is involved in a multitude of developmental decisions and its aberrant activation is linked to many diseases, including cancers. One example is the neural stem cell tumours that arise from constitutive Notch activity in Drosophila neuroblasts. To investigate how hyperactivation of Notch in larval neuroblasts leads to tumours, we combined results from profiling the upregulated mRNAs and mapping the regions bound by the core Notch pathway transcription factor Su(H). This identified 246 putative direct Notch targets. These genes were highly enriched for transcription factors and overlapped significantly with a previously identified regulatory programme dependent on the proneural transcription factor Asense. Included were genes associated with the neuroblast maintenance and self-renewal programme that we validated as Notch regulated in vivo. Another group were the so-called temporal transcription factors, which have been implicated in neuroblast maturation. Normally expressed in specific time windows, several temporal transcription factors were ectopically expressed in the stem cell tumours, suggesting that Notch had reprogrammed their normal temporal regulation. Indeed, the Notch-induced hyperplasia was reduced by mutations affecting two of the temporal factors, which, conversely, were sufficient to induce mild hyperplasia on their own. Altogether, the results suggest that Notch induces neuroblast tumours by directly promoting the expression of genes that contribute to stem cell identity and by reprogramming the expression of factors that could regulate maturity.

  8. Subthreshold K+ Channel Dynamics Interact With Stimulus Spectrum to Influence Temporal Coding in an Auditory Brain Stem Model

    Science.gov (United States)

    Day, Mitchell L.; Doiron, Brent; Rinzel, John

    2013-01-01

    Neurons in the auditory brain stem encode signals with exceptional temporal precision. A low-threshold potassium current, IKLT, present in many auditory brain stem structures and thought to enhance temporal encoding, facilitates spike selection of rapid input current transients through an associated dynamic gate. Whether the dynamic nature of IKLT interacts with the timescales in spectrally rich input to influence spike encoding remains unclear. We examine the general influence of IKLT on spike encoding of stochastic stimuli using a pattern classification analysis between spike responses from a ventral cochlear nucleus (VCN) model containing IKLT, and the same model with the dynamics removed. The influence of IKLT on spike encoding depended on the spectral content of the current stimulus such that maximal IKLT influence occurred for stimuli with power concentrated at frequencies low enough (<500 Hz) to allow IKLT activation. Further, broadband stimuli significantly decreased the influence of IKLT on spike encoding, suggesting that broadband stimuli are not well suited for investigating the influence of some dynamic membrane nonlinearities. Finally, pattern classification on spike responses was performed for physiologically realistic conductance stimuli created from various sounds filtered through an auditory nerve (AN) model. Regardless of the sound, the synaptic input arriving at VCN had similar low-pass power spectra, which led to a large influence of IKLT on spike encoding, suggesting that the subthreshold dynamics of IKLT plays a significant role in shaping the response of real auditory brain stem neurons. PMID:18057115

  9. Identification of Embryoid-Abundant Genes That Are Temporally Expressed during Pollen Embryogenesis in Wheat Anther Cultures.

    Science.gov (United States)

    Reynolds, T L; Kitto, S L

    1992-12-01

    Uninucleate microspores in anther cultures of bread wheat (Triticum aestivum cv Pavon) are capable of producing haploid pollen embryoids and plants. To gain an understanding of this alternate pathway of pollen development, we constructed a cDNA library to young pollen embryoids, isolated embryoid-specific genes, and analyzed their expression patterns during morphogenesis. Two embryoid-abundant clones, pEMB4 and 94, were expressed very early during culture, suggesting that these genes are associated with development and are not simply expressed as a consequence of differentiation. The accumulation patterns of five cloned mRNAs may indicate the activation of specific genes associated with the major morphological and physiological activities connected with the differentiation of embryoids in vitro. These results suggest that embryoid-abundant gene expression is causally related to this pathway because gene expression is spatially and temporally specific and is not observed when microspores are cultured under noninductive conditions.

  10. Variation within the Huntington's disease gene influences normal brain structure.

    Directory of Open Access Journals (Sweden)

    Mark Mühlau

    Full Text Available Genetics of the variability of normal and diseased brain structure largely remains to be elucidated. Expansions of certain trinucleotide repeats cause neurodegenerative disorders of which Huntington's disease constitutes the most common example. Here, we test the hypothesis that variation within the IT15 gene on chromosome 4, whose expansion causes Huntington's disease, influences normal human brain structure. In 278 normal subjects, we determined CAG repeat length within the IT15 gene on chromosome 4 and analyzed high-resolution T1-weighted magnetic resonance images by the use of voxel-based morphometry. We found an increase of GM with increasing long CAG repeat and its interaction with age within the pallidum, which is involved in Huntington's disease. Our study demonstrates that a certain trinucleotide repeat influences normal brain structure in humans. This result may have important implications for the understanding of both the healthy and diseased brain.

  11. An approximation to the temporal order in endogenous circadian rhythms of genes implicated in human adipose tissue metabolism.

    Science.gov (United States)

    Garaulet, Marta; Ordovás, José M; Gómez-Abellán, Purificación; Martínez, Jose A; Madrid, Juan A

    2011-08-01

    Although it is well established that human adipose tissue (AT) shows circadian rhythmicity, published studies have been discussed as if tissues or systems showed only one or few circadian rhythms at a time. To provide an overall view of the internal temporal order of circadian rhythms in human AT including genes implicated in metabolic processes such as energy intake and expenditure, insulin resistance, adipocyte differentiation, dyslipidemia, and body fat distribution. Visceral and subcutaneous abdominal AT biopsies (n=6) were obtained from morbid obese women (BMI≥40 kg/m(2) ). To investigate rhythmic expression pattern, AT explants were cultured during 24-h and gene expression was analyzed at the following times: 08:00, 14:00, 20:00, 02:00 h using quantitative real-time PCR. Clock genes, glucocorticoid metabolism-related genes, leptin, adiponectin and their receptors were studied. Significant differences were found both in achrophases and relative-amplitude among genes (P30%). When interpreting the phase map of gene expression in both depots, data indicated that circadian rhythmicity of the genes studied followed a predictable physiological pattern, particularly for subcutaneous AT. Interesting are the relationships between adiponectin, leptin, and glucocorticoid metabolism-related genes circadian profiles. Their metabolic significance is discussed. Visceral AT behaved in a different way than subcutaneous for most of the genes studied. For every gene, protein mRNA levels fluctuated during the day in synchrony with its receptors. We have provided an overall view of the internal temporal order of circadian rhythms in human adipose tissue.

  12. The absence of the CD163 receptor has distinct temporal influences on intracerebral hemorrhage outcomes.

    Science.gov (United States)

    Leclerc, Jenna L; Lampert, Andrew S; Loyola Amador, Claudia; Schlakman, Brandon; Vasilopoulos, Terrie; Svendsen, Pia; Moestrup, Søren K; Doré, Sylvain

    2017-01-01

    Hemoglobin (Hb) toxicity precipitates secondary brain damage following intracerebral hemorrhage (ICH). CD163 is an anti-inflammatory Hb scavenger receptor and CD163-positive macrophages/microglia locally accumulate post-bleed, yet no studies have investigated the role of CD163 after ICH. ICH was induced in wildtype and CD163(-/-) mice and various anatomical and functional outcomes were assessed. At 3 d, CD163(-/-) mice have 43.4 ± 5.0% (p = 0.0002) and 34.8 ± 3.4% (p = 0.0003) less hematoma volume and tissue injury, respectively. Whereas, at 10 d, CD163(-/-) mice have 49.2 ± 15.0% larger lesions (p = 0.0385). An inflection point was identified, where CD163(-/-) mice perform better on neurobehavioral testing and have less mortality before 4 d, but increased mortality and worse function after 4 d (p = 0.0389). At 3 d, CD163(-/-) mice have less Hb, iron, and blood-brain barrier dysfunction, increased astrogliosis and neovascularization, and no change in heme oxygenase 1 (HO1) expression. At 10 d, CD163(-/-) mice have increased iron and VEGF immunoreactivity, but no significant change in HO1 or astrogliosis. These novel findings reveal that CD163 deficiency has distinct temporal influences following ICH, with early beneficial properties but delayed injurious effects. While it is unclear why CD163 deficiency is initially beneficial, the late injurious effects are consistent with the key anti-inflammatory role of CD163 in the recovery phase of tissue damage.

  13. Influence of temporal pressure on anticipatory postural control of medio-lateral stability during rapid leg flexion.

    Science.gov (United States)

    Yiou, E; Hussein, T; Larue, J

    2012-03-01

    During leg flexion from erect posture, postural stability along the medio-lateral direction is organized in advance during "anticipatory postural adjustments" (APAs). This study aimed to investigate the influence of temporal pressure on this anticipatory postural control of medio-lateral stability. Eight young healthy participants performed series of leg flexions (1) as soon as possible in response to an acoustic signal (reaction-time condition; condition with temporal pressure) and (2) in a self-initiated condition (no temporal pressure). Results showed that APAs duration was shorter in the reaction-time condition as compared to the self-initiated condition; this shortening was compensated by an increase in the medio-lateral center-of-pressure displacement so that the dynamic stability reached at foot-off, as measured by the "extrapolated center-of-mass", remained unchanged. It is concluded that when a complex task is performed under temporal pressure, the central nervous system is able to modulate the spatio-temporal features of APAs in a way to both hasten the initiation of the voluntary movement and maintain optimal conditions of dynamic stability. In other words, it seems that the central nervous system does not "trade off optimal stability for speed of movement initiation under reaction-time condition", as it had been proposed in the literature.

  14. Influence of Game Evolution and the Phase of Competition on Temporal Game Structure in High-Level Table Tennis Tournaments

    Directory of Open Access Journals (Sweden)

    Leite Jorge Vieira de Mello

    2017-01-01

    Full Text Available The aims of this study were: a to investigate the game temporal structure in high-level table tennis competitions; b to verify the influence of game evolution in international competitions from 2009 to 2012 (World Table Tennis Championships and the Olympic Games on game temporal structure; c to compare game temporal structure according to the phase of competition. Comparisons between the three international tournaments demonstrated that rally duration decreased significantly (p < 0.05 during the analyzed period (2009-2012, while the rest time increased (p < 0.05 from 2009 to 2011, but decreased (p < 0.05 from 2011 to 2012. In the competition phase analysis, it was found that rally duration decreased (p < 0.05 in the quarterfinals in relation to the semifinals and finals, while the rest time increased (p < 0.05 from the quarterfinals to semifinals and finals. Based on our findings and previous literature, we concluded that the performance level, game evolution and the competition phase influenced the game temporal structure of table tennis, considering longer rest periods adopted by elite athletes in relation to non-elite athletes, the reduction in rally duration and an increase in rest time over the 2009-2012 period and through the competition phases (quarterfinals to finals.

  15. Hybridizing Daphnia communities from ten neighbouring lakes: spatio-temporal dynamics, local processes, gene flow and invasiveness.

    Science.gov (United States)

    Yin, Mingbo; Gießler, Sabine; Griebel, Johanna; Wolinska, Justyna

    2014-04-12

    In natural communities of cyclical parthenogens, rapid response to environmental change is enabled by switching between two reproduction modes. While long periods of asexual reproduction allow some clones to outcompete others, and may result in "clonal erosion", sexual reproduction restores genetic variation in such systems. Moreover, sexual reproduction may result in the formation of interspecific hybrids. These hybrids can then reach high abundances, through asexual clonal reproduction. In the present study, we explored genetic variation in water fleas of the genus Daphnia. The focus was on the short-term dynamics within several clonal assemblages from the hybridizing Daphnia longispina complex and the impact of gene flow at small spatial scales. Daphnia individuals belonged either to the parental species D. galeata and D. longispina, or to different hybrid classes, as identified by 15 microsatellite markers. The distribution and genotypic structure of parental species, but not hybrids, corresponded well with the geographical positions of the lakes. Within parental species, the genetic distance among populations of D. galeata was lower than among populations of D. longispina. Moreover, D. galeata dominance was associated with higher phosphorous load. Finally, there was no evidence for clonal erosion. Our results suggest that the contemporary structure of hybridizing Daphnia communities from ten nearby lakes is influenced by colonization events from neighbouring habitats as well as by environmental factors. Unlike the parental species, however, there was little evidence for successful dispersal of hybrids, which seem to be produced locally. Finally, in contrast to temporary Daphnia populations, in which a decrease in clonal diversity was sometimes detectable over a single growing season, the high clonal diversity and lack of clonal erosion observed here might result from repeated hatching of sexually produced offspring. Overall, our study provides insights into

  16. A comparative analysis of green fluorescent protein and -glucuronidase protein-encoding genes as a reporter system for studying the temporal expression profiles of promoters

    Indian Academy of Sciences (India)

    P Kavita; Pradeep Kumar Burma

    2008-09-01

    The assessment of activity of promoters has been greatly facilitated by the use of reporter genes. However, the activity as assessed by reporter gene is a reflection of not only promoter strength, but also that of the stability of the mRNA and the protein encoded by the reporter gene. While a stable reporter gene product is an advantage in analysing activities of weak promoters, it becomes a major limitation for understanding temporal expression patterns of a promoter, as the reporter product persists even after the activity of the promoter ceases. In the present study we undertook a comparative analysis of two reporter genes, -glucuronidase (gus) and green fluorescent protein (sgfp), for studying the temporal expression pattern of tapetum-specific promoters A9 (Arabidopsis thaliana) and TA29 (Nicotiana tabacum). The activity of A9 and TA29 promoters as assessed by transcript profiles of the reporter genes (gus or sgfp) remained the same irrespective of the reporter gene used. However, while the deduced promoter activity using gus was extended temporally beyond the actual activity of the promoter, sgfp as recorded through its fluorescence correlated better with the transcription profile. Our results thus demonstrate that sgfp is a better reporter gene compared to gus for assessment of temporal activity of promoters. Although several earlier reports have commented on the possible errors in deducing temporal activities of promoters using GUS as a reporter protein, we experimentally demonstrate the advantage of using reporter genes such as gfp for analysis of temporal expression patterns.

  17. Garlic Influences Gene Expression In Vivo and In Vitro.

    Science.gov (United States)

    Charron, Craig S; Dawson, Harry D; Novotny, Janet A

    2016-02-01

    There is a large body of preclinical research aimed at understanding the roles of garlic and garlic-derived preparations in the promotion of human health. Most of this research has targeted the possible functions of garlic in maintaining cardiovascular health and in preventing and treating cancer. A wide range of outcome variables has been used to investigate the bioactivity of garlic, ranging from direct measures of health status such as cholesterol concentrations, blood pressure, and changes in tumor size and number, to molecular and biochemical measures such as mRNA gene expression, protein concentration, enzyme activity, and histone acetylation status. Determination of how garlic influences mRNA gene expression has proven to be a valuable approach to elucidating the mechanisms of garlic bioactivity. Preclinical studies investigating the health benefits of garlic far outnumber human studies and have made frequent use of mRNA gene expression measurement. There is an immediate need to understand mRNA gene expression in humans as well. Although safety and ethical constraints limit the types of available human tissue, peripheral whole blood is readily accessible, and measuring mRNA gene expression in whole blood may provide a unique window to understanding how garlic intake affects human health.

  18. Temporal variation of diatom benthic propagules in a monsoon-influenced tropical estuary

    Digital Repository Service at National Institute of Oceanography (India)

    Patil, J.S.; Anil, A

    Temporal variations in the diatom benthic propagule (DBP) community and their role in the phytoplankton community in a monsoon-affected tropical estuary, Zuari estuary, Goa (India) are presented. The DBP from the sediments was enumerated using...

  19. Validation of suitable reference genes for expression studies in different pilocarpine-induced models of mesial temporal lobe epilepsy.

    Directory of Open Access Journals (Sweden)

    Thalita Ewellyn Batista Sales Marques

    Full Text Available It is well recognized that the reference gene in a RT-qPCR should be properly validated to ensure that gene expression is unaffected by the experimental condition. We investigated eight potential reference genes in two different pilocarpine PILO-models of mesial temporal lobe epilepsy (MTLE performing a stability expression analysis using geNorm, NormFinder and BestKepeer softwares. Then, as a validation strategy, we conducted a relative expression analysis of the Gfap gene. Our results indicate that in the systemic PILO-model Actb, Gapdh, Rplp1, Tubb2a and Polr1a mRNAs were highly stable in hippocampus of rats from all experimental and control groups, whereas Gusb revealed to be the most variable one. In fact, we observed that using Gusb for normalization, the relative mRNA levels of the Gfap gene differed from those obtained with stable genes. On the contrary, in the intrahippocampal PILO-model, all softwares included Gusb as a stable gene, whereas B2m was indicated as the worst candidate gene. The results obtained for the other reference genes were comparable to those observed for the systemic Pilo-model. The validation of these data by the analysis of the relative expression of Gfap showed that the upregulation of the Gfap gene in the hippocampus of rats sacrificed 24 hours after status epilepticus (SE was undetected only when B2m was used as the normalizer. These findings emphasize that a gene that is stable in one pathology model may not be stable in a different experimental condition related to the same pathology and therefore, the choice of reference genes depends on study design.

  20. Spatially and temporally fluctuating selection at non-MHC immune genes: evidence from TAP polymorphism in populations of brown trout ( Salmo trutta , L.)

    DEFF Research Database (Denmark)

    Jensen, L.F.; Hansen, Michael Møller; Mensberg, Karen-Lise Dons;

    2008-01-01

    Temporal samples of Danish brown trout (Salmo trutta) from populations representing varying geographical scales were analysed using eight putatively neutral microsatellite loci and two microsatellite loci embedded in TAP genes (Transporter associated with Antigen Processing). These genes encode....... Moreover, signals of divergent selection among temporal samples within localities suggest that selection also might fluctuate at a temporal scale. These results suggest that immune genes other than the classical MHC class I and II might be subject to selection and warrant further studies of functional...

  1. Influence of the NRGN gene on intellectual ability in schizophrenia.

    Science.gov (United States)

    Ohi, Kazutaka; Hashimoto, Ryota; Yasuda, Yuka; Fukumoto, Motoyuki; Yamamori, Hidenaga; Umeda-Yano, Satomi; Fujimoto, Michiko; Iwase, Masao; Kazui, Hiroaki; Takeda, Masatoshi

    2013-10-01

    Genome-wide association studies have reported an association between schizophrenia and rs12807809 of the neurogranin (NRGN) gene. We have recently found that an rs12807809-rs12278912 haplotype of the gene is associated with schizophrenia in a Japanese population and that the NRGN expression of the high-risk TG haplotype is lower than that of the protective TA haplotype in immortalized lymphoblasts. In this study, we investigated the influences of neurogranin genotypes (rs12807809 and rs12278912), haplotypes and diplotypes and genetic variant-diagnosis interactions on intellectual ability in 414 Japanese patients with schizophrenia and healthy subjects. We detected possible effects of the genome-wide screen-supported rs12807809, haplotypes, diplotypes and their genetic variant-diagnosis interactions on intellectual abilities at the threshold level of Pintelligence quotient (CG/CG: P=3.9 × 10(-13); TA/TA: P=1.1 × 10(-7)) and TA/TA diplotype on performance intelligence quotient in patients with schizophrenia (P=8.2 × 10(-8)) remained significant. The intellectual abilities of the high-risk TG/TG diplotype of the neurogranin gene were lower compared to those with the non-risk TA/TA diplotype. Our findings suggest that the genetic risk variant in the neurogranin gene may be related to reduced intellectual ability.

  2. Temporal scaling of bacterial taxa is influenced by both stochastic and deterministic ecological factors.

    Science.gov (United States)

    van der Gast, Christopher J; Ager, Duane; Lilley, Andrew K

    2008-06-01

    Microorganisms operate at a range of spatial and temporal scales acting as key drivers of ecosystem properties. Therefore, many key questions in microbial ecology require the consideration of both spatial and temporal scales. Spatial scaling, in particular the species-area relationship (SAR), has a long history in ecology and has recently been addressed in microbial ecology. However, the temporal analogue of the SAR, the species-time relationship, has received far less attention even in the science of general ecology. Here we focus upon the role of temporal scaling in microbial ecological patterns by coupling molecular characterization of bacterial communities in discrete island (bioreactor) systems with a macroecological approach. Our findings showed that the temporal scaling exponent (slope), and therefore taxa turnover of the bacterial taxa-time relationship decreased as selective pressure (industrial wastewater concentration) increased. Also, as the concentration of industrial wastewater increased across the bioreactors, we observed a gradual switch from stochastic community assembly to more deterministic (niche)-based considerations. The identification of broad-scale statistical patterns is particularly relevant to microbial ecology, as it is frequently difficult to identify individual species or their functions. In this study, we identify wide-reaching statistical patterns of diversity and show that they are shaped by the prevalent underlying ecological factors.

  3. Temporal gene expression profiling reveals CEBPD as a candidate regulator of brain disease in prosaposin deficient mice

    Directory of Open Access Journals (Sweden)

    Ran Huimin

    2008-08-01

    Full Text Available Abstract Background Prosaposin encodes, in tandem, four small acidic activator proteins (saposins with specificities for glycosphingolipid (GSL hydrolases in lysosomes. Extensive GSL storage occurs in various central nervous system regions in mammalian prosaposin deficiencies. Results Our hypomorphic prosaposin deficient mouse, PS-NA, exhibited 45% WT levels of brain saposins and showed neuropathology that included neuronal GSL storage and Purkinje cell loss. Impairment of neuronal function was observed as early as 6 wks as demonstrated by the narrow bridges tests. Temporal transcriptome microarray analyses of brain tissues were conducted with mRNA from three prosaposin deficient mouse models: PS-NA, prosaposin null (PS-/- and a V394L/V394L glucocerebrosidase mutation combined with PS-NA (4L/PS-NA. Gene expression alterations in cerebrum and cerebellum were detectable at birth preceding the neuronal deficits. Differentially expressed genes encompassed a broad spectrum of cellular functions. The number of down-regulated genes was constant, but up-regulated gene numbers increased with age. CCAAT/enhancer-binding protein delta (CEBPD was the only up-regulated transcription factor in these two brain regions of all three models. Network analyses revealed that CEBPD has functional relationships with genes in transcription, pro-inflammation, cell death, binding, myelin and transport. Conclusion These results show that: 1 Regionally specific gene expression abnormalities precede the brain histological and neuronal function changes, 2 Temporal gene expression profiles provide insights into the molecular mechanism during the GSL storage disease course, and 3 CEBPD is a candidate regulator of brain disease in prosaposin deficiency to participate in modulating disease acceleration or progression.

  4. Temporal and Tissue-Specific Expression of Tomato 14-3-3 Gene Family in Response to Phosphorus Deficiency

    Institute of Scientific and Technical Information of China (English)

    XU Wei-Feng; SHI Wei-Ming; YAN Feng

    2012-01-01

    Plants adapt to phosphorus (P) deficiency through a complex of biological processes and many genes are involved.Tomato (Solanum lycopersicum L.'Hezuo906’) plants were selected to grown hydroponically to study the temporal and spatial gene expression patterns of the 14-3-3 gene family and their roles in response to P deficiency in tomato plants.Using real-time reverse-transcriptase polymerase chain reaction (RT-PCR),we investigated the expression profiles in different tissues (root,stem and leaf) at short-term and long-term P-deficient stress phases.Results revealed that i) four members of 14-3-3 gene family (TFT1,TFT4,TFT6 and TFT7)were involved in the adaptation of tomato plants to P deficiency,ii) TFT7 responded quickly to P deficiency in the root,while TFT6 responded slowly to P deficiency in the leaf,iii) expression response of TFT4 to P-deficient stress was widely distributed in different tissues (root,stem and leaf) while TFT8 only displayed stem-specific expression,and iv) temporal and tissues-specific expression patterns to P deficiency suggested that isoform specificity existed in tomato 14-3-3 gene family.We propose that TFT7 (one member of ε-like group in tomato 14-3-3 family) is the early responsive gene and may play a role in the adaptation of tomato plants to short-term P deficiency,while TFT6 (one member of non-ε group in tomato 14-3-3 family) is the later responsive gene and may play a role in the adaptation of tomato plants to long-term P deficiency.

  5. The influence of lexical statistics on temporal lobe cortical dynamics during spoken word listening

    Science.gov (United States)

    Cibelli, Emily S.; Leonard, Matthew K.; Johnson, Keith; Chang, Edward F.

    2015-01-01

    Neural representations of words are thought to have a complex spatio-temporal cortical basis. It has been suggested that spoken word recognition is not a process of feed-forward computations from phonetic to lexical forms, but rather involves the online integration of bottom-up input with stored lexical knowledge. Using direct neural recordings from the temporal lobe, we examined cortical responses to words and pseudowords. We found that neural populations were not only sensitive to lexical status (real vs. pseudo), but also to cohort size (number of words matching the phonetic input at each time point) and cohort frequency (lexical frequency of those words). These lexical variables modulated neural activity from the posterior to anterior temporal lobe, and also dynamically as the stimuli unfolded on a millisecond time scale. Our findings indicate that word recognition is not purely modular, but relies on rapid and online integration of multiple sources of lexical knowledge. PMID:26072003

  6. Combined effect between two functional polymorphisms of SLC6A12 gene is associated with temporal lobe epilepsy

    Indian Academy of Sciences (India)

    Jingyun Li; Hua Lin; Fenghe Niu; Xilin Zhu; Ning Shen; Xin Wang; Liping Li; Aihua Liu; Xiaopan Wu; Wei Sun; Yuping Wang; Ying Liu

    2015-12-01

    Temporal lobe epilepsy (TLE) is the most common epilepsy subtype with complex genetic structure. A recent study in four populations (Ireland, UK, Australia and Finland) reported an allelic association between betaine/GABA transporter-1 (-1 or 612) and mesial temporal lobe epilepsy with hippocampal sclerosis. To demonstrate the association between 612 gene polymorphisms and TLE, TaqMan method was used to genotype five single-nucleotide polymorphisms of 612 gene in 358 TLE patients and 596 nonepileptic control subjects of Chinese Han origin. Real-time PCR was used to detect the effects of variations on gene expression associated with TLE. Though, the single-marker analysis did not demonstrate allelic association with TLE, rs542736–rs557881 interaction showed significant association. The 612 expression levels in peripheral blood mononuclear cells were significantly higher in TLE patients than in control subjects and were correlated to rs542736 G–rs557881 A haplotypes. Our preliminary results suggested combined effect of two common polymorphisms on SLC6A12 gene may be associated with TLE, but the precise mechanism needs further investigation.

  7. SuperFly: a comparative database for quantified spatio-temporal gene expression patterns in early dipteran embryos.

    Science.gov (United States)

    Cicin-Sain, Damjan; Pulido, Antonio Hermoso; Crombach, Anton; Wotton, Karl R; Jiménez-Guri, Eva; Taly, Jean-François; Roma, Guglielmo; Jaeger, Johannes

    2015-01-01

    We present SuperFly (http://superfly.crg.eu), a relational database for quantified spatio-temporal expression data of segmentation genes during early development in different species of dipteran insects (flies, midges and mosquitoes). SuperFly has a special focus on emerging non-drosophilid model systems. The database currently includes data of high spatio-temporal resolution for three species: the vinegar fly Drosophila melanogaster, the scuttle fly Megaselia abdita and the moth midge Clogmia albipunctata. At this point, SuperFly covers up to 9 genes and 16 time points per species, with a total of 1823 individual embryos. It provides an intuitive web interface, enabling the user to query and access original embryo images, quantified expression profiles, extracted positions of expression boundaries and integrated datasets, plus metadata and intermediate processing steps. SuperFly is a valuable new resource for the quantitative comparative study of gene expression patterns across dipteran species. Moreover, it provides an interesting test set for systems biologists interested in fitting mathematical gene network models to data. Both of these aspects are essential ingredients for progress toward a more quantitative and mechanistic understanding of developmental evolution.

  8. Genetic, temporal and diurnal influences on L-dopa-induced dyskinesia in the 6-OHDA model.

    Science.gov (United States)

    Monville, Christelle; Torres, Eduardo M; Pekarik, Vladimir; Lane, Emma L; Dunnett, Stephen B

    2009-03-16

    Current treatments for Parkinson's disease rely on a dopamine replacement strategy and are reasonably effective, particularly in the early stages of the disease. However, chronic dopaminergic therapy is limited by the development of a range of side effects, including the onset of abnormal movements ('dyskinesia'). The neural mechanisms that underlie dyskinesia are far from clear but they have been associated with pulsatile stimulation of dopamine receptors, downstream changes in proteins and genes, and abnormalities in non-dopamine transmitter systems. However, there has been no pathophysiological explanation for the worsening motor symptoms in the afternoon and evening reported by Parkinsonian patients in long-term L-dopa therapy, and no direct relationship has been found with the pharmacokinetics of the drug. Moreover, there continues to be a debate about whether the development of dyskinesias in patients is dependent upon the duration of L-dopa treatment or on the degree of denervation/advanced stage of the disease, both factors that are difficult to resolve experimentally in the human disease. The objective of this study was to characterise, in an animal model, factors that predispose some individuals to develop dyskinesia after a prolonged treatment with L-dopa, whereas others continue to exhibit symptom alleviation without the side effects. We report that none of the parameters studied--genetic variation within and between strains, delay of treatment onset after lesion, or time of day of the drug treatment--were found to influence directly the formation of dyskinesias after L-dopa treatment. We conclude that a complex combination of individual factors are likely to interact to regulate the onset and development of abnormal movements in some animals but not others.

  9. Exploiting the full power of temporal gene expression profiling through a new statistical test: Application to the analysis of muscular dystrophy data

    Directory of Open Access Journals (Sweden)

    Turk Rolf

    2006-04-01

    Full Text Available Abstract Background The identification of biologically interesting genes in a temporal expression profiling dataset is challenging and complicated by high levels of experimental noise. Most statistical methods used in the literature do not fully exploit the temporal ordering in the dataset and are not suited to the case where temporal profiles are measured for a number of different biological conditions. We present a statistical test that makes explicit use of the temporal order in the data by fitting polynomial functions to the temporal profile of each gene and for each biological condition. A Hotelling T2-statistic is derived to detect the genes for which the parameters of these polynomials are significantly different from each other. Results We validate the temporal Hotelling T2-test on muscular gene expression data from four mouse strains which were profiled at different ages: dystrophin-, beta-sarcoglycan and gamma-sarcoglycan deficient mice, and wild-type mice. The first three are animal models for different muscular dystrophies. Extensive biological validation shows that the method is capable of finding genes with temporal profiles significantly different across the four strains, as well as identifying potential biomarkers for each form of the disease. The added value of the temporal test compared to an identical test which does not make use of temporal ordering is demonstrated via a simulation study, and through confirmation of the expression profiles from selected genes by quantitative PCR experiments. The proposed method maximises the detection of the biologically interesting genes, whilst minimising false detections. Conclusion The temporal Hotelling T2-test is capable of finding relatively small and robust sets of genes that display different temporal profiles between the conditions of interest. The test is simple, it can be used on gene expression data generated from any experimental design and for any number of conditions, and it

  10. Polymorphisms in MIR137HG and microRNA-137-regulated genes influence gray matter structure in schizophrenia.

    Science.gov (United States)

    Wright, C; Gupta, C N; Chen, J; Patel, V; Calhoun, V D; Ehrlich, S; Wang, L; Bustillo, J R; Perrone-Bizzozero, N I; Turner, J A

    2016-02-02

    Evidence suggests that microRNA-137 (miR-137) is involved in the genetic basis of schizophrenia. Risk variants within the miR-137 host gene (MIR137HG) influence structural and functional brain-imaging measures, and miR-137 itself is predicted to regulate hundreds of genes. We evaluated the influence of a MIR137HG risk variant (rs1625579) in combination with variants in miR-137-regulated genes TCF4, PTGS2, MAPK1 and MAPK3 on gray matter concentration (GMC). These genes were selected based on our previous work assessing schizophrenia risk within possible miR-137-regulated gene sets using the same cohort of subjects. A genetic risk score (GRS) was determined based on genotypes of these four schizophrenia risk-associated genes in 221 Caucasian subjects (89 schizophrenia patients and 132 controls). The effects of the rs1625579 genotype with the GRS of miR-137-regulated genes in a three-way interaction with diagnosis on GMC patterns were assessed using a multivariate analysis. We found that schizophrenia subjects homozygous for the MIR137HG risk allele show significant decreases in occipital, parietal and temporal lobe GMC with increasing miR-137-regulated GRS, whereas those carrying the protective minor allele show significant increases in GMC with GRS. No correlations of GMC and GRS were found in control subjects. Variants within or upstream of genes regulated by miR-137 in combination with the MIR137HG risk variant may influence GMC in schizophrenia-related regions in patients. Given that the genes evaluated here are involved in protein kinase A signaling, dysregulation of this pathway through alterations in miR-137 biogenesis may underlie the gray matter loss seen in the disease.

  11. New regulatory circuit controlling spatial and temporal gene expression in the sea urchin embryo oral ectoderm GRN.

    Science.gov (United States)

    Li, Enhu; Materna, Stefan C; Davidson, Eric H

    2013-10-01

    The sea urchin oral ectoderm gene regulatory network (GRN) model has increased in complexity as additional genes are added to it, revealing its multiple spatial regulatory state domains. The formation of the oral ectoderm begins with an oral-aboral redox gradient, which is interpreted by the cis-regulatory system of the nodal gene to cause its expression on the oral side of the embryo. Nodal signaling drives cohorts of regulatory genes within the oral ectoderm and its derived subdomains. Activation of these genes occurs sequentially, spanning the entire blastula stage. During this process the stomodeal subdomain emerges inside of the oral ectoderm, and bilateral subdomains defining the lateral portions of the future ciliary band emerge adjacent to the central oral ectoderm. Here we examine two regulatory genes encoding repressors, sip1 and ets4, which selectively prevent transcription of oral ectoderm genes until their expression is cleared from the oral ectoderm as an indirect consequence of Nodal signaling. We show that the timing of transcriptional de-repression of sip1 and ets4 targets which occurs upon their clearance explains the dynamics of oral ectoderm gene expression. In addition two other repressors, the direct Nodal target not, and the feed forward Nodal target goosecoid, repress expression of regulatory genes in the central animal oral ectoderm thereby confining their expression to the lateral domains of the animal ectoderm. These results have permitted construction of an enhanced animal ectoderm GRN model highlighting the repressive interactions providing precise temporal and spatial control of regulatory gene expression. © 2013 Elsevier Inc. All rights reserved.

  12. Temporal Gene Expression Analysis and RNA Silencing of Single and Multiple Members of Gene Family in the Lone Star Tick Amblyomma americanum

    Science.gov (United States)

    Karim, Shahid

    2016-01-01

    Saliva is an integral factor in the feeding success of veterinary and medically important ticks. Therefore, the characterization of the proteins present in tick saliva is an important area of tick research. Here, we confirmed previously generated sialotranscriptome data using quantitative real-time PCR. The information obtained in this in-depth study of gene expression was used to measure the effects of metalloprotease gene silencing on tick feeding. We analyzed the temporal expression of seven housekeeping genes and 44 differentially expressed salivary molecules selected from a previously published Amblyomma americanum sialotranscriptome. Separate reference genes were selected for the salivary glands and midgut from among the seven housekeeping genes, to normalize the transcriptional expression of differentially expressed genes. The salivary gland reference gene, ubiquitin, was used to normalize the expression of 44 salivary genes. Unsurprisingly, each gene family was expressed throughout the blood meal, but the expression of specific genes differed at each time point. To further clarify the complex nature of the many proteins found in the saliva, we disrupted the translation of several members of the metalloprotease family. Intriguingly, the nucleotide sequence similarity of the reprolysin metalloprotease gene family is so homologous that a single synthesized dsRNA sequence knocked down multiple members of the family. The use of multigene knockdown yielded a more significant picture of the role of metalloproteases in tick feeding success, and changes were observed in the female engorgement weight and larval hatching success. Interestingly, the depletion of metalloprotease transcripts also reduced the total number of bacteria present in the salivary glands. These data provide insight into the expression and functions of tick salivary proteins expressed while feeding on its host. PMID:26872360

  13. Temporal Gene Expression Analysis and RNA Silencing of Single and Multiple Members of Gene Family in the Lone Star Tick Amblyomma americanum.

    Science.gov (United States)

    Bullard, Rebekah L; Williams, Jaclyn; Karim, Shahid

    2016-01-01

    Saliva is an integral factor in the feeding success of veterinary and medically important ticks. Therefore, the characterization of the proteins present in tick saliva is an important area of tick research. Here, we confirmed previously generated sialotranscriptome data using quantitative real-time PCR. The information obtained in this in-depth study of gene expression was used to measure the effects of metalloprotease gene silencing on tick feeding. We analyzed the temporal expression of seven housekeeping genes and 44 differentially expressed salivary molecules selected from a previously published Amblyomma americanum sialotranscriptome. Separate reference genes were selected for the salivary glands and midgut from among the seven housekeeping genes, to normalize the transcriptional expression of differentially expressed genes. The salivary gland reference gene, ubiquitin, was used to normalize the expression of 44 salivary genes. Unsurprisingly, each gene family was expressed throughout the blood meal, but the expression of specific genes differed at each time point. To further clarify the complex nature of the many proteins found in the saliva, we disrupted the translation of several members of the metalloprotease family. Intriguingly, the nucleotide sequence similarity of the reprolysin metalloprotease gene family is so homologous that a single synthesized dsRNA sequence knocked down multiple members of the family. The use of multigene knockdown yielded a more significant picture of the role of metalloproteases in tick feeding success, and changes were observed in the female engorgement weight and larval hatching success. Interestingly, the depletion of metalloprotease transcripts also reduced the total number of bacteria present in the salivary glands. These data provide insight into the expression and functions of tick salivary proteins expressed while feeding on its host.

  14. The Influence of Temporal Resolution Power and Working Memory Capacity on Psychometric Intelligence

    Science.gov (United States)

    Troche, Stefan J.; Rammsayer, Thomas H.

    2009-01-01

    According to the temporal resolution power (TRP) hypothesis, higher TRP as reflected by better performance on psychophysical timing tasks accounts for faster speed of information processing and increased efficiency of information processing leading to better performance on tests of psychometric intelligence. An alternative explanation of…

  15. Does Mandarin spatial metaphor for time influence Chinese deaf signers’ spatio-temporal reasoning?

    NARCIS (Netherlands)

    Gu, Yan; Zheng, Yeqiu; Swerts, Marc; Gunzelmann, G.; Howes, A.; Tenbrink, T.; Davelaar, E. J.

    2017-01-01

    In Mandarin Chinese, the space-time word “前/qian” is used to express both the spatial concept of front/forward and the temporal concept of early/before (e.g., “前天/qian-tian”, literally front day, meaning the day before yesterday). This is consistent with the fact that Mandarin speakers can gesture

  16. Interactions between the spatial and temporal stimulus factors that influence multisensory integration in human performance

    Science.gov (United States)

    Stevenson, Ryan A.; Fister, Juliane Krueger; Barnett, Zachary P.; Nidiffer, Aaron R.; Wallace, Mark T.

    2012-01-01

    In natural environments, human sensory systems work in a coordinated and integrated manner to perceive and respond to external events. Previous research has shown that the spatial and temporal relationships of sensory signals are paramount in determining how information is integrated across sensory modalities, but in ecologically plausible settings, these factors are not independent. In the current study we provide a novel exploration of the impact on behavioral performance for systematic manipulations of the spatial location and temporal synchrony of a visual-auditory stimulus pair. Simple auditory and visual stimuli were presented across a range of spatial locations and stimulus onset asynchronies (SOAs), and participants performed both a spatial localization and simultaneity judgment task. Response times in localizing paired visual-auditory stimuli were slower in the periphery and at larger SOAs, but most importantly, an interaction was found between the two factors, in which the effect of SOA was greater in peripheral as opposed to central locations. Simultaneity judgments also revealed a novel interaction between space and time: individuals were more likely to judge stimuli as synchronous occurring in the periphery at large SOAs. The results of this study provide novel insights into (a) how the speed of spatial localization of an audiovisual stimulus is affected by location and temporal coincidence and the interaction between these two factors, and (b) how the location of a multisensory stimulus impacts judgments concerning the temporal relationship of the paired stimuli. These findings provide strong evidence for a complex interdependency between spatial location and temporal structure in determining the ultimate behavioral and perceptual outcome associated with a paired multisensory (i.e., visual-auditory) stimulus. PMID:22447249

  17. Green light: gross primary production influences seasonal stream N export by controlling fine-scale temporal N dynamics

    Science.gov (United States)

    Bernal, S.; Lupon, A.; Sabater, F.; Martí Roca, E.

    2015-12-01

    The contribution of in-stream processes to nitrogen (N) exports remains unclear because stream water chemistry integrates biogeochemical processes occurring at different spatial and temporal scales within upland, riparian and aquatic ecosystems. Monitoring nutrient concentrations at fine-scale temporal resolution can provide insights on in-stream N processing. Yet, the mechanisms underlying fine-scale temporal nutrient dynamics and their implications for flux budgets at catchment scale are still poorly understood. Here, we investigated patterns and controls of diel variation in stream nitrate (NO3-) concentration and the influence of these on N fluxes along a stream continuum with increasing riparian area and channel width. We tested two alternative hypotheses: that diel variation in stream NO3- concentration is driven (a) by stream metabolism, or (b) by riparian groundwater inputs. Although productivity in this stream was extremely low, patterns of diel variation in stream NO3- concentration emerged in early-spring and they were highly correlated with the daily regime of irradiance and gross primary production (GPP). In addition, diel NO3- patterns agreed with those predicted from GPP and biofilm C:N ratios, but not with diel variations predicted from changes in riparian groundwater inputs. These results point at in-stream photoautotrophic N uptake as the most likely driver of diel fluctuations in stream NO3- concentration. From a network perspective, the occurrence of diel variations in stream NO3- concentration, and thus their influence on stream N fluxes, increased along the stream continuum likely because of increases in light inputs and water temperature. This study evidences that monitoring of nutrient concentrations at fine-scale temporal resolution can provide mechanistic explanations about the relevance of in-stream and terrestrial processes on regulating stream N dynamics and their contribution to N export at catchment scale.

  18. Coordinated Regulation of Anthocyanin Biosynthesis Genes Confers Varied Phenotypic and Spatial-Temporal Anthocyanin Accumulation in Radish (Raphanus sativus L.

    Directory of Open Access Journals (Sweden)

    Everlyne M'mbone Muleke

    2017-07-01

    Full Text Available Anthocyanins are natural pigments that have important functions in plant growth and development. Radish taproots are rich in anthocyanins which confer different taproot colors and are potentially beneficial to human health. The crop differentially accumulates anthocyanin during various stages of growth, yet molecular mechanisms underlying this differential anthocyanin accumulation remains unknown. In the present study, transcriptome analysis was used to concisely identify putative genes involved in anthocyanin biosynthesis in radish. Spatial-temporal transcript expressions were then profiled in four color variant radish cultivars. From the total transcript sequences obtained through illumina sequencing, 102 assembled unigenes, and 20 candidate genes were identified to be involved in anthocyanin biosynthesis. Fifteen genomic sequences were isolated and sequenced from radish taproot. The length of these sequences was between 900 and 1,579 bp, and the unigene coverage to all of the corresponding cloned sequences was more than 93%. Gene structure analysis revealed that RsF3′H is intronless and anthocyanin biosynthesis genes (ABGs bear asymmetrical exons, except RsSAM. Anthocyanin accumulation showed a gradual increase in the leaf of the red radish and the taproot of colored cultivars during development, with a rapid increase at 30 days after sowing (DAS, and the highest content at maturity. Spatial-temporal transcriptional analysis of 14 genes revealed detectable expressions of 12 ABGs in various tissues at different growth levels. The investigation of anthocyanin accumulation and gene expression in four color variant radish cultivars, at different stages of development, indicated that total anthocyanin correlated with transcript levels of ABGs, particularly RsUFGT, RsF3H, RsANS, RsCHS3 and RsF3′H1. Our results suggest that these candidate genes play key roles in phenotypic and spatial-temporal anthocyanin accumulation in radish through

  19. Spatio-Temporal Expression Pattern of Six Novel Candidate Genes in Ginsenoside Biosynthesis from Panax ginseng C.A. Meyer

    Institute of Scientific and Technical Information of China (English)

    Zhi-Yong LUO; Shui-Ping LIU; Xiang-Hui CHEN; Ying RUAN; Jian-Qing LUO; Bin WEN; Chun-Lin LIU; Wei-Xin HU

    2005-01-01

    To explore the mode of the spatio-temporal expression of six newly discovered ginsenoside biosynthesis candidate gene transcripts, both Northern blotting and semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR) were used to elucidate the mRNA expression levels of the transcripts in various tissues and organs of Panax ginseng C. A. Meyer during different growth development stages. The six gene transcripts were all differentially expressed in cultured callus, root, stem, leaf, and seed.The mRNA expression levels were significantly higher in four-year-old roots than in one-year-old roots, and results of semi-quantitative RT-PCR assays were in accordance with those of Northern blotting analyses.The results strongly suggest that all six genes were differentially expressed at root-specific developmental stages. In particular, when a quiescent early stage culture suspension of P. ginseng cells was exposed to the ginsenoside biosynthesis-promoting elicitor Aspergillus niger polysaccharide, the GBR6 gene transcript response showed time-dependent increments and was parallel with ginsenoside productivity (P < 0.01).Overexpression of the GBR6 gene is likely to play a critically important role in the biosynthesis of ginsenosides.The results of the present study provided a background for the further elucidation of the structure and physiological function of these six candidate genes.

  20. A influência das perdas auditivas sensorioneurais na ordenação temporal The influence of sensoryneural hearing loss on temporal ordering

    Directory of Open Access Journals (Sweden)

    Giselle Goulart de Oliveira Matos

    2013-01-01

    examination, basic audiological testing and hearing process screening with the Dichotic Digit Test. After this process, the participants were allocated into three groups, namely: G1 (normal hearing for the averages of 0.5 / 1 / 2 and 3/4/6 KHz, G2 (mild hearing loss in at least one of the averages and G3 (moderate loss in at least one of the averages. The results were analyzed through comparison between normal hearing and the presence of hearing loss (G2 + G3 and among the three groups described. The normality index used was 70% of successes. For statistical analysis, the tests used were Nonparametric Mann-Whitney, Kruskal-Wallis ANOVA, "One-way" Analysis of Variance, student's t and chi-square. The determining criterion of significance adopted was level 5%. RESULTS: there was a significant presence of men with hearing loss in the group. The percentage of correct answers in the overall sample was 62.3%, revealing no statistically significant difference among groups. CONCLUSION: the temporal ordering ability evaluated by the Duration Pattern Test is not influenced by mild to moderate sensoryneural hearing loss.

  1. Using the temporal self-regulation theory to examine the influence of environmental cues on maintaining a healthy lifestyle.

    Science.gov (United States)

    Booker, Liesel; Mullan, Barbara

    2013-11-01

    The aim of the current study is to explore the predictive utility of the temporal self-regulation theory (TST) for maintaining a healthy lifestyle (Hall & Fong, 2007, Health Psychology Review, 1, 6). According to TST, the influence of intention, self-regulation, and behavioural prepotency differs depending on the environmental context in which the behaviour is performed. This study examined the influence of perceptions about the supportiveness of the environmental context on TST-related factors. Temporal self-regulation theory was tested using a prospective design with a 1-week follow-up. One hundred and fifty-two undergraduates were administered three executive functioning tasks and an online questionnaire regarding their intentions to maintain a healthy lifestyle, environmental responsiveness, and previous behaviour. One week later, they completed a follow-up questionnaire. Participants who were supported by the environment were significantly more likely to maintain a healthy lifestyle than those distracted by the environment. Behavioural prepotency was significantly predictive of behaviour performance for 'supported' participants. Behavioural prepotency, planning, and response inhibition were significantly predictive of 'unsupported' participants' behaviour. These findings provided preliminary support for the use of TST for the prediction of healthy lifestyle behaviour. Importantly, this study provided support for the contention that the influence of TST-related factors would vary according to the perceived supportiveness of the environment. These findings suggest that environmental responsiveness may be an important determinant to close the intention-behaviour gap for maintaining a healthy lifestyle. © 2012 The British Psychological Society.

  2. Temporal feeding pattern may influence reproduction efficiency, the example of breeding mares.

    Science.gov (United States)

    Benhajali, Haifa; Ezzaouia, Mohammed; Lunel, Christophe; Charfi, Faouzia; Hausberger, Martine

    2013-01-01

    Discomfort in farm animals may be induced by inappropriate types or timing of food supplies. Thus, time restriction of meals and lack of roughage have been shown to be one source of emergence of oral stereotypies and abnormal behaviour in horses which have evolved to eat high-fibre diets in small amounts over long periods of time. This feeding pattern is often altered in domestic environment where horses are often fed low fibre meals that can be rapidly consumed. This study aimed at determining the effect of the temporal pattern of feeding on reproductive efficiency of breeding mares, One hundred Arab breeding mares were divided into two groups that differed only in the temporal pattern of roughage availability: only at night for the standard feeding pattern group (SFP mares), night and day for the "continuous feeding" group (CF mares). The total amount of roughage provided was the same as the CF mares received half of the hay during the day while in paddock (haynets). Mares were tested for oestrus detection by teasing with one stallion and were then examined clinically by rectal palpations and ultrasound before being mated naturally or inseminated by fresh or frozen semen. Multivariate logistic regression was used to analyse data. The treatment affected significantly the reproductive efficiency of the mares with fewer oestrus abnormalities (p = 0.0002) and more fertility (p = 0.024) in CF mares (conception rate = 81% versus 55% in SFP mares). Ensuring semi-continous feeding by providing roughage may be a way of fulfilling the basic physiological needs of the horses' digestive system, reducing stress and associated inhibitors of reproduction. To our knowledge, this study provides the first evidence of an impact of temporal feeding patterns on reproductive success in a Mammal. Temporal patterns of feeding may be a major and underestimated factor in breeding.

  3. Temporal feeding pattern may influence reproduction efficiency, the example of breeding mares.

    Directory of Open Access Journals (Sweden)

    Haifa Benhajali

    Full Text Available Discomfort in farm animals may be induced by inappropriate types or timing of food supplies. Thus, time restriction of meals and lack of roughage have been shown to be one source of emergence of oral stereotypies and abnormal behaviour in horses which have evolved to eat high-fibre diets in small amounts over long periods of time. This feeding pattern is often altered in domestic environment where horses are often fed low fibre meals that can be rapidly consumed. This study aimed at determining the effect of the temporal pattern of feeding on reproductive efficiency of breeding mares, One hundred Arab breeding mares were divided into two groups that differed only in the temporal pattern of roughage availability: only at night for the standard feeding pattern group (SFP mares, night and day for the "continuous feeding" group (CF mares. The total amount of roughage provided was the same as the CF mares received half of the hay during the day while in paddock (haynets. Mares were tested for oestrus detection by teasing with one stallion and were then examined clinically by rectal palpations and ultrasound before being mated naturally or inseminated by fresh or frozen semen. Multivariate logistic regression was used to analyse data. The treatment affected significantly the reproductive efficiency of the mares with fewer oestrus abnormalities (p = 0.0002 and more fertility (p = 0.024 in CF mares (conception rate = 81% versus 55% in SFP mares. Ensuring semi-continous feeding by providing roughage may be a way of fulfilling the basic physiological needs of the horses' digestive system, reducing stress and associated inhibitors of reproduction. To our knowledge, this study provides the first evidence of an impact of temporal feeding patterns on reproductive success in a Mammal. Temporal patterns of feeding may be a major and underestimated factor in breeding.

  4. Temporal gene expression profile after acute electroconvulsive stimulation in the rat.

    Science.gov (United States)

    Dyrvig, Mads; Christiansen, Søren H; Woldbye, David P D; Lichota, Jacek

    2014-04-10

    Electroconvulsive therapy (ECT) remains one of the most effective treatments of major depression. It has been suggested that the mechanisms of action involve gene expression. In recent decades there have been several investigations of gene expression following both acute and chronic electroconvulsive stimulation (ECS). These studies have focused on several distinct gene targets but have generally included only few time points after ECS for measuring gene expression. Here we measured gene expression of three types of genes: Immediate early genes, synaptic proteins, and neuropeptides at six time points following an acute ECS. We find significant increases for c-Fos, Egr1, Neuritin 1 (Nrn 1), Bdnf, Snap29, Synaptotagmin III (Syt 3), Synapsin I (Syn 1), and Psd95 at differing time points after ECS. For some genes these changes are prolonged whereas for others they are transient. Npy expression significantly increases whereas the gene expression of its receptors Npy1r, Npy2r, and Npy5r initially decreases. These decreases are followed by a significant increase for Npy2r, suggesting anticonvulsive adaptations following seizures. In summary, we find distinct changes in mRNA quantities that are characteristic for each gene. Considering the observed transitory and inverse changes in expression patterns, these data underline the importance of conducting measurements at several time points post-ECS.

  5. RNA splicing regulates the temporal order of TNF-induced gene expression.

    Science.gov (United States)

    Hao, Shengli; Baltimore, David

    2013-07-16

    When cells are induced to express inflammatory genes by treatment with TNF, the mRNAs for the induced genes appear in three distinct waves, defining gene groups I, II, and III, or early, intermediate, and late genes. To examine the basis for these different kinetic classes, we have developed a PCR-based procedure to distinguish pre-mRNAs from mRNAs. It shows that the three groups initiate transcription virtually simultaneously but that delays in splicing characterize groups II and III. We also examined the elongation times, concluding that pre-mRNA synthesis is coordinate but splicing differences directly regulate the timing of mRNA production.

  6. Two-Component Signal Transduction Systems That Regulate the Temporal and Spatial Expression of Myxococcus xanthus Sporulation Genes.

    Science.gov (United States)

    Sarwar, Zaara; Garza, Anthony G

    2015-09-14

    When starved for nutrients, Myxococcus xanthus produces a biofilm that contains a mat of rod-shaped cells, known as peripheral rods, and aerial structures called fruiting bodies, which house thousands of dormant and stress-resistant spherical spores. Because rod-shaped cells differentiate into spherical, stress-resistant spores and spore differentiation occurs only in nascent fruiting bodies, many genes and multiple levels of regulation are required. Over the past 2 decades, many regulators of the temporal and spatial expression of M. xanthus sporulation genes have been uncovered. Of these sporulation gene regulators, two-component signal transduction circuits, which typically contain a histidine kinase sensor protein and a transcriptional regulator known as response regulator, are among the best characterized. In this review, we discuss prototypical two-component systems (Nla6S/Nla6 and Nla28S/Nla28) that regulate an early, preaggregation phase of sporulation gene expression during fruiting body development. We also discuss orphan response regulators (ActB and FruA) that regulate a later phase of sporulation gene expression, which begins during the aggregation stage of fruiting body development. In addition, we summarize the research on a complex two-component system (Esp) that is important for the spatial regulation of sporulation. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  7. Identification of Embryoid-Abundant Genes That Are Temporally Expressed during Pollen Embryogenesis in Wheat Anther Cultures 1

    Science.gov (United States)

    Reynolds, Thomas L.; Kitto, Sherry L.

    1992-01-01

    Uninucleate microspores in anther cultures of bread wheat (Triticum aestivum cv Pavon) are capable of producing haploid pollen embryoids and plants. To gain an understanding of this alternate pathway of pollen development, we constructed a cDNA library to young pollen embryoids, isolated embryoid-specific genes, and analyzed their expression patterns during morphogenesis. Two embryoid-abundant clones, pEMB4 and 94, were expressed very early during culture, suggesting that these genes are associated with development and are not simply expressed as a consequence of differentiation. The accumulation patterns of five cloned mRNAs may indicate the activation of specific genes associated with the major morphological and physiological activities connected with the differentiation of embryoids in vitro. These results suggest that embryoid-abundant gene expression is causally related to this pathway because gene expression is spatially and temporally specific and is not observed when microspores are cultured under noninductive conditions. Images Figure 1 Figure 2 Figure 3 PMID:16653192

  8. Impulsive social influence increases impulsive choices on a temporal discounting task in young adults.

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    Jodi M Gilman

    Full Text Available Adolescents and young adults who affiliate with friends who engage in impulsive behavior are more likely to engage in impulsive behaviors themselves, and those who associate with prosocial (i.e. more prudent, future oriented peers are more likely to engage in prosocial behavior. However, it is difficult to disentangle the contribution of peer influence vs. peer selection (i.e., whether individuals choose friends with similar traits when interpreting social behaviors. In this study, we combined a novel social manipulation with a well-validated delay discounting task assessing impulsive behavior to create a social influence delay discounting task, in which participants were exposed to both impulsive (smaller, sooner or SS payment and non-impulsive (larger, later or LL payment choices from their peers. Young adults in this sample, n = 51, aged 18-25 had a higher rate of SS choices after exposure to impulsive peer influence than after exposure to non-impulsive peer influence. Interestingly, in highly susceptible individuals, the rate of non-impulsive choices did not increase after exposure to non-impulsive influence. There was a positive correlation between self-reported suggestibility and degree of peer influence on SS choices. These results suggest that, in young adults, SS choices appear to be influenced by the choices of same-aged peers, especially for individuals who are highly susceptible to influence.

  9. Temporal variation of pharmaceuticals in an urban and agriculturally influenced stream

    Energy Technology Data Exchange (ETDEWEB)

    Veach, Allison M., E-mail: amveach@k-state.edu; Bernot, Melody J., E-mail: mjbernot@bsu.edu

    2011-10-01

    Pharmaceuticals have become ubiquitous in the aquatic environment. Previous studies consistently demonstrate the prevalence of pharmaceuticals in freshwater but we do not yet know how concentrations vary over time within a given system. Two sites in central Indiana with varying land use in the surrounding watershed (suburban and agricultural) were sampled monthly for pharmaceutical concentrations and stream physiochemical parameters. Sediment samples were also collected at each sampling event for measurement of {delta}{sup 15}N natural abundance and sediment organic content. Across sites and sampling events, twelve pharmaceuticals were detected including acetaminophen, caffeine, carbamazepine, cotinine, N,N-diethyl-meta-toluamide (DEET), gemfibrozil, ibuprofen, sulfadimethoxine, sulfamethazine, sulfamethoxazole, triclosan, and trimethoprim. Sulfathiazole, lincomycin, and tylosin were not detected at either site at any time. The agriculturally-influenced site had comparable pharmaceutical concentrations to the urban-influenced site. In general, pharmaceutical concentrations increased during winter at both sites and decreased during spring and summer. Multiple regression analyses indicated that water column dissolved oxygen, the number of days since precipitation, and solar radiation influenced total pharmaceutical concentration in the urban-influenced site; whereas pH, chlorophyll a concentration, and total amount of rainfall in the previous 10 days influenced total pharmaceutical concentrations in the agriculturally-influenced site. Pharmaceutical concentrations were not correlated with sediment {delta}{sup 15}N across or within sites. However, sediment in the urban-influenced site had higher mean {delta}{sup 15}N signatures relative to sediment in the agriculturally-influenced site. These data indicate pharmaceuticals are persistent in aquatic ecosystems influenced by both agricultural and suburban activity. Pharmaceuticals are designed to have a physiological

  10. How molecular competition influences fluxes in gene expression networks.

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    Dirk De Vos

    Full Text Available Often, in living cells different molecular species compete for binding to the same molecular target. Typical examples are the competition of genes for the transcription machinery or the competition of mRNAs for the translation machinery. Here we show that such systems have specific regulatory features and how they can be analysed. We derive a theory for molecular competition in parallel reaction networks. Analytical expressions for the response of network fluxes to changes in the total competitor and common target pools indicate the precise conditions for ultrasensitivity and intuitive rules for competitor strength. The calculations are based on measurable concentrations of the competitor-target complexes. We show that kinetic parameters, which are usually tedious to determine, are not required in the calculations. Given their simplicity, the obtained equations are easily applied to networks of any dimension. The new theory is illustrated for competing sigma factors in bacterial transcription and for a genome-wide network of yeast mRNAs competing for ribosomes. We conclude that molecular competition can drastically influence the network fluxes and lead to negative response coefficients and ultrasensitivity. Competitors that bind a large fraction of the target, like bacterial σ(70, tend to influence competing pathways strongly. The less a competitor is saturated by the target, the more sensitive it is to changes in the concentration of the target, as well as to other competitors. As a consequence, most of the mRNAs in yeast turn out to respond ultrasensitively to changes in ribosome concentration. Finally, applying the theory to a genome-wide dataset we observe that high and low response mRNAs exhibit distinct Gene Ontology profiles.

  11. Genetic variation in the serotonin transporter gene influences ERP old/new effects during recognition memory.

    Science.gov (United States)

    Ross, Robert S; Medrano, Paolo; Boyle, Kaitlin; Smolen, Andrew; Curran, Tim; Nyhus, Erika

    2015-11-01

    Recognition memory is defined as the ability to recognize a previously encountered stimulus and has been associated with spatially and temporally distinct event-related potentials (ERPs). Allelic variations of the serotonin transporter gene (SLC6A4) have recently been shown to impact memory performance. Common variants of the serotonin transporter-linked polymorphic region (5HTTLPR) of the SLC6A4 gene result in long (l) and short (s) allelic variants with carriers of the s allele having lowered transcriptional efficiency. Thus, the current study examines the effects polymorphisms of the SLC6A4 gene have on performance and ERP amplitudes commonly associated with recognition memory. Electroencephalogram (EEG), genetic, and behavioral data were collected from sixty participants as they performed an item and source memory recognition task. In both tasks, participants studied and encoded 200 words, which were then mixed with 200 new words during retrieval. Participants were monitored with EEG during the retrieval portion of each memory task. EEG electrodes were grouped into four ROIs, left anterior superior, right anterior superior, left posterior superior, and right posterior superior. ERP mean amplitudes during hits in the item and source memory task were compared to correctly recognizing new items (correct rejections). Results show that s-carriers have decreased mean hit amplitudes in both the right anterior superior ROI 1000-1500ms post stimulus during the source memory task and the left anterior superior ROI 300-500ms post stimulus during the item memory task. These results suggest that individual differences due to genetic variation of the serotonin transporter gene influences recognition memory.

  12. Remote preoperative tonic-clonic seizures do not influence outcome after surgery for temporal lobe epilepsy.

    Science.gov (United States)

    Asadi-Pooya, Ali A; Rabiei, Amin H; Gracely, Edward J; Sperling, Michael R

    2016-10-15

    Tonic-clonic seizures are associated with greater chance of seizure relapse after anterior temporal lobectomy. We investigated whether the interval between the last preoperative tonic-clonic seizure and surgery relates to seizure outcome in patients with drug-resistant mesial temporal lobe epilepsy (MTLE). In this retrospective study, patients were prospectively registered in a database from 1986 through 2014. Postsurgical outcome was categorized as seizure freedom or relapse. The relationship between surgical outcome and the interval between the last preoperative tonic-clonic seizure and surgery was investigated. One-hundred seventy-one patients were studied. Seventy nine (46.2%) patients experienced tonic-clonic seizures before surgery. Receiver operating characteristic curve of timing of the last preoperative tonic-clonic seizure was a moderate indicator to anticipate surgery failure (area under the curve: 0.657, significance; 0.016). The best cutoff that maximizes sensitivity and specificity was 27months; with a sensitivity of 0.76 and specificity of 0.60. Cox-Mantel analysis confirmed that the chance of becoming free of seizures after surgery in patients with no or remote history of preoperative tonic-clonic seizures was significantly higher compared with patients with a recent history (i.e., in 27months before surgery) (p=0.0001). The more remote the occurrence of preoperative tonic-clonic seizures, the better the postsurgical seizure outcome, with at least a two year gap being more favorable. A recent history of tonic-clonic seizures in a patient with MTLE may reflect more widespread epileptogenicity extending beyond the borders of mesial temporal structures. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Long-Term and Annual Influence of Aswan Reservoir (Egypt) on the Local Seismicity: A Spatio-Temporal Statistical Analysis

    Science.gov (United States)

    Gahalaut, Kalpna; Hassoup, Awad; Hamed, Haggag; Kundu, Bhaskar; Gahalaut, Vineet

    2016-09-01

    Earthquakes continue to occur in the Kalabsha embayment region near the Aswan reservoir for more than three decades. These earthquakes, including the 1981 mainshock (M 5.3), have been considered to be reservoir triggered and pore pressure appears to be the main factor for their occurrence. However, influence of reservoir water levels on the earthquakes of the region, which is significant in the initial period, is reported to be weakening with time. We statistically analyse the influence of the reservoir water levels on spatio-temporal distribution of the earthquakes for the period 1982-2013. We divided the seismicity of various zones in different time windows, depending upon their clustering, and employed the power spectrum and singular spectrum analysis (SSA). The influence of long-term and annual variations in the water level on the seismicity is very much apparent in SSA. In the 45 years of reservoir filling history, episodes of water levels more than 170 m, which lead to filling of the embayment region, appear to be correlated with the increase in seismicity of the Aswan region. In the power spectrum analysis, a strong annual peak is found for water level time series. However, in the earthquake time series, on an average, a moderate and weak annual period cycle is present in the initial (1982-1988) and in the later (2001-2013) period, respectively. In the intermediate period (1989-2000) when the water level was the least in the embayment area, a very weak annual cycle is present. Non-consideration of spatio-temporal variation in the seismicity leads to erroneous and misleading results of no or weaker reservoir influence in the later period. This also highlights that the time and space dependent pore pressure diffusion process is likely responsible for earthquake triggering in the Aswan region.

  14. Long-Term and Annual Influence of Aswan Reservoir (Egypt) on the Local Seismicity: A Spatio-Temporal Statistical Analysis

    Science.gov (United States)

    Gahalaut, Kalpna; Hassoup, Awad; Hamed, Haggag; Kundu, Bhaskar; Gahalaut, Vineet

    2017-01-01

    Earthquakes continue to occur in the Kalabsha embayment region near the Aswan reservoir for more than three decades. These earthquakes, including the 1981 mainshock (M 5.3), have been considered to be reservoir triggered and pore pressure appears to be the main factor for their occurrence. However, influence of reservoir water levels on the earthquakes of the region, which is significant in the initial period, is reported to be weakening with time. We statistically analyse the influence of the reservoir water levels on spatio-temporal distribution of the earthquakes for the period 1982-2013. We divided the seismicity of various zones in different time windows, depending upon their clustering, and employed the power spectrum and singular spectrum analysis (SSA). The influence of long-term and annual variations in the water level on the seismicity is very much apparent in SSA. In the 45 years of reservoir filling history, episodes of water levels more than 170 m, which lead to filling of the embayment region, appear to be correlated with the increase in seismicity of the Aswan region. In the power spectrum analysis, a strong annual peak is found for water level time series. However, in the earthquake time series, on an average, a moderate and weak annual period cycle is present in the initial (1982-1988) and in the later (2001-2013) period, respectively. In the intermediate period (1989-2000) when the water level was the least in the embayment area, a very weak annual cycle is present. Non-consideration of spatio-temporal variation in the seismicity leads to erroneous and misleading results of no or weaker reservoir influence in the later period. This also highlights that the time and space dependent pore pressure diffusion process is likely responsible for earthquake triggering in the Aswan region.

  15. Effect of pregabalin on apoptotic regulatory genes in hippocampus of rats with chronic temporal lobe epilepsy

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    ZHANG Yi-dan

    2012-04-01

    Full Text Available Objective To observe the effect of pregabalin on the expression of Bcl-2 and Bax in hippocampus of chronic epileptic rats induced by pilocarpine, to explore the anti-epileptic pharmacology mechanism of pregabalin, and its anti-apoptotic effect on hippocampal neurons of rats. Methods The model of chronic temporal lobe epileptic rats induced by lithium-pilocarpine was established, then the rats in pregabalin treatment group received intraperitoneal injection of pregabalin (40 mg/kg once daily for three weeks. The expression of Bcl-2 and Bax in hippocampus of all rats was detected by immunohistochemical technique and Western blotting. Results Compared with normal saline group rats, the expression of Bcl-2 and Bax in hippocampus of rats with chronic temporal lobe epilepsy was significantly increased (P = 0.000, for all. Pregabalin can down-regulate the expression of Bax and up-regulate the expression of Bcl-2 in hippocampus of rats compared to model group rats (P = 0.000, for all. Conclusion Pregabalin may have the effects of inhibiting cell apoptosis and protecting neurons through lowing Bax level and increasing Bcl-2 level in hippocampus of chronic temporal lobe epileptic rats.

  16. Identification of temporal and region-specific myocardial gene expression patterns in response to infarction in swine.

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    Cristina Prat-Vidal

    Full Text Available Molecular mechanisms associated with pathophysiological changes in ventricular remodelling due to myocardial infarction (MI remain poorly understood. We analyzed changes in gene expression by microarray technology in porcine myocardial tissue at 1, 4, and 6 weeks post-MI.MI was induced by coronary artery ligation in 9 female pigs (30-40 kg. Animals were randomly sacrificed at 1, 4, or 6 weeks post-MI (n = 3 per group and 3 healthy animals were also included as control group. Total RNA from myocardial samples was hybridized to GeneChip® Porcine Genome Arrays. Functional analysis was obtained with the Ingenuity Pathway Analysis (IPA online tool. Validation of microarray data was performed by quantitative real-time PCR (qRT-PCR.More than 8,000 different probe sets showed altered expression in the remodelling myocardium at 1, 4, or 6 weeks post-MI. Ninety-seven percent of altered transcripts were detected in the infarct core and 255 probe sets were differentially expressed in the remote myocardium. Functional analysis revealed 28 genes de-regulated in the remote myocardial region in at least one of the three temporal analyzed stages, including genes associated with heart failure (HF, systemic sclerosis and coronary artery disease. In the infarct core tissue, eight major time-dependent gene expression patterns were recognized among 4,221 probe sets commonly altered over time. Altered gene expression of ACVR2B, BID, BMP2, BMPR1A, LMNA, NFKBIA, SMAD1, TGFB3, TNFRSF1A, and TP53 were further validated.The clustering of similar expression patterns for gene products with related function revealed molecular footprints, some of them described for the first time, which elucidate changes in biological processes at different stages after MI.

  17. A chemoprotective fish oil- and pectin-containing diet temporally alters gene expression profiles in exfoliated rat colonocytes throughout oncogenesis.

    Science.gov (United States)

    Cho, Youngmi; Kim, Hyemee; Turner, Nancy D; Mann, John C; Wei, Jiawei; Taddeo, Stella S; Davidson, Laurie A; Wang, Naisyin; Vannucci, Marina; Carroll, Raymond J; Chapkin, Robert S; Lupton, Joanne R

    2011-06-01

    We have demonstrated that fish oil- and pectin-containing (FO/P) diets protect against colon cancer compared with corn oil and cellulose (CO/C) by upregulating apoptosis and suppressing proliferation. To elucidate the mechanisms whereby FO/P diets induce apoptosis and suppress proliferation during the tumorigenic process, we analyzed the temporal gene expression profiles from exfoliated rat colonocytes. Rats consumed diets containing FO/P or CO/C and were injected with azoxymethane (AOM; 2 times, 15 mg/kg body weight, subcutaneously). Feces collected at initiation (24 h after AOM injection) and at aberrant crypt foci (ACF) (7 wk postinjection) and tumor (28 wk postinjection) stages of colon cancer were used for poly (A)+ RNA extraction. Gene expression signatures were determined using Codelink arrays. Changes in phenotypes (ACF, apoptosis, proliferation, and tumor incidence) were measured to establish the regulatory controls contributing to the chemoprotective effects of FO/P. At initiation, FO/P downregulated the expression of 3 genes involved with cell adhesion and enhanced apoptosis compared with CO/C. At the ACF stage, the expression of genes involved in cell cycle regulation was modulated by FO/P and the zone of proliferation was reduced in FO/P rats compared with CO/C rats. FO/P also increased apoptosis and the expression of genes that promote apoptosis at the tumor endpoint compared with CO/C. We conclude that the effects of chemotherapeutic diets on epithelial cell gene expression can be monitored noninvasively throughout the tumorigenic process and that a FO/P diet is chemoprotective in part due to its ability to affect expression of genes involved in apoptosis and cell cycle regulation throughout all stages of tumorigenesis.

  18. Influence of isoflurane on Immediate-Early Gene expression

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    Kristopher M Bunting

    2016-01-01

    Full Text Available Background: Anterograde amnesia is a hallmark effect of volatile anesthetics. Isoflurane is known to affect both the translation and transcription of plasticity-associated genes required for normal memory formation in many brain regions. What is not known is whether isoflurane anesthesia prevents the initiation of transcription or whether it halts transcription already in progress. We tested the hypothesis that general anesthesia with isoflurane prevents learning-induced initiation of transcription of several memory-associated immediate-early genes (IEGs correlated with amnesia; we also assessed whether it stops transcription initiated prior to anesthetic administration.Methods: Using a Tone Fear Conditioning paradigm, rats were trained to associate a tone with foot-shock. Animals received either no anesthesia, anesthesia immediately after training, or anesthesia before, during, and after training. Animals were either sacrificed after training or tested 24 hours later for memory. Using Cellular Compartment Analysis of Temporal Activity by Fluorescence in situ Hybridization (catFISH, we examined the percentage of neurons expressing the IEGs Arc/Arg3.1 and Zif268/Egr1/Ngfi-A/Krox-24 in the dorsal hippocampus, primary somatosensory cortex, and primary auditory cortex.Results: On a cellular level, isoflurane administered at high doses (general anesthesia prevented initiation of transcription, but did not stop transcription of Arc and Zif268 mRNA initiated prior to anesthesia. On a behavioral level, the same level of isoflurane anesthesia produced anterograde amnesia for fear conditioning when administered before and during training, but did not produce retrograde amnesia when administered immediately after training. Conclusions: General anesthesia with isoflurane prevents initiation of learning-related transcription but does not stop ongoing transcription of two plasticity-related IEGs, Arc and Zif268, a pattern of disruption that parallels the

  19. Temporal asymmetry in precipitation time series and its influence on flow simulations in combined sewer systems

    Science.gov (United States)

    Müller, Thomas; Schütze, Manfred; Bárdossy, András

    2017-09-01

    A property of natural processes is temporal irreversibility. However, this property cannot be reflected by most statistics used to describe precipitation time series and, consequently, is not considered in most precipitation models. In this paper, a new statistic, the asymmetry measure, is introduced and applied to precipitation enabling to detect and quantify irreversibility. It is used to analyze two different data sets of Singapore and Germany. The data of both locations show a significant asymmetry for high temporal resolutions. The asymmetry is more pronounced for Singapore where the climate is dominated by convective precipitation events. The impact of irreversibility on applications is analyzed on two different hydrological sewer system models. The results show that the effect of the irreversibility can lead to biases in combined sewer overflow statistics. This bias is in the same order as the effect that can be achieved by real time control of sewer systems. Consequently, wrong conclusion can be drawn if synthetic time series are used for sewer systems if asymmetry is present, but not considered in precipitation modeling.

  20. Differential DNA Methylation of MicroRNA Genes in Temporal Cortex from Alzheimer’s Disease Individuals

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    Darine Villela

    2016-01-01

    Full Text Available This study investigated for the first time the genomewide DNA methylation changes of noncoding RNA genes in the temporal cortex samples from individuals with Alzheimer’s disease (AD. The methylome of 10 AD individuals and 10 age-matched controls were obtained using Illumina 450 K methylation array. A total of 2,095 among the 15,258 interrogated noncoding RNA CpG sites presented differential methylation, 161 of which were associated with miRNA genes. In particular, 10 miRNA CpG sites that were found to be hypermethylated in AD compared to control brains represent transcripts that have been previously associated with the disease. This miRNA set is predicted to target 33 coding genes from the neuregulin receptor complex (ErbB signaling pathway, which is required for the neurons myelination process. For 6 of these miRNA genes (MIR9-1, MIR9-3, MIR181C, MIR124-1, MIR146B, and MIR451, the hypermethylation pattern is in agreement with previous results from literature that shows downregulation of miR-9, miR-181c, miR-124, miR-146b, and miR-451 in the AD brain. Our data implicate dysregulation of miRNA methylation as contributor to the pathogenesis of AD.

  1. Functional Brachyury binding sites establish a temporal read-out of gene expression in the Ciona notochord.

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    Lavanya Katikala

    2013-10-01

    Full Text Available The appearance of the notochord represented a milestone in Deuterostome evolution. The notochord is necessary for the development of the chordate body plan and for the formation of the vertebral column and numerous organs. It is known that the transcription factor Brachyury is required for notochord formation in all chordates, and that it controls transcription of a large number of target genes. However, studies of the structure of the cis-regulatory modules (CRMs through which this control is exerted are complicated in vertebrates by the genomic complexity and the pan-mesodermal expression territory of Brachyury. We used the ascidian Ciona, in which the single-copy Brachyury is notochord-specific and CRMs are easily identifiable, to carry out a systematic characterization of Brachyury-downstream notochord CRMs. We found that Ciona Brachyury (Ci-Bra controls most of its targets directly, through non-palindromic binding sites that function either synergistically or individually to activate early- and middle-onset genes, respectively, while late-onset target CRMs are controlled indirectly, via transcriptional intermediaries. These results illustrate how a transcriptional regulator can efficiently shape a shallow gene regulatory network into a multi-tiered transcriptional output, and provide insights into the mechanisms that establish temporal read-outs of gene expression in a fast-developing chordate embryo.

  2. Temporal Microbial Community Dynamics in Microbial Electrolysis Cells – Influence of Acetate and Propionate Concentration

    KAUST Repository

    Rao, Hari Ananda

    2017-07-20

    Microbial electrolysis cells (MECs) are widely considered as a next generation wastewater treatment system. However, fundamental insight on the temporal dynamics of microbial communities associated with MEC performance under different organic types with varied loading concentrations is still unknown, nevertheless this knowledge is essential for optimizing this technology for real-scale applications. Here, the temporal dynamics of anodic microbial communities associated with MEC performance was examined at low (0.5 g COD/L) and high (4 g COD/L) concentrations of acetate or propionate, which are important intermediates of fermentation of municipal wastewaters and sludge. The results showed that acetate-fed reactors exhibited higher performance in terms of maximum current density (I: 4.25 ± 0.23 A/m), coulombic efficiency (CE: 95 ± 8%), and substrate degradation rate (98.8 ± 1.2%) than propionate-fed reactors (I: 2.7 ± 0.28 A/m; CE: 68 ± 9.5%; substrate degradation rate: 84 ± 13%) irrespective of the concentrations tested. Despite of the repeated sampling of the anodic biofilm over time, the high-concentration reactors demonstrated lower and stable performance in terms of current density (I: 1.1 ± 0.14 to 4.2 ± 0.21 A/m), coulombic efficiency (CE: 44 ± 4.1 to 103 ± 7.2%) and substrate degradation rate (64.9 ± 6.3 to 99.7 ± 0.5%), while the low-concentration reactors produced higher and dynamic performance (I: 1.1 ± 0.12 to 4.6 ± 0.1 A/m; CE: 52 ± 2.5 to 105 ± 2.7%; substrate degradation rate: 87.2 ± 0.2 to 99.9 ± 0.06%) with the different substrates tested. Correlating reactor\\'s performance with temporal dynamics of microbial communities showed that relatively similar anodic microbial community composition but with varying relative abundances was observed in all the reactors despite differences in the substrate and concentrations tested. Particularly, Geobacter was the predominant bacteria on the anode biofilm of all MECs over time suggesting its

  3. Aging and Temporal Influences on Speech Perception in Reverberation and Noise.

    Science.gov (United States)

    Helfer, Karen S.

    The present study examined the interactions of age, temporal resolution, hearing loss, and consonant perception under realistic listening conditions. Four subject groups were employed, with N = 8 per group: young adults with normal hearing or sloping sensorineural hearing loss; and elderly individuals with minimal peripheral hearing loss or presbycusis. Copies of the CUNY Nonsense Syllable Test (NST) were re-recorded under four levels of reverberation in quiet and in +10 signal-to-noise ratio of cafeteria noise. The test stimuli were presented binaurally to the subjects via TDH-49 headphones. In addition, a diotic wideband gap detection task, using a 72 dBSPL presentation level, was used as a measure of temporal resolution. Results of the present investigation demonstrated that all other subject groups performed significantly poorer than the young, normal hearing adults. Scores decreased as the amount of distortion increased, although there was very little difference between performance in the two highest reverberation conditions. For reverberation alone, the young, hearing-impaired listeners obtained the lowest scores; for reverberation + noise, the older, hearing-impaired subjects performed poorest. Large within-group variability was noted in the size of the gap thresholds, and only the two groups of young subjects differed significantly on this task of temporal resolution. Correlation analyses demonstrated a strong inverse relation between age and performance in reverberation + noise, even when degree of hearing loss was partialed out. Pure -tone average, as well as NST scores in quiet and in noise alone were related strongly to performance in reverberation. Multiple regression analyses demonstrated that nonsense syllable perception in reverberation could be predicted from a combination of age, pure-tone thresholds, scores in quiet and noise, and gap threshold. Gap threshold was the strongest predictor variable for reverberation alone, while the NST score

  4. The influence of forest cover on landslide occurrence explored with spatio-temporal information

    Science.gov (United States)

    Schmaltz, Elmar M.; Steger, Stefan; Glade, Thomas

    2017-08-01

    Multi-temporal landslide inventories in widely forested landscapes are scarce and further studies are required to face the challenges of producing reliable inventories in woodland areas. An elaboration of valuable empirical relationships between shallow landslides and forest cover based on recent remote sensing data alone is often hampered due to constant land cover changes, differing ages of landslides within a landslide inventory and the fact that usage of different data sets for mapping might lead to various systematic mapping biases. Within this study, we attempted to overcome these difficulties in order to explore the effect of forest cover on shallow landslide occurrences. Thus, forest dynamics were examined on the basis of 9 orthophoto series from 1950s to 2015, distinguishing 3 forest classes, based on the wood type. These classes were furthermore distinguished in 12 subclasses, considering stand density and age. A multi-temporal landslide inventory was compiled for the same period based on the aerial photography, 2 airborne LiDAR imageries, 8 field surveys and archive data. We derived topographical parameters (slope, topographical positioning index and convergency index) from the digital elevation model for areal correction and accounting for topographical confounders within a logistic regression model. Empirical relationships were assessed by means of (a) areal changes of forests and logged areas, (b) spatio-temporal distribution of shallow translational landslides, (c) frequency ratios and (d) logistic regression analysis. The findings revealed that forests increased by 16.2% from 1950s to 2015. 311 landslides of 351 in total that where mapped in total could be assigned to the observed time series and were considered for our analyses. Frequency ratios and odds ratios indicated a stabilising effect of all forest classes on landslide occurrences. Odds ratios observed for the models based on aggregated data sets (3 forest classes) indicated provided

  5. Temporal network based analysis of cell specific vein graft transcriptome defines key pathways and hub genes in implantation injury.

    Directory of Open Access Journals (Sweden)

    Manoj Bhasin

    Full Text Available Vein graft failure occurs between 1 and 6 months after implantation due to obstructive intimal hyperplasia, related in part to implantation injury. The cell-specific and temporal response of the transcriptome to vein graft implantation injury was determined by transcriptional profiling of laser capture microdissected endothelial cells (EC and medial smooth muscle cells (SMC from canine vein grafts, 2 hours (H to 30 days (D following surgery. Our results demonstrate a robust genomic response beginning at 2 H, peaking at 12-24 H, declining by 7 D, and resolving by 30 D. Gene ontology and pathway analyses of differentially expressed genes indicated that implantation injury affects inflammatory and immune responses, apoptosis, mitosis, and extracellular matrix reorganization in both cell types. Through backpropagation an integrated network was built, starting with genes differentially expressed at 30 D, followed by adding upstream interactive genes from each prior time-point. This identified significant enrichment of IL-6, IL-8, NF-κB, dendritic cell maturation, glucocorticoid receptor, and Triggering Receptor Expressed on Myeloid Cells (TREM-1 signaling, as well as PPARα activation pathways in graft EC and SMC. Interactive network-based analyses identified IL-6, IL-8, IL-1α, and Insulin Receptor (INSR as focus hub genes within these pathways. Real-time PCR was used for the validation of two of these genes: IL-6 and IL-8, in addition to Collagen 11A1 (COL11A1, a cornerstone of the backpropagation. In conclusion, these results establish causality relationships clarifying the pathogenesis of vein graft implantation injury, and identifying novel targets for its prevention.

  6. Gene Regulatory Mechanisms Underlying the Spatial and Temporal Regulation of Target-Dependent Gene Expression in Drosophila Neurons.

    Directory of Open Access Journals (Sweden)

    Anthony J E Berndt

    2015-12-01

    Full Text Available Neuronal differentiation often requires target-derived signals from the cells they innervate. These signals typically activate neural subtype-specific genes, but the gene regulatory mechanisms remain largely unknown. Highly restricted expression of the FMRFa neuropeptide in Drosophila Tv4 neurons requires target-derived BMP signaling and a transcription factor code that includes Apterous. Using integrase transgenesis of enhancer reporters, we functionally dissected the Tv4-enhancer of FMRFa within its native cellular context. We identified two essential but discrete cis-elements, a BMP-response element (BMP-RE that binds BMP-activated pMad, and a homeodomain-response element (HD-RE that binds Apterous. These cis-elements have low activity and must be combined for Tv4-enhancer activity. Such combinatorial activity is often a mechanism for restricting expression to the intersection of cis-element spatiotemporal activities. However, concatemers of the HD-RE and BMP-RE cis-elements were found to independently generate the same spatiotemporal expression as the Tv4-enhancer. Thus, the Tv4-enhancer atypically combines two low-activity cis-elements that confer the same output from distinct inputs. The activation of target-dependent genes is assumed to 'wait' for target contact. We tested this directly, and unexpectedly found that premature BMP activity could not induce early FMRFa expression; also, we show that the BMP-insensitive HD-RE cis-element is activated at the time of target contact. This led us to uncover a role for the nuclear receptor, seven up (svp, as a repressor of FMRFa induction prior to target contact. Svp is normally downregulated immediately prior to target contact, and we found that maintaining Svp expression prevents cis-element activation, whereas reducing svp gene dosage prematurely activates cis-element activity. We conclude that the target-dependent FMRFa gene is repressed prior to target contact, and that target-derived BMP

  7. Temporal gene expression profiling of the rat knee joint capsule during immobilization-induced joint contractures.

    Science.gov (United States)

    Wong, Kayleigh; Sun, Fangui; Trudel, Guy; Sebastiani, Paola; Laneuville, Odette

    2015-05-26

    Contractures of the knee joint cause disability and handicap. Recovering range of motion is recognized by arthritic patients as their preference for improved health outcome secondary only to pain management. Clinical and experimental studies provide evidence that the posterior knee capsule prevents the knee from achieving full extension. This study was undertaken to investigate the dynamic changes of the joint capsule transcriptome during the progression of knee joint contractures induced by immobilization. We performed a microarray analysis of genes expressed in the posterior knee joint capsule following induction of a flexion contracture by rigidly immobilizing the rat knee joint over a time-course of 16 weeks. Fold changes of expression values were measured and co-expressed genes were identified by clustering based on time-series analysis. Genes associated with immobilization were further analyzed to reveal pathways and biological significance and validated by immunohistochemistry on sagittal sections of knee joints. Changes in expression with a minimum of 1.5 fold changes were dominated by a decrease in expression for 7732 probe sets occurring at week 8 while the expression of 2251 probe sets increased. Clusters of genes with similar profiles of expression included a total of 162 genes displaying at least a 2 fold change compared to week 1. Functional analysis revealed ontology categories corresponding to triglyceride metabolism, extracellular matrix and muscle contraction. The altered expression of selected genes involved in the triglyceride biosynthesis pathway; AGPAT-9, and of the genes P4HB and HSP47, both involved in collagen synthesis, was confirmed by immunohistochemistry. Gene expression in the knee joint capsule was sensitive to joint immobility and provided insights into molecular mechanisms relevant to the pathophysiology of knee flexion contractures. Capsule responses to immobilization was dynamic and characterized by modulation of at least three

  8. Hepatic temporal gene expression profiling in Helicobacter hepaticus-infected A/JCr mice.

    Science.gov (United States)

    Boutin, Samuel R; Rogers, Arlin B; Shen, Zeli; Fry, Rebecca C; Love, Jennifer A; Nambiar, Prashant R; Suerbaum, Sebastian; Fox, James G

    2004-01-01

    Helicobacter hepaticus infection of A/JCr mice is a model of infectious liver cancer. We monitored hepatic global gene expression profiles in H. hepaticus infected and control male A/JCr mice at 3 months, 6 months, and 1 year of age using an Affymetrix-based oligonucleotide microarray platform on the premise that a specific genetic expression signature at isolated time points would be indicative of disease status. Model based expression index comparisons generated by dChip yielded consistent profiles of differential gene expression for H. hepaticus infected male mice with progressive liver disease versus uninfected control mice within each age group. Linear discriminant analysis and principal component analysis allowed segregation of mice based on combined age and lesion status, or age alone. Up-regulation of putative tumor markers correlated with advancing hepatocellular dysplasia. Transcriptionally down-regulated genes in mice with liver lesions included those related to peroxisome proliferator, fatty acid, and steroid metabolism pathways. In conclusion, transcriptional profiling of hepatic genes documented gene expression signatures in the livers of H. hepaticus infected male A/JCr mice with chronic progressive hepatitis and preneoplastic liver lesions, complemented the histopathological diagnosis, and suggested molecular targets for the monitoring and intervention of disease progression prior to the onset of hepatocellular neoplasia.

  9. Temporal Expression of the Clock Genes in the Water Flea Daphnia pulex (Crustacea: Cladocera).

    Science.gov (United States)

    Bernatowicz, Piotr P; Kotwica-Rolinska, Joanna; Joachimiak, Ewa; Sikora, Anna; Polanska, Marta A; Pijanowska, Joanna; Bębas, Piotr

    2016-04-01

    The timekeeping mechanisms that operate at the core of circadian clocks (oscillators) are based on interacting molecular feedback loops consisting of clock and clock-associated genes. However, there is a lack of comprehensive studies on the expression of clock genes (particularly those forming its core) in single crustacean species at the mRNA and protein levels, and these studies could serve as a basis for constructing a model of the crustacean molecular oscillator. Studies on Daphnia pulex are well suited to fill this gap because this species is the only representative crustacean whose genome has been sequenced. We analyzed the abundance of 20 gene transcripts throughout the day in the whole bodies of D. pulex (single clone); we found that 15 of these genes were transcriptionally active, and most had daily expression level changes. According to the functional classification of their homologues in insects, these genes may represent elements of the Daphnia molecular oscillator core and its input and output pathways. Studies of PERIOD (PER) protein, one of the main clock components, revealed its rhythmic expression pattern in the epidermis, gut, and ovaries. Finally, the cycling levels of many of these clock components observed in animals reared in continuous light led to the conclusion that the Daphnia oscillator, even if it is structurally similar to the oscillators of other arthropods, can be considered a particularly important adaptive mechanism for living in environments with extreme photoperiods. © 2016 Wiley Periodicals, Inc.

  10. The Roles of L1 Influence and Lexical Aspect in the Acquisition of Temporal Morphology.

    Science.gov (United States)

    Collins, Laura

    2002-01-01

    Two cross-sectional studies used a replication design to investigate the degree to which adult Francophone English-as-a-Second-Language learners' use of tense/aspect markers in past contexts supported the predictions of the aspect hypothesis and the degree to which it showed first language influence. (Author/VWL)

  11. Temporal global changes in gene expression during temperature transition in Yersinia pestis.

    Science.gov (United States)

    Motin, Vladimir L; Georgescu, Anca M; Fitch, Joseph P; Gu, Pauline P; Nelson, David O; Mabery, Shalini L; Garnham, Janine B; Sokhansanj, Bahrad A; Ott, Linda L; Coleman, Matthew A; Elliott, Jeffrey M; Kegelmeyer, Laura M; Wyrobek, Andrew J; Slezak, Thomas R; Brubaker, Robert R; Garcia, Emilio

    2004-09-01

    DNA microarrays encompassing the entire genome of Yersinia pestis were used to characterize global regulatory changes during steady-state vegetative growth occurring after shift from 26 to 37 degrees C in the presence and absence of Ca2+. Transcriptional profiles revealed that 51, 4, and 13 respective genes and open reading frames (ORFs) on pCD, pPCP, and pMT were thermoinduced and that the majority of these genes carried by pCD were downregulated by Ca2+. In contrast, Ca2+ had little effect on chromosomal genes and ORFs, of which 235 were thermally upregulated and 274 were thermally downregulated. The primary consequence of these regulatory events is profligate catabolism of numerous metabolites available in the mammalian host.

  12. Simulated microgravity influenced the expression of DNA damage repair genes

    Science.gov (United States)

    Zhang, Meng; Sun, Yeqing; Jiawei, Liu; Wang, Ting

    2016-07-01

    Ionizing radiation and microgravity were considered to be the most important stress factors of space environmental the respective study of the biological effects of the radiation and microgravity carried out earlier, but the interaction of the effects of radiation with microgravity started later, and due to difference of the materials and methods the result of this experiment were not consistent. To further investigate the influence of microgravity on the expression of the radiation damage repair genes, the seed of Arabidopsis (Col) and its gravity-insensitive mutant (PIN2) were exposed to 0.1Gy of the dose of energetic carbon-ion beam radiation (LET = 30KeV / μm), and the germinated seed were than fixed in the 3D random positioning apparatus immediately for a 10-day simulated microgravity. By measuring the deflection angle of root tip and the changes of the expression of Ku70 and RAD51 protein, we investigated the impact of microgravity effect on radiation damage repair systems. The results shown that radiation, microgravity and microgravity with radiation could increase the angle of the root of the Col significantly, but no obvious effect on PIN2 type. The radiation could increase the expression of Ku70 significantly in both Col and PIN2, microgravity does not affect the expression, but the microgravity with radiation could decrease the expression of Ku70. This result shown that the microgravity could influence the radiation damage repair systems in molecular level. Moreover, our findings were important to understand the molecular mechanism of the impact of microgravity effect on radiation damage repair systems in vivo.

  13. Spatial and temporal distribution of genes involved in polyamine metabolism during tomato fruit development.

    Science.gov (United States)

    Tsaniklidis, Georgios; Kotsiras, Anastasios; Tsafouros, Athanasios; Roussos, Peter A; Aivalakis, Georgios; Katinakis, Panagiotis; Delis, Costas

    2016-03-01

    Polyamines are organic compounds involved in various biological roles in plants, including cell growth and organ development. In the present study, the expression profile, the accumulation of free polyamines and the transcript localisation of the genes involved in Put metabolism, such as Ornithine decarboxylase (ODC), Arginine decarboxylase (ADC) and copper containing Amine oxidase (CuAO), were examined during Solanum lycopersicum cv. Chiou fruit development and maturation. Moreover, the expression of genes coding for enzymes involved in higher polyamine metabolism, including Spermidine synthase (SPDS), Spermine synthase (SPMS), S-adenosylmethionine decarboxylase (SAMDC) and Polyamine oxidase (PAO), were studied. Most genes participating in PAs biosynthesis and metabolism exhibited an increased accumulation of transcripts at the early stages of fruit development. In contrast, CuAO and SPMS were mostly expressed later, during the development stages of the fruits where a massive increase in fruit volume occurs, while the SPDS1 gene exhibited a rather constant expression with a peak at the red ripe stage. Although Put, Spd and Spm were all exhibited decreasing levels in developing immature fruits, Put levels maxed late during fruit ripening. In contrast to Put both Spd and Spm levels continue to decrease gradually until full ripening. It is worth noticing that in situ RNA-RNA hybridisation is reported for the first time in tomato fruits. The localisation of ADC2, ODC1 and CuAO gene transcripts at tissues such as the locular parenchyma and the vascular bundles fruits, supports the theory that all genes involved in Put biosynthesis and catabolism are mostly expressed in fast growing tissues. The relatively high expression levels of CuAO at the ImG4 stage of fruit development (fruits with a diameter of 3 cm), mature green and breaker stages could possibly be attributed to the implication of polyamines in physiological processes taking place during fruit ripening.

  14. IL18 Gene Variants Influence the Susceptibility to Chagas Disease

    Science.gov (United States)

    Leon Rodriguez, Daniel A; Carmona, F. David; Echeverría, Luis Eduardo; González, Clara Isabel; Martin, Javier

    2016-01-01

    Chagas disease is a parasitic disorder caused by the infection with the flagellated protozoan Trypanosoma cruzi. According to the World Health Organization, more than six million people are currently infected in endemic regions. Genetic factors have been proposed to influence predisposition to infection and development of severe clinical phenotypes like chronic Chagas cardiomyopathy (CCC). Interleukin 18 (IL18) encodes a proinflammatory cytokine that has been proposed to be involved in controlling T. cruzi infection. In this study, we analyzed the possible role of six IL18 gene variants (rs5744258, rs360722, rs2043055, rs187238, rs1946518 and rs360719), which cover most of the variation within the locus, in the susceptibility to infection by T. cruzi and/or CCC. In total, 1,171 individuals from a Colombian region endemic for Chagas disease, classified as seronegative (n = 595), seropositive asymptomatic (n = 175) and CCC (n = 401), were genotyped using TaqMan probes. Significant associations with T. cruzi infection were observed when comparing seronegative and seropositive individuals for rs187238 (P = 2.18E-03, OR = 0.77), rs360719 (P = 1.49E-03, OR = 0.76), rs2043055 (P = 2.52E-03, OR = 1.29), and rs1946518 (P = 0.0162, OR = 1.22). However, dependence analyses suggested that the association was mainly driven by the polymorphism rs360719. This variant is located within the promoter region of the IL18 gene, and it has been described that it creates a binding site for the transcription factor OCT-1 affecting IL-18 expression levels. In addition, no evidence of association was observed between any of the analyzed IL18 gene polymorphisms and the development of CCC. In summary, our data suggest that genetic variation within the promoter region of IL18 is directly involved in the susceptibility to infection by T. cruzi, which provides novel insight into disease pathophysiology and adds new perspectives to achieve a more effective disease control. PMID:27027876

  15. Temporal Global Changes in Gene Expression during Temperature Transition in Yersinia pestis

    OpenAIRE

    Motin, Vladimir L; Georgescu, Anca M.; Fitch, Joseph P.; Gu, Pauline P.; Nelson, David O.; Mabery, Shalini L.; Garnham, Janine B.; Sokhansanj, Bahrad A.; Ott, Linda L.; Matthew A Coleman; Elliott, Jeffrey M.; Kegelmeyer, Laura M.; Wyrobek, Andrew J.; Slezak, Thomas R.; Brubaker, Robert R.

    2004-01-01

    DNA microarrays encompassing the entire genome of Yersinia pestis were used to characterize global regulatory changes during steady-state vegetative growth occurring after shift from 26 to 37°C in the presence and absence of Ca2+. Transcriptional profiles revealed that 51, 4, and 13 respective genes and open reading frames (ORFs) on pCD, pPCP, and pMT were thermoinduced and that the majority of these genes carried by pCD were downregulated by Ca2+. In contrast, Ca2+ had little effect on chrom...

  16. Temporal repression of endogenous pluripotency genes during reprogramming of porcine induced pluripotent stem cells

    DEFF Research Database (Denmark)

    Hall, Vanessa Jane; Christensen, Marianne; Rasmussen, Mikkel Aabech;

    2012-01-01

    transgenes on the expression of the porcine endogenous pluripotency machinery. Endogenous and exogenous gene expression of OCT4, NANOG, SOX2, KLF4, and cMYC was determined at passages 5, 10, 15, and 20, both in cells cultured at 1¿µg/mL doxycycline or 4¿µg/mL doxycycline. Our results revealed that endogenous....... Despite the ability for some endogenous genes to be expressed in these lines, the piPSC-like cells still cannot be maintained without doxycycline, indicating that the culture system of piPSCs may not be optimal or that the reprogramming factor combination used may not currently be optimal for maintaining...

  17. Scene complexity: influence on perception, memory, and development in the medial temporal lobe

    Directory of Open Access Journals (Sweden)

    Xiaoqian J Chai

    2010-03-01

    Full Text Available Regions in the medial temporal lobe (MTL and prefrontal cortex (PFC are involved in memory formation for scenes in both children and adults. The development in children and adolescents of successful memory encoding for scenes has been associated with increased activation in PFC, but not MTL, regions. However, evidence suggests that a functional subregion of the MTL that supports scene perception, located in the parahippocampal gyrus (PHG, goes through a prolonged maturation process. Here we tested the hypothesis that maturation of scene perception supports the development of memory for complex scenes. Scenes were characterized by their levels of complexity defined by the number of unique object categories depicted in the scene. Recognition memory improved with age, in participants ages 8-24, for high, but not low, complexity scenes. High-complexity compared to low-complexity scenes activated a network of regions including the posterior PHG. The difference in activations for high- versus low- complexity scenes increased with age in the right posterior PHG. Finally, activations in right posterior PHG were associated with age-related increases in successful memory formation for high-, but not low-, complexity scenes. These results suggest that functional maturation of the right posterior PHG plays a critical role in the development of enduring long-term recollection for high-complexity scenes.

  18. Scene complexity: influence on perception, memory, and development in the medial temporal lobe.

    Science.gov (United States)

    Chai, Xiaoqian J; Ofen, Noa; Jacobs, Lucia F; Gabrieli, John D E

    2010-01-01

    Regions in the medial temporal lobe (MTL) and prefrontal cortex (PFC) are involved in memory formation for scenes in both children and adults. The development in children and adolescents of successful memory encoding for scenes has been associated with increased activation in PFC, but not MTL, regions. However, evidence suggests that a functional subregion of the MTL that supports scene perception, located in the parahippocampal gyrus (PHG), goes through a prolonged maturation process. Here we tested the hypothesis that maturation of scene perception supports the development of memory for complex scenes. Scenes were characterized by their levels of complexity defined by the number of unique object categories depicted in the scene. Recognition memory improved with age, in participants ages 8-24, for high-, but not low-, complexity scenes. High-complexity compared to low-complexity scenes activated a network of regions including the posterior PHG. The difference in activations for high- versus low-complexity scenes increased with age in the right posterior PHG. Finally, activations in right posterior PHG were associated with age-related increases in successful memory formation for high-, but not low-, complexity scenes. These results suggest that functional maturation of the right posterior PHG plays a critical role in the development of enduring long-term recollection for high-complexity scenes.

  19. Local spatial and temporal factors influencing population and societal vulnerability to natural disasters.

    Science.gov (United States)

    Zhou, Yang; Li, Ning; Wu, Wenxiang; Wu, Jidong; Shi, Peijun

    2014-04-01

    The identification of societal vulnerable counties and regions and the factors contributing to social vulnerability are crucial for effective disaster risk management. Significant advances have been made in the study of social vulnerability over the past two decades, but we still know little regarding China's societal vulnerability profiles, especially at the county level. This study investigates the county-level spatial and temporal patterns in social vulnerability in China from 1980 to 2010. Based on China's four most recent population censuses of 2,361 counties and their corresponding socioeconomic data, a social vulnerability index for each county was created using factor analysis. Exploratory spatial data analysis, including global and local autocorrelations, was applied to reveal the spatial patterns of county-level social vulnerability. The results demonstrate that the dynamic characteristics of China's county-level social vulnerability are notably distinct, and the dominant contributors to societal vulnerability for all of the years studied were rural character, development (urbanization), and economic status. The spatial clustering patterns of social vulnerability to natural disasters in China exhibited a gathering-scattering-gathering pattern over time. Further investigations indicate that many counties in the eastern coastal area of China are experiencing a detectable increase in social vulnerability, whereas the societal vulnerability of many counties in the western and northern areas of China has significantly decreased over the past three decades. These findings will provide policymakers with a sound scientific basis for disaster prevention and mitigation decisions.

  20. Temporal variability in emission category influence on organic matter aerosols in the Indian region

    Science.gov (United States)

    Cherian, R.; Venkataraman, C.; Ramachandran, S.

    2009-03-01

    The dependence of carbonaceous aerosol properties, like radiation absorption and hygroscopicity, on the emission source of origin motivate this work. The influence of emission categories, including crop residue and forest burning, biofuel combustion, brick kilns, thermal power plants, diesel transport and ``other industry'', is estimated on organic matter (OM) surface concentrations in the Indian ocean region. The approach uses general circulation model predicted OM surface concentrations during a ship cruise, identifies probable source regions for high concentration episodes using the potential source contribution function, and estimates collocated OM emissions resolved by category. Distinct source regions identified, are the Indo-Gangetic Plain during 20-30th January, 1999, and central/south India during 1-11th March, 1999. Contributing emission categories are primarily biofuel combustion (18 Gg) during 20-30th January, but a combination of forest burning (8 Gg), biofuel combustion (7 Gg) and crop residue (5 Gg) during 1-11th March. The magnitude of emission flux rather than spatial extent of an emission category, was seen to increase its influence on the receptor. This approach can be used to investigate seasonal and inter-annual variability in emission category influence on atmospheric pollutants.

  1. Inducible defenses stay up late: temporal patterns of immune gene expression in Tenebrio molitor.

    Science.gov (United States)

    Johnston, Paul R; Makarova, Olga; Rolff, Jens

    2013-12-06

    The course of microbial infection in insects is shaped by a two-stage process of immune defense. Constitutive defenses, such as engulfment and melanization, act immediately and are followed by inducible defenses, archetypically the production of antimicrobial peptides, which eliminate or suppress the remaining microbes. By applying RNAseq across a 7-day time course, we sought to characterize the long-lasting immune response to bacterial challenge in the mealworm beetle Tenebrio molitor, a model for the biochemistry of insect immunity and persistent bacterial infection. By annotating a hybrid de novo assembly of RNAseq data, we were able to identify putative orthologs for the majority of components of the conserved insect immune system. Compared with Tribolium castaneum, the most closely related species with a reference genome sequence and a manually curated immune system annotation, the T. molitor immune gene count was lower, with lineage-specific expansions of genes encoding serine proteases and their countervailing inhibitors accounting for the majority of the deficit. Quantitative mapping of RNAseq reads to the reference assembly showed that expression of genes with predicted functions in cellular immunity, wound healing, melanization, and the production of reactive oxygen species was transiently induced immediately after immune challenge. In contrast, expression of genes encoding antimicrobial peptides or components of the Toll signaling pathway and iron sequestration response remained elevated for at least 7 days. Numerous genes involved in metabolism and nutrient storage were repressed, indicating a possible cost of immune induction. Strikingly, the expression of almost all antibacterial peptides followed the same pattern of long-lasting induction, regardless of their spectra of activity, signaling possible interactive roles in vivo.

  2. The influence of age and high-frequency hearing loss on sensitivity to temporal fine structure at low frequencies (L).

    Science.gov (United States)

    Moore, Brian C J; Glasberg, Brian R; Stoev, Martin; Füllgrabe, Christian; Hopkins, Kathryn

    2012-02-01

    Sensitivity to temporal fine structure (TFS) at low frequencies may be adversely affected by hearing loss at high frequencies even when absolute thresholds at low frequencies are within the normal range. However, in several studies suggesting this, the effects of hearing loss and age were confounded. Here, interaural phase discrimination (IPD) thresholds for pure tones at 500 and 750 Hz were measured for 39 subjects with ages from 61 to 83 yr. All subjects had near-normal audiometric thresholds at low frequencies, but thresholds varied across subjects at high frequencies. IPD thresholds were correlated with age. IPD thresholds for the test frequency of 750 Hz were weakly correlated with absolute thresholds at high frequencies, but these correlations became non-significant when the effect of age was partialed out. The results do not confirm that sensitivity to TFS at low frequencies is influenced by hearing loss at high frequencies, independently of age.

  3. Influence of nutrient inputs, hexadecane, and temporal variations on denitrification and community composition of river biofilms.

    Science.gov (United States)

    Chénier, M R; Beaumier, D; Fortin, N; Roy, R; Driscoll, B T; Lawrence, J R; Greer, C W

    2006-01-01

    Biofilms were cultivated on polycarbonate strips in rotating annular reactors using South Saskatchewan River water during the fall of 1999 and the fall of 2001, supplemented with carbon (glucose), nitrogen (NH4Cl), phosphorus (KH2PO4), or combined nutrients (CNP), with or without hexadecane, a model compound representing aliphatic hydrocarbons used to simulate a pollutant. In fall 1999 and fall 2001, comparable denitrification activities and catabolic potentials were observed in the biofilms, implying that denitrifying populations showed similar activity patterns and catabolic potentials during the fall from year to year in this river ecosystem, when environmental conditions were similar. Both nirS and nirK denitrification genes were detected by PCR amplification, suggesting that both denitrifying bacterial subpopulations can potentially contribute to total denitrification. Between 91.7 and 99.8% of the consumed N was emitted in the form of N2, suggesting that emission of N2O, a major potent greenhouse gas, by South Saskatchewan River biofilms is low. Denitrification was markedly stimulated by the addition of CNP, and nirS and nirK genes were predominant only in the presence of CNP. In contrast, individual nutrients had no impact on denitrification and on the occurrence of nirS and nirK genes detected by PCR amplification. Similarly, only CNP resulted in significant increases in algal and bacterial biomass relative to control biofilms. Biomass measurements indicated a linkage between autotrophic and heterotrophic populations in the fall 1999 biofilms. Correlation analyses demonstrated a significant relationship (P < or = 0.05) between the denitrification rate and the biomass of algae and heterotrophic bacteria but not cyanobacteria. At the concentration assessed (1 ppb), hexadecane partially inhibited denitrification in both years, slightly more in the fall of 2001. This study suggested that the response of the anaerobic heterotrophic biofilm community may be

  4. Occurrence and temporal variation of antibiotic resistance genes (ARGs) in shrimp aquaculture: ARGs dissemination from farming source to reared organisms.

    Science.gov (United States)

    Su, Haochang; Liu, Shan; Hu, Xiaojuan; Xu, Xiangrong; Xu, Wujie; Xu, Yu; Li, Zhuojia; Wen, Guoliang; Liu, Yousheng; Cao, Yucheng

    2017-12-31

    Considerable attention has been paid to the occurrence and abundance of antibiotic resistance genes (ARGs) in aquatic environments. However, the temporal variation and dissemination of ARGs in aquaculture environments and reared organisms need further study. This study investigated the abundance and diversity of ARGs and bacterial community in water source, shrimp pond water, sediment, and shrimps during the rearing period in Pearl River Delta region, South China. The results showed that sul1, qnrD, cmlA, and floR were the predominant ARGs in the aquaculture samples. A trend of decreasing abundance of ARGs was observed for pond water samples during the rearing period, whereas an increasing trend was observed in the sediment and shrimp samples. The total concentration of ARGs in water source was significantly higher than that in shrimp pond water (pshrimps were 4.48-19.0 times higher than those in juvenile shrimps. Similar to water source and pond water, cmlA and sul1 were the predominant ARGs in shrimp intestinal tract. The bacterial community in the shrimp intestinal tract changed greatly from juvenile to adult. The results of the present study indicated that the abundances of ARGs in aquaculture varied temporally during the rearing period. Water source was an important medium disseminating ARGs to the aquaculture environments and reared organisms. Sul1 could be used as a potential indicator for ARGs in both water and sediment in aquaculture in the estuary of the Pearl River Delta, South China. This study represents a case study for the temporal variation of abundance and dissemination of ARGs in aquaculture and is a reference for potential risks to food safety and human health. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. On the influence of temporal change on the validity of landslide susceptibility maps in an alpine catchment, Switzerland

    Science.gov (United States)

    Meusburger, K.; Alewell, C.

    2009-04-01

    Global change (as a combination of climate and land use change) poses a risk to stability of alpine soils, and may enhance landslide hazard. The occurrence of landslides depends on static catchment characteristics (e.g. geology, topography etc.), as well as triggering factors that are variable in time (dynamic factors), such as event characteristics and land use. However, in literature the effects of temporal change are still discussed controversially and most statistical landslide prediction models rely on static catchment characteristics alone. In this study, we aim to assess the additional influence of dynamic factors on landslide susceptibility and on the validity of commonly used statistical landslide models. The Urseren Valley (Central Swiss Alps) was chosen as study area due to the evidence of climate and land use change. To assess the influence of catchment characteristics on landslide susceptibility, we set up a logistic regression model using 20 static predictor variables. The additional impact of dynamic risk factors was evaluated with historic data (aerial photographs and meteorological time series). We found that geology, slope and stream density were the most significant static predictors and could explain 70% of the landslide variation. However, the area affected by landslides increased by 92% from 1959 to 2004, which highlights the crucial role of dynamic landslide triggering factors. Furthermore, more recent landslides (since 2000) could only in part be predicted, which confirmed our proposed hypothesis that the validity of statistical hazard models may worsen over time. Discrepancies between predicted susceptibility and observed landslides mainly occurred in areas that have undergone land use changes. Consequently, slopes, that have formerly been classified as only "medium" landslide susceptibility may nonetheless have a high probability to fail under changed management. Spatial information of the impact of land use on landslide susceptibility

  6. Radiation dose optimization in pediatric temporal bone computed tomography: influence of tube tension on image contrast and image quality

    Energy Technology Data Exchange (ETDEWEB)

    Nauer, Claude Bertrand [University Hospital Berne, Institute of Diagnostic and Interventional Neuroradiology, Berne (Switzerland); Zentrales Roentgeninstitut, Kantonsspital Graubuenden, Chur (Switzerland); Zubler, Christoph; Weisstanner, Christian [University Hospital Berne, Institute of Diagnostic and Interventional Neuroradiology, Berne (Switzerland); Stieger, Christof [University Berne, Group for Artificial Hearing Research, ARTORG Center, Berne (Switzerland); Senn, Pascal [University Hospital Berne, Department of ENT, Head and Neck Surgery, Berne (Switzerland); Arnold, Andreas [University Berne, Group for Artificial Hearing Research, ARTORG Center, Berne (Switzerland); University Hospital Berne, Department of ENT, Head and Neck Surgery, Berne (Switzerland)

    2012-03-15

    The purpose of this experimental study was to investigate the effect of tube tension reduction on image contrast and image quality in pediatric temporal bone computed tomography (CT). Seven lamb heads with infant-equivalent sizes were scanned repeatedly, using four tube tensions from 140 to 80 kV while the CT-Dose Index (CTDI) was held constant. Scanning was repeated with four CTDI values from 30 to 3 mGy. Image contrast was calculated for the middle ear as the Hounsfield unit (HU) difference between bone and air and for the inner ear as the HU difference between bone and fluid. The influence of tube tension on high-contrast detail delineation was evaluated using a phantom. The subjective image quality of eight middle and inner ear structures was assessed using a 4-point scale (scores 1-2 = insufficient; scores 3-4 = sufficient). Middle and inner ear contrast showed a near linear increase with tube tension reduction (r = -0.94/-0.88) and was highest at 80 kV. Tube tension had no influence on spatial resolution. Subjective image quality analysis showed significantly better scoring at lower tube tensions, with highest image quality at 80 kV. However, image quality improvement was most relevant for low-dose scans. Image contrast in the temporal bone is significantly higher at low tube tensions, leading to a better subjective image quality. Highest contrast and best quality were found at 80 kV. This image quality improvement might be utilized to further reduce the radiation dose in pediatric low-dose CT protocols. (orig.)

  7. Temporal Variations of Water Productivity in Irrigated Corn: An Analysis of Factors Influencing Yield and Water Use across Central Nebraska.

    Science.gov (United States)

    Carr, Tony; Yang, Haishun; Ray, Chittaranjan

    2016-01-01

    Water Productivity (WP) of a crop defines the relationship between the economic or physical yield of the crop and its water use. With this concept it is possible to identify disproportionate water use or water-limited yield gaps and thereby support improvements in agricultural water management. However, too often important qualitative and quantitative environmental factors are not part of a WP analysis and therefore neglect the aspect of maintaining a sustainable agricultural system. In this study, we examine both the physical and economic WP in perspective with temporally changing environmental conditions. The physical WP analysis was performed by comparing simulated maximum attainable corn yields per unit of water using the crop model Hybrid-Maize with observed data from 2005 through 2013 from 108 farm plots in the Central Platte and the Tri Basin Natural Resource Districts of Nebraska. In order to expand the WP analysis on external factors influencing yields, a second model, Maize-N, was used to estimate optimal nitrogen (N)-fertilizer rate for specific fields in the study area. Finally, a vadose zone flow and transport model, HYDRUS-1D for simulating vertical nutrient transport in the soil, was used to estimate locations of nitrogen pulses in the soil profile. The comparison of simulated and observed data revealed that WP was not on an optimal level, mainly due to large amounts of irrigation used in the study area. The further analysis illustrated year-to-year variations of WP during the nine consecutive years, as well as the need to improve fertilizer management to favor WP and environmental quality. In addition, we addressed the negative influence of groundwater depletion on the economic WP through increasing pumping costs. In summary, this study demonstrated that involving temporal variations of WP as well as associated environmental and economic issues can represent a bigger picture of WP that can help to create incentives to sustainably improve

  8. Temporal Gene Expression of the Cyanobacterium Arthrospira in Response to Gamma Rays.

    Science.gov (United States)

    Badri, Hanène; Monsieurs, Pieter; Coninx, Ilse; Nauts, Robin; Wattiez, Ruddy; Leys, Natalie

    2015-01-01

    The edible cyanobacterium Arthrospira is resistant to ionising radiation. The cellular mechanisms underlying this radiation resistance are, however, still largely unknown. Therefore, additional molecular analysis was performed to investigate how these cells can escape from, protect against, or repair the radiation damage. Arthrospira cells were shortly exposed to different doses of 60Co gamma rays and the dynamic response was investigated by monitoring its gene expression and cell physiology at different time points after irradiation. The results revealed a fast switch from an active growth state to a kind of 'survival modus' during which the cells put photosynthesis, carbon and nitrogen assimilation on hold and activate pathways for cellular protection, detoxification, and repair. The higher the radiation dose, the more pronounced this global emergency response is expressed. Genes repressed during early response, suggested a reduction of photosystem II and I activity and reduced tricarboxylic acid (TCA) and Calvin-Benson-Bassham (CBB) cycles, combined with an activation of the pentose phosphate pathway (PPP). For reactive oxygen species detoxification and restoration of the redox balance in Arthrospira cells, the results suggested a powerful contribution of the antioxidant molecule glutathione. The repair mechanisms of Arthrospira cells that were immediately switched on, involve mainly proteases for damaged protein removal, single strand DNA repair and restriction modification systems, while recA was not induced. Additionally, the exposed cells showed significant increased expression of arh genes, coding for a novel group of protein of unknown function, also seen in our previous irradiation studies. This observation confirms our hypothesis that arh genes are key elements in radiation resistance of Arthrospira, requiring further investigation. This study provides new insights into phasic response and the cellular pathways involved in the radiation resistance of

  9. Temporal Gene Expression of the Cyanobacterium Arthrospira in Response to Gamma Rays.

    Directory of Open Access Journals (Sweden)

    Hanène Badri

    Full Text Available The edible cyanobacterium Arthrospira is resistant to ionising radiation. The cellular mechanisms underlying this radiation resistance are, however, still largely unknown. Therefore, additional molecular analysis was performed to investigate how these cells can escape from, protect against, or repair the radiation damage. Arthrospira cells were shortly exposed to different doses of 60Co gamma rays and the dynamic response was investigated by monitoring its gene expression and cell physiology at different time points after irradiation. The results revealed a fast switch from an active growth state to a kind of 'survival modus' during which the cells put photosynthesis, carbon and nitrogen assimilation on hold and activate pathways for cellular protection, detoxification, and repair. The higher the radiation dose, the more pronounced this global emergency response is expressed. Genes repressed during early response, suggested a reduction of photosystem II and I activity and reduced tricarboxylic acid (TCA and Calvin-Benson-Bassham (CBB cycles, combined with an activation of the pentose phosphate pathway (PPP. For reactive oxygen species detoxification and restoration of the redox balance in Arthrospira cells, the results suggested a powerful contribution of the antioxidant molecule glutathione. The repair mechanisms of Arthrospira cells that were immediately switched on, involve mainly proteases for damaged protein removal, single strand DNA repair and restriction modification systems, while recA was not induced. Additionally, the exposed cells showed significant increased expression of arh genes, coding for a novel group of protein of unknown function, also seen in our previous irradiation studies. This observation confirms our hypothesis that arh genes are key elements in radiation resistance of Arthrospira, requiring further investigation. This study provides new insights into phasic response and the cellular pathways involved in the radiation

  10. Temporal regulation of polygalacturonase gene expression in fruits of normal, mutant, and heterozygous tomato genotypes.

    Science.gov (United States)

    Biggs, M S; Handa, A K

    1989-01-01

    Molecular cloning of polygalacturonase (PG; EC 3.2. 1.15) from fruits of tomato (Lycopersicon esculentum Mill cv Rutgers) was accomplished by constructing a cDNA library from turning stage poly(A)(+) RNA in lambdagtll and immunoscreening with polyclonal antibodies raised against purified PG2. Both PG cDNA and antibody probes were used to quantify changes in PG gene expression in pericarp from normal, mutant, and heterozygous genotypes. Results show that PG mRNA, protein, and enzyme activity sequentially peak at the turning, ripe, and red ripe stages of Rutgers pericarp ripening, respectively. PG gene expression was attenuated greatly (0-15% of normal on a gram fresh weight basis) for PG mRNA, protein, and enzyme activity in five ripening-impaired mutants (rin, nor, Nr, Gr, and Long Keeper) tested. Maximum expression of the PG gene in heterozygotes of rin, nor, Nr, Gr, and Long Keeper (crosses with Rutgers) at the mRNA level was about 25, 13, 17, 5, and 62% of the Rutgers turning stage, at the protein level was about 166, 110, 15, 6, and 104% of the Rutgers ripe stage, and at the enzyme activity level was about 69, 37, 4, 1, and 50% of the Rutgers red ripe stage, respectively. No PG gene expression was found in preclimacteric fruits or vegetative tissues. PG mRNA was localized on both free and membrane-bound polyribosomes of ripening pericarp. In addition to transcriptional regulation, mechanisms contributing to mRNA stability, delayed protein accumulation, and posttranslational modifications may play important roles in the overall accumulation of PG activity during fruit ripening.

  11. Temporal dynamics of oocyte growth and vitellogenin gene expression in zebrafish (Danio rerio).

    Science.gov (United States)

    Connolly, Michelle H; Dutkosky, Rachel M; Heah, Tze P; Sayler, Gary S; Henry, Theodore B

    2014-04-01

    Little is known about how hepatic vitellogenin gene (vtg) expression relates to oogenesis in fish, especially among fractional spawners. The objective of this study was to relate hepatic vtg 1A/B expression to stage-specific oocyte development in zebrafish (Danio rerio), an asynchronous spawning fish. Liver samples were collected at seven time points postspawning (1-32 days) and fish were preserved for subsequent histological analyses. Relative vtg 1A/B expression among liver samples was quantified by reverse transcription-quantitative PCR and oogenesis was evaluated following standard hematoxylin and eosin staining of serial ovarian sections. Histological analyses indicate that a subset of previtellogenic oocytes (stages 1-2) transitioned into postvitellogenic oocytes (stages 3-4) within 4 days (96 h) postspawning. By 8 days postspawning (192 h), the majority of the ovary was occupied by mature (stage 4) oocytes, a trend that continued through 32 days postspawning. Hepatic vtg 1A/B gene expression was upregulated 3.89-fold 1-h postspawning relative to the average gene expression across all time points, but was not correlated to stage-specific oogenesis. Follicular atresia among fish sampled 32 days postspawning highlights the importance of regular spawning in zebrafish and suggests that the event of spawning itself may be integral to the regulation of oocyte development.

  12. SPC-Cre-ERT2 transgenic mouse for temporal gene deletion in alveolar epithelial cells.

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    Yao-Song Gui

    Full Text Available Although several Cre-loxP-based gene knockout mouse models have been generated for the study of gene function in alveolar epithelia in the lung, their applications are still limited. In this study, we developed a SPC-Cre-ER(T2 mouse model, in which a tamoxifen-inducible Cre recombinase (Cre-ER(T2 is under the control of the human surfactant protein C (SPC promoter. The specificity and efficiency of Cre-ER(T2 activity was first evaluated by crossing SPC-Cre-ER(T2 mouse with ROSA26R mouse, a β-galactosidase reporter strain. We found that Cre-ER(T2 was expressed in 30.7% type II alveolar epithelial cells of SPC-Cre-ER(T2/ROSA26R mouse lung tissues in the presence of tamoxifen. We then tested the tamoxifen-inducible recombinase activity of Cre-ER(T2 in a mouse strain bearing TSC1 conditional knockout alleles (TSC1(fx/fx. TSC1 deletion was detected in the lungs of tamoxifen treated SPC-Cre-ER(T2/TSC1(fx/fx mice. Therefore this SPC-Cre-ER(T2 mouse model may be a valuable tool to investigate functions of genes in lung development, physiology and disease.

  13. SPC-Cre-ERT2 transgenic mouse for temporal gene deletion in alveolar epithelial cells.

    Science.gov (United States)

    Gui, Yao-Song; Wang, Lianmei; Tian, Xinlun; Feng, Ruie; Ma, Aiping; Cai, Baiqiang; Zhang, Hongbing; Xu, Kai-Feng

    2012-01-01

    Although several Cre-loxP-based gene knockout mouse models have been generated for the study of gene function in alveolar epithelia in the lung, their applications are still limited. In this study, we developed a SPC-Cre-ER(T2) mouse model, in which a tamoxifen-inducible Cre recombinase (Cre-ER(T2)) is under the control of the human surfactant protein C (SPC) promoter. The specificity and efficiency of Cre-ER(T2) activity was first evaluated by crossing SPC-Cre-ER(T2) mouse with ROSA26R mouse, a β-galactosidase reporter strain. We found that Cre-ER(T2) was expressed in 30.7% type II alveolar epithelial cells of SPC-Cre-ER(T2)/ROSA26R mouse lung tissues in the presence of tamoxifen. We then tested the tamoxifen-inducible recombinase activity of Cre-ER(T2) in a mouse strain bearing TSC1 conditional knockout alleles (TSC1(fx/fx)). TSC1 deletion was detected in the lungs of tamoxifen treated SPC-Cre-ER(T2)/TSC1(fx/fx) mice. Therefore this SPC-Cre-ER(T2) mouse model may be a valuable tool to investigate functions of genes in lung development, physiology and disease.

  14. Temporal and regional regulation of gene expression by calcium-stimulated adenylyl cyclase activity during fear memory.

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    Lindsay Wieczorek

    Full Text Available BACKGROUND: The Ca2+-stimulated adenylyl cyclases (ACs, AC1 and AC8, are key components of long-term memory processing. AC1 and AC8 double knockout mice (Adcy1(-/-Adcy8(-/-; DKO display impaired fear memory processing; the mechanism of this impairment is largely unknown. METHODOLOGY/PRINCIPAL FINDINGS: We hypothesize that the Ca2+-stimulated ACs modulate long-lasting transcriptional changes essential for fear memory consolidation and maintenance. Here, we report a genome-wide study of gene expression changes associated with conditioned fear (CF memory in wild-type and DKO mice to identify AC-dependent gene regulatory changes that occur in the amygdala and hippocampus at baseline and different time points after CF learning. We observed an overall decrease in transcriptional changes in DKO mice across all time points, but most strikingly, at periods when memory consolidation and retention should be occurring. Further, we identified a shared set of transcription factor binding sites in genes upregulated in wild-type mice that were associated with downregulated genes in DKO mice. To prove the temporal and regional importance of AC activity on different stages of memory processing, the tetracycline-off system was used to produce mice with forebrain-specific inducible expression of AC8 on a DKO background. CF behavioral results reveal that adult restoration of AC8 activity in the forebrain is sufficient for intact learning, while cessation of this expression at any time point across learning causes memory deficits. CONCLUSIONS/SIGNIFICANCE: Overall, these studies demonstrate that the Ca2+-stimulated ACs contribute to the formation and maintenance of fear memory by a network of long-term transcriptional changes.

  15. Temporal changes of antibiotic-resistance genes and bacterial communities in two contrasting soils treated with cattle manure.

    Science.gov (United States)

    Hu, Hang-Wei; Han, Xue-Mei; Shi, Xiu-Zhen; Wang, Jun-Tao; Han, Li-Li; Chen, Deli; He, Ji-Zheng

    2016-02-01

    The emerging environmental spread of antibiotic-resistance genes (ARGs) and their subsequent acquisition by clinically relevant microorganisms is a major threat to public health. Animal manure has been recognized as an important reservoir of ARGs; however, the dissemination of manure-derived ARGs and the impacts of manure application on the soil resistome remain obscure. Here, we conducted a microcosm study to assess the temporal succession of total bacteria and a broad spectrum of ARGs in two contrasting soils following manure application from cattle that had not been treated with antibiotics. High-capacity quantitative PCR detected 52 unique ARGs across all the samples, with β-lactamase as the most dominant ARG type. Several genes of soil indigenous bacteria conferring resistance to β-lactam, which could not be detected in manure, were found to be highly enriched in manure-treated soils, and the level of enrichment was maintained over the entire course of 140 days. The enriched β-lactam resistance genes had significantly positive relationships with the relative abundance of the integrase intI1 gene, suggesting an increasing mobility potential in manure-treated soils. The changes in ARG patterns were accompanied by a significant effect of cattle manure on the total bacterial community compositions. Our study indicates that even in the absence of selective pressure imposed by agricultural use of antibiotics, manure application could still strongly impact the abundance, diversity and mobility potential of a broad spectrum of soil ARGs. Our findings are important for reliable prediction of ARG behaviors in soil environment and development of appropriate strategies to minimize their dissemination.

  16. Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering.

    Science.gov (United States)

    You, Yuan; Sawikowska, Aneta; Neumann, Manuela; Posé, David; Capovilla, Giovanna; Langenecker, Tobias; Neher, Richard A; Krajewski, Paweł; Schmid, Markus

    2017-05-17

    Plants can produce organs throughout their entire life from pluripotent stem cells located at their growing tip, the shoot apical meristem (SAM). At the time of flowering, the SAM of Arabidopsis thaliana switches fate and starts producing flowers instead of leaves. Correct timing of flowering in part determines reproductive success, and is therefore under environmental and endogenous control. How epigenetic regulation contributes to the floral transition has eluded analysis so far, mostly because of the poor accessibility of the SAM. Here we report the temporal dynamics of the chromatin modifications H3K4me3 and H3K27me3 and their correlation with transcriptional changes at the SAM in response to photoperiod-induced flowering. Emphasizing the importance of tissue-specific epigenomic analyses we detect enrichments of chromatin states in the SAM that were not apparent in whole seedlings. Furthermore, our results suggest that regulation of translation might be involved in adjusting meristem function during the induction of flowering.

  17. Forecasting Temporal and Spatial Climatological Influence for Land Suitability Evaluation in Bentota Sri Lanka

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    Gayani Ranasinghe

    2017-01-01

    Full Text Available Climate change has raised much concern regarding its impacts on future land use planning, varying by region, time, and socio-economic development path. The principle purpose of land suitability evaluation is to predict the potential and limitation of the land for crop production and other land uses. This study was carried out to predict the temperature and rainfall trends as one of the major factor for evaluating land suitability. Climatic data such as monthly mean temperature, total monthly rainfall, maximum daily rainfall and total annual rainfall during last 30 years of all weather stations located in Bentota River basin was collected and analyzed applying time series analysis, correlation analysis and Manna Kendall trend test methods. Spatial distribution of forecast rainfall values was illustrated applying Arc GIS software. The findings revealed that monthly mean temperature and maximum daily rainfall had a general increasing trend whereas, total monthly rainfall and total annual rainfall showed a general decreasing trend in  Bentota area. It was indicated relatively high rainfall situations during May and October while low rainfall situations during January and February by occurring flood situation in once per five year. During Yala season the area will be received comparatively more rainfall (331mm than Maha season (300mm in future. Community and the farmers in this area can be aware about the anticipated spatial distribution of total monthly rainfall during two major seasons and flood occurrence periods. Decision makers should evaluate land suitability of Bentota area by considering above climatological influences and its spatial distribution pattern that identified as major outcome of this research. The approach and the methodology adopted in this study will be useful for other researchers, agriculturalist and planners to identify the future climatological influences and its spatial distribution pattern for land suitability evaluations

  18. Dysregulation of Autophagy, Mitophagy, and Apoptotic Genes in the Medial Temporal Lobe Cortex in an Ischemic Model of Alzheimer’s Disease

    Science.gov (United States)

    Ułamek-Kozioł, Marzena; Kocki, Janusz; Bogucka-Kocka, Anna; Petniak, Alicja; Gil-Kulik, Paulina; Januszewski, Sławomir; Bogucki, Jacek; Jabłoński, Mirosław; Furmaga-Jabłońska, Wanda; Brzozowska, Judyta; Czuczwar, Stanisław J.; Pluta, Ryszard

    2016-01-01

    Ischemic brain damage is a pathological incident that is often linked with medial temporal lobe cortex injury and finally its atrophy. Post-ischemic brain injury associates with poor prognosis since neurons of selectively vulnerable ischemic brain areas are disappearing by apoptotic program of neuronal death. Autophagy has been considered, after brain ischemia, as a guardian against neurodegeneration. Consequently, we have examined changes in autophagy (BECN 1), mitophagy (BNIP 3), and apoptotic (caspase 3) genes in the medial temporal lobe cortex with the use of quantitative reverse-transcriptase PCR following transient 10-min global brain ischemia in rats with survival 2, 7, and 30 days. The intense significant overexpression of BECN 1 gene was noted on the 2nd day, while on days 7–30 the expression of this gene was still upregulated. BNIP 3 gene was downregulated on the 2nd day, but on days 7–30 post-ischemia, there was a significant reverse tendency. Caspase 3 gene, associated with apoptotic neuronal death, was induced in the same way as BNIP 3 gene after brain ischemia. Thus, the demonstrated changes indicate that the considerable dysregulation of expression of BECN 1, BNIP 3, and caspase 3 genes may be connected with a response of neuronal cells in medial temporal lobe cortex to transient complete brain ischemia. PMID:27472881

  19. Iroquois genes influence proximo-distal morphogenesis during rat lung development

    NARCIS (Netherlands)

    W.G. van Tuyl (Minke); J. Liu (Jason); F. Groenman (Frederick); R. Ridsdale (Ross); R.N.N. Han (Robin N.); V. Venkatesh (Vikram); D. Tibboel (Dick); M.R. Post (Martin)

    2006-01-01

    textabstractLung development is a highly regulated process directed by mesenchymal-epithelial interactions, which coordinate the temporal and spatial expression of multiple regulatory factors required for proper lung formation. The Iroquois homeobox (Irx) genes have been implicated in the patterning

  20. Association between Vitamin D Receptor Gene Polymorphisms with Childhood Temporal Lobe Epilepsy

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    Pei Jiang

    2015-10-01

    Full Text Available Vitamin D (VD is implicated in multiple aspects of human physiology and vitamin D receptor (VDR polymorphisms are associated with a variety of neuropsychiatric disorders. Although VD deficiency is highly prevalent in epilepsy patients and converging evidence indicates a role for VD in the development of epilepsy, no data is available on the possible relationship between epilepsy and genetic variations of VDR. In this study, 150 controls and 82 patients with temporal lobe epilepsy (TLE were genotyped for five common VDR polymorphisms (Cdx-2, FokI, BsmI, ApaI and TaqI by the polymerase chain reaction-ligase detection reaction method. Our results revealed that the frequency of FokI AC genotype was significantly higher in the control group than in the patients (p = 0.003, OR = 0.39, 95% CI = 0.21–0.73, whereas the AA genotype of ApaI SNP was more frequent in patients than in controls (p = 0.018, OR = 2.92, 95% CI = 1.2–7.1. However, no statistically significant association was found between Cdx-2, BsmI and TaqI polymorphisms and epilepsy. Additionally, in haplotype analysis, we found the haplotype GAT (BsmI/ApaI/TaqI conferred significantly increased risk for developing TLE (p = 0.039, OR = 1.62, 95% CI = 1.02–2.56. As far as we know, these results firstly underline the importance of VDR polymorphisms for the genetic susceptibility to epilepsy.

  1. Gene expression variance in hippocampal tissue of temporal lobe epilepsy patients corresponds to differential memory performance.

    Science.gov (United States)

    Bungenberg, Julia; Surano, Natascha; Grote, Alexander; Surges, Rainer; Pernhorst, Katharina; Hofmann, Andrea; Schoch, Susanne; Helmstaedter, Christoph; Becker, Albert J

    2016-02-01

    Temporal lobe epilepsy (TLE) is a severe brain disorder affecting particularly young adults. TLE is frequently associated with memory deterioration and neuronal damage of the hippocampal formation. It thereby reveals striking parallels to neurodegenerative disorders including Alzheimer's disease (AD). TLE patients differ with respect to their cognitive performance, but currently little is known about relevant molecular-genetic factors. Here, we correlated differential memory performance of pharmacoresistant TLE patients undergoing neurosurgery for seizure control with in-vitro findings of their hippocampal tissues. We analyzed mRNA transcripts and subsequently promoter variants specifically altered in brain tissue of individuals with 'very severe' memory impairment. TLE patients (n=79) were stratified according to preoperative memory impairment using an established four-tiered grading system ranging from 'average' to 'very severely'. Multimodal cluster analyses revealed molecules specifically associated with synaptic function and abundantly expressed in TLE patients with very impaired memory performance. In a subsequent promoter analysis, we found the single nucleotide polymorphism rs744373 C-allele to be associated with high mRNA levels of bridging integrator 1 (BIN1)/Amphiphysin 2, i.e. a major component of the endocytotic machinery and located in a crucial genetic AD risk locus. Using in vitro luciferase transfection assays, we found that BIN1 promoter activation is genotype dependent and strongly increased by reduced binding of the transcriptional repressor TGIF. Our data indicate that poor memory performance in patients with TLE strongly corresponds to distinctly altered neuronal transcript signatures, which - as demonstrated for BIN1 - can correlate with a particular allelic promoter variant. Our data suggest aberrant transcriptional signaling to significantly impact synaptic dynamics in TLE resulting in impaired memory performance and may serve as basis for

  2. Interleukin (IL)1beta, IL-1alpha, and IL-1 receptor antagonist gene polymorphisms in patients with temporal lobe epilepsy.

    Science.gov (United States)

    Kanemoto, K; Kawasaki, J; Miyamoto, T; Obayashi, H; Nishimura, M

    2000-05-01

    Proinflammatory cytokines, including interleukin (IL)-1beta, are known to modulate effects of neurotoxic neurotransmitters discharged during excitation or inflammation in the central nervous system (CNS). They also regulate development of glial scars at sites of CNS injury. To elucidate a genetic predisposition of temporal lobe epilepsy with hippocampal sclerosis (TLE-HS+), we studied polymorphisms in the IL-1beta, IL-1alpha, and IL-1 receptor antagonist (IL-1RA) genes in 50 patients with TLE-HS+ and in 112 controls. Fifty-three patients who had TLE without HS were also examined (TLE-HS-) as disease controls. The distribution of the biallelic polymorphism in the promoter region at position -511 of the IL-1beta gene (IL-1B-511) was significantly different both between TLE-HS+ patients and controls and between TLE-HS+ and TLE-HS- patients. The differences were due to overrepresentation of the homozygotes for IL-1B-511*2, which is suggested to be a high producer of IL-1beta, in TLE-HS+ patients compared with both controls and TLE-HS- patients. In contrast, there was no difference between TLE-HS- patients and controls. Our data suggest that, in the homozygotes for IL-IB-511*2, minor events in development such as febrile convulsions could set up a cascade leading to HS.

  3. Gene expression analyses of the spatio-temporal relationships of human medulloblastoma subgroups during early human neurogenesis.

    Directory of Open Access Journals (Sweden)

    Cornelia M Hooper

    Full Text Available Medulloblastoma is the most common form of malignant paediatric brain tumour and is the leading cause of childhood cancer related mortality. The four molecular subgroups of medulloblastoma that have been identified - WNT, SHH, Group 3 and Group 4 - have molecular and topographical characteristics suggestive of different cells of origin. Definitive identification of the cell(s of origin of the medulloblastoma subgroups, particularly the poorer prognosis Group 3 and Group 4 medulloblastoma, is critical to understand the pathogenesis of the disease, and ultimately for the development of more effective treatment options. To address this issue, the gene expression profiles of normal human neural tissues and cell types representing a broad neuro-developmental continuum, were compared to those of two independent cohorts of primary human medulloblastoma specimens. Clustering, co-expression network, and gene expression analyses revealed that WNT and SHH medulloblastoma may be derived from distinct neural stem cell populations during early embryonic development, while the transcriptional profiles of Group 3 and Group 4 medulloblastoma resemble cerebellar granule neuron precursors at weeks 10-15 and 20-30 of embryogenesis, respectively. Our data indicate that Group 3 medulloblastoma may arise through abnormal neuronal differentiation, whereas deregulation of synaptic pruning-associated apoptosis may be driving Group 4 tumorigenesis. Overall, these data provide significant new insight into the spatio-temporal relationships and molecular pathogenesis of the human medulloblastoma subgroups, and provide an important framework for the development of more refined model systems, and ultimately improved therapeutic strategies.

  4. Spatial and temporal variation in selection of genes associated with pearl millet varietal quantitative traits in situ

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    Cedric Mariac

    2016-07-01

    Full Text Available Ongoing global climate changes imply new challenges for agriculture. Whether plants and crops can adapt to such rapid changes is still a widely debated question. We previously showed adaptation in the form of earlier flowering in pearl millet at the scale of a whole country over three decades. However, this analysis did not deal with variability of year to year selection. To understand and possibly manage plant and crop adaptation, we need more knowledge of how selection acts in situ. Is selection gradual, abrupt, and does it vary in space and over time? In the present study, we tracked the evolution of allele frequency in two genes associated with pearl millet phenotypic variation in situ. We sampled 17 populations of cultivated pearl millet over a period of two years. We tracked changes in allele frequencies in these populations by genotyping more than seven thousand individuals. We demonstrate that several allele frequencies changes are compatible with selection, by correcting allele frequency changes associated with genetic drift. We found marked variation in allele frequencies from year to year, suggesting a variable selection effect in space and over time. We estimated the strength of selection associated with variations in allele frequency. Our results suggest that the polymorphism maintained at the genes we studied is partially explained by the spatial and temporal variability of selection. In response to environmental changes, traditional pearl millet varieties could rapidly adapt thanks to this available functional variability.

  5. Influence of photoperiodism on the spatio-temporal accumulation of steviol glycosides in Stevia rebaudiana (Bertoni).

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    Ceunen, Stijn; Geuns, Jan M C

    2013-01-01

    The effect of photoperiodism on steviol glycoside (SVgly) accumulation was investigated in Stevia rebaudiana. Topped plants were cultivated to develop new branches under a 16h or 8h photoperiod. During different ontogenetic phases, leaves, stems, lateral shoots, roots and reproductive organs were collected and analysed for nine SVglys. Long-day (LD) conditions prolonged vegetative growth, significantly increasing leaf biomass and total SVgly content. In both photoperiods, declines in SVglys were observed during reproductive development, occurring mainly in mature leaves under LDs or young leaves under SDs. When lateral shoots were included in plants under LDs, total leaf and SVgly yield per branch significantly increased, indicating a harvest during flowering is possible. The ratio of rebaudioside A (Reb A) to stevioside (ST) amounts was influenced by ontogeny and daylength, with larger ratios during vegetative growth under SDs. Linear correlations were observed between dry matter and total SVglys and between the major SVglys individually. Minor SVglys showed larger fluctuations, especially under SDs. Under LDs, the Reb A to ST ratio was inversely correlated with both leaf dry matter and total SVglys. The highly dynamic nature of the observed patterns suggests a complex regulation of SVgly metabolism on molecular and biochemical level.

  6. Temporal dynamics of immediate early gene expression during cellular consolidation of spatial memory.

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    Barry, Daniel N; Commins, Sean

    2017-06-01

    The consolidation of newly acquired memories on a cellular level is thought to take place in the first few hours following learning. This process is dependent on de novo protein synthesis during this time, which ultimately leads to long-term structural and functional neuronal changes and the stabilisation of a memory trace. Immediate early genes (IEGs) are rapidly expressed in neurons following learning, and previous research has suggested more than one wave of IEG expression facilitates consolidation in the hours following learning. We analysed the expression of Zif268, c-Fos and Arc protein in a number of brain regions involved in spatial learning either 90min, 4h or 8h following training in the Morris water maze task. Consistent with the role of IEGs in the earliest stages of consolidation, a single wave of expression was observed in most brain regions at 90min, however a subsequent wave of expression was not observed at 8h. In fact, Zif268 expression was observed to fall below the levels of naïve controls at this time-point in the medial prefrontal and perirhinal cortices. This may be indicative of synaptic downscaling in these regions in the hours following learning, and an important marker of the consolidation of spatial memory. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. How and When Accentuation Influences Temporally Selective Attention and Subsequent Semantic Processing during On-Line Spoken Language Comprehension: An ERP Study

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    Li, Xiao-qing; Ren, Gui-qin

    2012-01-01

    An event-related brain potentials (ERP) experiment was carried out to investigate how and when accentuation influences temporally selective attention and subsequent semantic processing during on-line spoken language comprehension, and how the effect of accentuation on attention allocation and semantic processing changed with the degree of…

  8. How Can Students' Academic Performance in Statistics Be Improved? Testing the Influence of Social and Temporal-Self Comparison Feedback in a Web-Based Training Environment

    Science.gov (United States)

    Delaval, Marine; Michinov, Nicolas; Le Bohec, Olivier; Le Hénaff, Benjamin

    2017-01-01

    The aim of this study was to examine how social or temporal-self comparison feedback, delivered in real-time in a web-based training environment, could influence the academic performance of students in a statistics examination. First-year psychology students were given the opportunity to train for a statistics examination during a semester by…

  9. How the Number of Alleles Influences Gene Expression

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    Hat, Beata; Paszek, Pawel; Kimmel, Marek; Piechor, Kazimierz; Lipniacki, Tomasz

    2007-07-01

    The higher organisms, eukaryotes, are diploid and most of their genes have two homological copies (alleles). However, the number of alleles in a cell is not constant. In the S phase of the cell cycle all the genome is duplicated and then in the G2 phase and mitosis, which together last for several hours, most of the genes have four copies instead of two. Cancer development is, in many cases, associated with a change in allele number. Several genetic diseases are caused by haploinsufficiency: Lack of one of the alleles or its improper functioning. In the paper we consider the stochastic expression of a gene having a variable number of copies. We applied our previously developed method in which the reaction channels are split into slow (connected with change of gene state) and fast (connected with mRNA/protein synthesis/decay), the later being approximated by deterministic reaction rate equations. As a result we represent gene expression as a piecewise deterministic time-continuous Markov process, which is further related with a system of partial differential hyperbolic equations for probability density functions (pdfs) of protein distribution. The stationary pdfs are calculated analytically for haploidal gene or numerically for diploidal and tetraploidal ones. We distinguished nine classes of simultaneous activation of haploid, diploid and tetraploid genes. This allows for analysis of potential consequences of gene duplication or allele loss. We show that when gene activity is autoregulated by a positive feedback, the change in number of gene alleles may have dramatic consequences for its regulation and may not be compensated by the change of efficiency of mRNA synthesis per allele.

  10. Major genes and QTL influencing wool production and quality: a review

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    Purvis Ian

    2005-12-01

    Full Text Available Abstract The opportunity exists to utilise our knowledge of major genes that influence the economically important traits in wool sheep. Genes with Mendelian inheritance have been identified for many important traits in wool sheep. Of particular importance are genes influencing pigmentation, wool quality and the keratin proteins, the latter of which are important for the morphology of the wool fibre. Gene mapping studies have identified some chromosomal regions associated with variation in wool quality and production traits. The challenge now is to build on this knowledge base in a cost-effective way to deliver molecular tools that facilitate enhanced genetic improvement programs for wool sheep.

  11. Influence of leukotriene gene polymorphisms on chronic rhinosinusitis

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    Duval Melanie

    2008-03-01

    Full Text Available Abstract Background Chronic rhinosinusitis (CRS is increasingly viewed as an inflammatory condition of the sinonasal mucosa interacting with bacteria and/or fungi. However, factors conferring susceptibility to disease remain unknown. Advances in genomics offer powerful tools to explore this disorder. The goal of this study was to evaluate the effect of single nucleotide polymorphisms (SNP on CRS in a panel of genes related to cysteinyl leukotriene metabolism. Methods Severe cases of CRS and postal code match controls were recruited prospectively. A total of 206 cases and 200 controls were available for the present study. Using a candidate gene approach, five genes related to cysteinyl leukotriene metabolism were assessed. For each gene, we selected the maximally informative set of common SNPs (tagSNPs using the European-derived (CEU HapMap dataset. These SNPs are in arachidonate 5-lipoxygenase (ALOX5, arachidonate 5-lipoxygenase-activating protein (ALOX5AP, leukotriene C4 synthase (LTC4S, cysteinyl leukotriene receptor 1 (CYSLTR1 and cysteinyl leukotriene receptor 2 (CYSLTR2 genes. Results A total of 59 SNPs were genotyped to capture the common genetic variations within these genes. Three SNPs located within the ALOX5, CYSLTR1 and ALOX5AP genes reached the nominal p-value threshold (p Conclusion While these initial results do not support that polymorphsims in genes assessed involved in the leukotriene pathways are contributing to the pathogenesis of CRS, this initial study was not powered to detect polymorphisms with relative risk of 2.0 or less, where we could expect many gene effects for complex diseases to occur. Thus, despite this lack of significant association noted in this study, we believe that validation with external populations and the use of better-powered studies in the future may allow more conclusive findings.

  12. Genes influencing circadian differences in blood pressure in hypertensive mice.

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    Francine Z Marques

    Full Text Available Essential hypertension is a common multifactorial heritable condition in which increased sympathetic outflow from the central nervous system is involved in the elevation in blood pressure (BP, as well as the exaggerated morning surge in BP that is a risk factor for myocardial infarction and stroke in hypertensive patients. The Schlager BPH/2J mouse is a genetic model of hypertension in which increased sympathetic outflow from the hypothalamus has an important etiological role in the elevation of BP. Schlager hypertensive mice exhibit a large variation in BP between the active and inactive periods of the day, and also show a morning surge in BP. To investigate the genes responsible for the circadian variation in BP in hypertension, hypothalamic tissue was collected from BPH/2J and normotensive BPN/3J mice at the 'peak' (n = 12 and 'trough' (n = 6 of diurnal BP. Using Affymetrix GeneChip® Mouse Gene 1.0 ST Arrays, validation by quantitative real-time PCR and a statistical method that adjusted for clock genes, we identified 212 hypothalamic genes whose expression differed between 'peak' and 'trough' BP in the hypertensive strain. These included genes with known roles in BP regulation, such as vasopressin, oxytocin and thyrotropin releasing hormone, as well as genes not recognized previously as regulators of BP, including chemokine (C-C motif ligand 19, hypocretin and zinc finger and BTB domain containing 16. Gene ontology analysis showed an enrichment of terms for inflammatory response, mitochondrial proton-transporting ATP synthase complex, structural constituent of ribosome, amongst others. In conclusion, we have identified genes whose expression differs between the peak and trough of 24-hour circadian BP in BPH/2J mice, pointing to mechanisms responsible for diurnal variation in BP. The findings may assist in the elucidation of the mechanism for the morning surge in BP in essential hypertension.

  13. Genes influencing circadian differences in blood pressure in hypertensive mice.

    Science.gov (United States)

    Marques, Francine Z; Campain, Anna E; Davern, Pamela J; Yang, Yee Hwa J; Head, Geoffrey A; Morris, Brian J

    2011-04-26

    Essential hypertension is a common multifactorial heritable condition in which increased sympathetic outflow from the central nervous system is involved in the elevation in blood pressure (BP), as well as the exaggerated morning surge in BP that is a risk factor for myocardial infarction and stroke in hypertensive patients. The Schlager BPH/2J mouse is a genetic model of hypertension in which increased sympathetic outflow from the hypothalamus has an important etiological role in the elevation of BP. Schlager hypertensive mice exhibit a large variation in BP between the active and inactive periods of the day, and also show a morning surge in BP. To investigate the genes responsible for the circadian variation in BP in hypertension, hypothalamic tissue was collected from BPH/2J and normotensive BPN/3J mice at the 'peak' (n = 12) and 'trough' (n = 6) of diurnal BP. Using Affymetrix GeneChip® Mouse Gene 1.0 ST Arrays, validation by quantitative real-time PCR and a statistical method that adjusted for clock genes, we identified 212 hypothalamic genes whose expression differed between 'peak' and 'trough' BP in the hypertensive strain. These included genes with known roles in BP regulation, such as vasopressin, oxytocin and thyrotropin releasing hormone, as well as genes not recognized previously as regulators of BP, including chemokine (C-C motif) ligand 19, hypocretin and zinc finger and BTB domain containing 16. Gene ontology analysis showed an enrichment of terms for inflammatory response, mitochondrial proton-transporting ATP synthase complex, structural constituent of ribosome, amongst others. In conclusion, we have identified genes whose expression differs between the peak and trough of 24-hour circadian BP in BPH/2J mice, pointing to mechanisms responsible for diurnal variation in BP. The findings may assist in the elucidation of the mechanism for the morning surge in BP in essential hypertension.

  14. Spatio-Temporal Pattern and Influencing Factors of Hemorrhagic Fever with Renal Syndrome (HFRS) in Hubei Province (China) between 2005 and 2014

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    Ge, Liang; Zhao, Youlin; Zhou, Kui; Mu, Xiangming; Yu, Haibo; Wang, Yongfeng; Wang, Ning; Fan, Hong; Guo, Liqiang; Huo, XiXiang

    2016-01-01

    Hemorrhagic Fever with Renal Syndrome (HFRS) is considered as a globally distributed infectious disease, which results in many deaths annually in Hubei Province, China. The outbreak of HFRS is usually characterized with spatio-temporal heterogeneity and is seasonally distributed. Further, it might also be impacted by the influencing factors such as socio-economic and geographical environment. To better understand and predict the outbreak of HFRS in the Hubei Province, the spatio-temporal pattern and influencing factors were investigated in this study. Moran’s I Index value was adopted in spatial global autocorrelation analysis to identify the overall spatio-temporal pattern of HFRS outbreak. Kulldorff scan statistical analysis was performed to further identify the changing trends of the clustering patterns of HFRS outbreak. Spearman's rank correlation analysis was used to explore the possible influencing factors on HFRS epidemics such as climate and geographic. The results demonstrated that HFRS outbreak in Hubei Province decreased from 2005 to 2012 in general while increasing slightly from 2012 to 2014. The spatial and temporal scan statistical analysis indicated that HFRS epidemic was temporally clustered in summer and autumn from 2005 to 2014 except 2008 and 2011. The seasonal epidemic pattern of HFRS in Hubei Province was characterized by a bimodal pattern (March to May and September to November) while peaks often occurring in the spring time. SEOV-type HFRS was presumed to influence more on the total number of HFRS incidence than HTNV-type HFRS do. The average humidity and human population density were the main influencing factors during these years. HFRS outbreaks were more in plains than in other areas of Hubei Province. We did not find that whether the terrain of the wetland (water system) plays a significant role in the outbreak of HFRS incidence. With a better understanding of rodent infection rate, socio-economic status and ecological environment

  15. Temporal and spatial variations in microclimate influence the larval foraging behaviors and performance of a conifer-feeding sawfly.

    Science.gov (United States)

    Johns, R C; Boone, J; Leggo, J J; Smith, S; Carleton, D; Quiring, D T

    2012-06-01

    Herbivorous insects are often exposed to broad temporal and spatial variations in microclimate conditions within their host plants and have adapted a variety of behaviors, such as avoidance or basking, to either offset or benefit from such variation. Field experiments were carried out to investigate the influence of daily and intratree variations in microclimate on the behaviors (feeding, resting, dispersal, and hiding) and associated performance of late-instar larvae of the yellowheaded spruce sawfly, Pikonema alaskensis (Rohwer) (Hymenoptera: Tenthredinidae) within crowns of 1.25-1.5 m tall black spruce (Picea mariana [Miller] Britton Sterns Poggenburg); late instars feed on developing shoots of young spruce and are often exposed to microclimatic extremes with unknown effects on performance. Larvae fed diurnally from just after dawn (0800 h) until dusk (2000 h) and rested throughout the night, with brief periods of dispersal occurring in the morning and evening. Neither larval behavior nor abiotic conditions differed significantly between the upper and lower crowns of trees. Temperature, humidity, and solar insolation all explained >90% of variation in feeding; however, sunrise and sunset were the most likely cues influencing diurnal behavior. Most larvae (94%) fed on the bottom, shaded side of shoots, and field experiments indicated that this behavior is adaptive with respect to microclimate, probably reducing hygrothermal stress. Thus, behavioral adaptations by P. alaskensis to daily and within-shoot microclimatic variation may reduce the risk of hygrothermal stress during dispersal or feeding, while still allowing larvae to feed on the preferred and highly nutritious upper crown foliage of young spruce.

  16. The anterior temporal cortex is a primary semantic source of top-down influences on object recognition.

    Science.gov (United States)

    Chiou, Rocco; Lambon Ralph, Matthew A

    2016-06-01

    Perception emerges from a dynamic interplay between feed-forward sensory input and feedback modulation along the cascade of neural processing. Prior knowledge, a major form of top-down modulatory signal, benefits perception by enabling efficacious inference and resolving ambiguity, particularly under circumstances of degraded visual input. Despite semantic information being a potentially critical source of this top-down influence, to date, the core neural substrate of semantic knowledge (the anterolateral temporal lobe - ATL) has not been considered as a key component of the feedback system. Here we provide direct evidence of its significance for visual cognition - the ATL underpins the semantic aspect of object recognition, amalgamating sensory-based (amount of accumulated sensory input) and semantic-based (representational proximity between exemplars and typicality of appearance) influences. Using transcranial theta-burst stimulation combined with a novel visual identification paradigm, we demonstrate that the left ATL contributes to discrimination between visual objects. Crucially, its contribution is especially vital under situations where semantic knowledge is most needed for supplementing deficiency of input (brief visual exposure), discerning analogously-coded exemplars (close representational distance), and resolving discordance (target appearance violating the statistical typicality of its category). Our findings characterise functional properties of the ATL in object recognition: this neural structure is summoned to augment the visual system when the latter is overtaxed by challenging conditions (insufficient input, overlapped neural coding, and conflict between incoming signal and expected configuration). This suggests a need to revisit current theories of object recognition, incorporating the ATL that interfaces high-level vision with semantic knowledge.

  17. Spatial and temporal characterization of fish assemblages in a tropical coastal system influenced by freshwater inputs: northwestern Yucatan Peninsula.

    Science.gov (United States)

    Arceo-Carranza, Daniel; Vega-Cendejas, Ma Eugenia

    2009-01-01

    Coastal lagoons are important systems for freshwater, estuarine and marine organisms; they are considered important zones of reproduction, nursery and feeding for many fish species. The present study investigates the fish assemblages of the natural reserve of Dzilam and their relationship with the hydrologic variables. A total of 6 474 individuals (81 species) were collected, contributing with more than 50% considering the Importance Value Index (IVI), Sphoeroides testudineus, Fundulus persimilis, Anchoa mitchilli, Eucinostomus gula, Eucinostomus argenteus and Mugil trichodon. Differences in species composition were found between seasons the highest during the cold fronts. Spatially, differences were related with the presence of freshwater seeps, the highest in the ecological characterized eastern part and the lowest with higher difference in specific composition located in the western part of the internal zone, due to a higher abundance and dominance of L. rhomboides. Salinity and temperature were the variables that presented a higher influence in the distribution of some pelagic species such as A. mitchilli and A. hepsetus. Because of the abundant freshwater seeps characteristic of the coastal lagoons of Yucatan Peninsula their community structure and fish assemblage display spatial and temporal differences in specific composition.

  18. Influence of human leukocyte antigen genes on TCR V gene segment frequencies.

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    Genevée, C; Farace, F; Chung, V; Diu, A; Raffoux, C; Charron, D; Hercend, T; Triebel, F

    1994-10-01

    Human leukocyte antigen (HLA)-dependent selection mechanisms exerted during thymic maturation are supposed to be main contributing factors to the genetic predetermination of the TCR repertoire and may have a detectable effect on adult peripheral blood lymphocyte V segment frequencies. Here, we analyzed whether polymorphic or non-polymorphic HLA determinants are associated with selected expression of some V gene segment specificities. We first examined the reactivity of 17 V segment specific mAb on purified CD4+ and CD8+ cell fractions in 10 unrelated people. We found a significant overexpression of only three V segment products (V beta 2, V beta 5.1 and V beta 6.7) in CD4+ and none in CD8+ cell fractions in most individuals. Skewing of certain V beta segments by non-polymorphic HLA determinants (i.e. class II for CD4+ and class I for CD8+ cells) is therefore more limited (3/17) than previously thought. Considering the effects of polymorphic HLA determinants, we compared TCR V segment frequencies in HLA-identical siblings to sibling pairs who differ at one or both HLA haplotypes, using 13 V beta specific mAb. In pairwise comparisons, we found that the HLA complex had no detectable effect on TCR repertoire in five large families with multiple siblings. Together, these observations suggest that HLA-predicted selection mechanisms exerted during thymic maturation might not have a predominant influence shaping the TCR repertoire of normal adults.

  19. Sleep Deprivation Influences Circadian Gene Expression in the Lateral Habenula.

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    Zhang, Beilin; Gao, Yanxia; Li, Yang; Yang, Jing; Zhao, Hua

    2016-01-01

    Sleep is governed by homeostasis and the circadian clock. Clock genes play an important role in the generation and maintenance of circadian rhythms but are also involved in regulating sleep homeostasis. The lateral habenular nucleus (LHb) has been implicated in sleep-wake regulation, since LHb gene expression demonstrates circadian oscillation characteristics. This study focuses on the participation of LHb clock genes in regulating sleep homeostasis, as the nature of their involvement is unclear. In this study, we observed changes in sleep pattern following sleep deprivation in LHb-lesioned rats using EEG recording techniques. And then the changes of clock gene expression (Per1, Per2, and Bmal1) in the LHb after 6 hours of sleep deprivation were detected by using real-time quantitative PCR (qPCR). We found that sleep deprivation increased the length of Non-Rapid Eye Movement Sleep (NREMS) and decreased wakefulness. LHb-lesioning decreased the amplitude of reduced wake time and increased NREMS following sleep deprivation in rats. qPCR results demonstrated that Per2 expression was elevated after sleep deprivation, while the other two genes were unaffected. Following sleep recovery, Per2 expression was comparable to the control group. This study provides the basis for further research on the role of LHb Per2 gene in the regulation of sleep homeostasis.

  20. Sleep Deprivation Influences Circadian Gene Expression in the Lateral Habenula

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    Beilin Zhang

    2016-01-01

    Full Text Available Sleep is governed by homeostasis and the circadian clock. Clock genes play an important role in the generation and maintenance of circadian rhythms but are also involved in regulating sleep homeostasis. The lateral habenular nucleus (LHb has been implicated in sleep-wake regulation, since LHb gene expression demonstrates circadian oscillation characteristics. This study focuses on the participation of LHb clock genes in regulating sleep homeostasis, as the nature of their involvement is unclear. In this study, we observed changes in sleep pattern following sleep deprivation in LHb-lesioned rats using EEG recording techniques. And then the changes of clock gene expression (Per1, Per2, and Bmal1 in the LHb after 6 hours of sleep deprivation were detected by using real-time quantitative PCR (qPCR. We found that sleep deprivation increased the length of Non-Rapid Eye Movement Sleep (NREMS and decreased wakefulness. LHb-lesioning decreased the amplitude of reduced wake time and increased NREMS following sleep deprivation in rats. qPCR results demonstrated that Per2 expression was elevated after sleep deprivation, while the other two genes were unaffected. Following sleep recovery, Per2 expression was comparable to the control group. This study provides the basis for further research on the role of LHb Per2 gene in the regulation of sleep homeostasis.

  1. Temporal succession of soil antibiotic resistance genes following application of swine, cattle and poultry manures spiked with or without antibiotics.

    Science.gov (United States)

    Zhang, Yu-Jing; Hu, Hang-Wei; Gou, Min; Wang, Jun-Tao; Chen, Deli; He, Ji-Zheng

    2017-09-27

    Land application of animal manure is a common agricultural practice potentially leading to dispersal and propagation of antibiotic resistance genes (ARGs) in environmental settings. However, the fate of resistome in agro-ecosystems over time following application of different manure sources has never been compared systematically. Here, soil microcosm incubation was conducted to compare effects of poultry, cattle and swine manures spiked with or without the antibiotic tylosin on the temporal changes of soil ARGs. The high-throughput quantitative PCR detected a total of 185 unique ARGs, with Macrolide-Lincosamide-Streptogramin B resistance as the most frequently encountered ARG type. The diversity and abundance of ARGs significantly increased following application of manure and manure spiked with tylosin, with more pronounced effects observed in the swine and poultry manure treatments than in the cattle manure treatment. The level of antibiotic resistance gradually decreased over time in all manured soils but was still significantly higher in the soils treated with swine and poultry manures than in the untreated soils after 130 days' incubation. Tylosin-amended soils consistently showed higher abundances of ARGs than soils treated with manure only, suggesting a strong selection pressure of antibiotic-spiked manure on soil ARGs. The relative abundance of ARGs had significantly positive correlations with integrase and transposase genes, indicative of horizontal transfer potential of ARGs in manure and tylosin treated soils. Our findings provide evidence that application of swine and poultry manures might enrich more soil ARGs than cattle manure, which necessitates the appropriate treatment of raw animal manures prior to land application to minimise the spread of environmental ARGs. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Corpora amylacea deposition in the hippocampus of patients with mesial temporal lobe epilepsy: A new role for an old gene?

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    Abhijit Das

    2011-01-01

    Full Text Available Background: Mesial temporal lobe epilepsy (MTLE is the most common medically refractory epilepsy syndrome in adults, and hippocampal sclerosis (HS is the most frequently encountered lesion in patients with MTLE. Premature accumulation of corpora amylacea (CoA, which plays an important role in the sequestration of toxic cellular metabolites, is found in the hippocampus of 50-60% of the patients who undergo surgery for medically refractory MTLE-HS. However, the etiopathogenesis and clinical importance of this phenomenon are still uncertain. The ABCB1 gene product P-glycoprotein (P-gp plays a prominent role as an antiapoptotic factor in addition to its efflux transporter function. ABCB1 polymorphism has been found to be associated with downregulation of P-gp expression. We hypothesized that a similar polymorphism will be found in patients with CoA deposition, as the polymorphism predisposes the hippocampal neuronal and glial cells to seizure-induced excitotoxic damage and CoA formation ensues as a buffer response. Materials and Methods: We compared five single nucleotide polymorphisms in the ABCB1 gene Ex06+139C/T (rs1202168, Ex 12 C1236T (rs1128503, Ex 17-76T/A (rs1922242, Ex 21 G2677T/A (rs2032582, Ex26 C3435T (rs1045642 among 46 MTLE-HS patients of south Indian ancestry with and without CoA accumulation. Results: We found that subjects carrying the Ex-76T/A polymorphism (TA genotype had a five-times higher risk of developing CoA accumulation than subjects without this genotype (Odds ratio 5.0, 95% confidence intervals 1.34-18.55; P = 0.016. Conclusion: We speculate that rs1922242 polymorphism results in the downregulation of P-gp function, which predisposes the hippocampal cells to seizure-induced apoptosis, and CoA gets accumulated as a buffer response.

  3. Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets.

    Science.gov (United States)

    Zeng, Liping; Zhang, Ning; Zhang, Qiang; Endress, Peter K; Huang, Jie; Ma, Hong

    2017-05-01

    Explosive diversification is widespread in eukaryotes, making it difficult to resolve phylogenetic relationships. Eudicots contain c. 75% of extant flowering plants, are important for human livelihood and terrestrial ecosystems, and have probably experienced explosive diversifications. The eudicot phylogenetic relationships, especially among those of the Pentapetalae, remain unresolved. Here, we present a highly supported eudicot phylogeny and diversification rate shifts using 31 newly generated transcriptomes and 88 other datasets covering 70% of eudicot orders. A highly supported eudicot phylogeny divided Pentapetalae into two groups: one with rosids, Saxifragales, Vitales and Santalales; the other containing asterids, Caryophyllales and Dilleniaceae, with uncertainty for Berberidopsidales. Molecular clock analysis estimated that crown eudicots originated c. 146 Ma, considerably earlier than earliest tricolpate pollen fossils and most other molecular clock estimates, and Pentapetalae sequentially diverged into eight major lineages within c. 15 Myr. Two identified increases of diversification rate are located in the stems leading to Pentapetalae and asterids, and lagged behind the gamma hexaploidization. The nuclear genes from newly generated transcriptomes revealed a well-resolved eudicot phylogeny, sequential separation of major core eudicot lineages and temporal mode of diversifications, providing new insights into the evolutionary trend of morphologies and contributions to the diversification of eudicots. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  4. The influence of vegetation covers on soil moisture dynamics at high temporal resolution in scattered tree woodlands of Mediterranean climate

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    Lozano-Parra, Javier; Schnabel, Susanne; Ceballos-Barbancho, Antonio

    2015-04-01

    Soil water is a key factor that controls the organization and functioning of dryland ecosystems. However, in spite of its great importance in ecohydrological processes, most of the studies focus on daily or longer timescales, while its dynamics at shorter timescales are very little known. The main objective of this work was to determine the role of vegetation covers (grassland and tree canopy) in the soil hydrological response using measurements with high temporal resolution in evergreen oak woodland with Mediterranean climate. For this, soil water content was monitored continuously with a temporal resolution of 30 minutes and by means of capacitance sensors, mainly for the hydrological years 2010-2011 and 2011-2012. They were installed at 5, 10 and 15 cm, and 5 cm above the bedrock and depending on soil profile. This distribution along the soil profile is justified because soils are generally very shallow and most of the roots are concentrated in the upper layer. The sensors were gathered in 8 soil moisture stations in two contrasting situations characterized by different vegetation covers: under tree canopy and in open spaces or grasslands. Soil moisture variations were calculated at rainfall event scale at top soil layer and deepest depth by the difference between the final and initial soil moisture registered by a sensor at the finish and the beginning of the rainfall event, respectively. Besides, as soil moisture changes are strongly influenced by antecedent conditions, different antecedent soil moisture conditions or states, from driest to wettest, were also defined. The works were carried out in 3 experimental farms of the Spanish region of Extremadura. Results obtained revealed that rainwater amount bypassing vegetation covers and reaching the soil may temporarily be modified by covers according to precipitation properties and antecedent environmental conditions (from dry to wet) before the rain episode. Rainfall amounts triggering a positive soil

  5. Temporal Influence on Awareness

    Science.gov (United States)

    1995-12-01

    Noncausality 4.1 Background: Neurophysiological Timing in the Brain Michael S. Gazzaniga , commenting upon the nature of the conscious experience in the ex...1994. 8. Gazzaniga . "Brain Mechanisms and Conscious Experience," Experimental and Theoretical Studies of Consciousness, 247-262 (1993). 9. Gray, Charles

  6. KIR gene content in amerindians indicates influence of demographic factors.

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    Danillo Gardenal Augusto

    Full Text Available Although the KIR gene content polymorphism has been studied worldwide, only a few isolated or Amerindian populations have been analyzed. This extremely diverse gene family codifies receptors that are expressed mainly in NK cells and bind HLA class I molecules. KIR-HLA combinations have been associated to several diseases and population studies are important to comprehend their evolution and their role in immunity. Here we analyzed, by PCR-SSP (specific sequencing priming, 327 individuals from four isolated groups of two of the most important Brazilian Amerindian populations: Kaingang and Guarani. The pattern of KIR diversity among these and other ten Amerindian populations disclosed a wide range of variation for both KIR haplotypes and gene frequencies, indicating that demographic factors, such as bottleneck and founder effects, were the most important evolutionary factors in shaping the KIR polymorphism in these populations.

  7. Height in pre- and postmenopausal women is influenced by estrogen receptor alpha gene polymorphisms

    NARCIS (Netherlands)

    J.B.J. van Meurs (Joyce); A.P. Bergink (Arjan); M. van de Klift (Marjolein); Y. Fang (Yue); G. Leusink (Geraline); A.G. Uitterlinden (André); H.A.P. Pols (Huib); J.P.T.M. van Leeuwen (Hans); S.C.E. Schuit (Stephanie); A. Hofman (Albert)

    2004-01-01

    textabstractThe estrogen receptor alpha gene (ESR1) is known to be involved in metabolic pathways influencing growth. We have performed two population-based association studies using three common polymorphisms within this candidate gene to determine whether these are associated with variation in adu

  8. The Prader-Willi syndrome murine imprinting center is not involved in the spatio-temporal transcriptional regulation of the Necdin gene

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    Dandolo Luisa

    2005-01-01

    Full Text Available Abstract Background The human Prader-Willi syndrome (PWS domain and its mouse orthologue include a cluster of paternally expressed genes which imprinted expression is co-ordinately regulated by an imprinting center (IC closely associated to the Snurf-Snrpn gene. Besides their co-regulated imprinted expression, two observations suggest that the spatio-temporal expression of these genes could also be co-regulated. First, the PWS genes have all been reported to be expressed in the mouse nervous system. Second, Snurf-Snrpn and its associated IC are the most ancient elements of the domain which later acquired additional functional genes by retrotransposition. Although located at least 1.5 megabases from the IC, these retroposons acquired the same imprinted regulation as Snurf-Snrpn. In this study, we ask whether the IC, in addition to its function in imprinting, could also be involved in the spatio-temporal regulation of genes in the PWS domain. Results We compared the expression pattern of Snurf-Snrpn and C/D-box small nucleolar RNAs (snoRNAs MBII-85 and MBII-52 to the expression pattern of the two evolutionary related retroposons Ndn and Magel2, in the developing mouse embryo. We show that these genes have highly similar expression patterns in the central nervous system, suggesting that they share a common central nervous system-specific regulatory element. Among these genes, Ndn and Magel2 display the most similar expression patterns. Using transgenic mice containing the Ndn and Magel2 genes, we show that the transgenic Ndn gene whereas not imprinted is correctly expressed. Search for DNase I hypersensitive sites in the Ndn-Magel2 genomic region and comparative genomic analyses were performed in order to identify potential transcriptional cis-regulatory elements. Conclusions These results strongly suggest that paternally expressed genes of the PWS domain share a common central nervous system-specific regulatory element. We proposed that this

  9. Restriction genes for retroviruses influence the risk of multiple sclerosis

    DEFF Research Database (Denmark)

    Nexø, Bjørn A; Hansen, Bettina; Nissen, Kari K

    2013-01-01

    We recently described that the autoimmune, central nervous system disease, multiple sclerosis (MS), is genetically associated with the human endogenous retroviral locus, HERV-Fc1, in Scandinavians. A number of dominant human genes encoding factors that restrict retrovirus replication have been...

  10. How Molecular Competition Influences Fluxes in Gene Expression Networks

    NARCIS (Netherlands)

    De Vos, Dirk; Bruggeman, Frank J.; Westerhoff, Hans V.; Bakker, Barbara M.

    2011-01-01

    Often, in living cells different molecular species compete for binding to the same molecular target. Typical examples are the competition of genes for the transcription machinery or the competition of mRNAs for the translation machinery. Here we show that such systems have specific regulatory featur

  11. How molecular competition influences fluxes in gene expression networks

    NARCIS (Netherlands)

    Vos, D. de; Bruggeman, F.J.; Westerhoff, H.V.; Bakker, B.M.

    2011-01-01

    Often, in living cells different molecular species compete for binding to the same molecular target. Typical examples are the competition of genes for the transcription machinery or the competition of mRNAs for the translation machinery. Here we show that such systems have specific regulatory featur

  12. How Molecular Competition Influences Fluxes in Gene Expression Networks

    NARCIS (Netherlands)

    Vos, D. de; Bruggeman, F.J.; Westerhoff, H.V.; Bakker, B.M.

    2011-01-01

    Often, in living cells different molecular species compete for binding to the same molecular target. Typical examples are the competition of genes for the transcription machinery or the competition of mRNAs for the translation machinery. Here we show that such systems have specific regulatory featur

  13. Brain Plasticity, Intelligence and Schizophrenia: influence of genes and environment

    NARCIS (Netherlands)

    Hedman, A.M.

    2013-01-01

    This thesis shows that the adult human brain has plastic properties. These plastic properties are at least in part heritable and have functional significance. Identifying genes and environmental factors implicated in brain plasticity is an important next step to optimize brain development in health

  14. Maternal diet influences gene expression in intestine of offspring in chicken (Gallus gallus)

    NARCIS (Netherlands)

    Rebel, J.M.J.; Hemert, van S.; Hoekman, A.J.W.; Francis, R.M.; Balk, F.R.M.; Smits, M.A.

    2006-01-01

    The diet of the mother during pregnancy influences the onset of different diseases and health-related traits in the offspring. We investigated the influence of the mother hen diet on the intestinal gene expression pattern in the offspring. Hens received for 11 weeks either a commercial feed or a

  15. Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of Central Asian pastoralists.

    Science.gov (United States)

    Sengupta, Sanghamitra; Zhivotovsky, Lev A; King, Roy; Mehdi, S Q; Edmonds, Christopher A; Chow, Cheryl-Emiliane T; Lin, Alice A; Mitra, Mitashree; Sil, Samir K; Ramesh, A; Usha Rani, M V; Thakur, Chitra M; Cavalli-Sforza, L Luca; Majumder, Partha P; Underhill, Peter A

    2006-02-01

    Although considerable cultural impact on social hierarchy and language in South Asia is attributable to the arrival of nomadic Central Asian pastoralists, genetic data (mitochondrial and Y chromosomal) have yielded dramatically conflicting inferences on the genetic origins of tribes and castes of South Asia. We sought to resolve this conflict, using high-resolution data on 69 informative Y-chromosome binary markers and 10 microsatellite markers from a large set of geographically, socially, and linguistically representative ethnic groups of South Asia. We found that the influence of Central Asia on the pre-existing gene pool was minor. The ages of accumulated microsatellite variation in the majority of Indian haplogroups exceed 10,000-15,000 years, which attests to the antiquity of regional differentiation. Therefore, our data do not support models that invoke a pronounced recent genetic input from Central Asia to explain the observed genetic variation in South Asia. R1a1 and R2 haplogroups indicate demographic complexity that is inconsistent with a recent single history. Associated microsatellite analyses of the high-frequency R1a1 haplogroup chromosomes indicate independent recent histories of the Indus Valley and the peninsular Indian region. Our data are also more consistent with a peninsular origin of Dravidian speakers than a source with proximity to the Indus and with significant genetic input resulting from demic diffusion associated with agriculture. Our results underscore the importance of marker ascertainment for distinguishing phylogenetic terminal branches from basal nodes when attributing ancestral composition and temporality to either indigenous or exogenous sources. Our reappraisal indicates that pre-Holocene and Holocene-era--not Indo-European--expansions have shaped the distinctive South Asian Y-chromosome landscape.

  16. The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell Fusion

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    Rigzin Dekhang

    2017-01-01

    Full Text Available Light and the circadian clock have a profound effect on the biology of organisms through the regulation of large sets of genes. Toward understanding how light and the circadian clock regulate gene expression, we used genome-wide approaches to identify the direct and indirect targets of the light-responsive and clock-controlled transcription factor ADV-1 in Neurospora crassa. A large proportion of ADV-1 targets were found to be light- and/or clock-controlled, and enriched for genes involved in development, metabolism, cell growth, and cell fusion. We show that ADV-1 is necessary for transducing light and/or temporal information to its immediate downstream targets, including controlling rhythms in genes critical to somatic cell fusion. However, while ADV-1 targets are altered in predictable ways in Δadv-1 cells in response to light, this is not always the case for rhythmic target gene expression. These data suggest that a complex regulatory network downstream of ADV-1 functions to generate distinct temporal dynamics of target gene expression relative to the central clock mechanism.

  17. Effect of short-term feed restriction on temporal changes in milk components and mammary lipogenic gene expression in mid-lactation Holstein dairy cows.

    Science.gov (United States)

    Abdelatty, A M; Iwaniuk, M E; Garcia, M; Moyes, K M; Teter, B B; Delmonte, P; Kadegowda, A K G; Tony, M A; Mohamad, F F; Erdman, R A

    2017-02-22

    Investigations of the temporal changes in mammary gene expression that occur during sudden diet change have been limited by the use of mammary tissue as the source of RNA because of the invasive nature of mammary biopsy procedures. However, the cytosolic crescent, present in 1% of the largest milk fat globules, contains mammary epithelial cell RNA that has become trapped between the inner and outer milk fat globule membranes during final formation and secretion of milk fat into the lumen of the mammary alveoli. We hypothesized that cytosolic crescent RNA extracted from milk fat could be used as an alternative source of mammary epithelial cell RNA to measure the immediate temporal changes in gene expression as a result of changes in diet. In this experiment, feed restriction was used to mimic the state of negative energy balance observed in early lactation and induce a rapid change in milk fat yield and lipogenic gene expression. Ten multiparous Holstein dairy were fed a basal diet ad libitum during a 14-d preliminary period followed by a 4-d experimental period where 5 cows remained on ad libitum feeding and 5 cows were fed at 60% of their d 8-14 intakes (restricted) on d 15 to 18 and then returned to ad libitum feeding on d 19 to 21. Milk samples were collected from each milking on d 13 to 20 and the milk fat was immediately isolated, mixed with Trizol LS, and stored at -80°C for subsequent extraction of RNA that was used for measurement of gene expression. Feed restriction tended to increase milk fat percentage. However, total milk and milk fat production were reduced by 21 and 18%, respectively. Consistent with increased use of body fat for milk synthesis, serum nonesterified fatty acids increased 6-fold (0.78 mEq/L in the feed restriction vs. 0.13 mEq/L ad libitum group), whereas the milk fatty acids genes ACACA, FASN, and SCD1, and the transcription factor SREBF1 were downregulated by 59, 36, 35, and 43%, respectively, during the feed restriction period. In

  18. The immediate and chronic influence of spatio-temporal metaphors on the mental representations of time in english, mandarin, and mandarin-english speakers.

    Science.gov (United States)

    Lai, Vicky Tzuyin; Boroditsky, Lera

    2013-01-01

    In this paper we examine whether experience with spatial metaphors for time has an influence on people's representation of time. In particular we ask whether spatio-temporal metaphors can have both chronic and immediate effects on temporal thinking. In Study 1, we examine the prevalence of ego-moving representations for time in Mandarin speakers, English speakers, and Mandarin-English (ME) bilinguals. As predicted by observations in linguistic analyses, we find that Mandarin speakers are less likely to take an ego-moving perspective than are English speakers. Further, we find that ME bilinguals tested in English are less likely to take an ego-moving perspective than are English monolinguals (an effect of L1 on meaning-making in L2), and also that ME bilinguals tested in Mandarin are more likely to take an ego-moving perspective than are Mandarin monolinguals (an effect of L2 on meaning-making in L1). These findings demonstrate that habits of metaphor use in one language can influence temporal reasoning in another language, suggesting the metaphors can have a chronic effect on patterns in thought. In Study 2 we test Mandarin speakers using either horizontal or vertical metaphors in the immediate context of the task. We find that Mandarin speakers are more likely to construct front-back representations of time when understanding front-back metaphors, and more likely to construct up-down representations of time when understanding up-down metaphors. These findings demonstrate that spatio-temporal metaphors can also have an immediate influence on temporal reasoning. Taken together, these findings demonstrate that the metaphors we use to talk about time have both immediate and long-term consequences for how we conceptualize and reason about this fundamental domain of experience.

  19. Temporal patterns of charcoal burning suicides among the working age population in Hong Kong SAR: the influence of economic activity status and sex

    Science.gov (United States)

    2012-01-01

    Background Charcoal burning in a sealed room has recently emerged as the second most common suicide means in Hong Kong, causing approximately 200 deaths each year. As charcoal burning suicide victims have a unique sociodemographic profile (i.e., predominantly economically active men), they may commit suicide at specific times. However, little is known about the temporal patterns of charcoal burning suicides. Methods Suicide data from 2001 to 2008 on victims of usual working age (20–59) were obtained from the registered death files of the Census and Statistics Department of Hong Kong. A total of 1649 cases of charcoal burning suicide were analyzed using a two-step procedure, which first examined the temporal asymmetries in the incidence of suicide, and second investigated whether these asymmetries were influenced by sex and/or economic activity status. Poisson regression analyses were employed to model the monthly and daily patterns of suicide by economic activity status and sex. Results Our findings revealed pronounced monthly and daily temporal variations in the pattern of charcoal burning suicides in Hong Kong. Consistent with previous findings on overall suicide deaths, there was an overall spring peak in April, and Monday was the common high risk day for all groups. Although sex determined the pattern of variation in charcoal burning suicides, the magnitude of the variation was influenced by the economic activity status of the victims. Conclusion The traditional classification of suicide methods as either violent or nonviolent tends to elide the temporal variations of specific methods. The interaction between sex and economic activity status observed in the present study indicates that sex should be taken into consideration when investigating the influence of economic activity status on temporal variations of suicide. This finding also suggests that suicide prevention efforts should be both time- and subgroup-specific. PMID:22770504

  20. Spatial-Temporal Variations of Chlorophyll-a in the Adjacent Sea Area of the Yangtze River Estuary Influenced by Yangtze River Discharge

    Directory of Open Access Journals (Sweden)

    Ying Wang

    2015-05-01

    Full Text Available Carrying abundant nutrition, terrigenous freshwater has a great impact on the spatial and temporal heterogeneity of phytoplankton in coastal waters. The present study analyzed the spatial-temporal variations of Chlorophyll-a (Chl-a concentration under the influence of discharge from the Yangtze River, based on remotely sensed Chl-a concentrations. The study area was initially zoned to quantitatively investigate the spatial variation patterns of Chl-a. Then, the temporal variation of Chl-a in each zone was simulated by a sinusoidal curve model. The results showed that in the inshore waters, the terrigenous discharge was the predominant driving force determining the pattern of Chl-a, which brings the risk of red tide disasters; while in the open sea areas, Chl-a was mainly affected by meteorological factors. Furthermore, a diversity of spatial and temporal variations of Chl-a existed based on the degree of influences from discharge. The diluted water extended from inshore to the east of Jeju Island. This process affected the Chl-a concentration flowing through the area, and had a potential impact on the marine environment. The Chl-a from September to November showed an obvious response to the discharge from July to September with a lag of 1 to 2 months.

  1. Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors

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    Frank Emmert-Streib

    2013-02-01

    Full Text Available The inference of gene regulatory networks gained within recent years a considerable interest in the biology and biomedical community. The purpose of this paper is to investigate the influence that environmental conditions can exhibit on the inference performance of network inference algorithms. Specifically, we study five network inference methods, Aracne, BC3NET, CLR, C3NET and MRNET, and compare the results for three different conditions: (I observational gene expression data: normal environmental condition, (II interventional gene expression data: growth in rich media, (III interventional gene expression data: normal environmental condition interrupted by a positive spike-in stimulation. Overall, we find that different statistical inference methods lead to comparable, but condition-specific results. Further, our results suggest that non-steady-state data enhance the inferability of regulatory networks.

  2. Patrones fenologico de la provincia de Mendoza, Argentina: Mediante serie temporal de imágenes NOAA - AVHRR NDI GAC

    NARCIS (Netherlands)

    González Loyarte, M.M.; Menenti, M.; Roig, F.A.

    2010-01-01

    Phenological patterns of the province of Mendoza, Argentina, through a temporal series of NOAA-AVHRR NDVI GAC images. The temporal dynamics of vegetation in Mendoza is described through analysis of regional foliar phenology using a series of 108 monthly NOAA-AVHRR NDVI GAC images. A Fast Fourier

  3. Patrones fenologico de la provincia de Mendoza, Argentina: Mediante serie temporal de imágenes NOAA - AVHRR NDI GAC

    NARCIS (Netherlands)

    González Loyarte, M.M.; Menenti, M.; Roig, F.A.

    2010-01-01

    Phenological patterns of the province of Mendoza, Argentina, through a temporal series of NOAA-AVHRR NDVI GAC images. The temporal dynamics of vegetation in Mendoza is described through analysis of regional foliar phenology using a series of 108 monthly NOAA-AVHRR NDVI GAC images. A Fast Fourier Tra

  4. Temporal Dissection of Rate Limiting Transcriptional Events Using Pol II ChIP and RNA Analysis of Adrenergic Stress Gene Activation.

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    Daniel P Morris

    Full Text Available In mammals, increasing evidence supports mechanisms of co-transcriptional gene regulation and the generality of genetic control subsequent to RNA polymerase II (Pol II recruitment. In this report, we use Pol II Chromatin Immunoprecipitation to investigate relationships between the mechanistic events controlling immediate early gene (IEG activation following stimulation of the α1a-Adrenergic Receptor expressed in rat-1 fibroblasts. We validate our Pol II ChIP assay by comparison to major transcriptional events assessable by microarray and PCR analysis of precursor and mature mRNA. Temporal analysis of Pol II density suggests that reduced proximal pausing often enhances gene expression and was essential for Nr4a3 expression. Nevertheless, for Nr4a3 and several other genes, proximal pausing delayed the time required for initiation of productive elongation, consistent with a role in ensuring transcriptional fidelity. Arrival of Pol II at the 3' cleavage site usually correlated with increased polyadenylated mRNA; however, for Nfil3 and probably Gprc5a expression was delayed and accompanied by apparent pre-mRNA degradation. Intragenic pausing not associated with polyadenylation was also found to regulate and delay Gprc5a expression. Temporal analysis of Nr4a3, Dusp5 and Nfil3 shows that transcription of native IEG genes can proceed at velocities of 3.5 to 4 kilobases/min immediately after activation. Of note, all of the genes studied here also used increased Pol II recruitment as an important regulator of expression. Nevertheless, the generality of co-transcriptional regulation during IEG activation suggests temporal and integrated analysis will often be necessary to distinguish causative from potential rate limiting mechanisms.

  5. The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces

    Science.gov (United States)

    Mao, Xizeng; Zhang, Han; Yin, Yanbin; Xu, Ying

    2012-01-01

    The majority of bacterial genes are located on the leading strand, and the percentage of such genes has a large variation across different bacteria. Although some explanations have been proposed, these are at most partial explanations as they cover only small percentages of the genes and do not even consider the ones biased toward the lagging strand. We have carried out a computational study on 725 bacterial genomes, aiming to elucidate other factors that may have influenced the strand location of genes in a bacterium. Our analyses suggest that (i) genes of some functional categories such as ribosome have higher preferences to be on the leading strands; (ii) genes of some functional categories such as transcription factor have higher preferences on the lagging strands; (iii) there is a balancing force that tends to keep genes from all moving to the leading and more efficient strand and (iv) the percentage of leading-strand genes in an bacterium can be accurately explained based on the numbers of genes in the functional categories outlined in (i) and (ii), genome size and gene density, indicating that these numbers implicitly contain the information about the percentage of genes on the leading versus lagging strand in a genome. PMID:22735706

  6. Influence of the myopia gene on brain development.

    Science.gov (United States)

    Karlsson, J L

    1975-11-01

    Evaluation of the performance of 17-18-year-old high school students on standard intelligence tests confirms previous reports that nearsighted persons consistently achieve scores approximately eight I.O. points higher than non-myopes. Comparison of tests administered to the same students 10 years earlier suggests that the intellectual gain precedes the development of nearsightedness. Since there is convincing evidence from genetic studies that myopia is an inherited condition, probably transmitted as a recessive characteristic, it is concluded that the myopia gene has a stimulant action on the brain in addition to its effect on the eye. The high frequency of myopia in urbanized societies is explained in terms of an evolutionary adjustment, myopes probably having a survival advantage under conditions of industrialization.

  7. Chronic intermittent hypoxia increases encoding pigment epithelium-derived factor gene expression, although not that of the protein itself, in the temporal cortex of rats,

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    Guilherme Silva Julian

    2015-02-01

    Full Text Available Objective: Obstructive sleep apnea syndrome is mainly characterized by intermittent hypoxia (IH during sleep, being associated with several complications. Exposure to IH is the most widely used animal model of sleep apnea, short-term IH exposure resulting in cognitive and neuronal impairment. Pigment epithelium-derived factor (PEDF is a hypoxia-sensitive factor acting as a neurotrophic, neuroprotective, and antiangiogenic agent. Our study analyzed performance on learning and cognitive tasks, as well as PEDF gene expression and PEDF protein expression in specific brain structures, in rats exposed to long-term IH. Methods: Male Wistar rats were exposed to IH (oxygen concentrations of 21-5% for 6 weeks-the chronic IH (CIH group-or normoxia for 6 weeks-the control group. After CIH exposure, a group of rats were allowed to recover under normoxic conditions for 2 weeks (the CIH+N group. All rats underwent the Morris water maze test for learning and memory, PEDF gene expression and PEDF protein expression in the hippocampus, frontal cortex, and temporal cortex being subsequently assessed. Results: The CIH and CIH+N groups showed increased PEDF gene expression in the temporal cortex, PEDF protein expression remaining unaltered. PEDF gene expression and PEDF protein expression remained unaltered in the frontal cortex and hippocampus. Long-term exposure to IH did not affect cognitive function. Conclusions: Long-term exposure to IH selectively increases PEDF gene expression at the transcriptional level, although only in the temporal cortex. This increase is probably a protective mechanism against IH-induced injury.

  8. Age-related differences in motor coordination during simultaneous leg flexion and finger extension: influence of temporal pressure.

    Science.gov (United States)

    Hussein, Tarek; Yiou, Eric; Larue, Jacques

    2013-01-01

    Although the effect of temporal pressure on spatio-temporal aspects of motor coordination and posture is well established in young adults, there is a clear lack of data on elderly subjects. This work examined the aging-related effects of temporal pressure on movement synchronization and dynamic stability. Sixteen young and eleven elderly subjects performed series of simultaneous rapid leg flexions in an erect posture paired with ipsilateral index-finger extensions, minimizing the difference between heel and finger movement onsets. This task was repeated ten times under two temporal conditions (self-initiated [SI] vs. reaction-time [RT]). Results showed that, first, temporal pressure modified movement synchronization; the finger extension preceded swing heel-off in RT, and inversely in SI. Synchronization error and associated standard deviation were significantly greater in elderly than in young adults in SI only, i.e. in the condition where proprioception is thought to be crucial for temporal coordination. Secondly, both groups developed a significantly shorter mediolateral (ML) anticipatory postural adjustment duration in RT (high temporal pressure) than in SI. In both groups, this shortening was compensated by an increase in the anticipatory peak of centre-of-gravity (CoG) acceleration towards the stance-leg so that ML dynamic stability at foot-off, quantified with the "extrapolated centre-of-mass", remained unchanged across temporal conditions. This increased CoG acceleration was associated with an increased anticipatory peak of ML centre-of-pressure shift towards the swing-leg in young adults only. This suggested that the ability to accelerate the CoG with the centre-of-pressure shift was degraded in elderly, probably due to weakness in the lower limb muscles. Dynamic stability at foot-off was also degraded in elderly, with a consequent increased risk of ML imbalance and falling. The present study provides new insights into the ability of elderly adults to deal

  9. Age-related differences in motor coordination during simultaneous leg flexion and finger extension: influence of temporal pressure.

    Directory of Open Access Journals (Sweden)

    Tarek Hussein

    Full Text Available Although the effect of temporal pressure on spatio-temporal aspects of motor coordination and posture is well established in young adults, there is a clear lack of data on elderly subjects. This work examined the aging-related effects of temporal pressure on movement synchronization and dynamic stability. Sixteen young and eleven elderly subjects performed series of simultaneous rapid leg flexions in an erect posture paired with ipsilateral index-finger extensions, minimizing the difference between heel and finger movement onsets. This task was repeated ten times under two temporal conditions (self-initiated [SI] vs. reaction-time [RT]. Results showed that, first, temporal pressure modified movement synchronization; the finger extension preceded swing heel-off in RT, and inversely in SI. Synchronization error and associated standard deviation were significantly greater in elderly than in young adults in SI only, i.e. in the condition where proprioception is thought to be crucial for temporal coordination. Secondly, both groups developed a significantly shorter mediolateral (ML anticipatory postural adjustment duration in RT (high temporal pressure than in SI. In both groups, this shortening was compensated by an increase in the anticipatory peak of centre-of-gravity (CoG acceleration towards the stance-leg so that ML dynamic stability at foot-off, quantified with the "extrapolated centre-of-mass", remained unchanged across temporal conditions. This increased CoG acceleration was associated with an increased anticipatory peak of ML centre-of-pressure shift towards the swing-leg in young adults only. This suggested that the ability to accelerate the CoG with the centre-of-pressure shift was degraded in elderly, probably due to weakness in the lower limb muscles. Dynamic stability at foot-off was also degraded in elderly, with a consequent increased risk of ML imbalance and falling. The present study provides new insights into the ability of

  10. Temporal changes in the structure of a plant-frugivore network are influenced by bird migration and fruit availability

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    Michelle Ramos-Robles

    2016-06-01

    Full Text Available Background. Ecological communities are dynamic collections whose composition and structure change over time, making up complex interspecific interaction networks. Mutualistic plant–animal networks can be approached through complex network analysis; these networks are characterized by a nested structure consisting of a core of generalist species, which endows the network with stability and robustness against disturbance. Those mutualistic network structures can vary as a consequence of seasonal fluctuations and food availability, as well as the arrival of new species into the system that might disorder the mutualistic network structure (e.g., a decrease in nested pattern. However, there is no assessment on how the arrival of migratory species into seasonal tropical systems can modify such patterns. Emergent and fine structural temporal patterns are adressed here for the first time for plant-frugivorous bird networks in a highly seasonal tropical environment. Methods. In a plant-frugivorous bird community, we analyzed the temporal turnover of bird species comprising the network core and periphery of ten temporal interaction networks resulting from different bird migration periods. Additionally, we evaluated how fruit abundance and richness, as well as the arrival of migratory birds into the system, explained the temporal changes in network parameters such as network size, connectance, nestedness, specialization, interaction strength asymmetry and niche overlap. The analysis included data from 10 quantitative plant-frugivorous bird networks registered from November 2013 to November 2014. Results. We registered a total of 319 interactions between 42 plant species and 44 frugivorous bird species; only ten bird species were part of the network core. We witnessed a noteworthy turnover of the species comprising the network periphery during migration periods, as opposed to the network core, which did not show significant temporal changes in species

  11. Identification of endogenous reference genes for the analysis of microRNA expression in the hippocampus of the pilocarpine-induced model of mesial temporal lobe epilepsy.

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    Mykaella Andrade de Araújo

    Full Text Available Real-time quantitative RT-PCR (qPCR is one of the most powerful techniques for analyzing miRNA expression because of its sensitivity and specificity. However, in this type of analysis, a suitable normalizer is required to ensure that gene expression is unaffected by the experimental condition. To the best of our knowledge, there are no reported studies that performed a detailed identification and validation of suitable reference genes for miRNA qPCR during the epileptogenic process. Here, using a pilocarpine (PILO model of mesial temporal lobe epilepsy (MTLE, we investigated five potential reference genes, performing a stability expression analysis using geNorm and NormFinder softwares. As a validation strategy, we used each one of the candidate reference genes to measure PILO-induced changes in microRNA-146a levels, a gene whose expression pattern variation in the PILO injected model is known. Our results indicated U6SnRNA and SnoRNA as the most stable candidate reference genes. By geNorm analysis, the normalization factor should preferably contain at least two of the best candidate reference genes (snoRNA and U6SnRNA. In fact, when normalized using the best combination of reference genes, microRNA-146a transcripts were found to be significantly increased in chronic stage, which is consistent with the pattern reported in different models. Conversely, when reference genes were individually employed for normalization, we failed to detect up-regulation of the microRNA-146a gene in the hippocampus of epileptic rats. The data presented here support that the combination of snoRNA and U6SnRNA was the minimum necessary for an accurate normalization of gene expression at the different stages of epileptogenesis that we tested.

  12. Temporal pattern of loss/persistence of duplicate genes involved in signal transduction and metabolic pathways after teleost-specific genome duplication

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    Sato Yukuto

    2009-06-01

    Full Text Available Abstract Background Recent genomic studies have revealed a teleost-specific third-round whole genome duplication (3R-WGD event occurred in a common ancestor of teleost fishes. However, it is unclear how the genes duplicated in this event were lost or persisted during the diversification of teleosts, and therefore, how many of the duplicated genes contribute to the genetic differences among teleosts. This subject is also important for understanding the process of vertebrate evolution through WGD events. We applied a comparative evolutionary approach to this question by focusing on the genes involved in long-term potentiation, taste and olfactory transduction, and the tricarboxylic acid cycle, based on the whole genome sequences of four teleosts; zebrafish, medaka, stickleback, and green spotted puffer fish. Results We applied a state-of-the-art method of maximum-likelihood phylogenetic inference and conserved synteny analyses to each of 130 genes involved in the above biological systems of human. These analyses identified 116 orthologous gene groups between teleosts and tetrapods, and 45 pairs of 3R-WGD-derived duplicate genes among them. This suggests that more than half [(45×2/(116+45] = 56.5% of the loci, probably more than ten thousand genes, present in a common ancestor of the four teleosts were still duplicated after the 3R-WGD. The estimated temporal pattern of gene loss suggested that, after the 3R-WGD, many (71/116 of the duplicated genes were rapidly lost during the initial 75 million years (MY, whereas on average more than half (27.3/45 of the duplicated genes remaining in the ancestor of the four teleosts (45/116 have persisted for about 275 MY. The 3R-WGD-derived duplicates that have persisted for a long evolutionary periods of time had significantly larger number of interacting partners and longer length of protein coding sequence, implying that they tend to be more multifunctional than the singletons after the 3R-WGD. Conclusion

  13. Influence of hCG on inducible nitric oxide synthase gene expression in ram testicular arteries

    Directory of Open Access Journals (Sweden)

    Maria Matteo

    2014-09-01

    Full Text Available Background. Experimental evidence suggests a relationship between the vasodilatory effect of hCG and the NOS system in the testis. The influence of hCG administration on testicular vascular NOS gene expression has not been fully investigated. Objective: This study aimed to evaluate the presence of the nitric oxide syntheses gene in ram testicular arteries and the influence of hCG administration on its expression. Materials and methods: Both testicular arteries of sixteen rams were extracted before and after i.v. administration of 5000 IU of hCG or placebo. The expression of the iNOS gene was investigated by real time PCR. Data were analyzed by means of Wilcoxon and Mann-Whitney tests. A p value of < 0.05 was considered statistically significant. Results: PCR revealed the presence of iNOS mRNA in all basal samples but the expression of the iNOS gene was significantly reduced in all arteries obtained 24 h after the administration of either hCG or placebo. A significant reduction in the expression of iNOS gene was observed in the testicular arteries extracted after 24 h in both treated and placebo groups. On the other hand hCG stimulation did not significantly influence iNOS expression following its administration compared to a placebo. Conclusion: Ram testicular arteries express the iNOS gene but hCG stimulation did not significantly influence iNOS expression. A significant reduction in the expression of this gene was observed in the testicular arteries extracted after 24 h in both treated and placebo groups, suggesting that iNOS expression on the testicular artery could be influenced by the spermatic vessel ligation of the controlateral testis.

  14. Influence of CFH gene on symptom severity of schizophrenia

    Science.gov (United States)

    Zhang, Chen; Lv, Qinyu; Fan, Weixing; Tang, Wei; Yi, Zhenghui

    2017-01-01

    Objective Recent advances have provided compelling evidence for the role of excessive complement activity in the pathophysiology of schizophrenia. In this study, we aimed to detect the association of the gene encoding complement factor H (CFH), a regulator in complement activation, with schizophrenia. Materials and methods A sample of 1783 individuals with or without schizophrenia was recruited for genetic analysis. Genomic DNA samples were extracted from peripheral blood cells using multiplex polymerase chain reaction and the SNaPshot assay. A Database for Schizophrenia Genetic Research (SZDB) was used to detect the association of brain CFH expression with schizophrenia. Next, we performed a genotype–phenotype analysis to identify the relationship between CFH Y402H polymorphism and clinical features of schizophrenia. Results There was a significant association of hippocampal CFH expression with schizophrenia (P=0.017), whereas this significance did not survive after adjusting for false discovery rate (P=0.105). Comparing the genotype and allele frequencies of the genotyped single-nucleotide polymorphisms between case and control groups showed no significant difference. There were significant differences in the scores of negative symptoms and delayed memory between the patients with C allele and those without C allele (Pschizophrenia. PMID:28293111

  15. Number of X-chromosome genes influences social behavior and vasopressin gene expression in mice.

    Science.gov (United States)

    Cox, Kimberly H; Quinnies, Kayla M; Eschendroeder, Alex; Didrick, Paula M; Eugster, Erica A; Rissman, Emilie F

    2015-01-01

    Sex differences in behavior are widespread and often caused by hormonal differences between the sexes. In addition to hormones, the composition and numbers of the sex chromosomes also affect a variety of sex differences. In humans, X-chromosome genes are implicated in neurobehavioral disorders (i.e. fragile-X, autism). To investigate the role of X-chromosome genes in social behavior, we used a mouse model that has atypical sex chromosome configurations resembling Turner (45, XO) and Klinefelter syndromes (47, XXY). We examined a number of behaviors in juvenile mice. Mice with only one copy of most X-chromosome genes, regardless of gonadal sex, were less social in dyadic interaction and social preference tasks. In the elevated plus maze, mice with one X-chromosome spent less time in the distal ends of the open arms as compared to mice with two copies of X-chromosome genes. Using qRTPCR, we noted that amygdala from female mice with one X-chromosome had higher expression levels of vasopressin (Avp) as compared to mice in the other groups. Finally, in plasma from girls with Turner syndrome we detected reduced vasopressin (AVP) concentrations as compared to control patients. These novel findings link sex chromosome genes with social behavior via concentrations of AVP in brain, adding to our understanding of sex differences in neurobehavioral disorders.

  16. Beyond the single gene: How epistasis and gene-by-environment effects influence crop domestication.

    Science.gov (United States)

    Doust, Andrew N; Lukens, Lewis; Olsen, Kenneth M; Mauro-Herrera, Margarita; Meyer, Ann; Rogers, Kimberly

    2014-04-29

    Domestication is a multifaceted evolutionary process, involving changes in individual genes, genetic interactions, and emergent phenotypes. There has been extensive discussion of the phenotypic characteristics of plant domestication, and recent research has started to identify the specific genes and mutational mechanisms that control domestication traits. However, there is an apparent disconnect between the simple genetic architecture described for many crop domestication traits, which should facilitate rapid phenotypic change under selection, and the slow rate of change reported from the archeobotanical record. A possible explanation involves the middle ground between individual genetic changes and their expression during development, where gene-by-gene (epistatic) and gene-by-environment interactions can modify the expression of phenotypes and opportunities for selection. These aspects of genetic architecture have the potential to significantly slow the speed of phenotypic evolution during crop domestication and improvement. Here we examine whether epistatic and gene-by-environment interactions have shaped how domestication traits have evolved. We review available evidence from the literature, and we analyze two domestication-related traits, shattering and flowering time, in a mapping population derived from a cross between domesticated foxtail millet and its wild progenitor. We find that compared with wild progenitor alleles, those favored during domestication often have large phenotypic effects and are relatively insensitive to genetic background and environmental effects. Consistent selection should thus be able to rapidly change traits during domestication. We conclude that if phenotypic evolution was slow during crop domestication, this is more likely due to cultural or historical factors than epistatic or environmental constraints.

  17. Influences on gene expression in vivo by a Shine-Dalgarno sequence

    DEFF Research Database (Denmark)

    Jin, Haining; Zhao, Qing; Gonzalez de Valdivia, Ernesto I;

    2006-01-01

    The Shine-Dalgarno (SD+: 5'-AAGGAGG-3') sequence anchors the mRNA by base pairing to the 16S rRNA in the small ribosomal subunit during translation initiation. We have here compared how an SD+ sequence influences gene expression, if located upstream or downstream of an initiation codon....... The positive effect of an upstream SD+ is confirmed. A downstream SD+ gives decreased gene expression. This effect is also valid for appropriately modified natural Escherichia coli genes. If an SD+ is placed between two potential initiation codons, initiation takes place predominantly at the second start site...

  18. Influence of sublethal concentrations of common disinfectants on expression of virulence genes in Listeria monocytogenes

    DEFF Research Database (Denmark)

    Kastbjerg, Vicky Gaedt; Larsen, M. H.; Gram, Lone

    2010-01-01

    Listeria monocytogenes is a food-borne human pathogen that causes listeriosis, a relatively rare infection with a high fatality rate. The regulation of virulence gene expression is influenced by several environmental factors, and the aim of the present study was to determine how disinfectants used...... routinely in the food industry affect the expression of different virulence genes in L. monocytogenes when added at sublethal concentrations. An agar-based assay was developed to screen the effect of disinfectants on virulence gene promoter expression and was validated at the transcriptional level...... by Northern blot analysis. Eleven disinfectants representing four different groups of active components were evaluated in this study. Disinfectants with the same active ingredients had a similar effect on gene expression. Peroxy and chlorine compounds reduced the expression of the virulence genes...

  19. Genome size diversity in angiosperms and its influence on gene space.

    Science.gov (United States)

    Dodsworth, Steven; Leitch, Andrew R; Leitch, Ilia J

    2015-12-01

    Genome size varies c. 2400-fold in angiosperms (flowering plants), although the range of genome size is skewed towards small genomes, with a mean genome size of 1C=5.7Gb. One of the most crucial factors governing genome size in angiosperms is the relative amount and activity of repetitive elements. Recently, there have been new insights into how these repeats, previously discarded as 'junk' DNA, can have a significant impact on gene space (i.e. the part of the genome comprising all the genes and gene-related DNA). Here we review these new findings and explore in what ways genome size itself plays a role in influencing how repeats impact genome dynamics and gene space, including gene expression. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  20. 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.

  1. Representing Representation: Integration between the Temporal Lobe and the Posterior Cingulate Influences the Content and Form of Spontaneous Thought.

    Directory of Open Access Journals (Sweden)

    Jonathan Smallwood

    Full Text Available When not engaged in the moment, we often spontaneously represent people, places and events that are not present in the environment. Although this capacity has been linked to the default mode network (DMN, it remains unclear how interactions between the nodes of this network give rise to particular mental experiences during spontaneous thought. One hypothesis is that the core of the DMN integrates information from medial and lateral temporal lobe memory systems, which represent different aspects of knowledge. Individual differences in the connectivity between temporal lobe regions and the default mode network core would then predict differences in the content and form of people's spontaneous thoughts. This study tested this hypothesis by examining the relationship between seed-based functional connectivity and the contents of spontaneous thought recorded in a laboratory study several days later. Variations in connectivity from both medial and lateral temporal lobe regions was associated with different patterns of spontaneous thought and these effects converged on an overlapping region in the posterior cingulate cortex. We propose that the posterior core of the DMN acts as a representational hub that integrates information represented in medial and lateral temporal lobe and this process is important in determining the content and form of spontaneous thought.

  2. Representing Representation: Integration between the Temporal Lobe and the Posterior Cingulate Influences the Content and Form of Spontaneous Thought.

    Science.gov (United States)

    Smallwood, Jonathan; Karapanagiotidis, Theodoros; Ruby, Florence; Medea, Barbara; de Caso, Irene; Konishi, Mahiko; Wang, Hao-Ting; Hallam, Glyn; Margulies, Daniel S; Jefferies, Elizabeth

    2016-01-01

    When not engaged in the moment, we often spontaneously represent people, places and events that are not present in the environment. Although this capacity has been linked to the default mode network (DMN), it remains unclear how interactions between the nodes of this network give rise to particular mental experiences during spontaneous thought. One hypothesis is that the core of the DMN integrates information from medial and lateral temporal lobe memory systems, which represent different aspects of knowledge. Individual differences in the connectivity between temporal lobe regions and the default mode network core would then predict differences in the content and form of people's spontaneous thoughts. This study tested this hypothesis by examining the relationship between seed-based functional connectivity and the contents of spontaneous thought recorded in a laboratory study several days later. Variations in connectivity from both medial and lateral temporal lobe regions was associated with different patterns of spontaneous thought and these effects converged on an overlapping region in the posterior cingulate cortex. We propose that the posterior core of the DMN acts as a representational hub that integrates information represented in medial and lateral temporal lobe and this process is important in determining the content and form of spontaneous thought.

  3. Silencing of the SlNAP7 gene influences plastid development and lycopene accumulation in tomato

    Science.gov (United States)

    Fu, Da-Qi; Meng, Lan-Huan; Zhu, Ben-Zhong; Zhu, Hong-Liang; Yan, Hua-Xue; Luo, Yun-Bo

    2016-12-01

    Ripening is an important stage of fruit development. To screen the genes associated with pigment formation in tomato fruit, a suppression subtractive hybridization (SSH) cDNA library was constructed by using tomato fruit in the green ripe and break ripe stages, and 129 differential genes were obtained. Using redness as a screening marker, virus-induced gene silencing (VIGS) of the differential genes was performed with a sprout vacuum-infiltration system (SVI). The results showed that silencing the SlNAP7 gene affected the chloroplast development of tomato leaves, manifesting as a photo-bleaching phenotype, and silenced fruit significantly affected the accumulation of lycopene, manifested as a yellow phenotype. In our study, we found that silencing the SlNAP7 gene downregulates the expression of the POR and PORA genes and destroys the normal development of the chloroplast. The expression of related genes included in the lycopene biosynthesis pathway was not significantly changed, but lycopene accumulation was significantly reduced in tomato fruit. Perhaps it was caused by the destruction of the chromoplast, which leads to the oxidation of lycopene. The results show that the SlNAP7 gene influences chloroplast development and lycopene accumulation in tomato.

  4. Venom of the ectoparasitoid, Nasonia vitripennis, influences gene expression in Musca domestica hemocytes.

    Science.gov (United States)

    Qian, Cen; Liu, Yang; Fang, Qi; Min-Li, Yan; Liu, Shu-Sheng; Ye, Gong-Yin; Li, Yan-Min

    2013-08-01

    Insect hosts have evolved potent innate immunity against invasion by parasitoid wasps. Host/parasitoids live in co-evolutionary relationships. Nasonia vitripennis females inject venom into their dipteran hosts just prior to laying eggs on the host's outer integument. The parasitoid larvae are ectoparasitoids because they feed on their hosts within the puparium, but do not enter the host body. We investigated the influence of N. vitripennis venom on the gene expression profile of hemocytes of their hosts, pupae of the housefly, Musca domestica. We prepared venom by isolating venom glands and treated experimental host pupae with venom. We used suppression subtractive hybridization (SSH) to determine the influence of venom on hemocyte gene expression. At 1 h post treatment, we recorded decreases in transcript levels of 133 EST clones derived from forward a subtractive library of host hemocytes and upregulation in transcript levels of 111 EST clones from the reverse library. These genes are related to immune and stress response, cytoskeleton, cell cycle and apoptosis, metabolism, transport, and transcription/translation regulation. We verified the reliability of our data with reverse transcription quantitative real-time PCR analysis of randomly selected genes, and with assays of enzyme activities. These analyses showed that the expression level of all selected genes were downregulated after venom treatment. Outcomes of our experiments support the hypothesis that N. vitripennis venom influences the gene expression in host hemocytes. We conclude that the actions of venom on host gene expression influence host biology in ways that benefit the development and emergence of the next generation of parasitoids.

  5. Spatial and temporal characterization of fish assemblages in a tropical coastal system influenced by freshwater inputs: northwestern Yucatan peninsula

    Directory of Open Access Journals (Sweden)

    Daniel Arceo-Carranza

    2009-06-01

    Full Text Available Coastal lagoons are important systems for freshwater, estuarine and marine organisms; they are considered important zones of reproduction, nursery and feeding for many fish species. The present study investigates the fish assemblages of the natural reserve of Dzilam and their relationship with the hydrologic variables. A total of 6 474 individuals (81 species were collected, contributing with more than 50% considering the Importance Value Index (IVI, Sphoeroides testudineus, Fundulus persimilis, Anchoa mitchilli, Eucinostomus gula, Eucinostomus argenteus and Mugil trichodon. Differences in species composition were found between seasons the highest during the cold fronts. Spatially, differences were related with the presence of freshwater seeps, the highest in the ecological characterized eastern part and the lowest with higher difference in specific composition located in the western part of the internal zone, due to a higher abundance and dominance of L. rhomboides. Salinity and temperature were the variables that presented a higher influence in the distribution of some pelagic species such as A. mitchilli and A. hepsetus. Because of the abundant freshwater seeps characteristic of the coastal lagoons of Yucatan Peninsula their community structure and fish assemblage display spatial and temporal differences in specific composition. Rev. Biol. Trop. 57 (1-2: 89-103. Epub 2009 June 30.Las lagunas costeras son sistemas importantes para muchas especies de organismos dulceacuícolas, estuarinos y marinos, ya que son consideradas zonas de reproducción, refugio y alimentación de muchas especies de peces. El presente estudio analizó los ensamblajes de la comunidad íctica de la reserva de Dzilam y su relación con las variables hidrológicas. Se capturaron un total de 6 474 individuos (81 especies, en donde Sphoeroides testudineus, Fundulus persimilis, Anchoa mitchilli, Eucinostomus gula, Eucinostomus argenteus and Mugil trichodon contribuyeron con m

  6. Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries

    DEFF Research Database (Denmark)

    Jakobsen, Janus Schou; Waage, Johannes; Rapin, Nicolas

    2013-01-01

    quantified the genome-wide binding patterns of two key hepatocyte transcription factors, CEBPA and CEBPB (also known as C/EBPalpha and C/EBPbeta), at multiple time points during the highly dynamic process of liver regeneration elicited by partial hepatectomy in mouse. Combining these profiles with RNA...... polymerase II binding data, we find three temporal classes of transcription factor binding to be associated with distinct sets of regulated genes involved in the acute phase response, metabolic/homeostatic functions, or cell cycle progression. Moreover, we demonstrate a previously unrecognized early phase......-renewal of differentiated cells. Taken together, our work emphasizes the power of global temporal analyses of transcription factor occupancy to elucidate mechanisms regulating dynamic biological processes in complex higher organisms....

  7. Identification of key pathways and genes influencing prognosis in bladder urothelial carcinoma

    Directory of Open Access Journals (Sweden)

    Ning X

    2017-03-01

    enrichment of the cyclic guanosine monophosphate-protein kinase G signaling pathway, angiogenesis, cell proliferation, and differentiation, which are associated with tumor angiogenesis and cancer prognosis.Conclusion: Genes and pathways related to cell cycle and DNA damage and repair may play a crucial role in BUC pathogenesis, whereas those pertaining to tumor angiogenesis may be key factors in influencing BUC prognosis, especially in advanced disease stages. Keywords: bioinformatics analytical tools, bladder urothelial carcinoma, microarray, differentially expressed gene, prognosis 

  8. Temporal gene expression profile of human precursor B leukemia cells induced by adhesion receptor: identification of pathways regulating B-cell survival.

    Science.gov (United States)

    Astier, Anne Laurence; Xu, Ronghui; Svoboda, Marek; Hinds, Esther; Munoz, Olivier; de Beaumont, Rosalie; Crean, Colin Daniel; Gabig, Theodore; Freedman, Arnold Stephen

    2003-02-01

    The physical interactions between B cells and stromal cells from the lymphoid tissue microenvironment are critical to the survival of normal and malignant B cells. They are principally mediated by integrins expressed on B cells and counterreceptors on stromal cells. Specifically, alpha4beta1 integrin engagement rescues B cells from physiological or drug-induced apoptosis. Therefore, in order to understand the mechanisms by which integrins prevent apoptosis in leukemia B cells, we compared the temporal gene expression profiles induced by beta1-integrin ligation with fibronectin (Fn) or adhesion by poly-L-Lysine in serum-starved precursor B leukemia cells. Among the 38 selected differentially expressed genes, 6 genes involved in adhesion (VAV2, EPB41L1, CORO1A), proliferation (FRAP1, CCT4), and intercellular communication (GJB3) were validated by real-time quantitative polymerase chain reaction (RT-Q-PCR). Gene expression modulation could also be validated at the protein level for 5 other genes. We show that integrin stimulation up-regulated FBI-1 expression but inhibited CD79a, Requiem, c-Fos, and caspase 7 induction when the cells underwent apoptosis. We further demonstrate that Fn stimulation also inhibits caspase 3 activation but increases XIAP and survivin expression. Moreover, integrin stimulation also prevents caspase activation induced by doxorubicin. Therefore, we identified genes modulated by adhesion of human precursor B leukemia cells that regulate proliferation and apoptosis, highlighting new pathways that might provide insights into future therapy aiming at targeting apoptosis of leukemia cells.

  9. The spatial distribution and temporal variation of desert riparian forests and their influencing factors in the downstream Heihe River basin, China

    Science.gov (United States)

    Ding, Jingyi; Zhao, Wenwu; Daryanto, Stefani; Wang, Lixin; Fan, Hao; Feng, Qiang; Wang, Yaping

    2017-05-01

    Desert riparian forests are the main restored vegetation community in Heihe River basin. They provide critical habitats and a variety of ecosystem services in this arid environment. Since desert riparian forests are also sensitive to disturbance, examining the spatial distribution and temporal variation of these forests and their influencing factors is important to determine the limiting factors of vegetation recovery after long-term restoration. In this study, field experiment and remote sensing data were used to determine the spatial distribution and temporal variation of desert riparian forests and their relationship with the environmental factors. We classified five types of vegetation communities at different distances from the river channel. Community coverage and diversity formed a bimodal pattern, peaking at the distances of 1000 and 3000 m from the river channel. In general, the temporal normalized difference vegetation index (NDVI) trend from 2000 to 2014 was positive at different distances from the river channel, except for the region closest to the river bank (i.e. within 500 m from the river channel), which had been undergoing degradation since 2011. The spatial distribution of desert riparian forests was mainly influenced by the spatial heterogeneity of soil properties (e.g. soil moisture, bulk density and soil particle composition). Meanwhile, while the temporal variation of vegetation was affected by both the spatial heterogeneity of soil properties (e.g. soil moisture and soil particle composition) and to a lesser extent, the temporal variation of water availability (e.g. annual average and variability of groundwater, soil moisture and runoff). Since surface (0-30 cm) and deep (100-200 cm) soil moisture, bulk density and the annual average of soil moisture at 100 cm obtained from the remote sensing data were regarded as major determining factors of community distribution and temporal variation, conservation measures that protect the soil structure

  10. Data sets used in the analysis presented in the manuscript “Regional and Hemispheric Influences on Temporal Variability in Baseline Carbon Monoxide and Ozone over the Northeast US”

    Data.gov (United States)

    U.S. Environmental Protection Agency — This dataset documents that all of the data analyzed in the manuscript "Regional and Hemispheric Influences on Temporal Variability in Baseline Carbon Monoxide and...

  11. Genes unlinked to the leptin receptor influence urinary albumin excretion in obese Zucker rats

    NARCIS (Netherlands)

    Kim, K.; Warden, C.H.; Griffey, S.M.; Vilches-Moure, J.G.; Hansen, S.; Cuppen, E.; Nijman, I.J.; Chiu, S.; Stern, J.S.

    2010-01-01

    We have previously shown that 90% of outbred obese Zucker Lepr(fa/fa) rats die prematurely of renal disease. Thus, renal disease in obese Zucker Lepr(fa/fa) rats may be caused by the LEPR mutation on chromosome 5, by the obesity, or it may be influenced by Zucker susceptibility alleles of genes on o

  12. Influence of the IL6 Gene in Susceptibility to Systemic Sclerosis

    NARCIS (Netherlands)

    Cenit, M.C.; Simeon, C.P.; Vonk, M.C.; Callejas-Rubio, J.L.; Espinosa, G.; Carreira, P.; Blanco, F.J.; Narvaez, J.; Tolosa, C.; Roman-Ivorra, J.A.; Gomez-Garcia, I.; Garcia-Hernandez, F.J.; Gallego, M.; Garcia-Portales, R.; Egurbide, M.V.; Fonollosa, V.; Garcia de la Pena, P.; Lopez-Longo, F.J.; Gonzalez-Gay, M.A.; The Spanish Scleroderma, G.; Hesselstrand, R.; Riemekasten, G.; Witte, T.; Voskuyl, A.E.; Schuerwegh, A.J.; Madhok, R.; Fonseca, C.; Denton, C.; Nordin, A.; Palm, O.; Laar, J.M. van; Hunzelmann, N.; Distler, J.H.; Kreuter, A.; Herrick, A.; Worthington, J.; Koeleman, B.P.; Radstake, T.R.D.J.; Martin, J.

    2012-01-01

    OBJECTIVE: Systemic sclerosis (SSc) is a genetically complex autoimmune disease; the genetic component has not been fully defined. Interleukin 6 (IL-6) plays a crucial role in immunity and fibrosis, both key aspects of SSc. We investigated the influence of IL6 gene in the susceptibility and phenotyp

  13. Adaptive social learning strategies in temporally and spatially varying environments : how temporal vs. spatial variation, number of cultural traits, and costs of learning influence the evolution of conformist-biased transmission, payoff-biased transmission, and individual learning.

    Science.gov (United States)

    Nakahashi, Wataru; Wakano, Joe Yuichiro; Henrich, Joseph

    2012-12-01

    Long before the origins of agriculture human ancestors had expanded across the globe into an immense variety of environments, from Australian deserts to Siberian tundra. Survival in these environments did not principally depend on genetic adaptations, but instead on evolved learning strategies that permitted the assembly of locally adaptive behavioral repertoires. To develop hypotheses about these learning strategies, we have modeled the evolution of learning strategies to assess what conditions and constraints favor which kinds of strategies. To build on prior work, we focus on clarifying how spatial variability, temporal variability, and the number of cultural traits influence the evolution of four types of strategies: (1) individual learning, (2) unbiased social learning, (3) payoff-biased social learning, and (4) conformist transmission. Using a combination of analytic and simulation methods, we show that spatial-but not temporal-variation strongly favors the emergence of conformist transmission. This effect intensifies when migration rates are relatively high and individual learning is costly. We also show that increasing the number of cultural traits above two favors the evolution of conformist transmission, which suggests that the assumption of only two traits in many models has been conservative. We close by discussing how (1) spatial variability represents only one way of introducing the low-level, nonadaptive phenotypic trait variation that so favors conformist transmission, the other obvious way being learning errors, and (2) our findings apply to the evolution of conformist transmission in social interactions. Throughout we emphasize how our models generate empirical predictions suitable for laboratory testing.

  14. Temporal mortality-colonization dynamic can influence the coexistence and persistence patterns of cooperators and defectors in an evolutionary game model

    Directory of Open Access Journals (Sweden)

    YouHua Chen

    2014-03-01

    Full Text Available In the present report, the coexistence and persistence time patterns of Prisoners' Dilemma game players were explored in 2D spatial grid systems by considering the impacts of the mortality-colonization temporal dynamic specifically. Our results showed that the waiting time for triggering a colonization event could remarkably influence and change the extinction patterns of both cooperators and defectors. Interestingly, a relatively high frequency of stochastic colonization events could promote the persistence of defectors but not cooperators. In contrast, a low frequency of stochastic- or constant-time colonization events could facilitate the persistence of cooperators but not defectors. However, a long waiting time would be detrimental to the survival of both game players and drives them to go extinction in faster rates. At last, it was found that colonization strength played a relatively weak role on influencing the coexistence scenarios of both game players, but should be kept small if the coexistence of game players is needed to maintain. In conclusion, our study provides evidence showing that the temporal trade-off of mortality and colonization activities would influence the evolution of PD game and the persistence of cooperators and defectors.

  15. The immediate and chronic influence of spatio-temporal metaphors on the mental representations of time in English, Mandarin, and Mandarin-English speakers

    Directory of Open Access Journals (Sweden)

    Vicky T. Lai

    2013-04-01

    Full Text Available In this paper we examine whether experience with spatial metaphors for time has an influence on people’s representation of time. In particular we ask whether spatiotemporal metaphors can have both chronic and immediate effects on temporal thinking. In Study 1, we examine the prevalence of ego-moving representations for time in Mandarin speakers, English speakers, and Mandarin-English (ME bilinguals. As predicted by observations in linguistic analyses, we find that Mandarin speakers are less likely to take an ego-moving perspective than are English speakers. Further, we find that ME bilinguals tested in English are less likely to take an ego-moving perspective than are English monolinguals (an effect of L1 on meaning-making in L2, and also that ME bilinguals tested in Mandarin are more likely to take an ego-moving perspective than are Mandarin monolinguals (an effect of L2 on meaning-making in L1. These findings demonstrate that habits of metaphor use in one language can influence temporal reasoning in another language, suggesting the metaphors can have a chronic effect on patterns in thought. In Study 2 we test Mandarin speakers using either horizontal or vertical metaphors in the immediate context of the task. We find that Mandarin speakers are more likely to construct front-back representations of time when understanding front-back metaphors, and more likely to construct up-down representations of time when understanding up-down metaphors. These findings demonstrate that spatiotemporal metaphors can also have an immediate influence on temporal reasoning. Taken together, these findings demonstrate that the metaphors we use to talk about time have both immediate and long-term consequences for how we conceptualize and reason about this fundamental domain of experience.

  16. Multiple OPR genes influence personality traits in substance dependent and healthy subjects in two American populations.

    Science.gov (United States)

    Luo, Xingguang; Zuo, Lingjun; Kranzler, Henry; Zhang, Huiping; Wang, Shuang; Gelernter, Joel

    2008-10-05

    Personality traits are among the most complex quantitative traits. Certain personality traits are associated with substance dependence (SD); genetic factors may influence both. Associations between opioid receptor (OPR) genes and SD have been reported. This study investigated the relationship between OPR genes and personality traits in a case-control sample. We assessed dimensions of the five-factor model of personality in 556 subjects: 250 with SD [181 European-Americans (EAs) and 69 African-Americans (AAs)] and 306 healthy subjects (266 EAs and 40 AAs). We genotyped 20 OPRM1 markers, 8 OPRD1 markers, and 7 OPRK1 markers, and 38 unlinked ancestry-informative markers in these subjects. The relationships between OPR genes and personality traits were examined using MANCOVA, controlling for gene-gene interaction effects and potential confounders. Associations were decomposed by Roy-Bargmann Stepdown ANCOVA. We found that personality traits were associated as main or interaction effects with the haplotypes, diplotypes, alleles and genotypes at the three OPR genes (0.002 CAC/TAC had interaction effects on Openness (P = 0.010) after conservative correction for multiple testing. The present study demonstrates that the genes encoding the mu-, delta-, and kappa-opioid receptors may contribute to variation in personality traits. Further, the three OPR genes have significant interaction effects on personality traits. This work provides additional evidence that personality traits and SD have a partially overlapping genetic basis.

  17. Diurnal Variation Has Effect on Differential Gene Expression Analysis in the Hippocampus of the Pilocarpine-Induced Model of Mesial Temporal Lobe Epilepsy.

    Directory of Open Access Journals (Sweden)

    Evelin Antonieli da Silva Santos

    Full Text Available The molecular mechanisms underlying epileptogenesis have been widely investigated by differential gene expression approach, especially RT-qPCR methodology. However, controversial findings highlight the occurrence of unpredictable sources of variance in the experimental designs. Here, we investigated if diurnal rhythms of transcript's levels may impact on differential gene expression analysis in hippocampus of rats with experimental epilepsy. For this, we have selected six core clock genes (Per1, Per3, Bmal1, Clock, Cry1 and Cry2, whose rhythmic expression pattern in hippocampus had been previously reported. Initially, we identified Tubb2a/Rplp1 and Tubb2a/Ppia as suitable normalizers for circadian studies in hippocampus of rats maintained to 12:12 hour light:dark (LD cycle. Next, we confirmed the temporal profiling of Per1, Per3, Bmal1, Cry1 and Cry2 mRNA levels in the hippocampus of naive rats by both Acrophase and CircWave statistical tests for circadian analysis. Finally, we showed that temporal differences of sampling can change experimental results for Per1, Per3, Bmal1, Cry1 and Cry2, but not for Clock, which was consistently decreased in rats with epilepsy in all comparison to the naive group. In conclusion, our study demonstrates it is mandatory to consider diurnal oscillations, in order to avoid erroneous conclusions in gene expression analysis in hippocampus of rats with epilepsy. Investigators, therefore, should be aware that genes with circadian expression could be out of phase in different animals of experimental and control groups. Moreover, our results indicate that a sub-expression of Clock may be involved in epileptogenicity, although the functional significance of this remains to be investigated.

  18. Microgeographical population structure and adaptation in Atlantic cod Gadus morhua: spatio-temporal insights from gene-associated DNA markers

    DEFF Research Database (Denmark)

    Poulsen, Nina Aagaard; Hemmer-Hansen, Jakob; Loeschcke, V.;

    2011-01-01

    Recent technical advances have stimulated studies on spatial scales of adaptive genetic variation in marine fishes. However, very few studies have combined spatial and temporal sampling to investigate adaptive genetic structuring at local and microgeographical scales, i.e. scales at which neutral...

  19. Identification of febrile seizure susceptibility genes : studies in mouse chromosome substitution strains and temporal lobe epilepsy patients

    NARCIS (Netherlands)

    Hessel, E.V.S.

    2010-01-01

    Febrile Seizures (FS) are the most common seizure type in children and recurrent FS are a risk factor for developing temporal lobe epilepsy (TLE). Although the mechanisms underlying FS are largely unknown, recent family, twin and animal studies indicate that genetics are important in FS

  20. Identification of febrile seizure susceptibility genes : studies in mouse chromosome substitution strains and temporal lobe epilepsy patients

    NARCIS (Netherlands)

    Hessel, E.V.S.

    2010-01-01

    Febrile Seizures (FS) are the most common seizure type in children and recurrent FS are a risk factor for developing temporal lobe epilepsy (TLE). Although the mechanisms underlying FS are largely unknown, recent family, twin and animal studies indicate that genetics are important in FS susceptibili

  1. Development of genomic resources for a thraustochytrid pathogen and investigation of temperature influences on gene expression.

    Directory of Open Access Journals (Sweden)

    Ana Elisa Garcia-Vedrenne

    Full Text Available Understanding how environmental changes influence the pathogenicity and virulence of infectious agents is critical for predicting epidemiological patterns of disease. Thraustochytrids, part of the larger taxonomic class Labyrinthulomycetes, contain several highly pathogenic species, including the hard clam pathogen quahog parasite unknown (QPX. QPX has been associated with large-scale mortality events along the northeastern coast of North America. Growth and physiology of QPX is temperature-dependent, and changes in local temperature profiles influence pathogenicity. In this study we characterize the partial genome of QPX and examine the influence of temperature on gene expression. Genes involved in several biological processes are differentially expressed upon temperature change, including those associated with altered growth and metabolism and virulence. The genomic and transcriptomic resources developed in this study provide a foundation for better understanding virulence, pathogenicity and life history of thraustochytrid pathogens.

  2. Spatial and temporal gene expression differences in core and periinfarct areas in experimental stroke: a microarray analysis.

    Directory of Open Access Journals (Sweden)

    Jaime Ramos-Cejudo

    Full Text Available BACKGROUND: A large number of genes are regulated to promote brain repair following stroke. The thorough analysis of this process can help identify new markers and develop therapeutic strategies. This study analyzes gene expression following experimental stroke. METHODOLOGY/PRINCIPAL FINDINGS: A microarray study of gene expression in the core, periinfarct and contralateral cortex was performed in adult Sprague-Dawley rats (n = 60 after 24 hours (acute phase or 3 days (delayed stage of permanent middle cerebral artery (MCA occlusion. Independent qRT-PCR validation (n = 12 was performed for 22 of the genes. Functional data were evaluated by Ingenuity Pathway Analysis. The number of genes differentially expressed was 2,612 (24 h and 5,717 (3 d in the core; and 3,505 (24 h and 1,686 (3 d in the periinfarct area (logFC>|1|; adjP<0.05. Expression of many neurovascular unit development genes was altered at 24 h and 3 d including HES2, OLIG2, LINGO1 and NOGO-A; chemokines like CXCL1 and CXCL12, stress-response genes like HIF-1A, and trophic factors like BDNF or BMP4. Nearly half of the detected genes (43% had not been associated with stroke previously. CONCLUSIONS: This comprehensive study of gene regulation in the core and periinfarct areas at different times following permanent MCA occlusion provides new data that can be helpful in translational research.

  3. The Tibetan medicine Zuotai influences clock gene expression in the liver of mice

    Directory of Open Access Journals (Sweden)

    Huan Li

    2016-01-01

    Full Text Available Background. The circadian clock is involved in drug metabolism, efficacy and toxicity. Drugs could in turn affect the biological clock as a mechanism of their actions. Zuotai is an essential component of many popular Tibetan medicines for sedation, tranquil and “detoxification,” and is mainly composed of metacinnabar (β-HgS. The pharmacological and/or toxicological basis of its action is unknown. This study aimed to examine the effect of Zuotai on biological clock gene expression in the liver of mice. Materials and methods. Mice were orally given Zuotai (10 mg/kg, 1.5-fold of clinical dose daily for 7 days, and livers were collected every 4 h during the 24 h period. Total RNA was extracted and subjected to real-time RT-PCR analysis of circadian clock gene expression. Results. Zuotai decreased the oscillation amplitude of the clock core gene Clock, neuronal PAS domain protein 2 (Npas2, Brain and muscle Arnt-like protein-1 (Bmal1 at 10:00. For the clock feedback negative control genes, Zuotai had no effect on the oscillation of the clock gene Cryptochrome (Cry1 and Period genes (Per1–3. For the clock-driven target genes, Zuotai increased the oscillation amplitude of the PAR-bZip family member D-box-binding protein (Dbp, decreased nuclear factor interleukin 3 (Nfil3 at 10:00, but had no effect on thyrotroph embryonic factor (Tef; Zuotai increased the expression of nuclear receptor Rev-Erbα (Nr1d1 at 18:00, but had little influence on the nuclear receptor Rev-Erbβ (Nr1d2 and RORα. Conclusion. The Tibetan medicine Zuotai could influence the expression of clock genes, which could contribute to pharmacological and/or toxicological effects of Zuotai.

  4. Study of the influence of genes related to muscle oxidative processes on beef color.

    Science.gov (United States)

    Falomir-Lockhart, A H; Rogberg-Muñoz, A; Papaleo-Mazzucco, J; Goszczynski, D E; Lirón, J P; Fernández, M E; Añon, M C; Melucci, L M; Giovambattista, G

    2015-10-01

    The biochemical bases of meat color are determined by the concentration and redox state of myoglobin, hemoglobin, cytochromes, and other pigments. Post-mortem depletion of cellular oxygen results in oxidative stresses that consume NADH and affects reducing activity, while enzymatic detoxification influences the cellular oxidative processes, both affecting meat color. The aim of this work was to study the influence of several genes related to cellular oxidative processes that could affect CIELAB meat color parameters. The study was performed in steers that received a grass-based diet combined with grain, hays and silages. Results suggest a possible link between colorimetric parameters (a*, b* and chroma) and SNPs in the GSTP1 gene (P<0.05). Although the influence of the enzymes, encoded by GSTP1 gene, on meat color has been proposed previously at biochemical level and protein expression level, further association studies in different populations and functional studies of proteins are needed to confirm the genetic determination of that gene on meat color.

  5. Transcriptional Analysis of the Genetic Element pSSVx: Differential and Temporal Regulation of Gene Expression Reveals Correlation between Transcription and Replication

    DEFF Research Database (Denmark)

    Contursi, Patrizia; Cannio, Raffaele; Prato, Santina

    2007-01-01

    long transcriptional unit comprised the genes for the plasmid copy number control protein ORF60 (CopG), ORF91, and the replication protein ORF892 (RepA). We propose that a termination readthrough mechanism might be responsible for the formation of more than one RNA species from a single 5' end......pSSVx from Sulfolobus islandicus strain REY15/4 is a hybrid between a plasmid and a fusellovirus. A systematic study performed by a combination of Northern blot analysis, primer extension, and reverse transcriptase PCR revealed the presence of nine major transcripts whose expression...... was differentially and temporally regulated over the growth cycle of S. islandicus. The map positions of the RNAs as well as the clockwise and the anticlockwise directions of their transcription were determined. Some genes were clustered and appeared to be transcribed as polycistronic messengers, among which one...

  6. Temporal profiling of cytokine-induced genes in pancreatic β-cells by meta-analysis and network inference

    DEFF Research Database (Denmark)

    Lopes, Miguel; Kutlu, Burak; Miani, Michela;

    2014-01-01

    Type 1 Diabetes (T1D) is an autoimmune disease where local release of cytokines such as IL-1β and IFN-γ contributes to β-cell apoptosis. To identify relevant genes regulating this process we performed a meta-analysis of 8 datasets of β-cell gene expression after exposure to IL-1β and IFN-γ. Two o...

  7. Spatial and temporal variation of biochemical biomarkers in Gobius niger (Gobiidae) from a southern Mediterranean lagoon (Bizerta lagoon, Tunisia): Influence of biotic and abiotic factors.

    Science.gov (United States)

    Louiz, Ibtissem; Ben Hassine, Oum Kalthoum; Palluel, Olivier; Ben-Attia, Mossadok; Aït-Aïssa, Sélim

    2016-06-15

    This study aims at evaluating both the influence of natural and some anthropogenic pressures on spatio-temporal variations on biomarker responses in sedentary benthic fish Gobius niger. For this purpose, variability of biotransformation enzymes and oxidative stress parameters response were studied in six stations from Bizerta lagoon as well as a reference station located in Ghar El Melh lagoon. Biomarker responses were shown to vary according to both physico-chemical parameters and anthropogenic pressures, but no influence of sex was reported. Based on multivariate analyses, the responses of biomarkers, obtained after covariate analysis in order to weigh the effect of physico-chemical parameters, allowed us to discriminate all stations, with a good classification rate for those that are highly contaminated. Altogether, this study shows the usefulness of G. niger as a sentinel species and stresses the necessity of integrating natural variables for data interpretation.

  8. Optimization of reporter gene assay: several factors influencing detection of promoter activity

    Institute of Scientific and Technical Information of China (English)

    XUE Li-xiang; WENG Mo; ZHANG Zong-yu; TONG Tan-jun

    2007-01-01

    Background Promoter analysis is currently applied to detect the expression of the targeted gene in studies of signal transduction and transcriptional regulation. As a reporter gene, luciferase plays an important role and has been used widely in the promoter assay.Methods Human embryonic lung fibroblast cells (2BS), HeLa cells and MCF-7 cells were transfected with various genes embedded by lipofectamine. This study determined various factors that affect promoter activity determination,such as the selection of the reporter genes and internal references, the dose and the type of the vectors carrying the transcription factors, the host cells and the instruments.Results The sensitivity of the luciferase assay was much higher than that of enhanced green fluorescence protein (EGFP). Moreover, promoter activity is increased in a dose-related manner only in certain ranges outside of which the results may be reversed and the promoter activity is related to the expression vector which is carrying the cDNA.Otherwise, the length of the promoter, internal references and the host cell can also influence the promoter activity.Conclusions To detect the promoter activity accurately, a few factors including dose, vector, length and host cell which influence reporter gene assay aforementioned should be considered.

  9. On the influence of temporal and spatial resolution of aircraft emission inventories for mesoscale modeling of pollutant dispersion

    Energy Technology Data Exchange (ETDEWEB)

    Franzkowiak, V.; Petry, H.; Ebel, A. [Cologne Univ. (Germany). Inst. for Geophysics and Meteorology

    1997-12-31

    The sensitivity of a mesoscale chemistry transport model to the temporal and spatial resolution of aircraft emission inventories is evaluated. A statistical analysis of air traffic in the North-Atlantic flight corridor is carried out showing a highly variable, fine structured spatial distribution and a pronounced daily variation. Sensitivity studies comparing different emission scenarios reveal a strong dependency to the emission time and location of both transport and response in chemical formation of subsequent products. The introduction of a pronounced daily variation leads to a 30% higher ozone production in comparison to uniformly distributed emissions. (author) 9 refs.

  10. Influence of temporal resolution and processing of exposure data on modeling of chloride ingress and reinforcement corrosion in concrete

    DEFF Research Database (Denmark)

    Flint, Madeleine; Michel, Alexander; Billington, Sarah L.;

    2014-01-01

    The impacts of temporal resolution and processing of exposure data on the long-term chloride ingress and reinforcement corrosion in concrete were studied. Exposure data from one simulated and two real climates was processed to create boundary conditions for a one-dimensional geometry studied using...... resolution of the exposure data has a considerable impact on long-term hygrothermal distribution, chloride ingress, and reinforcement section loss results. Use of time-averaged exposure data in the heat and mass transport model reduces the rate of chloride ingress in concrete and affects prediction...

  11. Molecular landscape of arthrofibrosis: Microarray and bioinformatic analysis of the temporal expression of 380 genes during contracture genesis.

    Science.gov (United States)

    Morrey, Mark E; Abdel, Matthew P; Riester, Scott M; Dudakovic, Amel; van Wijnen, Andre J; Morrey, Bernard F; Sanchez-Sotelo, Joaquin

    2017-04-30

    Inflammatory changes are suspected in the pathophysiology of arthrofibrosis formation and require early molecular examination. Here, we assessed the hypothesis that early inflammatory genes are related to arthrofibrosis by ascertaining gene expression during the early stages of contracture genesis in an animal model. Joint trauma was incited surgically in a cohort of rabbits (n=36) knees followed by immobilization in a model of contracture. Six groups of 6 rabbits were sacrificed at multiple time points (0, 6, 12, 24, 72h and 2weeks). Microarray expression and RT-qPCR profiling were performed to determine genes that are significantly up or downregulated. Bioinformatic analysis was carried out to understand which biological programs and functional groups of genes are modulated in arthrofibrosis. Gene expression profiling revealed a large number biologically relevant genes (>100) that are either upregulated or downregulated by at least a 1.5 fold (log2) during the first two weeks after joint injury during contracture development. Gene ontology analysis identified molecular pathways and programs that act during the course of fibrosis and joint contracture. Our main finding is that the development of contractures occur concomitant with modulation of genes mediating inflammatory responses, ECM remodeling and the epithelial-to-mesenchymal transition. The genesis of joint contracture reflects an imbalance between pro- and anti-fibrotic expression. Our study indicates that inflammatory genes may be involved in the process of contracture genesis and initiated at relatively early stages. Our findings also may inform clinical practice in the future by suggesting potential therapeutic targets in preventing the long-term development of arthrofibrosis. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Detecting shifts in gene regulatory networks during time-course experiments at single-time-point temporal resolution.

    Science.gov (United States)

    Takenaka, Yoichi; Seno, Shigeto; Matsuda, Hideo

    2015-10-01

    Comprehensively understanding the dynamics of biological systems is one of the greatest challenges in biology. Vastly improved biological technologies have provided vast amounts of information that must be understood by bioinformatics and systems biology researchers. Gene regulations have been frequently modeled by ordinary differential equations or graphical models based on time-course gene expression profiles. The state-of-the-art computational approaches for analyzing gene regulations assume that their models are same throughout time-course experiments. However, these approaches cannot easily analyze transient changes at a time point, such as diauxic shift. We propose a score that analyzes the gene regulations at each time point. The score is based on the information gains of information criterion values. The method detects the shifts in gene regulatory networks (GRNs) during time-course experiments with single-time-point resolution. The effectiveness of the method is evaluated on the diauxic shift from glucose to lactose in Escherichia coli. Gene regulation shifts were detected at two time points: the first corresponding to the time at which the growth of E. coli ceased and the second corresponding to the end of the experiment, when the nutrient sources (glucose and lactose) had become exhausted. According to these results, the proposed score and method can appropriately detect the time of gene regulation shifts. The method based on the proposed score provides a new tool for analyzing dynamic biological systems. Because the score value indicates the strength of gene regulation at each time point in a gene expression profile, it can potentially infer hidden GRNs from time-course experiments.

  13. Impact of mosquito gene drive on malaria elimination in a computational model with explicit spatial and temporal dynamics

    Science.gov (United States)

    Eckhoff, Philip A.; Wenger, Edward A.; Godfray, H. Charles J.; Burt, Austin

    2017-01-01

    The renewed effort to eliminate malaria and permanently remove its tremendous burden highlights questions of what combination of tools would be sufficient in various settings and what new tools need to be developed. Gene drive mosquitoes constitute a promising set of tools, with multiple different possible approaches including population replacement with introduced genes limiting malaria transmission, driving-Y chromosomes to collapse a mosquito population, and gene drive disrupting a fertility gene and thereby achieving population suppression or collapse. Each of these approaches has had recent success and advances under laboratory conditions, raising the urgency for understanding how each could be deployed in the real world and the potential impacts of each. New analyses are needed as existing models of gene drive primarily focus on nonseasonal or nonspatial dynamics. We use a mechanistic, spatially explicit, stochastic, individual-based mathematical model to simulate each gene drive approach in a variety of sub-Saharan African settings. Each approach exhibits a broad region of gene construct parameter space with successful elimination of malaria transmission due to the targeted vector species. The introduction of realistic seasonality in vector population dynamics facilitates gene drive success compared with nonseasonal analyses. Spatial simulations illustrate constraints on release timing, frequency, and spatial density in the most challenging settings for construct success. Within its parameter space for success, each gene drive approach provides a tool for malaria elimination unlike anything presently available. Provided potential barriers to success are surmounted, each achieves high efficacy at reducing transmission potential and lower delivery requirements in logistically challenged settings. PMID:28028208

  14. Joint QTL mapping and gene expression analysis identify positional candidate genes influencing pork quality traits

    Science.gov (United States)

    González-Prendes, Rayner; Quintanilla, Raquel; Cánovas, Angela; Manunza, Arianna; Figueiredo Cardoso, Tainã; Jordana, Jordi; Noguera, José Luis; Pena, Ramona N.; Amills, Marcel

    2017-01-01

    Meat quality traits have an increasing importance in the pig industry because of their strong impact on consumer acceptance. Herewith, we have combined phenotypic and microarray expression data to map loci with potential effects on five meat quality traits recorded in the longissimus dorsi (LD) and gluteus medius (GM) muscles of 350 Duroc pigs, i.e. pH at 24 hours post-mortem (pH24), electric conductivity (CE) and muscle redness (a*), lightness (L*) and yellowness (b*). We have found significant genome-wide associations for CE of LD on SSC4 (~104 Mb), SSC5 (~15 Mb) and SSC13 (~137 Mb), while several additional regions were significantly associated with meat quality traits at the chromosome-wide level. There was a low positional concordance between the associations found for LD and GM traits, a feature that reflects the existence of differences in the genetic determinism of meat quality phenotypes in these two muscles. The performance of an eQTL search for SNPs mapping to the regions associated with meat quality traits demonstrated that the GM a* SSC3 and pH24 SSC17 QTL display positional concordance with cis-eQTL regulating the expression of several genes with a potential role on muscle metabolism. PMID:28054563

  15. The Temporal Program of Peripheral Blood Gene Expression in the Response of Nonhuman Primates to Ebola Hemorrhagic Fever

    Science.gov (United States)

    2007-08-28

    exhibited a highly homogeneous, time-dependent pattern of gene expression (Figure 1). Given the massive path- ologic changes, physiologic instability, and...compression. It is very likely that the observed gene expression patterns reflect many physiologic changes caused by systemic filoviral infection (for example...trafficking pathway. J Virol 2005, 79:547-553. 54. Simmons G, Wool-Lewis RJ, Baribaud F, Netter RC, Bates P: Ebola virus glycoproteins induce global

  16. Spatial and temporal assessment of pollen- and seed-mediated gene flow from genetically engineered plum Prunus domestica.

    Science.gov (United States)

    Scorza, Ralph; Kriss, Alissa B; Callahan, Ann M; Webb, Kevin; Demuth, Mark; Gottwald, Tim

    2013-01-01

    Pollen flow from a 0.46 ha plot of genetically engineered (GE) Prunus domestica located in West Virginia, USA was evaluated from 2000-2010. Sentinel plum trees were planted at distances ranging from 132 to 854 m from the center of the GE orchard. Plots of mixed plum varieties and seedlings were located at 384, 484 and 998 m from the GE plot. Bee hives (Apis mellifera) were dispersed between the GE plum plot and the pollen flow monitoring sites. Pollen-mediated gene flow from out of the GE plum plot to non-GE plums under the study conditions was low, only occurring at all in 4 of 11 years and then in only 0.31% of the 12,116 seeds analyzed. When it occurred, gene flow, calculated as the number of GUS positive embryos/total embryos sampled, ranged from 0.215% at 132 m from the center of the GE plum plot (28 m from the nearest GE plum tree) to 0.033-0.017% at longer distances (384-998 m). Based on the percentage of GUS positive seeds per individual sampled tree the range was 0.4% to 12%. Within the GE field plot, gene flow ranged from 4.9 to 39%. Gene flow was related to distance and environmental conditions. A single year sample from a sentinel plot 132 m from the center of the GE plot accounted for 65% of the total 11-year gene flow. Spatial modeling indicated that gene flow dramatically decreased at distances over 400 m from the GE plot. Air temperature and rainfall were, respectively, positively and negatively correlated with gene flow, reflecting the effects of weather conditions on insect pollinator activity. Seed-mediated gene flow was not detected. These results support the feasibility of coexistence of GE and non-GE plum orchards.

  17. The temporal dynamics of differential gene expression in Aspergillus fumigatus interacting with human immature dendritic cells in vitro.

    LENUS (Irish Health Repository)

    Morton, Charles O

    2011-01-01

    Dendritic cells (DC) are the most important antigen presenting cells and play a pivotal role in host immunity to infectious agents by acting as a bridge between the innate and adaptive immune systems. Monocyte-derived immature DCs (iDC) were infected with viable resting conidia of Aspergillus fumigatus (Af293) for 12 hours at an MOI of 5; cells were sampled every three hours. RNA was extracted from both organisms at each time point and hybridised to microarrays. iDC cell death increased at 6 h in the presence of A. fumigatus which coincided with fungal germ tube emergence; >80% of conidia were associated with iDC. Over the time course A. fumigatus differentially regulated 210 genes, FunCat analysis indicated significant up-regulation of genes involved in fermentation, drug transport, pathogenesis and response to oxidative stress. Genes related to cytotoxicity were differentially regulated but the gliotoxin biosynthesis genes were down regulated over the time course, while Aspf1 was up-regulated at 9 h and 12 h. There was an up-regulation of genes in the subtelomeric regions of the genome as the interaction progressed. The genes up-regulated by iDC in the presence of A. fumigatus indicated that they were producing a pro-inflammatory response which was consistent with previous transcriptome studies of iDC interacting with A. fumigatus germ tubes. This study shows that A. fumigatus adapts to phagocytosis by iDCs by utilising genes that allow it to survive the interaction rather than just up-regulation of specific virulence genes.

  18. Monocular inhibition reveals temporal and spatial changes in gene expression in the primary visual cortex of marmoset.

    Directory of Open Access Journals (Sweden)

    Yuki eNakagami

    2013-04-01

    Full Text Available We investigated the time course of the expression of several activity-dependent genes evoked by visual inputs in the primary visual cortex (V1 in adult marmosets. In order to examine the rapid time course of activity-dependent gene expression, marmosets were first monocularly inactivated by tetrodotoxin (TTX, kept in darkness for two days, and then exposed to various length of light stimulation. Activity-dependent genes including HTR1B, HTR2A, whose activity-dependency were previously reported by us, and well-known immediate early genes (IEGs, c-FOS, ZIF268, and ARC, were examined by in situ hybridization. Using this system, first, we demonstrated the ocular dominance type of gene expression pattern in V1 under this condition. IEGs were expressed in columnar patterns throughout layers II-VI of all the tested monocular marmosets. Second, we showed the regulation of HTR1B and HTR2A expressions by retinal spontaneous activity, because HTR1B and HTR2A mRNA expressions sustained a certain level regardless of visual stimulation and were inhibited by a blockade of the retinal activity with TTX. Third, IEGs dynamically changed its laminar distribution from half an hour to several hours upon a stimulus onset with the unique time course for each gene. The expression patterns of these genes were different in neurons of each layer as well. These results suggest that the regulation of each neuron in the primary visual cortex of marmosets is subjected to different regulation upon the change of activities from retina. It should be related to a highly differentiated laminar structure of primate visual systems, reflecting the functions of the activity-dependent gene expression in marmoset V1.

  19. The temporal dynamics of differential gene expression in Aspergillus fumigatus interacting with human immature dendritic cells in vitro.

    Directory of Open Access Journals (Sweden)

    Charles O Morton

    Full Text Available Dendritic cells (DC are the most important antigen presenting cells and play a pivotal role in host immunity to infectious agents by acting as a bridge between the innate and adaptive immune systems. Monocyte-derived immature DCs (iDC were infected with viable resting conidia of Aspergillus fumigatus (Af293 for 12 hours at an MOI of 5; cells were sampled every three hours. RNA was extracted from both organisms at each time point and hybridised to microarrays. iDC cell death increased at 6 h in the presence of A. fumigatus which coincided with fungal germ tube emergence; >80% of conidia were associated with iDC. Over the time course A. fumigatus differentially regulated 210 genes, FunCat analysis indicated significant up-regulation of genes involved in fermentation, drug transport, pathogenesis and response to oxidative stress. Genes related to cytotoxicity were differentially regulated but the gliotoxin biosynthesis genes were down regulated over the time course, while Aspf1 was up-regulated at 9 h and 12 h. There was an up-regulation of genes in the subtelomeric regions of the genome as the interaction progressed. The genes up-regulated by iDC in the presence of A. fumigatus indicated that they were producing a pro-inflammatory response which was consistent with previous transcriptome studies of iDC interacting with A. fumigatus germ tubes. This study shows that A. fumigatus adapts to phagocytosis by iDCs by utilising genes that allow it to survive the interaction rather than just up-regulation of specific virulence genes.

  20. Spatial and temporal assessment of pollen- and seed-mediated gene flow from genetically engineered plum Prunus domestica.

    Directory of Open Access Journals (Sweden)

    Ralph Scorza

    Full Text Available Pollen flow from a 0.46 ha plot of genetically engineered (GE Prunus domestica located in West Virginia, USA was evaluated from 2000-2010. Sentinel plum trees were planted at distances ranging from 132 to 854 m from the center of the GE orchard. Plots of mixed plum varieties and seedlings were located at 384, 484 and 998 m from the GE plot. Bee hives (Apis mellifera were dispersed between the GE plum plot and the pollen flow monitoring sites. Pollen-mediated gene flow from out of the GE plum plot to non-GE plums under the study conditions was low, only occurring at all in 4 of 11 years and then in only 0.31% of the 12,116 seeds analyzed. When it occurred, gene flow, calculated as the number of GUS positive embryos/total embryos sampled, ranged from 0.215% at 132 m from the center of the GE plum plot (28 m from the nearest GE plum tree to 0.033-0.017% at longer distances (384-998 m. Based on the percentage of GUS positive seeds per individual sampled tree the range was 0.4% to 12%. Within the GE field plot, gene flow ranged from 4.9 to 39%. Gene flow was related to distance and environmental conditions. A single year sample from a sentinel plot 132 m from the center of the GE plot accounted for 65% of the total 11-year gene flow. Spatial modeling indicated that gene flow dramatically decreased at distances over 400 m from the GE plot. Air temperature and rainfall were, respectively, positively and negatively correlated with gene flow, reflecting the effects of weather conditions on insect pollinator activity. Seed-mediated gene flow was not detected. These results support the feasibility of coexistence of GE and non-GE plum orchards.

  1. Genetic influences on insight problem solving: the role of catechol-O-methyltransferase (COMT) gene polymorphisms.

    Science.gov (United States)

    Jiang, Weili; Shang, Siyuan; Su, Yanjie

    2015-01-01

    People may experience an "aha" moment, when suddenly realizing a solution of a puzzling problem. This experience is called insight problem solving. Several findings suggest that catecholamine-related genes may contribute to insight problem solving, among which the catechol-O-methyltransferase (COMT) gene is the most promising candidate. The current study examined 753 healthy individuals to determine the associations between 7 candidate single nucleotide polymorphisms on the COMT gene and insight problem-solving performance, while considering gender differences. The results showed that individuals carrying A allele of rs4680 or T allele of rs4633 scored significantly higher on insight problem-solving tasks, and the COMT gene rs5993883 combined with gender interacted with correct solutions of insight problems, specifically showing that this gene only influenced insight problem-solving performance in males. This study presents the first investigation of the genetic impact on insight problem solving and provides evidence that highlights the role that the COMT gene plays in insight problem solving.

  2. Genetic influences on insight problem solving: The role of catechol-o-methyltransferase (COMT gene polymorphisms

    Directory of Open Access Journals (Sweden)

    Weili eJiang

    2015-10-01

    Full Text Available People may experience an aha moment, when suddenly realizing a solution of a puzzling problem. This experience is called insight problem solving. Several findings suggest that catecholamine-related genes may contribute to insight problem solving, among which the catechol-o-methyltransferase (COMT gene is the most promising candidate. The current study examined 753 healthy individuals to determine the associations between 7 candidate single nucleotide polymorphisms on the COMT gene and insight problem-solving performance, while considering gender differences. The results showed that individuals carrying A allele of rs4680 or T allele of rs4633 scored significantly higher on insight problem-solving tasks, and the COMT gene rs5993883 combined with gender interacted with correct solutions of insight problems, specifically showing that this gene only influenced insight problem-solving performance in males. This study presents the first investigation of the genetic impact on insight problem solving and provides evidence that highlights the role that the COMT gene plays in insight problem solving.

  3. Influence of testosterone and a novel SARM on gene expression in whole blood of Macaca fascicularis.

    Science.gov (United States)

    Riedmaier, Irmgard; Tichopad, Ales; Reiter, Martina; Pfaffl, Michael W; Meyer, Heinrich H D

    2009-04-01

    Anabolic hormones, including testosterone, have been suggested as a therapy for aging-related conditions, such as osteoporosis and sarcopenia. These therapies are sometimes associated with severe androgenic side effects. A promising alternative to testosterone replacement therapy are selective androgen receptor modulators (SARMs). SARMs have the potential to mimic the desirable central and peripheral androgenic anabolic effects of testosterone without having its side effects. In this study we evaluated the effects of LGD2941, in comparison to testosterone, on mRNA expression of selected target genes in whole blood in an non-human model. The regulated genes can act as potential blood biomarker candidates in future studies with AR ligands. Cynomolgus monkeys (Macaca fascicularis) were treated either with testosterone or LGD2941 for 90 days in order to compare their effects on mRNA expression in blood. Blood samples were taken before SARM application, on day 16 and on day 90 of treatment. Gene expression of 37 candidate genes was measured using quantitative real-time RT-PCR (qRT-PCR) technology. Our study shows that both testosterone and LGD2941 influence mRNA expression of 6 selected genes out of 37 in whole blood. The apoptosis regulators CD30L, Fas, TNFR1 and TNFR2 and the interleukins IL-12B and IL-15 showed significant changes in gene expression between control and the treatment groups and represent potential biomarkers for androgen receptor ligands in whole blood.

  4. The spatial-temporal pattern and influencing factors of negative air ions in urban forests, Shanghai, China

    Institute of Scientific and Technical Information of China (English)

    Hong Liang; Xiaoshuang Chen; Junguang Yin; Liangjun Da

    2014-01-01

    Negative air ions are natural components of the air we breathe. Forests are the main continuous natural source of negative air ions (NAI). The spatio-temporal patterns of negative air ions were explored in Shanghai, based on monthly monitoring in 15 parks from March 2009 to February 2010. In each park, sampling sites were selected in forests and open spaces. The annual variation in negative air ion concentrations (NAIC) showed peak values from June to October and minimum values from December to January. NAIC were highest in summer and autumn, intermediate in spring, and lowest in winter. During spring and summer, NAIC in open spaces were significantly higher in rural areas than those in suburban areas. However, there were no significant differences in NAIC at forest sites among seasons. For open spaces, total suspended particles (TSP) were the dominant determining factor of NAIC in sum-mer, and air temperature and air humidity were the dominant determining factors of NAIC in spring, which were tightly correlated with Shanghai’s ongoing urbanization and its impacts on the environment. It is suggested that urbanization could induce variation in NAIC along the urban-rural gradient, but that may not change the temporal variation pattern. Fur-thermore, the effects of urbanization on NAIC were limited in non-vegetated or less-vegetated sites, such as open spaces, but not in well-vegetated areas, such as urban forests. Therefore, we suggest that urban greening, especially urban forest, has significant resistance to the effect of urbanization on NAIC.

  5. Comparing the influence of distinct kinds of temporal disorder in a low-dimensional absorbing transition model

    Science.gov (United States)

    Solano, C. M. D.; de Oliveira, M. M.; Fiore, C. E.

    2016-10-01

    Recently it was stated that temporal disorder constitutes a relevant perturbation in absorbing phase transitions for all dimensions. However, its effect on systems other than the standard contact process (CP), its competition with other ingredients (e.g., particle diffusion), and other kinds of disorder (besides the standard types) are unknown. In order to shed some light on the above-mentioned points, we investigate a variant of the usual CP, namely, the triplet annihilation model, in which the competition between triplet annihilation and single particle diffusion leads to an unusual phase diagram behavior, with reentrant shape and endless activity for sufficiently large diffusion rates. Two kinds of time-dependent disorder have been considered. In the former, it is introduced in the creation-annihilation parameters (as commonly considered in recent studies), whereas in the latter, the diffusion rate D is allowed to be time dependent. In all cases, the disorder follows a uniform distribution with fixed mean and width σ . Two values of σ have been considered in order to exemplify the regime of "weaker" and "stronger" temporal disorder strengths. Our results show that in the former approach, the disorder suppresses the reentrant phase diagram with a critical behavior deviating from the directed percolation (DP) universality class in the regime of low diffusion rates, while they strongly suggest that the DP class is recovered for larger hopping rates. An opposite scenario is found in the latter disorder approach, with a substantial increase of reentrant shape and the maximum diffusion, in which the reentrant shape also displays a critical behavior consistent with the DP universality class (in similarity with the pure model). In order to compare with very recent claims, the results from taking a bimodal distribution and critical behavior in the limit of strong disorder are presented. Also, the results derived from the mean-field theory are performed, presenting

  6. Identification of landscape features influencing gene flow: How useful are habitat selection models?

    Science.gov (United States)

    Roffler, Gretchen H.; Schwartz, Michael K.; Pilgrim, Kristy L.; Talbot, Sandra; Sage, Kevin; Adams, Layne G.; Luikart, Gordon

    2016-01-01

    Understanding how dispersal patterns are influenced by landscape heterogeneity is critical for modeling species connectivity. Resource selection function (RSF) models are increasingly used in landscape genetics approaches. However, because the ecological factors that drive habitat selection may be different from those influencing dispersal and gene flow, it is important to consider explicit assumptions and spatial scales of measurement. We calculated pairwise genetic distance among 301 Dall's sheep (Ovis dalli dalli) in southcentral Alaska using an intensive noninvasive sampling effort and 15 microsatellite loci. We used multiple regression of distance matrices to assess the correlation of pairwise genetic distance and landscape resistance derived from an RSF, and combinations of landscape features hypothesized to influence dispersal. Dall's sheep gene flow was positively correlated with steep slopes, moderate peak normalized difference vegetation indices (NDVI), and open land cover. Whereas RSF covariates were significant in predicting genetic distance, the RSF model itself was not significantly correlated with Dall's sheep gene flow, suggesting that certain habitat features important during summer (rugged terrain, mid-range elevation) were not influential to effective dispersal. This work underscores that consideration of both habitat selection and landscape genetics models may be useful in developing management strategies to both meet the immediate survival of a species and allow for long-term genetic connectivity.

  7. Vascular endothelial growth factor (VEGF) gene polymorphisms may influence the efficacy of thalidomide in multiple myeloma

    DEFF Research Database (Denmark)

    Andersen, Niels Frost; Vogel, Ulla Birgitte; Klausen, Tobias W;

    2012-01-01

    Vascular endothelial growth factor (VEGF) is a potent proangiogenic factor. Several single nucleotide polymorphisms (SNPs) in the VEGF gene with influence on VEGF expression have been described. In multiple myeloma, VEGF stimulates angiogenesis which is correlated with disease progression...... and prognosis. In this study, we evaluated the association between genetic variations in the VEGF gene in patients with multiple myeloma and time to treatment failure (TTF) after high-dose melphalan and stem cell support (HDT), overall survival (OS) and efficacy of the anti-angiogenic drug thalidomide....... Retrospectively, the SNPs -2,578C>A (rs699947), -460C>T (rs833061), +405G>C (rs2010963) and +936C>T (rs3025039) in the VEGF gene were examined in 348 patients with newly diagnosed multiple myeloma initially treated with HDT, where 176 patients were treated with thalidomide at relapse. None of the examined geno...

  8. Factors influencing electroporation-mediated gene transfer to Stylosanthes guianensis (Aubl. Sw. protoplasts

    Directory of Open Access Journals (Sweden)

    Quecini V.M.

    2002-01-01

    Full Text Available In order to develop a high-efficiency and reproducible transformation protocol for Stylosanthes guianensis we assessed the biological and physical parameters affecting plant electroporation protoplasts. Energy input, as combinations of electric field strengths discharged by different capacitors, electroporation buffer and DNA form were evaluated. Transformation efficiency was assayed in vivo as transient reporter gene expression, using the GFP-coding gene mgfp5 driven by a CaMV 35S constitutive promoter. Energy input and electric field strength had a critical influence on transgene expression with higher transformation levels being achieved with 250 V.cm-1 discharged by 900 and 1000 muF capacitors. Linear plasmid DNA, the absence of chloride and the presence of calcium ions also increased transient gene expression, albeit not significantly.

  9. Differential methylation at the RELN gene promoter in temporal cortex from autistic and typically developing post-puberal subjects.

    Science.gov (United States)

    Lintas, Carla; Sacco, Roberto; Persico, Antonio M

    2016-01-01

    Reelin plays a pivotal role in neurodevelopment and in post-natal synaptic plasticity and has been implicated in the pathogenesis of autism spectrum disorder (ASD). The reelin (RELN) gene expression is significantly decreased in ASD, both in the brain and peripherally. Methylation at the RELN gene promoter is largely triggered at puberty, and hypermethylation has been found in post-mortem brains of schizophrenic and bipolar patients. In this study, we assessed RELN gene methylation status in post-mortem temporocortical tissue samples (BA41/42 or 22) of six pairs of post-puberal individuals with ASD and typically developing subjects, matched for sex (male:female, M:F = 5:1), age, and post-mortem interval. ASD patients display a significantly higher number of methylated CpG islands and heavier methylation in the 5' region of the RELN gene promoter, spanning from -458 to -223 bp, whereas controls have more methylated CpG positions and greater extent of methylation at the 3' promoter region, spanning from -222 to +1 bp. The most upstream promoter region (-458 to -364 bp) is methylated only in ASD brains, while the most downstream region (-131 to +1 bp) is methylated exclusively in control brains. Within this general framework, three different methylation patterns are discernible, each correlated with different extents of reduction in reelin gene expression among ASD individuals compared to controls. The methylation pattern is different in ASD and control post-mortem brains. ASD-specific CpG positions, located in the most upstream gene promoter region, may exert a functional role potentially conferring ASD risk by blunting RELN gene expression.

  10. Transcriptome Dynamics of Developing Photoreceptors in Three-Dimensional Retina Cultures Recapitulates Temporal Sequence of Human Cone and Rod Differentiation Revealing Cell Surface Markers and Gene Networks.

    Science.gov (United States)

    Kaewkhaw, Rossukon; Kaya, Koray Dogan; Brooks, Matthew; Homma, Kohei; Zou, Jizhong; Chaitankar, Vijender; Rao, Mahendra; Swaroop, Anand

    2015-12-01

    The derivation of three-dimensional (3D) stratified neural retina from pluripotent stem cells has permitted investigations of human photoreceptors. We have generated a H9 human embryonic stem cell subclone that carries a green fluorescent protein (GFP) reporter under the control of the promoter of cone-rod homeobox (CRX), an established marker of postmitotic photoreceptor precursors. The CRXp-GFP reporter replicates endogenous CRX expression in vitro when the H9 subclone is induced to form self-organizing 3D retina-like tissue. At day 37, CRX+ photoreceptors appear in the basal or middle part of neural retina and migrate to apical side by day 67. Temporal and spatial patterns of retinal cell type markers recapitulate the predicted sequence of development. Cone gene expression is concomitant with CRX, whereas rod differentiation factor neural retina leucine zipper protein (NRL) is first observed at day 67. At day 90, robust expression of NRL and its target nuclear receptor NR2E3 is evident in many CRX+ cells, while minimal S-opsin and no rhodopsin or L/M-opsin is present. The transcriptome profile, by RNA-seq, of developing human photoreceptors is remarkably concordant with mRNA and immunohistochemistry data available for human fetal retina although many targets of CRX, including phototransduction genes, exhibit a significant delay in expression. We report on temporal changes in gene signatures, including expression of cell surface markers and transcription factors; these expression changes should assist in isolation of photoreceptors at distinct stages of differentiation and in delineating coexpression networks. Our studies establish the first global expression database of developing human photoreceptors, providing a reference map for functional studies in retinal cultures.

  11. Arabidopsis FLOWERING LOCUS D influences systemic-acquiredresistance-induced expression and histone modifications of WRKY genes

    Indian Academy of Sciences (India)

    Vijayata Singh; Shweta Roy; Deepjyoti Singh; Ashis Kumar Nandi

    2014-03-01

    A plant that is in part infected by a pathogen is more resistant throughout its whole body to subsequent infections – a phenomenon known as systemic acquired resistance (SAR). Mobile signals are synthesized at the site of infection and distributed throughout the plant through vascular tissues. Mechanism of SAR development subsequent to reaching the mobile signal in the distal tissue is largely unknown. Recently we showed that FLOWERING LOCUS D (FLD) gene of Arabidopsis thaliana is required in the distal tissue to activate SAR. FLD codes for a homologue of human-lysine-specific histone demethylase. Here we show that FLD function is required for priming (SAR induced elevated expression during challenge inoculation) of WRKY29 and WRKY6 genes. FLD also differentially influences basal and SAR-induced expression of WRKY38, WRKY65 and WRKY53 genes. In addition, we also show that FLD partly localizes in nucleus and influences histone modifications at the promoters of WRKY29 and WRKY6 genes. The results altogether indicate to the possibility of FLD’s involvement in epigenetic regulation of SAR.

  12. Mutualism and asexual reproduction influence recognition genes in a fungal symbiont.

    Science.gov (United States)

    van der Nest, Magriet A; Steenkamp, Emma T; Wilken, Markus P; Stenlid, Jan; Wingfield, Mike J; Wingfield, Brenda D; Slippers, Bernard

    2013-06-01

    Mutualism between microbes and insects is common and alignment of the reproductive interests of microbial symbionts with this lifestyle typically involves clonal reproduction and vertical transmission by insect partners. Here the Amylostereum fungus-Sirex woodwasp mutualism was used to consider whether their prolonged association and predominance of asexuality have affected the mating system of the fungal partner. Nucleotide information for the pheromone receptor gene rab1, as well as the translation elongation factor 1α gene and ribosomal RNA internal transcribed spacer region were utilized. The identification of rab1 alleles in Amylostereum chailletii and Amylostereum areolatum populations revealed that this gene is more polymorphic than the other two regions, although the diversity of all three regions was lower than what has been observed in free-living Agaricomycetes. Our data suggest that suppressed recombination might be implicated in the diversification of rab1, while no evidence of balancing selection was detected. We also detected positive selection at only two codons, suggesting that purifying selection is important for the evolution of rab1. The symbiotic relationship with their insect partners has therefore influenced the diversity of this gene and influenced the manner in which selection drives and maintains this diversity in A. areolatum and A. chailletii.

  13. Common variants within oxidative phosphorylation genes influence risk of ischemic stroke and intracerebral hemorrhage.

    Science.gov (United States)

    Anderson, Christopher D; Biffi, Alessandro; Nalls, Michael A; Devan, William J; Schwab, Kristin; Ayres, Alison M; Valant, Valerie; Ross, Owen A; Rost, Natalia S; Saxena, Richa; Viswanathan, Anand; Worrall, Bradford B; Brott, Thomas G; Goldstein, Joshua N; Brown, Devin; Broderick, Joseph P; Norrving, Bo; Greenberg, Steven M; Silliman, Scott L; Hansen, Björn M; Tirschwell, David L; Lindgren, Arne; Slowik, Agnieszka; Schmidt, Reinhold; Selim, Magdy; Roquer, Jaume; Montaner, Joan; Singleton, Andrew B; Kidwell, Chelsea S; Woo, Daniel; Furie, Karen L; Meschia, James F; Rosand, Jonathan

    2013-03-01

    Previous studies demonstrated association between mitochondrial DNA variants and ischemic stroke (IS). We investigated whether variants within a larger set of oxidative phosphorylation (OXPHOS) genes encoded by both autosomal and mitochondrial DNA were associated with risk of IS and, based on our results, extended our investigation to intracerebral hemorrhage (ICH). This association study used a discovery cohort of 1643 individuals, a validation cohort of 2432 individuals for IS, and an extension cohort of 1476 individuals for ICH. Gene-set enrichment analysis was performed on all structural OXPHOS genes, as well as genes contributing to individual respiratory complexes. Gene-sets passing gene-set enrichment analysis were tested by constructing genetic scores using common variants residing within each gene. Associations between each variant and IS that emerged in the discovery cohort were examined in validation and extension cohorts. IS was associated with genetic risk scores in OXPHOS as a whole (odds ratio [OR], 1.17; P=0.008) and complex I (OR, 1.06; P=0.050). Among IS subtypes, small vessel stroke showed association with OXPHOS (OR, 1.16; P=0.007), complex I (OR, 1.13; P=0.027), and complex IV (OR, 1.14; P=0.018). To further explore this small vessel association, we extended our analysis to ICH, revealing association between deep hemispheric ICH and complex IV (OR, 1.08; P=0.008). This pathway analysis demonstrates association between common genetic variants within OXPHOS genes and stroke. The associations for small vessel stroke and deep ICH suggest that genetic variation in OXPHOS influences small vessel pathobiology. Further studies are needed to identify culprit genetic variants and assess their functional consequences.

  14. Common genetic variants in NEFL influence gene expression and neuroblastoma risk.

    Science.gov (United States)

    Capasso, Mario; Diskin, Sharon; Cimmino, Flora; Acierno, Giovanni; Totaro, Francesca; Petrosino, Giuseppe; Pezone, Lucia; Diamond, Maura; McDaniel, Lee; Hakonarson, Hakon; Iolascon, Achille; Devoto, Marcella; Maris, John M

    2014-12-01

    The genetic etiology of sporadic neuroblastoma is still largely obscure. In a genome-wide association study, we identified single-nucleotide polymorphisms (SNP) associated with neuroblastoma at the CASC15, BARD1, LMO1, DUSP12, HSD17B12, HACE1, and LIN28B gene loci, but these explain only a small fraction of neuroblastoma heritability. Other neuroblastoma susceptibility genes are likely hidden among signals discarded by the multiple testing corrections. In this study, we evaluated eight additional genes selected as candidates for further study based on proven involvement in neuroblastoma differentiation. SNPs at these candidate genes were tested for association with disease susceptibility in 2,101 cases and 4,202 controls, with the associations found replicated in an independent cohort of 459 cases and 809 controls. Replicated associations were further studied for cis-effect using gene expression, transient overexpression, silencing, and cellular differentiation assays. The neurofilament gene NEFL harbored three SNPs associated with neuroblastoma (rs11994014: Pcombined = 0.0050; OR, 0.88; rs2979704: Pcombined = 0.0072; OR, 0.87; rs1059111: Pcombined = 0.0049; OR, 0.86). The protective allele of rs1059111 correlated with increased NEFL expression. Biologic investigations showed that ectopic overexpression of NEFL inhibited cell growth specifically in neuroblastoma cells carrying the protective allele. NEFL overexpression also enhanced differentiation and impaired the proliferation and anchorage-independent growth of cells with protective allele and basal NEFL expression, while impairing invasiveness and proliferation of cells homozygous for the risk genotype. Clinically, high levels of NEFL expression in primary neuroblastoma specimens were associated with better overall survival (P = 0.03; HR, 0.68). Our results show that common variants of NEFL influence neuroblastoma susceptibility and they establish that NEFL expression influences disease initiation and

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

    Science.gov (United States)

    Mouser, P. J.

    2010-12-01

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

  16. Influence of neonatal hypothyroidism on hepatic gene expression and lipid metabolism in adulthood

    DEFF Research Database (Denmark)

    Santana-Farré, Ruymán; Mirecki-Garrido, Mercedes; Bocos, Carlos

    2012-01-01

    Thyroid hormones are required for normal growth and development in mammals. Congenital-neonatal hypothyroidism (CH) has a profound impact on physiology, but its specific influence in liver is less understood. Here, we studied how CH influences the liver gene expression program in adulthood......, triglyceride assembly, bile acid synthesis, and lipogenesis. These changes were associated with a decrease of intrahepatic lipids. Finally, CH rats responded to the onset of hypothyroidism in adulthood with a reduction of serum fatty acids and hepatic cholesteryl esters and to T3 replacement with an enhanced...... activation of malic enzyme. In summary, we provide in vivo evidence that neonatal hypothyroidism influences the hepatic transcriptional program and tissue sensitivity to hormone treatment in adulthood. This highlights the critical role that a euthyroid state during development plays on normal liver...

  17. Temporal Changes in Cortical and Hippocampal Expression of Genes Important for Brain Glucose Metabolism Following Controlled Cortical Impact Injury in Mice

    Directory of Open Access Journals (Sweden)

    June Zhou

    2017-09-01

    Full Text Available Traumatic brain injury (TBI causes transient increases and subsequent decreases in brain glucose utilization. The underlying molecular pathways are orchestrated processes and poorly understood. In the current study, we determined temporal changes in cortical and hippocampal expression of genes important for brain glucose/lactate metabolism and the effect of a known neuroprotective drug telmisartan on the expression of these genes after experimental TBI. Adult male C57BL/6J mice (n = 6/group underwent sham or unilateral controlled cortical impact (CCI injury. Their ipsilateral and contralateral cortex and hippocampus were collected 6 h, 1, 3, 7, 14, 21, and 28 days after injury. Expressions of several genes important for brain glucose utilization were determined by qRT-PCR. In results, (1 mRNA levels of three key enzymes in glucose metabolism [hexo kinase (HK 1, pyruvate kinase, and pyruvate dehydrogenase (PDH] were all increased 6 h after injury in the contralateral cortex, followed by decreases at subsequent times in the ipsilateral cortex and hippocampus; (2 capillary glucose transporter Glut-1 mRNA increased, while neuronal glucose transporter Glut-3 mRNA decreased, at various times in the ipsilateral cortex and hippocampus; (3 astrocyte lactate transporter MCT-1 mRNA increased, whereas neuronal lactate transporter MCT-2 mRNA decreased in the ipsilateral cortex and hippocampus; (4 HK2 (an isoform of hexokinase expression increased at all time points in the ipsilateral cortex and hippocampus. GPR81 (lactate receptor mRNA increased at various time points in the ipsilateral cortex and hippocampus. These temporal alterations in gene expression corresponded closely to the patterns of impaired brain glucose utilization reported in both TBI patients and experimental TBI rodents. The observed changes in hippocampal gene expression were delayed and prolonged, when compared with those in the cortex. The patterns of alterations were specific

  18. The influence of hydrodynamics on the spatial and temporal variation of phytoplankton pigments in a large, sub-tropical coastal lake (Brazil

    Directory of Open Access Journals (Sweden)

    Luciana de Souza Cardoso

    2004-08-01

    Full Text Available This study evaluated the spatial and temporal distribution of phytoplankton pigments in Itapeva Lake and its relationship with hydrodynamic aspects. Regarding spatial distribution, a decreasing N®S gradient was generally observed for the pigments, except in summer. This inversion observed during the summer was influenced by the predominant fetch (N-E. The horizontal heterogeneity was proved (ANOVA for all seasons of the year, except spring. Spatially in spring, the vertical variance was much more significant (pEste estudo avalia a distribuição espaço-temporal dos pigmentos fitoplanctônicos na Lagoa Itapeva e sua relação com aspectos hidrodinâmicos. Com relação à distribuição espacial, geralmente um gradiente decrescente no sentido N®S foi observado para os pigmentos, com exceção do verão. Esta inversão observada durante o verão foi influenciada pelo fetch predominante (N-E. Excetuando a primavera, ficou comprovada a existência de heterogeneidade horizontal (ANOVA nas demais estações do ano. Espacialmente, na primavera a variância vertical foi muito mais significativa (p<0,05 que a horizontal. Os turnos de amostragem sempre exibiram um grau de variabilidade entre as estações do ano, mostrando a existência de um ciclo diurno com relação à concentração de clorofila a. Este comportamento esteve relacionado com o fetch principalmente dos quadrantes NE-SW, perturbando o sistema por ser uma lagoa rasa. Com isso, ficou constatada a influência do regime hidrodinâmico da Lagoa Itapeva na distribuição espaço-temporal dos pigmentos fitoplanctônicos.

  19. Language impairment and dyslexia genes influence language skills in children with autism spectrum disorders.

    Science.gov (United States)

    Eicher, John D; Gruen, Jeffrey R

    2015-04-01

    Language and communication development is a complex process influenced by numerous environmental and genetic factors. Many neurodevelopment disorders include deficits in language and communication skills in their diagnostic criteria, including autism spectrum disorders (ASD), language impairment (LI), and dyslexia. These disorders are polygenic and complex with a significant genetic component contributing to each. The similarity of language phenotypes and comorbidity of these disorders suggest that they may share genetic contributors. To test this, we examined the association of genes previously implicated in dyslexia, LI, and/or language-related traits with language skills in children with ASD. We used genetic and language data collected in the Autism Genome Research Exchange (AGRE) and Simons Simplex Collection (SSC) cohorts to perform a meta-analysis on performance on a receptive vocabulary task. There were associations with LI risk gene ATP2C2 and dyslexia risk gene MRPL19. Additionally, we found suggestive evidence of association with CMIP, GCFC2, KIAA0319L, the DYX2 locus (ACOT13, GPLD1, and FAM65B), and DRD2. Our results show that LI and dyslexia genes also contribute to language traits in children with ASD. These associations add to the growing literature of generalist genes that contribute to multiple related neurobehavioral traits. Future studies should examine whether other genetic contributors may be shared among these disorders and how risk variants interact with each other and the environment to modify clinical presentations. © 2014 International Society for Autism Research, Wiley Periodicals, Inc.

  20. Renin-Angiotensin System Gene Variants and Type 2 Diabetes Mellitus: Influence of Angiotensinogen.

    Science.gov (United States)

    Joyce-Tan, Siew Mei; Zain, Shamsul Mohd; Abdul Sattar, Munavvar Zubaid; Abdullah, Nor Azizan

    2016-01-01

    Genome-wide association studies (GWAS) have been successfully used to call for variants associated with diseases including type 2 diabetes mellitus (T2DM). However, some variants are not included in the GWAS to avoid penalty in multiple hypothetic testing. Thus, candidate gene approach is still useful even at GWAS era. This study attempted to assess whether genetic variations in the renin-angiotensin system (RAS) and their gene interactions are associated with T2DM risk. We genotyped 290 T2DM patients and 267 controls using three genes of the RAS, namely, angiotensin converting enzyme (ACE), angiotensinogen (AGT), and angiotensin II type 1 receptor (AGTR1). There were significant differences in allele frequencies between cases and controls for AGT variants (P = 0.05) but not for ACE and AGTR1. Haplotype TCG of the AGT was associated with increased risk of T2DM (OR 1.92, 95% CI 1.15-3.20, permuted P = 0.012); however, no evidence of significant gene-gene interactions was seen. Nonetheless, our analysis revealed that the associations of the AGT variants with T2DM were independently associated. Thus, this study suggests that genetic variants of the RAS can modestly influence the T2DM risk.

  1. The transcription factor ultraspiracle influences honey bee social behavior and behavior-related gene expression.

    Directory of Open Access Journals (Sweden)

    Seth A Ament

    Full Text Available Behavior is among the most dynamic animal phenotypes, modulated by a variety of internal and external stimuli. Behavioral differences are associated with large-scale changes in gene expression, but little is known about how these changes are regulated. Here we show how a transcription factor (TF, ultraspiracle (usp; the insect homolog of the Retinoid X Receptor, working in complex transcriptional networks, can regulate behavioral plasticity and associated changes in gene expression. We first show that RNAi knockdown of USP in honey bee abdominal fat bodies delayed the transition from working in the hive (primarily "nursing" brood to foraging outside. We then demonstrate through transcriptomics experiments that USP induced many maturation-related transcriptional changes in the fat bodies by mediating transcriptional responses to juvenile hormone. These maturation-related transcriptional responses to USP occurred without changes in USP's genomic binding sites, as revealed by ChIP-chip. Instead, behaviorally related gene expression is likely determined by combinatorial interactions between USP and other TFs whose cis-regulatory motifs were enriched at USP's binding sites. Many modules of JH- and maturation-related genes were co-regulated in both the fat body and brain, predicting that usp and cofactors influence shared transcriptional networks in both of these maturation-related tissues. Our findings demonstrate how "single gene effects" on behavioral plasticity can involve complex transcriptional networks, in both brain and peripheral tissues.

  2. Renin-Angiotensin System Gene Variants and Type 2 Diabetes Mellitus: Influence of Angiotensinogen

    Directory of Open Access Journals (Sweden)

    Siew Mei Joyce-Tan

    2016-01-01

    Full Text Available Genome-wide association studies (GWAS have been successfully used to call for variants associated with diseases including type 2 diabetes mellitus (T2DM. However, some variants are not included in the GWAS to avoid penalty in multiple hypothetic testing. Thus, candidate gene approach is still useful even at GWAS era. This study attempted to assess whether genetic variations in the renin-angiotensin system (RAS and their gene interactions are associated with T2DM risk. We genotyped 290 T2DM patients and 267 controls using three genes of the RAS, namely, angiotensin converting enzyme (ACE, angiotensinogen (AGT, and angiotensin II type 1 receptor (AGTR1. There were significant differences in allele frequencies between cases and controls for AGT variants (P=0.05 but not for ACE and AGTR1. Haplotype TCG of the AGT was associated with increased risk of T2DM (OR 1.92, 95% CI 1.15–3.20, permuted P=0.012; however, no evidence of significant gene-gene interactions was seen. Nonetheless, our analysis revealed that the associations of the AGT variants with T2DM were independently associated. Thus, this study suggests that genetic variants of the RAS can modestly influence the T2DM risk.

  3. How complexity increases in development: An analysis of the spatial-temporal dynamics of 1218 genes in Drosophila melanogaster.

    Science.gov (United States)

    Salvador-Martínez, Irepan; Salazar-Ciudad, Isaac

    2015-09-15

    One of the most apparent phenomena in development is that it starts with something apparently simple and leads to something clearly complex with a specific and functional structure. At the level of gene expression it seems also clear that the embryo becomes progressively compartmentalized over time and space. However, there have not been any systematic attempts to quantify how this occurs. Here, we present a quantitative analysis of the compartmentalization and spatial complexity of gene expression in Drosophila melanogaster over developmental time by analyzing thousands of gene expression spatial patterns from FlyExpress database. We use three different mathematical measures of compartmentalization of gene expression in space. All these measures show a similar non-linear increase in compartmentalization over time, with the most dramatic change occurring from the maternal to the early gastrula stage. Transcription factors and growth factors showed an earlier compartmentalization. Finally, we partitioned the embryo space in 257 equally sized regions and clustered them depending on their expression similarity, within and between stages. This provides a global overview about the effective degree of differentiation and compartmentalization between body parts at each developmental stage and when and where in the embryo there are more changes, due to signaling or movement.

  4. Endo-(1,4-β-Glucanase gene families in the grasses: temporal and spatial Co-transcription of orthologous genes1

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    Buchanan Margaret

    2012-12-01

    Full Text Available Abstract Background Endo-(1,4-β-glucanase (cellulase glycosyl hydrolase GH9 enzymes have been implicated in several aspects of cell wall metabolism in higher plants, including cellulose biosynthesis and degradation, modification of other wall polysaccharides that contain contiguous (1,4-β-glucosyl residues, and wall loosening during cell elongation. Results The endo-(1,4-β-glucanase gene families from barley (Hordeum vulgare, maize (Zea mays, sorghum (Sorghum bicolor, rice (Oryza sativa and Brachypodium (Brachypodium distachyon range in size from 23 to 29 members. Phylogenetic analyses show variations in clade structure between the grasses and Arabidopsis, and indicate differential gene loss and gain during evolution. Map positions and comparative studies of gene structures allow orthologous genes in the five species to be identified and synteny between the grasses is found to be high. It is also possible to differentiate between homoeologues resulting from ancient polyploidizations of the maize genome. Transcript analyses using microarray, massively parallel signature sequencing and quantitative PCR data for barley, rice and maize indicate that certain members of the endo-(1,4-β-glucanase gene family are transcribed across a wide range of tissues, while others are specifically transcribed in particular tissues. There are strong correlations between transcript levels of several members of the endo-(1,4-β-glucanase family and the data suggest that evolutionary conservation of transcription exists between orthologues across the grass family. There are also strong correlations between certain members of the endo-(1,4-β-glucanase family and other genes known to be involved in cell wall loosening and cell expansion, such as expansins and xyloglucan endotransglycosylases. Conclusions The identification of these groups of genes will now allow us to test hypotheses regarding their functions and joint participation in wall synthesis, re

  5. Temporal and tissue specific regulation of RP-associated splicing factor genes PRPF3, PRPF31 and PRPC8--implications in the pathogenesis of RP.

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    Huibi Cao

    Full Text Available BACKGROUND: Genetic mutations in several ubiquitously expressed RNA splicing genes such as PRPF3, PRP31 and PRPC8, have been found to cause retina-specific diseases in humans. To understand this intriguing phenomenon, most studies have been focused on testing two major hypotheses. One hypothesis assumes that these mutations interrupt retina-specific interactions that are important for RNA splicing, implying that there are specific components in the retina interacting with these splicing factors. The second hypothesis suggests that these mutations have only a mild effect on the protein function and thus affect only the metabolically highly active cells such as retinal photoreceptors. METHODOLOGY/PRINCIPAL FINDINGS: We examined the second hypothesis using the PRPF3 gene as an example. We analyzed the spatial and temporal expression of the PRPF3 gene in mice and found that it is highly expressed in retinal cells relative to other tissues and its expression is developmentally regulated. In addition, we also found that PRP31 and PRPC8 as well as snRNAs are highly expressed in retinal cells. CONCLUSIONS/SIGNIFICANCE: Our data suggest that the retina requires a relatively high level of RNA splicing activity for optimal tissue-specific physiological function. Because the RP18 mutation has neither a debilitating nor acute effect on protein function, we suggest that retinal degeneration is the accumulative effect of decades of suboptimal RNA splicing due to the mildly impaired protein.

  6. Genome-wide scan of healthy human connectome discovers SPON1 gene variant influencing dementia severity

    Science.gov (United States)

    Jahanshad, Neda; Rajagopalan, Priya; Hua, Xue; Hibar, Derrek P.; Nir, Talia M.; Toga, Arthur W.; Jack, Clifford R.; Saykin, Andrew J.; Green, Robert C.; Weiner, Michael W.; Medland, Sarah E.; Montgomery, Grant W.; Hansell, Narelle K.; McMahon, Katie L.; de Zubicaray, Greig I.; Martin, Nicholas G.; Wright, Margaret J.; Thompson, Paul M.; Weiner, Michael; Aisen, Paul; Weiner, Michael; Aisen, Paul; Petersen, Ronald; Jack, Clifford R.; Jagust, William; Trojanowski, John Q.; Toga, Arthur W.; Beckett, Laurel; Green, Robert C.; Saykin, Andrew J.; Morris, John; Liu, Enchi; Green, Robert C.; Montine, Tom; Petersen, Ronald; Aisen, Paul; Gamst, Anthony; Thomas, Ronald G.; Donohue, Michael; Walter, Sarah; Gessert, Devon; Sather, Tamie; Beckett, Laurel; Harvey, Danielle; Gamst, Anthony; Donohue, Michael; Kornak, John; Jack, Clifford R.; Dale, Anders; Bernstein, Matthew; Felmlee, Joel; Fox, Nick; Thompson, Paul; Schuff, Norbert; Alexander, Gene; DeCarli, Charles; Jagust, William; Bandy, Dan; Koeppe, Robert A.; Foster, Norm; Reiman, Eric M.; Chen, Kewei; Mathis, Chet; Morris, John; Cairns, Nigel J.; Taylor-Reinwald, Lisa; Trojanowki, J.Q.; Shaw, Les; Lee, Virginia M.Y.; Korecka, Magdalena; Toga, Arthur W.; Crawford, Karen; Neu, Scott; Saykin, Andrew J.; Foroud, Tatiana M.; Potkin, Steven; Shen, Li; Khachaturian, Zaven; Frank, Richard; Snyder, Peter J.; Molchan, Susan; Kaye, Jeffrey; Quinn, Joseph; Lind, Betty; Dolen, Sara; Schneider, Lon S.; Pawluczyk, Sonia; Spann, Bryan M.; Brewer, James; Vanderswag, Helen; Heidebrink, Judith L.; Lord, Joanne L.; Petersen, Ronald; Johnson, Kris; Doody, Rachelle S.; Villanueva-Meyer, Javier; Chowdhury, Munir; Stern, Yaakov; Honig, Lawrence S.; Bell, Karen L.; Morris, John C.; Ances, Beau; Carroll, Maria; Leon, Sue; Mintun, Mark A.; Schneider, Stacy; Marson, Daniel; Griffith, Randall; Clark, David; Grossman, Hillel; Mitsis, Effie; Romirowsky, Aliza; deToledo-Morrell, Leyla; Shah, Raj C.; Duara, Ranjan; Varon, Daniel; Roberts, Peggy; Albert, Marilyn; Onyike, Chiadi; Kielb, Stephanie; Rusinek, Henry; de Leon, Mony J.; Glodzik, Lidia; De Santi, Susan; Doraiswamy, P. Murali; Petrella, Jeffrey R.; Coleman, R. Edward; Arnold, Steven E.; Karlawish, Jason H.; Wolk, David; Smith, Charles D.; Jicha, Greg; Hardy, Peter; Lopez, Oscar L.; Oakley, MaryAnn; Simpson, Donna M.; Porsteinsson, Anton P.; Goldstein, Bonnie S.; Martin, Kim; Makino, Kelly M.; Ismail, M. Saleem; Brand, Connie; Mulnard, Ruth A.; Thai, Gaby; Mc-Adams-Ortiz, Catherine; Womack, Kyle; Mathews, Dana; Quiceno, Mary; Diaz-Arrastia, Ramon; King, Richard; Weiner, Myron; Martin-Cook, Kristen; DeVous, Michael; Levey, Allan I.; Lah, James J.; Cellar, Janet S.; Burns, Jeffrey M.; Anderson, Heather S.; Swerdlow, Russell H.; Apostolova, Liana; Lu, Po H.; Bartzokis, George; Silverman, Daniel H.S.; Graff-Radford, Neill R.; Parfitt, Francine; Johnson, Heather; Farlow, Martin R.; Hake, Ann Marie; Matthews, Brandy R.; Herring, Scott; van Dyck, Christopher H.; Carson, Richard E.; MacAvoy, Martha G.; Chertkow, Howard; Bergman, Howard; Hosein, Chris; Black, Sandra; Stefanovic, Bojana; Caldwell, Curtis; Hsiung, Ging-Yuek Robin; Feldman, Howard; Mudge, Benita; Assaly, Michele; Kertesz, Andrew; Rogers, John; Trost, Dick; Bernick, Charles; Munic, Donna; Kerwin, Diana; Mesulam, Marek-Marsel; Lipowski, Kristina; Wu, Chuang-Kuo; Johnson, Nancy; Sadowsky, Carl; Martinez, Walter; Villena, Teresa; Turner, Raymond Scott; Johnson, Kathleen; Reynolds, Brigid; Sperling, Reisa A.; Johnson, Keith A.; Marshall, Gad; Frey, Meghan; Yesavage, Jerome; Taylor, Joy L.; Lane, Barton; Rosen, Allyson; Tinklenberg, Jared; Sabbagh, Marwan; Belden, Christine; Jacobson, Sandra; Kowall, Neil; Killiany, Ronald; Budson, Andrew E.; Norbash, Alexander; Johnson, Patricia Lynn; Obisesan, Thomas O.; Wolday, Saba; Bwayo, Salome K.; Lerner, Alan; Hudson, Leon; Ogrocki, Paula; Fletcher, Evan; Carmichael, Owen; Olichney, John; DeCarli, Charles; Kittur, Smita; Borrie, Michael; Lee, T.-Y.; Bartha, Rob; Johnson, Sterling; Asthana, Sanjay; Carlsson, Cynthia M.; Potkin, Steven G.; Preda, Adrian; Nguyen, Dana; Tariot, Pierre; Fleisher, Adam; Reeder, Stephanie; Bates, Vernice; Capote, Horacio; Rainka, Michelle; Scharre, Douglas W.; Kataki, Maria; Zimmerman, Earl A.; Celmins, Dzintra; Brown, Alice D.; Pearlson, Godfrey D.; Blank, Karen; Anderson, Karen; Saykin, Andrew J.; Santulli, Robert B.; Schwartz, Eben S.; Sink, Kaycee M.; Williamson, Jeff D.; Garg, Pradeep; Watkins, Franklin; Ott, Brian R.; Querfurth, Henry; Tremont, Geoffrey; Salloway, Stephen; Malloy, Paul; Correia, Stephen; Rosen, Howard J.; Miller, Bruce L.; Mintzer, Jacobo; Longmire, Crystal Flynn; Spicer, Kenneth; Finger, Elizabeth; Rachinsky, Irina; Rogers, John; Kertesz, Andrew; Drost, Dick

    2013-01-01

    Aberrant connectivity is implicated in many neurological and psychiatric disorders, including Alzheimer’s disease and schizophrenia. However, other than a few disease-associated candidate genes, we know little about the degree to which genetics play a role in the brain networks; we know even less about specific genes that influence brain connections. Twin and family-based studies can generate estimates of overall genetic influences on a trait, but genome-wide association scans (GWASs) can screen the genome for specific variants influencing the brain or risk for disease. To identify the heritability of various brain connections, we scanned healthy young adult twins with high-field, high-angular resolution diffusion MRI. We adapted GWASs to screen the brain’s connectivity pattern, allowing us to discover genetic variants that affect the human brain’s wiring. The association of connectivity with the SPON1 variant at rs2618516 on chromosome 11 (11p15.2) reached connectome-wide, genome-wide significance after stringent statistical corrections were enforced, and it was replicated in an independent subsample. rs2618516 was shown to affect brain structure in an elderly population with varying degrees of dementia. Older people who carried the connectivity variant had significantly milder clinical dementia scores and lower risk of Alzheimer’s disease. As a posthoc analysis, we conducted GWASs on several organizational and topological network measures derived from the matrices to discover variants in and around genes associated with autism (MACROD2), development (NEDD4), and mental retardation (UBE2A) significantly associated with connectivity. Connectome-wide, genome-wide screening offers substantial promise to discover genes affecting brain connectivity and risk for brain diseases. PMID:23471985

  7. The influence of riparian woodland on the spatial and temporal variability of stream water temperatures in an upland salmon stream

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    I. A. Malcolm

    2004-01-01

    Full Text Available The spatio-temporal variability of stream water temperatures was investigated at six locations on the Girnock Burn (30km2 catchment, Cairngorms, Scotland over three hydrological years between 1998 and 2002. The key site-specific factors affecting the hydrology and climatology of the sampling points were investigated as a basis for physical process inference. Particular emphasis was placed on assessing the effects of riparian forest in the lower catchment versus the heather moorland riparian zones that are spatially dominant in the upper catchment. The findings were related to river heat budget studies that provided process detail. Gross changes in stream temperature were affected by the annual cycle of incoming solar radiation and seasonal changes in hydrological and climatological conditions. Inter-annual variation in these controlling variables resulted in inter-annual variability in thermal regime. However, more subtle inter-site differences reflected the impact of site-specific characteristics on various components of the river energy budget. Inter-site variability was most apparent at shorter time scales, during the summer months and for higher stream temperatures. Riparian woodland in the lower catchment had a substantial impact on thermal regime, reducing diel variability (over a period of 24 hours and temperature extremes. Observed inter-site differences are likely to have a substantial effect on freshwater ecology in general and salmonid fish in particular. Keywords: temperature, thermal regime, forest, salmon, hydrology, Girnock Burn, Cairngorm

  8. Temporal dynamics of airborne fungi in Havana (Cuba) during dry and rainy seasons: influence of meteorological parameters

    Science.gov (United States)

    Almaguer, Michel; Aira, María-Jesús; Rodríguez-Rajo, F. Javier; Rojas, Teresa I.

    2014-09-01

    The aim of this paper was to determine for first time the influence of the main meteorological parameters on the atmospheric fungal spore concentration in Havana (Cuba). This city is characterized by a subtropical climate with two different marked annual rainfall seasons during the year: a "dry season" and a "rainy season". A nonviable volumetric methodology (Lanzoni VPPS-2000 sampler) was used to sample airborne spores. The total number of spores counted during the 2 years of study was 293,594, belonging to 30 different genera and five spore types. Relative humidity was the meteorological parameter most influencing the atmospheric concentration of the spores, mainly during the rainy season of the year. Winds coming from the SW direction also increased the spore concentration in the air. In terms of spore intradiurnal variation we found three different patterns: morning maximum values for Cladosporium, night peaks for Coprinus and Leptosphaeria, and uniform behavior throughout the whole day for Aspergillus/ Penicillium."

  9. Atmospheric Fossil Fuel CO2 Traced by Δ(14)C in Beijing and Xiamen, China: Temporal Variations, Inland/Coastal Differences and Influencing Factors.

    Science.gov (United States)

    Niu, Zhenchuan; Zhou, Weijian; Wu, Shugang; Cheng, Peng; Lu, Xuefeng; Xiong, Xiaohu; Du, Hua; Fu, Yunchong; Wang, Gehui

    2016-06-07

    One year of atmospheric Δ(14)CO2 were observed in 2014 in the inland city of Beijing and coastal city of Xiamen, China, to trace temporal CO2ff variations and to determine the factors influencing them. The average CO2ff concentrations at the sampling sites in Beijing and Xiamen were 39.7 ± 36.1 ppm and 13.6 ± 12.3 ppm, respectively. These contributed 75.2 ± 14.6% and 59.1 ± 26.8% to their respective annual ΔCO2 offsets over background CO2 concentrations. Significantly (p < 0.05) high CO2ff values were observed in winter in Beijing. We did not find any significant differences in CO2ff values between weekdays and weekends. Diurnal CO2ff variations were plainly evident, with high values between midnight and 4:00, and during morning and afternoon rush hours. The sampling site in the inland city of Beijing displayed much higher CO2ff inputs and overall temporal variations than the site in the coastal city of Xiamen. The variations of CO2ff at both sites were controlled by a combination of emission sources, topography, and atmospheric dispersion. In particular, diurnal observations at the urban site in Beijing showed that CO2ff was easily accumulated under the southeast wind conditions.

  10. MSTN genotypes in Thoroughbred horses influence skeletal muscle gene expression and racetrack performance.

    Science.gov (United States)

    McGivney, Beatrice A; Browne, John A; Fonseca, Rita G; Katz, Lisa M; Machugh, David E; Whiston, Ronan; Hill, Emmeline W

    2012-12-01

    Myostatin, encoded by the MSTN gene, is a member of the TGF-β superfamily that regulates skeletal muscle development. A MSTN SNP significantly associated with Thoroughbred horse racing phenotypes has recently been identified as well as significant reductions in Thoroughbred skeletal muscle gene expression for three transcripts 400-1500 base pairs downstream of the MSTN gene following a period of training. Together, these findings indicate that MSTN genotypes may influence MSTN gene expression. To investigate this, MSTN mRNA expression was measured in biopsies from the middle gluteal muscle from 60 untrained yearling Thoroughbreds (C/C, n = 15; C/T, n = 28; T/T, n = 17) using two independent real-time qRT-PCR assays. MSTN gene expression was also evaluated in a subset (N = 33) of these animals using samples collected after a ten-month period of training. A significant association was observed between genotype and mRNA abundance for the untrained horses (assay I, P = 0.0237; assay II, P = 0.003559), with the C/C cohort having the highest MSTN mRNA levels, the T/T group the lowest levels and the C/T group intermediate levels. Following training, there was a significant decrease in MSTN mRNA (-3.35-fold; P = 6.9 × 10(-7) ), which was most apparent for the C/C cohort (-5.88-fold, P = 0.001). These data demonstrate the tight relationship between phenotype, genotype and gene expression at the MSTN gene in Thoroughbred racehorses.

  11. INFLUENCE OF THE POLYMORPHISM OF THE RENIN-ANGIOTENSIN SYSTEM GENES ON THE CARDIAC ARRHYTHMIAS IN CHILDREN WITH HYPERTROPHIC CARDIOMYOPATHY

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    N. A. Berezneva

    2013-01-01

    Full Text Available Hypertrophic cardiomyopathy (HCMP is a genetically determined myocardial disease, characterized by massive hypertrophy of the myocardium of the left and/or (rarely the right ventricle, often associated with obstruction of the left ventricular outflow tract and diastolic dysfunction. The course of disease can be complicated by development of various cardiac arrhythmias.  It was reported that severity of HCMP course depends at certain degree on polymorphism of candidate genes, including genes of the renin angiotensin system (RAS. Influence of RAS genes polymorphism on the frequency and character of cardiac arrhythmias in childhood is almost not studied. Aim: to determine the influence of RAS genes polymorphism on the prevalence and structure of cardiac arrhythmias in children with HCMP. Patients and methods: analysis of influence of RAS genes polymorphism on the prevalence and structure of cardiac arrhythmias was performed in 32 children with HCMP. All the patients were carried out ECG, cardiac ultrasound and ECG Holter monitoring. Polymorphism of the RAS genes (renin gene (REN G83A, angiotensinogen gene (AGT M235T, angiotensin-converting enzyme gene (ACE I/D, angiotensin II receptor type 1 gene (AGTR1 A1166C. Results: in patients with HCMP was established a higher frequency of TT-genotype and T-alleles of angiotensinogen gene than in comparison group. In homozygous patients with T-allele of angiotensinogen gene ventricular arrhythmia was found reliably more often than in patients with MT- and MM-genotypes, which suggested that M235T polymorphism of angiotensinogen gene influenced on intensity of ventricular arrhythmias in children with HCMP. Conclusions: in children with HCMP and cardiac arrhythmias analysis of M235T polymorphism of angiotensinogen gene can be used as an additional criterion for revealing of patients with high risk of arrhythmic complications and for development of preventative measures.

  12. Genetic control of responses to Trypanosoma cruzi in mice: multiple genes influencing parasitemia and survival.

    Science.gov (United States)

    Wrightsman, R; Krassner, S; Watson, J

    1982-05-01

    Inbred strains of mice can be divided into two groups based on the level of parasitemia which develops after injection with 10(3) trypomastigotes of Trypanosoma cruzi (Peru). Strains which developed parasitemias of greater than 10(7) trypomastigotes per ml by day 17, including C3H/HeJ, BALB/c, and CBA/N mice, were termed high parasitemia strains. Low parasitemia strains, including C57BL/6J and DBA/2J mice, developed parasitemias of less than 5 x 10(6) trypomastigotes per ml by day 17 of infection. Congenic mice from C57BL/10J, C57BL/6J, and BALB/c backgrounds which differed at the H-2 region were injected with 10(3) trypomastigotes to determine the effect of the H-2 locus on response to infection. The H-2 locus had no effect on the level of parasitemia attained during infection. However, one strain, B10.S (H-2s), was unusual in that most of the mice survived infection. The results of infection of F1 hybrid progeny with T. cruzi (Peru) suggest that the low parasitemia response in inherited in a dominant manner and that survival may be influenced by several other genes. The response to T. cruzi infection in inbred mice, as measured by parasitemia and survival time, was influenced by several genes. One or more genes, located outside the H-2 region, were involved in regulating the level of parasitemia reached during infection. Another H-2-linked gene(s) was involved in survival of the infection and appeared to be unique to the H-2s haplotype.

  13. Structural influence of gene networks on their inference: analysis of C3NET

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    Emmert-Streib Frank

    2011-06-01

    Full Text Available Abstract Background The availability of large-scale high-throughput data possesses considerable challenges toward their functional analysis. For this reason gene network inference methods gained considerable interest. However, our current knowledge, especially about the influence of the structure of a gene network on its inference, is limited. Results In this paper we present a comprehensive investigation of the structural influence of gene networks on the inferential characteristics of C3NET - a recently introduced gene network inference algorithm. We employ local as well as global performance metrics in combination with an ensemble approach. The results from our numerical study for various biological and synthetic network structures and simulation conditions, also comparing C3NET with other inference algorithms, lead a multitude of theoretical and practical insights into the working behavior of C3NET. In addition, in order to facilitate the practical usage of C3NET we provide an user-friendly R package, called c3net, and describe its functionality. It is available from https://r-forge.r-project.org/projects/c3net and from the CRAN package repository. Conclusions The availability of gene network inference algorithms with known inferential properties opens a new era of large-scale screening experiments that could be equally beneficial for basic biological and biomedical research with auspicious prospects. The availability of our easy to use software package c3net may contribute to the popularization of such methods. Reviewers This article was reviewed by Lev Klebanov, Joel Bader and Yuriy Gusev.

  14. Influence of environmental factors on abundance and temporal variation of benthic fauna resources in the eutrophic Tha Chin estuary, Samut Sakhon province, Thailand.

    Science.gov (United States)

    Ritnim, Nittaya; Meksumpun, Charumas

    2011-01-01

    The influence of environmental factors on the abundance and temporal variation of benthic fauna resources was studied in the eutrophic Tha Chin estuary located in Samut Sakhon province. The objectives were to analyze the status of abundance and temporal variation of the benthic fauna and to clarify the impacts from environmental factors (water and sediment quality). Field surveys were conducted monthly from August 2007 to March 2008 at 11 sampling stations in the estuary. Based on freshwater runoff volumes, the high-, medium-, and low-loading periods were categorized to be from August to October 2007, November to December 2007, and January to March 2008, respectively. The benthic fauna resources were composed of 57 species in eight phyla. Annelids were the dominant species (with the maximum density being 19,885 individuals/m2), followed by the mollusks. Both densities decreased during the low-loading period in 2008. Water quality deteriorated during the high-loading period. Land-based wastewater discharges decreased the levels of salinity and dissolved oxygen but dramatically increased various nutrients. Consequently, the sediment quality deteriorated during the medium-loading period. Bottom deposits during this time depicted high accumulation of acid volatile sulfides (more than 0.76 mg/g dry weight). Analyzing the environmental relationships, deposit feeders (for example, Nereis sp. and Prionospio sp.) and a clam (Arcuatula sp.) showed potential as bio-indicators for environmental monitoring. The overall results revealed the importance of changes in the water and sediment qualities that had an influence on related benthic resources. The increase in the level of NH4(+)-N had a negative impact on the economic clam species, while the sedimentary TOM showed positive correlation (P land-based runoff should be controlled for the protection of resources. Further effective sustainable management will be enhanced by giving serious consideration to an eco-based zoning

  15. Epigenetic Influence of Dam Methylation on Gene Expression and Attachment in Uropathogenic Escherichia coli.

    Science.gov (United States)

    Stephenson, Stacy Ann-Marie; Brown, Paul D

    2016-01-01

    Urinary tract infections (UTI) are among the most frequently encountered infections in clinical practice globally. Predominantly a burden among female adults and infants, UTIs primarily caused by uropathogenic Escherichia coli (UPEC) results in high morbidity and fiscal health strains. During pathogenesis, colonization of the urinary tract via fimbrial adhesion to mucosal cells is the most critical point in infection and has been linked to DNA methylation. Furthermore, with continuous exposure to antibiotics as the standard therapeutic strategy, UPEC has evolved to become highly adaptable in circumventing the effect of antimicrobial agents and host defenses. Hence, the need for alternative treatment strategies arises. Since differential DNA methylation is observed as a critical precursor to virulence in various pathogenic bacteria, this body of work sought to assess the influence of the DNA adenine methylase (dam) gene on gene expression and cellular adhesion in UPEC and its potential as a therapeutic target. To monitor the influence of dam on attachment and FQ resistance, selected UPEC dam mutants created via one-step allelic exchange were transformed with cloned qnrA and dam complement plasmid for comparative analysis of growth rate, antimicrobial susceptibility, biofilm formation, gene expression, and mammalian cell attachment. The absence of DNA methylation among dam mutants was apparent. Varying deficiencies in cell growth, antimicrobial resistance and biofilm formation, alongside low-level increases in gene expression (recA and papI), and adherence to HEK-293 and HTB-9 mammalian cells were also detected as a factor of SOS induction to result in increased mutability. Phenotypic characteristics of parental strains were restored in dam complement strains. Dam's vital role in DNA methylation and gene expression in local UPEC isolates was confirmed. Similarly to dam-deficient Enterohemorrhagic E. coli (EHEC), these findings suggest unsuccessful therapeutic use of

  16. Influence of temporal relationships between serotonergic and dopaminergic precursors on the regulation of gonadal development in birds.

    Science.gov (United States)

    Chaturvedi, Chandra Mohini; Yadav, Suneeta

    2013-09-01

    This article is focused on the effect of specific phase relation of serotonergic and dopaminergic oscillations on the gonadal responses of different avian species. These species include (i) summer breeding birds - Red headed bunting (exhibiting post-reproductive absolute photorefractoriness) and Indian Weaver bird (which lacks absolute photorefractoriness), (ii) autumn breeding - Spotted munia and Lal munia (photoperiodic responses of which are distinctly different from that of any long day birds described thus far) and (iii) domesticated Japanese quail (which under natural day length breeds in summer, exhibits relative photorefractoriness, but breeds continuously if maintained in long photoperiod). Previous experiments have shown that daily administration of serotonin precursor 5-hydroxytryptophan and dopamine precursor L-dihydroxyphenylalanine given 8h apart during progressive phase of gonadal cycle can lead to a significant decrease in gonadal activity. However, if given at an interval of 12h it leads to an increase in gonadal activity and the effect of other intervals (0-, 4-, 16- and 20-h) were not different from control. Similar effects were observed during regressive phase of the gonadal cycle of above species except in those which display absolute photorefractory phase in their breeding cycle. This shows that, gonad of such species not only develop post-reproductive photorefractoriness but also becomes insensitive to the stimulatory effects of 5-HTP and L-DOPA when given at the interval of 12h. It is suggested that, temporal phase relation of circadian serotonergic and dopaminergic oscillations is the basis of seasonality in birds and may alter the activity of neuroendocrine-gonadal axis not only under natural day length but also under experimental/different photoperiodic conditions. These results are in agreement with the internal coincidence model of photoperiodic time measurement and indicate that birds can detect specific phase relationship between the

  17. Spatio-temporal distribution of vegetation index and its influencing factors—a case study of the Jiaozhou Bay, China

    Science.gov (United States)

    Zheng, Yang; Yu, Ge

    2016-10-01

    The coastal zone is an area characterized by intense interaction between land and sea, high sensitivity to regional environmental changes, and concentrated human activities. Little research has investigated vegetation cover changes in coastal zones resulting from climate change and land-use change, with a lack of knowledge about the driving mechanism. Normalized difference vegetation index (NDVI) can be used as an indicator for change of the coastal environment. In this study, we analyzed the interannual changes and spatial distribution of NDVI in the coastal zone around Jiaozhou Bay in Qingdao, a coastal city undergoing rapid urbanization in northeast China. The underlying causes of NDVI variations were discussed in the context of climate change and land-use change. Results showed that the spatio-temporal distribution of NDVI displayed high spatial variability in the study area and showed a typical trend of gradually increasing from coastal to inland regions. The significant increase area of NDVI was mainly found in newly added construction land, extending along the coastline towards the inland. Land vegetation cover demonstrated a certain response relationship to sea-land climate change and land-based activities. The impact of land-based human activities was slightly greater than that of sea-land climate change for land vegetation cover. The results indicate that promoting ecological policies can build an ecological security framework of vegetation suitable for the resource characteristics of coastal cities. The framework will buffer the negative effects of sea-land climate change and land-based human activities on vegetation cover and thereby achieve the balance of regional development and ecological benefits in the coastal zone.

  18. Influence of apolipoprotein-E gene on lipid profile, physical activity and body fat relationship

    Directory of Open Access Journals (Sweden)

    Thales Boaventura Rachid Nascimento

    2012-03-01

    Full Text Available Physical activity and body fat modify lipemia, and this effect seems to be influenced by apolipoprotein-E (APOE gene polymorphism. Thus, the purpose of this article was to review main results of studies that have analyzed the relation of APOE gene with physical activity and body fat on triglycerides, total cholesterol and low (LDL and high density lipoprotein (HDL concentrations. The Scientific Electronic Library Online – SciELO, Web of Science and PubMed database were used to locate the articles. The keywords used in combination were: apoe genotype, apolipoprotein-E polymorphism, physical exercise, physical activity, aerobic exercise, body fat and obesity. Originals scientific investigations performed with humans were included, and excluded those ones which involved samples with diseases, except obesity and/or lipemic disorders. It was observed a trend, that ε2 allele carriers are the ones with the greater improvements on lipemia from physical exercise. In addition, the body fat impact on the elevation of triglycerides and LDL are stronger in carriers of the ε2 and ε4 allele, respectively. Considering the small number of originals scientific investigations and their divergent results, reliable inferences can not be made about the APOE gene polymorphism influences on physical activity and body fat effect on lipemia. Thus, further studies with others populations and more volunteers for allele, as well as others exercise modalities and intensities, are necessary.

  19. Social environment influences the relationship between genotype and gene expression in wild baboons.

    Science.gov (United States)

    Runcie, Daniel E; Wiedmann, Ralph T; Archie, Elizabeth A; Altmann, Jeanne; Wray, Gregory A; Alberts, Susan C; Tung, Jenny

    2013-05-19

    Variation in the social environment can have profound effects on survival and reproduction in wild social mammals. However, we know little about the degree to which these effects are influenced by genetic differences among individuals, and conversely, the degree to which social environmental variation mediates genetic reaction norms. To better understand these relationships, we investigated the potential for dominance rank, social connectedness and group size to modify the effects of genetic variation on gene expression in the wild baboons of the Amboseli basin. We found evidence for a number of gene-environment interactions (GEIs) associated with variation in the social environment, encompassing social environments experienced in adulthood as well as persistent effects of early life social environment. Social connectedness, maternal dominance rank and group size all interacted with genotype to influence gene expression in at least one sex, and either in early life or in adulthood. These results suggest that social and behavioural variation, akin to other factors such as age and sex, can impact the genotype-phenotype relationship. We conclude that GEIs mediated by the social environment are important in the evolution and maintenance of individual differences in wild social mammals, including individual differences in responses to social stressors.

  20. A temporal switch in the insulin-signalling pathway that regulates hepatic IGF-binding protein-1 gene expression

    OpenAIRE

    2006-01-01

    PUBLISHED Insulin regulation of hepatic gene transcription is a vital component of glucose homeostasis. Understanding the molecular regulationof thisprocess aids the searchfor the defect(s) that promotesinsulin-resistant states, such asdiabetesmellitus. We havepreviously shownthat the insulin regulationof hepatic IGF-binding protein-1 (IGFBP1) expression requiresthe signalling proteins phosphatidylinositol 3-kinase (PI 3-kinase) and mammalian target of rapamycin (mTOR). In this report, we ...

  1. Emergent Self-Organized Criticality in Gene Expression Dynamics: Temporal Development of Global Phase Transition Revealed in a Cancer Cell Line

    Science.gov (United States)

    Tsuchiya, Masa; Giuliani, Alessandro; Hashimoto, Midori; Erenpreisa, Jekaterina; Yoshikawa, Kenichi

    2015-01-01

    Background The underlying mechanism of dynamic control of the genome-wide expression is a fundamental issue in bioscience. We addressed it in terms of phase transition by a systemic approach based on both density analysis and characteristics of temporal fluctuation for the time-course mRNA expression in differentiating MCF-7 breast cancer cells. Methodology In a recent work, we suggested criticality as an essential aspect of dynamic control of genome-wide gene expression. Criticality was evident by a unimodal-bimodal transition through flattened unimodal expression profile. The flatness on the transition suggests the existence of a critical transition at which up- and down-regulated expression is balanced. Mean field (averaging) behavior of mRNAs based on the temporal expression changes reveals a sandpile type of transition in the flattened profile. Furthermore, around the transition, a self-similar unimodal-bimodal transition of the whole expression occurs in the density profile of an ensemble of mRNA expression. These singular and scaling behaviors identify the transition as the expression phase transition driven by self-organized criticality (SOC). Principal Findings Emergent properties of SOC through a mean field approach are revealed: i) SOC, as a form of genomic phase transition, consolidates distinct critical states of expression, ii) Coupling of coherent stochastic oscillations between critical states on different time-scales gives rise to SOC, and iii) Specific gene clusters (barcode genes) ranging in size from kbp to Mbp reveal similar SOC to genome-wide mRNA expression and ON-OFF synchronization to critical states. This suggests that the cooperative gene regulation of topological genome sub-units is mediated by the coherent phase transitions of megadomain-scaled conformations between compact and swollen chromatin states. Conclusion and Significance In summary, our study provides not only a systemic method to demonstrate SOC in whole-genome expression

  2. Environmental influence on the worldwide prevalence of a 776C->G variant in the transcobalamin gene (TCN2)

    National Research Council Canada - National Science Library

    Guéant, Jean-Louis; Chabi, Nicodème W; Guéant-Rodriguez, Rosa-Maria; Mutchinick, Osvaldo M; Debard, Renée; Payet, Corinne; Lu, Xiaohong; Villaume, Christian; Bronowicki, Jean-Pierre; Quadros, Edward V; Sanni, Ambaliou; Amouzou, Emile; Xia, Bing; Chen, Min; Anello, Guido; Bosco, Paolo; Romano, Corrado; Arrieta, Heidy R; Sánchez, Beatríz E; Romano, Antonino; Herbeth, Bernard; Anwar, Wafaa; Namour, Fares

    2007-01-01

    A 776C-->G variant (dbSNP ID: rs1801198) in the transcobalamin gene (TCN2; MIM# 275350) decreases the cellular and plasma concentration of transcobalamin and thereby influences the cellular availability of vitamin B...

  3. Temporal variations in the gene expression levels of cyanobacterial anti-oxidant enzymes through geological history: implications for biological evolution during the Great Oxidation Event

    Science.gov (United States)

    Harada, M.; Furukawa, R.; Yokobori, S. I.; Tajika, E.; Yamagishi, A.

    2016-12-01

    A significant rise in atmospheric O2 levels during the GOE (Great Oxidation Event), ca. 2.45-2.0 Ga, must have caused a great stress to biosphere, enforcing life to adapt to oxic conditions. Cyanobacteria, oxygenic photosynthetic bacteria that had been responsible for the GOE, are at the same time one of the organisms that would have been greatly affected by the rise of O2 level in the surface environments. Knowledge on the evolution of cyanobacteria is not only important to elucidate the cause of the GOE, but also helps us to better understand the adaptive evolution of life in response to the GOE. Here we performed phylogenetic analysis of an anti-oxidant enzyme Fe-SOD (iron superoxide dismutase) of cyanobacteria, to assess the adaptive evolution of life under the GOE. The rise of O2 level must have increased the level of toxic reactive oxygen species in cyanobacterial cells, thus forced them to change activities or the gene expression levels of Fe-SOD. In the present study, we focus on the change in the gene expression levels of the enzyme, which can be estimated from the promoter sequences of the gene. Promoters are DNA sequences found upstream of protein encoding regions, where RNA polymerase binds and initiates transcription. "Strong" promoters that efficiently interact with RNA polymerase induce high rates of transcription, leading to high levels of gene expression. Thus, from the temporal changes in the promoter sequences, we can estimate the variations in the gene expression levels during the geological time. Promoter sequences of Fe-SOD at each ancestral node of cyanobacteria were predicted from phylogenetic analysis, and the ancestral promoter sequences were compared to the promoters of known highly expressed genes. The similarity was low at the time of the emergence of cyanobacteria; however, increased at the branching nodes diverged 2.4 billon years ago. This roughly coincided with the onset of the GOE, implying that the transition from low to high gene

  4. Spatio-Temporal Gene Expression Profiling during In Vivo Early Ovarian Folliculogenesis: Integrated Transcriptomic Study and Molecular Signature of Early Follicular Growth.

    Directory of Open Access Journals (Sweden)

    Agnes Bonnet

    Full Text Available The successful achievement of early ovarian folliculogenesis is important for fertility and reproductive life span. This complex biological process requires the appropriate expression of numerous genes at each developmental stage, in each follicular compartment. Relatively little is known at present about the molecular mechanisms that drive this process, and most gene expression studies have been performed in rodents and without considering the different follicular compartments.We used RNA-seq technology to explore the sheep transcriptome during early ovarian follicular development in the two main compartments: oocytes and granulosa cells. We documented the differential expression of 3,015 genes during this phase and described the gene expression dynamic specific to these compartments. We showed that important steps occurred during primary/secondary transition in sheep. We also described the in vivo molecular course of a number of pathways. In oocytes, these pathways documented the chronology of the acquisition of meiotic competence, migration and cellular organization, while in granulosa cells they concerned adhesion, the formation of cytoplasmic projections and steroid synthesis. This study proposes the involvement in this process of several members of the integrin and BMP families. The expression of genes such as Kruppel-like factor 9 (KLF9 and BMP binding endothelial regulator (BMPER was highlighted for the first time during early follicular development, and their proteins were also predicted to be involved in gene regulation. Finally, we selected a data set of 24 biomarkers that enabled the discrimination of early follicular stages and thus offer a molecular signature of early follicular growth. This set of biomarkers includes known genes such as SPO11 meiotic protein covalently bound to DSB (SPO11, bone morphogenetic protein 15 (BMP15 and WEE1 homolog 2 (S. pombe(WEE2 which play critical roles in follicular development but other biomarkers

  5. Influence of light on growth, fumonisin biosynthesis and FUM1 gene expression by Fusarium proliferatum.

    Science.gov (United States)

    Fanelli, Francesca; Schmidt-Heydt, Markus; Haidukowski, Miriam; Geisen, Rolf; Logrieco, Antonio; Mulè, Giuseppina

    2012-02-01

    Fumonisins are a group of mycotoxins, mainly found in maize and maize-based food and feed, associated with several diseases in animals. The impact of these toxins on the economy and health worldwide has driven several efforts to clarify the role of environmental factors that can influence fumonisin biosynthesis by the toxigenic species. We analyzed the influence of light of varying wavelength on growth and fumonisin biosynthesis by the fungus Fusarium proliferatum ITEM 1719. Light in general had a positive influence on growth, with a mean increase of the grow rate of about 40% under light exposure in comparison to the dark incubation. Wavelengths from both sides of the spectrum, from long (627 nm) to short wavelength (470-455 nm) had a stimulating effect on fumonisin biosynthesis compared to the dark incubation: fumonisins B(1) (FB(1)) and B(2) (FB(2)) production increased of about 40 fold under red, 35 fold under blue, 20 fold under royal blue, 10 fold under green, 5 fold under yellow and 3 fold under white light in comparison to the dark incubation. The transcriptional regulation of the FUM1 fumonisin biosynthesis gene was analyzed by Real time reverse transcriptase PCR quantification, revealing a correlation between fumonisin biosynthesis and gene expression. These findings show a role of light on the growth and the modulation of fumonisin biosynthesis and provide new information on the physiology of an important toxigenic maize pathogen. Copyright © 2011 Elsevier B.V. All rights reserved.

  6. Differential induction of two different cystatin genes during pathogenesis of Karnal bunt (Tilletia indica) in wheat under the influence of jasmonic acid.

    Science.gov (United States)

    Dutt, Shriparna; Gaur, Vikram Singh; Taj, Gohar; Kumar, Anil

    2012-09-10

    In the present study, expression patterns of two different wheat cystatins (WCs) were studied under the influence of jasmonate signaling in triggering resistance against Karnal bunt (KB). Cystatins are cysteine proteinase inhibitors (CPI) constituting a multigene family which regulate the activity of endo- and/or exogenous cysteine proteinases (CP). Two wheat varieties HD-29 (resistant, R) and WH-542 (susceptible, S) were pre-conditioned with jasmonate and then artificially inoculated with sporidial suspension of Tilletia indica to study its influence in inducing defense by regulating cystatin genes. On the transcriptional level, WC4 and WC5 gave different temporal expression patterns. Expression of WC4 was higher in boot emergence stage which is most susceptible to KB and then slowly declined in both varieties. Expression of WC5 showed an entirely reverse pattern of expression, which kept on rising as the grains matured. Cystatin activity determination by inhibitor assay gave higher activity in resistant variety and under JA treatment. Estimation of specific activity of total cystatin at different days after inoculation (DAI) showed that JA positively induced cystatin expression in both varieties but R variety always registered a greater cystatin expression than the susceptible one (Pcystatin activity which gradually decreased 7 DAI when compared with the un-inoculated plants. Based on these findings it is clearly demonstrated that jasmonate acts as a potential activator of induced resistance by up-regulating cystatin expression and provides the conditioning effect prior to infection through the maintenance of critical balance of CP/CPI interaction. However, different cystatin genes show different temporal expression patterns and may play different roles at various developmental stages of the grain.

  7. Temporal properties of stereopsis

    Science.gov (United States)

    Gheorghiu, E.

    2005-03-01

    The goal of the research presented in this thesis was to investigate temporal properties of disparity processing and depth perception in human subjects, in response to dynamic stimuli. The results presented in various chapters, reporting findings about different temporal aspects of disparity processing, are based on psychophysical experiments and computational model analysis. In chapter 1 we investigated which processes of binocular depth perception in dynamic random-dot stereograms (DRS), i.e., tolerance for interocular delays and temporal integration of correlation, are responsible for the temporal flexibility of the stereoscopic system. Our results demonstrate that (i) disparities from simultaneous monocular inputs dominate those from interocular delayed inputs; (ii) stereopsis is limited by temporal properties of monocular luminance mechanisms; (iii) depth perception in DRS results from cross-correlation-like operation on two simultaneous monocular inputs that represent the retinal images after having been subjected to a process of monocular temporal integration of luminance. In chapter 2 we examined what temporal information is exploited by the mechanisms underlying stereoscopic motion in depth. We investigated systematically the influence of temporal frequency on binocular depth perception in temporally correlated and temporally uncorrelated DRS. Our results show that disparity-defined depth is judged differently in temporally correlated and uncorrelated DRS above a temporal frequency of about 3 Hz. The results and simulations indicate that: (i) above about 20 Hz, the complete absence of stereomotion is caused by temporal integration of luminance; (ii) the difference in perceived depth in temporally correlated and temporally uncorrelated DRS for temporal frequencies between 20 and 3 Hz, is caused by temporal integration of disparity. In chapter 3 we investigated temporal properties of stereopsis at different spatial scales in response to sustained and

  8. Genetic influences on adolescent sexual behavior: Why genes matter for environmentally oriented researchers.

    Science.gov (United States)

    Harden, K Paige

    2014-03-01

    There are dramatic individual differences among adolescents in how and when they become sexually active adults, and early sexual activity is frequently cited as a cause of concern for scientists, policymakers, and the general public. Understanding the causes and developmental impact of adolescent sexual activity can be furthered by considering genes as a source of individual differences. Quantitative behavioral genetics (i.e., twin and family studies) and candidate gene association studies now provide clear evidence for the genetic underpinnings of individual differences in adolescent sexual behavior and related phenotypes. Genetic influences on sexual behavior may operate through a variety of direct and indirect mechanisms, including pubertal development, testosterone levels, and dopaminergic systems. Genetic differences may be systematically associated with exposure to environments that are commonly treated as causes of sexual behavior (gene-environment correlation). Possible gene-environment correlations pose a serious challenge for interpreting the results of much behavioral research. Multivariate, genetically informed research on adolescent sexual behavior compares twins and family members as a form of quasi experiment: How do twins who differ in their sexual experiences differ in their later development? The small but growing body of genetically informed research has already challenged dominant assumptions regarding the etiology and sequelae of adolescent sexual behavior, with some studies indicating possible positive effects of teenage sexuality. Studies of Gene × Environment interaction may further elucidate the mechanisms by which genes and environments combine to shape the development of sexual behavior and its psychosocial consequences. Overall, the existence of heritable variation in adolescent sexual behavior has profound implications for environmentally oriented theory and research.

  9. Genetic Influences on Adolescent Sexual Behavior: Why Genes Matter for Environmentally-Oriented Researchers

    Science.gov (United States)

    Harden, K. Paige

    2013-01-01

    There are dramatic individual differences among adolescents in how and when they become sexually active adults, and “early” sexual activity is frequently cited as a cause of concern for scientists, policymakers, and the general public. Understanding the causes and developmental impact of adolescent sexual activity can be furthered by considering genes as a source of individual differences. Quantitative behavioral genetics (i.e., twin and family studies) and candidate gene association studies now provide clear evidence for the genetic underpinnings of individual differences in adolescent sexual behavior and related phenotypes. Genetic influences on sexual behavior may operate through a variety of direct and indirect mechanisms, including pubertal development, testosterone levels, and dopaminergic systems. Genetic differences may be systematically associated with exposure to environments that are commonly treated as causes of sexual behavior (gene-environment correlation). Possible gene-environment correlations pose a serious challenge for interpreting the results of much behavioral research. Multivariate, genetically-informed research on adolescent sexual behavior compares twins and family members as a form of “quasi-experiment”: How do twins who differ in their sexual experiences differ in their later development? The small but growing body of genetically-informed research has already challenged dominant assumptions regarding the etiology and sequelae of adolescent sexual behavior, with some studies indicating possible positive effects of teenage sexuality. Studies of gene × environment interaction may further elucidate the mechanisms by which genes and environments combine to shape the development of sexual behavior and its psychosocial consequences. Overall, the existence of heritable variation in adolescent sexual behavior has profound implications for environmentally-oriented theory and research. PMID:23855958

  10. Determinants of nucleosome positioning and their influence on plant gene expression.

    Science.gov (United States)

    Liu, Ming-Jung; Seddon, Alexander E; Tsai, Zing Tsung-Yeh; Major, Ian T; Floer, Monique; Howe, Gregg A; Shiu, Shin-Han

    2015-08-01

    Nucleosome positioning influences the access of transcription factors (TFs) to their binding sites and gene expression. Studies in plant, animal, and fungal models demonstrate similar nucleosome positioning patterns along genes and correlations between occupancy and expression. However, the relationships among nucleosome positioning, cis-regulatory element accessibility, and gene expression in plants remain undefined. Here we showed that plant nucleosome depletion occurs on specific 6-mer motifs and this sequence-specific nucleosome depletion is predictive of expression levels. Nucleosome-depleted regions in Arabidopsis thaliana tend to have higher G/C content, unlike yeast, and are centered on specific G/C-rich 6-mers, suggesting that intrinsic sequence properties, such as G/C content, cannot fully explain plant nucleosome positioning. These 6-mer motif sites showed higher DNase I hypersensitivity and are flanked by strongly phased nucleosomes, consistent with known TF binding sites. Intriguingly, this 6-mer-specific nucleosome depletion pattern occurs not only in promoter but also in genic regions and is significantly correlated with higher gene expression level, a phenomenon also found in rice but not in yeast. Among the 6-mer motifs enriched in genes responsive to treatment with the defense hormone jasmonate, there are no significant changes in nucleosome occupancy, suggesting that these sites are potentially preconditioned to enable rapid response without changing chromatin state significantly. Our study provides a global assessment of the joint contribution of nucleosome occupancy and motif sequences that are likely cis-elements to the control of gene expression in plants. Our findings pave the way for further understanding the impact of chromatin state on plant transcriptional regulatory circuits.

  11. Advanced Large Scale Cross Domain Temporal Topic Modeling Algorithms to Infer the Influence of Recent Research on IPCC Assessment Reports

    Science.gov (United States)

    Sleeman, J.; Halem, M.; Finin, T.; Cane, M. A.

    2016-12-01

    Approximately every five years dating back to 1989, thousands of climate scientists, research centers and government labs volunteer to prepare comprehensive Assessment Reports for the Intergovernmental Panel on Climate Change. These are highly curated reports distributed to 200 nation policy makers. There have been five IPCC Assessment Reports to date, the latest leading to a Paris Agreement in Dec. 2016 signed thus far by 172 nations to limit the amount of global Greenhouse gases emitted to producing no more than a 20 C warming of the atmosphere. These reports are a living evolving big data collection tracing 30 years of climate science research, observations, and model scenario intercomparisons. They contain more than 200,000 citations over a 30 year period that trace the evolution of the physical basis of climate science, the observed and predicted impact, risk and adaptation to increased greenhouse gases and mitigation approaches, pathways, policies for climate change. Document-topic and topic-term probability distributions are built from the vocabularies of the respective assessment report chapters and citations. Using Microsoft Bing, we retrieve 150,000 citations referenced across chapters and convert those citations to text. Using a word n-gram model based on a heterogeneous set of climate change terminology, lemmatization, noise filtering and stopword elimination, we calculate word frequencies for chapters and citations. Temporal document sets are built based on the assessment period. In addition to topic modeling, we employ cross domain correlation measures. Using the Jensen-Shannon divergence and Pearson correlation we build correlation matrices for chapter and citations topics. The shared vocabulary acts as the bridge between domains resulting in chapter-citation point pairs in space. Pairs are established based on a document-topic probability distribution. Each chapter and citation is associated with a vector of topics and based on the n most probable

  12. β3 Integrin Haplotype Influences Gene Regulation and Plasma von Willebrand Factor Activity

    Science.gov (United States)

    Payne, Katie E; Bray, Paul F; Grant, Peter J; Carter, Angela M

    2008-01-01

    The Leu33Pro polymorphism of the gene encoding β3 integrin (ITGB3) is associated with acute coronary syndromes and influences platelet aggregation. Three common promoter polymorphisms have also been identified. The aims of this study were to (1) investigate the influence of the ITGB3 −400C/A, −425A/C and −468G/A promoter polymorphisms on reporter gene expression and nuclear protein binding and (2) determine genotype and haplotype associations with platelet αIIbβ3 receptor density. Promoter haplotypes were introduced into an ITGB3 promoter-pGL3 construct by site directed mutagenesis and luciferase reporter gene expression analysed in HEL and HMEC-1 cells. Binding of nuclear proteins was assessed by electrophoretic mobility shift assay. The association of ITGB3 haplotype with platelet αIIbβ3 receptor density was determined in 223 subjects. Species conserved motifs were identified in the ITGB3 promoter in the vicinity of the 3 polymorphisms. The GAA, GCC, AAC, AAA and ACC constructs induced ~50% increased luciferase expression relative to the GAC construct in both cell types. Haplotype analysis including Leu33Pro indicated 5 common haplotypes; no associations between ITGB3 haplotypes and receptor density were found. However, the GCC-Pro33 haplotype was associated with significantly higher vWF activity (128.6 [112.1–145.1]%) compared with all other haplotypes (107.1 [101.2–113.0]%, p=0.02). In conclusion, the GCC-Pro33 haplotype was associated with increased vWF activity but not with platelet αIIbβ3 receptor density, which may indicate ITGB3 haplotype influences endothelial function. PMID:18045606

  13. Characterization of optical turbulence at the GREGOR solar telescope: temporal and local behavior and its influence on the solar observations

    Science.gov (United States)

    Sprung, D.; Sucher, E.; Stein, K.; von der Lühe, O.; Berkefeld, Th.

    2016-10-01

    Local atmospheric turbulence at the telescope level is regarded as a major reason for affecting the performance of the adaptive optics systems using wavelengths in the visible and infrared for solar observations. During the day the air masses around the telescope dome are influenced by flow distortions. Additionally heating of the infrastructure close to telescope causes thermal turbulence. Thereby optical turbulence is produced and leads to quality changes in the local seeing throughout the day. Image degradation will be yielded affecting the performance of adaptive optical systems. The spatial resolution of the solar observations will be reduced. For this study measurements of the optical turbulence, represented by the structure function parameter of the refractive index Cn2 were performed on several locations at the GREGOR telescope at the Teide observatory at Tenerife at the Canary Islands / Spain. Since September 2012 measurements of Cn2 were carried out between the towers of the Vacuum Tower Telescope (VTT) and of GREGOR with a laser-scintillometer. The horizontal distance of the measurement path was about 75 m. Additional from May 2015 up to March 2016 the optical turbulence was determined at three additional locations close to the solar telescope GREGOR. The optical turbulence is derived from sonic anemometer measurements. Time series of the sonic temperature are analyzed and compared to the direct measurements of the laser scintillometer. Meteorological conditions are investigated, especially the influence of the wind direction. Turbulence of upper atmospheric layers is not regarded. The measured local turbulence is compared to the system performance of the GREGOR telescopes. It appears that the mountain ridge effects on turbulence are more relevant than any local causes of seeing close to the telescope. Results of these analyses and comparison of nearly one year of measurements are presented and discussed.

  14. Temporal expression of staphylococcal enterotoxin h in comparison with accessory gene regulator-dependent and -independent enterotoxins.

    Science.gov (United States)

    Lis, Elżbieta; Podkowik, Magdalena; Bystroń, Jarosław; Stefaniak, Tadeusz; Bania, Jacek

    2012-02-01

    Using sandwich enzyme-linked immunosorbent assay (ELISA), the production of staphylococcal enterotoxin (SE) H was determined in 22 Staphylococcus aureus isolates bearing the seh gene. Samples of supernatants were taken at four time points corresponding to exponential phase (optical density at 600 nm [OD(600)] 0.3 to 0.6), late exponential phase (OD(600) 2 to 4), early stationary phase (OD(600) 4 to 6), and late stationary phase (OD(600) 7 to 12). In four isolates, SEH was detectable at a very low level at the first time point. In 18 isolates, the earliest SEH production was detected in the late exponential phase. For all isolates, there was an increase of SEH concentration with time. Western blot analysis revealed that SEH production, similar to SEA, started in the early exponential phase (OD(600) ∼ 0.5). Isolates with high SEH productivity, as measured by ELISA, demonstrated a higher seh transcription as well. sec transcription was induced in the stationary phase. An induction in the sea transcript was observed during mid- to late exponential phase. Expression profile of seh was similar to that of sea. We showed that the seh expression profile is similar to that of Agr-independent sea and not to that of Agr-dependent sec genes. SEH can be effectively expressed at low bacterial counts, meaning that even in an environment not favorable for S. aureus growth, seh-bearing strains can pose a risk for food safety.

  15. Influence of climatic teleconnections on the temporal isotopic variability as recorded in a firn core from the coastal Dronning Maud Land, East Antarctica

    Indian Academy of Sciences (India)

    Sushant S Naik; Meloth Thamban; A Rajakumar; Witty D’Souza; C M Laluraj; Arun Chaturvedi

    2010-02-01

    Ice and firn core studies provide one of the most valuable tools for understanding the past climate change. In order to evaluate the temporal isotopic variability recorded in ice and its relevance to environmental changes, stable isotopes of oxygen and hydrogen were studied in a firn core from coastal Dronning Maud Land, East Antarctica. The annual 18O profile of the core shows a close relation to the El Niño Southern Oscillation (ENSO) variability. The ENSO indices show significant correlation with the surface air temperatures and 18O values of this region during the austral summer season and support an additional influence related to the Southern Annular Mode (SAM). The correlation between the combined ENSO-SAM index and the summer 18O record seems to have been caused through an atmospheric mechanism. Snow accumulation in this region illustrates a decreasing trend with opposite relationships with 18O data and surface air temperature prior and subsequent to the year 1997. A reorganization of the local water cycle is further indicated by the deuterium excess data showing a shift around 1997, consistent with a change in evaporation conditions. The present study thus illustrates the utility of ice-core studies in the reconstruction of past climate change and suggests possible influence of climatic teleconnections on the snow accumulation rates and isotopic profiles of snow in the coastal regions of east Antarctica.

  16. Does my brain want what my eyes like? - How food liking and choice influence spatio-temporal brain dynamics of food viewing.

    Science.gov (United States)

    Bielser, Marie-Laure; Crézé, Camille; Murray, Micah M; Toepel, Ulrike

    2016-12-01

    How food valuation and decision-making influence the perception of food is of major interest to better understand food intake behavior and, by extension, body weight management. Our study investigated behavioral responses and spatio-temporal brain dynamics by means of visual evoked potentials (VEPs) in twenty-two normal-weight participants when viewing pairs of food photographs. Participants rated how much they liked each food item (valuation) and subsequently chose between the two alternative food images. Unsurprisingly, strongly liked foods were also chosen most often. Foods were rated faster as strongly liked than as mildly liked or disliked irrespective of whether they were subsequently chosen over an alternative. Moreover, strongly liked foods were subsequently also chosen faster than the less liked alternatives. Response times during valuation and choice were positively correlated, but only when foods were liked; the faster participants rated foods as strongly liked, the faster they were in choosing the food item over an alternative. VEP modulations by the level of liking attributed as well as the subsequent choice were found as early as 135-180ms after food image onset. Analyses of neural source activity patterns over this time interval revealed an interaction between liking and the subsequent choice within the insula, dorsal frontal and superior parietal regions. The neural responses to food viewing were found to be modulated by the attributed level of liking only when foods were chosen, not when they were dismissed for an alternative. Therein, the responses to disliked foods were generally greater than those to foods that were liked more. Moreover, the responses to disliked but chosen foods were greater than responses to disliked foods which were subsequently dismissed for an alternative offer. Our findings show that the spatio-temporal brain dynamics to food viewing are immediately influenced both by how much foods are liked and by choices taken on them

  17. Regional and hemispheric influences on temporal variability in baseline carbon monoxide and ozone over the Northeast US

    Science.gov (United States)

    Zhou, Y.; Mao, H.; Demerjian, K.; Hogrefe, C.; Liu, J.

    2017-09-01

    Interannual variability in baseline carbon monoxide (CO) and ozone (O3), defined as mixing ratios under minimal influence of recent and local emissions, was studied for seven rural sites in the Northeast US over 2001-2010. Annual baseline CO exhibited statistically significant decreasing trends (-4.3 to -2.3 ppbv yr-1), while baseline O3 did not display trends at any site. In examining the data by season, wintertime and springtime baseline CO at the two highest sites (1.5 km and 2 km asl) did not experience significant trends. Decadal increasing trends (∼2.55 ppbv yr-1) were found in springtime and wintertime baseline O3 in southern New Hampshire, which was associated with anthropogenic NOx emission reductions from the urban corridor. Biomass burning emissions impacted summertime baseline CO with ∼38% variability from wildfire emissions in Russia and ∼22% from Canada at five sites and impacted baseline O3 at the two high elevation sites only with ∼27% variability from wildfires in both Russia and Canada. The Arctic Oscillation was negatively correlated with summertime baseline O3, while the North Atlantic Oscillation was positively correlated with springtime baseline O3. This study suggested that anthropogenic and biomass burning emissions, and meteorological conditions were important factors working together to determine baseline O3 and CO in the Northeast U.S. during the 2000s.

  18. Evaluation of anthropogenic influences on the Luhuitou fringing reef via spatial and temporal analyses (from isotopic values)

    Science.gov (United States)

    Cao, D.; Cao, W.; Yu, K.; Wu, G.; Yang, J.; Su, X.; Wang, F.

    2017-05-01

    Coral reefs have suffered remarkable declines worldwide. Nutrient overenrichment is considered to be one of the primary local causes. The Luhuitou fringing reef in southern China is a well-known tourist destination that is subject to enormous coastal renovation. The mean δ13C, δ15N value, and carbon over nitrogen ratio (C/N) of particulate organic matter were -21.56 ± 1.94‰, 7.04 ± 3.81‰, and 5.81 ± 1.86, respectively, suggesting mixed sources of carbon and nitrogen. The IsoError calculations suggested that marine phytoplankton and marine benthic algae dominated the majority of carbon sources, while anthropogenic and terrestrial organic nitrogen dominated the nitrogen sources. A tendency toward greater terrestrial detritus and anthropogenic-derived discharges was found during dry seasons and greater marine-derived organic matter during wet seasons. These results demonstrated the existence of anthropogenic influences and high dissolved inorganic nitrogen concentrations and C/N ratios. Anthropogenic nutrient discharge moderated nitrogen limitation, whereas phosphorus became more important to the reef ecosystem. Despite the marine carbon sources dominated, freshwater and terrestrial-derived organic carbon sources were also very important. Meanwhile, anthropogenic and terrestrial organic nitrogen sources were dominant. Therefore, pollution from more extensive region and anthropogenic activities from riverine sewage discharges adjacent to reefs should be focused to effectively reduce human-derived nutrients on reefs.

  19. Environmental factors influencing the spatio-temporal distribution of Carybdea marsupialis (Lineo, 1978, Cubozoa) in South-Western Mediterranean coasts.

    Science.gov (United States)

    Canepa, Antonio; Fuentes, Verónica; Bosch-Belmar, Mar; Acevedo, Melissa; Toledo-Guedes, Kilian; Ortiz, Antonio; Durá, Elia; Bordehore, César; Gili, Josep-Maria

    2017-01-01

    Jellyfish blooms cause important ecological and socio-economic problems. Among jellyfish, cubozoans are infamous for their painful, sometimes deadly, stings and are a major public concern in tropical to subtropical areas; however, there is little information about the possible causes of their outbreaks. After a bloom of the cubomedusa Carybdea marsupialis (Carybdeidae) along the coast of Denia (SW Mediterranean, Spain) in 2008 with negative consequences for local tourism, the necessity to understand the ecological restrictions on medusae abundance was evident. Here we use different models (GAM and zero-inflated models) to understand the environmental and human related factors influencing the abundance and distribution of C. marsupialis along the coast of Denia. Selected variables differed among medusae size classes, showing different environmental restriction associated to the developmental stages of the species. Variables implicated with dispersion (e.g. wind and current) affected mostly small and medium size classes. Sea surface temperature, salinity and proxies of primary production (chl a, phosphates, nitrates) were related to the abundances of small and large size classes, highlighting the roles of springtime salinity changes and increased primary production that may promote and maintain high densities of this species. The increased primary (and secondary) production due to anthropogenic impact is implicated as the factor enabling high numbers of C. marsupialis to thrive. Recommendations for monitoring blooms of this species along the study area and applicable to Mediterranean Sea include focus effort in coastal waters where productivity have been enriched by anthropogenic activities.

  20. Molecular Phylogenetics and Temporal Diversification in the Genus Aeromonas Based on the Sequences of Five Housekeeping Genes

    Science.gov (United States)

    Lorén, J. Gaspar; Farfán, Maribel; Fusté, M. Carmen

    2014-01-01

    Several approaches have been developed to estimate both the relative and absolute rates of speciation and extinction within clades based on molecular phylogenetic reconstructions of evolutionary relationships, according to an underlying model of diversification. However, the macroevolutionary models established for eukaryotes have scarcely been used with prokaryotes. We have investigated the rate and pattern of cladogenesis in the genus Aeromonas (γ-Proteobacteria, Proteobacteria, Bacteria) using the sequences of five housekeeping genes and an uncorrelated relaxed-clock approach. To our knowledge, until now this analysis has never been applied to all the species described in a bacterial genus and thus opens up the possibility of establishing models of speciation from sequence data commonly used in phylogenetic studies of prokaryotes. Our results suggest that the genus Aeromonas began to diverge between 248 and 266 million years ago, exhibiting a constant divergence rate through the Phanerozoic, which could be described as a pure birth process. PMID:24586399

  1. Proinflammatory chemokine gene expression influences survival of patients with non-Hodgkin’s lymphoma

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    Kazimierz Kuliczkowski

    2011-07-01

    Full Text Available The migration, survival and proliferation of cells is the basis for all physiologic and pathologic processes in the human body. All these reactions are regulated by a complex chemokine network that guides lymphocytes homing, chemotaxis, adhesion and interplay between immunologic system response cells. Chemokines are also responsible for metastatic dissemination of cancers, including Hodgkin’s and non-Hodgkin’s lymphomas. The purpose of this study was to determine chemokine gene expression (CXCL8, CXCL10, CCL2, CCL3, CCL4 and CCL5 in lymphoma lymph nodes compared to their expression in reactive lymph nodes. We also analyzed the influence of chemokine gene expression on the survival of lymphoma patients. Chemokine gene expression was evaluated in 37 lymphoma lymph nodes and in 25 samples of reactive lymph nodes. Gene expression of chemokines CXCL8, CXCL10, CCL2, CCL3, CCL4 and CCL5 was measured using the PCR method. Statistical analysis was performed using CSS Statistica for Windows (version 7.0 software. Probability values < < 0.05 were considered statistically significant and those between 0.05 and 0.1 as indicative of a trend. We found lower CXCL8 and CXCL10 gene expression in lymphoma lymph nodes compared to reactive lymph nodes. In the cases of CCL2 and CCL3, expression in lymphomas was higher than in reactive lymph nodes. Patients with high expression of CCL2 and CXCL10 had shorter survival. (Folia Histochemica et Cytobiologica 2011; Vol. 49, No. 2, pp. 240–247

  2. Nucleotides upstream of the Kozak sequence strongly influence gene expression in the yeast S. cerevisiae.

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    Li, Jing; Liang, Qiang; Song, Wenjiang; Marchisio, Mario Andrea

    2017-01-01

    In the yeast Saccharomyces cerevisiae, as in every eukaryotic organism, the mRNA 5(')-untranslated region (UTR) is important for translation initiation. However, the patterns and mechanisms that determine the efficiency with which ribozomes bind mRNA, the elongation of ribosomes through the 5(')-UTR, and the formation of a stable translation initiation complex are not clear. Genes that are highly expressed in S. cerevisiae seem to prefer a 5(')-UTR rich in adenine and poor in guanine, particularly in the Kozak sequence, which occupies roughly the first six nucleotides upstream of the START codon. We measured the fluorescence produced by 58 synthetic versions of the S. cerevisiae minimal CYC1 promoter (pCYC1min), each containing a different 5(')-UTR. First, we replaced with adenine the last 15 nucleotides of the original pCYC1min 5(')-UTR-a theoretically optimal configuration for high gene expression. Next, we carried out single and multiple point mutations on it. Protein synthesis was highly affected by both single and multiple point mutations upstream of the Kozak sequence. RNAfold simulations revealed that significant changes in the mRNA secondary structures occur by mutating more than three adenines into guanines between positions -15 and -9. Furthermore, the effect of point mutations turned out to be strongly context-dependent, indicating that adenines placed just upstream of the START codon do not per se guarantee an increase in gene expression, as previously suggested. New synthetic eukaryotic promoters, which differ for their translation initiation rate, can be built by acting on the nucleotides upstream of the Kozak sequence. Translation efficiency could, potentially, be influenced by another portion of the 5(')-UTR further upstream of the START codon. A deeper understanding of the role of the 5(')-UTR in gene expression would improve criteria for choosing and using promoters inside yeast synthetic gene circuits.

  3. Francisella tularensis subsp. tularensis induces a unique pulmonary inflammatory response: role of bacterial gene expression in temporal regulation of host defense responses.

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    Kathie-Anne Walters

    Full Text Available Pulmonary exposure to Francisella tularensis is associated with severe lung pathology and a high mortality rate. The lack of induction of classical inflammatory mediators, including IL1-β and TNF-α, during early infection has led to the suggestion that F. tularensis evades detection by host innate immune surveillance and/or actively suppresses inflammation. To gain more insight into the host response to Francisella infection during the acute stage, transcriptomic analysis was performed on lung tissue from mice exposed to virulent (Francisella tularensis ssp tularensis SchuS4. Despite an extensive transcriptional response in the lungs of animals as early as 4 hrs post-exposure, Francisella tularensis was associated with an almost complete lack of induction of immune-related genes during the initial 24 hrs post-exposure. This broad subversion of innate immune responses was particularly evident when compared to the pulmonary inflammatory response induced by other lethal (Yersinia pestis and non-lethal (Legionella pneumophila, Pseudomonas aeruginosa pulmonary infections. However, the unique induction of a subset of inflammation-related genes suggests a role for dysregulation of lymphocyte function and anti-inflammatory pathways in the extreme virulence of Francisella. Subsequent activation of a classical inflammatory response 48 hrs post-exposure was associated with altered abundance of Francisella-specific transcripts, including those associated with bacterial surface components. In summary, virulent Francisella induces a unique pulmonary inflammatory response characterized by temporal regulation of innate immune pathways correlating with altered bacterial gene expression patterns. This study represents the first simultaneous measurement of both host and Francisella transcriptome changes that occur during in vivo infection and identifies potential bacterial virulence factors responsible for regulation of host inflammatory pathways.

  4. The spatial and temporal expression of Ch-en, the engrailed gene in the polychaete Chaetopterus, does not support a role in body axis segmentation

    Science.gov (United States)

    Seaver, E. C.; Paulson, D. A.; Irvine, S. Q.; Martindale, M. Q.

    2001-01-01

    We are interested in understanding whether the annelids and arthropods shared a common segmented ancestor and have approached this question by characterizing the expression pattern of the segment polarity gene engrailed (en) in a basal annelid, the polychaete Chaetopterus. We have isolated an en gene, Ch-en, from a Chaetopterus cDNA library. Genomic Southern blotting suggests that this is the only en class gene in this animal. The predicted protein sequence of the 1.2-kb cDNA clone contains all five domains characteristic of en proteins in other taxa, including the en class homeobox. Whole-mount in situ hybridization reveals that Ch-en is expressed throughout larval life in a complex spatial and temporal pattern. The Ch-en transcript is initially detected in a small number of neurons associated with the apical organ and in the posterior portion of the prototrochophore. At later stages, Ch-en is expressed in distinct patterns in the three segmented body regions (A, B, and C) of Chaetopterus. In all segments, Ch-en is expressed in a small set of segmentally iterated cells in the CNS. In the A region, Ch-en is also expressed in a small group of mesodermal cells at the base of the chaetal sacs. In the B region, Ch-en is initially expressed broadly in the mesoderm that then resolves into one band/segment coincident with morphological segmentation. The mesodermal expression in the B region is located in the anterior region of each segment, as defined by the position of ganglia in the ventral nerve cord, and is involved in the morphogenesis of segment-specific feeding structures late in larval life. We observe banded mesodermal and ectodermal staining in an anterior-posterior sequence in the C region. We do not observe a segment polarity pattern of expression of Ch-en in the ectoderm, as is observed in arthropods. Copyright 2001 Academic Press.

  5. Spatio-temporal structure and influence of environmental parameters on the Tipuloidea (Insecta: Diptera) assemblage of Neotropical salt marshes

    Science.gov (United States)

    Rodrigues, Lucas; Carrasco, Daiane; Proietti, Maíra

    2017-10-01

    that compose the detritivorous and/or succivorous trophic guild, and consequently influence the upper trophic levels of the salt marsh environment.

  6. C-reactive protein levels are influenced by common IL-1 gene variations.

    Science.gov (United States)

    Berger, Peter; McConnell, Joseph P; Nunn, Martha; Kornman, Kenneth S; Sorrell, Julian; Stephenson, Katherine; Duff, Gordon W

    2002-02-21

    Elevated markers of systemic inflammation are associated with the development of acute coronary syndromes, but there is no current explanation for increased inflammation in overtly healthy individuals. The influence of genetic control of the inflammatory response on the observed variability is unknown. We studied the frequency of four polymorphisms in interleukin (IL) 1 genes, known to modulate inflammation, in 454 individuals undergoing coronary angiography and analysed their influence on plasma C-reactive protein (CRP) and fibrinogen levels. Females and smokers had higher levels of CRP than males (Pi = 0.001) and non-smokers (Pi = 0.001). Patients with genotype 2.2 for the IL-1B(+3954) polymorphism had twice the median CRP levels of patients who were genotype 1.1 (4.33 vs 2.01 mg/l; P = 0.001). Patients with genotype 1.2 or 2.2 at the IL-1A(+4845) polymorphism also had higher median CRP (2.92 vs 2.05 mg/l, Pi = 0.023). In multivariate analyses, CRP levels remained significantly associated with IL-1 polymorphisms after adjustment for smoking, gender and age. Fibrinogen levels had similar associations with the IL-1 genotypes. These data indicate that IL-1 gene polymorphisms known to affect the inflammatory response are highly related to plasma levels of CRP and fibrinogen in patients referred for coronary angiography.

  7. Sirolimus and Everolimus Pathway: Reviewing Candidate Genes Influencing Their Intracellular Effects

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    Simona Granata

    2016-05-01

    Full Text Available Sirolimus (SRL and everolimus (EVR are mammalian targets of rapamycin inhibitors (mTOR-I largely employed in renal transplantation and oncology as immunosuppressive/antiproliferative agents. SRL was the first mTOR-I produced by the bacterium Streptomyces hygroscopicus and approved for several medical purposes. EVR, derived from SRL, contains a 2-hydroxy-ethyl chain in the 40th position that makes the drug more hydrophilic than SRL and increases oral bioavailability. Their main mechanism of action is the inhibition of the mTOR complex 1 and the regulation of factors involved in a several crucial cellular functions including: protein synthesis, regulation of angiogenesis, lipid biosynthesis, mitochondrial biogenesis and function, cell cycle, and autophagy. Most of the proteins/enzymes belonging to the aforementioned biological processes are encoded by numerous and tightly regulated genes. However, at the moment, the polygenic influence on SRL/EVR cellular effects is still not completely defined, and its comprehension represents a key challenge for researchers. Therefore, to obtain a complete picture of the cellular network connected to SRL/EVR, we decided to review major evidences available in the literature regarding the genetic influence on mTOR-I biology/pharmacology and to build, for the first time, a useful and specific “SRL/EVR genes-focused pathway”, possibly employable as a starting point for future in-depth research projects.

  8. Social environment influences performance in a cognitive task in natural variants of the foraging gene.

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    Nancy R Kohn

    Full Text Available In Drosophila melanogaster, natural genetic variation in the foraging gene affects the foraging behaviour of larval and adult flies, larval reward learning, adult visual learning, and adult aversive training tasks. Sitters (for(s are more sedentary and aggregate within food patches whereas rovers (for(R have greater movement within and between food patches, suggesting that these natural variants are likely to experience different social environments. We hypothesized that social context would differentially influence rover and sitter behaviour in a cognitive task. We measured adult rover and sitter performance in a classical olfactory training test in groups and alone. All flies were reared in groups, but fly training and testing were done alone and in groups. Sitters trained and tested in a group had significantly higher learning performances compared to sitters trained and tested alone. Rovers performed similarly when trained and tested alone and in a group. In other words, rovers learning ability is independent of group training and testing. This suggests that sitters may be more sensitive to the social context than rovers. These differences in learning performance can be altered by pharmacological manipulations of PKG activity levels, the foraging (for gene's gene product. Learning and memory is also affected by the type of social interaction (being in a group of the same strain or in a group of a different strain in rovers, but not in sitters. These results suggest that for mediates social learning and memory in D. melanogaster.

  9. Quadruplex-single nucleotide polymorphisms (Quad-SNP) influence gene expression difference among individuals.

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    Baral, Aradhita; Kumar, Pankaj; Halder, Rashi; Mani, Prithvi; Yadav, Vinod Kumar; Singh, Ankita; Das, Swapan K; Chowdhury, Shantanu

    2012-05-01

    Non-canonical guanine quadruplex structures are not only predominant but also conserved among bacterial and mammalian promoters. Moreover recent findings directly implicate quadruplex structures in transcription. These argue for an intrinsic role of the structural motif and thereby posit that single nucleotide polymorphisms (SNP) that compromise the quadruplex architecture could influence function. To test this, we analysed SNPs within quadruplex motifs (Quad-SNP) and gene expression in 270 individuals across four populations (HapMap) representing more than 14,500 genotypes. Findings reveal significant association between quadruplex-SNPs and expression of the corresponding gene in individuals (P analysis of Quad-SNPs obtained from population-scale sequencing of 1000 human genomes showed relative selection bias against alteration of the structural motif. To directly test the quadruplex-SNP-transcription connection, we constructed a reporter system using the RPS3 promoter-remarkable difference in promoter activity in the 'quadruplex-destabilized' versus 'quadruplex-intact' promoter was noticed. As a further test, we incorporated a quadruplex motif or its disrupted counterpart within a synthetic promoter reporter construct. The quadruplex motif, and not the disrupted-motif, enhanced transcription in human cell lines of different origin. Together, these findings build direct support for quadruplex-mediated transcription and suggest quadruplex-SNPs may play significant role in mechanistically understanding variations in gene expression among individuals.

  10. Transcriptional interference by independently regulated genes occurs in any relative arrangement of the genes and is influenced by chromosomal integration position.

    Science.gov (United States)

    Eszterhas, Susan K; Bouhassira, Eric E; Martin, David I K; Fiering, Steven

    2002-01-01

    Transcriptional interference is the influence, generally suppressive, of one active transcriptional unit on another unit linked in cis. Its wide occurrence in experimental systems suggests that it may also influence transcription in many loci, but little is known about its precise nature or underlying mechanisms. Here we report a study of the interaction of two nearly identical transcription units juxtaposed in various arrangements. Each reporter gene in the constructs has its own promoter and enhancer and a strong polyadenylation signal. We used recombinase-mediated cassette exchange (RMCE) to insert the constructs into previously tagged genomic sites in cultured cells. This strategy also allows the constructs to be assessed in both orientations with respect to flanking chromatin. In each of the possible arrangements (tandem, divergent, and convergent), the presence of two genes strongly suppresses expression of both genes compared to that of an identical single gene at the same integration site. The suppression is most severe with the convergent arrangement and least severe in total with the divergent arrangement, while the tandem arrangement is most strongly influenced by the integration site and the genes' orientation within the site. These results suggest that transcriptional interference could underlie some position effects and contribute to the regulation of genes in complex loci.

  11. The methylenetetrahydrofolate reductase gene variant C677T influences susceptibility to migraine with aura

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    Sundholm James

    2004-02-01

    Full Text Available Abstract Background The C677T variant in the methylenetetrahydrofolate reductase (MTHFR gene is associated with increased levels of circulating homocysteine and is a mild risk factor for vascular disease. Migraine, with and without aura (MA and MO, is a prevalent and complex neurovascular disorder that may also be affected by genetically influenced hyperhomocysteinaemia. To determine whether the C677T variant in the MTHFR gene is associated with migraine susceptibility we utilised unrelated and family-based case-control study designs. Methods A total of 652 Caucasian migraine cases were investigated in this study. The MTHFR C677T variant was genotyped in 270 unrelated migraine cases and 270 controls as well as 382 affected subjects from 92 multiplex pedigrees. Results In the unrelated case-control sample we observed an over-representation of the 677T allele in migraine patients compared to controls, specifically for the MA subtype (40% vs. 33% (χ2 = 5.70, P = 0.017. The Armitage test for trend indicated a significant dosage effect of the risk allele (T for MA (χ2 = 5.72, P = 0.017. This linear trend was also present in the independent family-based sample (χ2 = 4.25, Padjusted = 0.039. Overall, our results indicate that the T/T genotype confers a modest, yet significant, increase in risk for the MA subtype (odds ratio: 2.0 – 2.5. No increased risk for the MO subtype was observed (P > 0.05. Conclusions In Caucasians, the C677T variant in the MTHFR gene influences susceptibility to MA, but not MO. Investigation into the enzyme activity of MTHFR and the role of homocysteine in the pathophysiology of migraine is warranted.

  12. The influence of Angiotensin converting enzyme and angiotensinogen gene polymorphisms on hypertrophic cardiomyopathy.

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    Rong Luo

    Full Text Available Some studies have reported that angiotensin converting enzyme (ACE and angiotensinogen (AGT genes have been associated with hypertrophic cardiomyopathy (HCM. However, there have been inconsonant results among different studies. To clarify the influence of ACE and AGT on HCM, a systemic review and meta-analysis of case-control studies were performed. The following databases were searched to indentify related studies: PubMed database, the Embase database, the Cochrane Central Register of Controlled Trials database, China National Knowledge Information database, and Chinese Scientific and Technological Journal database. Search terms included "hypertrophic cardiomyopathy", "angiotensin converting enzyme" (ACE or "ACE" and "polymorphism or mutation". For the association of AGT M235T polymorphism and HCM, "angiotensin converting enzyme" or "ACE" was replaced with "angiotensinogen". A total of seventeen studies were included in our review. For the association of ACE I/D polymorphism and HCM, eleven literatures were included in the meta-analysis on association of penetrance and genotype. Similarly, six case-control studies were included in the meta-analysis for AGT M235T. For ACE I/D polymorphism, the comparison of DI/II genotype vs DD genotype was performed in the present meta-analysis. The OR was 0.73 (95% CI: 0.527, 0.998, P = 0.049, power = 94%, alpha = 0.05 after the study which deviated from Hardy-Weinberg Equilibrium was excluded, indicating that the ACE I/D gene polymorphism might be associated with HCM. The AGT M235T polymorphism did not significantly affect the risk of HCM. In addition, ACE I/D gene polymorphism did not significantly influence the interventricular septal thickness in HCM patients. In conclusion, the ACE I/D polymorphism might be associated with the risk of HCM.

  13. Lithium and GSK-3β promoter gene variants influence cortical gray matter volumes in bipolar disorder.

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    Benedetti, Francesco; Poletti, Sara; Radaelli, Daniele; Locatelli, Clara; Pirovano, Adele; Lorenzi, Cristina; Vai, Benedetta; Bollettini, Irene; Falini, Andrea; Smeraldi, Enrico; Colombo, Cristina

    2015-04-01

    Lithium is the mainstay for the treatment of bipolar disorder (BD) and inhibits glycogen synthase kinase-3β (GSK-3β). The less active GSK-3β promoter gene variants have been associated with less detrimental clinical features of BD. GSK-3β gene variants and lithium can influence brain gray and white matter structure in psychiatric conditions, so we studied their combined effect in BD. The aim of this study is to investigate the effects of ongoing long-term lithium treatment and GSK-3β promoter rs334558 polymorphism on regional gray matter (GM) volumes of patients with BD. GM volumes were estimated with 3.0 Tesla MRI in 150 patients affected by a major depressive episode in course of BD. Duration of lifetime lithium treatment was retrospectively assessed. Analyses were performed by searching for significant effects of lithium and rs334558 in the whole brain. The less active GSK-3β rs334558*G gene promoter variant and the long-term administration of lithium were synergistically associated with increased GM volumes in the right frontal lobe, in a large cluster encompassing the boundaries of subgenual and orbitofrontal cortex (including Brodmann areas 25, 11, and 47). Effects of lithium on GM revealed in rs334558*G carriers only, consistent with previously reported clinical effects in these genotype groups, and were proportional to the duration of treatment. Lithium and rs334558 influenced GM volumes in areas critical for the generation and control of affect, which have been widely implicated in the process of BD pathophysiology. In the light of the protective effects of lithium on white matter integrity, our results suggest that the clinical effects of lithium associate with a neurotrophic effect on the whole brain, probably mediated by GSK-3β inhibition.

  14. Lithium and GSK3-β promoter gene variants influence white matter microstructure in bipolar disorder.

    Science.gov (United States)

    Benedetti, Francesco; Bollettini, Irene; Barberi, Ignazio; Radaelli, Daniele; Poletti, Sara; Locatelli, Clara; Pirovano, Adele; Lorenzi, Cristina; Falini, Andrea; Colombo, Cristina; Smeraldi, Enrico

    2013-01-01

    Lithium is the mainstay for the treatment of bipolar disorder (BD) and inhibits glycogen synthase kinase 3-β (GSK3-β). The less active GSK3-β promoter gene variants have been associated with less detrimental clinical features of BD. GSK3-β gene variants and lithium can influence brain gray matter structure in psychiatric conditions. Diffusion tensor imaging (DTI) measures of white matter (WM) integrity showed widespred disruption of WM structure in BD. In a sample of 70 patients affected by a major depressive episode in course of BD, we investigated the effect of ongoing long-term lithium treatment and GSK3-β promoter rs334558 polymorphism on WM microstructure, using DTI and tract-based spatial statistics with threshold-free cluster enhancement. We report that the less active GSK3-β rs334558*C gene-promoter variants, and the long-term administration of the GSK3-β inhibitor lithium, were associated with increases of DTI measures of axial diffusivity (AD) in several WM fiber tracts, including corpus callosum, forceps major, anterior and posterior cingulum bundle (bilaterally including its hippocampal part), left superior and inferior longitudinal fasciculus, left inferior fronto-occipital fasciculus, left posterior thalamic radiation, bilateral superior and posterior corona radiata, and bilateral corticospinal tract. AD reflects the integrity of axons and myelin sheaths. We suggest that GSK3-β inhibition and lithium could counteract the detrimental influences of BD on WM structure, with specific benefits resulting from effects on specific WM tracts contributing to the functional integrity of the brain and involving interhemispheric, limbic, and large frontal, parietal, and fronto-occipital connections.

  15. Dietary intake alters gene expression in colon tissue: possible underlying mechanism for the influence of diet on disease.

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    Pellatt, Andrew J; Slattery, Martha L; Mullany, Lila E; Wolff, Roger K; Pellatt, Daniel F

    2016-06-01

    Although the association between diet and disease is well documented, the biologic mechanisms involved have not been entirely elucidated. In this study, we evaluate how dietary intake influences gene expression to better understand the underlying mechanisms through which diet operates. We used data from 144 individuals who had comprehensive dietary intake and gene expression data from RNAseq using normal colonic mucosa. Using the DESeq2 statistical package, we identified genes that showed statistically significant differences in expression between individuals in high-intake and low-intake categories for several dietary variables of interest adjusting for age and sex. We examined total calories, total fats, vegetable protein, animal protein, carbohydrates, trans-fatty acids, mutagen index, red meat, processed meat, whole grains, vegetables, fruits, fiber, folate, dairy products, calcium, and prudent and western dietary patterns. Using a false discovery rate of less than 0.1, meat-related foods were statistically associated with 68 dysregulated genes, calcium with three dysregulated genes, folate with four dysregulated genes, and nonmeat-related foods with 65 dysregulated genes. With a more stringent false discovery rate of less than 0.05, there were nine meat-related dysregulated genes and 23 nonmeat-related genes. Ingenuity pathway analysis identified three major networks among genes identified as dysregulated with respect to meat-related dietary variables and three networks among genes identified as dysregulated with respect to nonmeat-related variables. The top networks (Ingenuity Pathway Analysis network score >30) associated with meat-related genes were (i) cancer, organismal injury, and abnormalities, tumor morphology, and (ii) cellular function and maintenance, cellular movement, cell death, and survival. Among genes related to nonmeat consumption variables, the top networks were (i) hematological system development and function, nervous system development

  16. Influence of simulation time-step (temporal-scale) on optimal parameter estimation and runoff prediction performance in hydrological modeling

    Science.gov (United States)

    Loizu, Javier; Álvarez-Mozos, Jesús; Casalí, Javier; Goñi, Mikel

    2015-04-01

    Nowadays, most hydrological catchment models are designed to allow their use for streamflow simulation at different time-scales. While this permits models to be applied for broader purposes, it can also be a source of error in hydrological processes simulation at catchment scale. Those errors seem not to affect significantly simple conceptual models, but this flexibility may lead to large behavior errors in physically based models. Equations used in processes such as those related to soil moisture time-variation are usually representative at certain time-scales but they may not characterize properly water transfer in soil layers at larger scales. This effect is especially relevant as we move from detailed hourly scale to daily time-step, which are common time scales used at catchment streamflow simulation for different research and management practices purposes. This study aims to provide an objective methodology to identify the degree of similarity of optimal parameter values when hydrological catchment model calibration is developed at different time-scales. Thus, providing information for an informed discussion of physical parameter significance on hydrological models. In this research, we analyze the influence of time scale simulation on: 1) the optimal values of six highly sensitive parameters of the TOPLATS model and 2) the streamflow simulation efficiency, while optimization is carried out at different time scales. TOPLATS (TOPMODEL-based Land-Atmosphere Transfer Scheme) has been applied on its lumped version on three catchments of varying size located in northern Spain. The model has its basis on shallow groundwater gradients (related to local topography) that set up spatial patterns of soil moisture and are assumed to control infiltration and runoff during storm events and evaporation and drainage in between storm events. The model calculates the saturated portion of the catchment at each time step based on Topographical Index (TI) intervals. Surface

  17. Selection of suitable endogenous reference genes for qPCR in kidney and hypothalamus of rats under testosterone influence.

    Science.gov (United States)

    Gholami, Khadijeh; Loh, Su Yi; Salleh, Naguib; Lam, Sau Kuen; Hoe, See Ziau

    2017-01-01

    Real-time quantitative PCR (qPCR) is the most reliable and accurate technique for analyses of gene expression. Endogenous reference genes are being used to normalize qPCR data even though their expression may vary under different conditions and in different tissues. Nonetheless, verification of expression of reference genes in selected studied tissue is essential in order to accurately assess the level of expression of target genes of interest. Therefore, in this study, we attempted to examine six commonly used reference genes in order to identify the gene being expressed most constantly under the influence of testosterone in the kidneys and hypothalamus. The reference genes include glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin beta (ACTB), beta-2 microglobulin (B2m), hypoxanthine phosphoribosyltransferase 1 (HPRT), peptidylprolylisomerase A (Ppia) and hydroxymethylbilane synthase (Hmbs). The cycle threshold (Ct) value for each gene was determined and data obtained were analyzed using the software programs NormFinder, geNorm, BestKeeper, and rank aggregation. Results showed that Hmbs and Ppia genes were the most stably expressed in the hypothalamus. Meanwhile, in kidneys, Hmbs and GAPDH appeared to be the most constant genes. In conclusion, variations in expression levels of reference genes occur in kidneys and hypothalamus under similar conditions; thus, it is important to verify reference gene levels in these tissues prior to commencing any studies.

  18. A model for quantitative correction of coronary calcium scores on multidetector, dual source, and electron beam computed tomography for influences of linear motion, calcification density, and temporal resolution : A cardiac phantom study

    NARCIS (Netherlands)

    Greuter, M. J. W.; Groen, J. M.; Nicolai, L. J.; Dijkstra, H.; Oudkerk, M.

    2009-01-01

    Purpose: The objective of this study is to quantify the influence of linear motion, calcification density, and temporal resolution on coronary calcium determination using multidetector computed tomography (MDCT), dual source CT (DSCT), and electron beam tomography (EBT) and to find a quantitative me

  19. Differential expression of miR-184 in temporal lobe epilepsy patients with and without hippocampal sclerosis - Influence on microglial function.

    Science.gov (United States)

    Danis, Bénédicte; van Rikxoort, Marijke; Kretschmann, Anita; Zhang, Jiong; Godard, Patrice; Andonovic, Lidija; Siegel, Franziska; Niehusmann, Pitt; Hanon, Etienne; Delev, Daniel; von Lehe, Marec; Kaminski, Rafal M; Pfeifer, Alexander; Foerch, Patrik

    2016-09-26

    Epilepsy is one of the most common neurological disorders characterized by recurrent seizures due to neuronal hyperexcitability. Here we compared miRNA expression patterns in mesial temporal lobe epilepsy with and without hippocampal sclerosis (mTLE + HS and mTLE -HS) to investigate the regulatory mechanisms differentiating both patient groups. Whole genome miRNA sequencing in surgically resected hippocampi did not reveal obvious differences in expression profiles between the two groups of patients. However, one microRNA (miR-184) was significantly dysregulated, which was confirmed by qPCR. We observed that overexpression of miR-184 inhibited cytokine release after LPS stimulation in primary microglial cells, while it did not affect the viability of murine primary neurons and primary astrocytes. Pathway analysis revealed that miR-184 is potentially involved in the regulation of inflammatory signal transduction and apoptosis. Dysregulation of some the potential miR-184 target genes was confirmed by qPCR and 3'UTR luciferase reporter assay. The reduced expression of miR-184 observed in patients with mTLE + HS together with its anti-inflammatory effects indicate that miR-184 might be involved in the modulation of inflammatory processes associated with hippocampal sclerosis which warrants further studies elucidating the role of miR-184 in the pathophysiology of mTLE.

  20. Differential expression of miR-184 in temporal lobe epilepsy patients with and without hippocampal sclerosis – Influence on microglial function

    Science.gov (United States)

    Danis, Bénédicte; van Rikxoort, Marijke; Kretschmann, Anita; Zhang, Jiong; Godard, Patrice; Andonovic, Lidija; Siegel, Franziska; Niehusmann, Pitt; Hanon, Etienne; Delev, Daniel; von Lehe, Marec; Kaminski, Rafal M.; Pfeifer, Alexander; Foerch, Patrik

    2016-01-01

    Epilepsy is one of the most common neurological disorders characterized by recurrent seizures due to neuronal hyperexcitability. Here we compared miRNA expression patterns in mesial temporal lobe epilepsy with and without hippocampal sclerosis (mTLE + HS and mTLE −HS) to investigate the regulatory mechanisms differentiating both patient groups. Whole genome miRNA sequencing in surgically resected hippocampi did not reveal obvious differences in expression profiles between the two groups of patients. However, one microRNA (miR-184) was significantly dysregulated, which was confirmed by qPCR. We observed that overexpression of miR-184 inhibited cytokine release after LPS stimulation in primary microglial cells, while it did not affect the viability of murine primary neurons and primary astrocytes. Pathway analysis revealed that miR-184 is potentially involved in the regulation of inflammatory signal transduction and apoptosis. Dysregulation of some the potential miR-184 target genes was confirmed by qPCR and 3′UTR luciferase reporter assay. The reduced expression of miR-184 observed in patients with mTLE + HS together with its anti-inflammatory effects indicate that miR-184 might be involved in the modulation of inflammatory processes associated with hippocampal sclerosis which warrants further studies elucidating the role of miR-184 in the pathophysiology of mTLE. PMID:27666871

  1. Influence of catechol-O-methyltransferase (COMT) gene polymorphisms in pain sensibility of Brazilian fibromialgia patients.

    Science.gov (United States)

    Barbosa, Flávia Regina; Matsuda, Josie Budag; Mazucato, Mendelson; de Castro França, Suzelei; Zingaretti, Sônia Marli; da Silva, Lucienir Maria; Martinez-Rossi, Nilce Maria; Júnior, Milton Faria; Marins, Mozart; Fachin, Ana Lúcia

    2012-02-01

    Fibromyalgia syndrome (FS) is a rheumatic syndrome affecting to 2-3% of individuals of productive age, mainly women. Neuroendocrine and genetic factors may play a significant role in development of the disease which is characterized by diffuse chronic pain and presence of tender points. Several studies have suggested an association between FS, especially pain sensitivity, and polymorphism of the catechol-O-methyltransferase (COMT) gene. The aim of the present study was to characterize the SNPs rs4680 and rs4818 of the COMT gene and assess its influence in pain sensitivity of patients with fibromyalgia screened by the Fibromyalgia Impact Questionnaire (FIQ). DNA was extracted from peripheral blood of 112 patients with fibromyalgia and 110 healthy individuals and was used as template in PCR for amplification of a 185-bp fragment of the COMT gene. The amplified fragment was sequenced for analyses of the SNPs rs4680 and rs4818. The frequency of mutant genotype AA of SNP rs6860 was 77.67% in patients with FS and 28.18% for the control group. For the SNP rs4818, the frequency of mutant genotype CC was 73.21 and 39.09% for patients with FS and controls, respectively. Moreover, the FIQ score was higher in patients with the homozygous mutant genotype for SNPs rs4680 (87.92 points) and rs4818 (86.14 points). These results suggest that SNPs rs4680 and rs4818 of the COMT gene may be associated with fibromyalgia and pain sensitivity in FS Brazilian patients.

  2. Influence of EARLI1-like genes on flowering time and lignin synthesis of Arabidopsis thaliana.

    Science.gov (United States)

    Shi, Y; Zhang, X; Xu, Z-Y; Li, L; Zhang, C; Schläppi, M; Xu, Z-Q

    2011-09-01

    EARLI1 encodes a 14.7 kDa protein in the cell wall, is a member of the PRP (proline-rich protein) family and has multiple functions, including resistance to low temperature and fungal infection. RNA gel blot analyses in the present work indicated that expression of EARLI1-like genes, EARLI1, At4G12470 and At4G12490, was down-regulated in Col-FRI-Sf2 RNAi plants derived from transformation with Agrobacterium strain ABI, which contains a construct encoding a double-strand RNA targeting 8CM of EARLI1. Phenotype analyses revealed that Col-FRI-Sf2 RNAi plants of EARLI1 flowered earlier than Col-FRI-Sf2 wild-type plants. The average bolting time of Col-FRI-Sf2 and Col-FRI-Sf2 RNAi plants was 39.7 and 19.4 days, respectively, under a long-day photoperiod. In addition, there were significant differences in main stem length, internode number and rosette leaf number between Col-FRI-Sf2 and Col-FRI-Sf2 RNAi plants. RT-PCR showed that EARLI1-like genes might delay flowering time through the autonomous and long-day photoperiod pathways by maintaining the abundance of FLC transcripts. In Col-FRI-Sf2 RNAi plants, transcription of FLC was repressed, while expression of SOC1 and FT was activated. Microscopy observations showed that EARLI1-like genes were also associated with morphogenesis of leaf cells in Arabidopsis. Using histochemical staining, EARLI1-like genes were found to be involved in regulation of lignin synthesis in inflorescence stems, and Col-FRI-Sf2 and Col-FRI-Sf2 RNAi plants had 9.67% and 8.76% dry weight lignin, respectively. Expression analysis revealed that cinnamoyl-CoA reductase, a key enzyme in lignin synthesis, was influenced by EARLI1-like genes. These data all suggest that EARLI1-like genes could control the flowering process and lignin synthesis in Arabidopsis.

  3. Cytokine and apoptosis gene polymorphisms influence the outcome of hepatitis C virus infection

    Institute of Scientific and Technical Information of China (English)

    Leila Ksiaa Cheikhrouhou; Imen Sfar; Hajer Aounallah-Skhiri; Houda Aouadi; Salwa Jendoubi-Ayed; Taieb Ben Abdallah; Khaled Ayed; Yousr Lakhoua-Gorgi

    2011-01-01

    BACKGROUND: Hepatitis C virus (HCV) infection is thought to be chronic and the factors leading to viral clearance or persistence are poorly understood. This study was undertaken to investigate the possibility of a significant relationship between the spontaneous clearance or the persistence of hepatitis C virus (HCV) infection and cytokine and apoptosis gene polymorphisms in Tunisian patients on hemodialysis. METHODS: Polymorphisms of the genes IL-1 (-889 IL-1α, -511 and +3954 IL-1β, IL-1Ra), IL-18 (-137 and -607), IL-12 (-1188) and Apo1/Fas (-670) were determined by PCR-RFLP, PCR-SSP and PCR-VNTR in 100 healthy blood donors and 100 patients infected with HCV and undergoing hemodialysis. The patients were classified into two groups: G1 consisted of 76 active chronic hepatitis patients (positive for HCV RNA) and G2 consisted of 24 hemodialysed patients who spontaneously eliminated the virus (negativeforHCVRNA). RESULTS: The frequency of genotype association [-137GC/-607CA] IL-18 was higher in G2 (41.7%) than in G1 (15.8%) (P=0.008; OR=0.26; 95% CI, 0.10-0.73). We also found a higher frequency of the AA genotype of the Apo1/Fas gene in G2 (41.6%) than in G1 (17.5%) (P=0.026; OR=3.49; 95%CI, 1.13-10.69). Adjustment for known covariate factors (age, gender and genotype) confirmed these univariate findings and revealed that the genotype association GC-CA of the (-137 and -607) IL-18 gene and the AA genotype of the Apo1/Fas gene were associated with the clearance of HCV (P=0.041 and 0.017, respectively). CONCLUSION: The two genotypes GC-CA of the (-137 and-607) IL-18 polymorphism and the AA genotype of the Apo1/Fas gene influence the outcome of HCV infection in Tunisian patients on hemodialysis.

  4. The Influence of Greenland melt water on the temporal and spatial response of the Holocene Thermal Maximum in the Nordic Seas: a modelling study

    Science.gov (United States)

    Blaschek, M.; Renssen, H.

    2012-04-01

    In the early-to-mid Holocene a period of relatively warm climate, known as the Holocene thermal maximum (HTM, 11-5 kyr BP), has been associated with the orbitally-forced northern hemisphere summer insolation maximum at approximately 10 kyr BP. Although the HTM is orbitally forced, the spatial and temporal response of its climate signature is diverse. At 9 kyr BP remnants of glacial ice sheets, most importantly the Laurentide Ice Sheet (LIS), modified the climate of the North Atlantic region by freshening the ocean surface through melt water discharge, and by altering the surface albedo and topography. A previous climate modelling study (Renssen et al. 2009) has shown that the LIS delayed the HTM in the Nordic Seas by up to 3000 years. We extend this approach by introducing another source of melt water in the early Holocene, the Greenland Ice Sheet (GIS). The GIS was likely up to 25% larger (at 9 kyr BP) in volume than at present-day (Vinther et al. 2009, Peltier, 2004) and is therefore potentially an important regional contributor to climate change in the Nordic Seas. We present here simulations performed with the LOVECLIM1.2 global ocean-atmosphere-vegetation model. These simulations seek to highlight the spatial and temporal impact of GIS melting on the early Holocene climate, in terms of sea surface temperature (SST). Several sensitivity experiments with fixed 9 kyr BP forcings were performed for different Greenland melt water fluxes to test model and climate sensitivity. These melt water fluxes range from 0 to 52 mSv. The sensitivity experiments show that GIS melting considerably influences sea surface conditions around the southern part of Greenland, and that 13 to 26 mSv of GIS melting, in a combination with the LIS background melting, agrees better in that region with proxy-based SST reconstructions. In a further step, transient simulations exhibit the long term (9 to 0 kyr BP) impact of GIS melting on the development of the Holocene climate. Transient

  5. Temporal Variation in Natural Gas Seep Rate and Influence Factors in the Lingtou Promontory Seep Field of the Northern South China Sea

    Directory of Open Access Journals (Sweden)

    Pengfei Di

    2014-01-01

    Full Text Available Natural hydrocarbon seeps in marine environment are important sources of methane and other greenhouse gases into the ocean and the atmosphere. This greenhouse gas seepage influences the global methane budget and global climate change. Hydrocarbon seeps on the shallow seabed produce a near-shore gas bubble zone along the western coast of Hainan Island, in the northern South China Sea. However, few studies on the quantitative value of the methane flux and on temporal variation and influence factors of hydrocarbon seeps have been conducted until now. This study describes the results of continuous gas vent measurements for 420 hours on the seabed of the Lingtou promontory shore. The amount of gas released from a single gas vent was 30.5 m3 during the measurement period. The gas flow rate ranged from 22 - 72 L h-1, with an average rate of 53.4 L h-1. The time series analyses of the 420-hour record clearly show three principal tidal components with periods of 5.4, 4.6, and 2.4 hours, which are the main factors controlling the gas flow rate. Low flow rates were associated with high tide and high flow rates associated with low tide. A 1-m increase in seawater height results in a decrease of 20 - 30 L h-1 or 35 - 56% of the hourly flow rate. Therefore, the changes in gas volume escape from the pore could be attributed to the hydrostatic pressure effect induced by water depth. This dominant mechanism controlled pore activation as well as the gas flow rate, suggesting that in the marine environment, especially the shallow-water shelf area, sea level changes may result in great variations in methane release into the ocean and atmosphere.

  6. Temporal variability of the microbial food web (viruses to ciliates under the influence of the Black Sea Water inflow (N. Aegean, E. Mediterranean

    Directory of Open Access Journals (Sweden)

    A. GIANNAKOUROU

    2015-01-01

    Full Text Available Τhe entire pelagic microbial food web was studied during the winter-spring period in the frontal area of the North Aegean Sea. Abundance of viruses, heterotrophic bacteria, cyanobacteria, auto- and hetero-trophic flagellates, and ciliates, as well as bacterial production, were measured at three stations (MD1, MD2, MD3 situated along a N-S transect between the area directly influenced by the inflowing Black Sea water and the area covered by the Levantine water. Samples were collected in December 2009, and January, March, April, and May 2011. Station MD1 exhibited the highest values of abundance and integrated biomass of all microbial groups and bacterial production during all months, and MD3 the lowest. Bacteria dominated the total integrated biomass at all stations and months, followed by cyanobacteria, auto-, hetero-trophic flagellates and ciliates. On a temporal scale, the microbial food web was less important in March as all microbial parameters at all stations showed the lowest values. After the phytoplankton bloom in March, the heterotrophic part of the microbial food web (mainly strongly increased, though the intensity of the phenomenon was diminished from North to South. Pico-sized plankton was found to be heterotrophic whereas nanoplankton was autotrophic. It seems that the influence of the Black Sea water on station MD1, permanent throughout the study period of early winter to late spring, was reflected in all microbial populations studied, and produced a more productive pelagic food web system, with potential consequences for the upper trophic levels.

  7. Identification of genes influencing dendrite morphogenesis in developing peripheral sensory and central motor neurons

    Directory of Open Access Journals (Sweden)

    Chwalla Barbara

    2008-07-01

    Full Text Available Abstract Background Developing neurons form dendritic trees with cell type-specific patterns of growth, branching and targeting. Dendrites of Drosophila peripheral sensory neurons have emerged as a premier genetic model, though the molecular mechanisms that underlie and regulate their morphogenesis remain incompletely understood. Still less is known about this process in central neurons and the extent to which central and peripheral dendrites share common organisational principles and molecular features. To address these issues, we have carried out two comparable gain-of-function screens for genes that influence dendrite morphologies in peripheral dendritic arborisation (da neurons and central RP2 motor neurons. Results We found 35 unique loci that influenced da neuron dendrites, including five previously shown as required for da dendrite patterning. Several phenotypes were class-specific and many resembled those of known mutants, suggesting that genes identified in this study may converge with and extend known molecular pathways for dendrite development in da neurons. The second screen used a novel technique for cell-autonomous gene misexpression in RP2 motor neurons. We found 51 unique loci affecting RP2 dendrite morphology, 84% expressed in the central nervous system. The phenotypic classes from both screens demonstrate that gene misexpression can affect specific aspects of dendritic development, such as growth, branching and targeting. We demonstrate that these processes are genetically separable. Targeting phenotypes were specific to the RP2 screen, and we propose that dendrites in the central nervous system are targeted to territories defined by Cartesian co-ordinates along the antero-posterior and the medio-lateral axes of the central neuropile. Comparisons between the screens suggest that the dendrites of peripheral da and central RP2 neurons are shaped by regulatory programs that only partially overlap. We focused on one common

  8. Influence of Biomass Burning on Temporal and Diurnal Variations of Acidic Gases, Particulate Nitrate, and Sulfate in a Tropical Urban Atmosphere

    Directory of Open Access Journals (Sweden)

    Sailesh N. Behera

    2014-01-01

    Full Text Available The present study investigated the temporal and diurnal distributions of atmospheric acidic gases (sulphur dioxide (SO2, nitrous acid (HONO, and nitric acid (HNO3 and those of particulate nitrate (NO3- and sulfate (SO42- through a comprehensive field campaign during the largest smoke haze episode in Singapore, a representative country in Southeast Asia (SEA. To identify the atmospheric behavior of these pollutants during the smoke haze period, the data generated from the measurement campaign were divided into three distinct periods: prehaze, during haze, and posthaze periods. The 24 hr average data indicated that ambient SO2, HONO, and HNO3 during the smoke haze episodes increased by a factor ranging from 1.2 to 2.6 compared to those during the prehaze and posthaze periods. Similarly, in the case of particulates SO42- and NO3-, the factor ranged from 2.3 to 4.2. Backward air trajectories were constructed and used to find the sources of biomass burning to the recurring smoke haze in this region. The air trajectory analysis showed that the smoke haze episodes experienced in Singapore were influenced by transboundary air pollution, caused by severe biomass burning events in the islands of Indonesia.

  9. Ebola Virus Infections in Nonhuman Primates Are Temporally Influenced by Glycoprotein Poly-U Editing Site Populations in the Exposure Material.

    Science.gov (United States)

    Trefry, John C; Wollen, Suzanne E; Nasar, Farooq; Shamblin, Joshua D; Kern, Steven J; Bearss, Jeremy J; Jefferson, Michelle A; Chance, Taylor B; Kugelman, Jeffery R; Ladner, Jason T; Honko, Anna N; Kobs, Dean J; Wending, Morgan Q S; Sabourin, Carol L; Pratt, William D; Palacios, Gustavo F; Pitt, M Louise M

    2015-12-19

    Recent experimentation with the variants of the Ebola virus that differ in the glycoprotein's poly-uridine site, which dictates the form of glycoprotein produced through a transcriptional stutter, has resulted in questions regarding the pathogenicity and lethality of the stocks used to develop products currently undergoing human clinical trials to combat the disease. In order to address these concerns and prevent the delay of these critical research programs, we designed an experiment that permitted us to intramuscularly challenge statistically significant numbers of naïve and vaccinated cynomolgus macaques with either a 7U or 8U variant of the Ebola virus, Kikwit isolate. In naïve animals, no difference in survivorship was observed; however, there was a significant delay in the disease course between the two groups. Significant differences were also observed in time-of-fever, serum chemistry, and hematology. In vaccinated animals, there was no statistical difference in survivorship between either challenge groups, with two succumbing in the 7U group compared to 1 in the 8U challenge group. In summary, survivorship was not affected, but the Ebola virus disease course in nonhuman primates is temporally influenced by glycoprotein poly-U editing site populations.

  10. Influence of the temporal and spatial variation of nitrate reductase, glutamine synthetase and soil composition in the N species content in lettuce (Lactuca sativa).

    Science.gov (United States)

    Pinto, Edgar; Fidalgo, Fernanda; Teixeira, Jorge; Aguiar, Ana A; Ferreira, Isabel M P L V O

    2014-04-01

    The variation of nitrate reductase (NR), glutamine synthetase (GS) and N content in lettuce was evaluated at 5 stages of lettuce growth. Soil physicochemical properties and its N content were also assessed to elucidate the soil-to-plant transfer of inorganic N and potential leaching to groundwater. A decrease of NR activity and an increase of NO3(-) and N-Kjeldahl content in lettuces were observed during plant growth, whereas GS activity and NH4(+) increased during the first few weeks of lettuce growth and then decreased. Although the temporal variation was similar in lettuces grown in different soils, quantitative differences were observed, indicating that high NO3(-) content in soil caused a higher NO3(-) accumulation in lettuce despite the higher NR activity during the initial stage of plant growth. Higher levels of NO3(-) and NH4(+) were correlated with higher levels of N-Kjeldahl in lettuce suggesting a positive effect of these N species in the biosynthesis of organic forms of N. Soil physicochemical properties influenced the mobility of inorganic N within the groundwater-soil-plant system. Sandy soils with low OM content allowed NO3(-) leaching, which was confirmed by higher NO3(-) levels in groundwater. Therefore, lettuces grown in those soils presented lower N content and the inputs of N to the environment were higher. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  11. The influence of tungsten on the chemical composition of a temporally evolving nanostructure of a model Ni-Al-Cr superalloy.

    Science.gov (United States)

    Sudbrack, Chantal K; Isheim, Dieter; Noebe, Ronald D; Jacobson, Nathan S; Seidman, David N

    2004-06-01

    The influence of W on the temporal evolution of gamma' precipitation toward equilibrium in a model Ni-Al-Cr alloy is investigated by three-dimensional atom-probe (3DAP) microscopy and transmission electron microscopy (TEM). We report on the alloys Ni-10 Al-8.5 Cr (at.%) and Ni-10 Al-8.5 Cr-2 W (at.%), which were aged isothermally in the gamma + gamma' two-phase field at 1073 K, for times ranging from 0.25 to 264 h. Spheroidal-shaped gamma' precipitates, 5-15 nm diameter, form during quenching from above the solvus temperature in both alloys at a high number density (approximately 1023 m-3). As gamma' precipitates grow with aging at 1073 K, a transition from spheroidal- to cuboidal-shaped precipitates is observed in both alloys. The elemental partitioning and spatially resolved concentration profiles across the gamma' precipitates are obtained as a function of aging time from three-dimensional atom-by-atom reconstructions. Proximity histogram concentration profiles (Hellman et al., 2000) of the quaternary alloy demonstrate that W concentration gradients exist in gamma' precipitates in the as-quenched and 0.25-h aging states, which disappear after 1 h of aging. The diffusion coefficient of W in gamma' is estimated to be 6.2 x 10-20 m2 s-1 at 1073 K. The W addition decreases the coarsening rate constant, and leads to stronger partitioning of Al to gamma' and Cr to gamma.

  12. The Influence of Tungsten on the Chemical Composition of a Temporally Evolving Nanostructure of a Model Ni-Al-Cr Superalloy

    Science.gov (United States)

    Sudbrack, Chantal K.; Isheim, Dieter; Noebe, Ronald D.; Jacobson, Nathan S.; Seidman, David N.

    2004-01-01

    The influence of W on the temporal evolution of gamma' precipitation toward equilibrium in a model Ni-Al-Cr alloy is investigated by three-dimensional atom-probe (3DAP) microscopy and transmission electron microscopy (TEM). We report on the alloys Ni-10 Al-8.5 Cr (at.%) and Ni-10 Al-8.5 Cr-2 W (at.%), which were aged isothermally in the gamma + gamma' two-phase field at 1073 K, for times ranging from 0.25 to 264 h. Spheroidal-shaped gamma' precipitates, 5-15 nm diameter, form during quenching from above the solvus temperature in both alloys at a high number density (approx. 10(exp 23/cu m). As gamma' precipitates grow with aging at 1073 K, a transition from spheriodal- to cuboidal-shaped precipitates is observed in both alloys. The elemental partitioning and spatially resolved concentration profiles across the gamma' precipitates are obtained as a function of aging time from three-dimensional atom-by-atom reconstructions. Proximity histogram concentration profiles of the quaternary alloy demonstrate that W concentration gradients exist in gamma' precipitates in the as-quenched and 0.25-h aging states, which disappear after 1 h of aging. The diffusion coefficient of W in gamma' is estimated to be 6.2 x 10(exp -20) sq m/s at 1073 K. The W addition decreases the coarsening rate constant, and leads to stronger partitioning of Al to gamma' and Cr to gamma.

  13. Influence of specific training on spatio-temporal parameters at the onset of goal-directed reaching in infants: a controlled trial

    Directory of Open Access Journals (Sweden)

    Andréa B. Cunha

    2013-07-01

    Full Text Available BACKGROUND: There is evidence that long-term experience can promote functional changes in infants. However, much remains unknown about how a short-term experience affects performance of a task. OBJECTIVE: This study aims to investigate the influence of a single training session at the onset of goal-directed reaching on the spatio-temporal parameters of reaching and whether there are differences in the effects of training across different reaching positions. METHOD: Thirty-three infants were divided into three groups: 1 a control group; 2 a group that was reach trained in a reclined position; and 3 a group trained in the supine position. The infants were submitted to two assessments (pre- and post-training in two testing positions (supine and reclined at 45°. RESULTS: The short-duration training sessions were effective in promoting shorter reaches in the specific position in which the training was conducted. Training in the reclined position was associated with shorter and faster reaches upon assessment in the reclined position. CONCLUSIONS: A few minutes of reach training are effective in facilitating reaching behavior in infants at the onset of reaching. The improvements in reaching were specific to the position in which the infants were trained.

  14. The Influence of Tungsten on the Chemical Composition of a Temporally Evolving Nanostructure of a Model Ni-Al-Cr Superalloy

    Science.gov (United States)

    Sudbrack, Chantal K.; Isheim, Dieter; Noebe, Ronald D.; Jacobson, Nathan S.; Seidman, David N.

    2004-01-01

    The influence of W on the temporal evolution of gamma' precipitation toward equilibrium in a model Ni-Al-Cr alloy is investigated by three-dimensional atom-probe (3DAP) microscopy and transmission electron microscopy (TEM). We report on the alloys Ni-10 Al-8.5 Cr (at.%) and Ni-10 Al-8.5 Cr-2 W (at.%), which were aged isothermally in the gamma + gamma' two-phase field at 1073 K, for times ranging from 0.25 to 264 h. Spheroidal-shaped gamma' precipitates, 5-15 nm diameter, form during quenching from above the solvus temperature in both alloys at a high number density (approx. 10(exp 23/cu m). As gamma' precipitates grow with aging at 1073 K, a transition from spheriodal- to cuboidal-shaped precipitates is observed in both alloys. The elemental partitioning and spatially resolved concentration profiles across the gamma' precipitates are obtained as a function of aging time from three-dimensional atom-by-atom reconstructions. Proximity histogram concentration profiles of the quaternary alloy demonstrate that W concentration gradients exist in gamma' precipitates in the as-quenched and 0.25-h aging states, which disappear after 1 h of aging. The diffusion coefficient of W in gamma' is estimated to be 6.2 x 10(exp -20) sq m/s at 1073 K. The W addition decreases the coarsening rate constant, and leads to stronger partitioning of Al to gamma' and Cr to gamma.

  15. Ebola Virus Infections in Nonhuman Primates Are Temporally Influenced by Glycoprotein Poly-U Editing Site Populations in the Exposure Material

    Directory of Open Access Journals (Sweden)

    John C. Trefry

    2015-12-01

    Full Text Available Recent experimentation with the variants of the Ebola virus that differ in the glycoprotein’s poly-uridine site, which dictates the form of glycoprotein produced through a transcriptional stutter, has resulted in questions regarding the pathogenicity and lethality of the stocks used to develop products currently undergoing human clinical trials to combat the disease. In order to address these concerns and prevent the delay of these critical research programs, we designed an experiment that permitted us to intramuscularly challenge statistically significant numbers of naïve and vaccinated cynomolgus macaques with either a 7U or 8U variant of the Ebola virus, Kikwit isolate. In naïve animals, no difference in survivorship was observed; however, there was a significant delay in the disease course between the two groups. Significant differences were also observed in time-of-fever, serum chemistry, and hematology. In vaccinated animals, there was no statistical difference in survivorship between either challenge groups, with two succumbing in the 7U group compared to 1 in the 8U challenge group. In summary, survivorship was not affected, but the Ebola virus disease course in nonhuman primates is temporally influenced by glycoprotein poly-U editing site populations.

  16. Spatially- and temporally-controlled postnatal p53 knockdown cooperates with embryonic Schwann cell precursor Nf1 gene loss to promote malignant peripheral nerve sheath tumor formation.

    Science.gov (United States)

    Hirbe, Angela C; Dahiya, Sonika; Friedmann-Morvinski, Dinorah; Verma, Inder M; Clapp, D Wade; Gutmann, David H

    2016-02-16

    Malignant peripheral nerve sheath tumors (MPNSTs) are highly aggressive sarcomas that arise sporadically or in association with the Neurofibromatosis type 1 (NF1) cancer predisposition syndrome. In individuals with NF1, MPNSTs are hypothesized to arise from Nf1-deficient Schwann cell precursor cells following the somatic acquisition of secondary cooperating genetic mutations (e.g., p53 loss). To model this sequential genetic cooperativity, we coupled somatic lentivirus-mediated p53 knockdown in the adult right sciatic nerve with embryonic Schwann cell precursor Nf1 gene inactivation in two different Nf1 conditional knockout mouse strains. Using this approach, ~60% of mice with Periostin-Cre-mediated Nf1 gene inactivation (Periostin-Cre; Nf1(flox/flox) mice) developed tumors classified as low-grade MPNSTs following p53 knockdown (mean, 6 months). Similarly, ~70% of Nf1+/- mice with GFAP-Cre-mediated Nf1 gene inactivation (GFAP-Cre; Nf1(flox/null) mice) developed low-grade MPNSTs following p53 knockdown (mean, 3 months). In addition, wild-type and Nf1+/- mice with GFAP-Cre-mediated Nf1 loss develop MPNSTs following somatic p53 knockout with different latencies, suggesting potential influences of Nf1+/- stromal cells in MPNST pathogenesis. Collectively, this new MPNST model system permits the analysis of somatically-acquired events as well as tumor microenvironment signals that potentially cooperate with Nf1 loss in the development and progression of this deadly malignancy.

  17. Influence of heat stress, sex and genetic groups on reference genes stability in muscle tissue of chicken.

    Science.gov (United States)

    Cedraz de Oliveira, Haniel; Pinto Garcia, Antonio Amandio; Gonzaga Gromboni, Juliana Gracielle; Vasconcelos Farias Filho, Ronaldo; Souza do Nascimento, Carlos; Arias Wenceslau, Amauri

    2017-01-01

    Quantitative RT-PCR is an important technique for assessing gene expression. However, a proper normalization of reference genes prior to expression analyses of target genes is necessary. The best normalizer is that gene which remains stable in all samples from different treatments. The aim of this study was to identify stable reference genes for normalization of target genes in muscle tissue from three genetically divergent chickens groups (Peloco, Cobb 500® and Caneluda) under environmental (heat stress and comfort) and sex influence. Expressions of ten reference genes were tested for stability in breast muscular tissue (Pectoralis major muscle). Samples were obtained from 36 males and females of two backyard breeds (Caneluda and Peloco) and one commercial line (Cobb 500®) under two environments. The heat stress and comfort temperature were 39 and 23°C, respectively. Animals were housed in the Animal Science Department at Universidade Estadual do Sudoeste da Bahia. We analyzed the expression data by four statistical tools (SLqPCR, NormFinder, Bestkeeper and Comparative CT). According to these tools, genes stability varied according to sex, genetic group and environment, however, some genes remained stable in all analyzes. There was no difference between the most stable genes for sex effect, being MRPS27 more stable for both males and females. In general, MRPS27 was the most stable gene. Within the three genetic groups, the most stable genes were RPL5, HMBS and EEF1 to Cobb 500®, Peloco and Caneluda, respectively. Within the environment, the most stable gene under comfort and heat stress conditions was HMBS and MRPS27, respectively. BestKeeper and Comparative Ct were less correlated (28%) and SLqPCR and NormFinder were the most correlated (98%). MRPS27, RPL5 and MRPS30 genes were considered stable according the overall ranking and can be used as normalizer of relative expression of target genes in muscle tissue of chickens under heat stress.

  18. Transcriptional Activity of HTLV-I Tax Influences the Expression of Marker Genes Associated with Cellular Transformation

    Directory of Open Access Journals (Sweden)

    Francene J. Lemoine

    2001-01-01

    Full Text Available Human T cell leukemia virus type I (HTLV-I has been identified as the etiologic agent of adult T cell leukemia (ATL. HTLV-I encodes a transcriptional regulatory protein, Tax, which also functions as the viral transforming protein. Through interactions with a number of cellular transcription factors Tax can modulate cellular gene expression. Since the majority of Tax-responsive cellular genes are important regulators of cellular proliferation, the transactivating functions of Tax appear to be necessary for cellular transformation by HTLV-I. Gaining a complete understanding of the broad range of genes regulated by Tax, the temporal pattern of their expression, and their effects on cell function may identify early markers of disease progression mediated by this virus.

  19. Project Temporalities

    DEFF Research Database (Denmark)

    Tryggestad, Kjell; Justesen, Lise; Mouritsen, Jan

    2013-01-01

    into account. This may require investments in new project management technologies. Originality/value – This paper adds to the literatures on project temporalities and stakeholder theory by connecting them to the question of non-human stakeholders and to project management technologies.......Purpose – The purpose of this paper is to explore how animals can become stakeholders in interaction with project management technologies and what happens with project temporalities when new and surprising stakeholders become part of a project and a recognized matter of concern to be taken...... into account. Design/methodology/approach – The paper is based on a qualitative case study of a project in the building industry. The authors use actor-network theory (ANT) to analyze the emergence of animal stakeholders, stakes and temporalities. Findings – The study shows how project temporalities can...

  20. Gene expression and biological processes influenced by deletion of Stat3 in pulmonary type II epithelial cells

    Directory of Open Access Journals (Sweden)

    Whitsett Jeffrey A

    2007-12-01

    Full Text Available Abstract Background The signal transducer and activator of transcription 3 (STAT3 mediates gene expression in response to numerous growth factors and cytokines, playing an important role in many cellular processes. To better understand the molecular mechanisms by which Stat3 influences gene expression in the lung, the effect of pulmonary epithelial cell specific deletion of Stat3 on genome wide mRNA expression profiling was assessed. Differentially expressed genes were identified from Affymetrix Murine GeneChips analysis and subjected to gene ontology classification, promoter analysis, pathway mapping and literature mining. Results Total of 791 mRNAs were significantly increased and 314 mRNAs were decreased in response to the deletion of Stat3Δ/Δ in the lung. STAT is the most enriched cis-elements in the promoter regions of those differentially expressed genes. Deletion of Stat3 induced genes influencing protein metabolism, transport, chemotaxis and apoptosis and decreased the expression of genes mediating lipid synthesis and metabolism. Expression of Srebf1 and 2, genes encoding key regulators of fatty acid and steroid biosynthesis, was decreased in type II cells from the Stat3Δ/Δ mice, consistent with the observation that lung surfactant phospholipids content was decreased. Stat3 influenced both pro- and anti-apoptotic pathways that determine cell death or survival. Akt, a potential transcriptional target of Stat3, was identified as an important participant in Stat3 mediated pathways including Jak-Stat signaling, apoptosis, Mapk signaling, cholesterol and fatty acid biosynthesis. Conclusion Deletion of Stat3 from type II epithelial cells altered the expression of genes regulating diverse cellular processes, including cell growth, apoptosis and lipid metabolism. Pathway analysis indicates that STAT3 regulates cellular homeostasis through a complex regulatory network that likely enhances alveolar epithelial cell survival and surfactant

  1. Fatty acid translocase gene CD36 rs1527483 variant influences oral fat perception in Malaysian subjects.

    Science.gov (United States)

    Ong, Hing-Huat; Tan, Yen-Nee; Say, Yee-How

    2017-01-01

    We determined whether single nucleotide polymorphisms (SNPs; rs1761667 and rs1527483) in the fatty acid translocase CD36 gene - a receptor for fatty acids - is associated with oral fat perception (OFP) of different fat contents in custards and commercially-available foods, and obesity measures in Malaysian subjects (n=313; 118 males, 293 ethnic Chinese; 20 ethnic Indians). A 170-mm visual analogue scale was used to assess the ratings of perceived fat content, oiliness and creaminess of 0%, 2%, 6% and 10% fat content-by-weight custards and low-fat/regular versions of commercially-available milk, mayonnaise and cream crackers. Overall, the subjects managed to significantly discriminate the fat content, oiliness and creaminess between low-fat/regular versions of milk and mayonnaise. Females rated the perception of fat content and oiliness of both milks higher, but ethnicity, obesity and adiposity status did not seem to play a role in influencing most of OFP. The overall minor allele frequencies for rs1761667 and rs1527483 were 0.30 and 0.26, respectively. Females and individuals with rs1527483 TT genotype significantly perceived greater creaminess of 10% fat-by-weight custard. Also, individuals with rs1527483 TT genotype and T allele significantly perceived greater fat content of cream crackers, independent of fat concentration. rs1761667 SNP did not significantly affect OFP, except for cream crackers. Both gene variants were also not associated with obesity measures. Taken together, this study supports the notion that CD36 - specifically rs1527483, plays a role in OFP, but not in influencing obesity in Malaysian subjects. Besides, gender is an important factor for OFP, where females had higher sensitivity. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Population dynamics of the red shrimp Aristeus antennatus in the Balearic Islands (western Mediterranean): Short spatio-temporal differences and influence of environmental factors

    Science.gov (United States)

    Guijarro, Beatriz; Massutí, Enric; Moranta, Joan; Díaz, Paz

    2008-06-01

    The red shrimp Aristeus antennatus is one of the target species of the bottom trawl fishery of the Balearic Islands. The objective of the present paper is to study the short spatial and temporal differences of this important economic resource between two different locations off Mallorca (Cabrera: CA; Sóller: SO), where a fleet mobility pattern has been detected, and to study the influence of environmental conditions on this species. Six simultaneous bottom-trawl and oceanographic surveys were carried out at these two locations in order to collect data from the demersal species, hydrography (temperature and salinity), trophic resources and sediment characteristics. The commercial fleet from both locations was monitored by monthly on-board sampling, log-books and daily landings obtained from sales slips. Additional data was obtained from other fishing surveys. Short spatial and temporal differences have been detected between both locations. The population at CA was more demographically homogeneous, while that at SO showed important variations, like high abundance of juveniles recruiting to fishing grounds in autumn-winter and high abundance of large females during summer. Several differences have also been found in the biology of the species between locations, such as males were more abundant in SO than in CA. Also, the reproductive period started sooner in SO than in CA, and the condition of pre-spawning females was better in SO. The percentage of total lipids in the hepatopancreas was minimal during the spawning period, showing their importance as a reserve of energy for the ovary ripening. Water masses could play an important role in these differences, the characteristics of water masses being more stable in CA than in SO. Red shrimp adult females seemed to be more correlated with the warmer and more saline Levantine Intermediate Waters, while juveniles (males and females) and adult males were more correlated with the colder Western Mediterranean Deep Waters

  3. Ketamine influences CLOCK:BMAL1 function leading to altered circadian gene expression.

    Directory of Open Access Journals (Sweden)

    Marina M Bellet

    Full Text Available Major mood disorders have been linked to abnormalities in circadian rhythms, leading to disturbances in sleep, mood, temperature, and hormonal levels. We provide evidence that ketamine, a drug with rapid antidepressant effects, influences the function of the circadian molecular machinery. Ketamine modulates CLOCK:BMAL1-mediated transcriptional activation when these regulators are ectopically expressed in NG108-15 neuronal cells. Inhibition occurs in a dose-dependent manner and is attenuated after treatment with the GSK3β antagonist SB21673. We analyzed the effect of ketamine on circadian gene expression and observed a dose-dependent reduction in the amplitude of circadian transcription of the Bmal1, Per2, and Cry1 genes. Finally, chromatin-immunoprecipitation analyses revealed that ketamine altered the recruitment of the CLOCK:BMAL1 complex on circadian promoters in a time-dependent manner. Our results reveal a yet unsuspected molecular mode of action of ketamine and thereby may suggest possible pharmacological antidepressant strategies.

  4. Epistatic interactions of genes influence within-individual variation of physical activity traits in mice.

    Science.gov (United States)

    Leamy, Larry J; Pomp, Daniel; Lightfoot, J Timothy

    2011-06-01

    A number of quantitative trait loci (QTLs) recently have been discovered that affect various activity traits in mice, but their collective impact does not appear to explain the consistently moderate to high heritabilities for these traits. We previously suggested interactions of genes, or epistasis, might account for additional genetic variability of activity, and tested this for the average distance, duration and speed run by mice during a 3 week period. We found abundant evidence for epistasis affecting these traits, although, recognized that epistatic effects may well vary within individuals over time. We therefore conducted a full genome scan for epistatic interactions affecting these traits in each of seven three-day intervals. Our intent was to assess the extent and trends in epistasis affecting these traits in each of the intervals. We discovered a number of epistatic interactions of QTLs that influenced the activity traits in the mice, the majority of which were not previously found and appeared to affect the activity traits (especially distance and speed) primarily in the early or in the late age intervals. The overall impact of epistasis was considerable, its contribution to the total phenotypic variance varying from an average of 22-35% in the three traits across all age intervals. It was concluded that epistasis is more important than single-locus effects of genes on activity traits at specific ages and it is therefore an essential component of the genetic architecture of physical activity.

  5. Evidence that genetic variation in the oxytocin receptor (OXTR) gene influences social cognition in ADHD.

    Science.gov (United States)

    Park, J; Willmott, M; Vetuz, G; Toye, C; Kirley, A; Hawi, Z; Brookes, K J; Gill, M; Kent, L

    2010-05-30

    Some children with ADHD also have social and communication difficulties similar to those seen in children with autistic spectrum disorders and this may be due to shared genetic liability. As the oxytocin receptor (OXTR) gene has been implicated in social cognition and autistic spectrum disorders, this study investigated whether OXTR polymorphisms previously implicated in autism were associated with ADHD and whether they influenced OXTR mRNA expression in 27 normal human amygdala brain samples. The family-based association sample consisted of 450 DSM-IV diagnosed ADHD probands and their parents. Although there was no association with the ADHD phenotype, an association with social cognitive impairments in a subset of the ADHD probands (N=112) was found for SNP rs53576 (F=5.24, p=0.007) with post-hoc tests demonstrating that the AA genotype was associated with better social ability compared to the AG genotype. Additionally, significant association was also found for rs13316193 (F=3.09, p=0.05) with post-hoc tests demonstrating that the CC genotype was significantly associated with poorer social ability than the TT genotype. No significant association between genotype and OXTR mRNA expression was found. This study supports previous evidence that the OXTR gene is implicated in social cognition.

  6. Leber Hereditary Optic Neuropathy: Do Folate Pathway Gene Alterations Influence the Expression of Mitochondrial DNA Mutation?

    Directory of Open Access Journals (Sweden)

    A Aleyasin

    2010-09-01

    Full Text Available "nBackground: Leber hereditary optic neuropathy (LHON is an inherited form of bilateral optic atrophy leading to the loss of central vision.  The primary cause of vision loss is mutation in the mitochondrial DNA (mtDNA, however, unknown secon­dary genetic and/or epigenetic risk factors are suggested to influence its neuropathology.  In this study folate gene polymor­phisms were examined as a possible LHON secondary genetic risk factor in Iranian patients."nMethods: Common polymorphisms in the MTHFR (C677T and A1298C and MTRR (A66G genes were tested in 21 LHON patients and 150 normal controls."nResults:  Strong associations were observed between the LHON syndrome and C677T (P= 0.00 and A66G (P= 0.00 polymor­phisms.  However, no significant association was found between A1298C (P =0.69 and the LHON syndrome."nConclusion: This is the first study that shows MTHFR C677T and MTRR A66G polymorphisms play a role in the etiology of the LHON syndrome.  This finding may help in the better understanding of mechanisms involved in neural degeneration and vision loss by LHON and hence the better treatment of patients.

  7. An SNP site in pri-miR-124, a brain expressed miRNA gene, no contribution to mesial temporal lobe epilepsy in an Italian sample.

    Science.gov (United States)

    Manna, Ida; Labate, Angelo; Borzì, Giuseppe; Mumoli, Laura; Cavalli, Salvatore Maria; Sturniolo, Miriam; Quattrone, Aldo; Gambardella, Antonio

    2016-08-01

    Mesial temporal lobe epilepsy (MTLE) is the most common type of refractory epilepsy and is usually associated with hippocampal sclerosis (Hs). The pathogenesis of MTLE involves many biological pathways, some of which seem to be regulated by microRNAs (miRNAs). Increasing evidence shows that single nucleotide polymorphisms (SNPs) or mutations in miRNAs sequence may affect the processing and function of miRNAs and participate in the occurrence of diseases. In this study, the effect of the SNP of one neuronal miRNA, miR-124, on susceptibility to MTLE was investigated using a case control study. To understand the role, a common C/G polymorphism designated rs531564 in the molecular mechanisms of MTLE, we sought to determine whether this genetic variant could influence susceptibility to disease in a cohort of 307 MTLE patients and 306 healthy controls, using TaqMan allelic discrimination assay, on an Applied Biosystems PCR platform. No statistically significant differences were found in the allele or genotype distributions of the miR-124 rs531564 polymorphism among MTLE patients and MTLE-free control subjects (p > 0.05). Our results demonstrate that this SNP has no major role in genetic susceptibility to MTLE, at least in the population studied here.

  8. Dietary intake alters gene expression in colon tissue: possible underlying mechanism for the influence of diet on disease

    OpenAIRE

    Pellatt, Andrew J.; Slattery, Martha L.; Mullany, Lila E.; Wolff, Roger K.; Pellatt, Daniel F.

    2016-01-01

    Background Although the association between diet and disease is well documented, the biologic mechanisms involved have not been entirely elucidated. In this study, we evaluate how dietary intake influences gene expression to better understand the underlying mechanisms through which diet operates. Methods We used data from 144 individuals who had comprehensive dietary intake and gene expression data from RNAseq using normal colonic mucosa. Using the DESeq2 statistical package, we identified ge...

  9. Influence of PRKCH gene polymorphism on antihypertensive response to amlodipine and telmisartan.

    Science.gov (United States)

    Zhang, Zan-Ling; Zhu, Miao-Miao; Li, Hui-Lan; Shi, Li-Hong; Chen, Xiao-Ping; Luo, Jia; Zhao, Jin-Feng

    2017-06-22

    This study aimed to evaluate the effect of PRKCH rs2230500 genetic polymorphism on efficacy of amlodipine and telmisartan for patients with hypertension. A total of 136 essential hypertension (EH) patients were treated with amlodipine (70 patients) or telmisartan (66 patients), respectively. Genetic polymorphism was genotyped by Sanger sequencing. Both baseline and post-treatment blood pressure (BP) and heart rate were measured to evaluate the influence of genetic polymorphism on the antihypertensive response. No significant difference in the absolute decrease in diastolic blood pressure (DBP),systolic blood pressure (SBP), and mean arterial pressure (MAP) was observed among PRKCH rs2230500 genotypes after 4-week amlodipine or telmisartan therapy (p > 0.05). However, when compared with carriers or GG genotype, the antihypertensive effect of PRKCH rs2230500 GA/AA carriers was superior in telmisartan treatment group. PRKCH rs2230500 gene polymorphism is significantly related to the efficiency in telmisartan therapy (p = 0.02). The PRKCH rs2230500 may influence the antihypertensive efficacy of telmisartan in Chinese EH patients, and further studies are needed to confirm these findings.

  10. Regulation of 11beta-HSD genes in human adipose tissue: influence of central obesity and weight loss.

    Science.gov (United States)

    Engeli, Stefan; Böhnke, Jana; Feldpausch, Mareike; Gorzelniak, Kerstin; Heintze, Ute; Janke, Jürgen; Luft, Friedrich C; Sharma, Arya M

    2004-01-01

    The activity of adipose 11beta-hydroxysteroid dehydrogenase (11beta-HSD) 1 is increased in obese subjects, and animal data suggest that increased cortisol formation in adipose tissue contributes to the development of the metabolic syndrome. The aim of this study was to determine whether up-regulation of human adipose 11beta-HSD1 in obesity can also be found at the gene expression level. 11beta-HSD gene expression in subcutaneous adipose tissue biopsies of 70 postmenopausal women was studied by real-time reverse-transcription polymerase chain reaction. The influence of weight reduction and in vitro effects of several modulators of adipocyte gene expression on 11beta-HSD genes in human adipocytes were also studied. The 11beta-HSD1 gene was highly expressed in human adipose tissue. 11beta-HSD2 mRNA was also detectable at lower levels. Adipose 11beta-HSD1 gene expression was increased by two-fold and was positively correlated with waist circumference and homeostasis model assessment index of insulin resistance. 11beta-HSD2 gene expression was reduced by half in obese women. Weight reduction did not change gene expression levels of 11beta-HSD1 or 11beta-HSD2. Cortisol increased 11beta-HSD1 gene expression in isolated human adipocytes in vitro, whereas estradiol, triiodothyronine, angiotensin II, and pioglitazone had no influence. Our data suggest that increased expression of the 11beta-HSD1 gene is associated with metabolic abnormalities in obese women and that increased expression of this gene may contribute to the previously reported increased local conversion of cortisone to cortisol in adipose tissue of obese individuals.

  11. Temporal and anatomical host resistance to chronic Salmonella infection is quantitatively dictated by Nramp1 and influenced by host genetic background.

    Directory of Open Access Journals (Sweden)

    Wendy P Loomis

    Full Text Available The lysosomal membrane transporter, Nramp1, plays a key role in innate immunity and resistance to infection with intracellular pathogens such as non-typhoidal Salmonella (NTS. NTS-susceptible C57BL/6 (B6 mice, which express the mutant Nramp1D169 allele, are unable to control acute infection with Salmonella enterica serovar Typhimurium following intraperitoneal or oral inoculation. Introducing functional Nramp1G169 into the B6 host background, either by constructing a congenic strain carrying Nramp1G169 from resistant A/J mice (Nramp-Cg or overexpressing Nramp1G169 from a transgene (Nramp-Tg, conferred equivalent protection against acute Salmonella infection. In contrast, the contributions of Nramp1 for controlling chronic infection are more complex, involving temporal and anatomical differences in Nramp1-dependent host responses. Nramp-Cg, Nramp-Tg and NTS-resistant 129×1/SvJ mice survived oral Salmonella infection equally well for the first 2-3 weeks, providing evidence that Nramp1 contributes to the initial control of NTS bacteremia preceding establishment of chronic Salmonella infection. By day 30, increased host Nramp1 expression (Tg>Cg provided greater protection as indicated by decreased splenic bacterial colonization (Tggenes other than Nramp1 also contribute to the ability of NTS-resistant 129×1/SvJ mice to control bacterial replication during chronic infection.

  12. Temporal and anatomical host resistance to chronic Salmonella infection is quantitatively dictated by Nramp1 and influenced by host genetic background.

    Science.gov (United States)

    Loomis, Wendy P; Johnson, Matthew L; Brasfield, Alicia; Blanc, Marie-Pierre; Yi, Jaehun; Miller, Samuel I; Cookson, Brad T; Hajjar, Adeline M

    2014-01-01

    The lysosomal membrane transporter, Nramp1, plays a key role in innate immunity and resistance to infection with intracellular pathogens such as non-typhoidal Salmonella (NTS). NTS-susceptible C57BL/6 (B6) mice, which express the mutant Nramp1D169 allele, are unable to control acute infection with Salmonella enterica serovar Typhimurium following intraperitoneal or oral inoculation. Introducing functional Nramp1G169 into the B6 host background, either by constructing a congenic strain carrying Nramp1G169 from resistant A/J mice (Nramp-Cg) or overexpressing Nramp1G169 from a transgene (Nramp-Tg), conferred equivalent protection against acute Salmonella infection. In contrast, the contributions of Nramp1 for controlling chronic infection are more complex, involving temporal and anatomical differences in Nramp1-dependent host responses. Nramp-Cg, Nramp-Tg and NTS-resistant 129×1/SvJ mice survived oral Salmonella infection equally well for the first 2-3 weeks, providing evidence that Nramp1 contributes to the initial control of NTS bacteremia preceding establishment of chronic Salmonella infection. By day 30, increased host Nramp1 expression (Tg>Cg) provided greater protection as indicated by decreased splenic bacterial colonization (Tggenes other than Nramp1 also contribute to the ability of NTS-resistant 129×1/SvJ mice to control bacterial replication during chronic infection.

  13. The Temporal and Spatial Characteristics of IGF-I Gene Expression in Broilers%肉鸡IGF-I基因mRNA的时空表达模式

    Institute of Scientific and Technical Information of China (English)

    顾海娟; 王星果; 王慧娟; 邵芳; 顾志良

    2014-01-01

    In this experiment, the real-time fluorescence quantitative PCR was applied to investigate the tissue expressional patterns of IGF-I mRNA in breast muscle, thigh muscle, adipose, heart, liver, spleen, lung, kidney, glandular stomach, muscular stomach, intestine, brain tissues and in various developmental stages (d1, w1, w2, w3, w4, w5, w6 and w7) of thigh muscle, liver, adipose tissue in three different broilers, and β-actin gene stan-dards was used as an inner control. The results showed that the expression of IGF-I gene in liver was significant-ly higher than that of the other tissues, and expressed at a certain amount of IGF-I gene in all tissues except for kidney, that the highest expression of IGF-I mRNA in thigh muscle was at age of six-week old, and the rest of the stage was also higher than one day, that the highest expression of IGF-I mRNA in liver was at three-week, and then declined, that the highest expression in adipose was at three-week, and then its expression gradually decreased with increasing age. These research results revealed the temporal and spatial expression characteris-tics of IGF-I mRNA gene in early growth broilers, and would contribute to the further study on genes related to growth axis regulation of growth and development in broilers.%采用实时荧光定量PCR技术,以β-actin为内参,检测了白羽AA肉鸡在4周龄时其胸肌、腿肌、脂肪、心、肝、脾、肺、肾、腺胃、肌胃、肠、脑共12个组织和在1日龄及1、2、3、4、5、6、7周龄时腿肌、肝脏、脂肪中类胰岛素生长因子-I(IGF-I)的表达量变化。结果显示,除肾外其余组织均表达一定量的IGF-I mRNA表达,且在肝脏中表达量显著高于其他组织;腿肌6周时IGF-I mRNA表达量达到最大值,其余各时期也都高于1日龄时的表达;肝脏中表达量最高时期是3周,然后又呈下降趋势;脂肪中在3周时表达量最高,然后其表达量随年龄增长而逐渐

  14. INFLUENCE OF GENETIC POLYMORPHISM IN FABP3 AND LEPR GENES ON INTRAMUSCULAR FAT CONTENT IN PIG CARCASSES

    Directory of Open Access Journals (Sweden)

    Kristina Budimir

    2014-06-01

    Full Text Available Intensive production conditions, selection directed to increase the percentage of muscle tissue in carcasses and consumer demand have led to a reduction of intramuscular fat content in pig carcasses. Intramuscular fat is a factor affecting the flavor, juiciness and tenderness of pork meat. FABP protein family causes the differences in the content of intramuscular fat in different pig breeds. FABP3 and LEPR gene are candidate genes for intramuscular fat content and their polymorphisms explain the variability that can occur in different pig breeds. The aim of this paper is to demonstrate the influence of genes on different intramuscular fat content in pig carcasses due to pigs genotype.

  15. Relationships between spatio-temporal environmental and genetic variation reveal an important influence of exogenous selection in a pupfish hybrid zone.

    Science.gov (United States)

    Carson, Evan W; Tobler, Michael; Minckley, W L; Ainsworth, Ryan J; Dowling, Thomas E

    2012-03-01

    The importance of exogenous selection in a natural hybrid zone between the pupfishes Cyprinodon atrorus and Cyprinodon bifasciatus was tested via spatio-temporal analyses of environmental and genetic change over winter, spring and summer for three consecutive years. A critical influence of exogenous selection on hybrid zone regulation was demonstrated by a significant relationship between environmental (salinity and temperature) and genetic (three diagnostic nuDNA loci) variation over space and time (seasons) in the Rio Churince system, Cuatro Ciénegas, Mexico. At sites environmentally more similar to parental habitats, the genetic composition of hybrids was stable and similar to the resident parental species, whereas complex admixtures of parental and hybrid genotypic classes characterized intermediate environments, as did the greatest change in allelic and genotypic frequencies across seasons. Within hybrids across the entire Rio Churince system, seasonal changes in allelic and genotypic frequencies were consistent with results from previous reciprocal transplant experiments, which showed C. bifasciatus to suffer high mortality (75%) when exposed to the habitat of C. atrorus in winter (extreme temperature lows and variability) and summer (abrupt salinity change and extreme temperature highs and variability). Although unconfirmed, the distributional limits of C. atrorus and C. atrorus-like hybrids appear to be governed by similar constraints (predation or competition). The argument favouring evolutionary significance of hybridization in animals is bolstered by the results of this study, which links the importance of exogenous selection in a contemporary hybrid zone between C. atrorus and C. bifasciatus to previous demonstration of the long-term evolutionary significance of environmental variation and introgression on the phenotypic diversification Cuatro Ciénegas Cyprinodon. © 2012 Blackwell Publishing Ltd.

  16. Socio-environmental and endocrine influences on developmental and caste-regulatory gene expression in the eusocial termite Reticulitermes flavipes

    Directory of Open Access Journals (Sweden)

    Zhou Xuguo

    2010-04-01

    Full Text Available Abstract Background Strict regulation of caste differentiation, at the molecular level, is thought to be important to maintain social structure in insect societies. Previously, a number of extrinsic and intrinsic factors have been shown to influence caste composition in termite colonies. One important factor is the influence of nestmates; in particular, soldier termites are known to inhibit hormone-dependent worker-to-soldier differentiation. However, soldier influences on nestmates at the molecular level are virtually unknown. Here, to test the hypothesis that soldiers can influence nestmate gene expression, we investigated the impact of four treatments on whole-body gene expression in totipotent Reticulitermes flavipes workers: (i juvenile hormone III (JHIII; a morphogenetic hormone, (ii soldier head extracts (SHE, (iii JHIII+SHE, and (iv live soldiers. Results Using quantitative-real-time PCR we determined the expression patterns of 49 previously identified candidate genes in response to the four treatments at assay days 1, 5, and 10. Thirty-eight total genes from three categories (chemical production/degradation, hemolymph protein, and developmental showed significant differential expression among treatments. Most importantly, SHE and live soldier treatments had a significant impact on a number of genes from families known to play roles in insect development, supporting previous findings and hypotheses that soldiers regulate nestmate caste differentiation via terpene primer pheromones contained in their heads. Conclusions This research provides new insights into the impacts that socio-environmental factors (JH, soldiers, primer pheromones can have on termite gene expression and caste differentiation, and reveals a number of socially-relevant genes for investigation in subsequent caste differentiation research.

  17. The urease gene cluster of Vibrio parahaemolyticus does not influence the expression of the thermostable direct hemolysin (TDH) gene or the TDH-related hemolysin gene.

    Science.gov (United States)

    Nakaguchi, Yoshitsugu; Okuda, Jun; Iida, Tetsuya; Nishibuchi, Mitsuaki

    2003-01-01

    In order to investigate why the thermostable direct hemolysin (TDH) and the TDH-related hemolysin (TRH) of Vibrio parahaemolyticus are produced at low levels from urease-positive strains, the effect of the functional urease gene cluster of V. parahaemolyticus on the expression of the tdh and trh genes was examined. Transcriptional lacZ fusions with the tdh1, tdh2, trh1 and trh2 genes representing variants of the tdh and trh genes were integrated into the chromosome of an Escherichia coli strain and a urease-negative V. parahaemolyticus strain. The plasmid-borne urease gene cluster introduced and expressed in these constructs did not affect expression of any of the fusion genes. The amount of TDH produced from a Kanagawa phenomenon-positive V. parahaemolyticus did not change by introduction of the urease gene cluster either. It was concluded therefore that the urease gene cluster is not involved in the regulation of tdh and trh expression.

  18. Temporal and spatial expression of polygalacturonase gene family members reveals divergent regulation during fleshy fruit ripening and abscission in the monocot species oil palm

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    Roongsattham Peerapat

    2012-08-01

    Full Text Available Abstract Background Cell separation that occurs during fleshy fruit abscission and dry fruit dehiscence facilitates seed dispersal, the final stage of plant reproductive development. While our understanding of the evolutionary context of cell separation is limited mainly to the eudicot model systems tomato and Arabidopsis, less is known about the mechanisms underlying fruit abscission in crop species, monocots in particular. The polygalacturonase (PG multigene family encodes enzymes involved in the depolymerisation of pectin homogalacturonan within the primary cell wall and middle lamella. PG activity is commonly found in the separation layers during organ abscission and dehiscence, however, little is known about how this gene family has diverged since the separation of monocot and eudicots and the consequence of this divergence on the abscission process. Results The objective of the current study was to identify PGs responsible for the high activity previously observed in the abscission zone (AZ during fruit shedding of the tropical monocot oil palm, and to analyze PG gene expression during oil palm fruit ripening and abscission. We identified 14 transcripts that encode PGs, all of which are expressed in the base of the oil palm fruit. The accumulation of five PG transcripts increase, four decrease and five do not change during ethylene treatments that induce cell separation. One PG transcript (EgPG4 is the most highly induced in the fruit base, with a 700–5000 fold increase during the ethylene treatment. In situ hybridization experiments indicate that the EgPG4 transcript increases preferentially in the AZ cell layers in the base of the fruit in response to ethylene prior to cell separation. Conclusions The expression pattern of EgPG4 is consistent with the temporal and spatial requirements for cell separation to occur during oil palm fruit shedding. The sequence diversity of PGs and the complexity of their expression in the oil palm fruit

  19. Myosin Light Chain Kinase (MLCK) Gene Influences Exercise Induced Muscle Damage during a Competitive Marathon.

    Science.gov (United States)

    Del Coso, Juan; Valero, Marjorie; Lara, Beatriz; Salinero, Juan José; Gallo-Salazar, César; Areces, Francisco

    2016-01-01

    Myosin light chain kinase (MLCK) phosphorylates the regulatory light chain (RLC) of myosin producing increases in force development during skeletal muscle contraction. It has been suggested that MLCK gene polymorphisms might alter RLC phosphorylation thereby decreasing the ability to produce force and to resist strain during voluntary muscle contractions. Thus, the genetic variations in the MLCK gene might predispose some individuals to higher values of muscle damage during exercise, especially during endurance competitions. The aim of this investigation was to determine the influence of MLCK genetic variants on exercise-induced muscle damage produced during a marathon. Sixty-seven experienced runners competed in a marathon race. The MLCK genotype (C37885A) of these marathoners was determined. Before and after the race, a sample of venous blood was obtained to assess changes in serum myoglobin concentrations and leg muscle power changes were measured during a countermovement jump. Self-reported leg muscle pain and fatigue were determined by questionnaires. A total of 59 marathoners (88.1%) were CC homozygotes and 8 marathoners (11.9%) were CA heterozygotes. The two groups of participants completed the race with a similar time (228 ± 33 vs 234 ± 39 min; P = 0.30) and similar self-reported values for fatigue (15 ± 2 vs 16 ± 2 A.U.; P = 0.21) and lower-limb muscle pain (6.2 ± 1.7 vs 6.6 ± 1.8 cm; P = 0.29). However, CC marathoners presented higher serum myoglobin concentrations (739 ± 792 vs 348 ± 144 μg·mL-1; P = 0.03) and greater pre-to-post- race leg muscle power reduction (-32.7 ± 15.7 vs -21.2 ± 21.6%; P = 0.05) than CA marathoners. CA heterozygotes for MLCK C37885A might present higher exercise-induced muscle damage after a marathon competition than CC counterparts.

  20. Genetic Variation in Autophagy-Related Genes Influences the Risk and Phenotype of Buruli Ulcer.

    Directory of Open Access Journals (Sweden)

    Carlos Capela

    2016-04-01

    Full Text Available Buruli ulcer (BU is a severe necrotizing human skin disease caused by Mycobacterium ulcerans. Clinically, presentation is a sum of these diverse pathogenic hits subjected to critical immune-regulatory mechanisms. Among them, autophagy has been demonstrated as a cellular process of critical importance. Since microtubules and dynein are affected by mycolactone, the critical pathogenic exotoxin produced by M. ulcerans, cytoskeleton-related changes might potentially impair the autophagic process and impact the risk and progression of infection.Genetic variants in the autophagy-related genes NOD2, PARK2 and ATG16L1 has been associated with susceptibility to mycobacterial diseases. Here, we investigated their association with BU risk, its severe phenotypes and its progression to an ulcerative form.Genetic variants were genotyped using KASPar chemistry in 208 BU patients (70.2% with an ulcerative form and 28% in severe WHO category 3 phenotype and 300 healthy endemic controls.The rs1333955 SNP in PARK2 was significantly associated with increased susceptibility to BU [odds ratio (OR, 1.43; P = 0.05]. In addition, both the rs9302752 and rs2066842 SNPs in NOD2 gee significantly increased the predisposition of patients to develop category 3 (OR, 2.23; P = 0.02; and OR 12.7; P = 0.03, respectively, whereas the rs2241880 SNP in ATG16L1 was found to significantly protect patients from presenting the ulcer phenotype (OR, 0.35; P = 0.02.Our findings indicate that specific genetic variants in autophagy-related genes influence susceptibility to the development of BU and its progression to severe phenotypes.

  1. Influence of pre-exercise muscle glycogen content on exercise-induced transcriptional regulation of metabolic genes

    DEFF Research Database (Denmark)

    Pilegaard, Henriette; Keller, Charlotte; Steensberg, Adam

    2002-01-01

    Transcription of metabolic genes is transiently induced during recovery from exercise in skeletal muscle of humans. To determine whether pre-exercise muscle glycogen content influences the magnitude and/or duration of this adaptive response, six male subjects performed one-legged cycling exercise...

  2. Interaction between serotonin 5-HT2A receptor gene and dopamine transporter (DAT1) gene polymorphisms influences personality trait of persistence in Austrian Caucasians.

    Science.gov (United States)

    Schosser, Alexandra; Fuchs, Karoline; Scharl, Theresa; Schloegelhofer, Monika; Kindler, Jochen; Mossaheb, Nilufar; Kaufmann, Rainer M; Leisch, Friedrich; Kasper, Siegfried; Sieghart, Werner; Aschauer, Harald N

    2010-03-01

    We examined 89 normal volunteers using Cloninger's Temperament and Character Inventory (TCI). Genotyping the 102T/C polymorphism of the serotonin 5HT2A receptor gene and the ser9gly polymorphism in exon 1 of the dopamine D3 receptor (DRD3) gene was performed using PCR-RFLP, whereas the dopamine transporter (DAT1) gene variable number of tandem repeats (VNTR) polymorphism was investigated using PCR amplification followed by electrophoresis in an 8% acrylamide gel with a set of size markers. We found a nominally significant association between gender and harm avoidance (P=0.017; women showing higher scores). There was no association of either DAT1, DRD3 or 5HT2A alleles or genotypes with any dimension of the TCI applying Kruskal-Wallis rank-sum tests. Comparing homozygote and heterozygote DAT1 genotypes, we found higher novelty seeking scores in homozygotes (P=0.054). We further found a nominally significant interaction between DAT1 and 5HT2A homo-/heterozygous gene variants (P=0.0071; DAT1 and 5HT2A genotypes P value of 0.05), performing multivariate analysis of variance (MANOVA). Examining the temperamental TCI subscales, this interaction was associated with persistence (genotypes: P=0.004; homo-/heterozygous gene variants: P=0.0004). We conclude that an interaction between DAT1 and 5HT2A genes might influence the temperamental personality trait persistence.

  3. Hormone-replacement therapy influences gene expression profiles and is associated with breast-cancer prognosis: a cohort study

    Directory of Open Access Journals (Sweden)

    Skoog Lambert

    2006-06-01

    Full Text Available Abstract Background Postmenopausal hormone-replacement therapy (HRT increases breast-cancer risk. The influence of HRT on the biology of the primary tumor, however, is not well understood. Methods We obtained breast-cancer gene expression profiles using Affymetrix human genome U133A arrays. We examined the relationship between HRT-regulated gene profiles, tumor characteristics, and recurrence-free survival in 72 postmenopausal women. Results HRT use in patients with estrogen receptor (ER protein positive tumors (n = 72 was associated with an altered regulation of 276 genes. Expression profiles based on these genes clustered ER-positive tumors into two molecular subclasses, one of which was associated with HRT use and had significantly better recurrence free survival despite lower ER levels. A comparison with external data suggested that gene regulation in tumors associated with HRT was negatively correlated with gene regulation induced by short-term estrogen exposure, but positively correlated with the effect of tamoxifen. Conclusion Our findings suggest that post-menopausal HRT use is associated with a distinct gene expression profile related to better recurrence-free survival and lower ER protein levels. Tentatively, HRT-associated gene expression in tumors resembles the effect of tamoxifen exposure on MCF-7 cells.

  4. Effect of Brahman genetic influence on collagen enzymatic crosslinking gene expression and meat tenderness.

    Science.gov (United States)

    Gonzalez, J M; Johnson, D D; Elzo, M A; White, M C; Stelzleni, A M; Johnson, S E

    2014-01-01

    The objective of the study was to examine the effect of Brahman genetics on collagen enzymatic crosslinking gene expression and meat tenderness. Steers were randomly selected to represent a high percentage Brahman genetics (n = 13), Half-Blood genetics (n = 13), Brangus genetics (n = 13), and a high percentage Angus genetics (n = 13). Muscle samples from the Longissimus lumborum muscle were collected at weaning and harvest and reverse transcription quantitative PCR (qPCR) analysis was conducted to measure the mRNA expression of lysyl oxidase (LOX), bone morphogenetic protein 1 (BMP1), and cystatin C (CYS). Steaks from subject animals were collected at harvest, aged for 14 d and subjected to collagen analysis, Warner-Bratzler Shear Force (WBS) and trained sensory panel analysis (tenderness, juiciness, and connective tissue). Data indicated that Half-Blood and Brahman steers had greater (PBrahman and Half-Blood steaks when compared to Angus and Brangus steaks (P 0.10). At harvest, Brangus and Angus steers had greater LOX mRNA expression than Brahman cattle (P Brahman genetic influence.

  5. Variation at genes influencing facial morphology are not associated with developmental imprecision in human faces.

    Directory of Open Access Journals (Sweden)

    Sonja Windhager

    Full Text Available Facial asymmetries are commonly used as a proxy for human developmental imprecision resulting from inbreeding, and thus reduced genetic heterozygosity. Several environmental factors influence human facial asymmetry (e.g., health care, parasites, but the generalizability of findings on genetic stressors has been limited in humans by sample characteristics (island populations, endogamy and indirect genetic assessment (inference from pedigrees. In a sample of 3215 adult humans from the Rotterdam Study, we therefore studied the relationship of facial asymmetry, estimated from nine mid-facial landmarks, with genetic variation at 102 single nucleotide polymorphism (SNP loci recently associated with facial shape variation. We further tested whether the degree of individual heterozygosity is negatively correlated with facial asymmetry. An ANOVA tree regression did not identify any SNP relating to either fluctuating asymmetry or total asymmetry. In a general linear model, only age and sex--but neither heterozygosity nor any SNP previously reported to covary with facial shape--was significantly related to total or fluctuating asymmetry of the midface. Our study does not corroborate the common assumption in evolutionary and behavioral biology that morphological asymmetries reflect heterozygosity. Our results, however, may be affected by a relatively small degree of inbreeding, a relatively stable environment, and an advanced age in the Rotterdam sample. Further large-scale genetic studies, including gene expression studies, are necessary to validate the genetic and developmental origin of morphological asymmetries.

  6. [Influence of genetic mutations on clinical presentation of subretinal neovascularization. Report 2: The impact of HTRA and VEGF genes polymorphism].

    Science.gov (United States)

    Budzinskaia, M V; Pogoda, T V; Strelkova, I D; Chikun, E A; Shchegoleva, I V; Kazarian, É É; Galoian, N S

    2011-01-01

    A detailed analysis of influence of HTRA (serine peptidase) and VEGF (vascular endothelial growth factor) genes mutations is presented. The presence of one gene copy with allele of A- polymorphism rs1120638 of HTRA1 gen, T- polymorphism rs10490924 and de11443in54 of ARMS2 gene increases the risk of CNV in patients with AMD. The feature of clinical presentation in patients with CNV associated with (-625) A mutation of promoter region of HTRA1 gene in two chromosomes was fulminant course of the disease from exudative to scarring processes with fibrous tissue formation not just with sub-, but also intra- and preretinal localization. Genetic screening showed that combination of studied mutations (402H, (-625) A and (-251) A in both gene copies of CFH, HTRA and IL-8) results in the most severe and rapidly progressing form of the disease. Two new mutations were revealed in promoter region of VEGF gene: G > A replacement in position of (-72) nucleotide from transcription start and G > A replacement in 5'-nontranslated region of the 1st gene exon in position of (+31) nucleotide from transcription start.

  7. Influences of the G2350A polymorphism in the ACE Gene on cardiac structure and function of ball game players

    Directory of Open Access Journals (Sweden)

    Jang Yongwoo

    2012-01-01

    Full Text Available Abstract Background Except for the I/D polymorphism in the angiotensin I-converting enzyme (ACE gene, there were few reports about the relationship between other genetic polymorphisms in this gene and the changes in cardiac structure and function of athletes. Thus, we investigated whether the G2350A polymorphism in the ACE gene is associated with the changes in cardiac structure and function of ball game players. Total 85 healthy ball game players were recruited in this study, and they were composed of 35 controls and 50 ball game players, respectively. Cardiac structure and function were measured by 2-D echocardiography, and the G2350A polymorphism in the ACE gene analyzed by the SNaPshot method. Results There were significant differences in left ventricular mass index (LVmassI value among each sporting discipline studied. Especially in the athletes of basketball disciplines, indicated the highest LVmassI value than those of other sporting disciplines studied (p ACE gene in the both controls and ball game players. Conclusions Our data suggests that the G2350A polymorphism in the ACE gene may not significantly contribute to the changes in cardiac structure and function of ball game players, although sporting disciplines of ball game players may influence the changes in LVmassI value of these athletes. Further studies using a larger sample size and other genetic markers in the ACE gene will be needed.

  8. How contemporary human reproductive behaviors influence the role of fertility-related genes: the example of the p53 gene.

    Directory of Open Access Journals (Sweden)

    Rosa Maria Corbo

    Full Text Available Studies on human fertility genes have identified numerous risk/protective alleles involved in the occurrence of reproductive system diseases causing infertility or subfertility. Investigations we carried out in populations at natural fertility seem to suggest that the clinical relevance that some fertility genes are now acquiring depends on their interaction with contemporary reproductive behaviors (birth control, delayed childbearing, and spacing birth order, among others. In recent years, a new physiological role in human fertility regulation has emerged for the tumor- suppressor p53 gene (P53, and the P53 Arg72Pro polymorphism has been associated with recurrent implantation failure in humans. To lend support to our previous observations, we examined the impact of Arg72Pro polymorphism on fertility in two samples of Italian women not selected for impaired fertility but collected from populations with different (premodern and modern reproductive behaviors. Among the women at near-natural fertility (n = 98, the P53 genotypes were not associated with different reproductive efficiency, whereas among those with modern reproductive behaviors (n = 68, the P53 genotypes were associated with different mean numbers of children [Pro/Pro = 0.75genes may have become "detrimental" following exposure to modern reproductive patterns and might therefore be associated with reduced reproductive success. Set within an evolutionary framework, this change could lead to the selection of a set of gene variants fitter to current reproductive behaviors as the

  9. The influence of dopaminergic gene variants on decision making in the ultimatum game

    Directory of Open Access Journals (Sweden)

    Martin eReuter

    2013-06-01

    Full Text Available One of the most prominent paradigms in neuroeconomics is the Ultimatum Game (UG that provides a framework for the study of pro-social behavior in two players interacting anonymously with each other: Player 1 has to split an endowment with player 2. Player 2 can either accept or reject the offer from player 1. If player 2 accepts the offer then the money is split as proposed by player 1. In case of rejection both players get nothing. Until now only one twin study investigated the heritability of the behavior in the UG. Results indicated a strong heritability for the decision behavior of player 2 whereas no genetic influence on player 1 behavior could be detected. Further studies are mandatory to validate these heritability estimates. However, a first candidate polymorphism, the DRD4 exon III, constituting the biological basis of the heritability in the responder behavior has already been identified in a Chinese sample (Zhong et al., 2010. Until now genetic studies in Caucasians on the UG are lacking. The present study wants to fill this gap by investigating the UG in a healthy German sample. Moreover, we intend to find candidate genes that are associated with the first-mover-behavior. In a sample of N=130 healthy participants an online version of the UG was conducted and polymorphisms of the dopamine D2 receptor gene (DRD2 and the DRD4 exon III VNTR were genotyped. We could confirm the DRD4 exon III effect on the responder behavior and the absence of an effect on the proposer behavior reported before. In line with Zhong et al. (2010 carriers of the 4/4 genotype showed a significant higher minimal acceptable offer (p=0.023 than subjects with any other genotype. Furthermore, a DRD2-haplotype-block containing the single nucleotide polymorphisms rs1800497 and rs2283265 was significantly associated with the amount player1 offered (p=.005 but not with the decision of player 2. Results support the importance of the dopaminergic system for pro

  10. The influence of dopaminergic gene variants on decision making in the ultimatum game.

    Science.gov (United States)

    Reuter, Martin; Felten, Andrea; Penz, Sabrina; Mainzer, Anna; Markett, Sebastian; Montag, Christian

    2013-01-01

    One of the most prominent paradigms in neuroeconomics is the ultimatum game (UG) that provides a framework for the study of pro-social behavior in two players interacting anonymously with each other: Player 1 has to split an endowment with player 2. Player 2 can either accept or reject the offer from player 1. If player 2 accepts the offer then the money is split as proposed by player 1. In case of rejection both players get nothing. Until now only one twin study investigated the heritability of the behavior in the UG. Results indicated a strong heritability for the decision behavior of player 2 whereas no genetic influence on player 1 behavior could be detected. Further studies are mandatory to validate these heritability estimates. However, a first candidate polymorphism, the DRD4 exon III, constituting the biological basis of the heritability in the responder behavior has already been identified in a Chinese sample (Zhong et al., 2010). Until now genetic studies in Caucasians on the UG are lacking. The present study wants to fill this gap by investigating the UG in a healthy German sample. Moreover, we intend to find candidate genes that are associated with the first-mover-behavior. In a sample of N = 130 healthy participants an online version of the UG was conducted and polymorphisms of the dopamine D2 receptor gene (DRD2) and the DRD4 exon III VNTR were genotyped. We could confirm the DRD4 exon III effect on the responder behavior and the absence of an effect on the proposer behavior reported before. In line with Zhong et al. (2010) carriers of the 4/4 genotype showed a significant higher minimal acceptable offer (p = 0.023) than subjects with any other genotype. Furthermore, a DRD2-haplotype-block containing the single nucleotide polymorphisms rs1800497 and rs2283265 was significantly associated with the amount player1 offered (p = 0.005) but not with the decision of player 2. Results support the importance of the dopaminergic system for pro-social behavior.

  11. A gene-gene interaction between polymorphisms in the OCT2 and MATE1 genes influences the renal clearance of metformin

    DEFF Research Database (Denmark)

    Hougaard Christensen, Mette Marie; Pedersen, Rasmus Steen; Stage, Tore Bjerregaard;

    2013-01-01

    The aim of this study was to determine the association between the renal clearance (CL(renal)) of metformin in healthy Caucasian volunteers and the single-nucleotide polymorphism (SNP) c.808G>T (rs316019) in OCT2 as well as the relevance of the gene-gene interactions between this SNP and (a...

  12. Protocols for screening antimicrobial peptides that influence virulence gene expression in Staphylococcus aureus

    DEFF Research Database (Denmark)

    Bojer, Martin Saxtorph; Baldry, Mara; Ingmer, Hanne

    2017-01-01

    Compounds that inhibit virulence gene expression in bacterial pathogens have received increasing interest as possible alternatives to the traditional antibiotic treatment of infections. For the human pathogen Staphylococcus aureus, we have developed two simple assays based on reporter gene fusion...... is quantitative and can be employed to address whether a compound is acting on the central quorum sensing regulatory system, agr, that controls a large number of virulence genes in S. aureus.......Compounds that inhibit virulence gene expression in bacterial pathogens have received increasing interest as possible alternatives to the traditional antibiotic treatment of infections. For the human pathogen Staphylococcus aureus, we have developed two simple assays based on reporter gene fusions...

  13. Lupanine Improves Glucose Homeostasis by Influencing KATP Channels and Insulin Gene Expression

    Directory of Open Access Journals (Sweden)

    Mats Wiedemann

    2015-10-01

    Full Text Available The glucose-lowering effects of lupin seeds involve the combined action of several components. The present study investigates the influence of one of the main quinolizidine alkaloids, lupanine, on pancreatic beta cells and in an animal model of type-2 diabetes mellitus. In vitro studies were performed with insulin-secreting INS-1E cells or islets of C57BL/6 mice. In the in vivo experiments, hyperglycemia was induced in rats by injecting streptozotocin (65 mg/kg body weight. In the presence of 15 mmol/L glucose, insulin secretion was significantly elevated by 0.5 mmol/L lupanine, whereas the alkaloid did not stimulate insulin release with lower glucose concentrations. In islets treated with l-arginine, the potentiating effect of lupanine already occurred at 8 mmol/L glucose. Lupanine increased the expression of the Ins-1 gene. The potentiating effect on secretion was correlated to membrane depolarization and an increase in the frequency of Ca2+ action potentials. Determination of the current through ATP-dependent K+ channels (KATP channels revealed that lupanine directly inhibited the channel. The effect was dose-dependent but, even with a high lupanine concentration of 1 mmol/L or after a prolonged exposure time (12 h, the KATP channel block was incomplete. Oral administration of lupanine did not induce hypoglycemia. By contrast, lupanine improved glycemic control in response to an oral glucose tolerance test in streptozotocin-diabetic rats. In summary, lupanine acts as a positive modulator of insulin release obviously without a risk for hypoglycemic episodes.

  14. Analysis of the influence of PTPN22 gene polymorphisms in systemic sclerosis

    Science.gov (United States)

    Diaz-Gallo, LM; Gourh, P; Broen, J; Simeon, C; Fonollosa, V; Ortego-Centeno, N; Agarwal, S; Vonk, MC; Coenen, M; Riemekasten, G; Hunzelmann, N; Hesselstrand, R; Tan, FK; Reveille, JD; Assassi, S; García-Hernandez, FJ; Carreira, P; Camps, MT; Fernandez-Nebro, A; de la Peña, P Garcia; Nearney, T; Hilda, D; González-Gay, MA; Airo, P; Beretta, L; Scorza, R; Herrick, A; Worthington, J; Pros, A; Gómez-Gracia, I; Trapiella, L; Espinosa, G; Castellvi, I; Witte, T; de Keyser, F; Vanthuyne, M; Mayes, MD; Radstake, TRDJ; Arnett, FC; Martin, J; Rueda, B

    2011-01-01

    Objective Two functional single nucleotide polymorphisms (SNP) in the PTPN22 gene (rs24746601 and rs33996649) have been associated with autoimmunity. The aim of this study was to investigate the role of the R263Q SNP for the first time and to re-evaluate the role of the R620W SNP in the genetic predisposition to systemic sclerosis (SSc) susceptibility and clinical phenotypes. Methods 3422 SSc patients (2020 with limited cutaneous SSc and 1208 with diffuse cutaneous SSc) and 3638 healthy controls of Caucasian ancestry from an initial case--control set of Spain and seven additional independent replication cohorts were included in our study. Both rs33996649 and rs2476601 PTPN22 polymorphisms were genotyped by TaqMan allelic discrimination assay. A meta-analysis was performed to test the overall effect of these PTPN22 polymorphisms in SSc. Results The meta-analysis revealed evidence of association of the rs2476601 T allele with SSc susceptibility (pFDRcorrected=0.03 pooled, OR 1.15, 95% CI 1.03 to 1.28). In addition, the rs2476601 T allele was significantly associated with anticentromere-positive status (pFDRcorrected=0.02 pooled, OR 1.22, 95% CI 1.05 to 1.42). Although the rs33996649 A allele was significantly associated with SSc in the Spanish population (pFDRcorrected=0.04, OR 0.58, 95% CI 0.36 to 0.92), this association was not confirmed in the meta-analysis (p=0.36 pooled, OR 0.89, 95% CI 0.72 to 1.1). Conclusion The study suggests that the PTPN22 R620W polymorphism influences SSc genetic susceptibility but the novel R263Q genetic variant does not. These data strengthen evidence that the R620W mutation is a common risk factor in autoimmune diseases. PMID:21131644

  15. INFLUENCE OF NEOADJUVANT INTRAARTERIAL INFUSION CHEMOTHERAPY ON APOPTOSIS AND MULTIDRUG RESISTANCE ASSOCIATED GENES OF ENDOMETRIAL CANCER

    Institute of Scientific and Technical Information of China (English)

    朱雪琼; 岳天孚; 张颖; 惠京; 王德华

    2002-01-01

    Objective: Through investigating the influence of neoadjuvant intraarterial infusion chemotherapy (NIAC) on the timing changes of apoptosis, PCNA and multiple drug resistance associated genes of endometrial cancer, to study the mechanism of chemotherapy and to define the best operation time. Methods: Twenty patients were subjected to neoadjuvant consecutive uterine arterial infusion with CDDP 100 mg and ADM 50 mg. The biopsy of endometrial tumor tissues was performed before, immediate after and 1, 2-2+3 w, 3+3-4 w after chemotherapy. Apoptosis index (AI) was estimated by a combination of histologic and TUNEL assays. Proliferative index (PI) was examined by SABC immunohistochemical staining. Expressions of multidrug resistance 1 (MDR1), multidrug resistance-associated protein (MRP) and lung resistance protein (LRP) were detected by reverse transcription polymerase chain reaction (RT-PCR). Results: The AI of endometrial cancer cells immediate after and 1, 2-2+3 w, after chemotherapy were 3.03%, 3.47% and 5.04%, respectively, much higher than that before chemotherapy which was 2.31%. After chemotherapy, AI/PI gradually increased. It was highest in 2-2+3 w, while 3+3-4 w after chemotherapy the AI and AI/PI were both significantly lower than that before chemotherapy. The expression of MDR1, MRP and LRP all decreased temporarily after chemotherapy, while 3+3-4 w after chemotherapy they all increased to levels higher than that before chemotherapy, but the difference were not significant (P>0.05). Conclusion: Neoadjuvant consecutive intra-arterial infusion chemotherapy via uterine artery can inhibit tumor cells proliferation and induce apoptosis effectively. To evaluate the response of intra-arterial chemotherapy the change of apoptosis index and cell proliferation should be analyzed. The most suitable time for the operation is 3 weeks after intra-arterial infusion chemotherapy.

  16. Bidirectional promoters of insects: genome-wide comparison, evolutionary implication and influence on gene expression.

    Science.gov (United States)

    Behura, Susanta K; Severson, David W

    2015-01-30

    Bidirectional promoters are widespread in insect genomes. By analyzing 23 insect genomes we show that the frequency of bidirectional gene pairs varies according to genome compactness and density of genes among the species. The density of bidirectional genes expected based on number of genes per megabase of genome explains the observed density suggesting that bidirectional pairing of genes may be due to random event. We identified specific transcription factor binding motifs that are enriched in bidirectional promoters across insect species. Furthermore, we observed that bidirectional promoters may act as transcriptional hotspots in insect genomes where protein coding genes tend to aggregate in significantly biased (p promoters. Natural selection seems to have an association with the extent of bidirectionality of genes among the species. The rate of non-synonymous-to-synonymous changes (dN/dS) shows a second-order polynomial distribution with bidirectionality between species indicating that bidirectionality is dependent upon evolutionary pressure acting on the genomes. Analysis of genome-wide microarray expression data of multiple insect species suggested that bidirectionality has a similar association with transcriptome variation across species. Furthermore, bidirectional promoters show significant association with correlated expression of the divergent gene pairs depending upon their motif composition. Analysis of gene ontology showed that bidirectional genes tend to have a common association with functions related to "binding" (including ion binding, nucleotide binding and protein binding) across genomes. Such functional constraint of bidirectional genes may explain their widespread persistence in genome of diverse insect species.

  17. Temporal Variations in Cigarette Tobacco Bacterial Community Composition and Tobacco-Specific Nitrosamine Content Are Influenced by Brand and Storage Conditions

    Science.gov (United States)

    Chopyk, Jessica; Chattopadhyay, Suhana; Kulkarni, Prachi; Smyth, Eoghan M.; Hittle, Lauren E.; Paulson, Joseph N.; Pop, Mihai; Buehler, Stephanie S.; Clark, Pamela I.; Mongodin, Emmanuel F.; Sapkota, Amy R.

    2017-01-01

    Tobacco products, specifically cigarettes, are home to microbial ecosystems that may play an important role in the generation of carcinogenic tobacco-specific nitrosamines (TSNAs), as well as the onset of multiple adverse human health effects associated with the use of these products. Therefore, we conducted time-series experiments with five commercially available brands of cigarettes that were either commercially mentholated, custom-mentholated, user-mentholated, or non-mentholated. To mimic user storage conditions, the cigarettes were incubated for 14 days under three different temperatures and relative humidities (i.e., pocket, refrigerator, and room). Overall, 360 samples were collected over the course of 2 weeks and total DNA was extracted, PCR amplified for the V3V4 hypervariable region of the 16S rRNA gene and sequenced using Illumina MiSeq. A subset of samples (n = 32) was also analyzed via liquid chromatography with tandem mass spectrometry for two TSNAs: N’-nitrosonornicotine (NNN) and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). Comparative analyses of the five tobacco brands revealed bacterial communities dominated by Pseudomonas, Pantoea, and Bacillus, with Pseudomonas relatively stable in abundance regardless of storage condition. In addition, core bacterial operational taxonomic units (OTUs) were identified in all samples and included Bacillus pumilus, Rhizobium sp., Sphingomonas sp., unknown Enterobacteriaceae, Pantoea sp., Pseudomonas sp., Pseudomonas oryzihabitans, and P. putida. Additional OTUs were identified that significantly changed in relative abundance between day 0 and day 14, influenced by brand and storage condition. In addition, small but statistically significant increases in NNN levels were observed in user- and commercially mentholated brands between day 0 and day 14 at pocket conditions. These data suggest that manufacturing and user manipulations, such as mentholation and storage conditions, may directly impact the

  18. Functional differentiation and spatial-temporal co-expression networks of the NBS-encoding gene family in Jilin ginseng, Panax ginseng C.A. Meyer.

    Science.gov (United States)

    Yin, Rui; Zhao, Mingzhu; Wang, Kangyu; Lin, Yanping; Wang, Yanfang; Sun, Chunyu; Wang, Yi; Zhang, Meiping

    2017-01-01

    Ginseng, Panax ginseng C.A. Meyer, is one of the most important medicinal plants for human health and medicine. It has been documented that over 80% of genes conferring resistance to bacteria, viruses, fungi and nematodes are contributed by the nucleotide binding site (NBS)-encoding gene family. Therefore, identification and characterization of NBS genes expressed in ginseng are paramount to its genetic improvement and breeding. However, little is known about the NBS-encoding genes in ginseng. Here we report genome-wide identification and systems analysis of the NBS genes actively expressed in ginseng (PgNBS genes). Four hundred twelve PgNBS gene transcripts, derived from 284 gene models, were identified from the transcriptomes of 14 ginseng tissues. These genes were classified into eight types, including TNL, TN, CNL, CN, NL, N, RPW8-NL and RPW8-N. Seven conserved motifs were identified in both the Toll/interleukine-1 receptor (TIR) and coiled-coil (CC) typed genes whereas six were identified in the RPW8 typed genes. Phylogenetic analysis showed that the PgNBS gene family is an ancient family, with a vast majority of its genes originated before ginseng originated. In spite of their belonging to a family, the PgNBS genes have functionally dramatically differentiated and been categorized into numerous functional categories. The expressions of the across tissues, different aged roots and the roots of different genotypes. However, they are coordinating in expression, forming a single co-expression network. These results provide a deeper understanding of the origin, evolution and functional differentiation and expression dynamics of the NBS-encoding gene family in plants in general and in ginseng particularly, and a NBS gene toolkit useful for isolation and characterization of disease resistance genes and for enhanced disease resistance breeding in ginseng and related species.

  19. Macrodissection versus microdissection of rectal carcinoma: minor influence of stroma cells to tumor cell gene expression profiles

    Directory of Open Access Journals (Sweden)

    Medema Jan

    2005-10-01

    Full Text Available Abstract Background The molecular determinants of carcinogenesis, tumor progression and patient prognosis can be deduced from simultaneous comparison of thousands of genes by microarray analysis. However, the presence of stroma cells in surgically excised carcinoma tissues might obscure the tumor cell-specific gene expression profiles of these samples. To circumvent this complication, laser microdissection can be performed to separate tumor epithelium from the surrounding stroma and healthy tissue. In this report, we compared RNAs isolated from macrodissected, of which only surrounding healthy tissue had been removed, and microdissected rectal carcinoma samples by microarray analysis in order to determine the most reliable approach to detect the expression of tumor cell-derived genes by microarray analysis. Results As microdissection yielded low tissue and RNA quantities, extra rounds of mRNA amplification were necessary to obtain sufficient RNA for microarray experiments. These second rounds of amplification influenced the gene expression profiles. Moreover, the presence of stroma cells in macrodissected samples had a minor contribution to the tumor cell gene expression profiles, which can be explained by the observation that more RNA is extracted from tumor epithelial cells than from stroma. Conclusion These data demonstrate that the more convenient procedure of macrodissection can be adequately used and yields reliable data regarding the identification of tumor cell-specific gene expression profiles.

  20. The influence of gene flow and drift on genetic and phenotypic divergence in two species of Zosterops in Vanuatu.

    Science.gov (United States)

    Clegg, Sonya M; Phillimore, Albert B

    2010-04-12

    Colonization of an archipelago sets the stage for adaptive radiation. However, some archipelagos are home to spectacular radiations, while others have much lower levels of diversification. The amount of gene flow among allopatric populations is one factor proposed to contribute to this variation. In island colonizing birds, selection for reduced dispersal ability is predicted to produce changing patterns of regional population genetic structure as gene flow-dominated systems give way to drift-mediated divergence. If this transition is important in facilitating phenotypic divergence, levels of genetic and phenotypic divergence should be associated. We consider population genetic structure and phenotypic divergence among two co-distributed, congeneric (Genus: Zosterops) bird species inhabiting the Vanuatu archipelago. The more recent colonist, Z. lateralis, exhibits genetic patterns consistent with a strong influence of distance-mediated gene flow. However, complex patterns of asymmetrical gene flow indicate variation in dispersal ability or inclination among populations. The endemic species, Z. flavifrons, shows only a partial transition towards a drift-mediated system, despite a long evolutionary history on the archipelago. We find no strong evidence that gene flow constrains phenotypic divergence in either species, suggesting that levels of inter-island gene flow do not explain the absence of a radiation across this archipelago.

  1. Influence of prolonged bed-rest on spectral and temporal electromyographic motor control characteristics of the superficial lumbo-pelvic musculature.

    NARCIS (Netherlands)

    Belavy, D.L.; Ng, J.K.; Wilson, S.J.; Armbrecht, G.; Stegeman, D.F.; Rittweger, J.; Felsenberg, D.; Richardson, C.A.

    2010-01-01

    Little is known about the motor control of the lumbo-pelvic musculature in microgravity and its simulation (bed-rest). Analysis of spectral and temporal electromyographic variables can provide information on motor control relevant for normal function. This study examined the effect of 56-days of bed

  2. Temperature and Food Influence Shell Growth and Mantle Gene Expression of Shell Matrix Proteins in the Pearl Oyster Pinctada margaritifera

    Science.gov (United States)

    Joubert, Caroline; Linard, Clémentine; Le Moullac, Gilles; Soyez, Claude; Saulnier, Denis; Teaniniuraitemoana, Vaihiti; Ky, Chin Long; Gueguen, Yannick

    2014-01-01

    In this study, we analyzed the combined effect of microalgal concentration and temperature on the shell growth of the bivalve Pinctada margaritifera and the molecular mechanisms underlying this biomineralization process. Shell growth was measured after two months of rearing in experimental conditions, using calcein staining of the calcified structures. Molecular mechanisms were studied though the expression of 11 genes encoding proteins implicated in the biomineralization process, which was assessed in the mantle. We showed that shell growth is influenced by both microalgal concentration and temperature, and that these environmental factors also regulate the expression of most of the genes studied. Gene expression measurement of shell matrix protein thereby appears to be an appropriate indicator for the evaluation of the biomineralization activity in the pearl oyster P. margaritifera under varying environmental conditions. This study provides valuable information on the molecular mechanisms of mollusk shell growth and its environmental control. PMID:25121605

  3. Temperature and food influence shell growth and mantle gene expression of shell matrix proteins in the pearl oyster Pinctada margaritifera.

    Directory of Open Access Journals (Sweden)

    Caroline Joubert

    Full Text Available In this study, we analyzed the combined effect of microalgal concentration and temperature on the shell growth of the bivalve Pinctada margaritifera and the molecular mechanisms underlying this biomineralization process. Shell growth was measured after two months of rearing in experimental conditions, using calcein staining of the calcified structures. Molecular mechanisms were studied though the expression of 11 genes encoding proteins implicated in the biomineralization process, which was assessed in the mantle. We showed that shell growth is influenced by both microalgal concentration and temperature, and that these environmental factors also regulate the expression of most of the genes studied. Gene expression measurement of shell matrix protein thereby appears to be an appropriate indicator for the evaluation of the biomineralization activity in the pearl oyster P. margaritifera under varying environmental conditions. This study provides valuable information on the molecular mechanisms of mollusk shell growth and its environmental control.

  4. Arabidopsis flowering locus D influences systemic-acquired-resistance- induced expression and histone modifications of WRKY genes.

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    Singh, Vijayata; Roy, Shweta; Singh, Deepjyoti; Nandi, Ashis Kumar

    2014-03-01

    A plant that is in part infected by a pathogen is more resistant throughout its whole body to subsequent infections--a phenomenon known as systemic acquired resistance (SAR). Mobile signals are synthesized at the site of infection and distributed throughout the plant through vascular tissues. Mechanism of SAR development subsequent to reaching the mobile signal in the distal tissue is largely unknown. Recently we showed that flowering locus D (FLD) gene of Arabidopsis thaliana is required in the distal tissue to activate SAR. FLD codes for a homologue of human-lysine-specific histone demethylase. Here we show that FLD function is required for priming (SAR induced elevated expression during challenge inoculation) of WRKY29 and WRKY6 genes. FLD also differentially influences basal and SAR-induced expression of WRKY38, WRKY65 and WRKY53 genes. In addition, we also show that FLD partly localizes in nucleus and influences histone modifications at the promoters of WRKY29 and WRKY6 genes. The results altogether indicate to the possibility of FLD's involvement in epigenetic regulation of SAR.

  5. Transcriptional regulator PerA influences biofilm-associated, platelet binding, and metabolic gene expression in Enterococcus faecalis.

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    Scott M Maddox

    Full Text Available Enterococcus faecalis is an opportunistic pathogen and a leading cause of nosocomial infections, traits facilitated by the ability to quickly acquire and transfer virulence determinants. A 150 kb pathogenicity island (PAI comprised of genes contributing to virulence is found in many enterococcal isolates and is known to undergo horizontal transfer. We have shown that the PAI-encoded transcriptional regulator PerA contributes to pathogenicity in the mouse peritonitis infection model. In this study, we used whole-genome microarrays to determine the PerA regulon. The PerA regulon is extensive, as transcriptional analysis showed 151 differentially regulated genes. Our findings reveal that PerA coordinately regulates genes important for metabolism, amino acid degradation, and pathogenicity. Further transcriptional analysis revealed that PerA is influenced by bicarbonate. Additionally, PerA influences the ability of E. faecalis to bind to human platelets. Our results suggest that PerA is a global transcriptional regulator that coordinately regulates genes responsible for enterococcal pathogenicity.

  6. Expression of energy balance regulatory genes in the developing ovine fetal hypothalamus at midgestation and the influence of hyperglycemia.

    Science.gov (United States)

    Adam, Clare L; Findlay, Patricia A; Chanet, Audrey; Aitken, Raymond P; Milne, John S; Wallace, Jacqueline M

    2008-06-01

    Evidence suggests that the prenatal nutritional environment influences the risk of developing obesity, a major health problem worldwide. It is hypothesized that fetal nutrition influences the developing neuroendocrine hypothalamus, the integrative control center for postnatal energy balance regulation. The present aim was to determine whether relevant hypothalamic genes are expressed in midgestation and whether they are nutritionally (glucose) sensitive at this time. Hypothalami from a cohort of 81-day singleton sheep fetuses, with varying glycemia by virtue of maternal dietary and/or growth hormone treatment, were subject to in situ hybridization analysis for primary orexigenic, anorexigenic, and related receptor genes (term = 147 days, n = 24). Neuropeptide Y, agouti-related peptide, proopiomelanocortin (POMC), cocaine- and amphetamine-regulated transcript (CART), and insulin receptor mRNAs were all localized in the hypothalamic arcuate nucleus (ARC) of all fetuses, whereas leptin receptor mRNA was expressed more abundantly in the ventromedial hypothalamic nucleus. ARC expression levels of POMC and CART genes, but none of the other genes, were positively correlated with fetal plasma glucose concentrations. Therefore, key central components of adult energy balance regulation were already present as early as midgestation (equivalent to 22 wk in humans), and two anorexigenic components were upregulated by elevated glycemia. Such changes provide a potential mechanism for the prenatal origins of postnatal energy balance dysregulation and obesity.

  7. SNCA Gene, but Not MAPT, Influences Onset Age of Parkinson’s Disease in Chinese and Australians

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    Yue Huang

    2015-01-01

    Full Text Available Background. α-Synuclein (SNCA and microtubule-associated protein tau (MAPT are the two major genes independently, but not jointly, associated with susceptibility for Parkinson’s disease (PD. The SNCA gene has recently been identified as a major modifier of age of PD onset. Whether MAPT gene synergistically influences age of onset of PD is unknown. Objective. To investigate independent and joint effects of MAPT and SNCA on PD onset age. Methods. 412 patients with PD were recruited from the Australian PD Research Network (123 and the Neurology Department, Ruijin Hospital Affiliated to Shanghai Jiaotong University, China (289. MAPT (rs17650901 tagging H1/H2 haplotype and SNCA (Rep1 were genotyped in the Australian cohort, and MAPT (rs242557, rs3744456 and SNCA (rs11931074, rs894278 were genotyped in the Chinese cohort. SPSS regression analysis was used to test genetic effects on age at onset of PD in each cohort. Results. SNCA polymorphisms associated with the onset age of PD in both populations. MAPT polymorphisms did not enhance such association in either entire cohort. Conclusion. This study suggests that, in both ethnic groups, SNCA gene variants influence the age at onset of PD and α-synuclein plays a key role in the disease course of PD.

  8. Epistatic interaction between beta2-adrenergic receptor and neuropeptide Y genes influences LDL-cholesterol in hypertension.

    Science.gov (United States)

    Tomaszewski, Maciej; Charchar, Fadi J; Lacka, Beata; Pesonen, Ullamari; Wang, William Y S; Zukowska-Szczechowska, Ewa; Grzeszczak, Wladyslaw; Dominiczak, Anna F

    2004-11-01

    Beta2-adrenergic receptor gene and neuropeptide Y gene may potentially influence lipid metabolism and overall energy balance. Therefore, we examined associations of these genes with lipid fractions and obesity-related phenotypes in hypertensive subjects. A total of 638 white individuals from 212 Polish families with clustering of essential hypertension were phenotyped for cardiovascular risk determinants. Each subject was genotyped for functional polymorphisms of beta2-adrenergic receptor gene (Arg16Gly and Gln27Glu) and neuropeptide Y (Leu7Pro). Of 3 common haplotypes of beta2-adrenergic receptor gene, Arg16Gln27 was overtransmitted to offspring with elevated levels of total cholesterol (Z=2.2; P=0.026) and LDL-cholesterol (Z=3.2; P=0.002). Individually, Leu7Pro was not associated with any of the metabolic phenotypes in family-based tests or case-control analyses. However, in the presence of Arg allele of Arg16Gly and Gln allele of Gln27Glu, homozygosity for Leu variant of the Leu7Pro polymorphism was associated with 2.1-increased odds ratio (confidence interval, 1.10 to 3.81; P=0.024) of elevated LDL in hypertensive subjects, independent of age, gender, body mass index, adjusted blood pressures, antihypertensive therapy, and use of nonselective beta-blockers and diuretics. Consistently, there was a significant multilocus association among variants of Arg16Gly, Gln27Glu, and Leu7Pro in hypertensive probands with elevated LDL (cases; P=0.028) but not in hypertensive subjects with normal LDL (controls). This study revealed an association of LDL-cholesterol with beta2-adrenergic receptor gene haplotype and provided evidence for epistatic interaction between beta2-adrenergic receptor gene and neuropeptide Y gene in determination of LDL-cholesterol in patients with essential hypertension.

  9. Influence of SLCO1B1 and CYP2C8 gene polymorphisms on rosiglitazone pharmacokinetics in healthy volunteers

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    Aquilante Christina L

    2008-09-01

    Full Text Available Abstract Polymorphisms in drug transporter genes and/or drug-metabolising enzyme genes may contribute to inter-individual variability in rosiglitazone pharmacokinetics in humans. We sought to determine the joint effects of polymorphisms in the SLCO1B1 drug transporter gene and the cytochrome P450 (CYP 2C8-metabolising enzyme gene on rosiglitazone pharmacokinetics in healthy volunteers. Healthy Caucasian subjects were prospectively enrolled on the basis of SLCO1B1 521 T > C genotype. Additionally, subjects were genotyped for SLCO1B1 11187 G > A, - 10499 A > C and 388 A > G polymorphisms, and the CYP2C8*3 polymorphism. SLCO1B1 haplotypes and diplotypes were computationally assigned. Rosiglitazone plasma concentrations were determined by high-performance liquid chromatography and analysed using non-compartmental methods. The study population consisted of 26 subjects, with a mean age of 33 ± 9 years, and a mean weight of 66.6 ± 11.7 kg. There were no significant differences in rosiglitazone pharmacokinetic parameters between SLCO1B1 diplotype groups. Subjects with the CYP2C8*1/*3 genotype (n = 7, however, had significantly lower rosiglitazone area under the plasma concentration-time curve (AUC and significantly higher rosiglitazone oral clearance, compared with CYP2C8 wild-type homozygotes (n = 19. Stepwise linear regression analysis revealed that CYP2C8 genotype (p = 0.006 and weight (p = 0.022 were significant predictors of rosiglitazone AUC (overall p = 0.002; R2 = 41.6 per cent. We concluded that polymorphisms in the CYP2C8 drug-metabolising enzyme gene, but not the SLCO1B1 drug transporter gene, significantly influence rosiglitazone disposition in humans. Future studies examining the influence of CYP2C8 genotypes and haplotypes on thiazolidinedione disposition and response in patients with type 2 diabetes are warranted.

  10. Sterile DJH rearrangements reveal that distance between gene segments on the human Ig H chain locus influences their ability to rearrange

    DEFF Research Database (Denmark)

    Hansen, Tina Østergaard; Lange, Anders Blaabjerg; Barington, Torben

    2015-01-01

    Rearrangement of the Ig locus occurs in two steps. First, a JH gene is rearranged to a D gene followed by a VH gene rearranging to the DJH rearrangement. By next generation sequencing, we analyzed 9969 unique DJH rearrangements and 5919 unique VHDJH rearrangements obtained from peripheral blood B...... frequently than JH locus distal D genes, whereas VH locus proximal D genes were observed more frequently in nonproductive VHDJH rearrangements. We further demonstrate that the distance between VH, D, and JH gene segments influence their ability to rearrange within the human Ig locus....

  11. The Influence of Major Life Events on Economic Attitudes in a World of Gene-Environment Interplay

    Science.gov (United States)

    Hatemi, Peter K.

    2014-01-01

    The role of “genes” on political attitudes has gained attention across disciplines. However, person-specific experiences have yet to be incorporated into models that consider genetic influences. Relying on a gene-environment interplay approach, this study explicates how life-events, such as losing one’s job or suffering a financial loss, influence economic policy attitudes. The results indicate genetic and environmental variance on support for unions, immigration, capitalism, socialism and property tax is moderated by financial risks. Changes in the magnitude of genetic influences, however, are temporary. After two years, the phenotypic effects of the life events remain on most attitudes, but changes in the sources of individual differences do not. Univariate twin models that estimate the independent contributions of genes and environment on the variation of attitudes appear to provide robust baseline indicators of sources of individual differences. These estimates, however, are not event or day specific. In this way, genetic influences add stability, while environment cues change, and this process is continually updated. PMID:24860199

  12. Dietary fat influences the expression of contractile and metabolic genes in rat skeletal muscle.

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    Wataru Mizunoya

    Full Text Available Dietary fat plays a major role in obesity, lipid metabolism, and cardiovascular diseases. To determine whether the intake of different types of dietary fats affect the muscle fiber types that govern the metabolic and contractile properties of the skeletal muscle, we fed male Wistar rats with a 15% fat diet derived from different fat sources. Diets composed of soybean oil (n-6 polyunsaturated fatty acids (PUFA-rich, fish oil (n-3 PUFA-rich, or lard (low in PUFAs were ad