To Nap, Perchance to DREAM: A Factor Analysis of College Students' Self-Reported Reasons for Napping.

PubMed

Duggan, Katherine A; McDevitt, Elizabeth A; Whitehurst, Lauren N; Mednick, Sara C

2018-01-01

Although napping has received attention because of its associations with health and use as a method to understand the function of sleep, to our knowledge no study has systematically and statistically assessed reasons for napping. Using factor analysis, we determined the underlying structure of reasons for napping in diverse undergraduates (N = 430, 59% female) and examined their relationships with self-reported sleep, psychological health, and physical health. The five reasons for napping can be summarized using the acronym DREAM (Dysregulative, Restorative, Emotional, Appetitive, and Mindful). Only Emotional reasons for napping were uniformly related to lower well-being. The use of factor analysis raises possibilities for future research, including examining the stability, structure, and psychological and physical health processes related to napping throughout the lifespan.

To nap, perchance to DREAM: A factor analysis of college students’ self-reported reasons for napping

PubMed Central

Duggan, Katherine A.; McDevitt, Elizabeth A.; Whitehurst, Lauren N.; Mednick, Sara C.

2017-01-01

Although napping has received attention because of its associations with health and use as a method to understand the function of sleep, to our knowledge no study has systematically and statistically assessed reasons for napping. Using factor analysis, we determined the underlying structure of reasons for napping in diverse undergraduates (N=430, 59% female) and examined their relationships with self-reported sleep, psychological, and physical health. The 5 reasons for napping can be summarized using the acronym DREAM (Dysregulative, Restorative, Emotional, Appetitive, and Mindful). Only Emotional reasons for napping were uniformly related to lower well-being. The use of factor analysis raises possibilities for future research, including examining the stability, structure, and psychological and physical health processes related to napping throughout the lifespan. PMID:27347727

The nitrate-reduction gene cluster components exert lineage-dependent contributions to optimization of Sinorhizobium symbiosis with soybeans.

PubMed

Liu, Li Xue; Li, Qin Qin; Zhang, Yun Zeng; Hu, Yue; Jiao, Jian; Guo, Hui Juan; Zhang, Xing Xing; Zhang, Biliang; Chen, Wen Xin; Tian, Chang Fu

2017-12-01

Receiving nodulation and nitrogen fixation genes does not guarantee rhizobia an effective symbiosis with legumes. Here, variations in gene content were determined for three Sinorhizobium species showing contrasting symbiotic efficiency on soybeans. A nitrate-reduction gene cluster absent in S. sojae was found to be essential for symbiotic adaptations of S. fredii and S. sp. III. In S. fredii, the deletion mutation of the nap (nitrate reductase), instead of nir (nitrite reductase) and nor (nitric oxide reductase), led to defects in nitrogen-fixation (Fix - ). By contrast, none of these core nitrate-reduction genes were required for the symbiosis of S. sp. III. However, within the same gene cluster, the deletion of hemN1 (encoding oxygen-independent coproporphyrinogen III oxidase) in both S. fredii and S. sp. III led to the formation of nitrogen-fixing (Fix + ) but ineffective (Eff - ) nodules. These Fix + /Eff - nodules were characterized by significantly lower enzyme activity of glutamine synthetase indicating rhizobial modulation of nitrogen-assimilation by plants. A distant homologue of HemN1 from S. sojae can complement this defect in S. fredii and S. sp. III, but exhibited a more pleotropic role in symbiosis establishment. These findings highlighted the lineage-dependent optimization of symbiotic functions in different rhizobial species associated with the same host. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Words to Sleep On: Naps Facilitate Verb Generalization in Habitually and Nonhabitually Napping Preschoolers

ERIC Educational Resources Information Center

Sandoval, Michelle; Leclerc, Julia A.; Gómez, Rebecca L.

2017-01-01

A nap soon after encoding leads to better learning in infancy. However, whether napping plays the same role in preschoolers' learning is unclear. In Experiment 1 (N = 39), 3-year-old habitual and nonhabitual nappers learned novel verbs before a nap or a period of wakefulness and received a generalization test examining word extension to novel…

Naps Enhance Executive Attention in Preschool-Aged Children.

PubMed

Cremone, Amanda; McDermott, Jennifer M; Spencer, Rebecca M C

2017-09-01

Executive attention is impaired following sleep loss in school-aged children, adolescents, and adults. Whether naps improve attention relative to nap deprivation in preschool-aged children is unknown. The aim of this study was to compare executive attention in preschool children following a nap and an interval of wake. Sixty-nine children, 35-70 months of age, completed a Flanker task to assess executive attention following a nap and an equivalent interval of wake. Overall, accuracy was greater after the nap compared with the wake interval. Reaction time(s) did not differ between the nap and wake intervals. Results did not differ between children who napped consistently and those who napped inconsistently, suggesting that naps benefit executive attention of preschoolers regardless of nap habituality. These results indicate that naps enhance attention in preschool children. As executive attention supports executive functioning and learning, nap promotion may improve early education outcomes. © The Author 2017. Published by Oxford University Press on behalf of the Society of Pediatric Psychology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Is Daytime Napping Associated With Inflammation In Adolescents?

PubMed Central

Jakubowski, Karen P.; Hall, Martica H.; Marsland, Anna L.; Matthews, Karen A.

2016-01-01

Objective Daytime napping has been associated with poor health outcomes in adults. It is not known whether daytime napping is similarly linked to adverse health in adolescents, although many report napping. The present study evaluated associations between daytime napping and two markers of increased inflammation, high sensitivity C-reactive protein (hs-CRP) and interleukin-6 (IL-6), in healthy high school students. Methods 234 black and white high school students completed a week of actigraph and diary measures of sleep and napping and provided a fasting blood sample. Napping measures were the proportion of days napped and the average minutes napped across one week during the school year. Results Linear regressions adjusted for age, sex, race, average nocturnal sleep duration, time between sleep protocol and blood draw, and BMI percentile demonstrated that proportion of days napped measured by actigraphy [B(SE)=.41(.19), p<.05] across the full week was positively associated with IL-6. Higher proportions of school days napped between 2 p.m. and 6 p.m. [B(SE)=.40(.20), p<.05] and between 6 p.m. and 10 p.m. [B(SE)=.57(.28), p<.05] were associated with increased IL-6. No associations emerged between average actigraphy-assessed nap duration and either study outcome. Diary-reported napping was unrelated to either study outcome. Conclusions Actigraphy-assessed napping and IL-6 are associated but the direction of the relationship remains to be determined. Overall, napping is an important factor to consider in order to better understand the relationship between short sleep and cardiovascular health in adolescents. PMID:27253429

Is daytime napping associated with inflammation in adolescents?

PubMed

Jakubowski, Karen P; Hall, Martica H; Marsland, Anna L; Matthews, Karen A

2016-12-01

Daytime napping has been associated with poor health outcomes in adults. It is not known whether daytime napping is similarly linked to adverse health in adolescents, although many report napping. The present study evaluated associations between daytime napping and 2 markers of increased inflammation, high-sensitivity C-reactive protein and interleukin-6 (IL-6), in healthy high school students. Two hundred thirty-four Black and White high school students completed a week of actigraph and diary measures of sleep and napping and provided a fasting blood sample. Napping measures were the proportion of days napped and the average minutes napped across 1 week during the school year. Linear regressions adjusted for age, sex, race, average nocturnal sleep duration, time between sleep protocol and blood draw, and body mass index percentile demonstrated that proportion of days napped measured by actigraphy, B(SE) = .41(.19), p < .05, across the full week was positively associated with IL-6. Higher proportions of school days napped between 2 p.m. and 6 p.m., B(SE) = .40(.20), p < .05, and between 6 p.m. and 10 p.m., B(SE) = .57(.28), p < .05, were associated with increased IL-6. No associations emerged between average actigraphy-assessed nap duration and either study outcome. Diary-reported napping was unrelated to either study outcome. Actigraphy-assessed napping and IL-6 are associated but the direction of the relationship remains to be determined. Overall, napping is an important factor to consider to better understand the relationship between short sleep and cardiovascular health in adolescents. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Multiconstrained gene clustering based on generalized projections

PubMed Central

2010-01-01

Background Gene clustering for annotating gene functions is one of the fundamental issues in bioinformatics. The best clustering solution is often regularized by multiple constraints such as gene expressions, Gene Ontology (GO) annotations and gene network structures. How to integrate multiple pieces of constraints for an optimal clustering solution still remains an unsolved problem. Results We propose a novel multiconstrained gene clustering (MGC) method within the generalized projection onto convex sets (POCS) framework used widely in image reconstruction. Each constraint is formulated as a corresponding set. The generalized projector iteratively projects the clustering solution onto these sets in order to find a consistent solution included in the intersection set that satisfies all constraints. Compared with previous MGC methods, POCS can integrate multiple constraints from different nature without distorting the original constraints. To evaluate the clustering solution, we also propose a new performance measure referred to as Gene Log Likelihood (GLL) that considers genes having more than one function and hence in more than one cluster. Comparative experimental results show that our POCS-based gene clustering method outperforms current state-of-the-art MGC methods. Conclusions The POCS-based MGC method can successfully combine multiple constraints from different nature for gene clustering. Also, the proposed GLL is an effective performance measure for the soft clustering solutions. PMID:20356386

To nap or not to nap: excessive daytime napping is associated with elevated evening cortisol in nursing home residents with dementia.

PubMed

Woods, Diana Lynn; Kim, Haesook; Yefimova, Maria

2013-04-01

Alterations in the sleep-wake cycle, including daytime napping, are consistently reported in persons with dementia (PWD). A dysregulation in the hypothalamic-pituitary-adrenal (HPA) axis, indexed by elevated evening cortisol, may offer one explanation for these alterations. Alternatively, excessive daytime sleeping may alter cortisol rhythm and increase intraindividual variability, potentially contributing to increased environmental reactivity and behavioral symptoms. The purpose of this substudy (N = 12) was to examine the association between daytime napping and basal cortisol diurnal rhythm in nursing home residents with dementia. In this within-individual longitudinal design, saliva samples were obtained daily for 5 consecutive days upon waking and 30-45 min, 6 hr, and 12 hr after waking to obtain a cortisol diurnal rhythm. Behavior and sleep-wake state (nap/no nap) were observed and recorded every 20 min for 12 hr per day for 5 days. Participants were categorized as high nappers (HNs) or low nappers (LNs). There was a significant difference in evening cortisol levels (t = -2.38, p = .032) and continence (t = 3.37, p = .007) between groups, with HNs exhibiting higher evening cortisol levels. There were no other significant differences in resident characteristics between the two groups. These data suggest a link between excessive daytime napping and elevated evening cortisol in PWD consistent with findings in children. Elevated evening cortisol is an indication of a dysregulation in the HPA axis. These preliminary data support a close association between the sleep-wake cycle and HPA-axis regulation in PWD.

Characteristics of napping in community-dwelling insomnia patients.

PubMed

Jang, Kwang Ho; Lee, Jung Hie; Kim, Seong Jae; Kwon, Hyo Jeong

2018-05-01

We aimed to determine napping characteristics of community-dwelling patients with insomnia disorder (ID) compared to characteristics of normal controls (NC), and to examine the effect of napping on nocturnal sleep. Adult volunteers who were more than 18 years old were recruited from three rural public health centers in Korea. Data from actigraphy recording and a sleep diary filled out for seven days were obtained. Finally, 115 ID patients and 80 NC subjects were included in this study. Parameters and timing of nocturnal sleep and nap were compared between the ID and NC groups. Two-way analysis of covariance (ANCOVA) was performed to determine the effect of ID diagnosis and napping on sleep parameters. Sleep efficiency (SE) in the ID group was significantly lower (p = 0.010), and wake time after sleep onset (WASO) was significantly greater (p = 0.023), compared to the NC group. There was no significant difference in nocturnal sleep or nap timing between the two groups. Nap frequency in the ID group was significantly higher than that in the NC group (p = 0.025). Although ID diagnosis and napping had no independent effect on fragmentation index, their interaction had a significant effect on fragmentation index (p = 0.021). Nap frequency was positively correlated with PSQI score (r = 0.166, p = 0.033). Insomnia patients showed no significant difference in nap timing or nap duration compared to NC subjects. However, insomnia patients showed higher nap frequency. Frequent napping was associated with poorer subjective sleep quality. Therefore, although napping might not have a negative impact on nocturnal sleep maintenance in NC subjects, it did have an effect on nocturnal sleep in insomnia patients. Copyright © 2018 Elsevier B.V. All rights reserved.

Finding approximate gene clusters with Gecko 3.

PubMed

Winter, Sascha; Jahn, Katharina; Wehner, Stefanie; Kuchenbecker, Leon; Marz, Manja; Stoye, Jens; Böcker, Sebastian

2016-11-16

Gene-order-based comparison of multiple genomes provides signals for functional analysis of genes and the evolutionary process of genome organization. Gene clusters are regions of co-localized genes on genomes of different species. The rapid increase in sequenced genomes necessitates bioinformatics tools for finding gene clusters in hundreds of genomes. Existing tools are often restricted to few (in many cases, only two) genomes, and often make restrictive assumptions such as short perfect conservation, conserved gene order or monophyletic gene clusters. We present Gecko 3, an open-source software for finding gene clusters in hundreds of bacterial genomes, that comes with an easy-to-use graphical user interface. The underlying gene cluster model is intuitive, can cope with low degrees of conservation as well as misannotations and is complemented by a sound statistical evaluation. To evaluate the biological benefit of Gecko 3 and to exemplify our method, we search for gene clusters in a dataset of 678 bacterial genomes using Synechocystis sp. PCC 6803 as a reference. We confirm detected gene clusters reviewing the literature and comparing them to a database of operons; we detect two novel clusters, which were confirmed by publicly available experimental RNA-Seq data. The computational analysis is carried out on a laptop computer in <40 min. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

The effects of napping on cognitive function in preschoolers.

PubMed

Lam, Janet C; Mahone, E Mark; Mason, Thornton; Scharf, Steven M

2011-01-01

To determine the relationship between napping and cognitive function in preschool-aged children. Daytime napping, nighttime sleep, and cognitive function were assessed in 59 typically developing children aged 3 to 5 years, who were enrolled in full-time childcare. Participants wore an actigraphy watch for 7 days to measure sleep and napping patterns and completed neuropsychological testing emphasizing attention, response control, and vocabulary. Parents of participants completed behavior ratings and sleep logs during the study. Sleep/wake cycles were scored with the Sadeh algorithm. Children who napped more on weekdays were also more likely to nap during weekends. Weekday napping and nighttime sleep were inversely correlated, such that those who napped more slept less at night, although total weekday sleep remained relatively constant. Weekday napping was significantly (negatively) correlated with vocabulary and auditory attention span, and weekday nighttime sleep was positively correlated with vocabulary. Nighttime sleep was also significantly negatively correlated with performance, such that those who slept less at night made more impulsive errors on a computerized go/no-go test. Daytime napping is actually negatively correlated with neurocognitive function in preschoolers. Nighttime sleep seems to be more critical for development of cognitive performance. Cessation of napping may serve as a developmental milestone of brain maturation. Children who nap less do not appear to be sleep deprived, especially if they compensate with increased nighttime sleep. An alternative explanation is that children who sleep less at night are sleep deprived and require a nap. A randomized trial of nap restriction would be the next step in understanding the relationship between napping and neurocognitive performance.

The Effects of Napping on Cognitive Function in Preschoolers

PubMed Central

Lam, Janet C.; Mahone, E. Mark; Mason, Thornton B.A.; Scharf, Steven M.

2011-01-01

Objective To determine the relationship between napping and cognitive function in preschool-aged children. Methods Daytime napping, nighttime sleep and cognitive function were assessed in fifty-nine typically developing children ages 3-5 years, who were enrolled in full-time childcare. Participants wore an actigraphy watch for 7 days to measure sleep and napping patterns, and completed neuropsychological testing emphasizing attention, response control, and vocabulary. Parents of participants completed behavior ratings and sleep logs during the study. Sleep/wake cycles were scored with the Sadeh algorithm. Results Children who napped more on weekdays were also more likely to nap during weekends. Weekday napping and nighttime sleep were inversely correlated, such that those who napped more slept less at night, while total weekday sleep remained relatively constant. Weekday napping was significantly (negatively) correlated with vocabulary and auditory attention span, and weekday nighttime sleep was positively correlated with vocabulary. Nighttime sleep was also significantly negatively correlated with performance, such that those who slept less at night made more impulsive errors on a computerized go/no-go test. Conclusions Daytime napping is actually negatively correlated with neurocognitive function in preschoolers. Nighttime sleep appears to be more critical for development of cognitive performance. Cessation of napping may serve as a developmental milestone of brain maturation. Children who nap less do not appear to be sleep deprived, especially if they compensate with increased nighttime sleep. An alternative explanation is that children who sleep less at night are sleep deprived and require a nap. A randomized trial of nap restriction would be the next step in understanding the relationship between napping and neurocognitive performance. PMID:21217402

Daydreams and nap dreams: Content comparisons.

PubMed

Carr, Michelle; Nielsen, Tore

2015-11-01

Differences between nighttime REM and NREM dreams are well-established but only rarely are daytime REM and NREM nap dreams compared with each other or with daydreams. Fifty-one participants took daytime naps (with REM or NREM awakenings) and provided both waking daydream and nap dream reports. They also provided ratings of their bizarreness, sensory experience, and emotion intensity. Recall rates for REM (96%) and NREM (89%) naps were elevated compared to typical recall rates for nighttime dreams (80% and 43% respectively), suggesting an enhanced circadian influence. All attribute ratings were higher for REM than for NREM dreams, replicating findings for nighttime dreams. Compared with daydreams, NREM dreams had lower ratings for emotional intensity and sensory experience while REM dreams had higher ratings for bizarreness and sensory experience. Results support using daytime naps in dream research and suggest that there occurs selective enhancement and inhibition of specific dream attributes by REM, NREM and waking state mechanisms. Copyright © 2015 Elsevier Inc. All rights reserved.

The Periplasmic Nitrate Reductase Nap Is Required for Anaerobic Growth and Involved in Redox Control of Magnetite Biomineralization in Magnetospirillum gryphiswaldense

PubMed Central

Li, Yingjie; Katzmann, Emanuel; Borg, Sarah

2012-01-01

The magnetosomes of many magnetotactic bacteria consist of membrane-enveloped magnetite crystals, whose synthesis is favored by a low redox potential. However, the cellular redox processes governing the biomineralization of the mixed-valence iron oxide have remained unknown. Here, we show that in the alphaproteobacterium Magnetospirillum gryphiswaldense, magnetite biomineralization is linked to dissimilatory nitrate reduction. A complete denitrification pathway, including gene functions for nitrate (nap), nitrite (nir), nitric oxide (nor), and nitrous oxide reduction (nos), was identified. Transcriptional gusA fusions as reporters revealed that except for nap, the highest expression of the denitrification genes coincided with conditions permitting maximum magnetite synthesis. Whereas microaerobic denitrification overlapped with oxygen respiration, nitrate was the only electron acceptor supporting growth in the entire absence of oxygen, and only the deletion of nap genes, encoding a periplasmic nitrate reductase, and not deletion of nor or nos genes, abolished anaerobic growth and also delayed aerobic growth in both nitrate and ammonium media. While loss of nosZ or norCB had no or relatively weak effects on magnetosome synthesis, deletion of nap severely impaired magnetite biomineralization and resulted in fewer, smaller, and irregular crystals during denitrification and also microaerobic respiration, probably by disturbing the proper redox balance required for magnetite synthesis. In contrast to the case for the wild type, biomineralization in Δnap cells was independent of the oxidation state of carbon substrates. Altogether, our data demonstrate that in addition to its essential role in anaerobic respiration, the periplasmic nitrate reductase Nap has a further key function by participating in redox reactions required for magnetite biomineralization. PMID:22730130

Napping-Ultra Flash Profile as a Tool for Category Identification and Subsequent Model System Formulation of Caramel Corn Products.

PubMed

Mayhew, Emily; Schmidt, Shelly; Lee, Soo-Yeun

2016-07-01

In a novel approach to formulation, the flash descriptive profiling technique Napping-Ultra Flash Profile (Napping-UFP) was used to characterize a wide range of commercial caramel corn products. The objectives were to identify product categories, develop model systems based on product categories, and correlate analytical parameters with sensory terms generated through the Napping-UFP exercise. In one 2 h session, 12 panelists participated in 4 Napping-UFP exercises, describing and grouping, on a 43×56 cm paper sheet, 12 commercial caramel corn samples by degree of similarity, globally and in terms of aroma-by-mouth, texture, and taste. The coordinates of each sample's placement on the paper sheet and descriptive terms generated by the panelists were used to conduct Multiple Factor Analysis (MFA) and hierarchical clustering of the samples. Strong trends in the clustering of samples across the 4 Napping-UFP exercises resulted in the determination of 3 overarching types of commercial caramel corn: "small-scale dark" (typified by burnt, rich caramel corn), "large-scale light" (typified by light and buttery caramel corn), and "large-scale dark" (typified by sweet and molasses-like caramel corn). Representative samples that best exemplified the properties of each category were used as guides in the formulation of 3 model systems that represent the spread of commercial caramel corn products. Analytical testing of the commercial products, including aw measurement, moisture content determination, and thermal characterization via differential scanning calorimetry, were conducted and results related to sensory descriptors using Spearman's correlation. © 2016 Institute of Food Technologists®

Daytime napping associated with increased symptom severity in fibromyalgia syndrome.

PubMed

Theadom, Alice; Cropley, Mark; Kantermann, Thomas

2015-02-07

Previous qualitative research has revealed that people with fibromyalgia use daytime napping as a coping strategy for managing symptoms against clinical advice. Yet there is no evidence to suggest whether daytime napping is beneficial or detrimental for people with fibromyalgia. The purpose of this study was to explore how people use daytime naps and to determine the links between daytime napping and symptom severity in fibromyalgia syndrome. A community based sample of 1044 adults who had been diagnosed with fibromyalgia syndrome by a clinician completed an online questionnaire. Associations between napping behavior, sleep quality and fibromyalgia symptoms were explored using Spearman correlations, with possible predictors of napping behaviour entered into a logistic regression model. Differences between participants who napped on a daily basis and those who napped less regularly, as well as nap duration were explored. Daytime napping was significantly associated with increased pain, depression, anxiety, fatigue, memory difficulties and sleep problems. Sleep problems and fatigue explained the greatest amount of variance in napping behaviour, p < 0.010. Those who engaged in daytime naps for >30 minutes had higher memory difficulties (t = -3.45) and levels of depression (t = -2.50) than those who napped for shorter periods (<30 mins) (p < 0.010). Frequent use and longer duration of daytime napping was linked with greater symptom severity in people with fibromyalgia. Given the common use of daytime napping in people with fibromyalgia evidence based guidelines on the use of daytime napping in people with chronic pain are urgently needed.

Napping on the Night Shift: A Two-Hospital Implementation Project

PubMed Central

Brown, Jeanne Geiger; Sagherian, Knar; Zhu, Shijun; Wieroniey, Margaret; Blair, Lori; Warren, Joan; Hinds, Pamela; Szeles, Rose

2015-01-01

Some nurses who work the night shift experience high levels of sleepiness. Napping has been adopted as an effective countermeasure to sleepiness and fatigue in other safety-sensitive industries but has not had widespread acceptance in nursing. In this two-hospital implementation project, napping was offered to six nursing units where nurse executives had previously approved nap implementation for the night shift as a pilot project. Successful implementation occurred in only one of the six units with partial success in a second unit. Barriers primarily occurred at the point of seeking unit-based nursing leadership approval. On the successful unit, one hundred fifty three 30-minutes naps were taken during the 3-month pilot period. A Nap Experience Survey measured sleepiness prior to the nap, the nap duration and perceived sleep, sleep inertia after the nap, and the perceived helpfulness of the nap. A high level of sleepiness was present at the beginning of 44% of naps. For over half of naps, nurses reported sleeping slightly (43%) or deeply (14%). Sleep inertia was rare (very groggy or sluggish on arising, 1.3%). The average score of helpfulness of napping was high (7.3 on a 1–10 scale). Nurses who napped reported being less drowsy while driving home after their shift. These data suggest that when barriers to napping are overcome, napping on the nightshift is feasible and can reduce sleepiness and drowsy driving in nurses. PMID:27082421

Napping facilitates word learning in early lexical development.

PubMed

Horváth, Klára; Myers, Kyle; Foster, Russell; Plunkett, Kim

2015-10-01

Little is known about the role that night-time sleep and daytime naps play in early cognitive development. Our aim was to investigate how napping affects word learning in 16-month-olds. Thirty-four typically developing infants were assigned randomly to nap and wake groups. After teaching two novel object-word pairs to infants, we tested their initial performance with an intermodal preferential looking task in which infants are expected to increase their target looking time compared to a distracter after hearing its auditory label. A second test session followed after approximately a 2-h delay. The delay contained sleep for the nap group or no sleep for the wake group. Looking behaviour was measured with an automatic eye-tracker. Vocabulary size was assessed using the Oxford Communicative Development Inventory. A significant interaction between group and session was found in preferential looking towards the target picture. The performance of the nap group increased after the nap, whereas that of the wake group did not change. The gain in performance correlated positively with the expressive vocabulary size in the nap group. These results indicate that daytime napping helps consolidate word learning in infancy. © 2015 European Sleep Research Society.

Conversion events in gene clusters

PubMed Central

2011-01-01

Background Gene clusters containing multiple similar genomic regions in close proximity are of great interest for biomedical studies because of their associations with inherited diseases. However, such regions are difficult to analyze due to their structural complexity and their complicated evolutionary histories, reflecting a variety of large-scale mutational events. In particular, conversion events can mislead inferences about the relationships among these regions, as traced by traditional methods such as construction of phylogenetic trees or multi-species alignments. Results To correct the distorted information generated by such methods, we have developed an automated pipeline called CHAP (Cluster History Analysis Package) for detecting conversion events. We used this pipeline to analyze the conversion events that affected two well-studied gene clusters (α-globin and β-globin) and three gene clusters for which comparative sequence data were generated from seven primate species: CCL (chemokine ligand), IFN (interferon), and CYP2abf (part of cytochrome P450 family 2). CHAP is freely available at http://www.bx.psu.edu/miller_lab. Conclusions These studies reveal the value of characterizing conversion events in the context of studying gene clusters in complex genomes. PMID:21798034

Spotlight on daytime napping during early childhood.

PubMed

Horváth, Klára; Plunkett, Kim

2018-01-01

Daytime napping undergoes a remarkable change in early childhood, and research regarding its relationship to cognitive development has recently accelerated. In this review, we summarize our current understanding of this relationship focusing on children aged <5 years. First, we evaluate different studies on the basis of the experimental design used and the specific cognitive processes they investigate. Second, we analyze how the napping status of children may modulate the relationship between learning and napping. Third, the possible role of sleep spindles, ie, specific electroencephalographic components during sleep, in cognitive development is explored. We conclude that daytime napping is crucial in early memory development.

Napping in English preschool children and the association with parents' attitudes.

PubMed

Jones, Caroline Helen Dorothy; Ball, Helen Louise

2013-04-01

Age-independent variability in childrens' napping duration may be influenced by parental preference and attitudes and childrens' availability or lack of opportunity to nap. Our study examined English preschool childrens' napping duration, frequency and location, and the association of daily nap duration with parents' attitudes towards napping. Parents of three-year-old children in deprived and nondeprived areas of a town in North-East England were interviewed regarding their attitudes towards child napping and completed four-day and five night sleep diaries documenting their childrens' daytime and nighttime sleep. Of 84 children, half had at least one nap during the four-day study period (median [interquartile range] daily nap duration across all children was 1 [21] min; for nappers only was 21 [34] min). Naps tended to be infrequent and short and few (6%) occurred in a bedroom. Children whose parents allowed or encouraged napping had significantly longer daily nap duration (n=25, median [interquartile range] daily nap duration 21 [34] min) compared to those whose parents tried to prevent them from napping (n=29, 1 [21] min), and those whose parents reported that children did not want to nap (n=30, 0 [0] min) (U=23.21; p<.001). Positive parental attitude towards napping was associated with longer child nap duration. Napping appeared to be mainly sporadic and opportunistic and was negatively perceived and prevented by one-third of parents. The consequences of premature nap cessation are not known; given the importance of sufficient sleep in childhood, we should possibly consider enabling young children to nap more freely. Copyright © 2013 Elsevier B.V. All rights reserved.

Sleep spindles in midday naps enhance learning in preschool children

PubMed Central

Kurdziel, Laura; Duclos, Kasey; Spencer, Rebecca M. C.

2013-01-01

Despite the fact that midday naps are characteristic of early childhood, very little is understood about the structure and function of these sleep bouts. Given that sleep benefits memory in young adults, it is possible that naps serve a similar function for young children. However, children transition from biphasic to monophasic sleep patterns in early childhood, eliminating the nap from their daily sleep schedule. As such, naps may contain mostly light sleep stages and serve little function for learning and memory during this transitional age. Lacking scientific understanding of the function of naps in early childhood, policy makers may eliminate preschool classroom nap opportunities due to increasing curriculum demands. Here we show evidence that classroom naps support learning in preschool children by enhancing memories acquired earlier in the day compared with equivalent intervals spent awake. This nap benefit is greatest for children who nap habitually, regardless of age. Performance losses when nap-deprived are not recovered during subsequent overnight sleep. Physiological recordings of naps support a role of sleep spindles in memory performance. These results suggest that distributed sleep is critical in early learning; when short-term memory stores are limited, memory consolidation must take place frequently. PMID:24062429

Sleep spindles in midday naps enhance learning in preschool children.

PubMed

Kurdziel, Laura; Duclos, Kasey; Spencer, Rebecca M C

2013-10-22

Despite the fact that midday naps are characteristic of early childhood, very little is understood about the structure and function of these sleep bouts. Given that sleep benefits memory in young adults, it is possible that naps serve a similar function for young children. However, children transition from biphasic to monophasic sleep patterns in early childhood, eliminating the nap from their daily sleep schedule. As such, naps may contain mostly light sleep stages and serve little function for learning and memory during this transitional age. Lacking scientific understanding of the function of naps in early childhood, policy makers may eliminate preschool classroom nap opportunities due to increasing curriculum demands. Here we show evidence that classroom naps support learning in preschool children by enhancing memories acquired earlier in the day compared with equivalent intervals spent awake. This nap benefit is greatest for children who nap habitually, regardless of age. Performance losses when nap-deprived are not recovered during subsequent overnight sleep. Physiological recordings of naps support a role of sleep spindles in memory performance. These results suggest that distributed sleep is critical in early learning; when short-term memory stores are limited, memory consolidation must take place frequently.

Alertness management in flight operations - Strategic napping

NASA Technical Reports Server (NTRS)

Rosekind, Mark R.; Gander, Philippa H.; Dinges, David F.

1991-01-01

Strategic napping in two different flight operation environments is considered to illustrate its application as a fatigue countermeasure. Data obtained from commercial short-haul and long-haul operations demonstrated the utility and current practices of strategic napping. A preplanned cockpit nap acted as an acute 'safety valve' for the sleep loss, circadian disruption, and fatigue that occurs in long-haul flying.

Association between Nighttime Sleep and Napping in Older Adults

PubMed Central

Goldman, Suzanne E.; Hall, Martica; Boudreau, Robert; Matthews, Karen A.; Cauley, Jane A.; Ancoli-Israel, Sonia; Stone, Katie L.; Rubin, Susan M.; Satterfield, Suzanne; Simonsick, Eleanor M.; Newman, Anne B.

2008-01-01

Study Objectives: Napping might indicate deficiencies in nighttime sleep, but the relationship is not well defined. We assessed the association of nighttime sleep duration and fragmentation with subsequent daytime sleep. Design: Cross-sectional study. Participants: 235 individuals (47.5% men, 29.7% black), age 80.1 (2.9) years. Measurements and Results: Nighttime and daytime sleep were measured with wrist actigraphy and sleep diaries for an average of 6.8 (SD 0.7) nights. Sleep parameters included total nighttime sleep (h), movement and fragmentation index (fragmentation), and total daytime sleep (h). The relationship of total nighttime sleep and fragmentation to napping (yes/no) was assessed using logistic regression. In individuals who napped, mixed random effects models were used to determine the association between the previous night sleep duration and fragmentation and nap duration, and nap duration and subsequent night sleep duration. All models were adjusted for age, race, gender, BMI, cognitive status, depression, cardiovascular disease, respiratory symptoms, diabetes, pain, fatigue, and sleep medication use. Naps were recorded in sleep diaries by 178 (75.7%) participants. The odds ratios (95% CI) for napping were higher for individuals with higher levels of nighttime fragmentation (2.1 [0.8, 5.7]), respiratory symptoms (2.4 [1.1, 5.4]), diabetes (6.1 [1.2, 30.7]), and pain (2.2 [1.0, 4.7]). Among nappers, neither sleep duration nor fragmentation the preceding night was associated with nap duration the next day. Conclusion: More sleep fragmentation was associated with higher odds of napping although not with nap duration. Further research is needed to determine the causal association between sleep fragmentation and daytime napping. Citation: Goldman SE; Hall M; Boudreau R; Matthews KA; Cauley JA; Ancoli-Israel S; Stone KL; Rubin SM; Satterfield S; Simonsick EM; Newman AB. Association between nighttime sleep and napping in older adults. SLEEP 2008

Spotlight on daytime napping during early childhood

PubMed Central

Horváth, Klára; Plunkett, Kim

2018-01-01

Daytime napping undergoes a remarkable change in early childhood, and research regarding its relationship to cognitive development has recently accelerated. In this review, we summarize our current understanding of this relationship focusing on children aged <5 years. First, we evaluate different studies on the basis of the experimental design used and the specific cognitive processes they investigate. Second, we analyze how the napping status of children may modulate the relationship between learning and napping. Third, the possible role of sleep spindles, ie, specific electroencephalographic components during sleep, in cognitive development is explored. We conclude that daytime napping is crucial in early memory development. PMID:29576733

Association between Daytime Napping and Chronic Diseases in China.

PubMed

Zhou, Junmin; Kessler, Asia Sikora; Su, Dejun

2016-03-01

To explore the relationship between daytime napping and incidence of chronic diseases over the past 6 months among adults in China. Based on data collected from 13,469 respondents over age 40 in the Chinese Family Panel Studies in 2010, logistic regression models were estimated to examine the association between daytime napping and the incidence of any chronic diseases and 3 specific chronic diseases (hypertension, diabetes, and heart disease) after adjusting for confounders. Differences of risks by sex and age were also investigated. In the sample, 50.8% were women and 32.2% were over 60 years old. Adjusted estimates show respondents with daytime napping had elevated odds of developing any chronic diseases, hypertension, and diabetes compared to those who did not nap; having over 60 minutes of daytime napping had weaker association compared with shorter duration of daytime napping. The association between daytime napping and hypertension was found in women but not in men. Daytime napping appears to be associated with elevated risk of incidence of any chronic diseases, hypertension, and diabetes.

Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus

PubMed Central

Cowley, Michael; Wood, Andrew J.; Böhm, Sabrina; Schulz, Reiner; Oakey, Rebecca J.

2012-01-01

Alternative polyadenylation increases transcriptome diversity by generating multiple transcript isoforms from a single gene. It is thought that this process can be subject to epigenetic regulation, but few specific examples of this have been reported. We previously showed that the Mcts2/H13 locus is subject to genomic imprinting and that alternative polyadenylation of H13 transcripts occurs in an allele-specific manner, regulated by epigenetic mechanisms. Here, we demonstrate that allele-specific polyadenylation occurs at another imprinted locus with similar features. Nap1l5 is a retrogene expressed from the paternally inherited allele, is situated within an intron of a ‘host’ gene Herc3, and overlaps a CpG island that is differentially methylated between the parental alleles. In mouse brain, internal Herc3 polyadenylation sites upstream of Nap1l5 are used on the paternally derived chromosome, from which Nap1l5 is expressed, whereas a downstream site is used more frequently on the maternally derived chromosome. Ablating DNA methylation on the maternal allele at the Nap1l5 promoter increases the use of an internal Herc3 polyadenylation site and alters exon splicing. These changes demonstrate the influence of epigenetic mechanisms in regulating Herc3 alternative mRNA processing. Internal Herc3 polyadenylation correlates with expression levels of Nap1l5, suggesting a possible role for transcriptional interference. Similar mechanisms may regulate alternative polyadenylation elsewhere in the genome. PMID:22790983

Napping in college students and its relationship with nighttime sleep.

PubMed

Ye, Lichuan; Hutton Johnson, Stacy; Keane, Kathleen; Manasia, Michael; Gregas, Matt

2015-01-01

Abstract. To examine the habit of napping and its relationship with nighttime sleep in college students. Four hundred and forty undergraduate students who responded to an anonymous online survey in April 2010. Three questions were asked to determine the frequency, length, and timing of napping during the past month. Sleep quality was measured by the Pittsburgh Sleep Quality Index (PSQI). The PSQI score significantly differed among self-reported nap-frequency (p=.047) and nap-length (p=.017) groups, with those who napped more than 3 times per week and those who napped more than 2 hours having the poorest sleep quality. Students who napped between 6 and 9 pm had shorter sleep on school nights compared with students in other nap-timing groups (p=.002). College students who are self-reported frequent, long, and late nappers may have a higher risk of poor nighttime sleep quality and more severe sleep deprivation.

Finding gene clusters for a replicated time course study

PubMed Central

2014-01-01

Background Finding genes that share similar expression patterns across samples is an important question that is frequently asked in high-throughput microarray studies. Traditional clustering algorithms such as K-means clustering and hierarchical clustering base gene clustering directly on the observed measurements and do not take into account the specific experimental design under which the microarray data were collected. A new model-based clustering method, the clustering of regression models method, takes into account the specific design of the microarray study and bases the clustering on how genes are related to sample covariates. It can find useful gene clusters for studies from complicated study designs such as replicated time course studies. Findings In this paper, we applied the clustering of regression models method to data from a time course study of yeast on two genotypes, wild type and YOX1 mutant, each with two technical replicates, and compared the clustering results with K-means clustering. We identified gene clusters that have similar expression patterns in wild type yeast, two of which were missed by K-means clustering. We further identified gene clusters whose expression patterns were changed in YOX1 mutant yeast compared to wild type yeast. Conclusions The clustering of regression models method can be a valuable tool for identifying genes that are coordinately transcribed by a common mechanism. PMID:24460656

Napping reduces emotional attention bias during early childhood.

PubMed

Cremone, Amanda; Kurdziel, Laura B F; Fraticelli-Torres, Ada; McDermott, Jennifer M; Spencer, Rebecca M C

2017-07-01

Sleep loss alters processing of emotional stimuli in preschool-aged children. However, the mechanism by which sleep modifies emotional processing in early childhood is unknown. We tested the hypothesis that a nap, compared to an equivalent time spent awake, reduces biases in attention allocation to affective information. Children (n = 43; M = 55.40 months, SD = 8.05 months) completed a Dot Probe task, which provides a measure of attention biases to emotional stimuli, following a mid-day nap and an equivalent interval spent awake. No emotional attention biases emerged when children napped. However, when nap-deprived, children exhibited biases towards negative and positive stimuli. This emotional bias after wake was greater in children who napped habitually. Gender differences also emerged such that females were more attentive to positive emotional stimuli whereas males showed heightened attention to negative emotional stimuli, regardless of having napped or not. Moreover, greater slow wave activity (SWA) during the nap was associated with faster responding, which suggests that SWA may promote efficiency of attention allocation. A video abstract of this article can be viewed at: https://www.youtube.com/watch?v=JIoZ8mzxQgg. © 2016 John Wiley & Sons Ltd.

Constrained clusters of gene expression profiles with pathological features.

PubMed

Sese, Jun; Kurokawa, Yukinori; Monden, Morito; Kato, Kikuya; Morishita, Shinichi

2004-11-22

Gene expression profiles should be useful in distinguishing variations in disease, since they reflect accurately the status of cells. The primary clustering of gene expression reveals the genotypes that are responsible for the proximity of members within each cluster, while further clustering elucidates the pathological features of the individual members of each cluster. However, since the first clustering process and the second classification step, in which the features are associated with clusters, are performed independently, the initial set of clusters may omit genes that are associated with pathologically meaningful features. Therefore, it is important to devise a way of identifying gene expression clusters that are associated with pathological features. We present the novel technique of 'itemset constrained clustering' (IC-Clustering), which computes the optimal cluster that maximizes the interclass variance of gene expression between groups, which are divided according to the restriction that only divisions that can be expressed using common features are allowed. This constraint automatically labels each cluster with a set of pathological features which characterize that cluster. When applied to liver cancer datasets, IC-Clustering revealed informative gene expression clusters, which could be annotated with various pathological features, such as 'tumor' and 'man', or 'except tumor' and 'normal liver function'. In contrast, the k-means method overlooked these clusters.

Effects of napping on neuromuscular fatigue in myasthenia gravis.

PubMed

Kassardjian, Charles D; Murray, Brian J; Kokokyi, Seint; Jewell, Dana; Barnett, Carolina; Bril, Vera; Katzberg, Hans D

2013-11-01

The relationship between sleep and neuromuscular fatigue is understood poorly. The goal of this study was to evaluate the effects of napping on quantitative measures of neuromuscular fatigue in patients with myasthenia gravis (MG). Eight patients with mild to moderate MG were recruited. Patients underwent maintenance of wakefulness tests (MWT) and multiple sleep latency tests (MSLT). The Quantitative Myasthenia Gravis Score (QMGS) was measured before nap and after each nap to examine the effects of napping and sleep on neuromuscular weakness. Results showed that QMGS improves only after naps where patients slept more than 5 min but not where patients did not sleep or slept less than 5 min. Daytime napping mitigates neuromuscular fatigue in patients with MG, especially if patients slept for more than 5 min. Copyright © 2013 Wiley Periodicals, Inc.

Napping Characteristics and Restricted Participation in Valued Activities Among Older Adults.

PubMed

Owusu, Jocelynn T; Ramsey, Christine M; Tzuang, Marian; Kaufmann, Christopher N; Parisi, Jeanine M; Spira, Adam P

2018-03-02

Napping is associated with both positive and negative health outcomes among older adults. However, the association between particular napping characteristics (eg, frequency, duration, and whether naps were intentional) and daytime function is unclear. Participants were 2,739 community-dwelling Medicare beneficiaries aged ≥65 years from the nationally representative National Health and Aging Trends Study. Participants reported napping frequency, duration, and whether naps were intentional versus unintentional. Restricted participation in valued activities was measured by self-report. After adjusting for potential confounders and nighttime sleep duration, those who took intentional and unintentional naps had a greater odds of any valued activity restriction (ie, ≥1 valued activity restriction), compared to those who rarely/never napped (unintentional odds ratio [OR] = 1.34, 95% confidence interval [CI] 1.01, 1.79, intentional OR = 1.49, 95% CI 1.09, 2.04). There was no difference between unintentional napping and intentional napping with respect to any valued activity restriction after adjustment for demographics. Compared to participants napping "some days," those napping most days/every day had a greater odds of any valued activity restriction (OR = 1.68, 95% CI 1.30, 2.16). Moreover, each 30-minute increase in average nap duration was associated with a 25% greater odds of any valued activity restriction (OR = 1.25, 95% CI 1.10, 1.43). Older adults who took more frequent or longer naps were more likely to report activity restrictions, as were those who took intentional or unintentional naps. Additional longitudinal studies with objective measures of sleep are needed to further our understanding of associations between napping characteristics and daytime dysfunction. © The Author 2017. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Genomic analyses of bacterial porin-cytochrome gene clusters

DOE PAGES

Shi, Liang; Fredrickson, James K.; Zachara, John M.

2014-11-26

In this study, the porin-cytochrome (Pcc) protein complex is responsible for trans-outer membrane electron transfer during extracellular reduction of Fe(III) by the dissimilatory metal-reducing bacterium Geobacter sulfurreducens PCA. The identified and characterized Pcc complex of G. sulfurreducens PCA consists of a porin-like outer-membrane protein, a periplasmic 8-heme c type cytochrome (c-Cyt) and an outer-membrane 12-heme c-Cyt, and the genes encoding the Pcc proteins are clustered in the same regions of genome (i.e., the pcc gene clusters) of G. sulfurreducens PCA. A survey of additionally microbial genomes has identified the pcc gene clusters in all sequenced Geobacter spp. and other bacteriamore » from six different phyla, including Anaeromyxobacter dehalogenans 2CP-1, A. dehalogenans 2CP-C, Anaeromyxobacter sp. K, Candidatus Kuenenia stuttgartiensis, Denitrovibrio acetiphilus DSM 12809, Desulfurispirillum indicum S5, Desulfurivibrio alkaliphilus AHT2, Desulfurobacterium thermolithotrophum DSM 11699, Desulfuromonas acetoxidans DSM 684, Ignavibacterium album JCM 16511, and Thermovibrio ammonificans HB-1. The numbers of genes in the pcc gene clusters vary, ranging from two to nine. Similar to the metal-reducing (Mtr) gene clusters of other Fe(III)-reducing bacteria, such as Shewanella spp., additional genes that encode putative c-Cyts with predicted cellular localizations at the cytoplasmic membrane, periplasm and outer membrane often associate with the pcc gene clusters. This suggests that the Pcc-associated c-Cyts may be part of the pathways for extracellular electron transfer reactions. The presence of pcc gene clusters in the microorganisms that do not reduce solid-phase Fe(III) and Mn(IV) oxides, such as D. alkaliphilus AHT2 and I. album JCM 16511, also suggests that some of the pcc gene clusters may be involved in extracellular electron transfer reactions with the substrates other than Fe(III) and Mn(IV) oxides.« less

NAP enzyme recruitment in simultaneous bioremediation and nanoparticles synthesis.

PubMed

Eltarahony, Marwa; Zaki, Sahar; Kheiralla, Zeinab; Abd-El-Haleem, Desouky

2018-06-01

The periplasmic nitrate reductase enzyme (NAP) has become attractive catalyst, whose exploitation has emerged as one of the indispensable strategies toward environmentally benign applications. To achieve them efficiently and overcome the sensitivity of NAP in harsh environmental circumstances, the immobilization for denitrifying bacteria and NAP enzyme for simultaneous bioremediation and bionanoparticles synthesis was studied. NAP catalyzed NO 3 - reduction at V max of 0.811 μM/min and K m of 14.02 mM. Concurrently, the immobilized MMT cells completely removed NO 3 - upon 192 h with AgNPs synthesis ranging from 23.26 to 58.14 nm as indicated by SEM. Wherase, immobilized NAP exhibited lower efficiency with 28.6% of NO 3 - elimination within 288 h and large aggregated AgNPs ranging from 94.44 nm to 172.22 nm. To the best of author knowledge, the immobilization for denitrifying bacteria and NAP enzyme for simultaneous bioremediation and bionanoparticles synthesis was not studied before.

Cockpit napping

NASA Technical Reports Server (NTRS)

Graeber, R. Curtis; Rosekind, Mark R.; Connell, Linda J.; Dinges, David F.

1990-01-01

The results of a NASA-sponsored study examining the effectiveness of a brief, preplanned cockpit rest period to improve pilot alertness and performance in nonaugmented long-haul flight operations are discussed. Four regularly scheduled trans-Pacific flight legs were studied. The shortest flight legs were about 7 h and the longest about 9.5 h, with duty periods averaging about 11 h and layovers about 25 h. Three-person B747 crews were divided randomly into two volunteer pilot groups. These crews were nonaugmented, and therefore no relief pilots were available. The rest group, consisting of four crews, was allowed a 40 min opportunity to rest during the overwater cruise portion of the flight. On a preplanned, rotating basis, individual crew members were allowed to nap. It is concluded that a preplanned cockpit nap is associated with significantly better behavioral performance and higher levels of physiological alertness and that this can be accomplished without disrupting normal flight operations or compromising safety.

Temporal Relationships Between Napping and Nocturnal Sleep in Healthy Adolescents.

PubMed

Jakubowski, Karen P; Hall, Martica H; Lee, Laisze; Matthews, Karen A

2017-01-01

Many adolescents do not achieve the recommended 9 hr of sleep per night and report daytime napping, perhaps because it makes up for short nocturnal sleep. This article tests temporal relationships between daytime naps and nighttime sleep as measured by actigraphy and diary among 236 healthy high school students during one school week. Mixed model analyses adjusted for age, race, and gender demonstrated that shorter actigraphy-assessed nocturnal sleep duration predicted longer napping (measured by actigraphy and diary) the next day. Napping (by actigraphy and diary) predicted shorter nocturnal sleep duration and worse sleep efficiency that night measured by actigraphy. Diary-reported napping also predicted poorer self-reported sleep quality that night. Frequent napping may interfere with nocturnal sleep during adolescence.

C-NAP1 and rootletin restrain DNA damage-induced centriole splitting and facilitate ciliogenesis.

PubMed

Conroy, Pauline C; Saladino, Chiara; Dantas, Tiago J; Lalor, Pierce; Dockery, Peter; Morrison, Ciaran G

2012-10-15

Cilia are found on most human cells and exist as motile cilia or non-motile primary cilia. Primary cilia play sensory roles in transducing various extracellular signals, and defective ciliary functions are involved in a wide range of human diseases. Centrosomes are the principal microtubule-organizing centers of animal cells and contain two centrioles. We observed that DNA damage causes centriole splitting in non-transformed human cells, with isolated centrioles carrying the mother centriole markers CEP170 and ninein but not kizuna or cenexin. Loss of centriole cohesion through siRNA depletion of C-NAP1 or rootletin increased radiation-induced centriole splitting, with C-NAP1-depleted isolated centrioles losing mother markers. As the mother centriole forms the basal body in primary cilia, we tested whether centriole splitting affected ciliogenesis. While irradiated cells formed apparently normal primary cilia, most cilia arose from centriolar clusters, not from isolated centrioles. Furthermore, C-NAP1 or rootletin knockdown reduced primary cilium formation. Therefore, the centriole cohesion apparatus at the proximal end of centrioles may provide a target that can affect primary cilium formation as part of the DNA damage response.

Prokaryotic Gene Clusters: A Rich Toolbox for Synthetic Biology

PubMed Central

Fischbach, Michael; Voigt, Christopher A.

2014-01-01

Bacteria construct elaborate nanostructures, obtain nutrients and energy from diverse sources, synthesize complex molecules, and implement signal processing to react to their environment. These complex phenotypes require the coordinated action of multiple genes, which are often encoded in a contiguous region of the genome, referred to as a gene cluster. Gene clusters sometimes contain all of the genes necessary and sufficient for a particular function. As an evolutionary mechanism, gene clusters facilitate the horizontal transfer of the complete function between species. Here, we review recent work on a number of clusters whose functions are relevant to biotechnology. Engineering these clusters has been hindered by their regulatory complexity, the need to balance the expression of many genes, and a lack of tools to design and manipulate DNA at this scale. Advances in synthetic biology will enable the large-scale bottom-up engineering of the clusters to optimize their functions, wake up cryptic clusters, or to transfer them between organisms. Understanding and manipulating gene clusters will move towards an era of genome engineering, where multiple functions can be “mixed-and-matched” to create a designer organism. PMID:21154668

Do night naps impact driving performance and daytime recovery sleep?

PubMed

Centofanti, Stephanie A; Dorrian, Jillian; Hilditch, Cassie J; Banks, Siobhan

2017-02-01

Short, nighttime naps are used as a fatigue countermeasure in night shift work, and may offer protective benefits on the morning commute. However, there is a concern that nighttime napping may impact upon the quality of daytime sleep. The aim of the current project was to investigate the influence of short nighttime naps (<30min) on simulated driving performance and subsequent daytime recovery sleep. Thirty-one healthy subjects (aged 21-35 y; 18 females) participated in a 3-day laboratory study. After a 9-h baseline sleep opportunity (22:00h-07:00h), subjects were kept awake the following night with random assignment to: a 10-min nap ending at 04:00h plus a 10-min nap at 07:00h; a 30-min nap ending at 04:00h; or a no-nap control. A 40-min driving simulator task was administered at 07:00h and 18:30h post-recovery sleep. All conditions had a 6-h daytime recovery sleep opportunity (10:00h-16:00h) the next day. All sleep periods were recorded polysomnographically. Compared to control, the napping conditions did not significantly impact upon simulated driving lane variability, percentage of time in a safe zone, or time to first crash on morning or evening drives (p>0.05). Short nighttime naps did not significantly affect daytime recovery total sleep time (p>0.05). Slow wave sleep (SWS) obtained during the 30-min nighttime nap resulted in a significant reduction in SWS during subsequent daytime recovery sleep (p<0.05), such that the total amount of SWS in 24-h was preserved. Therefore, short naps did not protect against performance decrements during a simulated morning commute, but they also did not adversely affect daytime recovery sleep following a night shift. Further investigation is needed to examine the optimal timing, length or combination of naps for reducing performance decrements on the morning commute, whilst still preserving daytime sleep quality. Copyright © 2015 Elsevier Ltd. All rights reserved.

Gene Cluster Encoding Cholate Catabolism in Rhodococcus spp.

PubMed Central

Wilbrink, Maarten H.; Casabon, Israël; Stewart, Gordon R.; Liu, Jie; van der Geize, Robert; Eltis, Lindsay D.

2012-01-01

Bile acids are highly abundant steroids with important functions in vertebrate digestion. Their catabolism by bacteria is an important component of the carbon cycle, contributes to gut ecology, and has potential commercial applications. We found that Rhodococcus jostii RHA1 grows well on cholate, as well as on its conjugates, taurocholate and glycocholate. The transcriptome of RHA1 growing on cholate revealed 39 genes upregulated on cholate, occurring in a single gene cluster. Reverse transcriptase quantitative PCR confirmed that selected genes in the cluster were upregulated 10-fold on cholate versus on cholesterol. One of these genes, kshA3, encoding a putative 3-ketosteroid-9α-hydroxylase, was deleted and found essential for growth on cholate. Two coenzyme A (CoA) synthetases encoded in the cluster, CasG and CasI, were heterologously expressed. CasG was shown to transform cholate to cholyl-CoA, thus initiating side chain degradation. CasI was shown to form CoA derivatives of steroids with isopropanoyl side chains, likely occurring as degradation intermediates. Orthologous gene clusters were identified in all available Rhodococcus genomes, as well as that of Thermomonospora curvata. Moreover, Rhodococcus equi 103S, Rhodococcus ruber Chol-4 and Rhodococcus erythropolis SQ1 each grew on cholate. In contrast, several mycolic acid bacteria lacking the gene cluster were unable to grow on cholate. Our results demonstrate that the above-mentioned gene cluster encodes cholate catabolism and is distinct from a more widely occurring gene cluster encoding cholesterol catabolism. PMID:23024343

A review of short naps and sleep inertia: do naps of 30 min or less really avoid sleep inertia and slow-wave sleep?

PubMed

Hilditch, Cassie J; Dorrian, Jillian; Banks, Siobhan

2017-04-01

Napping is a widely used countermeasure to sleepiness and impaired performance caused by sleep loss and circadian pressure. Sleep inertia, the period of grogginess and impaired performance experienced after waking, is a potential side effect of napping. Many industry publications recommend naps of 30 min or less to avoid this side effect. However, the evidence to support this advice is yet to be thoroughly reviewed. Electronic databases were searched, and defined criteria were applied to select articles for review. The review covers literature on naps of 30 min or less regarding (a) sleep inertia, (b) slow-wave sleep (SWS) and (c) the relationship between sleep inertia and SWS. The review found that although the literature on short afternoon naps is relatively comprehensive, there are very few studies on naps of 30 min or less at night. Studies have mixed results regarding the onset of SWS and the duration and severity of sleep inertia following short naps, making guidelines regarding their use unclear. The varying results are likely due to differing sleep/wake profiles before the nap of interest and the time of the day at waking. The review highlights the need to have more detailed guidelines about the implementation of short naps according to the time of the day and prior sleep/wake history. Without this context, such a recommendation is potentially misleading. Further research is required to better understand the interactions between these factors, especially at night, and to provide more specific recommendations. Copyright © 2017 Elsevier B.V. All rights reserved.

Microtubules (tau) as an emerging therapeutic target: NAP (davunetide).

PubMed

Gozes, Illana

2011-01-01

This review focuses on the discovery of activity-dependent neuroprotective protein (ADNP) and the ensuing discovery of NAP (davunetide) toward clinical development with emphasis on microtubule protection. ADNP immunoreactivity was shown to occasionally decorate microtubules and ADNP silencing inhibited neurite outgrowth as measured by microtubule associated protein 2 (MAP2) labeling. ADNP knockout is lethal, while 50% reduction in ADNP (ADNP haploinsufficiency) resulted in the microtubule associated protein tau pathology coupled to cognitive dysfunction and neurodegeneration. NAP (davunetide), an eight amino acid peptide derived from ADNP partly ameliorated deficits associated with ADNP deficiency. NAP (davunetide) interacted with microtubules, protected against microtubule toxicity associated with zinc, nocodazole and oxidative stress in vitro and against tau pathology and MAP6 (stable tubuleonly polypeptide - STOP) pathology in vivo. NAP (davunetide) provided neurotrophic functions promoting neurite outgrowth as measured by increases in MAP2 immunoreactivity and synapse formation by increasing synaptophysin expression. NAP (davunetide) protection against neurodegeneration has recently been shown to extend to katanin-related microtubule disruption under conditions of tau deficiencies. In conclusion, NAP (davunetide) provided potent neuroprotection in a broad range of neurodegenerative models, protecting the neuroglial cytoskeleton in vitro and inhibiting tau pathology (tauopathy) in vivo. Based on these extensive preclinical results, davunetide (NAP) is now being evaluated in a Phase II/III study of the tauopathy, progressive supranuclear palsy (PSP); (Allon Therapeutics Inc.).

Clustering Algorithms: Their Application to Gene Expression Data

PubMed Central

Oyelade, Jelili; Isewon, Itunuoluwa; Oladipupo, Funke; Aromolaran, Olufemi; Uwoghiren, Efosa; Ameh, Faridah; Achas, Moses; Adebiyi, Ezekiel

2016-01-01

Gene expression data hide vital information required to understand the biological process that takes place in a particular organism in relation to its environment. Deciphering the hidden patterns in gene expression data proffers a prodigious preference to strengthen the understanding of functional genomics. The complexity of biological networks and the volume of genes present increase the challenges of comprehending and interpretation of the resulting mass of data, which consists of millions of measurements; these data also inhibit vagueness, imprecision, and noise. Therefore, the use of clustering techniques is a first step toward addressing these challenges, which is essential in the data mining process to reveal natural structures and identify interesting patterns in the underlying data. The clustering of gene expression data has been proven to be useful in making known the natural structure inherent in gene expression data, understanding gene functions, cellular processes, and subtypes of cells, mining useful information from noisy data, and understanding gene regulation. The other benefit of clustering gene expression data is the identification of homology, which is very important in vaccine design. This review examines the various clustering algorithms applicable to the gene expression data in order to discover and provide useful knowledge of the appropriate clustering technique that will guarantee stability and high degree of accuracy in its analysis procedure. PMID:27932867

CORM: An R Package Implementing the Clustering of Regression Models Method for Gene Clustering

PubMed Central

Shi, Jiejun; Qin, Li-Xuan

2014-01-01

We report a new R package implementing the clustering of regression models (CORM) method for clustering genes using gene expression data and provide data examples illustrating each clustering function in the package. The CORM package is freely available at CRAN from http://cran.r-project.org. PMID:25452684

CE: Original Research: Napping on the Night Shift: A Two-Hospital Implementation Project.

PubMed

Geiger-Brown, Jeanne; Sagherian, Knar; Zhu, Shijun; Wieroniey, Margaret Ann; Blair, Lori; Warren, Joan; Hinds, Pamela S; Szeles, Rose

2016-05-01

: Nurses who work the night shift often experience high levels of sleepiness. Napping has been adopted as an effective countermeasure to sleepiness and fatigue in other safety-sensitive industries, but has not had widespread acceptance in nursing. To assess the barriers to successful implementation of night-shift naps and to describe the nap experiences of night-shift nurses who took naps. In this two-hospital pilot implementation project, napping on the night shift was offered to six nursing units for which the executive nursing leadership had given approval. Unit nurse managers' approval was sought, and where granted, further explanation was given to the unit's staff nurses. A nap experience form, which included the Karolinska Sleepiness Scale, was used to assess pre-nap sleepiness level, nap duration and perceived sleep experience, post-nap sleep inertia, and the perceived helpfulness of the nap. Nurse managers and staff nurses were also interviewed at the end of the three-month study period. Successful implementation occurred on only one of the six units, with partial success seen on a second unit. Barriers primarily occurred at the point of seeking the unit nurse managers' approval. On the successful unit, 153 30-minutes naps were taken during the study period. A high level of sleepiness was present at the beginning of 44% of the naps. For more than half the naps, nurses reported achieving either light (43%) or deep (14%) sleep. Sleep inertia was rare. The average score of helpfulness of napping was high (7.3 on a 1-to-10 scale). Nurses who napped reported being less drowsy while driving home after their shift. These data suggest that when barriers to napping are overcome, napping on the night shift is feasible and can reduce nurses' workplace sleepiness and drowsy driving on the way home. Addressing nurse managers' perceptions of and concerns about napping may be essential to successful implementation.

A 30-Minute, but Not a 10-Minute Nighttime Nap is Associated with Sleep Inertia.

PubMed

Hilditch, Cassie J; Centofanti, Stephanie A; Dorrian, Jillian; Banks, Siobhan

2016-03-01

To assess sleep inertia following 10-min and 30-min naps during a simulated night shift. Thirty-one healthy adults (aged 21-35 y; 18 females) participated in a 3-day laboratory study that included one baseline (BL) sleep (22:00-07:00) and one experimental night involving randomization to either: total sleep deprivation (NO-NAP), a 10-min nap (10-NAP) or a 30-min nap (30-NAP). Nap opportunities ended at 04:00. A 3-min psychomotor vigilance task (PVT-B), digit-symbol substitution task (DSST), fatigue scale, sleepiness scale, and self-rated performance scale were undertaken pre-nap (03:00) and at 2, 17, 32, and 47 min post-nap. The 30-NAP (14.7 ± 5.7 min) had more slow wave sleep than the 10-NAP (0.8 ± 1.5 min; P < 0.001) condition. In the NO-NAP condition, PVT-B performance was worse than pre-nap (4.6 ± 0.3 1/sec) at 47 min post-nap (4.1 ± 0.4 1/sec; P < 0.001). There was no change across time in the 10-NAP condition. In the 30-NAP condition, performance immediately deteriorated from pre-nap (4.3 ± 0.3 1/sec) and was still worse at 47 min post-nap (4.0 ± 0.5 1/sec; P < 0.015). DSST performance deteriorated in the NO-NAP (worse than pre-nap from 17 to 47 min; P < 0.008), did not change in the 10-NAP, and was impaired 2 min post-nap in the 30-NAP condition (P = 0.028). All conditions self-rated performance as better than pre-nap for all post-nap test points (P < 0.001). This study is the first to show that a 10-min (but not a 30-min) nighttime nap had minimal sleep inertia and helped to mitigate short-term performance impairment during a simulated night shift. Self-rated performance did not reflect objective performance following a nap. © 2016 Associated Professional Sleep Societies, LLC.

Napping and Nighttime Sleep: Findings From an Occupation-Based Intervention

PubMed Central

Fogelberg, Donald; Sleight, Alix; Mallinson, Trudy; Vigen, Cheryl; Blanchard, Jeanine; Carlson, Mike; Clark, Florence

2016-01-01

OBJECTIVE. To describe sleeping behaviors and trends over time among an ethnically diverse group of community-living older adults. METHOD. A descriptive secondary data analysis of a subsample (n = 217) from the Lifestyle Redesign randomized controlled trial was done to explore baseline napping and sleeping patterns as well as 6-mo changes in these outcomes. RESULTS. At baseline, the average time sleeping was 8.2 hr daily (standard deviation = 1.7). Among all participants, 29% reported daytime napping at baseline, of which 36% no longer napped at follow-up. Among participants who stopped napping, those who received an occupation-based intervention (n = 98) replaced napping time with nighttime sleep, and those not receiving an intervention (n = 119) experienced a net loss of total sleep (p < .05). CONCLUSION. Among participants who stopped napping, the occupation-based intervention may be related to enhanced sleep. More research examining the role of occupation-based interventions in improving sleep is warranted. PMID:27294991

Napping and Nighttime Sleep: Findings From an Occupation-Based Intervention.

PubMed

Leland, Natalie E; Fogelberg, Donald; Sleight, Alix; Mallinson, Trudy; Vigen, Cheryl; Blanchard, Jeanine; Carlson, Mike; Clark, Florence

2016-01-01

To describe sleeping behaviors and trends over time among an ethnically diverse group of community-living older adults. A descriptive secondary data analysis of a subsample (n = 217) from the Lifestyle Redesign randomized controlled trial was done to explore baseline napping and sleeping patterns as well as 6-mo changes in these outcomes. At baseline, the average time sleeping was 8.2 hr daily (standard deviation = 1.7). Among all participants, 29% reported daytime napping at baseline, of which 36% no longer napped at follow-up. Among participants who stopped napping, those who received an occupation-based intervention (n = 98) replaced napping time with nighttime sleep, and those not receiving an intervention (n = 119) experienced a net loss of total sleep (p < .05). Among participants who stopped napping, the occupation-based intervention may be related to enhanced sleep. More research examining the role of occupation-based interventions in improving sleep is warranted. Copyright © 2016 by the American Occupational Therapy Association, Inc.

Analysis of temporal gene expression profiles: clustering by simulated annealing and determining the optimal number of clusters.

PubMed

Lukashin, A V; Fuchs, R

2001-05-01

Cluster analysis of genome-wide expression data from DNA microarray hybridization studies has proved to be a useful tool for identifying biologically relevant groupings of genes and samples. In the present paper, we focus on several important issues related to clustering algorithms that have not yet been fully studied. We describe a simple and robust algorithm for the clustering of temporal gene expression profiles that is based on the simulated annealing procedure. In general, this algorithm guarantees to eventually find the globally optimal distribution of genes over clusters. We introduce an iterative scheme that serves to evaluate quantitatively the optimal number of clusters for each specific data set. The scheme is based on standard approaches used in regular statistical tests. The basic idea is to organize the search of the optimal number of clusters simultaneously with the optimization of the distribution of genes over clusters. The efficiency of the proposed algorithm has been evaluated by means of a reverse engineering experiment, that is, a situation in which the correct distribution of genes over clusters is known a priori. The employment of this statistically rigorous test has shown that our algorithm places greater than 90% genes into correct clusters. Finally, the algorithm has been tested on real gene expression data (expression changes during yeast cell cycle) for which the fundamental patterns of gene expression and the assignment of genes to clusters are well understood from numerous previous studies.

Fast gene ontology based clustering for microarray experiments.

PubMed

Ovaska, Kristian; Laakso, Marko; Hautaniemi, Sampsa

2008-11-21

Analysis of a microarray experiment often results in a list of hundreds of disease-associated genes. In order to suggest common biological processes and functions for these genes, Gene Ontology annotations with statistical testing are widely used. However, these analyses can produce a very large number of significantly altered biological processes. Thus, it is often challenging to interpret GO results and identify novel testable biological hypotheses. We present fast software for advanced gene annotation using semantic similarity for Gene Ontology terms combined with clustering and heat map visualisation. The methodology allows rapid identification of genes sharing the same Gene Ontology cluster. Our R based semantic similarity open-source package has a speed advantage of over 2000-fold compared to existing implementations. From the resulting hierarchical clustering dendrogram genes sharing a GO term can be identified, and their differences in the gene expression patterns can be seen from the heat map. These methods facilitate advanced annotation of genes resulting from data analysis.

Napping reverses increased pain sensitivity due to sleep restriction.

PubMed

Faraut, Brice; Léger, Damien; Medkour, Terkia; Dubois, Alexandre; Bayon, Virginie; Chennaoui, Mounir; Perrot, Serge

2015-01-01

To investigate pain sensitivity after sleep restriction and the restorative effect of napping. A strictly controlled randomized crossover study with continuous polysomnography monitoring was performed. Laboratory-based study. 11 healthy male volunteers. Volunteers attended two three-day sessions: "sleep restriction" alone and "sleep restriction and nap". Each session involved a baseline night of normal sleep, a night of sleep deprivation and a night of free recovery sleep. Participants were allowed to sleep only from 02:00 to 04:00 during the sleep deprivation night. During the "sleep restriction and nap" session, volunteers took two 30-minute naps, one in the morning and one in the afternoon. Quantitative sensory testing was performed with heat, cold and pressure, at 10:00 and 16:00, on three areas: the supraspinatus, lower back and thigh. After sleep restriction, quantitative sensory testing revealed differential changes in pain stimuli thresholds, but not in thermal threshold detection: lower back heat pain threshold decreased, pressure pain threshold increased in the supraspinatus area and no change was observed for the thigh. Napping restored responses to heat pain stimuli in the lower back and to pressure stimuli in the supraspinatus area. Sleep restriction induces different types of hypersensitivity to pain stimuli in different body areas, consistent with multilevel mechanisms, these changes being reversed by napping. The napping restorative effect on pain thresholds result principally from effects on pain mechanisms, since it was independent of vigilance status.

The utility of a 5(th) nap in multiple sleep latency test.

PubMed

Muza, Rexford; Lykouras, Dimosthenis; Rees, Kate

2016-02-01

This is the first study that aimed to look specifically at the utility of the 5(th) nap in the multiple sleep latency test (MSLT), a test used to assist in the diagnosis of narcolepsy. Data was retrospectively collected from the Sleep Disorders Centre of a Tertiary Hospital on patients that had a 5(th) nap during their MSLT from the 08(th) November 2011 to 12(th) November 2014. Fifty-three patients had a 5(th) nap performed out of 378 MSLT studies. In 16% of cases a diagnosis of narcolepsy was given directly due to the inclusion of the 5(th) nap on the MSLT. Here a 5(th) nap allowed diagnostic criteria of mean sleep latency <8 minutes and >2 SOREMPS to be met. In 53% of cases the mean sleep latency increased due to 5(th) nap inclusion; the mean sleep latency of the first four naps was 5.6 vs. 6.7 after inclusion of the 5(th) nap. The 5(th) nap is not often performed within the MSLT studies. Our study shows that only a few patients may benefit from a 5(th) nap opportunity which also led to increase of the mean sleep latency at the expense of extra time, cost, labour and increased patient anxiety.

A 30-Minute, but Not a 10-Minute Nighttime Nap is Associated with Sleep Inertia

PubMed Central

Hilditch, Cassie J.; Centofanti, Stephanie A.; Dorrian, Jillian; Banks, Siobhan

2016-01-01

Study Objectives: To assess sleep inertia following 10-min and 30-min naps during a simulated night shift. Methods: Thirty-one healthy adults (aged 21–35 y; 18 females) participated in a 3-day laboratory study that included one baseline (BL) sleep (22:00–07:00) and one experimental night involving randomization to either: total sleep deprivation (NO-NAP), a 10-min nap (10-NAP) or a 30-min nap (30-NAP). Nap opportunities ended at 04:00. A 3-min psychomotor vigilance task (PVT-B), digit-symbol substitution task (DSST), fatigue scale, sleepiness scale, and self-rated performance scale were undertaken pre-nap (03:00) and at 2, 17, 32, and 47 min post-nap. Results: The 30-NAP (14.7 ± 5.7 min) had more slow wave sleep than the 10-NAP (0.8 ± 1.5 min; P < 0.001) condition. In the NO-NAP condition, PVT-B performance was worse than pre-nap (4.6 ± 0.3 1/sec) at 47 min post-nap (4.1 ± 0.4 1/sec; P < 0.001). There was no change across time in the 10-NAP condition. In the 30-NAP condition, performance immediately deteriorated from pre-nap (4.3 ± 0.3 1/sec) and was still worse at 47 min post-nap (4.0 ± 0.5 1/sec; P < 0.015). DSST performance deteriorated in the NO-NAP (worse than pre-nap from 17 to 47 min; P < 0.008), did not change in the 10-NAP, and was impaired 2 min post-nap in the 30-NAP condition (P = 0.028). All conditions self-rated performance as better than pre-nap for all post-nap test points (P < 0.001). Conclusions: This study is the first to show that a 10-min (but not a 30-min) nighttime nap had minimal sleep inertia and helped to mitigate short-term performance impairment during a simulated night shift. Self-rated performance did not reflect objective performance following a nap. Citation: Hilditch CJ, Centofanti SA, Dorrian J, Banks S. A 30-minute, but not a 10-minute nighttime nap is associated with sleep inertia. SLEEP 2016;39(3):675–685. PMID:26715234

Scheduled napping as a countermeasure to sleepiness in air traffic controllers.

PubMed

Signal, Tracey Leigh; Gander, Philippa H; Anderson, Howard; Brash, Sue

2009-03-01

The aims of this study were to measure sleep during a planned nap on the night shift; and to use objective measures of performance and alertness to compare the effects of the nap opportunity versus staying awake. Twenty-eight air traffic controllers (mean age 36 years, nine women) completed four night shifts (two with early starts and two with late starts). Each type of night shift (early/late start) included a 40-min planned nap opportunity on one occasion and no nap on the other. Polysomnographic data were used to measure sleep and waking alertness [spectral power in the electroencephalogram (EEG) during the last hour of the night shift and the occurrence of slow rolling eye movements (SEMs) subsequent to the nap]. Psychomotor performance task [Psychomotor Vigilance Task (PVT)] was completed at the beginning and end of the shift, and after the nap (or an equivalent time if no nap was taken). Nap sleep latencies were relatively long (mean = 19 min) and total sleep time short (mean = 18 min), with minimal slow wave sleep (SWS, mean = 0%), and no rapid eye movement sleep. Nap sleep resulted in improved PVT performance (mean and slowest 10% of reaction time events), decreased spectral power in the EEG and reduced the likelihood of SEMs. The occurrence of SWS in the nap decreased spectral power in the EEG. This study indicates that although sleep taken at work is likely to be short and of poor quality it still results in an improvement in objective measures of alertness and performance.

Short Daytime Naps Briefly Attenuate Objectively Measured Sleepiness Under Chronic Sleep Restriction.

PubMed

Saletin, Jared M; Hilditch, Cassie J; Dement, William C; Carskadon, Mary A

2017-09-01

Napping is a useful countermeasure to the negative effects of acute sleep loss on alertness. The efficacy of naps to recover from chronic sleep loss is less well understood. Following 2 baseline nights (10 hours' time-in-bed), participants were restricted to 7 nights of 5-hour sleep opportunity. Ten adults participated in the No-Nap condition, and a further 9 were assigned to a Nap condition with a daily 45-minute nap opportunity at 1300 h. Sleepiness was assessed using the multiple sleep latency test and a visual analogue scale at 2-hour intervals. Both objective and subjective indexes of sleepiness were normalized within subject as a difference from those at baseline prior to sleep restriction. Mixed-effects models examined how the daytime nap opportunity altered sleepiness across the day and across the protocol. Short daytime naps attenuated sleepiness due to chronic sleep restriction for up to 6-8 hours after the nap. Benefits of the nap did not extend late into evening. Subjective sleepiness demonstrated a similar short-lived benefit that emerged later in the day when objective sleepiness already returned to pre-nap levels. Neither measure showed a benefit of the nap the following morning after the subsequent restriction night. These data indicate a short daytime nap may attenuate sleepiness in chronic sleep restriction, yet subjective and objective benefits emerge at different time scales. Because neither measure showed a benefit the next day, the current study underscores the need for careful consideration before naps are used as routine countermeasures to chronic sleep loss. © Sleep Research Society 2017. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.

The Relationship Between Midday Napping And Neurocognitive Function in Early Adolescents.

PubMed

Ji, Xiaopeng; Li, Junxin; Liu, Jianghong

2018-02-01

The impact of midday napping on neurocognitive function in adolescents has not been well established. This study aimed to investigate the relationship between self-reported midday-napping behaviors and neurocognitive function in early adolescents. The sample was comprised of 363 early adolescents (12.00 ± 0.38 years old) from Jintan, China. Midday napping, nighttime sleep duration, and sleep quality were measured by self-reported questionnaires. Neurocognitive function was measured by the Penn Computerized Neurocognitive Battery (accuracy and reaction times). Generalized linear regression was used to analyze the relationships. Sixty-four percent of our sample took more than 3 naps per week, and 70.11% reported nap durations of over 30 min. Participants with higher frequencies or longer durations of midday napping reported significantly better nighttime sleep quality (p < 0.05). Adjusted models showed that frequent nappers (5-7d/week) were significantly associated with heightened accuracy on tasks that measured sustained attention and nonverbal reasoning and faster reaction times on spatial memory compared with other frequency groups (ps < 0.05). For napping duration subgroups, early adolescents who took naps of any length were estimated to have faster reaction speeds on the sustained attention task compared with participants who never napped (ps < 0.05). However, only nappers with a moderate duration (31-60 min) tended to achieve both faster speeds (β = -38.28, p = 0.02) and better accuracy (β = 3.90, p = 0.04) on the sustained attention task. Our findings suggest that there is an association between habitual midday napping and neurocognitive function in early adolescents, especially in China, where midday napping is a cultural practice.

Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications

PubMed Central

Siegel, Nicol; Hoegg, Simone; Salzburger, Walter; Braasch, Ingo; Meyer, Axel

2007-01-01

Background The evolutionary lineage leading to the teleost fish underwent a whole genome duplication termed FSGD or 3R in addition to two prior genome duplications that took place earlier during vertebrate evolution (termed 1R and 2R). Resulting from the FSGD, additional copies of genes are present in fish, compared to tetrapods whose lineage did not experience the 3R genome duplication. Interestingly, we find that ParaHox genes do not differ in number in extant teleost fishes despite their additional genome duplication from the genomic situation in mammals, but they are distributed over twice as many paralogous regions in fish genomes. Results We determined the DNA sequence of the entire ParaHox C1 paralogon in the East African cichlid fish Astatotilapia burtoni, and compared it to orthologous regions in other vertebrate genomes as well as to the paralogous vertebrate ParaHox D paralogons. Evolutionary relationships among genes from these four chromosomal regions were studied with several phylogenetic algorithms. We provide evidence that the genes of the ParaHox C paralogous cluster are duplicated in teleosts, just as it had been shown previously for the D paralogon genes. Overall, however, synteny and cluster integrity seems to be less conserved in ParaHox gene clusters than in Hox gene clusters. Comparative analyses of non-coding sequences uncovered conserved, possibly co-regulatory elements, which are likely to contain promoter motives of the genes belonging to the ParaHox paralogons. Conclusion There seems to be strong stabilizing selection for gene order as well as gene orientation in the ParaHox C paralogon, since with a few exceptions, only the lengths of the introns and intergenic regions differ between the distantly related species examined. The high degree of evolutionary conservation of this gene cluster's architecture in particular – but possibly clusters of genes more generally – might be linked to the presence of promoter, enhancer or inhibitor

Fractal Clustering and Knowledge-driven Validation Assessment for Gene Expression Profiling.

PubMed

Wang, Lu-Yong; Balasubramanian, Ammaiappan; Chakraborty, Amit; Comaniciu, Dorin

2005-01-01

DNA microarray experiments generate a substantial amount of information about the global gene expression. Gene expression profiles can be represented as points in multi-dimensional space. It is essential to identify relevant groups of genes in biomedical research. Clustering is helpful in pattern recognition in gene expression profiles. A number of clustering techniques have been introduced. However, these traditional methods mainly utilize shape-based assumption or some distance metric to cluster the points in multi-dimension linear Euclidean space. Their results shows poor consistence with the functional annotation of genes in previous validation study. From a novel different perspective, we propose fractal clustering method to cluster genes using intrinsic (fractal) dimension from modern geometry. This method clusters points in such a way that points in the same clusters are more self-affine among themselves than to the points in other clusters. We assess this method using annotation-based validation assessment for gene clusters. It shows that this method is superior in identifying functional related gene groups than other traditional methods.

Hox gene clusters in the Indonesian coelacanth, Latimeria menadoensis

PubMed Central

Koh, Esther G. L.; Lam, Kevin; Christoffels, Alan; Erdmann, Mark V.; Brenner, Sydney; Venkatesh, Byrappa

2003-01-01

The Hox genes encode transcription factors that play a key role in specifying body plans of metazoans. They are organized into clusters that contain up to 13 paralogue group members. The complex morphology of vertebrates has been attributed to the duplication of Hox clusters during vertebrate evolution. In contrast to the single Hox cluster in the amphioxus (Branchiostoma floridae), an invertebrate-chordate, mammals have four clusters containing 39 Hox genes. Ray-finned fishes (Actinopterygii) such as zebrafish and fugu possess more than four Hox clusters. The coelacanth occupies a basal phylogenetic position among lobe-finned fishes (Sarcopterygii), which gave rise to the tetrapod lineage. The lobe fins of sarcopterygians are considered to be the evolutionary precursors of tetrapod limbs. Thus, the characterization of Hox genes in the coelacanth should provide insights into the origin of tetrapod limbs. We have cloned the complete second exon of 33 Hox genes from the Indonesian coelacanth, Latimeria menadoensis, by extensive PCR survey and genome walking. Phylogenetic analysis shows that 32 of these genes have orthologs in the four mammalian HOX clusters, including three genes (HoxA6, D1, and D8) that are absent in ray-finned fishes. The remaining coelacanth gene is an ortholog of hoxc1 found in zebrafish but absent in mammals. Our results suggest that coelacanths have four Hox clusters bearing a gene complement more similar to mammals than to ray-finned fishes, but with an additional gene, HoxC1, which has been lost during the evolution of mammals from lobe-finned fishes. PMID:12547909

Hox gene clusters in the Indonesian coelacanth, Latimeria menadoensis.

PubMed

Koh, Esther G L; Lam, Kevin; Christoffels, Alan; Erdmann, Mark V; Brenner, Sydney; Venkatesh, Byrappa

2003-02-04

The Hox genes encode transcription factors that play a key role in specifying body plans of metazoans. They are organized into clusters that contain up to 13 paralogue group members. The complex morphology of vertebrates has been attributed to the duplication of Hox clusters during vertebrate evolution. In contrast to the single Hox cluster in the amphioxus (Branchiostoma floridae), an invertebrate-chordate, mammals have four clusters containing 39 Hox genes. Ray-finned fishes (Actinopterygii) such as zebrafish and fugu possess more than four Hox clusters. The coelacanth occupies a basal phylogenetic position among lobe-finned fishes (Sarcopterygii), which gave rise to the tetrapod lineage. The lobe fins of sarcopterygians are considered to be the evolutionary precursors of tetrapod limbs. Thus, the characterization of Hox genes in the coelacanth should provide insights into the origin of tetrapod limbs. We have cloned the complete second exon of 33 Hox genes from the Indonesian coelacanth, Latimeria menadoensis, by extensive PCR survey and genome walking. Phylogenetic analysis shows that 32 of these genes have orthologs in the four mammalian HOX clusters, including three genes (HoxA6, D1, and D8) that are absent in ray-finned fishes. The remaining coelacanth gene is an ortholog of hoxc1 found in zebrafish but absent in mammals. Our results suggest that coelacanths have four Hox clusters bearing a gene complement more similar to mammals than to ray-finned fishes, but with an additional gene, HoxC1, which has been lost during the evolution of mammals from lobe-finned fishes.

Conditions for the Evolution of Gene Clusters in Bacterial Genomes

PubMed Central

Ballouz, Sara; Francis, Andrew R.; Lan, Ruiting; Tanaka, Mark M.

2010-01-01

Genes encoding proteins in a common pathway are often found near each other along bacterial chromosomes. Several explanations have been proposed to account for the evolution of these structures. For instance, natural selection may directly favour gene clusters through a variety of mechanisms, such as increased efficiency of coregulation. An alternative and controversial hypothesis is the selfish operon model, which asserts that clustered arrangements of genes are more easily transferred to other species, thus improving the prospects for survival of the cluster. According to another hypothesis (the persistence model), genes that are in close proximity are less likely to be disrupted by deletions. Here we develop computational models to study the conditions under which gene clusters can evolve and persist. First, we examine the selfish operon model by re-implementing the simulation and running it under a wide range of conditions. Second, we introduce and study a Moran process in which there is natural selection for gene clustering and rearrangement occurs by genome inversion events. Finally, we develop and study a model that includes selection and inversion, which tracks the occurrence and fixation of rearrangements. Surprisingly, gene clusters fail to evolve under a wide range of conditions. Factors that promote the evolution of gene clusters include a low number of genes in the pathway, a high population size, and in the case of the selfish operon model, a high horizontal transfer rate. The computational analysis here has shown that the evolution of gene clusters can occur under both direct and indirect selection as long as certain conditions hold. Under these conditions the selfish operon model is still viable as an explanation for the evolution of gene clusters. PMID:20168992

Napping and associated factors: a Japanese nationwide general population survey.

PubMed

Furihata, Ryuji; Kaneita, Yoshitaka; Jike, Maki; Ohida, Takashi; Uchiyama, Makoto

2016-04-01

The objective of this study was to investigate napping habits and their associated factors in the Japanese adult general population. The cross-sectional survey was conducted in November 2007 for subjects selected randomly from among 300 districts throughout Japan. Data from 7664 people (3527 men and 4137 women), aged 20-99 years, were analyzed. Participants completed a self-administered questionnaire on frequency and duration of napping. The percentage of responders for high-frequency napping, four or more days per week, was 21.2% among men and 17.1% among women. The percentage of responders for long-duration napping, 2 h or more per one nap, was 2.9% among men and 2.6% among women. Multivariate logistic regression analyses revealed that men, older age, smoking, insomnia symptoms, long sleep duration, excessive daytime sleepiness, and having sufficient rest obtained by sleep were positively associated with high-frequency napping, whereas alcohol drinking showed a negative association. Older age was negatively associated with long-duration napping whereas living in a large community, smoking, long sleep duration, excessive daytime sleepiness, and psychological stress showed a positive association. These findings provide important data for future studies aimed at improvement of sleep habits. Copyright © 2016 Elsevier B.V. All rights reserved.

Maternal Habitual Midday Napping Duration and Frequency are Associated with High Birthweight.

PubMed

Zheng, Xiaoxuan; Zhang, Lina; Shen, Lijun; Song, Lulu; Li, Hui; Liu, Bingqing; Li, Yuanyuan; Xia, Wei; Zhang, Bin; Xu, Shunqing; Wang, Youjie

2017-09-05

Habitual midday napping is a common habit in China, especially for pregnant women. The purpose of this study was to examine whether duration and frequency of maternal habitual midday napping were associated with high birthweight (HBW). A total of 10,482 participants from Healthy Baby Cohort were include in our analysis. The information of the mothers and their infants were abstracted from medical records, or obtained from questionnaire. Logistic regression models were used to calculate the odds ratios (ORs) and 95% confidence intervals (CIs) of habitual midday napping duration and frequency with HBW. Of the participants, 8,705 (83.0%) reported having habitual midday napping. Duration and frequency of napping had a positive association with HBW without adjustment. After controlling for potential confounders, increasing risk of HBW was observed in participants who napped 1.5-2 hours (OR, 1.50, 95% CI, 1.14, 1.98), and ≥2 hours (OR, 1.35, 95% CI, 1.03, 1.78) compared with no habitual midday napping. Participants who took naps ≥5 days/week had a higher risk of HBW (OR, 1.37, 95% CI, 1.07, 1.77) compared with the women without naps. This suggests that longer (≥1.5 hours) and more frequent (≥5 days/week) maternal habitual midday napping were associated with an increased risk of HBW.

The Influence of Match-Day Napping in Elite Female Netball Athletes.

PubMed

O'Donnell, Shannon; Beaven, Christopher M; Driller, Matthew

2018-03-15

To assess the effect of match-day napping and duration of naps on perceptual and performance indices in elite female netball players over two consecutive netball seasons. Fourteen elite female netball athletes (mean ± SD; age = 23 ± 6 yr) participated in an observational study over 26 competition matches. On each match day, athletes provided information on their napping habits, perceived energy levels, and then performed 3 countermovement jumps (CMJ) 3h30 prior to the start of the match. One hour following the match, subjective player performance ratings from the players and two members of the coaching staff were obtained. Naps were characterized into 3 conditions for analysis; No Nap (NN), <20 min Nap (SHORT), and ≥20 min Nap (LONG). A significant difference in peak jump velocity was observed between the SHORT and the NN condition in favor of the shorter nap (3.23 ± 0.26 and 3.07 ± 0.36 m.s -1 , respectively, d = 0.34, p < 0.05). A moderate, significant difference (d = 0.85; p < 0.05) was observed for the coach rating of performance (out of 10) between the SHORT and the NN condition (7.2 ± 0.8 and 6.4 ± 0.9, respectively) in favor of SHORT. The findings from the study would suggest that a short nap (<20 min) on the day of competition can enhance jump velocity and improve subjective performance in elite netball players, as assessed by coaching staff.

Napping, nighttime sleep, and cardiovascular risk factors in mid-life adults.

PubMed

Owens, Jane F; Buysse, Daniel J; Hall, Martica; Kamarck, Thomas W; Lee, Laisze; Strollo, Patrick J; Reis, Steven E; Matthews, Karen A

2010-08-15

To evaluate the relations between sleep characteristics and cardiovascular risk factors and napping behavior, and to assess whether daytime napping leads to subsequent better or worse sleep. The sample consisted of 224 (African American, Caucasian, and Asian) middle-aged men and women. Sleep measures included nine nights of actigraphy and sleep diaries, sleep questionnaires, and one night of polysomnography to measure sleep disordered breathing. More frequent napping was associated with shorter nighttime sleep duration averaged across the nine nights of actigraphy (especially among African Americans), more daytime sleepiness, more pain and fatigue by diary, and increased body mass index and waist circumference. Shorter nighttime sleep duration was associated with taking a nap during the next day and taking a nap was associated with less efficient sleep the next night. Napping in middle-aged men and women is associated with overall less nighttime sleep in African Americans and lower sleep efficiency as measured by actigraphy, and increased BMI and central adiposity. These findings point to the importance of measuring of napping in understanding associations of sleep with cardiovascular risk.

Night work and BMI: is it related to on-shift napping?

PubMed

Silva-Costa, Aline; Griep, Rosane Härter; Rotenberg, Lúcia

2017-11-17

On-shift napping can benefit night workers regarding sleep loss, synchronization of circadian rhythms, and alertness. However, few studies on napping can be found in the literature focused on possible health benefits. This cross-sectional study has investigated the role of on-shift napping on the association between night work and BMI in 409 night-shift nursing professionals. The number of working nights and the years of exposure to night work were significantly associated with increased BMI levels among non-nappers, but not among nappers. Results suggest a benefit of napping for weight gain, thus subsidizing occupational health policies on the regulation of on-shift napping among nursing workers.

Association between habitual daytime napping and metabolic syndrome: a population-based study.

PubMed

Lin, Diaozhu; Sun, Kan; Li, Feng; Qi, Yiqin; Ren, Meng; Huang, Chulin; Tang, Juying; Xue, Shengneng; Li, Yan; Yan, Li

2014-12-01

Our objective was to evaluate the association between habitual daytime napping and the prevalence of metabolic syndrome. We conducted a population-based study of 8,547 subjects aged 40 years or older. Metabolic syndrome was defined according to a harmonized definition from a joint statement and the recommended thresholds for the Chinese population. Information about sleep duration was self-reported. The prevalence of metabolic syndrome in the no daytime napping group, the 0 to 1 hour daytime napping group and the more than 1 hour daytime napping group were 35.0%, 36.0% and 44.5% among the females (P<0.0001). Increased daytime napping hours were positively associated with parameters of metabolic syndrome in the female subjects, including waist circumference, systolic blood pressure, triglycerides and fasting plasma glucose (P<0.05 for all). Multivariate adjusted logistic regression analysis revealed that, compared to the no habitual daytime napping females, napping for more than 1 hour was independently associated with an increased prevalence of metabolic syndrome (odds ratio 1.39, 95% confidence interval, 1.13-1.72). Compared to the female subjects in the no daytime napping group, those habitually napped for more than 1 hour exhibited 46% and 26% increases in the prevalence of central obesity and hypertriglyceridemia (all P<0.05). No statistically significant associations were detected between daytime napping hours and metabolic syndrome among the male subjects. Daytime napping is associated with an increased prevalence of metabolic syndrome in middle-aged non-obese Chinese women. Copyright © 2014. Published by Elsevier Inc.

Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression

PubMed Central

Poole, William; Leinonen, Kalle; Shmulevich, Ilya

2017-01-01

Cancer researchers have long recognized that somatic mutations are not uniformly distributed within genes. However, most approaches for identifying cancer mutations focus on either the entire-gene or single amino-acid level. We have bridged these two methodologies with a multiscale mutation clustering algorithm that identifies variable length mutation clusters in cancer genes. We ran our algorithm on 539 genes using the combined mutation data in 23 cancer types from The Cancer Genome Atlas (TCGA) and identified 1295 mutation clusters. The resulting mutation clusters cover a wide range of scales and often overlap with many kinds of protein features including structured domains, phosphorylation sites, and known single nucleotide variants. We statistically associated these multiscale clusters with gene expression and drug response data to illuminate the functional and clinical consequences of mutations in our clusters. Interestingly, we find multiple clusters within individual genes that have differential functional associations: these include PTEN, FUBP1, and CDH1. This methodology has potential implications in identifying protein regions for drug targets, understanding the biological underpinnings of cancer, and personalizing cancer treatments. Toward this end, we have made the mutation clusters and the clustering algorithm available to the public. Clusters and pathway associations can be interactively browsed at m2c.systemsbiology.net. The multiscale mutation clustering algorithm is available at https://github.com/IlyaLab/M2C. PMID:28170390

Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression.

PubMed

Poole, William; Leinonen, Kalle; Shmulevich, Ilya; Knijnenburg, Theo A; Bernard, Brady

2017-02-01

Cancer researchers have long recognized that somatic mutations are not uniformly distributed within genes. However, most approaches for identifying cancer mutations focus on either the entire-gene or single amino-acid level. We have bridged these two methodologies with a multiscale mutation clustering algorithm that identifies variable length mutation clusters in cancer genes. We ran our algorithm on 539 genes using the combined mutation data in 23 cancer types from The Cancer Genome Atlas (TCGA) and identified 1295 mutation clusters. The resulting mutation clusters cover a wide range of scales and often overlap with many kinds of protein features including structured domains, phosphorylation sites, and known single nucleotide variants. We statistically associated these multiscale clusters with gene expression and drug response data to illuminate the functional and clinical consequences of mutations in our clusters. Interestingly, we find multiple clusters within individual genes that have differential functional associations: these include PTEN, FUBP1, and CDH1. This methodology has potential implications in identifying protein regions for drug targets, understanding the biological underpinnings of cancer, and personalizing cancer treatments. Toward this end, we have made the mutation clusters and the clustering algorithm available to the public. Clusters and pathway associations can be interactively browsed at m2c.systemsbiology.net. The multiscale mutation clustering algorithm is available at https://github.com/IlyaLab/M2C.

A tripartite clustering analysis on microRNA, gene and disease model.

PubMed

Shen, Chengcheng; Liu, Ying

2012-02-01

Alteration of gene expression in response to regulatory molecules or mutations could lead to different diseases. MicroRNAs (miRNAs) have been discovered to be involved in regulation of gene expression and a wide variety of diseases. In a tripartite biological network of human miRNAs, their predicted target genes and the diseases caused by altered expressions of these genes, valuable knowledge about the pathogenicity of miRNAs, involved genes and related disease classes can be revealed by co-clustering miRNAs, target genes and diseases simultaneously. Tripartite co-clustering can lead to more informative results than traditional co-clustering with only two kinds of members and pass the hidden relational information along the relation chain by considering multi-type members. Here we report a spectral co-clustering algorithm for k-partite graph to find clusters with heterogeneous members. We use the method to explore the potential relationships among miRNAs, genes and diseases. The clusters obtained from the algorithm have significantly higher density than randomly selected clusters, which means members in the same cluster are more likely to have common connections. Results also show that miRNAs in the same family based on the hairpin sequences tend to belong to the same cluster. We also validate the clustering results by checking the correlation of enriched gene functions and disease classes in the same cluster. Finally, widely studied miR-17-92 and its paralogs are analyzed as a case study to reveal that genes and diseases co-clustered with the miRNAs are in accordance with current research findings.

Night work and BMI: is it related to on-shift napping?

PubMed Central

Silva-Costa, Aline; Griep, Rosane Härter; Rotenberg, Lúcia

2017-01-01

ABSTRACT On-shift napping can benefit night workers regarding sleep loss, synchronization of circadian rhythms, and alertness. However, few studies on napping can be found in the literature focused on possible health benefits. This cross-sectional study has investigated the role of on-shift napping on the association between night work and BMI in 409 night-shift nursing professionals. The number of working nights and the years of exposure to night work were significantly associated with increased BMI levels among non-nappers, but not among nappers. Results suggest a benefit of napping for weight gain, thus subsidizing occupational health policies on the regulation of on-shift napping among nursing workers. PMID:29166450

Napping, Nighttime Sleep, and Cardiovascular Risk Factors in Mid-Life Adults

PubMed Central

Owens, Jane F.; Buysse, Daniel J.; Hall, Martica; Kamarck, Thomas W.; Lee, Laisze; Strollo, Patrick J.; Reis, Steven E.; Matthews, Karen A.

2010-01-01

Study Objectives: To evaluate the relations between sleep characteristics and cardiovascular risk factors and napping behavior, and to assess whether daytime napping leads to subsequent better or worse sleep. Methods: The sample consisted of 224 (African American, Caucasian, and Asian) middle-aged men and women. Sleep measures included nine nights of actigraphy and sleep diaries, sleep questionnaires, and one night of polysomnography to measure sleep disordered breathing. Results: More frequent napping was associated with shorter nighttime sleep duration averaged across the nine nights of actigraphy (especially among African Americans), more daytime sleepiness, more pain and fatigue by diary, and increased body mass index and waist circumference. Shorter nighttime sleep duration was associated with taking a nap during the next day and taking a nap was associated with less efficient sleep the next night. Conclusions: Napping in middle-aged men and women is associated with overall less nighttime sleep in African Americans and lower sleep efficiency as measured by actigraphy, and increased BMI and central adiposity. These findings point to the importance of measuring of napping in understanding associations of sleep with cardiovascular risk. Citation: Owens JF; Buysee DJ; Hall M; Kamarck TW; Lee L; Strollo PJ; Reis SE; Matthews KA. Napping, nighttime sleep, and cardiovascular risk factors in mid-life adults. J Clin Sleep Med 2010;6(4):330-335. PMID:20726280

Genes encoding cuticular proteins are components of the Nimrod gene cluster in Drosophila.

PubMed

Cinege, Gyöngyi; Zsámboki, János; Vidal-Quadras, Maite; Uv, Anne; Csordás, Gábor; Honti, Viktor; Gábor, Erika; Hegedűs, Zoltán; Varga, Gergely I B; Kovács, Attila L; Juhász, Gábor; Williams, Michael J; Andó, István; Kurucz, Éva

2017-08-01

The Nimrod gene cluster, located on the second chromosome of Drosophila melanogaster, is the largest synthenic unit of the Drosophila genome. Nimrod genes show blood cell specific expression and code for phagocytosis receptors that play a major role in fruit fly innate immune functions. We previously identified three homologous genes (vajk-1, vajk-2 and vajk-3) located within the Nimrod cluster, which are unrelated to the Nimrod genes, but are homologous to a fourth gene (vajk-4) located outside the cluster. Here we show that, unlike the Nimrod candidates, the Vajk proteins are expressed in cuticular structures of the late embryo and the late pupa, indicating that they contribute to cuticular barrier functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Identification of lethal cluster of genes in the yeast transcription network

NASA Astrophysics Data System (ADS)

Rho, K.; Jeong, H.; Kahng, B.

2006-05-01

Identification of essential or lethal genes would be one of the ultimate goals in drug designs. Here we introduce an in silico method to select the cluster with a high population of lethal genes, called lethal cluster, through microarray assay. We construct a gene transcription network based on the microarray expression level. Links are added one by one in the descending order of the Pearson correlation coefficients between two genes. As the link density p increases, two meaningful link densities pm and ps are observed. At pm, which is smaller than the percolation threshold, the number of disconnected clusters is maximum, and the lethal genes are highly concentrated in a certain cluster that needs to be identified. Thus the deletion of all genes in that cluster could efficiently lead to a lethal inviable mutant. This lethal cluster can be identified by an in silico method. As p increases further beyond the percolation threshold, the power law behavior in the degree distribution of a giant cluster appears at ps. We measure the degree of each gene at ps. With the information pertaining to the degrees of each gene at ps, we return to the point pm and calculate the mean degree of genes of each cluster. We find that the lethal cluster has the largest mean degree.

Napping: A public health issue. From epidemiological to laboratory studies.

PubMed

Faraut, Brice; Andrillon, Thomas; Vecchierini, Marie-Françoise; Leger, Damien

2017-10-01

Sleep specialists have proposed measures to counteract the negative short- and long-term consequences of sleep debt, and some have suggested the nap as a potential and powerful "public health tool". Here, we address this countermeasure aspect of napping viewed as an action against sleep deprivation rather than an action associated with poor health. We review the physiological functions that have been associated positively with napping in both public health and clinical settings (sleep-related accidents, work and school, and cardiovascular risk) and in laboratory-based studies with potential public health issues (cognitive performance, stress, immune function and pain sensitivity). We also discuss the circumstances in which napping-depending on several factors, including nap duration, frequency, and age-could be a potential public health tool and a countermeasure for sleep loss in terms of reducing accidents and cardiovascular events and improving sleep-restriction-sensitive working performance. However, the impact of napping and the nature of the sleep stage(s) involved still need to be evaluated, especially from the perspective of coping strategies in populations with chronic sleep debt, such as night and shift workers. Copyright © 2016 Elsevier Ltd. All rights reserved.

Napping and the Selective Consolidation of Negative Aspects of Scenes

PubMed Central

Payne, Jessica D.; Kensinger, Elizabeth A.; Wamsley, Erin; Spreng, R. Nathan; Alger, Sara; Gibler, Kyle; Schacter, Daniel L.; Stickgold, Robert

2018-01-01

After information is encoded into memory, it undergoes an offline period of consolidation that occurs optimally during sleep. The consolidation process not only solidifies memories, but also selectively preserves aspects of experience that are emotionally salient and relevant for future use. Here, we provide evidence that an afternoon nap is sufficient to trigger preferential memory for emotional information contained in complex scenes. Selective memory for negative emotional information was enhanced after a nap compared to wakefulness in two control conditions designed to carefully address interference and time-of-day confounds. Although prior evidence has connected negative emotional memory formation to rapid eye movement (REM) sleep physiology, we found that non-REM delta activity and the amount of slow wave sleep (SWS) in the nap were robustly related to the selective consolidation of negative information. These findings suggest that the mechanisms underlying memory consolidation benefits associated with napping and nighttime sleep are not always the same. Finally, we provide preliminary evidence that the magnitude of the emotional memory benefit conferred by sleep is equivalent following a nap and a full night of sleep, suggesting that selective emotional remembering can be economically achieved by taking a nap. PMID:25706830

The ergot alkaloid gene cluster in Claviceps purpurea: extension of the cluster sequence and intra species evolution.

PubMed

Haarmann, Thomas; Machado, Caroline; Lübbe, Yvonne; Correia, Telmo; Schardl, Christopher L; Panaccione, Daniel G; Tudzynski, Paul

2005-06-01

The genomic region of Claviceps purpurea strain P1 containing the ergot alkaloid gene cluster [Tudzynski, P., Hölter, K., Correia, T., Arntz, C., Grammel, N., Keller, U., 1999. Evidence for an ergot alkaloid gene cluster in Claviceps purpurea. Mol. Gen. Genet. 261, 133-141] was explored by chromosome walking, and additional genes probably involved in the ergot alkaloid biosynthesis have been identified. The putative cluster sequence (extending over 68.5kb) contains 4 different nonribosomal peptide synthetase (NRPS) genes and several putative oxidases. Northern analysis showed that most of the genes were co-regulated (repressed by high phosphate), and identified probable flanking genes by lack of co-regulation. Comparison of the cluster sequences of strain P1, an ergotamine producer, with that of strain ECC93, an ergocristine producer, showed high conservation of most of the cluster genes, but significant variation in the NRPS modules, strongly suggesting that evolution of these chemical races of C. purpurea is determined by evolution of NRPS module specificity.

Large clusters of co-expressed genes in the Drosophila genome.

PubMed

Boutanaev, Alexander M; Kalmykova, Alla I; Shevelyov, Yuri Y; Nurminsky, Dmitry I

2002-12-12

Clustering of co-expressed, non-homologous genes on chromosomes implies their co-regulation. In lower eukaryotes, co-expressed genes are often found in pairs. Clustering of genes that share aspects of transcriptional regulation has also been reported in higher eukaryotes. To advance our understanding of the mode of coordinated gene regulation in multicellular organisms, we performed a genome-wide analysis of the chromosomal distribution of co-expressed genes in Drosophila. We identified a total of 1,661 testes-specific genes, one-third of which are clustered on chromosomes. The number of clusters of three or more genes is much higher than expected by chance. We observed a similar trend for genes upregulated in the embryo and in the adult head, although the expression pattern of individual genes cannot be predicted on the basis of chromosomal position alone. Our data suggest that the prevalent mechanism of transcriptional co-regulation in higher eukaryotes operates with extensive chromatin domains that comprise multiple genes.

Arrangement of the Clostridium baratii F7 Toxin Gene Cluster with Identification of a σ Factor That Recognizes the Botulinum Toxin Gene Cluster Promoters

DOE PAGES

Dover, Nir; Barash, Jason R.; Burke, Julianne N.; ...

2014-05-22

Botulinum neurotoxin (BoNT) is the most poisonous substances known and its eight toxin types (A to H) are distinguished by the inability of polyclonal antibodies that neutralize one toxin type to neutralize any of the other seven toxin types. Infant botulism, an intestinal toxemia orphan disease, is the most common form of human botulism in the United States. It results from swallowed spores of Clostridium botulinum (or rarely, neurotoxigenic Clostridium butyricum or Clostridium baratii) that germinate and temporarily colonize the lumen of the large intestine, where, as vegetative cells, they produce botulinum toxin. Botulinum neurotoxin is encoded by the bontmore » gene that is part of a toxin gene cluster that includes several accessory genes. In this paper, we sequenced for the first time the complete botulinum neurotoxin gene cluster of nonproteolytic C. baratii type F7. Like the type E and the nonproteolytic type F6 botulinum toxin gene clusters, the C. baratii type F7 had an orfX toxin gene cluster that lacked the regulatory botR gene which is found in proteolytic C. botulinum strains and codes for an alternative σ factor. In the absence of botR, we identified a putative alternative regulatory gene located upstream of the C. baratii type F7 toxin gene cluster. This putative regulatory gene codes for a predicted σ factor that contains DNA-binding-domain homologues to the DNA-binding domains both of BotR and of other members of the TcdR-related group 5 of the σ 70 family that are involved in the regulation of toxin gene expression in clostridia. We showed that this TcdR-related protein in association with RNA polymerase core enzyme specifically binds to the C. baratii type F7 botulinum toxin gene cluster promoters. Finally, this TcdR-related protein may therefore be involved in regulating the expression of the genes of the botulinum toxin gene cluster in neurotoxigenic C. baratii.« less

Differential Retention of Gene Functions in a Secondary Metabolite Cluster.

PubMed

Reynolds, Hannah T; Slot, Jason C; Divon, Hege H; Lysøe, Erik; Proctor, Robert H; Brown, Daren W

2017-08-01

In fungi, distribution of secondary metabolite (SM) gene clusters is often associated with host- or environment-specific benefits provided by SMs. In the plant pathogen Alternaria brassicicola (Dothideomycetes), the DEP cluster confers an ability to synthesize the SM depudecin, a histone deacetylase inhibitor that contributes weakly to virulence. The DEP cluster includes genes encoding enzymes, a transporter, and a transcription regulator. We investigated the distribution and evolution of the DEP cluster in 585 fungal genomes and found a wide but sporadic distribution among Dothideomycetes, Sordariomycetes, and Eurotiomycetes. We confirmed DEP gene expression and depudecin production in one fungus, Fusarium langsethiae. Phylogenetic analyses suggested 6-10 horizontal gene transfers (HGTs) of the cluster, including a transfer that led to the presence of closely related cluster homologs in Alternaria and Fusarium. The analyses also indicated that HGTs were frequently followed by loss/pseudogenization of one or more DEP genes. Independent cluster inactivation was inferred in at least four fungal classes. Analyses of transitions among functional, pseudogenized, and absent states of DEP genes among Fusarium species suggest enzyme-encoding genes are lost at higher rates than the transporter (DEP3) and regulatory (DEP6) genes. The phenotype of an experimentally-induced DEP3 mutant of Fusarium did not support the hypothesis that selective retention of DEP3 and DEP6 protects fungi from exogenous depudecin. Together, the results suggest that HGT and gene loss have contributed significantly to DEP cluster distribution, and that some DEP genes provide a greater fitness benefit possibly due to a differential tendency to form network connections. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2017. This work is written by US Government employees and is in the public domain in the US.

Functional clustering of time series gene expression data by Granger causality

PubMed Central

2012-01-01

Background A common approach for time series gene expression data analysis includes the clustering of genes with similar expression patterns throughout time. Clustered gene expression profiles point to the joint contribution of groups of genes to a particular cellular process. However, since genes belong to intricate networks, other features, besides comparable expression patterns, should provide additional information for the identification of functionally similar genes. Results In this study we perform gene clustering through the identification of Granger causality between and within sets of time series gene expression data. Granger causality is based on the idea that the cause of an event cannot come after its consequence. Conclusions This kind of analysis can be used as a complementary approach for functional clustering, wherein genes would be clustered not solely based on their expression similarity but on their topological proximity built according to the intensity of Granger causality among them. PMID:23107425

Transcription factor clusters regulate genes in eukaryotic cells

PubMed Central

Hedlund, Erik G; Friemann, Rosmarie; Hohmann, Stefan

2017-01-01

Transcription is regulated through binding factors to gene promoters to activate or repress expression, however, the mechanisms by which factors find targets remain unclear. Using single-molecule fluorescence microscopy, we determined in vivo stoichiometry and spatiotemporal dynamics of a GFP tagged repressor, Mig1, from a paradigm signaling pathway of Saccharomyces cerevisiae. We find the repressor operates in clusters, which upon extracellular signal detection, translocate from the cytoplasm, bind to nuclear targets and turnover. Simulations of Mig1 configuration within a 3D yeast genome model combined with a promoter-specific, fluorescent translation reporter confirmed clusters are the functional unit of gene regulation. In vitro and structural analysis on reconstituted Mig1 suggests that clusters are stabilized by depletion forces between intrinsically disordered sequences. We observed similar clusters of a co-regulatory activator from a different pathway, supporting a generalized cluster model for transcription factors that reduces promoter search times through intersegment transfer while stabilizing gene expression. PMID:28841133

Identification of nitrogen-fixing genes and gene clusters from metagenomic library of acid mine drainage.

PubMed

Dai, Zhimin; Guo, Xue; Yin, Huaqun; Liang, Yili; Cong, Jing; Liu, Xueduan

2014-01-01

Biological nitrogen fixation is an essential function of acid mine drainage (AMD) microbial communities. However, most acidophiles in AMD environments are uncultured microorganisms and little is known about the diversity of nitrogen-fixing genes and structure of nif gene cluster in AMD microbial communities. In this study, we used metagenomic sequencing to isolate nif genes in the AMD microbial community from Dexing Copper Mine, China. Meanwhile, a metagenome microarray containing 7,776 large-insertion fosmids was constructed to screen novel nif gene clusters. Metagenomic analyses revealed that 742 sequences were identified as nif genes including structural subunit genes nifH, nifD, nifK and various additional genes. The AMD community is massively dominated by the genus Acidithiobacillus. However, the phylogenetic diversity of nitrogen-fixing microorganisms is much higher than previously thought in the AMD community. Furthermore, a 32.5-kb genomic sequence harboring nif, fix and associated genes was screened by metagenome microarray. Comparative genome analysis indicated that most nif genes in this cluster are most similar to those of Herbaspirillum seropedicae, but the organization of the nif gene cluster had significant differences from H. seropedicae. Sequence analysis and reverse transcription PCR also suggested that distinct transcription units of nif genes exist in this gene cluster. nifQ gene falls into the same transcription unit with fixABCX genes, which have not been reported in other diazotrophs before. All of these results indicated that more novel diazotrophs survive in the AMD community.

Identification of Nitrogen-Fixing Genes and Gene Clusters from Metagenomic Library of Acid Mine Drainage

PubMed Central

Yin, Huaqun; Liang, Yili; Cong, Jing; Liu, Xueduan

2014-01-01

Biological nitrogen fixation is an essential function of acid mine drainage (AMD) microbial communities. However, most acidophiles in AMD environments are uncultured microorganisms and little is known about the diversity of nitrogen-fixing genes and structure of nif gene cluster in AMD microbial communities. In this study, we used metagenomic sequencing to isolate nif genes in the AMD microbial community from Dexing Copper Mine, China. Meanwhile, a metagenome microarray containing 7,776 large-insertion fosmids was constructed to screen novel nif gene clusters. Metagenomic analyses revealed that 742 sequences were identified as nif genes including structural subunit genes nifH, nifD, nifK and various additional genes. The AMD community is massively dominated by the genus Acidithiobacillus. However, the phylogenetic diversity of nitrogen-fixing microorganisms is much higher than previously thought in the AMD community. Furthermore, a 32.5-kb genomic sequence harboring nif, fix and associated genes was screened by metagenome microarray. Comparative genome analysis indicated that most nif genes in this cluster are most similar to those of Herbaspirillum seropedicae, but the organization of the nif gene cluster had significant differences from H. seropedicae. Sequence analysis and reverse transcription PCR also suggested that distinct transcription units of nif genes exist in this gene cluster. nifQ gene falls into the same transcription unit with fixABCX genes, which have not been reported in other diazotrophs before. All of these results indicated that more novel diazotrophs survive in the AMD community. PMID:24498417

Hierarchical Dirichlet process model for gene expression clustering

PubMed Central

2013-01-01

Clustering is an important data processing tool for interpreting microarray data and genomic network inference. In this article, we propose a clustering algorithm based on the hierarchical Dirichlet processes (HDP). The HDP clustering introduces a hierarchical structure in the statistical model which captures the hierarchical features prevalent in biological data such as the gene express data. We develop a Gibbs sampling algorithm based on the Chinese restaurant metaphor for the HDP clustering. We apply the proposed HDP algorithm to both regulatory network segmentation and gene expression clustering. The HDP algorithm is shown to outperform several popular clustering algorithms by revealing the underlying hierarchical structure of the data. For the yeast cell cycle data, we compare the HDP result to the standard result and show that the HDP algorithm provides more information and reduces the unnecessary clustering fragments. PMID:23587447

Nurse managers' perception of night-shift napping: A cross-sectional survey.

PubMed

Dalky, Heyam F; Raeda, AbuAlRub F; Esraa, Aldalqamouni A

2017-10-04

Night-shift work often results in sleep deprivation, and this in turn results in fatigue that jeopardizes both nurse and patient safety. Napping is considered a viable deterrent to fatigue, yet hospital administration has been slow to adopt napping. To identify nurse managers' knowledge and approval of napping practices for nurses on night shifts. Nurse managers at nine Jordanian hospitals (n = 129) were surveyed using an Arabic version of a questionnaire previously used in a Canadian study. Descriptive statistics were used to describe results, and a one-way ANOVA was used to determine if relationships existed among nurse manager's approval of napping and nurse demographic characteristics. The majority of nurse managers (61%) knew nurses were napping during breaks. However, the managers reported there was no written policy for napping. A majority thought there were more benefits to napping than drawbacks. Some 55% of nurse managers recognized fatigue as a cause of errors or incidents regarding patient safety, and 40% perceived fatigue to be a factor in staff injuries. This study supports an urgent need for shared responsibility among nursing administration, and bedside nurses to develop evidence-based programs to counteract the effects of nurse fatigue. © 2017 Wiley Periodicals, Inc.

Prediction of operon-like gene clusters in the Arabidopsis thaliana genome based on co-expression analysis of neighboring genes.

PubMed

Wada, Masayoshi; Takahashi, Hiroki; Altaf-Ul-Amin, Md; Nakamura, Kensuke; Hirai, Masami Y; Ohta, Daisaku; Kanaya, Shigehiko

2012-07-15

Operon-like arrangements of genes occur in eukaryotes ranging from yeasts and filamentous fungi to nematodes, plants, and mammals. In plants, several examples of operon-like gene clusters involved in metabolic pathways have recently been characterized, e.g. the cyclic hydroxamic acid pathways in maize, the avenacin biosynthesis gene clusters in oat, the thalianol pathway in Arabidopsis thaliana, and the diterpenoid momilactone cluster in rice. Such operon-like gene clusters are defined by their co-regulation or neighboring positions within immediate vicinity of chromosomal regions. A comprehensive analysis of the expression of neighboring genes therefore accounts a crucial step to reveal the complete set of operon-like gene clusters within a genome. Genome-wide prediction of operon-like gene clusters should contribute to functional annotation efforts and provide novel insight into evolutionary aspects acquiring certain biological functions as well. We predicted co-expressed gene clusters by comparing the Pearson correlation coefficient of neighboring genes and randomly selected gene pairs, based on a statistical method that takes false discovery rate (FDR) into consideration for 1469 microarray gene expression datasets of A. thaliana. We estimated that A. thaliana contains 100 operon-like gene clusters in total. We predicted 34 statistically significant gene clusters consisting of 3 to 22 genes each, based on a stringent FDR threshold of 0.1. Functional relationships among genes in individual clusters were estimated by sequence similarity and functional annotation of genes. Duplicated gene pairs (determined based on BLAST with a cutoff of E<10(-5)) are included in 27 clusters. Five clusters are associated with metabolism, containing P450 genes restricted to the Brassica family and predicted to be involved in secondary metabolism. Operon-like clusters tend to include genes encoding bio-machinery associated with ribosomes, the ubiquitin/proteasome system, secondary

Napping during night shift: practices, preferences, and perceptions of critical care and emergency department nurses.

PubMed

Fallis, Wendy M; McMillan, Diana E; Edwards, Marie P

2011-04-01

Nurses working night shifts are at risk for sleep deprivation, which threatens patient and nurse safety. Little nursing research has addressed napping, an effective strategy to improve performance, reduce fatigue, and increase vigilance. To explore nurses' perceptions, experiences, barriers, and safety issues related to napping/not napping during night shift. A convenience sample of critical care nurses working night shift were interviewed to explore demographics, work schedule and environment, and napping/ not napping experiences, perceptions, and barriers. Transcripts were constantly compared, and categories and themes were identified. Participants were 13 critical care nurses with an average of 17 years' experience. Ten nurses napped regularly; 2 avoided napping because of sleep inertia. The need for and benefits of napping or not during night shift break were linked to patient and nurse safety. Ability to nap was affected by the demands of patient care and safety, staffing needs, and organizational and environmental factors. Nurses identified personal health, safety, and patient care issues supporting the need for a restorative nap during night shift. Barriers to napping exist within the organization/work environment.

Heterologous expression of pikromycin biosynthetic gene cluster using Streptomyces artificial chromosome system.

PubMed

Pyeon, Hye-Rim; Nah, Hee-Ju; Kang, Seung-Hoon; Choi, Si-Sun; Kim, Eung-Soo

2017-05-31

Heterologous expression of biosynthetic gene clusters of natural microbial products has become an essential strategy for titer improvement and pathway engineering of various potentially-valuable natural products. A Streptomyces artificial chromosomal conjugation vector, pSBAC, was previously successfully applied for precise cloning and tandem integration of a large polyketide tautomycetin (TMC) biosynthetic gene cluster (Nah et al. in Microb Cell Fact 14(1):1, 2015), implying that this strategy could be employed to develop a custom overexpression scheme of natural product pathway clusters present in actinomycetes. To validate the pSBAC system as a generally-applicable heterologous overexpression system for a large-sized polyketide biosynthetic gene cluster in Streptomyces, another model polyketide compound, the pikromycin biosynthetic gene cluster, was preciously cloned and heterologously expressed using the pSBAC system. A unique HindIII restriction site was precisely inserted at one of the border regions of the pikromycin biosynthetic gene cluster within the chromosome of Streptomyces venezuelae, followed by site-specific recombination of pSBAC into the flanking region of the pikromycin gene cluster. Unlike the previous cloning process, one HindIII site integration step was skipped through pSBAC modification. pPik001, a pSBAC containing the pikromycin biosynthetic gene cluster, was directly introduced into two heterologous hosts, Streptomyces lividans and Streptomyces coelicolor, resulting in the production of 10-deoxymethynolide, a major pikromycin derivative. When two entire pikromycin biosynthetic gene clusters were tandemly introduced into the S. lividans chromosome, overproduction of 10-deoxymethynolide and the presence of pikromycin, which was previously not detected, were both confirmed. Moreover, comparative qRT-PCR results confirmed that the transcription of pikromycin biosynthetic genes was significantly upregulated in S. lividans containing tandem

Clustering approaches to identifying gene expression patterns from DNA microarray data.

PubMed

Do, Jin Hwan; Choi, Dong-Kug

2008-04-30

The analysis of microarray data is essential for large amounts of gene expression data. In this review we focus on clustering techniques. The biological rationale for this approach is the fact that many co-expressed genes are co-regulated, and identifying co-expressed genes could aid in functional annotation of novel genes, de novo identification of transcription factor binding sites and elucidation of complex biological pathways. Co-expressed genes are usually identified in microarray experiments by clustering techniques. There are many such methods, and the results obtained even for the same datasets may vary considerably depending on the algorithms and metrics for dissimilarity measures used, as well as on user-selectable parameters such as desired number of clusters and initial values. Therefore, biologists who want to interpret microarray data should be aware of the weakness and strengths of the clustering methods used. In this review, we survey the basic principles of clustering of DNA microarray data from crisp clustering algorithms such as hierarchical clustering, K-means and self-organizing maps, to complex clustering algorithms like fuzzy clustering.

A Daytime Nap Facilitates Generalization of Word Meanings in Young Toddlers

PubMed Central

Horváth, Klára; Liu, Siying; Plunkett, Kim

2016-01-01

Study Objectives: One of the key processes in language development is generalization—the selection and extension of relevant features and information to similar objects and concepts. Little is known about how sleep influences generalization, and studies on the topic are inconclusive. Our aim was to investigate how a nap affects generalization in 16-mo-olds. We hypothesized that a nap is necessary for successful generalization of word meanings. Methods: Twenty-eight 16-mo-old, typically developing toddlers were randomly assigned to nap and wake groups. We trained toddlers with two novel object-word pairs and tested their initial ability to generalize. Toddlers took part in an intermodal preferential looking task, in which they were shown different colored versions of the original objects and heard one of the trained labels. If toddlers understand the label, they are expected to increase their looking time to the target. Looking behavior was measured with an automated eye tracker. Afterward, the nap group went to sleep, while the wake group stayed awake for approximately 2 h. We then repeated the test of their performance on the generalization task. Results: A significant interaction of group and session was found in preferential looking. The performance of the nap group increased after the nap, whereas that of the wake group did not change. Conclusions: Our results suggest that napping improves generalization in toddlers. Citation: Horváth K, Liu S, Plunkett K. A daytime nap facilitates generalization of word meanings in young toddlers. SLEEP 2016;39(1):203–207. PMID:26237777

Studies on nap sleep in young students. Relationships between polygraphic data and the occurrence of dreams in replacing naps.

PubMed

Islas-Marroquín, J; Delgado-Brambila, H A

1998-01-01

Afternoon nap sleep was studied in 32 young male medical students who take customary naps to replace loss in nocturnal sleep. From 16 subjects, a group called dreamers was formed, and the other 16 individuals were grouped as non-dreamers. Polygraphic recordings lasting 30 min were done at a fixed time in the afternoon, and the relationship between these data and the occurrence of dreams was investigated. We found that this replacing of nap sleep can adopt different sequences and relative durations of its phases, and can also show individual variations that have a systematic relationship with the occurrence of dreams. It was observed that dreaming was closely related to the appearance, during the first 10 minutes of the nap, of Stage I with Slow Eye Movements, interrupted by Sleep Onset REM Periods (SOREMPs) and, to a lesser degree, to phases IV and III of slow sleep. According to these findings, the existence of dreamers and non-dreamers depends upon the relationship between an internal sleep-waking rhythm, and an external rhythm imposed by the daytime resting-activity schedule on the habit of dreaming, and, to a certain extent, on the mental phenomena occurring between the generation of dreams and the moment of awakening.

A Stationary Wavelet Entropy-Based Clustering Approach Accurately Predicts Gene Expression

PubMed Central

Nguyen, Nha; Vo, An; Choi, Inchan

2015-01-01

Abstract Studying epigenetic landscapes is important to understand the condition for gene regulation. Clustering is a useful approach to study epigenetic landscapes by grouping genes based on their epigenetic conditions. However, classical clustering approaches that often use a representative value of the signals in a fixed-sized window do not fully use the information written in the epigenetic landscapes. Clustering approaches to maximize the information of the epigenetic signals are necessary for better understanding gene regulatory environments. For effective clustering of multidimensional epigenetic signals, we developed a method called Dewer, which uses the entropy of stationary wavelet of epigenetic signals inside enriched regions for gene clustering. Interestingly, the gene expression levels were highly correlated with the entropy levels of epigenetic signals. Dewer separates genes better than a window-based approach in the assessment using gene expression and achieved a correlation coefficient above 0.9 without using any training procedure. Our results show that the changes of the epigenetic signals are useful to study gene regulation. PMID:25383910

Improving alertness and performance in emergency department physicians and nurses: the use of planned naps.

PubMed

Smith-Coggins, Rebecca; Howard, Steven K; Mac, Dat T; Wang, Cynthia; Kwan, Sharon; Rosekind, Mark R; Sowb, Yasser; Balise, Raymond; Levis, Joel; Gaba, David M

2006-11-01

We examine whether a 40-minute nap opportunity at 3 AM can improve cognitive and psychomotor performance in physicians and nurses working 12-hour night shifts. This is a randomized controlled trial of 49 physicians and nurses working 3 consecutive night shifts in an academic emergency department. Subjects were randomized to a control group (no-nap condition=NONE) or nap intervention group (40-minute nap opportunity at 3 AM=NAP). The main outcome measures were Psychomotor Vigilance Task, Probe Recall Memory Task, CathSim intravenous insertion virtual reality simulation, and Profile of Mood States, which were administered before (6:30 PM), during (4 AM), and after (7:30 AM) night shifts. A 40-minute driving simulation was administered at 8 AM and videotaped for behavioral signs of sleepiness and driving accuracy. During the nap period, standard polysomnographic data were recorded. Polysomnographic data revealed that 90% of nap subjects were able to sleep for an average of 24.8 minutes (SD 11.1). At 7:30 AM, the nap group had fewer performance lapses (NAP 3.13, NONE 4.12; p<0.03; mean difference 0.99; 95% CI: -0.1-2.08), reported more vigor (NAP 4.44, NONE 2.39; p<0.03; mean difference 2.05; 95% CI: 0.63-3.47), less fatigue (NAP 7.4, NONE 10.43; p<0.05; mean difference 3.03; 95% CI: 1.11-4.95), and less sleepiness (NAP 5.36, NONE 6.48; p<0.03; mean difference 1.12; 95% CI: 0.41-1.83). They tended to more quickly complete the intravenous insertion (NAP 66.40 sec, NONE 86.48 sec; p=0.10; mean difference 20.08; 95% CI: 4.64-35.52), exhibit less dangerous driving and display fewer behavioral signs of sleepiness during the driving simulation. Immediately after the nap (4 AM), the subjects scored more poorly on Probed Recall Memory (NAP 2.76, NONE 3.7; p<0.05; mean difference 0.94; 95% CI: 0.20-1.68). A nap at 3 AM improved performance and subjective report in physicians and nurses at 7:30 AM compared to a no-nap condition. Immediately after the nap, memory temporarily

Napping during breaks on night shift: critical care nurse managers' perceptions.

PubMed

Edwards, Marie P; McMillan, Diana E; Fallis, Wendy M

2013-01-01

Fatigue associated with shiftwork can threaten the safety and health of nurses and the patients in their care. Napping during night shift breaks has been shown to be an effective strategy to decrease fatigue and enhance performance in a variety of work environments, but appears to have mixed support within health care. The purpose of this study was to explore critical care unit managers'perceptions of and experiences with their nursing staff's napping practices on night shift, including their perceptions of the benefits and barriers to napping/not napping in terms of patient safety and nurses'personal health and safety. A survey design was used. Forty-seven Canadian critical care unit managers who were members of the Canadian Association of Critical Care Nurses responded to the web-based survey. Data analysis involved calculation of frequencies and percentages for demographic data, use of the Friedman rank test for comparison of managers' perceptions, and content analysis for responses to open-ended questions. The findings of this study offer valuable insights into the complexities and conflicts perceived by managers with respect to napping on night shift breaks by nursing staff Staff and patient health and safety issues, work and break expectations and experiences, and strengths and deficits related to organizational napping resources and policy are considerations that will be instrumental in the development of effective napping strategies and guidelines.

An effective fuzzy kernel clustering analysis approach for gene expression data.

PubMed

Sun, Lin; Xu, Jiucheng; Yin, Jiaojiao

2015-01-01

Fuzzy clustering is an important tool for analyzing microarray data. A major problem in applying fuzzy clustering method to microarray gene expression data is the choice of parameters with cluster number and centers. This paper proposes a new approach to fuzzy kernel clustering analysis (FKCA) that identifies desired cluster number and obtains more steady results for gene expression data. First of all, to optimize characteristic differences and estimate optimal cluster number, Gaussian kernel function is introduced to improve spectrum analysis method (SAM). By combining subtractive clustering with max-min distance mean, maximum distance method (MDM) is proposed to determine cluster centers. Then, the corresponding steps of improved SAM (ISAM) and MDM are given respectively, whose superiority and stability are illustrated through performing experimental comparisons on gene expression data. Finally, by introducing ISAM and MDM into FKCA, an effective improved FKCA algorithm is proposed. Experimental results from public gene expression data and UCI database show that the proposed algorithms are feasible for cluster analysis, and the clustering accuracy is higher than the other related clustering algorithms.

Clustering Genes of Common Evolutionary History

PubMed Central

Gori, Kevin; Suchan, Tomasz; Alvarez, Nadir; Goldman, Nick; Dessimoz, Christophe

2016-01-01

Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent—due to events such as incomplete lineage sorting or horizontal gene transfer—it can be misleading to infer a single tree. To address this, many previous contributions have taken a mechanistic approach, by modeling specific processes. Alternatively, one can cluster loci without assuming how these incongruencies might arise. Such “process-agnostic” approaches typically infer a tree for each locus and cluster these. There are, however, many possible combinations of tree distance and clustering methods; their comparative performance in the context of tree incongruence is largely unknown. Furthermore, because standard model selection criteria such as AIC cannot be applied to problems with a variable number of topologies, the issue of inferring the optimal number of clusters is poorly understood. Here, we perform a large-scale simulation study of phylogenetic distances and clustering methods to infer loci of common evolutionary history. We observe that the best-performing combinations are distances accounting for branch lengths followed by spectral clustering or Ward’s method. We also introduce two statistical tests to infer the optimal number of clusters and show that they strongly outperform the silhouette criterion, a general-purpose heuristic. We illustrate the usefulness of the approach by 1) identifying errors in a previous phylogenetic analysis of yeast species and 2) identifying topological incongruence among newly sequenced loci of the globeflower fly genus Chiastocheta. We release treeCl, a new program to cluster genes of common evolutionary history (http://git.io/treeCl). PMID:26893301

The impact of short night-time naps on performance, sleepiness and mood during a simulated night shift.

PubMed

Centofanti, Stephanie A; Hilditch, Cassie J; Dorrian, Jillian; Banks, Siobhan

2016-01-01

Short naps on night shift are recommended in some industries. There is a paucity of evidence to verify the sustained recovery benefits of short naps in the last few hours of the night shift. Therefore, the current study aimed to investigate the sustained recovery benefits of 30 and 10-min nap opportunities during a simulated night shift. Thirty-one healthy participants (18F, 21-35 y) completed a 3-day, between-groups laboratory study with one baseline night (22:00-07:00 h time in bed), followed by one night awake (time awake from 07:00 h on day two through 10:00 h day three) with random allocation to: a 10-min nap opportunity ending at 04:00 h, a 30-min nap opportunity ending at 04:00 h or no nap (control). A neurobehavioral test bout was administered approximately every 2 h during wake periods. There were no significant differences between nap conditions for post-nap psychomotor vigilance performance after controlling for pre-nap scores (p > 0.05). The 30-min nap significantly improved subjective sleepiness compared to the 10-min nap and no-nap control (p < 0.05). The 10-min nap significantly worsened negative mood compared to the 30-min nap and no-nap control (p < 0.01). Contrary to some evidence suggesting "power naps" can help to alleviate performance decrements, a 30-min nap opportunity at approximately 04:00 h was found to improve subjective, but not objective sleepiness. A 10-min nap may lead to increased negative mood in the hours following the nap due to a "short nap aversion" effect.

Distribution and Genetic Diversity of Bacteriocin Gene Clusters in Rumen Microbial Genomes.

PubMed

Azevedo, Analice C; Bento, Cláudia B P; Ruiz, Jeronimo C; Queiroz, Marisa V; Mantovani, Hilário C

2015-10-01

Some species of ruminal bacteria are known to produce antimicrobial peptides, but the screening procedures have mostly been based on in vitro assays using standardized methods. Recent sequencing efforts have made available the genome sequences of hundreds of ruminal microorganisms. In this work, we performed genome mining of the complete and partial genome sequences of 224 ruminal bacteria and 5 ruminal archaea to determine the distribution and diversity of bacteriocin gene clusters. A total of 46 bacteriocin gene clusters were identified in 33 strains of ruminal bacteria. Twenty gene clusters were related to lanthipeptide biosynthesis, while 11 gene clusters were associated with sactipeptide production, 7 gene clusters were associated with class II bacteriocin production, and 8 gene clusters were associated with class III bacteriocin production. The frequency of strains whose genomes encode putative antimicrobial peptide precursors was 14.4%. Clusters related to the production of sactipeptides were identified for the first time among ruminal bacteria. BLAST analysis indicated that the majority of the gene clusters (88%) encoding putative lanthipeptides contained all the essential genes required for lanthipeptide biosynthesis. Most strains of Streptococcus (66.6%) harbored complete lanthipeptide gene clusters, in addition to an open reading frame encoding a putative class II bacteriocin. Albusin B-like proteins were found in 100% of the Ruminococcus albus strains screened in this study. The in silico analysis provided evidence of novel biosynthetic gene clusters in bacterial species not previously related to bacteriocin production, suggesting that the rumen microbiota represents an underexplored source of antimicrobial peptides. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Sleep duration, nap habits, and mortality in older persons.

PubMed

Cohen-Mansfield, Jiska; Perach, Rotem

2012-07-01

To examine the effect of nighttime sleep duration on mortality and the effect modification of daytime napping on the relationship between nighttime sleep duration and mortality in older persons. Prospective survey with 20-yr mortality follow-up. The Cross-Sectional and Longitudinal Aging Study, a multidimensional assessment of a stratified random sample of the older Jewish population in Israel conducted between 1989-1992. There were 1,166 self-respondent, community-dwelling participants age 75-94 yr (mean, 83.40, standard deviation, 5.30). Nighttime sleep duration, napping, functioning (activities of daily living, instrumental activities of daily living, Orientation Memory Concentration Test), health, and mortality. Duration of nighttime sleep of more than 9 hr was significantly related to increased mortality in comparison with sleeping 7-9 hr (hazard ratio [HR] = 1.31, P < 0.01) after adjusting for demographic, health, and function variables, whereas for short nighttime sleep of fewer than 7 hr mortality did not differ from that of 7-9 hr of sleep. For those who nap, sleeping more than 9 hr per night significantly increased mortality risk (HR = 1.385, P < 0.05) and shorter nighttime sleep reduced mortality significantly in the unadjusted model (HR = 0.71, P < 0.001) but only approached significance in the fully adjusted model (HR = 0.82, P = 0.054). For those who do not or sometimes nap, a short amount of sleep appears to be harmful up to age 84 yr and may be protective thereafter (HR = 1.51, confidence interval [CI] = 1.13-2.02, P < 0.01; HR = 0.76, CI = 0.49-1.17, in the fully adjusted model, respectively). The findings are novel in demonstrating the protective effect of short nighttime sleep duration in individuals who take daily naps and suggest that the examination of the effect of sleep needs to take into account sleep duration per 24 hr, rather than daytime napping or nighttime sleep per se. Cohen-Mansfield J; Perach R. Sleep duration, nap habits, and

Assembly and features of secondary metabolite biosynthetic gene clusters in Streptomyces ansochromogenes.

PubMed

Zhong, Xingyu; Tian, Yuqing; Niu, Guoqing; Tan, Huarong

2013-07-01

A draft genome sequence of Streptomyces ansochromogenes 7100 was generated using 454 sequencing technology. In combination with local BLAST searches and gap filling techniques, a comprehensive antiSMASH-based method was adopted to assemble the secondary metabolite biosynthetic gene clusters in the draft genome of S. ansochromogenes. A total of at least 35 putative gene clusters were identified and assembled. Transcriptional analysis showed that 20 of the 35 gene clusters were expressed in either or all of the three different media tested, whereas the other 15 gene clusters were silent in all three different media. This study provides a comprehensive method to identify and assemble secondary metabolite biosynthetic gene clusters in draft genomes of Streptomyces, and will significantly promote functional studies of these secondary metabolite biosynthetic gene clusters.

Relationships Among Daytime Napping and Fatigue, Sleep Quality, and Quality of Life in Cancer Patients.

PubMed

Sun, Jia-Ling; Lin, Chia-Chin

2016-01-01

The relationships among napping and sleep quality, fatigue, and quality of life (QOL) in cancer patients are not clearly understood. The aim of the study was to determine whether daytime napping is associated with nighttime sleep, fatigue, and QOL in cancer patients. In total, 187 cancer patients were recruited. Daytime napping, nighttime self-reported sleep, fatigue, and QOL were assessed using a questionnaire. Objective sleep parameters were collected using a wrist actigraph. According to waking-after-sleep-onset measurements, patients who napped during the day experienced poorer nighttime sleep than did patients who did not (t = -2.44, P = .02). Daytime napping duration was significantly negatively correlated with QOL. Patients who napped after 4 PM had poorer sleep quality (t = -1.93, P = .05) and a poorer Short-Form Health Survey mental component score (t = 2.06, P = .04) than did patients who did not. Fatigue, daytime napping duration, and sleep quality were significant predictors of the mental component score and physical component score, accounting for 45.7% and 39.3% of the variance, respectively. Daytime napping duration was negatively associated with QOL. Napping should be avoided after 4 PM. Daytime napping affects the QOL of cancer patients. Future research can determine the role of napping in the sleep hygiene of cancer patients.

Transcriptome Analysis of Aspergillus flavus Reveals veA-Dependent Regulation of Secondary Metabolite Gene Clusters, Including the Novel Aflavarin Cluster

PubMed Central

Cary, J. W.; Han, Z.; Yin, Y.; Lohmar, J. M.; Shantappa, S.; Harris-Coward, P. Y.; Mack, B.; Ehrlich, K. C.; Wei, Q.; Arroyo-Manzanares, N.; Uka, V.; Vanhaecke, L.; Bhatnagar, D.; Yu, J.; Nierman, W. C.; Johns, M. A.; Sorensen, D.; Shen, H.; De Saeger, S.; Diana Di Mavungu, J.

2015-01-01

The global regulatory veA gene governs development and secondary metabolism in numerous fungal species, including Aspergillus flavus. This is especially relevant since A. flavus infects crops of agricultural importance worldwide, contaminating them with potent mycotoxins. The most well-known are aflatoxins, which are cytotoxic and carcinogenic polyketide compounds. The production of aflatoxins and the expression of genes implicated in the production of these mycotoxins are veA dependent. The genes responsible for the synthesis of aflatoxins are clustered, a signature common for genes involved in fungal secondary metabolism. Studies of the A. flavus genome revealed many gene clusters possibly connected to the synthesis of secondary metabolites. Many of these metabolites are still unknown, or the association between a known metabolite and a particular gene cluster has not yet been established. In the present transcriptome study, we show that veA is necessary for the expression of a large number of genes. Twenty-eight out of the predicted 56 secondary metabolite gene clusters include at least one gene that is differentially expressed depending on presence or absence of veA. One of the clusters under the influence of veA is cluster 39. The absence of veA results in a downregulation of the five genes found within this cluster. Interestingly, our results indicate that the cluster is expressed mainly in sclerotia. Chemical analysis of sclerotial extracts revealed that cluster 39 is responsible for the production of aflavarin. PMID:26209694

Napping reverses the salivary interleukin-6 and urinary norepinephrine changes induced by sleep restriction.

PubMed

Faraut, Brice; Nakib, Samir; Drogou, Catherine; Elbaz, Maxime; Sauvet, Fabien; De Bandt, Jean-Pascal; Léger, Damien

2015-03-01

Neuroendocrine and immune stresses imposed by chronic sleep restriction are known to be involved in the harmful cardiovascular effects associated with poor sleep. Despite a well-known beneficial effect of napping on alertness, its effects on neuroendocrine stress and immune responses after sleep restriction are largely unknown. This study was a strictly controlled (sleep-wake status, light environment, caloric intake), crossover, randomized design in continuously polysomnography-monitored subjects. The study was conducted in a laboratory-based study. The subjects were 11 healthy young men. We investigated the effects on neuroendocrine and immune biomarkers of a night of sleep restricted to 2 h followed by a day without naps or with 30 minute morning and afternoon naps, both conditions followed by an ad libitum recovery night starting at 20:00. Salivary interleukin-6 and urinary catecholamines were assessed throughout the daytime study periods. The increase in norepinephrine values seen at the end of the afternoon after the sleep-restricted night was not present when the subjects had the opportunity to take naps. Interleukin-6 changes observed after sleep deprivation were also normalized after napping. During the recovery day in the no-nap condition, there were increased levels of afternoon epinephrine and dopamine, which was not the case in the nap condition. A recovery night after napping was associated with a reduced amount of slow-wave sleep compared to after the no-nap condition. Our data suggest that napping has stress-releasing and immune effects. Napping could be easily applied in real settings as a countermeasure to the detrimental health consequences of sleep debt.

Identifying a gene expression signature of cluster headache in blood

PubMed Central

Eising, Else; Pelzer, Nadine; Vijfhuizen, Lisanne S.; Vries, Boukje de; Ferrari, Michel D.; ‘t Hoen, Peter A. C.; Terwindt, Gisela M.; van den Maagdenberg, Arn M. J. M.

2017-01-01

Cluster headache is a relatively rare headache disorder, typically characterized by multiple daily, short-lasting attacks of excruciating, unilateral (peri-)orbital or temporal pain associated with autonomic symptoms and restlessness. To better understand the pathophysiology of cluster headache, we used RNA sequencing to identify differentially expressed genes and pathways in whole blood of patients with episodic (n = 19) or chronic (n = 20) cluster headache in comparison with headache-free controls (n = 20). Gene expression data were analysed by gene and by module of co-expressed genes with particular attention to previously implicated disease pathways including hypocretin dysregulation. Only moderate gene expression differences were identified and no associations were found with previously reported pathogenic mechanisms. At the level of functional gene sets, associations were observed for genes involved in several brain-related mechanisms such as GABA receptor function and voltage-gated channels. In addition, genes and modules of co-expressed genes showed a role for intracellular signalling cascades, mitochondria and inflammation. Although larger study samples may be required to identify the full range of involved pathways, these results indicate a role for mitochondria, intracellular signalling and inflammation in cluster headache. PMID:28074859

The human RHOX gene cluster: target genes and functional analysis of gene variants in infertile men.

PubMed

Borgmann, Jennifer; Tüttelmann, Frank; Dworniczak, Bernd; Röpke, Albrecht; Song, Hye-Won; Kliesch, Sabine; Wilkinson, Miles F; Laurentino, Sandra; Gromoll, Jörg

2016-11-15

The X-linked reproductive homeobox (RHOX) gene cluster encodes transcription factors preferentially expressed in reproductive tissues. This gene cluster has important roles in male fertility based on phenotypic defects of Rhox-mutant mice and the finding that aberrant RHOX promoter methylation is strongly associated with abnormal human sperm parameters. However, little is known about the molecular mechanism of RHOX function in humans. Using gene expression profiling, we identified genes regulated by members of the human RHOX gene cluster. Some genes were uniquely regulated by RHOXF1 or RHOXF2/2B, while others were regulated by both of these transcription factors. Several of these regulated genes encode proteins involved in processes relevant to spermatogenesis; e.g. stress protection and cell survival. One of the target genes of RHOXF2/2B is RHOXF1, suggesting cross-regulation to enhance transcriptional responses. The potential role of RHOX in human infertility was addressed by sequencing all RHOX exons in a group of 250 patients with severe oligozoospermia. This revealed two mutations in RHOXF1 (c.515G > A and c.522C > T) and four in RHOXF2/2B (-73C > G, c.202G > A, c.411C > T and c.679G > A), of which only one (c.202G > A) was found in a control group of men with normal sperm concentration. Functional analysis demonstrated that c.202G > A and c.679G > A significantly impaired the ability of RHOXF2/2B to regulate downstream genes. Molecular modelling suggested that these mutations alter RHOXF2/F2B protein conformation. By combining clinical data with in vitro functional analysis, we demonstrate how the X-linked RHOX gene cluster may function in normal human spermatogenesis and we provide evidence that it is impaired in human male fertility.

Many nonuniversal archaeal ribosomal proteins are found in conserved gene clusters

PubMed Central

WANG, JIACHEN; DASGUPTA, INDRANI; FOX, GEORGE E.

2009-01-01

The genomic associations of the archaeal ribosomal proteins, (r-proteins), were examined in detail. The archaeal versions of the universal r-protein genes are typically in clusters similar or identical and to those found in bacteria. Of the 35 nonuniversal archaeal r-protein genes examined, the gene encoding L18e was found to be associated with the conserved L13 cluster, whereas the genes for S4e, L32e and L19e were found in the archaeal version of the spc operon. Eleven nonuniversal protein genes were not associated with any common genomic context. Of the remaining 19 protein genes, 17 were convincingly assigned to one of 10 previously unrecognized gene clusters. Examination of the gene content of these clusters revealed multiple associations with genes involved in the initiation of protein synthesis, transcription or other cellular processes. The lack of such associations in the universal clusters suggests that initially the ribosome evolved largely independently of other processes. More recently it likely has evolved in concert with other cellular systems. It was also verified that a second copy of the gene encoding L7ae found in some bacteria is actually a homolog of the gene encoding L30e and should be annotated as such. PMID:19478915

The Concept of Qailulah (Midday Napping) from Neuroscientific and Islamic Perspectives.

PubMed

Tumiran, Mohd Amzari; Rahman, Noor Naemah Abdul; Saat, Rohaida Mohd; Kabir, Nurul; Zulkifli, Mohd Yakub; Adli, Durriyyah Sharifah Hasan

2015-08-13

Napping/siesta during the day is a phenomenon, which is widely practised in the world. However, the timing, frequency, and duration may vary. The basis of napping is also diverse, but it is mainly done for improvement in alertness and general well-being. Neuroscience reveals that midday napping improves memory, enhances alertness, boosts wakefulness and performance, and recovers certain qualities of lost night sleep. Interestingly, Islam, the religion of the Muslims, advocates midday napping primarily because it was a practice preferred by Prophet Muhammad (pbuh). The objectives of this review were to investigate and compare identical key points on focused topic from both neuroscientific and Islamic perspectives and make recommendations for future researches.

Effects of afternoon "siesta" naps on sleep, alertness, performance, and circadian rhythms in the elderly

NASA Technical Reports Server (NTRS)

Monk, T. H.; Buysse, D. J.; Carrier, J.; Billy, B. D.; Rose, L. R.

2001-01-01

STUDY OBJECTIVES: To determine the effects of a 90-minute afternoon nap regimen on nocturnal sleep, circadian rhythms, and evening alertness and performance levels in the healthy elderly. DESIGN AND SETTING: Nine healthy elderly subjects (4m, 5f, age range 74y-87y) each experienced both nap and no-nap conditions in two studies each lasting 17 days (14 at home, 3 in the laboratory). In the nap condition a 90-minute nap was enforced between 13:30 and 15:00 every day, in the no-nap condition daytime napping was prohibited, and activity encouraged in the 13:30-15:00 interval. The order of the two conditions was counterbalanced. PARTICIPANTS: N/A INTERVENTIONS: N/A MEASUREMENTS: Diary measures, pencil and paper alertness tests, and wrist actigraphy were used at home. In the 72 hour laboratory studies, these measures were augmented by polysomnographic sleep recording, continuous rectal temperature measurement, a daily evening single trial of a Multiple Sleep Latency Test (MSLT), and computerized tests of mood, activation and performance efficiency. RESULTS: By the second week in the "at home" study, an average of 58 minutes of sleep was reported per siesta nap; in the laboratory, polysomnography confirmed an average of 57 minutes of sleep per nap. When nap and no-nap conditions were compared, mixed effects on nocturnal sleep were observed. Diary measures indicated no significant difference in nocturnal sleep duration, but a significant increase (of 38 mins.) in 24-hour Total Sleep Time (TST) when nocturnal sleeps and naps were added together (p<0.025). The laboratory study revealed a decrease of 2.4% in nocturnal sleep efficiency in the nap condition (p<0.025), a reduction of nocturnal Total Sleep Time (TST) by 48 mins. in the nap condition (p<0.001) which resulted primarily from significantly earlier waketimes (p<0.005), but no reliable effects on Wake After Sleep Onset (WASO), delta sleep measures, or percent stages 1 & 2. Unlike the diary study, the laboratory study

Hox gene cluster of the ascidian, Halocynthia roretzi, reveals multiple ancient steps of cluster disintegration during ascidian evolution.

PubMed

Sekigami, Yuka; Kobayashi, Takuya; Omi, Ai; Nishitsuji, Koki; Ikuta, Tetsuro; Fujiyama, Asao; Satoh, Noriyuki; Saiga, Hidetoshi

2017-01-01

Hox gene clusters with at least 13 paralog group (PG) members are common in vertebrate genomes and in that of amphioxus. Ascidians, which belong to the subphylum Tunicata (Urochordata), are phylogenetically positioned between vertebrates and amphioxus, and traditionally divided into two groups: the Pleurogona and the Enterogona. An enterogonan ascidian, Ciona intestinalis ( Ci ), possesses nine Hox genes localized on two chromosomes; thus, the Hox gene cluster is disintegrated. We investigated the Hox gene cluster of a pleurogonan ascidian, Halocynthia roretzi ( Hr ) to investigate whether Hox gene cluster disintegration is common among ascidians, and if so, how such disintegration occurred during ascidian or tunicate evolution. Our phylogenetic analysis reveals that the Hr Hox gene complement comprises nine members, including one with a relatively divergent Hox homeodomain sequence. Eight of nine Hr Hox genes were orthologous to Ci-Hox1 , 2, 3, 4, 5, 10, 12 and 13. Following the phylogenetic classification into 13 PGs, we designated Hr Hox genes as Hox1, 2, 3, 4, 5, 10, 11/12/13.a , 11/12/13.b and HoxX . To address the chromosomal arrangement of the nine Hox genes, we performed two-color chromosomal fluorescent in situ hybridization, which revealed that the nine Hox genes are localized on a single chromosome in Hr , distinct from their arrangement in Ci . We further examined the order of the nine Hox genes on the chromosome by chromosome/scaffold walking. This analysis suggested a gene order of Hox1 , 11/12/13.b, 11/12/13.a, 10, 5, X, followed by either Hox4, 3, 2 or Hox2, 3, 4 on the chromosome. Based on the present results and those previously reported in Ci , we discuss the establishment of the Hox gene complement and disintegration of Hox gene clusters during the course of ascidian or tunicate evolution. The Hox gene cluster and the genome must have experienced extensive reorganization during the course of evolution from the ancestral tunicate to Hr and Ci

The ergot alkaloid gene cluster: functional analyses and evolutionary aspects.

PubMed

Lorenz, Nicole; Haarmann, Thomas; Pazoutová, Sylvie; Jung, Manfred; Tudzynski, Paul

2009-01-01

Ergot alkaloids and their derivatives have been traditionally used as therapeutic agents in migraine, blood pressure regulation and help in childbirth and abortion. Their production in submerse culture is a long established biotechnological process. Ergot alkaloids are produced mainly by members of the genus Claviceps, with Claviceps purpurea as best investigated species concerning the biochemistry of ergot alkaloid synthesis (EAS). Genes encoding enzymes involved in EAS have been shown to be clustered; functional analyses of EAS cluster genes have allowed to assign specific functions to several gene products. Various Claviceps species differ with respect to their host specificity and their alkaloid content; comparison of the ergot alkaloid clusters in these species (and of clavine alkaloid clusters in other genera) yields interesting insights into the evolution of cluster structure. This review focuses on recently published and also yet unpublished data on the structure and evolution of the EAS gene cluster and on the function and regulation of cluster genes. These analyses have also significant biotechnological implications: the characterization of non-ribosomal peptide synthetases (NRPS) involved in the synthesis of the peptide moiety of ergopeptines opened interesting perspectives for the synthesis of ergot alkaloids; on the other hand, defined mutants could be generated producing interesting intermediates or only single peptide alkaloids (instead of the alkaloid mixtures usually produced by industrial strains).

Duration of sleep inertia after napping during simulated night work and in extended operations.

PubMed

Signal, Tracey Leigh; van den Berg, Margo J; Mulrine, Hannah M; Gander, Philippa H

2012-07-01

Due to the mixed findings of previous studies, it is still difficult to provide guidance on how to best manage sleep inertia after waking from naps in operational settings. One of the few factors that can be manipulated is the duration of the nap opportunity. The aim of the present study was to investigate the magnitude and time course of sleep inertia after waking from short (20-, 40- or 60-min) naps during simulated night work and extended operations. In addition, the effect of sleep stage on awakening and duration of slow wave sleep (SWS) on sleep inertia was assessed. Two within-subject protocols were conducted in a controlled laboratory setting. Twenty-four healthy young men (Protocol 1: n = 12, mean age = 25.1 yrs; Protocol 2: n = 12, mean age = 23.2 yrs) were provided with nap opportunities of 20-, 40-, and 60-min (and a control condition of no nap) ending at 02:00 h after ∼20 h of wakefulness (Protocol 1 [P1]: simulated night work) or ending at 12:00 h after ∼30 h of wakefulness (Protocol 2 [P2]: simulated extended operations). A 6-min test battery, including the Karolinska Sleepiness Scale (KSS) and the 4-min 2-Back Working Memory Task (WMT), was repeated every 15 min the first hour after waking. Nap sleep was recorded polysomnographically, and in all nap opportunities sleep onset latency was short and sleep efficiency high. Mixed-model analyses of variance (ANOVA) for repeated measures were calculated and included the factors time (time post-nap), nap opportunity (duration of nap provided), order (order in which the four protocols were completed), and the interaction of these terms. Results showed no test x nap opportunity effect (i.e., no effect of sleep inertia) on KSS. However, WMT performance was impaired (slower reaction time, fewer correct responses, and increased omissions) on the first test post-nap, primarily after a 40- or 60-min nap. In P2 only, performance improvement was evident 45 min post-awakening for naps of 40 min or more. In ANOVAs

Clustered Genes Involved in Cyclopiazonic Acid Production are Next to the Aflatoxin Biosynthesis Gene Cluster in Aspergillus flavus

USDA-ARS?s Scientific Manuscript database

Cyclopiazonic acid (CPA), an indole-tetramic acid toxin, is produced by many species of Aspergillus and Penicillium. In addition to CPA Aspergillus flavus produces polyketide-derived carcinogenic aflatoxins (AFs). AF biosynthesis genes form a gene cluster in a subtelomeric region. Isolates of A. fla...

Unusual Gene Order and Organization of the Sea Urchin Hox Cluster

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

Cameron, R A; Rowen, L; Nesbitt, R

2005-10-11

The highly consistent gene order and axial colinear expression patterns found in vertebrate hox gene clusters are less well conserved across the rest of bilaterians. We report the first deuterostome instance of an intact hox cluster with a unique gene order where the paralog groups are not expressed in a sequential manner. The finished sequence from BAC clones from the genome of the sea urchin, Strongylocentrotus purpuratus, reveals a gene order wherein the anterior genes (Hox1, Hox2 and Hox3) lie nearest the posterior genes in the cluster such that the most 3 gene is Hox5. (The gene order is :more » 5-Hox1, 2, 3, 11/13c, 11/13b, 11/13a, 9/10, 8, 7, 6, 5 - 3). The finished sequence result is corroborated by restriction mapping evidence and BAC-end scaffold analyses. Comparisons with a putative ancestral deuterostome Hox gene cluster suggest that the rearrangements leading to the sea urchin gene order were many and complex.« less

Unusual Gene Order and Organization of the Sea Urchin HoxCluster

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

Richardson, Paul M.; Lucas, Susan; Cameron, R. Andrew

2005-05-10

The highly consistent gene order and axial colinear expression patterns found in vertebrate hox gene clusters are less well conserved across the rest of bilaterians. We report the first deuterostome instance of an intact hox cluster with a unique gene order where the paralog groups are not expressed in a sequential manner. The finished sequence from BAC clones from the genome of the sea urchin, Strongylocentrotus purpuratus, reveals a gene order wherein the anterior genes (Hox1, Hox2 and Hox3) lie nearest the posterior genes in the cluster such that the most 3' gene is Hox5. (The gene order is :more » 5'-Hox1,2, 3, 11/13c, 11/13b, '11/13a, 9/10, 8, 7, 6, 5 - 3)'. The finished sequence result is corroborated by restriction mapping evidence and BAC-end scaffold analyses. Comparisons with a putative ancestral deuterostome Hox gene cluster suggest that the rearrangements leading to the sea urchin gene order were many and complex.« less

clusterProfiler: an R package for comparing biological themes among gene clusters.

PubMed

Yu, Guangchuang; Wang, Li-Gen; Han, Yanyan; He, Qing-Yu

2012-05-01

Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters. The analysis module and visualization module were combined into a reusable workflow. Currently, clusterProfiler supports three species, including humans, mice, and yeast. Methods provided in this package can be easily extended to other species and ontologies. The clusterProfiler package is released under Artistic-2.0 License within Bioconductor project. The source code and vignette are freely available at http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html.

From hormones to secondary metabolism: the emergence of metabolic gene clusters in plants.

PubMed

Chu, Hoi Yee; Wegel, Eva; Osbourn, Anne

2011-04-01

Gene clusters for the synthesis of secondary metabolites are a common feature of microbial genomes. Well-known examples include clusters for the synthesis of antibiotics in actinomycetes, and also for the synthesis of antibiotics and toxins in filamentous fungi. Until recently it was thought that genes for plant metabolic pathways were not clustered, and this is certainly true in many cases; however, five plant secondary metabolic gene clusters have now been discovered, all of them implicated in synthesis of defence compounds. An obvious assumption might be that these eukaryotic gene clusters have arisen by horizontal gene transfer from microbes, but there is compelling evidence to indicate that this is not the case. This raises intriguing questions about how widespread such clusters are, what the significance of clustering is, why genes for some metabolic pathways are clustered and those for others are not, and how these clusters form. In answering these questions we may hope to learn more about mechanisms of genome plasticity and adaptive evolution in plants. It is noteworthy that for the five plant secondary metabolic gene clusters reported so far, the enzymes for the first committed steps all appear to have been recruited directly or indirectly from primary metabolic pathways involved in hormone synthesis. This may or may not turn out to be a common feature of plant secondary metabolic gene clusters as new clusters emerge. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species

PubMed Central

Lind, Abigail L.; Wisecaver, Jennifer H.; Lameiras, Catarina; Wiemann, Philipp; Palmer, Jonathan M.; Keller, Nancy P.; Rodrigues, Fernando; Goldman, Gustavo H.

2017-01-01

Filamentous fungi produce a diverse array of secondary metabolites (SMs) critical for defense, virulence, and communication. The metabolic pathways that produce SMs are found in contiguous gene clusters in fungal genomes, an atypical arrangement for metabolic pathways in other eukaryotes. Comparative studies of filamentous fungal species have shown that SM gene clusters are often either highly divergent or uniquely present in one or a handful of species, hampering efforts to determine the genetic basis and evolutionary drivers of SM gene cluster divergence. Here, we examined SM variation in 66 cosmopolitan strains of a single species, the opportunistic human pathogen Aspergillus fumigatus. Investigation of genome-wide within-species variation revealed 5 general types of variation in SM gene clusters: nonfunctional gene polymorphisms; gene gain and loss polymorphisms; whole cluster gain and loss polymorphisms; allelic polymorphisms, in which different alleles corresponded to distinct, nonhomologous clusters; and location polymorphisms, in which a cluster was found to differ in its genomic location across strains. These polymorphisms affect the function of representative A. fumigatus SM gene clusters, such as those involved in the production of gliotoxin, fumigaclavine, and helvolic acid as well as the function of clusters with undefined products. In addition to enabling the identification of polymorphisms, the detection of which requires extensive genome-wide synteny conservation (e.g., mobile gene clusters and nonhomologous cluster alleles), our approach also implicated multiple underlying genetic drivers, including point mutations, recombination, and genomic deletion and insertion events as well as horizontal gene transfer from distant fungi. Finally, most of the variants that we uncover within A. fumigatus have been previously hypothesized to contribute to SM gene cluster diversity across entire fungal classes and phyla. We suggest that the drivers of genetic

Analysis of lamprey clustered Fox genes: insight into Fox gene evolution and expression in vertebrates.

PubMed

Wotton, Karl R; Shimeld, Sebastian M

2011-12-01

In the human genome, members of the FoxC, FoxF, FoxL1, and FoxQ1 gene families are found in two paralagous clusters. One cluster contains the genes FOXQ1, FOXF2, FOXC1 and the second consists of FOXF1, FOXC2, and FOXL1. In jawed vertebrates these genes are known to be expressed in different pharyngeal tissues and all, except FoxQ1, are involved in patterning the early embryonic mesoderm. We have previously traced the evolution of this cluster in the bony vertebrates, and the gene content is identical in the dogfish, a member of the most basally branching lineage of the jawed vertebrates. Here we extend these analyses to jawless vertebrates. Using genomic searches and molecular approaches we have identified homologues of these genes from lampreys. We identify two FoxC genes, two FoxF genes, two FoxQ1 genes and single FoxL1 gene. We examine the embryonic expression of one predominantly mesodermally expressed gene family, FoxC, and the endodermally expressed member of the cluster, FoxQ1. We identified FoxQ1 transcripts in the pharyngeal endoderm, while the two FoxC genes are differentially expressed in the pharyngeal mesenchyme and ectoderm. Furthermore we identify conserved expression of lamprey FoxC genes in the paraxial and intermediate mesoderms. We interpret our results through a chordate-wide comparison of expression patterns and discuss gene content in the context of theories on the evolution of the vertebrate genome. 2011 Elsevier B.V. All rights reserved.

Identification and Functional Analysis of the Nocardithiocin Gene Cluster in Nocardia pseudobrasiliensis

PubMed Central

Sakai, Kanae; Komaki, Hisayuki; Gonoi, Tohru

2015-01-01

Nocardithiocin is a thiopeptide compound isolated from the opportunistic pathogen Nocardia pseudobrasiliensis. It shows a strong activity against acid-fast bacteria and is also active against rifampicin-resistant Mycobacterium tuberculosis. Here, we report the identification of the nocardithiocin gene cluster in N. pseudobrasiliensis IFM 0761 based on conserved thiopeptide biosynthesis gene sequence and the whole genome sequence. The predicted gene cluster was confirmed by gene disruption and complementation. As expected, strains containing the disrupted gene did not produce nocardithiocin while gene complementation restored nocardithiocin production in these strains. The predicted cluster was further analyzed using RNA-seq which showed that the nocardithiocin gene cluster contains 12 genes within a 15.2-kb region. This finding will promote the improvement of nocardithiocin productivity and its derivatives production. PMID:26588225

Lampreys, the jawless vertebrates, contain only two ParaHox gene clusters.

PubMed

Zhang, Huixian; Ravi, Vydianathan; Tay, Boon-Hui; Tohari, Sumanty; Pillai, Nisha E; Prasad, Aravind; Lin, Qiang; Brenner, Sydney; Venkatesh, Byrappa

2017-08-22

ParaHox genes ( Gsx , Pdx , and Cdx ) are an ancient family of developmental genes closely related to the Hox genes. They play critical roles in the patterning of brain and gut. The basal chordate, amphioxus, contains a single ParaHox cluster comprising one member of each family, whereas nonteleost jawed vertebrates contain four ParaHox genomic loci with six or seven ParaHox genes. Teleosts, which have experienced an additional whole-genome duplication, contain six ParaHox genomic loci with six ParaHox genes. Jawless vertebrates, represented by lampreys and hagfish, are the most ancient group of vertebrates and are crucial for understanding the origin and evolution of vertebrate gene families. We have previously shown that lampreys contain six Hox gene loci. Here we report that lampreys contain only two ParaHox gene clusters (designated as α- and β-clusters) bearing five ParaHox genes ( Gsxα , Pdxα , Cdxα , Gsxβ , and Cdxβ ). The order and orientation of the three genes in the α-cluster are identical to that of the single cluster in amphioxus. However, the orientation of Gsxβ in the β-cluster is inverted. Interestingly, Gsxβ is expressed in the eye, unlike its homologs in jawed vertebrates, which are expressed mainly in the brain. The lamprey Pdxα is expressed in the pancreas similar to jawed vertebrate Pdx genes, indicating that the pancreatic expression of Pdx was acquired before the divergence of jawless and jawed vertebrate lineages. It is likely that the lamprey Pdxα plays a crucial role in pancreas specification and insulin production similar to the Pdx of jawed vertebrates.

Afternoon nap and bright light exposure improve cognitive flexibility post lunch.

PubMed

Slama, Hichem; Deliens, Gaétane; Schmitz, Rémy; Peigneux, Philippe; Leproult, Rachel

2015-01-01

Beneficial effects of napping or bright light exposure on cognitive performance have been reported in participants exposed to sleep loss. Nonetheless, few studies investigated the effect of these potential countermeasures against the temporary drop in performance observed in mid-afternoon, and even less so on cognitive flexibility, a crucial component of executive functions. This study investigated the impact of either an afternoon nap or bright light exposure on post-prandial alterations in task switching performance in well-rested participants. Twenty-five healthy adults participated in two randomized experimental conditions, either wake versus nap (n=15), or bright light versus placebo (n=10). Participants were tested on a switching task three times (morning, post-lunch and late afternoon sessions). The interventions occurred prior to the post-lunch session. In the nap/wake condition, participants either stayed awake watching a 30-minute documentary or had the opportunity to take a nap for 30 minutes. In the bright light/placebo condition, participants watched a documentary under either bright blue light or dim orange light (placebo) for 30 minutes. The switch cost estimates cognitive flexibility and measures task-switching efficiency. Increased switch cost scores indicate higher difficulties to switch between tasks. In both control conditions (wake or placebo), accuracy switch-cost score increased post lunch. Both interventions (nap or bright light) elicited a decrease in accuracy switch-cost score post lunch, which was associated with diminished fatigue and decreased variability in vigilance. Additionally, there was a trend for a post-lunch benefit of bright light with a decreased latency switch-cost score. In the nap group, improvements in accuracy switch-cost score were associated with more NREM sleep stage N1. Thus, exposure to bright light during the post-lunch dip, a countermeasure easily applicable in daily life, results in similar beneficial effects as

Afternoon Nap and Bright Light Exposure Improve Cognitive Flexibility Post Lunch

PubMed Central

Schmitz, Rémy; Peigneux, Philippe; Leproult, Rachel

2015-01-01

Beneficial effects of napping or bright light exposure on cognitive performance have been reported in participants exposed to sleep loss. Nonetheless, few studies investigated the effect of these potential countermeasures against the temporary drop in performance observed in mid-afternoon, and even less so on cognitive flexibility, a crucial component of executive functions. This study investigated the impact of either an afternoon nap or bright light exposure on post-prandial alterations in task switching performance in well-rested participants. Twenty-five healthy adults participated in two randomized experimental conditions, either wake versus nap (n=15), or bright light versus placebo (n=10). Participants were tested on a switching task three times (morning, post-lunch and late afternoon sessions). The interventions occurred prior to the post-lunch session. In the nap/wake condition, participants either stayed awake watching a 30-minute documentary or had the opportunity to take a nap for 30 minutes. In the bright light/placebo condition, participants watched a documentary under either bright blue light or dim orange light (placebo) for 30 minutes. The switch cost estimates cognitive flexibility and measures task-switching efficiency. Increased switch cost scores indicate higher difficulties to switch between tasks. In both control conditions (wake or placebo), accuracy switch-cost score increased post lunch. Both interventions (nap or bright light) elicited a decrease in accuracy switch-cost score post lunch, which was associated with diminished fatigue and decreased variability in vigilance. Additionally, there was a trend for a post-lunch benefit of bright light with a decreased latency switch-cost score. In the nap group, improvements in accuracy switch-cost score were associated with more NREM sleep stage N1. Thus, exposure to bright light during the post-lunch dip, a countermeasure easily applicable in daily life, results in similar beneficial effects as

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants

DOE PAGES

Schläpfer, Pascal; Zhang, Peifen; Wang, Chuan; ...

2017-04-01

Plant metabolism underpins many traits of ecological and agronomic importance. Plants produce numerous compounds to cope with their environments but the biosynthetic pathways for most of these compounds have not yet been elucidated. To engineer and improve metabolic traits, we will need comprehensive and accurate knowledge of the organization and regulation of plant metabolism at the genome scale. Here, we present a computational pipeline to identify metabolic enzymes, pathways, and gene clusters from a sequenced genome. Using this pipeline, we generated metabolic pathway databases for 22 species and identified metabolic gene clusters from 18 species. This unified resource can bemore » used to conduct a wide array of comparative studies of plant metabolism. Using the resource, we discovered a widespread occurrence of metabolic gene clusters in plants: 11,969 clusters from 18 species. The prevalence of metabolic gene clusters offers an intriguing possibility of an untapped source for uncovering new metabolite biosynthesis pathways. For example, more than 1,700 clusters contain enzymes that could generate a specialized metabolite scaffold (signature enzymes) and enzymes that modify the scaffold (tailoring enzymes). In four species with sufficient gene expression data, we identified 43 highly coexpressed clusters that contain signature and tailoring enzymes, of which eight were characterized previously to be functional pathways. Finally, we identified patterns of genome organization that implicate local gene duplication and, to a lesser extent, single gene transposition as having played roles in the evolution of plant metabolic gene clusters.« less

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants

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

Schläpfer, Pascal; Zhang, Peifen; Wang, Chuan

Plant metabolism underpins many traits of ecological and agronomic importance. Plants produce numerous compounds to cope with their environments but the biosynthetic pathways for most of these compounds have not yet been elucidated. To engineer and improve metabolic traits, we will need comprehensive and accurate knowledge of the organization and regulation of plant metabolism at the genome scale. Here, we present a computational pipeline to identify metabolic enzymes, pathways, and gene clusters from a sequenced genome. Using this pipeline, we generated metabolic pathway databases for 22 species and identified metabolic gene clusters from 18 species. This unified resource can bemore » used to conduct a wide array of comparative studies of plant metabolism. Using the resource, we discovered a widespread occurrence of metabolic gene clusters in plants: 11,969 clusters from 18 species. The prevalence of metabolic gene clusters offers an intriguing possibility of an untapped source for uncovering new metabolite biosynthesis pathways. For example, more than 1,700 clusters contain enzymes that could generate a specialized metabolite scaffold (signature enzymes) and enzymes that modify the scaffold (tailoring enzymes). In four species with sufficient gene expression data, we identified 43 highly coexpressed clusters that contain signature and tailoring enzymes, of which eight were characterized previously to be functional pathways. Finally, we identified patterns of genome organization that implicate local gene duplication and, to a lesser extent, single gene transposition as having played roles in the evolution of plant metabolic gene clusters.« less

Poor sleep moderates the relationship between daytime napping and inflammation in Black and White men.

PubMed

Jakubowski, Karen P; Boylan, Jennifer M; Cundiff, Jenny M; Matthews, Karen A

2017-10-01

To test whether napping was associated with 2 inflammatory markers with known relationships to cardiovascular disease: high-sensitivity C-reactive protein (hsCRP) and interleukin-6 (IL-6). Because IL-6 is known to impact central inflammatory processes that relate to sleep regulation, including subjective fatigue, we tested whether this relationship was moderated by sleep duration, sleep efficiency, and self-reported sleep quality. Cross-sectional. A community sample of Black and White men (N=253) completed a week of actigraphy and diary measures of sleep and napping and provided a fasting blood sample. Napping was measured as the proportion of days with at least 30 minutes napped and the average minutes napped per day. Linear regressions adjusted for race, socioeconomic status, employment, body mass index, smoking, medications that affect sleep or inflammation, working the nightshift, and day-sleeping status, followed by interaction terms between napping and sleep duration, efficiency, and quality, respectively. There were no significant main effects of actigraphy- or diary-measured napping on IL-6 or hsCRP. Moderation analyses indicated elevated IL-6 values among men who napped more days (by actigraphy) and demonstrated short sleep duration (P=.03). Moderation analyses also indicated elevated IL-6 among men who demonstrated greater average minutes napped (by actigraphy) and short sleep duration (P<.001), low efficiency (P=.03), and poor quality (P=.03). Moderation analyses involving diary napping or hsCRP were not significant. Actigraphy-assessed daytime napping is related to higher IL-6 in men who demonstrate worse sleep characteristics. Daytime napping may pose additional risk for inflammation beyond the known risk conferred by short sleep. Copyright © 2017 National Sleep Foundation. Published by Elsevier Inc. All rights reserved.

Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi.

PubMed

Slot, Jason C; Rokas, Antonis

2011-01-25

Genes involved in intermediary and secondary metabolism in fungi are frequently physically linked or clustered. For example, in Aspergillus nidulans the entire pathway for the production of sterigmatocystin (ST), a highly toxic secondary metabolite and a precursor to the aflatoxins (AF), is located in a ∼54 kb, 23 gene cluster. We discovered that a complete ST gene cluster in Podospora anserina was horizontally transferred from Aspergillus. Phylogenetic analysis shows that most Podospora cluster genes are adjacent to or nested within Aspergillus cluster genes, although the two genera belong to different taxonomic classes. Furthermore, the Podospora cluster is highly conserved in content, sequence, and microsynteny with the Aspergillus ST/AF clusters and its intergenic regions contain 14 putative binding sites for AflR, the transcription factor required for activation of the ST/AF biosynthetic genes. Examination of ∼52,000 Podospora expressed sequence tags identified transcripts for 14 genes in the cluster, with several expressed at multiple life cycle stages. The presence of putative AflR-binding sites and the expression evidence for several cluster genes, coupled with the recent independent discovery of ST production in Podospora [1], suggest that this HGT event probably resulted in a functional cluster. Given the abundance of metabolic gene clusters in fungi, our finding that one of the largest known metabolic gene clusters moved intact between species suggests that such transfers might have significantly contributed to fungal metabolic diversity. PAPERFLICK: Copyright © 2011 Elsevier Ltd. All rights reserved.

Napping, development and health from 0 to 5 years: a systematic review.

PubMed

Thorpe, Karen; Staton, Sally; Sawyer, Emily; Pattinson, Cassandra; Haden, Catherine; Smith, Simon

2015-07-01

Duration and quality of sleep affect child development and health. Encouragement of napping in preschool children has been suggested as a health-promoting strategy. The aim of this study is to assess evidence regarding the effects of napping on measures of child development and health. This study is a systematic review of published, original research articles of any design. Children aged 0-5 years. Electronic database search was performed following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines and assessment of research quality was carried out following a Grading of Recommendations, Assessment, Development and Evaluations (GRADE) protocol. Twenty-six articles met inclusion criteria. These were of heterogeneous quality; all had observational designs (GRADE-low). Development and health outcomes included salivary cortisol, night sleep, cognition, behaviour, obesity and accidents. The findings regarding cognition, behaviour and health impacts were inconsistent, probably because of variation in age and habitual napping status of the samples. The most consistent finding was an association between napping and later onset, shorter duration and poorer quality of night sleep, with evidence strongest beyond the age of 2 years. Studies were not randomised. Most did not obtain data on the children's habitual napping status or the context of napping. Many were reliant on parent report rather than direct observation or physiological measurement of sleep behaviour. The evidence indicates that beyond the age of 2 years napping is associated with later night sleep onset and both reduced sleep quality and duration. The evidence regarding behaviour, health and cognition is less certain. There is a need for more systematic studies that use stronger designs. In preschool children presenting with sleep problems clinicians should investigate napping patterns. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted

The sirodesmin biosynthetic gene cluster of the plant pathogenic fungus Leptosphaeria maculans.

PubMed

Gardiner, Donald M; Cozijnsen, Anton J; Wilson, Leanne M; Pedras, M Soledade C; Howlett, Barbara J

2004-09-01

Sirodesmin PL is a phytotoxin produced by the fungus Leptosphaeria maculans, which causes blackleg disease of canola (Brassica napus). This phytotoxin belongs to the epipolythiodioxopiperazine (ETP) class of toxins produced by fungi including mammalian and plant pathogens. We report the cloning of a cluster of genes with predicted roles in the biosynthesis of sirodesmin PL and show via gene disruption that one of these genes (encoding a two-module non-ribosomal peptide synthetase) is essential for sirodesmin PL biosynthesis. Of the nine genes in the cluster tested, all are co-regulated with the production of sirodesmin PL in culture. A similar cluster is present in the genome of the opportunistic human pathogen Aspergillus fumigatus and is most likely responsible for the production of gliotoxin, which is also an ETP. Homologues of the genes in the cluster were also identified in expressed sequence tags of the ETP producing fungus Chaetomium globosum. Two other fungi with publicly available genome sequences, Magnaporthe grisea and Fusarium graminearum, had similar gene clusters. A comparative analysis of all four clusters is presented. This is the first report of the genes responsible for the biosynthesis of an ETP. Copyright 2004 Blackwell Publishing Ltd

NAP SACC UK: protocol for a feasibility cluster randomised controlled trial in nurseries and at home to increase physical activity and healthy eating in children aged 2-4 years.

PubMed

Kipping, R; Jago, R; Metcalfe, C; White, J; Papadaki, A; Campbell, R; Hollingworth, W; Ward, D; Wells, S; Brockman, R; Nicholson, A; Moore, L

2016-04-06

Systematic reviews have identified the lack of intervention studies with young children to prevent obesity. This feasibility study examines the feasibility and acceptability of adapting the Nutrition and Physical Activity Self-Assessment for Child Care (NAP SACC) intervention in the UK to inform a full-scale trial. A feasibility cluster randomised controlled trial in 12 nurseries in England, with 6 randomly assigned to the adapted NAP SACC UK intervention: nursery staff will receive training and support from an NAP SACC UK Partner to review the nursery environment (nutrition, physical activity, sedentary behaviours and oral health) and set goals for making changes. Parents will be invited to participate in a digital media-based home component to set goals for making changes in the home. As this is a feasibility study, the sample size was not based on a power calculation but will indicate the likely response rates and intracluster correlations. Measures will be assessed at baseline and 8-10 months later. We will estimate the recruitment rate of nurseries and children and adherence to the intervention and data. Nursery measurements will include the Environmental Policy Assessment and Observation score and the nursery staff's review of the nursery environment. Child measurements will include height and weight to calculate z-score body mass index (zBMI), accelerometer-determined minutes of moderate-to-vigorous physical activity per day and sedentary time, and diet using the Child and Diet Evaluation Tool. Questionnaires with nursery staff and parents will measure mediators. A process evaluation will assess fidelity of intervention delivery and views of participants. Ethical approval for this study was given by Wales 3 NHS Research Ethics Committee. Findings will be made available through publication in peer-reviewed journals, at conferences and to participants via the University of Bristol website. Data will be available from the University of Bristol Research Data

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants.

PubMed

Schläpfer, Pascal; Zhang, Peifen; Wang, Chuan; Kim, Taehyong; Banf, Michael; Chae, Lee; Dreher, Kate; Chavali, Arvind K; Nilo-Poyanco, Ricardo; Bernard, Thomas; Kahn, Daniel; Rhee, Seung Y

2017-04-01

Plant metabolism underpins many traits of ecological and agronomic importance. Plants produce numerous compounds to cope with their environments but the biosynthetic pathways for most of these compounds have not yet been elucidated. To engineer and improve metabolic traits, we need comprehensive and accurate knowledge of the organization and regulation of plant metabolism at the genome scale. Here, we present a computational pipeline to identify metabolic enzymes, pathways, and gene clusters from a sequenced genome. Using this pipeline, we generated metabolic pathway databases for 22 species and identified metabolic gene clusters from 18 species. This unified resource can be used to conduct a wide array of comparative studies of plant metabolism. Using the resource, we discovered a widespread occurrence of metabolic gene clusters in plants: 11,969 clusters from 18 species. The prevalence of metabolic gene clusters offers an intriguing possibility of an untapped source for uncovering new metabolite biosynthesis pathways. For example, more than 1,700 clusters contain enzymes that could generate a specialized metabolite scaffold (signature enzymes) and enzymes that modify the scaffold (tailoring enzymes). In four species with sufficient gene expression data, we identified 43 highly coexpressed clusters that contain signature and tailoring enzymes, of which eight were characterized previously to be functional pathways. Finally, we identified patterns of genome organization that implicate local gene duplication and, to a lesser extent, single gene transposition as having played roles in the evolution of plant metabolic gene clusters. © 2017 American Society of Plant Biologists. All Rights Reserved.

Napping Reverses Increased Pain Sensitivity Due to Sleep Restriction

PubMed Central

Faraut, Brice; Léger, Damien; Medkour, Terkia; Dubois, Alexandre; Bayon, Virginie; Chennaoui, Mounir; Perrot, Serge

2015-01-01

Study Objective To investigate pain sensitivity after sleep restriction and the restorative effect of napping. Design A strictly controlled randomized crossover study with continuous polysomnography monitoring was performed. Setting Laboratory-based study. Participants 11 healthy male volunteers. Interventions Volunteers attended two three-day sessions: “sleep restriction” alone and “sleep restriction and nap”. Each session involved a baseline night of normal sleep, a night of sleep deprivation and a night of free recovery sleep. Participants were allowed to sleep only from 02:00 to 04:00 during the sleep deprivation night. During the “sleep restriction and nap” session, volunteers took two 30-minute naps, one in the morning and one in the afternoon. Measurements and Results Quantitative sensory testing was performed with heat, cold and pressure, at 10:00 and 16:00, on three areas: the supraspinatus, lower back and thigh. After sleep restriction, quantitative sensory testing revealed differential changes in pain stimuli thresholds, but not in thermal threshold detection: lower back heat pain threshold decreased, pressure pain threshold increased in the supraspinatus area and no change was observed for the thigh. Napping restored responses to heat pain stimuli in the lower back and to pressure stimuli in the supraspinatus area. Conclusions Sleep restriction induces different types of hypersensitivity to pain stimuli in different body areas, consistent with multilevel mechanisms, these changes being reversed by napping. The napping restorative effect on pain thresholds result principally from effects on pain mechanisms, since it was independent of vigilance status. PMID:25723495

Fungal secondary metabolites - strategies to activate silent gene clusters.

PubMed

Brakhage, Axel A; Schroeckh, Volker

2011-01-01

Filamentous fungi produce a multitude of low molecular weight bioactive compounds. The increasing number of fungal genome sequences impressively demonstrated that their biosynthetic potential is far from being exploited. In fungi, the genes required for the biosynthesis of a secondary metabolite are clustered. Many of these bioinformatically newly discovered secondary metabolism gene clusters are silent under standard laboratory conditions. Consequently, no product can be found. This review summarizes the current strategies that have been successfully applied during the last years to activate these silent gene clusters in filamentous fungi, especially in the genus Aspergillus. The techniques take advantage of genome mining, vary from the simple search for compounds with bioinformatically predicted physicochemical properties up to methods that exploit a probable interaction of microorganisms. Until now, the majority of successful approaches have been based on molecular biology like the generation of gene "knock outs", promoter exchange, overexpression of transcription factors or other pleiotropic regulators. Moreover, strategies based on epigenetics opened a new avenue for the elucidation of the regulation of secondary metabolite formation and will certainly continue to play a significant role for the elucidation of cryptic natural products. The conditions under which a given gene cluster is naturally expressed are largely unknown. One technique is to attempt to simulate the natural habitat by co-cultivation of microorganisms from the same ecosystem. This has already led to the activation of silent gene clusters and the identification of novel compounds in Aspergillus nidulans. These simulation strategies will help discover new natural products in the future, and may also provide fundamental new insights into microbial communication. Copyright © 2010 Elsevier Inc. All rights reserved.

Daytime napping and increased risk of incident respiratory diseases: symptom, marker, or risk factor?

PubMed

Leng, Yue; Wainwright, Nick W J; Cappuccio, Francesco P; Surtees, Paul G; Hayat, Shabina; Luben, Robert; Brayne, Carol; Khaw, Kay-Tee

2016-07-01

We have identified a strong association between daytime napping and increased mortality risk from respiratory diseases, but little is known about the relationship between daytime napping and respiratory morbidity. Data were drawn from the European Prospective Investigation into Cancer and Nutrition-Norfolk cohort. Participants reported napping habits during 1998-2000 and were followed up for respiratory disease hospital admissions until March 2009. Cox proportional hazards regression was used to examine the association between daytime napping and respiratory disease incidence risk. The study sample included 10,978 men and women with a mean age of 61.9 years, and a total of 946 incident respiratory disease cases were recorded. After adjustment for age, sex, social class, education, marital status, employment status, nightshift work, body mass index, physical activity, smoking, alcohol intake, self-reported general health, hypnotic drug use, habitual sleep duration, and preexisting health conditions, daytime napping was associated with an increase in the overall respiratory disease incidence risk (hazard ratio (HR) = 1.32, 95% confidence interval (CI) 1.15, 1.52 for napping <1 h; HR = 1.54, 95% CI 1.14, 2.09 for napping ≥1 h). This association was more pronounced for lower respiratory diseases, especially for the risk of chronic lower respiratory diseases (HR = 1.52, 95% CI: 1.18, 1.96 for napping <1 h; HR = 1.72, 95% CI: 1.01, 2.92 for napping ≥1 h, overall p = 0.003). Excessive daytime napping might be a useful marker of future respiratory disease incidence risk. Further studies are required to confirm these findings and help understand potential mechanisms. Copyright © 2016 The Author(s). Published by Elsevier B.V. All rights reserved.

Comparing the benefits of caffeine, naps and placebo on verbal, motor and perceptual memory.

PubMed

Mednick, Sara C; Cai, Denise J; Kanady, Jennifer; Drummond, Sean P A

2008-11-03

Caffeine, the world's most common psychoactive substance, is used by approximately 90% of North Americans everyday. Little is known, however, about its benefits for memory. Napping has been shown to increase alertness and promote learning on some memory tasks. We directly compared caffeine (200mg) with napping (60-90min) and placebo on three distinct memory processes: declarative verbal memory, procedural motor skills, and perceptual learning. In the verbal task, recall and recognition for unassociated words were tested after a 7h retention period (with a between-session nap or drug intervention). A second, different, word list was administered post-intervention and memory was tested after a 20min retention period. The non-declarative tasks (finger tapping task (FTT) and texture discrimination task (TDT)) were trained before the intervention and then retested afterwards. Naps enhanced recall of words after a 7h and 20min retention interval relative to both caffeine and placebo. Caffeine significantly impaired motor learning compared to placebo and naps. Napping produced robust perceptual learning compared with placebo; however, naps and caffeine were not significantly different. These findings provide evidence of the limited benefits of caffeine for memory improvement compared with napping. We hypothesize that impairment from caffeine may be restricted to tasks that contain explicit information; whereas strictly implicit learning is less compromised.

Comparing the benefits of Caffeine, Naps and Placebo on Verbal, Motor and Perceptual Memory

PubMed Central

Mednick, Sara C.; Cai, Denise J.; Kanady, Jennifer; Drummond, Sean P.A.

2008-01-01

Caffeine, the world’s most common psychoactive substance, is used by approximately 90% of North Americans everyday. Little is known, however, about its benefits for memory. Napping has been shown to increase alertness and promote learning on some memory tasks. We directly compared caffeine (200mg) with napping (60–90 minutes) and placebo on three distinct memory processes: declarative verbal memory, procedural motor skills, and perceptual learning. In the verbal task, recall and recognition for unassociated words were tested after a 7hr retention period (with a between-session nap or drug intervention). A second, different, word list was administered post-intervention and memory was tested after a 20min retention period. The non-declarative tasks (finger tapping task and texture discrimination task) were trained before the intervention and then retested afterwards. Naps enhanced recall of words after a 7hr and 20min retention interval relative to both caffeine and placebo. Caffeine significantly impaired motor learning compared to placebo and naps. Napping produced robust perceptual learning compared with placebo; however, naps and caffeine were not significantly different. These findings provide evidence of the limited benefits of caffeine for memory improvement compared with napping. We hypothesize that impairment from caffeine may be restricted to tasks that contain explicit information; whereas strictly implicit learning is less compromised. PMID:18554731

Bacillus cereus-type polyhydroxyalkanoate biosynthetic gene cluster contains R-specific enoyl-CoA hydratase gene.

PubMed

Kihara, Takahiro; Hiroe, Ayaka; Ishii-Hyakutake, Manami; Mizuno, Kouhei; Tsuge, Takeharu

2017-08-01

Bacillus cereus and Bacillus megaterium both accumulate polyhydroxyalkanoate (PHA) but their PHA biosynthetic gene (pha) clusters that code for proteins involved in PHA biosynthesis are different. Namely, a gene encoding MaoC-like protein exists in the B. cereus-type pha cluster but not in the B. megaterium-type pha cluster. MaoC-like protein has an R-specific enoyl-CoA hydratase (R-hydratase) activity and is referred to as PhaJ when involved in PHA metabolism. In this study, the pha cluster of B. cereus YB-4 was characterized in terms of PhaJ's function. In an in vitro assay, PhaJ from B. cereus YB-4 (PhaJ YB4 ) exhibited hydration activity toward crotonyl-CoA. In an in vivo assay using Escherichia coli as a host for PHA accumulation, the recombinant strain expressing PhaJ YB4 and PHA synthase led to increased PHA accumulation, suggesting that PhaJ YB4 functioned as a monomer supplier. The monomer composition of the accumulated PHA reflected the substrate specificity of PhaJ YB4 , which appeared to prefer short chain-length substrates. The pha cluster from B. cereus YB-4 functioned to accumulate PHA in E. coli; however, it did not function when the phaJ YB4 gene was deleted. The B. cereus-type pha cluster represents a new example of a pha cluster that contains the gene encoding PhaJ.

Napping in College Students and Its Relationship with Nighttime Sleep

ERIC Educational Resources Information Center

Ye, Lichuan; Hutton Johnson, Stacy; Keane, Kathleen; Manasia, Michael; Gregas, Matt

2015-01-01

Objective: To examine the habit of napping and its relationship with nighttime sleep in college students. Participants: Four hundred and forty undergraduate students who responded to an anonymous online survey in April 2010. Methods: Three questions were asked to determine the frequency, length, and timing of napping during the past month. Sleep…

Hox cluster polarity in early transcriptional availability: a high order regulatory level of clustered Hox genes in the mouse.

PubMed

Roelen, Bernard A J; de Graaff, Wim; Forlani, Sylvie; Deschamps, Jacqueline

2002-11-01

The molecular mechanism underlying the 3' to 5' polarity of induction of mouse Hox genes is still elusive. While relief from a cluster-encompassing repression was shown to lead to all Hoxd genes being expressed like the 3'most of them, Hoxd1 (Kondo and Duboule, 1999), the molecular basis of initial activation of this 3'most gene, is not understood yet. We show that, already before primitive streak formation, prior to initial expression of the first Hox gene, a dramatic transcriptional stimulation of the 3'most genes, Hoxb1 and Hoxb2, is observed upon a short pulse of exogenous retinoic acid (RA), whereas it is not in the case for more 5', cluster-internal, RA-responsive Hoxb genes. In contrast, the RA-responding Hoxb1lacZ transgene that faithfully mimics the endogenous gene (Marshall et al., 1994) did not exhibit the sensitivity of Hoxb1 to precocious activation. We conclude that polarity in initial activation of Hoxb genes reflects a greater availability of 3'Hox genes for transcription, suggesting a pre-existing (susceptibility to) opening of the chromatin structure at the 3' extremity of the cluster. We discuss the data in the context of prevailing models involving differential chromatin opening in the directionality of clustered Hox gene transcription, and regarding the importance of the cluster context for correct timing of initial Hox gene expression.Interestingly, Cdx1 manifested the same early transcriptional availability as Hoxb1. Copyright 2002 Elsevier Science Ireland Ltd.

Racial Differences in Reported Napping and Nocturnal Sleep in 2- to 8-Year-Old Children

PubMed Central

Crosby, Brian; LeBourgeois, Monique K.; Harsh, John

2010-01-01

Objectives The objectives of this study were to examine racial differences in reported napping and nighttime sleep of 2- to 8-year-old children, to identify factors accounting for these differences, and to determine if variability in napping was related to psychosocial functioning. Methods Caretakers of 1043 children (73.5% non-Hispanic white; 50.4% male) 2 to 8 years old from a community sample reported on their children’s napping behavior and nighttime sleep. Caretakers of 255 preschool children (3–5 years old) also completed the Behavior Assessment System for Children. Results A more gradual age-related decline in napping was found for black children. At age 8, 39.1% of black children were reported to nap, compared with only 4.9% of white children. Black children also napped significantly more days per week, had shorter average nocturnal sleep durations, and slept significantly less on weekdays than on weekend nights. Despite differences in sleep distribution, total weekly sleep duration (diurnal and nocturnal) was nearly identical for the 2 racial groups at each year of age. Logistic regression analysis revealed that demographic variables were related to but did not fully explain napping differences. Napping in a subset of preschoolers was not significantly related to psychosocial functioning. Conclusions There are remarkable racial differences in reported napping and nighttime sleep patterns beginning as early as age 3 and extending to at least 8 years of age. These differences are independent of commonly investigated demographic factors. Differences in napping behavior do not seem to have psychosocial significance in a sample of preschool children. PMID:15866856

Naps promote flexible memory retrieval in 12-month-old infants.

PubMed

Konrad, Carolin; Seehagen, Sabine; Schneider, Silvia; Herbert, Jane S

2016-11-01

Flexibility in applying existing knowledge to similar cues is a corner stone of memory development in infants. Here, we examine the effect of sleep on the flexibility of memory retrieval using a deferred imitation paradigm. Forty-eight 12-month-old infants were randomly assigned to either a nap or a no-nap demonstration condition (scheduled around their natural daytime sleep schedule) or to a baseline control condition. In the demonstration conditions, infants watched an experimenter perform three target actions on a hand puppet. Immediately afterwards, infants were allowed to practice the target actions three times. In a test session 4-hr later, infants were given the opportunity to reproduce the actions with a novel hand puppet differing in color from the puppet used during the demonstration session. Only infants in the nap-condition performed significantly more target actions than infants in the baseline control condition. Furthermore, they were faster to carry out the first target action than infants in the no-nap condition. We conclude that sleep had a facilitative effect on infants' flexibility of memory retrieval. © 2016 Wiley Periodicals, Inc.

Delayed benefit of naps on motor learning in preschool children.

PubMed

Desrochers, Phillip C; Kurdziel, Laura B F; Spencer, Rebecca M C

2016-03-01

Sleep benefits memory consolidation across a variety of domains in young adults. However, while declarative memories benefit from sleep in young children, such improvements are not consistently seen for procedural skill learning. Here we examined whether performance improvements on a procedural task, although not immediately observed, are evident after a longer delay when augmented by overnight sleep (24 h after learning). We trained 47 children, aged 33-71 months, on a serial reaction time task and, using a within-subject design, evaluated performance at three time points: immediately after learning, after a daytime nap (nap condition) or equivalent wake opportunity (wake condition), and 24 h after learning. Consistent with previous studies, performance improvements following the nap did not differ from performance improvements following an equivalent interval spent awake. However, significant benefits of the nap were found when performance was assessed 24 h after learning. This research demonstrates that motor skill learning is benefited by sleep, but that this benefit is only evident after an extended period of time.

A cross-species bi-clustering approach to identifying conserved co-regulated genes.

PubMed

Sun, Jiangwen; Jiang, Zongliang; Tian, Xiuchun; Bi, Jinbo

2016-06-15

A growing number of studies have explored the process of pre-implantation embryonic development of multiple mammalian species. However, the conservation and variation among different species in their developmental programming are poorly defined due to the lack of effective computational methods for detecting co-regularized genes that are conserved across species. The most sophisticated method to date for identifying conserved co-regulated genes is a two-step approach. This approach first identifies gene clusters for each species by a cluster analysis of gene expression data, and subsequently computes the overlaps of clusters identified from different species to reveal common subgroups. This approach is ineffective to deal with the noise in the expression data introduced by the complicated procedures in quantifying gene expression. Furthermore, due to the sequential nature of the approach, the gene clusters identified in the first step may have little overlap among different species in the second step, thus difficult to detect conserved co-regulated genes. We propose a cross-species bi-clustering approach which first denoises the gene expression data of each species into a data matrix. The rows of the data matrices of different species represent the same set of genes that are characterized by their expression patterns over the developmental stages of each species as columns. A novel bi-clustering method is then developed to cluster genes into subgroups by a joint sparse rank-one factorization of all the data matrices. This method decomposes a data matrix into a product of a column vector and a row vector where the column vector is a consistent indicator across the matrices (species) to identify the same gene cluster and the row vector specifies for each species the developmental stages that the clustered genes co-regulate. Efficient optimization algorithm has been developed with convergence analysis. This approach was first validated on synthetic data and compared

Pichia stipitis genomics, transcriptomics, and gene clusters

Treesearch

Thomas W. Jeffries; Jennifer R. Headman Van Vleet

2009-01-01

Genome sequencing and subsequent global gene expression studies have advanced our understanding of the lignocellulose-fermenting yeast Pichia stipitis. These studies have provided an insight into its central carbon metabolism, and analysis of its genome has revealed numerous functional gene clusters and tandem repeats. Specialized physiological traits are often the...

EEG Changes Accompanying Successive Cycles of Sleep Restriction With and Without Naps in Adolescents

PubMed Central

Ong, Ju Lynn; Lo, June C.; Gooley, Joshua J.

2017-01-01

Abstract Study objectives: To investigate the temporal evolution of sleep EEG changes in adolescents across two cycles of sleep restriction and recovery simulating an intense school week and to examine the effect of an afternoon nap on nocturnal sleep. Methods: A parallel-group design, quasi-laboratory study was conducted in a student hostel. Fifty-seven adolescents (31 males, age = 15–19 years) were randomly assigned to nap or no nap groups. Participants underwent a 15-day protocol comprising two sleep restriction (5-hour time-in-bed [TIB]) and recovery (9-hour TIB) cycles. The nap group was also provided with a 1-hour nap opportunity at 14:00 following each sleep restriction night. Polysomnography recordings were obtained on nine nights and five nap episodes. Results: Naps reduced homeostatic sleep pressure on sleep restriction nights as evidenced by longer N2 latency and reduced total sleep time (TST), sleep efficiency (SE), and slow wave energy. Sleep debt accumulated in both groups, evidenced by increased TST, greater SE, and reduced wake after sleep onset on recovery compared to baseline nights. Changes were greater in the no nap group. Recovery sleep after the first cycle of sleep restriction did not restore sleep architecture to baseline in either group. SE, rapid eye movement (REM), and non-REM sleep increased, and N2 latency was reduced in the second sleep restriction period. Conclusions: Changes in sleep EEG induced by sleep restriction to 5-hour TIB for five nights were not eliminated after two nights of 9-hour recovery sleep. An afternoon nap helped but residual effects on the sleep EEG suggest that there is no substitute for adequate nocturnal sleep. PMID:28329386

Meta-Analysis of Self-Reported Daytime Napping and Risk of Cardiovascular or All-Cause Mortality

PubMed Central

Liu, Xiaokun; Zhang, Qi; Shang, Xiaoming

2015-01-01

Background Whether self-reported daytime napping is an independent predictor of cardiovascular or all-cause mortality remains unclear. The aim of this study was to investigate self-reported daytime napping and risk of cardiovascular or all-cause mortality by conducting a meta-analysis. Material/Methods A computerized literature search of PubMed, Embase, and Cochrane Library was conducted up to May 2014. Only prospective studies reporting risk ratio (RR) and corresponding 95% confidence intervals (CI) of cardiovascular or all-cause mortality with respect to baseline self-reported daytime napping were included. Results Seven studies with 98,163 subjects were included. Self-reported daytime napping was associated with a greater risk of all-cause mortality (RR 1.15; 95% CI 1.07–1.24) compared with non-nappers. Risk of all-cause mortality appeared to be more pronounced among persons with nap duration >60 min (RR 1.15; 95% CI 1.04–1.27) than persons with nap duration <60 min (RR 1.10; 95% CI 0.92–1.32). The pooled RR of cardiovascular mortality was 1.19 (95% CI 0.97–1.48) comparing daytime nappers to non-nappers. Conclusions Self-reported daytime napping is a mild but statistically significant predictor for all-cause mortality, but not for cardiovascular mortality. However, whether the risk is attributable to excessive sleep duration or napping alone remains controversial. More prospective studies stratified by sleep duration, napping periods, or age are needed. PMID:25937468

Meta-analysis of self-reported daytime napping and risk of cardiovascular or all-cause mortality.

PubMed

Liu, Xiaokun; Zhang, Qi; Shang, Xiaoming

2015-05-04

Whether self-reported daytime napping is an independent predictor of cardiovascular or all-cause mortality remains unclear. The aim of this study was to investigate self-reported daytime napping and risk of cardiovascular or all-cause mortality by conducting a meta-analysis. A computerized literature search of PubMed, Embase, and Cochrane Library was conducted up to May 2014. Only prospective studies reporting risk ratio (RR) and corresponding 95% confidence intervals (CI) of cardiovascular or all-cause mortality with respect to baseline self-reported daytime napping were included. Seven studies with 98,163 subjects were included. Self-reported daytime napping was associated with a greater risk of all-cause mortality (RR 1.15; 95% CI 1.07-1.24) compared with non-nappers. Risk of all-cause mortality appeared to be more pronounced among persons with nap duration >60 min (RR 1.15; 95% CI 1.04-1.27) than persons with nap duration <60 min (RR 1.10; 95% CI 0.92-1.32). The pooled RR of cardiovascular mortality was 1.19 (95% CI 0.97-1.48) comparing daytime nappers to non-nappers. Self-reported daytime napping is a mild but statistically significant predictor for all-cause mortality, but not for cardiovascular mortality. However, whether the risk is attributable to excessive sleep duration or napping alone remains controversial. More prospective studies stratified by sleep duration, napping periods, or age are needed.

Clustering change patterns using Fourier transformation with time-course gene expression data.

PubMed

Kim, Jaehee

2011-01-01

To understand the behavior of genes, it is important to explore how the patterns of gene expression change over a period of time because biologically related gene groups can share the same change patterns. In this study, the problem of finding similar change patterns is induced to clustering with the derivative Fourier coefficients. This work is aimed at discovering gene groups with similar change patterns which share similar biological properties. We developed a statistical model using derivative Fourier coefficients to identify similar change patterns of gene expression. We used a model-based method to cluster the Fourier series estimation of derivatives. We applied our model to cluster change patterns of yeast cell cycle microarray expression data with alpha-factor synchronization. It showed that, as the method clusters with the probability-neighboring data, the model-based clustering with our proposed model yielded biologically interpretable results. We expect that our proposed Fourier analysis with suitably chosen smoothing parameters could serve as a useful tool in classifying genes and interpreting possible biological change patterns.

An ergot alkaloid biosynthesis gene and clustered hypothetical genes from Aspergillus fumigatus.

PubMed

Coyle, Christine M; Panaccione, Daniel G

2005-06-01

The ergot alkaloids are a family of indole-derived mycotoxins with a variety of significant biological activities. Aspergillus fumigatus, a common airborne fungus and opportunistic human pathogen, and several fungi in the relatively distant taxon Clavicipitaceae (clavicipitaceous fungi) produce different sets of ergot alkaloids. The ergot alkaloids of these divergent fungi share a four-member ergoline ring but differ in the number, type, and position of the side chains. Several genes required for ergot alkaloid production are known in the clavicipitaceous fungi, and these genes are clustered in the genome of the ergot fungus Claviceps purpurea. We investigated whether the ergot alkaloids of A. fumigatus have a common biosynthetic and genetic origin with those of the clavicipitaceous fungi. A homolog of dmaW, the gene controlling the determinant step in the ergot alkaloid pathway of clavicipitaceous fungi, was identified in the A. fumigatus genome. Knockout of dmaW eliminated all known ergot alkaloids from A. fumigatus, and complementation of the mutation restored ergot alkaloid production. Clustered with dmaW in the A. fumigatus genome are sequences corresponding to five genes previously proposed to encode steps in the ergot alkaloid pathway of C. purpurea, as well as additional sequences whose deduced protein products are consistent with their involvement in the ergot alkaloid pathway. The corresponding genes have similarities in their nucleotide sequences, but the orientations and positions within the cluster of several of these genes differ. The data indicate that the ergot alkaloid biosynthetic capabilities in A. fumigatus and the clavicipitaceous fungi had a common origin.

An Ergot Alkaloid Biosynthesis Gene and Clustered Hypothetical Genes from Aspergillus fumigatus†

PubMed Central

Coyle, Christine M.; Panaccione, Daniel G.

2005-01-01

The ergot alkaloids are a family of indole-derived mycotoxins with a variety of significant biological activities. Aspergillus fumigatus, a common airborne fungus and opportunistic human pathogen, and several fungi in the relatively distant taxon Clavicipitaceae (clavicipitaceous fungi) produce different sets of ergot alkaloids. The ergot alkaloids of these divergent fungi share a four-member ergoline ring but differ in the number, type, and position of the side chains. Several genes required for ergot alkaloid production are known in the clavicipitaceous fungi, and these genes are clustered in the genome of the ergot fungus Claviceps purpurea. We investigated whether the ergot alkaloids of A. fumigatus have a common biosynthetic and genetic origin with those of the clavicipitaceous fungi. A homolog of dmaW, the gene controlling the determinant step in the ergot alkaloid pathway of clavicipitaceous fungi, was identified in the A. fumigatus genome. Knockout of dmaW eliminated all known ergot alkaloids from A. fumigatus, and complementation of the mutation restored ergot alkaloid production. Clustered with dmaW in the A. fumigatus genome are sequences corresponding to five genes previously proposed to encode steps in the ergot alkaloid pathway of C. purpurea, as well as additional sequences whose deduced protein products are consistent with their involvement in the ergot alkaloid pathway. The corresponding genes have similarities in their nucleotide sequences, but the orientations and positions within the cluster of several of these genes differ. The data indicate that the ergot alkaloid biosynthetic capabilities in A. fumigatus and the clavicipitaceous fungi had a common origin. PMID:15933009

Comparison of two schemes for automatic keyword extraction from MEDLINE for functional gene clustering.

PubMed

Liu, Ying; Ciliax, Brian J; Borges, Karin; Dasigi, Venu; Ram, Ashwin; Navathe, Shamkant B; Dingledine, Ray

2004-01-01

One of the key challenges of microarray studies is to derive biological insights from the unprecedented quatities of data on gene-expression patterns. Clustering genes by functional keyword association can provide direct information about the nature of the functional links among genes within the derived clusters. However, the quality of the keyword lists extracted from biomedical literature for each gene significantly affects the clustering results. We extracted keywords from MEDLINE that describes the most prominent functions of the genes, and used the resulting weights of the keywords as feature vectors for gene clustering. By analyzing the resulting cluster quality, we compared two keyword weighting schemes: normalized z-score and term frequency-inverse document frequency (TFIDF). The best combination of background comparison set, stop list and stemming algorithm was selected based on precision and recall metrics. In a test set of four known gene groups, a hierarchical algorithm correctly assigned 25 of 26 genes to the appropriate clusters based on keywords extracted by the TDFIDF weighting scheme, but only 23 og 26 with the z-score method. To evaluate the effectiveness of the weighting schemes for keyword extraction for gene clusters from microarray profiles, 44 yeast genes that are differentially expressed during the cell cycle were used as a second test set. Using established measures of cluster quality, the results produced from TFIDF-weighted keywords had higher purity, lower entropy, and higher mutual information than those produced from normalized z-score weighted keywords. The optimized algorithms should be useful for sorting genes from microarray lists into functionally discrete clusters.

Daytime napping, sleep duration and serum C reactive protein: a population-based cohort study

PubMed Central

Leng, Yue; Ahmadi-Abhari, Sara; Wainwright, Nick W J; Cappuccio, Francesco P; Surtees, Paul G; Luben, Robert; Brayne, Carol; Khaw, Kay-Tee

2014-01-01

Objectives To explore whether daytime napping and sleep duration are linked to serum C reactive protein (CRP), a pro-inflammatory marker, in an older aged British population. Design Cross-sectional study. Setting European Prospective Investigation into Cancer and Nutrition (EPIC)-Norfolk study. Participants A total of 5018 men and women aged 48–92 years reported their sleep habits and had serum CRP levels measured. Outcome and measures CRP was measured (mg/L) during 2006–2011 in fresh blood samples using high-sensitivity methods. Participants reported napping habits during 2002–2004, and reported sleep quantity during 2006–2007. Multivariable linear regression models were used to examine the association between napping and log-transformed CRP, and geometric mean CRP levels were calculated. Results After adjustment for age and sex, those who reported napping had 10% higher CRP levels compared with those not napping. The association was attenuated but remained borderline significant (β=0.05 (95% CI 0.00 to 0.10)) after further adjustment for social class, education, marital status, body mass index, physical activity, smoking, alcohol intake, self-reported health, pre-existing diseases, systolic blood pressure, hypnotic drug use, depression and in women-only hormone replacement therapy use. The geometric means (95% CI) of CRP levels were 2.38 (2.29 to 2.47) mg/L and 2.26 (2.21 to 2.32) mg/L for those who reported napping and no napping, respectively. A U-shaped association was observed between time spent in bed at night and CRP levels, and nighttime sleep duration was not associated with serum CRP levels. The association between napping and CRP was stronger for older participants, and among extremes of time spent in bed at night. Conclusions Daytime napping was associated with increased CRP levels in an older aged British population. Further studies are needed to determine whether daytime napping is a cause for systemic inflammation, or if it is a symptom

GraphTeams: a method for discovering spatial gene clusters in Hi-C sequencing data.

PubMed

Schulz, Tizian; Stoye, Jens; Doerr, Daniel

2018-05-08

Hi-C sequencing offers novel, cost-effective means to study the spatial conformation of chromosomes. We use data obtained from Hi-C experiments to provide new evidence for the existence of spatial gene clusters. These are sets of genes with associated functionality that exhibit close proximity to each other in the spatial conformation of chromosomes across several related species. We present the first gene cluster model capable of handling spatial data. Our model generalizes a popular computational model for gene cluster prediction, called δ-teams, from sequences to graphs. Following previous lines of research, we subsequently extend our model to allow for several vertices being associated with the same label. The model, called δ-teams with families, is particular suitable for our application as it enables handling of gene duplicates. We develop algorithmic solutions for both models. We implemented the algorithm for discovering δ-teams with families and integrated it into a fully automated workflow for discovering gene clusters in Hi-C data, called GraphTeams. We applied it to human and mouse data to find intra- and interchromosomal gene cluster candidates. The results include intrachromosomal clusters that seem to exhibit a closer proximity in space than on their chromosomal DNA sequence. We further discovered interchromosomal gene clusters that contain genes from different chromosomes within the human genome, but are located on a single chromosome in mouse. By identifying δ-teams with families, we provide a flexible model to discover gene cluster candidates in Hi-C data. Our analysis of Hi-C data from human and mouse reveals several known gene clusters (thus validating our approach), but also few sparsely studied or possibly unknown gene cluster candidates that could be the source of further experimental investigations.

Clusters of antibiotic resistance genes enriched together stay together in swine agriculture

DOE PAGES

Johnson, Timothy A.; Stedtfeld, Robert D.; Wang, Qiong; ...

2016-04-12

Antibiotic resistance is a worldwide health risk, but the influence of animal agriculture on the genetic context and enrichment of individual antibiotic resistance alleles remains unclear. Using quantitative PCR followed by amplicon sequencing, we quantified and sequenced 44 genes related to antibiotic resistance, mobile genetic elements, and bacterial phylogeny in microbiomes from U.S. laboratory swine and from swine farms from three Chinese regions. We identified highly abundant resistance clusters: groups of resistance and mobile genetic element alleles that cooccur. For example, the abundance of genes conferring resistance to six classes of antibiotics together with class 1 integrase and the abundancemore » of IS6100-type transposons in three Chinese regions are directly correlated. These resistance cluster genes likely colocalize in microbial genomes in the farms. Resistance cluster alleles were dramatically enriched (up to 1 to 10% as abundant as 16S rRNA) and indicate that multidrug-resistant bacteria are likely the norm rather than an exception in these communities. This enrichment largely occurred independently of phylogenetic composition; thus, resistance clusters are likely present in many bacterial taxa. Furthermore, resistance clusters contain resistance genes that confer resistance to antibiotics independently of their particular use on the farms. Selection for these clusters is likely due to the use of only a subset of the broad range of chemicals to which the clusters confer resistance. The scale of animal agriculture and its wastes, the enrichment and horizontal gene transfer potential of the clusters, and the vicinity of large human populations suggest that managing this resistance reservoir is important for minimizing human risk.Agricultural antibiotic use results in clusters of cooccurring resistance genes that together confer resistance to multiple antibiotics. The use of a single antibiotic could select for an entire suite of resistance

Clusters of antibiotic resistance genes enriched together stay together in swine agriculture

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

Johnson, Timothy A.; Stedtfeld, Robert D.; Wang, Qiong

Antibiotic resistance is a worldwide health risk, but the influence of animal agriculture on the genetic context and enrichment of individual antibiotic resistance alleles remains unclear. Using quantitative PCR followed by amplicon sequencing, we quantified and sequenced 44 genes related to antibiotic resistance, mobile genetic elements, and bacterial phylogeny in microbiomes from U.S. laboratory swine and from swine farms from three Chinese regions. We identified highly abundant resistance clusters: groups of resistance and mobile genetic element alleles that cooccur. For example, the abundance of genes conferring resistance to six classes of antibiotics together with class 1 integrase and the abundancemore » of IS6100-type transposons in three Chinese regions are directly correlated. These resistance cluster genes likely colocalize in microbial genomes in the farms. Resistance cluster alleles were dramatically enriched (up to 1 to 10% as abundant as 16S rRNA) and indicate that multidrug-resistant bacteria are likely the norm rather than an exception in these communities. This enrichment largely occurred independently of phylogenetic composition; thus, resistance clusters are likely present in many bacterial taxa. Furthermore, resistance clusters contain resistance genes that confer resistance to antibiotics independently of their particular use on the farms. Selection for these clusters is likely due to the use of only a subset of the broad range of chemicals to which the clusters confer resistance. The scale of animal agriculture and its wastes, the enrichment and horizontal gene transfer potential of the clusters, and the vicinity of large human populations suggest that managing this resistance reservoir is important for minimizing human risk.Agricultural antibiotic use results in clusters of cooccurring resistance genes that together confer resistance to multiple antibiotics. The use of a single antibiotic could select for an entire suite of resistance

Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture.

PubMed

Johnson, Timothy A; Stedtfeld, Robert D; Wang, Qiong; Cole, James R; Hashsham, Syed A; Looft, Torey; Zhu, Yong-Guan; Tiedje, James M

2016-04-12

Antibiotic resistance is a worldwide health risk, but the influence of animal agriculture on the genetic context and enrichment of individual antibiotic resistance alleles remains unclear. Using quantitative PCR followed by amplicon sequencing, we quantified and sequenced 44 genes related to antibiotic resistance, mobile genetic elements, and bacterial phylogeny in microbiomes from U.S. laboratory swine and from swine farms from three Chinese regions. We identified highly abundant resistance clusters: groups of resistance and mobile genetic element alleles that cooccur. For example, the abundance of genes conferring resistance to six classes of antibiotics together with class 1 integrase and the abundance of IS6100-type transposons in three Chinese regions are directly correlated. These resistance cluster genes likely colocalize in microbial genomes in the farms. Resistance cluster alleles were dramatically enriched (up to 1 to 10% as abundant as 16S rRNA) and indicate that multidrug-resistant bacteria are likely the norm rather than an exception in these communities. This enrichment largely occurred independently of phylogenetic composition; thus, resistance clusters are likely present in many bacterial taxa. Furthermore, resistance clusters contain resistance genes that confer resistance to antibiotics independently of their particular use on the farms. Selection for these clusters is likely due to the use of only a subset of the broad range of chemicals to which the clusters confer resistance. The scale of animal agriculture and its wastes, the enrichment and horizontal gene transfer potential of the clusters, and the vicinity of large human populations suggest that managing this resistance reservoir is important for minimizing human risk. Agricultural antibiotic use results in clusters of cooccurring resistance genes that together confer resistance to multiple antibiotics. The use of a single antibiotic could select for an entire suite of resistance genes if

The effects of nighttime napping on sleep, sleep inertia, and performance during simulated 16 h night work: a pilot study.

PubMed

Oriyama, Sanae; Miyakoshi, Yukiko

2018-03-27

This study aimed to elucidate the effects of two naps taken at night on morning waking state and performance. The participants were 12 women. The experiment was performed in a laboratory over 2 days (16:00-09:00). In this crossover comparative study, three experimental nap conditions were used (naps from 22:30 to 00:00 and from 02:30 to 03:00 (22:30-NAP), 00:30 to 02:00 and 04:30 to 05:00 (00:30-NAP), and no naps (NO-NAP), respectively). Measurement items were a Visual Analog Scale for sleepiness and fatigue, the Psychomotor Vigilance Test (PVT), and single-digit addition calculations (10 min) every hour for 18 h from 16:00 to 09:00, excluding nap times. Sleep inertia and sleepiness were noted directly after napping. Less sleepiness and fatigue were noted in the nap groups between 06:00 and 09:00 in the morning than in the NO-NAP condition and PVT response times were faster. Since participants in the nap groups were able to conduct more single-digit addition calculations, the performance of these groups appeared to be superior to that of the NO-NAP condition. Furthermore, the performance of calculations was significantly better in the 00:30-NAP than in the 22:30-NAP. Taking two naps during a simulated night shift helps improve sleepiness and fatigue and maintain performance. Taking a nap in the early morning appears to be promising for improving the waking state.

EEG Changes Accompanying Successive Cycles of Sleep Restriction With and Without Naps in Adolescents.

PubMed

Ong, Ju Lynn; Lo, June C; Gooley, Joshua J; Chee, Michael W L

2017-04-01

To investigate the temporal evolution of sleep EEG changes in adolescents across two cycles of sleep restriction and recovery simulating an intense school week and to examine the effect of an afternoon nap on nocturnal sleep. A parallel-group design, quasi-laboratory study was conducted in a student hostel. Fifty-seven adolescents (31 males, age = 15-19 years) were randomly assigned to nap or no nap groups. Participants underwent a 15-day protocol comprising two sleep restriction (5-hour time-in-bed [TIB]) and recovery (9-hour TIB) cycles. The nap group was also provided with a 1-hour nap opportunity at 14:00 following each sleep restriction night. Polysomnography recordings were obtained on nine nights and five nap episodes. Naps reduced homeostatic sleep pressure on sleep restriction nights as evidenced by longer N2 latency and reduced total sleep time (TST), sleep efficiency (SE), and slow wave energy. Sleep debt accumulated in both groups, evidenced by increased TST, greater SE, and reduced wake after sleep onset on recovery compared to baseline nights. Changes were greater in the no nap group. Recovery sleep after the first cycle of sleep restriction did not restore sleep architecture to baseline in either group. SE, rapid eye movement (REM), and non-REM sleep increased, and N2 latency was reduced in the second sleep restriction period. Changes in sleep EEG induced by sleep restriction to 5-hour TIB for five nights were not eliminated after two nights of 9-hour recovery sleep. An afternoon nap helped but residual effects on the sleep EEG suggest that there is no substitute for adequate nocturnal sleep. © Sleep Research Society 2017. Published by Oxford University Press [on behalf of the Sleep Research Society].

Objective measurement of daytime napping, cognitive dysfunction and subjective sleepiness in Parkinson's disease.

PubMed

Bolitho, Samuel J; Naismith, Sharon L; Salahuddin, Pierre; Terpening, Zoe; Grunstein, Ron R; Lewis, Simon J G

2013-01-01

Sleep-wake disturbances and concomitant cognitive dysfunction in Parkinson's disease (PD) contribute significantly to morbidity in patients and their carers. Subjectively reported daytime sleep disturbance is observed in over half of all patients with PD and has been linked to executive cognitive dysfunction. The current study used daytime actigraphy, a novel objective measure of napping and related this to neuropsychological performance in a sample of PD patients and healthy, age and gender-matched controls. Furthermore this study aimed to identify patients with PD who may benefit from pharmacologic and behavioural intervention to improve these symptoms. Eighty-five PD patients and 21 healthy, age-matched controls completed 14 days of wrist actigraphy within two weeks of neuropsychological testing. Objective napping measures were derived from actigraphy using a standardised protocol and subjective daytime sleepiness was recorded by the previously validated Epworth Sleepiness Scale. Patients with PD had a 225% increase in the mean nap time per day (minutes) as recorded by actigraphy compared to age matched controls (39.2 ± 35.2 vs. 11.5 ± 11.0 minutes respectively, p < 0.001). Significantly, differences in napping duration between patients, as recorded by actigraphy were not distinguished by their ratings on the subjective measurement of excessive daytime sleepiness. Finally, those patients with excessive daytime napping showed greater cognitive deficits in the domains of attention, semantic verbal fluency and processing speed. This study confirms increased levels of napping in PD, a finding that is concordant with subjective reports. However, subjective self-report measures of excessive daytime sleepiness do not robustly identify excessive napping in PD. Fronto-subcortical cognitive dysfunction was observed in those patients who napped excessively. Furthermore, this study suggests that daytime actigraphy, a non-invasive and inexpensive objective measure of

Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering

PubMed Central

2010-01-01

Background Cluster analysis, and in particular hierarchical clustering, is widely used to extract information from gene expression data. The aim is to discover new classes, or sub-classes, of either individuals or genes. Performing a cluster analysis commonly involve decisions on how to; handle missing values, standardize the data and select genes. In addition, pre-processing, involving various types of filtration and normalization procedures, can have an effect on the ability to discover biologically relevant classes. Here we consider cluster analysis in a broad sense and perform a comprehensive evaluation that covers several aspects of cluster analyses, including normalization. Result We evaluated 2780 cluster analysis methods on seven publicly available 2-channel microarray data sets with common reference designs. Each cluster analysis method differed in data normalization (5 normalizations were considered), missing value imputation (2), standardization of data (2), gene selection (19) or clustering method (11). The cluster analyses are evaluated using known classes, such as cancer types, and the adjusted Rand index. The performances of the different analyses vary between the data sets and it is difficult to give general recommendations. However, normalization, gene selection and clustering method are all variables that have a significant impact on the performance. In particular, gene selection is important and it is generally necessary to include a relatively large number of genes in order to get good performance. Selecting genes with high standard deviation or using principal component analysis are shown to be the preferred gene selection methods. Hierarchical clustering using Ward's method, k-means clustering and Mclust are the clustering methods considered in this paper that achieves the highest adjusted Rand. Normalization can have a significant positive impact on the ability to cluster individuals, and there are indications that background correction is

Chromatin organization and global regulation of Hox gene clusters

PubMed Central

Montavon, Thomas; Duboule, Denis

2013-01-01

During development, a properly coordinated expression of Hox genes, within their different genomic clusters is critical for patterning the body plans of many animals with a bilateral symmetry. The fascinating correspondence between the topological organization of Hox clusters and their transcriptional activation in space and time has served as a paradigm for understanding the relationships between genome structure and function. Here, we review some recent observations, which revealed highly dynamic changes in the structure of chromatin at Hox clusters, in parallel with their activation during embryonic development. We discuss the relevance of these findings for our understanding of large-scale gene regulation. PMID:23650639

The Association between Daytime Napping and Cognitive Functioning in Chronic Fatigue Syndrome

PubMed Central

Gotts, Zoe M.; Ellis, Jason G.; Deary, Vincent; Barclay, Nicola; Newton, Julia L.

2015-01-01

Objectives The precise relationship between sleep and physical and mental functioning in chronic fatigue syndrome (CFS) has not been examined directly, nor has the impact of daytime napping. This study aimed to examine self-reported sleep in patients with CFS and explore whether sleep quality and daytime napping, specific patient characteristics (gender, illness length) and levels of anxiety and depression, predicted daytime fatigue severity, levels of daytime sleepiness and cognitive functioning, all key dimensions of the illness experience. Methods 118 adults meeting the 1994 CDC case criteria for CFS completed a standardised sleep diary over 14 days. Momentary functional assessments of fatigue, sleepiness, cognition and mood were completed by patients as part of usual care. Levels of daytime functioning and disability were quantified using symptom assessment tools, measuring fatigue (Chalder Fatigue Scale), sleepiness (Epworth Sleepiness Scale), cognitive functioning (Trail Making Test, Cognitive Failures Questionnaire), and mood (Hospital Anxiety and Depression Scale). Results Hierarchical Regressions demonstrated that a shorter time since diagnosis, higher depression and longer wake time after sleep onset predicted 23.4% of the variance in fatigue severity (p <.001). Being male, higher depression and more afternoon naps predicted 25.6% of the variance in objective cognitive dysfunction (p <.001). Higher anxiety and depression and morning napping predicted 32.2% of the variance in subjective cognitive dysfunction (p <.001). When patients were classified into groups of mild and moderate sleepiness, those with longer daytime naps, those who mainly napped in the afternoon, and those with higher levels of anxiety, were more likely to be in the moderately sleepy group. Conclusions Napping, particularly in the afternoon is associated with poorer cognitive functioning and more daytime sleepiness in CFS. These findings have clinical implications for symptom management

The association between daytime napping and cognitive functioning in chronic fatigue syndrome.

PubMed

Gotts, Zoe M; Ellis, Jason G; Deary, Vincent; Barclay, Nicola; Newton, Julia L

2015-01-01

The precise relationship between sleep and physical and mental functioning in chronic fatigue syndrome (CFS) has not been examined directly, nor has the impact of daytime napping. This study aimed to examine self-reported sleep in patients with CFS and explore whether sleep quality and daytime napping, specific patient characteristics (gender, illness length) and levels of anxiety and depression, predicted daytime fatigue severity, levels of daytime sleepiness and cognitive functioning, all key dimensions of the illness experience. 118 adults meeting the 1994 CDC case criteria for CFS completed a standardised sleep diary over 14 days. Momentary functional assessments of fatigue, sleepiness, cognition and mood were completed by patients as part of usual care. Levels of daytime functioning and disability were quantified using symptom assessment tools, measuring fatigue (Chalder Fatigue Scale), sleepiness (Epworth Sleepiness Scale), cognitive functioning (Trail Making Test, Cognitive Failures Questionnaire), and mood (Hospital Anxiety and Depression Scale). Hierarchical Regressions demonstrated that a shorter time since diagnosis, higher depression and longer wake time after sleep onset predicted 23.4% of the variance in fatigue severity (p <.001). Being male, higher depression and more afternoon naps predicted 25.6% of the variance in objective cognitive dysfunction (p <.001). Higher anxiety and depression and morning napping predicted 32.2% of the variance in subjective cognitive dysfunction (p <.001). When patients were classified into groups of mild and moderate sleepiness, those with longer daytime naps, those who mainly napped in the afternoon, and those with higher levels of anxiety, were more likely to be in the moderately sleepy group. Napping, particularly in the afternoon is associated with poorer cognitive functioning and more daytime sleepiness in CFS. These findings have clinical implications for symptom management strategies.

Fragmentation of an aflatoxin-like gene cluster in a forest pathogen

USDA-ARS?s Scientific Manuscript database

Secondary metabolic pathway genes are typically clustered in fungi. An exception to this paradigm is seen for genes required for the production of dothistromin, an aflatoxin-like virulence factor produced by the pine needle pathogen Dothistroma septosporum. In contrast to the tight clustering of gen...

NAP SACC UK: protocol for a feasibility cluster randomised controlled trial in nurseries and at home to increase physical activity and healthy eating in children aged 2–4 years

PubMed Central

Kipping, R; Jago, R; Metcalfe, C; White, J; Papadaki, A; Campbell, R; Hollingworth, W; Ward, D; Wells, S; Brockman, R; Nicholson, A; Moore, L

2016-01-01

Introduction Systematic reviews have identified the lack of intervention studies with young children to prevent obesity. This feasibility study examines the feasibility and acceptability of adapting the Nutrition and Physical Activity Self-Assessment for Child Care (NAP SACC) intervention in the UK to inform a full-scale trial. Methods and analysis A feasibility cluster randomised controlled trial in 12 nurseries in England, with 6 randomly assigned to the adapted NAP SACC UK intervention: nursery staff will receive training and support from an NAP SACC UK Partner to review the nursery environment (nutrition, physical activity, sedentary behaviours and oral health) and set goals for making changes. Parents will be invited to participate in a digital media-based home component to set goals for making changes in the home. As this is a feasibility study, the sample size was not based on a power calculation but will indicate the likely response rates and intracluster correlations. Measures will be assessed at baseline and 8–10 months later. We will estimate the recruitment rate of nurseries and children and adherence to the intervention and data. Nursery measurements will include the Environmental Policy Assessment and Observation score and the nursery staff's review of the nursery environment. Child measurements will include height and weight to calculate z-score body mass index (zBMI), accelerometer-determined minutes of moderate-to-vigorous physical activity per day and sedentary time, and diet using the Child and Diet Evaluation Tool. Questionnaires with nursery staff and parents will measure mediators. A process evaluation will assess fidelity of intervention delivery and views of participants. Ethics and dissemination Ethical approval for this study was given by Wales 3 NHS Research Ethics Committee. Findings will be made available through publication in peer-reviewed journals, at conferences and to participants via the University of Bristol website. Data

Daytime napping, sleep duration and serum C reactive protein: a population-based cohort study.

PubMed

Leng, Yue; Ahmadi-Abhari, Sara; Wainwright, Nick W J; Cappuccio, Francesco P; Surtees, Paul G; Luben, Robert; Brayne, Carol; Khaw, Kay-Tee

2014-11-11

To explore whether daytime napping and sleep duration are linked to serum C reactive protein (CRP), a pro-inflammatory marker, in an older aged British population. Cross-sectional study. European Prospective Investigation into Cancer and Nutrition (EPIC)-Norfolk study. A total of 5018 men and women aged 48-92 years reported their sleep habits and had serum CRP levels measured. CRP was measured (mg/L) during 2006-2011 in fresh blood samples using high-sensitivity methods. Participants reported napping habits during 2002-2004, and reported sleep quantity during 2006-2007. Multivariable linear regression models were used to examine the association between napping and log-transformed CRP, and geometric mean CRP levels were calculated. After adjustment for age and sex, those who reported napping had 10% higher CRP levels compared with those not napping. The association was attenuated but remained borderline significant (β=0.05 (95% CI 0.00 to 0.10)) after further adjustment for social class, education, marital status, body mass index, physical activity, smoking, alcohol intake, self-reported health, pre-existing diseases, systolic blood pressure, hypnotic drug use, depression and in women-only hormone replacement therapy use. The geometric means (95% CI) of CRP levels were 2.38 (2.29 to 2.47) mg/L and 2.26 (2.21 to 2.32) mg/L for those who reported napping and no napping, respectively. A U-shaped association was observed between time spent in bed at night and CRP levels, and nighttime sleep duration was not associated with serum CRP levels. The association between napping and CRP was stronger for older participants, and among extremes of time spent in bed at night. Daytime napping was associated with increased CRP levels in an older aged British population. Further studies are needed to determine whether daytime napping is a cause for systemic inflammation, or if it is a symptom or consequence of underlying health problems. Published by the BMJ Publishing Group Limited

Day napping and short night sleeping are associated with higher risk of diabetes in older adults.

PubMed

Xu, Qun; Song, Yiqing; Hollenbeck, Albert; Blair, Aaron; Schatzkin, Arthur; Chen, Honglei

2010-01-01

To examine whether day napping or short night sleeping is associated with higher risk of diabetes. This was a prospective study of hours of day napping and night sleeping assessed in 1996-1997 in relation to diabetes diagnosed between 2000 and 2006 (n = 10,143) among 174,542 participants in the National Institutes of Health (NIH)-AARP Diet and Health Study. Odds ratios (ORs) and 95% CI were derived from multivariate logistic regression models. Longer day napping was associated with a higher risk of diabetes. After adjustment for potential confounders, ORs were 1.23 (95% CI 1.18-1.29) for those reporting <1 h and 1.55 (95% CI 1.45-1.66) for those reporting > or =1 h of napping compared with individuals who did not nap (P(trend) < 0.0001). For night sleeping, with 7-8 h as the referent, the OR was 1.46 (95% CI 1.31-1.63) for <5 h, 1.11 (1.06-1.16) for 5-6 h, and 1.11 (0.99-1.24) for > or =9 h. In both analyses, additional adjustment for BMI only modestly attenuated the associations. Further analysis showed a statistically significant interaction between hours of napping and sleeping on diabetes (P(interaction) < 0.0001). Among participants with no napping, only short night sleeping was associated with higher occurrence of diabetes, whereas among those with > or =1 h of napping, both long and short sleeping was associated with higher risk. Day napping and short night sleeping are associated with higher risk of diabetes. The association between sleep duration and diabetes may be modified by napping habit.

Characterization of the Nencki Affective Picture System by discrete emotional categories (NAPS BE).

PubMed

Riegel, Monika; Żurawski, Łukasz; Wierzba, Małgorzata; Moslehi, Abnoss; Klocek, Łukasz; Horvat, Marko; Grabowska, Anna; Michałowski, Jarosław; Jednoróg, Katarzyna; Marchewka, Artur

2016-06-01

The Nencki Affective Picture System (NAPS; Marchewka, Żurawski, Jednoróg, & Grabowska, Behavior Research Methods, 2014) is a standardized set of 1,356 realistic, high-quality photographs divided into five categories (people, faces, animals, objects, and landscapes). NAPS has been primarily standardized along the affective dimensions of valence, arousal, and approach-avoidance, yet the characteristics of discrete emotions expressed by the images have not been investigated thus far. The aim of the present study was to collect normative ratings according to categorical models of emotions. A subset of 510 images from the original NAPS set was selected in order to proportionally cover the whole dimensional affective space. Among these, using three available classification methods, we identified images eliciting distinguishable discrete emotions. We introduce the basic-emotion normative ratings for the Nencki Affective Picture System (NAPS BE), which will allow researchers to control and manipulate stimulus properties specifically for their experimental questions of interest. The NAPS BE system is freely accessible to the scientific community for noncommercial use as supplementary materials to this article.

Toddler's self-regulation strategies in a challenge context are nap-dependent.

PubMed

Miller, Alison L; Seifer, Ronald; Crossin, Rebecca; Lebourgeois, Monique K

2015-06-01

Early childhood represents a time of developmental changes in both sleep and self-regulation, a construct reflecting the ability to control one's behaviour, attention and emotions when challenged. Links between sleep and self-regulation processes have been proposed, but experimental evidence with young children is lacking. In the current study, we tested the effects of acute sleep restriction (nap deprivation) on toddlers' self-regulation. Healthy children (n = 12; four males; aged 30-36 months (33.9 ± 1.7)) slept on a strict schedule (verified with actigraphy and sleep diaries) for 5 days before each of two afternoon assessments following a nap and a no-nap condition (~11-day protocol). Children were videotaped while attempting an unsolvable puzzle, and 10 mutually exclusive self-regulation strategies were later coded. On average, children lost ~90 min of sleep on the no-nap versus the nap day. Nap deprivation resulted in moderate-to-large effects on self-regulation strategies, with decreases in scepticism (d = 0.77; 7% change), negative self-appraisal (d = 0.92; 5% change) and increases in physical self-soothing (d = 0.68; 10% change), focus on the puzzle piece that would not fit (perseveration; d = 0.50; 9% change) and insistence on completing the unsolvable puzzle (d = 0.91; 10% change). Results suggest that sleep serves an important role in the way that toddlers respond to challenging events in their daily lives. After losing daytime sleep, toddlers were less able to engage effectively in a difficult task and reverted to less mature self-regulation strategies than when they were well rested. Over time, chronically missed sleep may impair young children's self-regulation abilities, resulting in risk for social-emotional, behavioural and school problems. © 2014 European Sleep Research Society.

Nap-Dependent Learning in Infants

ERIC Educational Resources Information Center

Hupbach, Almut; Gomez, Rebecca L.; Bootzin, Richard R.; Nadel, Lynn

2009-01-01

Sleep has been shown to aid a variety of learning and memory processes in adults (Stickgold, 2005 ). Recently, we showed that infants' learning also benefits from subsequent sleep such that infants who nap are able to abstract the general grammatical pattern of a briefly presented artificial language (Gomez, Bootzin & Nadel, 2006 ). In the present…

The Effects of an Afternoon Nap on Episodic Memory in Young and Older Adults

PubMed Central

Fairley, Jacqueline; Decker, Michael J.; Bliwise, Donald L.

2017-01-01

Abstract Study Objectives: In young adults, napping is hypothesized to benefit episodic memory retention (eg, via consolidation). Whether this relationship is present in older adults has not been adequately tested but is an important question because older adults display marked changes in sleep and memory. Design: Between-subjects design. Setting: Sleep laboratory at Emory University School of Medicine. Participants: Fifty healthy young adults (18–29) and 45 community-dwelling older adults (58–83). Intervention: Participants were randomly assigned to a 90-minute nap opportunity or an equal interval of quiet wakefulness. Measurements and Results: Participants underwent an item-wise directed forgetting learning procedure in which they studied words that were individually followed by the instruction to “remember” or “forget.” Following a 90-minute retention interval filled with quiet wakefulness or a nap opportunity, they were asked to free recall and recognize those words. Young adults retained significantly more words following a nap interval than a quiet wakefulness interval on both free recall and recognition tests. There was modest evidence for greater nap-related retention of “remember” items relative to “forget” items for free recall but not recognition. Older adults’ memory retention did not differ across nap and quiet wakefulness conditions, although they demonstrated greater fragmentation, lower N3, and lower rapid eye movement duration than the young adults. Conclusions: In young adults, an afternoon nap benefits episodic memory retention, but such benefits decrease with advancing age. PMID:28329381

High-throughput platform for the discovery of elicitors of silent bacterial gene clusters.

PubMed

Seyedsayamdost, Mohammad R

2014-05-20

Over the past decade, bacterial genome sequences have revealed an immense reservoir of biosynthetic gene clusters, sets of contiguous genes that have the potential to produce drugs or drug-like molecules. However, the majority of these gene clusters appear to be inactive for unknown reasons prompting terms such as "cryptic" or "silent" to describe them. Because natural products have been a major source of therapeutic molecules, methods that rationally activate these silent clusters would have a profound impact on drug discovery. Herein, a new strategy is outlined for awakening silent gene clusters using small molecule elicitors. In this method, a genetic reporter construct affords a facile read-out for activation of the silent cluster of interest, while high-throughput screening of small molecule libraries provides potential inducers. This approach was applied to two cryptic gene clusters in the pathogenic model Burkholderia thailandensis. The results not only demonstrate a prominent activation of these two clusters, but also reveal that the majority of elicitors are themselves antibiotics, most in common clinical use. Antibiotics, which kill B. thailandensis at high concentrations, act as inducers of secondary metabolism at low concentrations. One of these antibiotics, trimethoprim, served as a global activator of secondary metabolism by inducing at least five biosynthetic pathways. Further application of this strategy promises to uncover the regulatory networks that activate silent gene clusters while at the same time providing access to the vast array of cryptic molecules found in bacteria.

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants1[OPEN

PubMed Central

Zhang, Peifen; Kim, Taehyong; Banf, Michael; Chavali, Arvind K.; Nilo-Poyanco, Ricardo; Bernard, Thomas

2017-01-01

Plant metabolism underpins many traits of ecological and agronomic importance. Plants produce numerous compounds to cope with their environments but the biosynthetic pathways for most of these compounds have not yet been elucidated. To engineer and improve metabolic traits, we need comprehensive and accurate knowledge of the organization and regulation of plant metabolism at the genome scale. Here, we present a computational pipeline to identify metabolic enzymes, pathways, and gene clusters from a sequenced genome. Using this pipeline, we generated metabolic pathway databases for 22 species and identified metabolic gene clusters from 18 species. This unified resource can be used to conduct a wide array of comparative studies of plant metabolism. Using the resource, we discovered a widespread occurrence of metabolic gene clusters in plants: 11,969 clusters from 18 species. The prevalence of metabolic gene clusters offers an intriguing possibility of an untapped source for uncovering new metabolite biosynthesis pathways. For example, more than 1,700 clusters contain enzymes that could generate a specialized metabolite scaffold (signature enzymes) and enzymes that modify the scaffold (tailoring enzymes). In four species with sufficient gene expression data, we identified 43 highly coexpressed clusters that contain signature and tailoring enzymes, of which eight were characterized previously to be functional pathways. Finally, we identified patterns of genome organization that implicate local gene duplication and, to a lesser extent, single gene transposition as having played roles in the evolution of plant metabolic gene clusters. PMID:28228535

Comparing the effects of nocturnal sleep and daytime napping on declarative memory consolidation.

PubMed

Lo, June C; Dijk, Derk-Jan; Groeger, John A

2014-01-01

Nocturnal sleep and daytime napping facilitate memory consolidation for semantically related and unrelated word pairs. We contrasted forgetting of both kinds of materials across a 12-hour interval involving either nocturnal sleep or daytime wakefulness (experiment 1) and a 2-hour interval involving either daytime napping or wakefulness (experiment 2). Beneficial effects of post-learning nocturnal sleep and daytime napping were greater for unrelated word pairs (Cohen's d=0.71 and 0.68) than for related ones (Cohen's d=0.58 and 0.15). While the size of nocturnal sleep and daytime napping effects was similar for unrelated word pairs, for related pairs, the effect of nocturnal sleep was more prominent. Together, these findings suggest that sleep preferentially facilitates offline memory processing of materials that are more susceptible to forgetting.

The interactive effects of nocturnal sleep and daytime naps in relation to serum C-reactive protein.

PubMed

Mantua, Janna; Spencer, Rebecca M C

2015-10-01

C-reactive protein (CRP) is a general marker of inflammation that has been differentially linked with sleep. Elevated CRP (ie, high inflammation) has been associated with either short/insufficient sleep duration or long sleep duration, both, or neither. Daytime napping has also been tied to increased and decreased inflammation. We attempted to unify these findings by examining the relationship between CRP and sleep duration in conjunction with napping in a healthy young adult cohort. Participants were young adults (mean age = 29.05 years, n = 2147) from the National Longitudinal Study of Adolescent Health (Add Health) cohort, a nationally representative longitudinal sample. Analysis of covariance (ANCOVA) tests examined whether self-reported sleep duration (short, medium, or long) and nap frequency (none-few days/week; most days/week; every day) interacted in relation to CRP. Standard covariates (ie, age, gender, race/ethnicity, body mass index, physical activity, depression, snoring, systolic blood pressure, clinical symptoms, and household income) were used. There was a linear increase in CRP with increased napping [contrast estimate = 0.265, 95% confidence interval (CI) (0.045-0.485), P = 0.018]. There was also an interaction between sleep duration and napping frequency in relation to CRP (F4,2128 = 2.90, P = 0.021). Inflammation differed between nap groups within the long and short sleep groups. Our results suggest that increased napping is an independent predictor of inflammation in young adults. These results also provide evidence for interactive effects of inflammation, nocturnal sleep, and daytime naps. Our findings confirm that excess sleep, insufficient sleep, frequent napping, and infrequent napping can all be linked with elevated CRP, but these relationships depend on both nocturnal and daytime sleep patterns. These analyses will guide future work to more specifically examine sleep-inflammation processes and directionality

Day Napping and Short Night Sleeping Are Associated With Higher Risk of Diabetes in Older Adults

PubMed Central

Xu, Qun; Song, Yiqing; Hollenbeck, Albert; Blair, Aaron; Schatzkin, Arthur; Chen, Honglei

2010-01-01

OBJECTIVE To examine whether day napping or short night sleeping is associated with higher risk of diabetes. RESEARCH DESIGN AND METHODS This was a prospective study of hours of day napping and night sleeping assessed in 1996–1997 in relation to diabetes diagnosed between 2000 and 2006 (n = 10,143) among 174,542 participants in the National Institutes of Health (NIH)-AARP Diet and Health Study. Odds ratios (ORs) and 95% CI were derived from multivariate logistic regression models. RESULTS Longer day napping was associated with a higher risk of diabetes. After adjustment for potential confounders, ORs were 1.23 (95% CI 1.18–1.29) for those reporting <1 h and 1.55 (95% CI 1.45–1.66) for those reporting ≥1 h of napping compared with individuals who did not nap (Ptrend < 0.0001). For night sleeping, with 7–8 h as the referent, the OR was 1.46 (95% CI 1.31–1.63) for <5 h, 1.11 (1.06–1.16) for 5–6 h, and 1.11 (0.99–1.24) for ≥9 h. In both analyses, additional adjustment for BMI only modestly attenuated the associations. Further analysis showed a statistically significant interaction between hours of napping and sleeping on diabetes (Pinteraction < 0.0001). Among participants with no napping, only short night sleeping was associated with higher occurrence of diabetes, whereas among those with ≥1 h of napping, both long and short sleeping was associated with higher risk. CONCLUSIONS Day napping and short night sleeping are associated with higher risk of diabetes. The association between sleep duration and diabetes may be modified by napping habit. PMID:19825823

[Association between insomnia symptoms, daytime napping, and falls in community-dwelling elderly].

PubMed

Pereira, Alexandre Alves; Ceolim, Maria Filomena; Neri, Anita Liberalesso

2013-03-01

This study focused on associations between insomnia symptoms, daytime napping, and falls in community-dwelling elderly, using a population-based cross-sectional design and probability sample with 689 community-dwelling elders. The protocol consisted of self-reported and physical performance variables. The study used univariate and multivariate logistic regression analysis with statistical significance set at p < 0.05. Prevalence rates for insomnia symptoms and daytime napping were 49.9% (n = 339) and 62.8% (n = 432), respectively. 14.4% reported a single fall and 11.9% reported multiple falls. Falls were associated with female gender (OR = 7.73; 95%CI: 3.03-19.72), age > 80 (OR = 3.48; 95%CI: 1.54-7.85), napping (OR = 2.24; 95%CI: 1.24-4.05), and depressive symptoms (OR = 1.98; 95%CI: 1.11-3.53). The association between daytime napping and falls corroborates data from international research. Identifying modifiable risk factors may help programs to prevent falls in the elderly.

Sex difference in the association between habitual daytime napping and prevalence of diabetes: a population-based study.

PubMed

Sun, Kan; Li, Feng; Qi, Yiqin; Lin, Diaozhu; Ren, Meng; Xu, Mingtong; Li, Fangping; Li, Yan; Yan, Li

2016-05-01

Our objective was to evaluate the associations between habitual daytime napping and diabetes and whether it varies by sex, menopause, and sleep quality. We conducted a population-based cross-sectional study in 8621 eligible individuals aged 40 years or older. Information on daytime napping hours, night-time sleep duration, history of menstruation, and sleep quality was self-reported. Diabetes was diagnosed according to the 1999 World Health Organization diagnostic criteria. The prevalence of diabetes was 19.4 % in men and 15.6 % in women. Increased daytime napping hours were positively associated with parameters of glycometabolism in women, such as fasting plasma glucose, oral glucose tolerance test (OGTT) 2-h plasma glucose, and Hemoglobin A1c (HbA1c, all P for trend <0.05). In women, the prevalence of diabetes in no-habitual daytime napping group, 0-1-h daytime napping group, and more than 1-h daytime napping group were 14.5, 15.6, and 20.8 %, respectively (P for trend = 0.0004). A similar trend was detected in postmenopausal women (P for trend = 0.002). In multivariate logistic regression analysis, compared with no-habitual daytime napping postmenopausal women, those with daytime napping more than 1 h had higher prevalent diabetes (odds ratios 1.36, 95 % confidence interval, 1.04-1.77). In subgroup analysis of postmenopausal women, associations of daytime napping levels and prevalent diabetes were detected in older, overweight participants with good sleep quality who have not retired from work. In conclusion, our study suggests that habitual daytime napping is associated with prevalence of diabetes in postmenopausal women.

Associations between longer habitual day napping and non-alcoholic fatty liver disease in an elderly Chinese population.

PubMed

Qu, Hua; Wang, Hang; Deng, Min; Wei, Huili; Deng, Huacong

2014-01-01

Both longer habitual day napping and Non-Alcoholic Fatty Liver Disease (NAFLD) are associated with diabetes and inflammation, but the association between day napping and NAFLD remains unexplored. To investigate the association between the duration of habitual day napping and NAFLD in an elderly Chinese population and to gain insight into the role of inflammatory cytokines in this association. We conducted a series of cross-sectional studies of the community population in Chongqing, China, from 2011 to 2012. Among 6998 participants aged 40 to 75 years, 6438 eligible participants were included in the first study and analyzed to observe the association between day napping duration and NAFLD. In a separate study, 80 non-nappers and 90 nappers were selected to identify the role of inflammatory cytokines in this association. Logistic regression models were used to examine the odds ratios (ORs) of day nap duration with NAFLD. Day nappers had a significantly higher prevalence of NAFLD (P<0.001). Longer day napping duration was associated in a dose-dependent manner with NAFLD (P trend <0.001). After adjustment for potential confounders, the ORs were 1.67 (95% CI 1.13-2.46) for those reporting 0.5-1 h and 1.49 (95% CI 1.01-2.19) for those reporting >1 h of day napping compared with individuals who did not take day naps (all P<0.05). Longer-duration day nappers had higher levels of IL-6 and progranulin (PGRN) but lower levels of Secreted frizzled-related protein-5 (SFRP5, all P trend <0.001). After adjusting for IL-6, PGRN, and SFRP5, the association between day napping duration and NAFLD disappeared (all P>0.05). Longer day napping duration is associated with a higher prevalence of NAFLD, and inflammatory cytokines may be an essential link between day napping and NAFLD.

Conservation of gene linkage in dispersed vertebrate NK homeobox clusters.

PubMed

Wotton, Karl R; Weierud, Frida K; Juárez-Morales, José L; Alvares, Lúcia E; Dietrich, Susanne; Lewis, Katharine E

2009-10-01

Nk homeobox genes are important regulators of many different developmental processes including muscle, heart, central nervous system and sensory organ development. They are thought to have arisen as part of the ANTP megacluster, which also gave rise to Hox and ParaHox genes, and at least some NK genes remain tightly linked in all animals examined so far. The protostome-deuterostome ancestor probably contained a cluster of nine Nk genes: (Msx)-(Nk4/tinman)-(Nk3/bagpipe)-(Lbx/ladybird)-(Tlx/c15)-(Nk7)-(Nk6/hgtx)-(Nk1/slouch)-(Nk5/Hmx). Of these genes, only NKX2.6-NKX3.1, LBX1-TLX1 and LBX2-TLX2 remain tightly linked in humans. However, it is currently unclear whether this is unique to the human genome as we do not know which of these Nk genes are clustered in other vertebrates. This makes it difficult to assess whether the remaining linkages are due to selective pressures or because chance rearrangements have "missed" certain genes. In this paper, we identify all of the paralogs of these ancestrally clustered NK genes in several distinct vertebrates. We demonstrate that tight linkages of Lbx1-Tlx1, Lbx2-Tlx2 and Nkx3.1-Nkx2.6 have been widely maintained in both the ray-finned and lobe-finned fish lineages. Moreover, the recently duplicated Hmx2-Hmx3 genes are also tightly linked. Finally, we show that Lbx1-Tlx1 and Hmx2-Hmx3 are flanked by highly conserved noncoding elements, suggesting that shared regulatory regions may have resulted in evolutionary pressure to maintain these linkages. Consistent with this, these pairs of genes have overlapping expression domains. In contrast, Lbx2-Tlx2 and Nkx3.1-Nkx2.6, which do not seem to be coexpressed, are also not associated with conserved noncoding sequences, suggesting that an alternative mechanism may be responsible for the continued clustering of these genes.

Eviction of linker histone H1 by NAP-family histone chaperones enhances activated transcription.

PubMed

Zhang, Qian; Giebler, Holli A; Isaacson, Marisa K; Nyborg, Jennifer K

2015-01-01

In the Metazoan nucleus, core histones assemble the genomic DNA to form nucleosome arrays, which are further compacted into dense chromatin structures by the linker histone H1. The extraordinary density of chromatin creates an obstacle for accessing the genetic information. Regulation of chromatin dynamics is therefore critical to cellular homeostasis, and histone chaperones serve as prominent players in these processes. In the current study, we examined the role of specific histone chaperones in negotiating the inherently repressive chromatin structure during transcriptional activation. Using a model promoter, we demonstrate that the human nucleosome assembly protein family members hNap1 and SET/Taf1β stimulate transcription in vitro during pre-initiation complex formation, prior to elongation. This stimulatory effect is dependent upon the presence of activators, p300, and Acetyl-CoA. We show that transcription from our chromatin template is strongly repressed by H1, and that both histone chaperones enhance RNA synthesis by overcoming H1-induced repression. Importantly, both hNap1 and SET/Taf1β directly bind H1, and function to enhance transcription by evicting the linker histone from chromatin reconstituted with H1. In vivo studies demonstrate that SET/Taf1β, but not hNap1, strongly stimulates activated transcription from the chromosomally-integrated model promoter, consistent with the observation that SET/Taf1β is nuclear, whereas hNap1 is primarily cytoplasmic. Together, these observations indicate that SET/Taf1β may serve as a critical regulator of H1 dynamics and gene activation in vivo. These studies uncover a novel function for SET that mechanistically couples transcriptional derepression with H1 dynamics. Furthermore, they underscore the significance of chaperone-dependent H1 displacement as an essential early step in the transition of a promoter from a dense chromatin state into one that is permissive to transcription factor binding and robust

A Cluster of Cuticle Protein Genes of Drosophila Melanogaster at 65a: Sequence, Structure and Evolution

PubMed Central

Charles, J. P.; Chihara, C.; Nejad, S.; Riddiford, L. M.

1997-01-01

A 36-kb genomic DNA segment of the Drosophila melanogaster genome containing 12 clustered cuticle genes has been mapped and partially sequenced. The cluster maps at 65A 5-6 on the left arm of the third chromosome, in agreement with the previously determined location of a putative cluster encompassing the genes for the third instar larval cuticle proteins LCP5, LCP6 and LCP8. This cluster is the largest cuticle gene cluster discovered to date and shows a number of surprising features that explain in part the genetic complexity of the LCP5, LCP6 and LCP8 loci. The genes encoding LCP5 and LCP8 are multiple copy genes and the presence of extensive similarity in their coding regions gives the first evidence for gene conversion in cuticle genes. In addition, five genes in the cluster are intronless. Four of these five have arisen by retroposition. The other genes in the cluster have a single intron located at an unusual location for insect cuticle genes. PMID:9383064

Modularity of Plant Metabolic Gene Clusters: A Trio of Linked Genes That Are Collectively Required for Acylation of Triterpenes in Oat[W][OA

PubMed Central

Mugford, Sam T.; Louveau, Thomas; Melton, Rachel; Qi, Xiaoquan; Bakht, Saleha; Hill, Lionel; Tsurushima, Tetsu; Honkanen, Suvi; Rosser, Susan J.; Lomonossoff, George P.; Osbourn, Anne

2013-01-01

Operon-like gene clusters are an emerging phenomenon in the field of plant natural products. The genes encoding some of the best-characterized plant secondary metabolite biosynthetic pathways are scattered across plant genomes. However, an increasing number of gene clusters encoding the synthesis of diverse natural products have recently been reported in plant genomes. These clusters have arisen through the neo-functionalization and relocation of existing genes within the genome, and not by horizontal gene transfer from microbes. The reasons for clustering are not yet clear, although this form of gene organization is likely to facilitate co-inheritance and co-regulation. Oats (Avena spp) synthesize antimicrobial triterpenoids (avenacins) that provide protection against disease. The synthesis of these compounds is encoded by a gene cluster. Here we show that a module of three adjacent genes within the wider biosynthetic gene cluster is required for avenacin acylation. Through the characterization of these genes and their encoded proteins we present a model of the subcellular organization of triterpenoid biosynthesis. PMID:23532069

Accurate prediction of secondary metabolite gene clusters in filamentous fungi.

PubMed

Andersen, Mikael R; Nielsen, Jakob B; Klitgaard, Andreas; Petersen, Lene M; Zachariasen, Mia; Hansen, Tilde J; Blicher, Lene H; Gotfredsen, Charlotte H; Larsen, Thomas O; Nielsen, Kristian F; Mortensen, Uffe H

2013-01-02

Biosynthetic pathways of secondary metabolites from fungi are currently subject to an intense effort to elucidate the genetic basis for these compounds due to their large potential within pharmaceutics and synthetic biochemistry. The preferred method is methodical gene deletions to identify supporting enzymes for key synthases one cluster at a time. In this study, we design and apply a DNA expression array for Aspergillus nidulans in combination with legacy data to form a comprehensive gene expression compendium. We apply a guilt-by-association-based analysis to predict the extent of the biosynthetic clusters for the 58 synthases active in our set of experimental conditions. A comparison with legacy data shows the method to be accurate in 13 of 16 known clusters and nearly accurate for the remaining 3 clusters. Furthermore, we apply a data clustering approach, which identifies cross-chemistry between physically separate gene clusters (superclusters), and validate this both with legacy data and experimentally by prediction and verification of a supercluster consisting of the synthase AN1242 and the prenyltransferase AN11080, as well as identification of the product compound nidulanin A. We have used A. nidulans for our method development and validation due to the wealth of available biochemical data, but the method can be applied to any fungus with a sequenced and assembled genome, thus supporting further secondary metabolite pathway elucidation in the fungal kingdom.

Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data

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

Data Analysis and Visualization; nternational Research Training Group ``Visualization of Large and Unstructured Data Sets,'' University of Kaiserslautern, Germany; Computational Research Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA

2008-05-12

The recent development of methods for extracting precise measurements of spatial gene expression patterns from three-dimensional (3D) image data opens the way for new analyses of the complex gene regulatory networks controlling animal development. We present an integrated visualization and analysis framework that supports user-guided data clustering to aid exploration of these new complex datasets. The interplay of data visualization and clustering-based data classification leads to improved visualization and enables a more detailed analysis than previously possible. We discuss (i) integration of data clustering and visualization into one framework; (ii) application of data clustering to 3D gene expression data; (iii)more » evaluation of the number of clusters k in the context of 3D gene expression clustering; and (iv) improvement of overall analysis quality via dedicated post-processing of clustering results based on visualization. We discuss the use of this framework to objectively define spatial pattern boundaries and temporal profiles of genes and to analyze how mRNA patterns are controlled by their regulatory transcription factors.« less

J-curve relation between daytime nap duration and type 2 diabetes or metabolic syndrome: A dose-response meta-analysis

PubMed Central

Yamada, Tomohide; Shojima, Nobuhiro; Yamauchi, Toshimasa; Kadowaki, Takashi

2016-01-01

Adequate sleep is important for good health, but it is not always easy to achieve because of social factors. Daytime napping is widely prevalent around the world. We performed a meta-analysis to investigate the association between napping (or excessive daytime sleepiness: EDS) and the risk of type 2 diabetes or metabolic syndrome, and to quantify the potential dose-response relation using cubic spline models. Electronic databases were searched for articles published up to 2016, with 288,883 Asian and Western subjects. Pooled analysis revealed that a long nap (≥60 min/day) and EDS were each significantly associated with an increased risk of type 2 diabetes versus no nap or no EDS (odds ratio 1.46 (95% CI 1.23–1.74, p < 0.01) for a long nap and 2.00 (1.58–2.53) for EDS). In contrast, a short nap (<60 min/day) was not associated with diabetes (p = 0.75). Dose-response meta-analysis showed a J-curve relation between nap time and the risk of diabetes or metabolic syndrome, with no effect of napping up to about 40 minutes/day, followed by a sharp increase in risk at longer nap times. In summary, longer napping is associated with an increased risk of metabolic disease. Further studies are needed to confirm the benefit of a short nap. PMID:27909305

Napping is associated with increased risk of type 2 diabetes: the Guangzhou Biobank Cohort Study.

PubMed

Lam, Kin-Bong Hubert; Jiang, Chao Qiang; Thomas, G Neil; Arora, Teresa; Zhang, Wei Sen; Taheri, Shahrad; Adab, Peymané; Lam, Tai Hing; Cheng, Kar Keung

2010-03-01

Intentional napping is very common, particularly in China. However, there are limited data regarding its potential health effects. We therefore examined the possible relationship between napping and type 2 diabetes. Cross-sectional analysis of baseline data from the Guangzhou Biobank Cohort Study. Community-based elderly association in Guangzhou, China. 19,567 Chinese men and women aged 50 years or older. Self-reported frequency of napping was obtained by questionnaire and type 2 diabetes was assessed by fasting blood glucose and/or self-reports of physician diagnosis or treatment. Participants reporting frequent naps (4-6 days/week and daily) were 42% to 52% more likely to have diabetes. The relationships remained essentially unchanged after adjustments were made for demographics, lifestyle and sleep habits, health status, adiposity, and metabolic markers (odds ratio for diabetes 1.36 [95% CI 1.17-1.57] in 4-6 days/week, 1.28 [1.15-1.44] in daily nappers). Similar associations were found between napping and impaired fasting glucose. Removal of those with potential ill health and daytime sleepiness did not alter the observed associations. Napping is associated with elevated prevalence of diabetes and impaired fasting glucose in this older Chinese sample. Our finding suggests that it is less likely that diabetes leads to daytime sleepiness. This raises the possibility that napping may increase the risk of diabetes. Confirmation by longitudinal studies is needed.

Variation in the fumonisin biosynthetic gene cluster in fumonisin-producing and nonproducing black aspergilli.

PubMed

Susca, Antonia; Proctor, Robert H; Butchko, Robert A E; Haidukowski, Miriam; Stea, Gaetano; Logrieco, Antonio; Moretti, Antonio

2014-12-01

The ability to produce fumonisin mycotoxins varies among members of the black aspergilli. Previously, analyses of selected genes in the fumonisin biosynthetic gene (fum) cluster in black aspergilli from California grapes indicated that fumonisin-nonproducing isolates of Aspergillus welwitschiae lack six fum genes, but nonproducing isolates of Aspergillus niger do not. In the current study, analyses of black aspergilli from grapes from the Mediterranean Basin indicate that the genomic context of the fum cluster is the same in isolates of A. niger and A. welwitschiae regardless of fumonisin-production ability and that full-length clusters occur in producing isolates of both species and nonproducing isolates of A. niger. In contrast, the cluster has undergone an eight-gene deletion in fumonisin-nonproducing isolates of A. welwitschiae. Phylogenetic analyses suggest each species consists of a mixed population of fumonisin-producing and nonproducing individuals, and that existence of both production phenotypes may provide a selective advantage to these species. Differences in gene content of fum cluster homologues and phylogenetic relationships of fum genes suggest that the mutation(s) responsible for the nonproduction phenotype differs, and therefore arose independently, in the two species. Partial fum cluster homologues were also identified in genome sequences of four other black Aspergillus species. Gene content of these partial clusters and phylogenetic relationships of fum sequences indicate that non-random partial deletion of the cluster has occurred multiple times among the species. This in turn suggests that an intact cluster and fumonisin production were once more widespread among black aspergilli. Copyright © 2014 Elsevier Inc. All rights reserved.

Sleep inertia associated with a 10-min nap before the commute home following a night shift: A laboratory simulation study.

PubMed

Hilditch, Cassie J; Dorrian, Jillian; Centofanti, Stephanie A; Van Dongen, Hans P; Banks, Siobhan

2017-02-01

Night shift workers are at risk of road accidents due to sleepiness on the commute home. A brief nap at the end of the night shift, before the commute, may serve as a sleepiness countermeasure. However, there is potential for sleep inertia, i.e. transient impairment immediately after awakening from the nap. We investigated whether sleep inertia diminishes the effectiveness of napping as a sleepiness countermeasure before a simulated commute after a simulated night shift. N=21 healthy subjects (aged 21-35 y; 12 females) participated in a 3-day laboratory study. After a baseline night, subjects were kept awake for 27h for a simulated night shift. They were randomised to either receive a 10-min nap ending at 04:00 plus a 10-min pre-drive nap ending at 07:10 (10-NAP) or total sleep deprivation (NO-NAP). A 40-min York highway driving task was performed at 07:15 to simulate the commute. A 3-min psychomotor vigilance test (PVT-B) and the Samn-Perelli Fatigue Scale (SP-Fatigue) were administered at 06:30 (pre-nap), 07:12 (post-nap), and 07:55 (post-drive). In the 10-NAP condition, total pre-drive nap sleep time was 9.1±1.2min (mean±SD), with 1.3±1.9min spent in slow wave sleep, as determined polysomnographically. There was no difference between conditions in PVT-B performance at 06:30 (before the nap). In the 10-NAP condition, PVT-B performance was worse after the nap (07:12) compared to before the nap (06:30); no change across time was found in the NO-NAP condition. There was no significant difference between conditions in PVT-B performance after the drive. SP-Fatigue and driving performance did not differ significantly between conditions. In conclusion, the pre-drive nap showed objective, but not subjective, evidence of sleep inertia immediately after awakening. The 10-min nap did not affect driving performance during the simulated commute home, and was not effective as a sleepiness countermeasure. Copyright © 2015 Elsevier Ltd. All rights reserved.

Comparing the Effects of Nocturnal Sleep and Daytime Napping on Declarative Memory Consolidation

PubMed Central

Lo, June C.; Dijk, Derk-Jan; Groeger, John A.

2014-01-01

Nocturnal sleep and daytime napping facilitate memory consolidation for semantically related and unrelated word pairs. We contrasted forgetting of both kinds of materials across a 12-hour interval involving either nocturnal sleep or daytime wakefulness (experiment 1) and a 2-hour interval involving either daytime napping or wakefulness (experiment 2). Beneficial effects of post-learning nocturnal sleep and daytime napping were greater for unrelated word pairs (Cohen’s d = 0.71 and 0.68) than for related ones (Cohen’s d = 0.58 and 0.15). While the size of nocturnal sleep and daytime napping effects was similar for unrelated word pairs, for related pairs, the effect of nocturnal sleep was more prominent. Together, these findings suggest that sleep preferentially facilitates offline memory processing of materials that are more susceptible to forgetting. PMID:25229457

Wide distribution of O157-antigen biosynthesis gene clusters in Escherichia coli.

PubMed

Iguchi, Atsushi; Shirai, Hiroki; Seto, Kazuko; Ooka, Tadasuke; Ogura, Yoshitoshi; Hayashi, Tetsuya; Osawa, Kayo; Osawa, Ro

2011-01-01

Most Escherichia coli O157-serogroup strains are classified as enterohemorrhagic E. coli (EHEC), which is known as an important food-borne pathogen for humans. They usually produce Shiga toxin (Stx) 1 and/or Stx2, and express H7-flagella antigen (or nonmotile). However, O157 strains that do not produce Stxs and express H antigens different from H7 are sometimes isolated from clinical and other sources. Multilocus sequence analysis revealed that these 21 O157:non-H7 strains tested in this study belong to multiple evolutionary lineages different from that of EHEC O157:H7 strains, suggesting a wide distribution of the gene set encoding the O157-antigen biosynthesis in multiple lineages. To gain insight into the gene organization and the sequence similarity of the O157-antigen biosynthesis gene clusters, we conducted genomic comparisons of the chromosomal regions (about 59 kb in each strain) covering the O-antigen gene cluster and its flanking regions between six O157:H7/non-H7 strains. Gene organization of the O157-antigen gene cluster was identical among O157:H7/non-H7 strains, but was divided into two distinct types at the nucleotide sequence level. Interestingly, distribution of the two types did not clearly follow the evolutionary lineages of the strains, suggesting that horizontal gene transfer of both types of O157-antigen gene clusters has occurred independently among E. coli strains. Additionally, detailed sequence comparison revealed that some positions of the repetitive extragenic palindromic (REP) sequences in the regions flanking the O-antigen gene clusters were coincident with possible recombination points. From these results, we conclude that the horizontal transfer of the O157-antigen gene clusters induced the emergence of multiple O157 lineages within E. coli and speculate that REP sequences may involve one of the driving forces for exchange and evolution of O-antigen loci.

Delineation of metabolic gene clusters in plant genomes by chromatin signatures

PubMed Central

Yu, Nan; Nützmann, Hans-Wilhelm; MacDonald, James T.; Moore, Ben; Field, Ben; Berriri, Souha; Trick, Martin; Rosser, Susan J.; Kumar, S. Vinod; Freemont, Paul S.; Osbourn, Anne

2016-01-01

Plants are a tremendous source of diverse chemicals, including many natural product-derived drugs. It has recently become apparent that the genes for the biosynthesis of numerous different types of plant natural products are organized as metabolic gene clusters, thereby unveiling a highly unusual form of plant genome architecture and offering novel avenues for discovery and exploitation of plant specialized metabolism. Here we show that these clustered pathways are characterized by distinct chromatin signatures of histone 3 lysine trimethylation (H3K27me3) and histone 2 variant H2A.Z, associated with cluster repression and activation, respectively, and represent discrete windows of co-regulation in the genome. We further demonstrate that knowledge of these chromatin signatures along with chromatin mutants can be used to mine genomes for cluster discovery. The roles of H3K27me3 and H2A.Z in repression and activation of single genes in plants are well known. However, our discovery of highly localized operon-like co-regulated regions of chromatin modification is unprecedented in plants. Our findings raise intriguing parallels with groups of physically linked multi-gene complexes in animals and with clustered pathways for specialized metabolism in filamentous fungi. PMID:26895889

A conserved gene cluster as a putative functional unit in insect innate immunity.

PubMed

Somogyi, Kálmán; Sipos, Botond; Pénzes, Zsolt; Andó, István

2010-11-05

The Nimrod gene superfamily is an important component of the innate immune response. The majority of its member genes are located in close proximity within the Drosophila melanogaster genome and they lie in a larger conserved cluster ("Nimrod cluster"), made up of non-related groups (families, superfamilies) of genes. This cluster has been a part of the Arthropod genomes for about 300-350 million years. The available data suggest that the Nimrod cluster is a functional module of the insect innate immune response. Copyright © 2010 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture

PubMed Central

Johnson, Timothy A.; Stedtfeld, Robert D.; Wang, Qiong; Cole, James R.; Hashsham, Syed A.; Looft, Torey; Zhu, Yong-Guan

2016-01-01

ABSTRACT   Antibiotic resistance is a worldwide health risk, but the influence of animal agriculture on the genetic context and enrichment of individual antibiotic resistance alleles remains unclear. Using quantitative PCR followed by amplicon sequencing, we quantified and sequenced 44 genes related to antibiotic resistance, mobile genetic elements, and bacterial phylogeny in microbiomes from U.S. laboratory swine and from swine farms from three Chinese regions. We identified highly abundant resistance clusters: groups of resistance and mobile genetic element alleles that cooccur. For example, the abundance of genes conferring resistance to six classes of antibiotics together with class 1 integrase and the abundance of IS6100-type transposons in three Chinese regions are directly correlated. These resistance cluster genes likely colocalize in microbial genomes in the farms. Resistance cluster alleles were dramatically enriched (up to 1 to 10% as abundant as 16S rRNA) and indicate that multidrug-resistant bacteria are likely the norm rather than an exception in these communities. This enrichment largely occurred independently of phylogenetic composition; thus, resistance clusters are likely present in many bacterial taxa. Furthermore, resistance clusters contain resistance genes that confer resistance to antibiotics independently of their particular use on the farms. Selection for these clusters is likely due to the use of only a subset of the broad range of chemicals to which the clusters confer resistance. The scale of animal agriculture and its wastes, the enrichment and horizontal gene transfer potential of the clusters, and the vicinity of large human populations suggest that managing this resistance reservoir is important for minimizing human risk. PMID:27073098

β-globin gene cluster haplotypes in ethnic minority populations of southwest China

PubMed Central

Sun, Hao; Liu, Hongxian; Huang, Kai; Lin, Keqin; Huang, Xiaoqin; Chu, Jiayou; Ma, Shaohui; Yang, Zhaoqing

2017-01-01

The genetic diversity and relationships among ethnic minority populations of southwest China were investigated using seven polymorphic restriction enzyme sites in the β-globin gene cluster. The haplotypes of 1392 chromosomes from ten ethnic populations living in southwest China were determined. Linkage equilibrium and recombination hotspot were found between the 5′ sites and 3′ sites of the β-globin gene cluster. 5′ haplotypes 2 (+−−−), 6 (−++−+), 9 (−++++) and 3′ haplotype FW3 (−+) were the predominant haplotypes. Notably, haplotype 9 frequency was significantly high in the southwest populations, indicating their difference with other Chinese. The interpopulation differentiation of southwest Chinese minority populations is less than those in populations of northern China and other continents. Phylogenetic analysis shows that populations sharing same ethnic origin or language clustered to each other, indicating current β-globin cluster diversity in the Chinese populations reflects their ethnic origin and linguistic affiliations to a great extent. This study characterizes β-globin gene cluster haplotypes in southwest Chinese minorities for the first time, and reveals the genetic variability and affinity of these populations using β-globin cluster haplotype frequencies. The results suggest that ethnic origin plays an important role in shaping variations of the β-globin gene cluster in the southwestern ethnic populations of China. PMID:28205625

Self-reported sleep duration and daytime napping are associated with renal hyperfiltration in general population.

PubMed

Lin, Miao; Su, Qing; Wen, Junping; Wei, Shichao; Yao, Jin; Huang, Huibin; Liang, Jixing; Li, Liantao; Lin, Wei; Lin, Lixiang; Lu, Jieli; Bi, Yufang; Wang, Weiqing; Ning, Guang; Chen, Gang

2018-03-01

Renal hyperfiltration (RHF) has emerged as a novel marker of early renal damage in various conditions such as diabetes and metabolic syndrome. Aberrant sleep duration and excessive daytime napping may affect the development of chronic kidney disease (CKD). In this study, the association between sleep duration, daytime napping, and renal hyperfiltration was assessed. This study was conducted in three communities in China. A total of 16,119 community volunteers (5735 males and 10,384 females) aged 40-65 years without CKD were included for the study. Participants with short sleep duration (<6 h/day) or long sleep duration (≥10 h/day) were at a significantly increased risk of renal hyperfiltration. The fully adjusted ORs (95% CI) were 2.112 (1.107, 4.031) and 2.071 (1.504, 2.853), respectively (P < 0.05). In addition, those who took naps longer than 1.5 h per day had a higher risk of renal hyperfiltration compared with those without napping (OR 1.400, 95% CI 1.018-1.924). Further joint analysis indicated that participants with long sleep duration (≥10 h/day) had a more than twofold increased risk of RHF regardless of nap status compared with those who slept 8-9 h per day without daytime napping. The association between sleep duration or daytime napping and RHF could not be explained by the influence of sleep quality. Additional subgroup analysis showed long sleep duration (≥9 h/day) and long daytime napping (≥1.5 h) were associated with an increased risk of RHF among individuals with good sleep quality. Sleep duration less than 6 h/day or more than 10 h/day and long daytime napping tend to be associated with an increased risk of renal hyperfiltration in middle-aged general population, and this relationship was independent of diabetes, hypertension, obesity, or poor sleep quality.

Iterative local Gaussian clustering for expressed genes identification linked to malignancy of human colorectal carcinoma.

PubMed

Wasito, Ito; Hashim, Siti Zaiton M; Sukmaningrum, Sri

2007-12-30

Gene expression profiling plays an important role in the identification of biological and clinical properties of human solid tumors such as colorectal carcinoma. Profiling is required to reveal underlying molecular features for diagnostic and therapeutic purposes. A non-parametric density-estimation-based approach called iterative local Gaussian clustering (ILGC), was used to identify clusters of expressed genes. We used experimental data from a previous study by Muro and others consisting of 1,536 genes in 100 colorectal cancer and 11 normal tissues. In this dataset, the ILGC finds three clusters, two large and one small gene clusters, similar to their results which used Gaussian mixture clustering. The correlation of each cluster of genes and clinical properties of malignancy of human colorectal cancer was analysed for the existence of tumor or normal, the existence of distant metastasis and the existence of lymph node metastasis.

The evolutionary life cycle of the polysaccharide biosynthetic gene cluster based on the Sphingomonadaceae.

PubMed

Wu, Mengmeng; Huang, Haidong; Li, Guoqiang; Ren, Yi; Shi, Zhong; Li, Xiaoyan; Dai, Xiaohui; Gao, Ge; Ren, Mengnan; Ma, Ting

2017-04-21

Although clustering of genes from the same metabolic pathway is a widespread phenomenon, the evolution of the polysaccharide biosynthetic gene cluster remains poorly understood. To determine the evolution of this pathway, we identified a scattered production pathway of the polysaccharide sanxan by Sphingomonas sanxanigenens NX02, and compared the distribution of genes between sphingan-producing and other Sphingomonadaceae strains. This allowed us to determine how the scattered sanxan pathway developed, and how the polysaccharide gene cluster evolved. Our findings suggested that the evolution of microbial polysaccharide biosynthesis gene clusters is a lengthy cyclic process comprising cluster 1 → scatter → cluster 2. The sanxan biosynthetic pathway proved the existence of a dispersive process. We also report the complete genome sequence of NX02, in which we identified many unstable genetic elements and powerful secretion systems. Furthermore, nine enzymes for the formation of activated precursors, four glycosyltransferases, four acyltransferases, and four polymerization and export proteins were identified. These genes were scattered in the NX02 genome, and the positive regulator SpnA of sphingans synthesis could not regulate sanxan production. Finally, we concluded that the evolution of the sanxan pathway was independent. NX02 evolved naturally as a polysaccharide producing strain over a long-time evolution involving gene acquisitions and adaptive mutations.

Co-clustering phenome–genome for phenotype classification and disease gene discovery

PubMed Central

Hwang, TaeHyun; Atluri, Gowtham; Xie, MaoQiang; Dey, Sanjoy; Hong, Changjin; Kumar, Vipin; Kuang, Rui

2012-01-01

Understanding the categorization of human diseases is critical for reliably identifying disease causal genes. Recently, genome-wide studies of abnormal chromosomal locations related to diseases have mapped >2000 phenotype–gene relations, which provide valuable information for classifying diseases and identifying candidate genes as drug targets. In this article, a regularized non-negative matrix tri-factorization (R-NMTF) algorithm is introduced to co-cluster phenotypes and genes, and simultaneously detect associations between the detected phenotype clusters and gene clusters. The R-NMTF algorithm factorizes the phenotype–gene association matrix under the prior knowledge from phenotype similarity network and protein–protein interaction network, supervised by the label information from known disease classes and biological pathways. In the experiments on disease phenotype–gene associations in OMIM and KEGG disease pathways, R-NMTF significantly improved the classification of disease phenotypes and disease pathway genes compared with support vector machines and Label Propagation in cross-validation on the annotated phenotypes and genes. The newly predicted phenotypes in each disease class are highly consistent with human phenotype ontology annotations. The roles of the new member genes in the disease pathways are examined and validated in the protein–protein interaction subnetworks. Extensive literature review also confirmed many new members of the disease classes and pathways as well as the predicted associations between disease phenotype classes and pathways. PMID:22735708

Associations between Longer Habitual Day Napping and Non-Alcoholic Fatty Liver Disease in an Elderly Chinese Population

PubMed Central

Qu, Hua; Wang, Hang; Deng, Min; Wei, Huili; Deng, Huacong

2014-01-01

Context Both longer habitual day napping and Non-Alcoholic Fatty Liver Disease (NAFLD) are associated with diabetes and inflammation, but the association between day napping and NAFLD remains unexplored. Objective To investigate the association between the duration of habitual day napping and NAFLD in an elderly Chinese population and to gain insight into the role of inflammatory cytokines in this association. Design and Setting We conducted a series of cross-sectional studies of the community population in Chongqing, China, from 2011 to 2012. Participants Among 6998 participants aged 40 to 75 years, 6438 eligible participants were included in the first study and analyzed to observe the association between day napping duration and NAFLD. In a separate study, 80 non-nappers and 90 nappers were selected to identify the role of inflammatory cytokines in this association. Logistic regression models were used to examine the odds ratios (ORs) of day nap duration with NAFLD. Results Day nappers had a significantly higher prevalence of NAFLD (P<0.001). Longer day napping duration was associated in a dose-dependent manner with NAFLD (P trend <0.001). After adjustment for potential confounders, the ORs were 1.67 (95% CI 1.13–2.46) for those reporting 0.5–1 h and 1.49 (95% CI 1.01–2.19) for those reporting >1 h of day napping compared with individuals who did not take day naps (all P<0.05). Longer-duration day nappers had higher levels of IL-6 and progranulin (PGRN) but lower levels of Secreted frizzled-related protein-5 (SFRP5, all P trend <0.001). After adjusting for IL-6, PGRN, and SFRP5, the association between day napping duration and NAFLD disappeared (all P>0.05). Conclusion Longer day napping duration is associated with a higher prevalence of NAFLD, and inflammatory cytokines may be an essential link between day napping and NAFLD. PMID:25140521

The effects of extended nap periods on cognitive, physiological and subjective responses under simulated night shift conditions.

PubMed

Davy, Jonathan; Göbel, Matthias

2018-02-01

Extended nap opportunities have been effective in maintaining alertness in the context of extended night shifts (+12 h). However, there is limited evidence of their efficacy during 8-h shifts. Thus, this study explored the effects of extended naps on cognitive, physiological and perceptual responses during four simulated, 8-h night shifts. In a laboratory setting, 32 participants were allocated to one of three conditions. All participants completed four consecutive, 8-h night shifts, with the arrangements differing by condition. The fixed night condition worked from 22h00 to 06h00, while the nap early group worked from 20h00 to 08h00 and napped between 00h00 and 03h20. The nap late group worked from 00h00 to 12h00 and napped between 04h00 and 07h20. Nap length was limited to 3 hours and 20 minutes. Participants performed a simple beading task during each shift, while also completing six to eight test batteries roughly every 2 h. During each shift, six test batteries were completed, in which the following measures were taken. Performance indicators included beading output, eye accommodation time, choice reaction time, visual vigilance, simple reaction time, processing speed and object recognition, working memory, motor response time and tracking performance. Physiological measures included heart rate and tympanic temperature, whereas subjective sleepiness and reported sleep length and quality while outside the laboratory constituted the self reported measures. Both naps reduced subjective sleepiness but did not alter the circadian and homeostatic-related changes in cognitive and physiological measures, relative to the fixed night condition. Additionally, there was evidence of sleep inertia following each nap, which resulted in transient reductions in certain perceptual cognitive performance measures. The present study suggested that there were some benefits associated with including an extended nap during 8-h night shifts. However, the effects of sleep inertia

Toddler’s Self-Regulation Strategies in a Challenge Context are Nap-Dependent

PubMed Central

Miller, Alison L.; Seifer, Ronald; Crossin, Rebecca; LeBourgeois, Monique K.

2015-01-01

SUMMARY Early childhood represents a time of developmental changes in both sleep and self-regulation, a construct reflecting the ability to control one’s behavior, attention, and emotion when challenged. Links between sleep and self-regulation processes have been proposed, but experimental evidence with young children is lacking. In the current study, we tested the effects of acute sleep restriction (nap deprivation) on toddlers’ self-regulation. Healthy children (n=12; 4 males; 30–36 months (33.9±1.7) slept on a strict schedule (verified with actigraphy and sleep diaries) for 5 days before each of two afternoon assessments following a Nap and a No-Nap condition (~11-day protocol). Children were videotaped while attempting an unsolvable puzzle, and 10 mutually exclusive self-regulation strategies were later coded. On average, children lost ~90 min of sleep on the No-Nap versus the Nap day. Nap deprivation resulted in moderate-to-large effects on self-regulation strategies, with decreases in skepticism (d=0.77; 7% change), negative self-appraisal (d=0.92; 5% change), and increases in physical self-soothing (d=0.68; 10% change), focus on the puzzle piece that would not fit (perseveration; d=0.50; 9% change), and insistence on completing the unsolvable puzzle (d=0.91; 10% change). Results suggest sleep serves an important role in the way toddlers respond to challenging events in their daily lives. After losing daytime sleep, toddlers were less able to effectively engage in a difficult task and reverted to less mature self-regulation strategies, than when they were well-rested. Over time, chronically missed sleep may impair young children’s self-regulation abilities, resulting in risk for social-emotional, behavioral, and school problems. PMID:25394169

Clustered Xenopus keratin genes: A genomic, transcriptomic, and proteomic analysis.

PubMed

Suzuki, Ken-Ichi T; Suzuki, Miyuki; Shigeta, Mitsuki; Fortriede, Joshua D; Takahashi, Shuji; Mawaribuchi, Shuuji; Yamamoto, Takashi; Taira, Masanori; Fukui, Akimasa

2017-06-15

Keratin genes belong to the intermediate filament superfamily and their expression is altered following morphological and physiological changes in vertebrate epithelial cells. Keratin genes are divided into two groups, type I and II, and are clustered on vertebrate genomes, including those of Xenopus species. Various keratin genes have been identified and characterized by their unique expression patterns throughout ontogeny in Xenopus laevis; however, compilation of previously reported and newly identified keratin genes in two Xenopus species is required for our further understanding of keratin gene evolution, not only in amphibians but also in all terrestrial vertebrates. In this study, 120 putative type I and II keratin genes in total were identified based on the genome data from two Xenopus species. We revealed that most of these genes are highly clustered on two homeologous chromosomes, XLA9_10 and XLA2 in X. laevis, and XTR10 and XTR2 in X. tropicalis, which are orthologous to those of human, showing conserved synteny among tetrapods. RNA-Seq data from various embryonic stages and adult tissues highlighted the unique expression profiles of orthologous and homeologous keratin genes in developmental stage- and tissue-specific manners. Moreover, we identified dozens of epidermal keratin proteins from the whole embryo, larval skin, tail, and adult skin using shotgun proteomics. In light of our results, we discuss the radiation, diversification, and unique expression of the clustered keratin genes, which are closely related to epidermal development and terrestrial adaptation during amphibian evolution, including Xenopus speciation. Copyright © 2016 Elsevier Inc. All rights reserved.

Objective Measurement of Daytime Napping, Cognitive Dysfunction and Subjective Sleepiness in Parkinson’s Disease

PubMed Central

Bolitho, Samuel J.; Naismith, Sharon L.; Salahuddin, Pierre; Terpening, Zoe; Grunstein, Ron R.; Lewis, Simon J. G.

2013-01-01

Introduction Sleep-wake disturbances and concomitant cognitive dysfunction in Parkinson’s disease (PD) contribute significantly to morbidity in patients and their carers. Subjectively reported daytime sleep disturbance is observed in over half of all patients with PD and has been linked to executive cognitive dysfunction. The current study used daytime actigraphy, a novel objective measure of napping and related this to neuropsychological performance in a sample of PD patients and healthy, age and gender-matched controls. Furthermore this study aimed to identify patients with PD who may benefit from pharmacologic and behavioural intervention to improve these symptoms. Methods Eighty-five PD patients and 21 healthy, age-matched controls completed 14 days of wrist actigraphy within two weeks of neuropsychological testing. Objective napping measures were derived from actigraphy using a standardised protocol and subjective daytime sleepiness was recorded by the previously validated Epworth Sleepiness Scale. Results Patients with PD had a 225% increase in the mean nap time per day (minutes) as recorded by actigraphy compared to age matched controls (39.2 ± 35.2 vs. 11.5 ± 11.0 minutes respectively, p < 0.001). Significantly, differences in napping duration between patients, as recorded by actigraphy were not distinguished by their ratings on the subjective measurement of excessive daytime sleepiness. Finally, those patients with excessive daytime napping showed greater cognitive deficits in the domains of attention, semantic verbal fluency and processing speed. Conclusion This study confirms increased levels of napping in PD, a finding that is concordant with subjective reports. However, subjective self-report measures of excessive daytime sleepiness do not robustly identify excessive napping in PD. Fronto-subcortical cognitive dysfunction was observed in those patients who napped excessively. Furthermore, this study suggests that daytime actigraphy, a non

Self-Reported Napping Behavior Change After Continuous Positive Airway Pressure Treatment in Older Adults with Obstructive Sleep Apnea.

PubMed

Hsieh, Cheng-Fang; Riha, Renata L; Morrison, Ian; Hsu, Chung-Yao

2016-08-01

To assess the effect of continuous positive airway pressure (CPAP) on napping behavior in adults aged 60 and older with obstructive sleep apnea-hypopnea syndrome (OSAHS). Retrospective cohort study using questionnaires. Sleep center. Individuals starting CPAP treatment between April 2010 and March 2012 (mean age 65.2 ± 4.7; M:F = 3.9:1; N = 107). All subjects underwent sleep studies, clinical reviews, and CPAP adherence checks and completed a questionnaire regarding CPAP adherence, current employment status, sleep patterns before and after CPAP, and factors affecting their current sleep patterns. CPAP treatment duration was 82.7 ± 30.0 weeks, and objective adherence was 5.4 ± 2.0 hours per night overall. Daytime nap frequency before CPAP treatment was higher in those with a history of stroke or cardiovascular disease. Both sexes had a significant reduction in daytime napping (men, P < .001; women, P = .008), evening napping (men, P < .001; women, P = .02), and daily nap duration (men, P < .001; women, P = .02). Logistic regression analysis showed that the reduction in self-reported daily nap duration was associated with younger age (odds ratio (OR) = 0.86, P = .04), a decrease in ESS score (OR = 1.20, P = .03), and longer self-reported daily nap duration at baseline (OR = 31.52, P < .001). Long-term CPAP treatment in older adults with OSAHS can play a significant role in reducing nap frequency and daily nap duration. Aging or shorter baseline daily nap duration may attenuate this effect. © 2016, Copyright the Authors Journal compilation © 2016, The American Geriatrics Society.

Underperception of Naps in Older Adults Referred for a Sleep Assessment: An Insomnia Trait and a Cognitive Problem?

PubMed

Nguyen-Michel, Vi-Huong; Lévy, Pierre-P; Pallanca, Olivier; Kinugawa, Kiyoka; Banica-Wolters, Raluca; Sebban, Claude; Mariani, Jean; Fournier, Emmanuel; Arnulf, Isabelle

2015-10-01

To examine the frequency and determinants of underperception of naps in older adults referred for a sleep assessment. Prospective study. Outpatient geriatric sleep clinic. Individuals aged 60 and older referred for insomnia complaints or suspected sleep apnea (N = 135). Tests included clinical interview, sleepiness scale, anxiety and depression scale, Insomnia Severity Index (ISI), Mini-Mental State Examination (MMSE), and overnight polysomnography, followed by multiple sleep latency tests. At the end of each of four nap opportunities, participants answered whether they had slept during the test. Nap underperception was defined as two or more unperceived naps. Of the 105 participants who napped at least twice, 42 (40%) did not perceive at least two naps. These participants had lower MMSE scores (P = .01) and were more likely to be taking benzodiazepines (P = .008) than the 63 participants who did not underperceive their naps but had similar demographic characteristics, sleep diagnoses, depression and anxiety scores, and polysomnography measures. Both groups had similarly short mean daytime sleep latencies (9.7 ± 4.5 minutes and 9.8 ± 3.7 minutes), but participants who underperceived their naps scored lower on the Epworth Sleepiness Scale (5.6 ± 4.0, vs 9.6 ± 4.8, P < .001). An ISI of 11 or greater, a MMSE score of 26 or less, and a sleepiness score of 8 or less were each independently associated with underperception of naps. The combination of these three factors yielded a positive predictive value of 93% and a negative predictive value of 71% for nap underperception. Older adults referred for sleep consultation with cognitive impairment and greater insomnia symptoms frequently underperceive naps, leading them to underestimate their level of sleepiness. In such cases, objective measures of daytime sleepiness would be better than the Epworth Sleepiness Scale. © 2015, Copyright the Authors Journal compilation © 2015, The American Geriatrics Society.

Napping Is Associated with Increased Risk of Type 2 Diabetes: The Guangzhou Biobank Cohort Study

PubMed Central

Lam, Kin-bong Hubert; Jiang, Chao Qiang; Thomas, G. Neil; Arora, Teresa; Zhang, Wei Sen; Taheri, Shahrad; Adab, Peymané; Lam, Tai Hing; Cheng, Kar Keung

2010-01-01

Study Objective: Intentional napping is very common, particularly in China. However, there are limited data regarding its potential health effects. We therefore examined the possible relationship between napping and type 2 diabetes. Design: Cross-sectional analysis of baseline data from the Guangzhou Biobank Cohort Study. Setting: Community-based elderly association in Guangzhou, China. Participants: 19,567 Chinese men and women aged 50 years or older. Measurements and Results: Self-reported frequency of napping was obtained by questionnaire and type 2 diabetes was assessed by fasting blood glucose and/or self-reports of physician diagnosis or treatment. Participants reporting frequent naps (4-6 days/week and daily) were 42% to 52% more likely to have diabetes. The relationships remained essentially unchanged after adjustments were made for demographics, lifestyle and sleep habits, health status, adiposity, and metabolic markers (odds ratio for diabetes 1.36 [95% CI 1.17–1.57] in 4-6 days/week, 1.28 [1.15–1.44] in daily nappers). Similar associations were found between napping and impaired fasting glucose. Removal of those with potential ill health and daytime sleepiness did not alter the observed associations. Conclusions: Napping is associated with elevated prevalence of diabetes and impaired fasting glucose in this older Chinese sample. Our finding suggests that it is less likely that diabetes leads to daytime sleepiness. This raises the possibility that napping may increase the risk of diabetes. Confirmation by longitudinal studies is needed. Citation: Lam KbH; Jiang CQ; Thomas GN; Arora T; Zhang WS; Taheri S; Adab P; Lam TH; Cheng KK. Napping is associated with increased risk of type 2 diabetes: the Guangzhou Biobank Cohort Study. SLEEP 2010;33(3):402-407. PMID:20337199

Longtime napping is associated with cardiovascular risk estimation according to Framingham risk score in postmenopausal women.

PubMed

Li, Feng; Sun, Kan; Lin, Diaozhu; Qi, Yiqin; Li, Yan; Yan, Li; Ren, Meng

2016-09-01

Menopause can affect the physiological timing system, which could result in circadian rhythm changes and development of napping habits. Whether longtime napping in postmenopausal women is associated with cardiovascular disease is, however, still debated. The present study aims to investigate this association. We conducted a population-based study in 4,616 postmenopausal Chinese women. Information on sleep duration was self-reported. The Framingham General Cardiovascular Risk Score was calculated and used to identify participants at high risk of coronary heart disease (CHD). Increased daytime napping hours were positively associated with cardiovascular disease risk factors in postmenopausal women, such as age, waist circumference, systolic blood pressure, triglycerides, fasting glucose, postload glucose, and hemoglobin A1C (all P for trend <0.05). The prevalence of high risk of CHD increased with daytime napping hours, and was 3.7%, 4.3%, and 6.9% in the no daytime napping group, the 0.1 to 1 hour group, and the more than 1 hour group, respectively (P for trend = 0.005). Compared with the no daytime napping group, postmenopausal women with daytime napping more than 1 hour had higher risk of CHD in both univariate (odds ratio 1.94, 95% CI, 1.29-2.95) and multivariate (odds ratio 1.61, 95% CI, 1.03-2.52) logistic regression analyses. No statistically significant association was detected between night sleeping hours and high risk of CHD in postmenopausal participants. Daytime napping is positively associated with estimated 10-year CHD risk in postmenopausal Chinese women.

Clustering gene expression regulators: new approach to disease subtyping.

PubMed

Pyatnitskiy, Mikhail; Mazo, Ilya; Shkrob, Maria; Schwartz, Elena; Kotelnikova, Ekaterina

2014-01-01

One of the main challenges in modern medicine is to stratify different patient groups in terms of underlying disease molecular mechanisms as to develop more personalized approach to therapy. Here we propose novel method for disease subtyping based on analysis of activated expression regulators on a sample-by-sample basis. Our approach relies on Sub-Network Enrichment Analysis algorithm (SNEA) which identifies gene subnetworks with significant concordant changes in expression between two conditions. Subnetwork consists of central regulator and downstream genes connected by relations extracted from global literature-extracted regulation database. Regulators found in each patient separately are clustered together and assigned activity scores which are used for final patients grouping. We show that our approach performs well compared to other related methods and at the same time provides researchers with complementary level of understanding of pathway-level biology behind a disease by identification of significant expression regulators. We have observed the reasonable grouping of neuromuscular disorders (triggered by structural damage vs triggered by unknown mechanisms), that was not revealed using standard expression profile clustering. For another experiment we were able to suggest the clusters of regulators, responsible for colorectal carcinoma vs adenoma discrimination and identify frequently genetically changed regulators that could be of specific importance for the individual characteristics of cancer development. Proposed approach can be regarded as biologically meaningful feature selection, reducing tens of thousands of genes down to dozens of clusters of regulators. Obtained clusters of regulators make possible to generate valuable biological hypotheses about molecular mechanisms related to a clinical outcome for individual patient.

Clustering Gene Expression Regulators: New Approach to Disease Subtyping

PubMed Central

Pyatnitskiy, Mikhail; Mazo, Ilya; Shkrob, Maria; Schwartz, Elena; Kotelnikova, Ekaterina

2014-01-01

One of the main challenges in modern medicine is to stratify different patient groups in terms of underlying disease molecular mechanisms as to develop more personalized approach to therapy. Here we propose novel method for disease subtyping based on analysis of activated expression regulators on a sample-by-sample basis. Our approach relies on Sub-Network Enrichment Analysis algorithm (SNEA) which identifies gene subnetworks with significant concordant changes in expression between two conditions. Subnetwork consists of central regulator and downstream genes connected by relations extracted from global literature-extracted regulation database. Regulators found in each patient separately are clustered together and assigned activity scores which are used for final patients grouping. We show that our approach performs well compared to other related methods and at the same time provides researchers with complementary level of understanding of pathway-level biology behind a disease by identification of significant expression regulators. We have observed the reasonable grouping of neuromuscular disorders (triggered by structural damage vs triggered by unknown mechanisms), that was not revealed using standard expression profile clustering. For another experiment we were able to suggest the clusters of regulators, responsible for colorectal carcinoma vs adenoma discrimination and identify frequently genetically changed regulators that could be of specific importance for the individual characteristics of cancer development. Proposed approach can be regarded as biologically meaningful feature selection, reducing tens of thousands of genes down to dozens of clusters of regulators. Obtained clusters of regulators make possible to generate valuable biological hypotheses about molecular mechanisms related to a clinical outcome for individual patient. PMID:24416320

Delineation of metabolic gene clusters in plant genomes by chromatin signatures.

PubMed

Yu, Nan; Nützmann, Hans-Wilhelm; MacDonald, James T; Moore, Ben; Field, Ben; Berriri, Souha; Trick, Martin; Rosser, Susan J; Kumar, S Vinod; Freemont, Paul S; Osbourn, Anne

2016-03-18

Plants are a tremendous source of diverse chemicals, including many natural product-derived drugs. It has recently become apparent that the genes for the biosynthesis of numerous different types of plant natural products are organized as metabolic gene clusters, thereby unveiling a highly unusual form of plant genome architecture and offering novel avenues for discovery and exploitation of plant specialized metabolism. Here we show that these clustered pathways are characterized by distinct chromatin signatures of histone 3 lysine trimethylation (H3K27me3) and histone 2 variant H2A.Z, associated with cluster repression and activation, respectively, and represent discrete windows of co-regulation in the genome. We further demonstrate that knowledge of these chromatin signatures along with chromatin mutants can be used to mine genomes for cluster discovery. The roles of H3K27me3 and H2A.Z in repression and activation of single genes in plants are well known. However, our discovery of highly localized operon-like co-regulated regions of chromatin modification is unprecedented in plants. Our findings raise intriguing parallels with groups of physically linked multi-gene complexes in animals and with clustered pathways for specialized metabolism in filamentous fungi. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Iterative local Gaussian clustering for expressed genes identification linked to malignancy of human colorectal carcinoma

PubMed Central

Wasito, Ito; Hashim, Siti Zaiton M; Sukmaningrum, Sri

2007-01-01

Gene expression profiling plays an important role in the identification of biological and clinical properties of human solid tumors such as colorectal carcinoma. Profiling is required to reveal underlying molecular features for diagnostic and therapeutic purposes. A non-parametric density-estimation-based approach called iterative local Gaussian clustering (ILGC), was used to identify clusters of expressed genes. We used experimental data from a previous study by Muro and others consisting of 1,536 genes in 100 colorectal cancer and 11 normal tissues. In this dataset, the ILGC finds three clusters, two large and one small gene clusters, similar to their results which used Gaussian mixture clustering. The correlation of each cluster of genes and clinical properties of malignancy of human colorectal cancer was analysed for the existence of tumor or normal, the existence of distant metastasis and the existence of lymph node metastasis. PMID:18305825

Neuroprotective effects of NAP against excitotoxic brain damage in the newborn mice: implications for cerebral palsy.

PubMed

Sokolowska, P; Passemard, S; Mok, A; Schwendimann, L; Gozes, I; Gressens, P

2011-01-26

Activity-dependent neuroprotective protein (ADNP) was shown to be essential for embryogenesis and brain development while NAP, an active motif of ADNP, is neuroprotective in a broad range of neurodegenerative disorders. In the present study, we examined the protective potential of ADNP/NAP in a mouse model of excitotoxic brain lesion mimicking brain damage associated with cerebral palsy. We demonstrated that NAP had a potent neuroprotective effect against ibotenate-induced excitotoxic damage in the cortical plate and the white matter of P5 mice, and moderate against brain lesions of P0 mice. In contrast, endogenous ADNP appears not to be involved in the response to excitotoxic challenge in the studied model. Our findings further show that NAP reduced the number of apoptotic neurons through activation of PI-3K/Akt pathway in the cortical plate or both PI-3K/Akt and MAPK/MEK1 kinases in the white matter. In addition, NAP prevented ibotenate-induced loss of pre-oligodendrocytes without affecting the number of astrocytes or activated microglia around the site of injection. These findings indicate that protective actions of NAP are mediated by triggering transduction pathways that are crucial for neuronal and oligodendroglial survival, thus, NAP might be a promising therapeutic agent for treating developing brain damage. © 2011 IBRO. Published by Elsevier Ltd. All rights reserved.

Patterning C. elegans: homeotic cluster genes, cell fates and cell migrations.

PubMed

Salser, S J; Kenyon, C

1994-05-01

Despite its simple body form, the nematode C. elegans expresses homeotic cluster genes similar to those of insects and vertebrates in the patterning of many cell types and tissues along the anteroposterior axis. In the ventral nerve cord, these genes program spatial patterns of cell death, fusion, division and neurotransmitter production; in migrating cells they regulate the direction and extent of movement. Nematode development permits an analysis at the cellular level of how homeotic cluster genes interact to specify cell fates, and how cell behavior can be regulated to assemble an organism.

A genomics based discovery of secondary metabolite biosynthetic gene clusters in Aspergillus ustus.

PubMed

Pi, Borui; Yu, Dongliang; Dai, Fangwei; Song, Xiaoming; Zhu, Congyi; Li, Hongye; Yu, Yunsong

2015-01-01

Secondary metabolites (SMs) produced by Aspergillus have been extensively studied for their crucial roles in human health, medicine and industrial production. However, the resulting information is almost exclusively derived from a few model organisms, including A. nidulans and A. fumigatus, but little is known about rare pathogens. In this study, we performed a genomics based discovery of SM biosynthetic gene clusters in Aspergillus ustus, a rare human pathogen. A total of 52 gene clusters were identified in the draft genome of A. ustus 3.3904, such as the sterigmatocystin biosynthesis pathway that was commonly found in Aspergillus species. In addition, several SM biosynthetic gene clusters were firstly identified in Aspergillus that were possibly acquired by horizontal gene transfer, including the vrt cluster that is responsible for viridicatumtoxin production. Comparative genomics revealed that A. ustus shared the largest number of SM biosynthetic gene clusters with A. nidulans, but much fewer with other Aspergilli like A. niger and A. oryzae. These findings would help to understand the diversity and evolution of SM biosynthesis pathways in genus Aspergillus, and we hope they will also promote the development of fungal identification methodology in clinic.

A Genomics Based Discovery of Secondary Metabolite Biosynthetic Gene Clusters in Aspergillus ustus

PubMed Central

Pi, Borui; Yu, Dongliang; Dai, Fangwei; Song, Xiaoming; Zhu, Congyi; Li, Hongye; Yu, Yunsong

2015-01-01

Secondary metabolites (SMs) produced by Aspergillus have been extensively studied for their crucial roles in human health, medicine and industrial production. However, the resulting information is almost exclusively derived from a few model organisms, including A. nidulans and A. fumigatus, but little is known about rare pathogens. In this study, we performed a genomics based discovery of SM biosynthetic gene clusters in Aspergillus ustus, a rare human pathogen. A total of 52 gene clusters were identified in the draft genome of A. ustus 3.3904, such as the sterigmatocystin biosynthesis pathway that was commonly found in Aspergillus species. In addition, several SM biosynthetic gene clusters were firstly identified in Aspergillus that were possibly acquired by horizontal gene transfer, including the vrt cluster that is responsible for viridicatumtoxin production. Comparative genomics revealed that A. ustus shared the largest number of SM biosynthetic gene clusters with A. nidulans, but much fewer with other Aspergilli like A. niger and A. oryzae. These findings would help to understand the diversity and evolution of SM biosynthesis pathways in genus Aspergillus, and we hope they will also promote the development of fungal identification methodology in clinic. PMID:25706180

Daytime Napping and the Risk of Cardiovascular Disease and All-Cause Mortality: A Prospective Study and Dose-Response Meta-Analysis.

PubMed

Yamada, Tomohide; Hara, Kazuo; Shojima, Nobuhiro; Yamauchi, Toshimasa; Kadowaki, Takashi

2015-12-01

To summarize evidence about the association between daytime napping and the risk of cardiovascular disease and all-cause mortality, and to quantify the potential dose-response relation. Meta-analysis of prospective cohort studies. Electronic databases were searched for articles published up to December 2014 using the terms nap, cardiovascular disease, and all-cause mortality. We selected well-adjusted prospective cohort studies reporting risk estimates for cardiovascular disease and all-cause mortality related to napping. Eleven prospective cohort studies were identified with 151,588 participants (1,625,012 person-years) and a mean follow-up period of 11 years (60% women, 5,276 cardiovascular events, and 18,966 all-cause deaths). Pooled analysis showed that a long daytime nap (≥ 60 min/day) was associated with a higher risk of cardiovascular disease (rate ratio [RR]: 1.82 [1.22-2.71], P = 0.003, I(2) = 37%) compared with not napping. All-cause mortality was associated with napping for ≥ 60 min/day (RR: 1.27 [1.11-1.45], P < 0.001, I(2) = 0%) compared with not napping. In contrast, napping for < 60 min/day was not associated with cardiovascular disease (P = 0.98) or all-cause mortality (P = 0.08). Meta-analysis demonstrated a significant J-curve dose-response relation between nap time and cardiovascular disease (P for nonlinearity = 0.01). The RR initially decreased from 0 to 30 min/day. Then it increased slightly until about 45 min/day, followed by a sharp increase at longer nap times. There was also a positive linear relation between nap time and all-cause mortality (P for non-linearity = 0.97). Nap time and cardiovascular disease may be associated via a J-curve relation. Further studies are needed to confirm the efficacy of a short nap. © 2015 Associated Professional Sleep Societies, LLC.

Relationship between napping during night shift work and household obligations of female nursing personnel.

PubMed

Silva-Costa, Aline; Fischer, Frida Marina; Griep, Rosane Harter; Rotenberg, Lúcia

2013-01-01

Night shift employment involves displacing sleep to the daytime. For female workers, the opportunity for daytime sleep is influenced by routine housework demands, which aggravates sleep deprivation. Allowing naps to be taken during the night shift of work is a frequent practice at some hospitals and can help reduce the effects of sleep deprivation. We hypothesize that an association between domestic work and the length of naps during night work exists for nursing professionals. To test this hypothesis, two cross-sectional studies were conducted in two different hospitals. In Study 1, female workers answered questionnaires regarding sleeping habits, professional work, and housework demands. In Study 2, data regarding napping during shifts was obtained by actigraphy, a noninvasive method of monitoring the human sleep-wake cycle. The demand for the performance of housework was measured by (i) domestic work hours (total time spent performing domestic work per week), and (ii) domestic workload, which considers the degree of sharing domestic tasks and the number of people living at home. The populations from the two studies were subdivided into groups, based on the duration of napping at work. Data on naps were analyzed according to domestic demands, using the Mann-Whitney and Chi-squared tests. Among the two study populations (Studies 1 and 2), those in Study 2 were older, had shorter professional weekly work hours, worked more night shifts, and dedicated more time to housework. significant associations were only found in Study 2, where greater time napping at work was associated with both greater time spent doing housework and greater domestic workload. The known benefits of napping during night shifts seem to be especially relevant for female workers who are more sleep-deprived from working more night shifts and who have higher demands for housework.

Napping and the risk of type 2 diabetes: a population-based prospective study.

PubMed

Hublin, Christer; Lehtovirta, Mikko; Partinen, Markku; Koskenvuo, Markku; Kaprio, Jaakko

2016-01-01

Some studies indicate an association between napping and increased risk of type 2 diabetes. We studied this prospectively in a sample representative of general population. A questionnaire was administered to the Finnish Twin Cohort in 1990 (response rate 77%, age 33-60 years). The study population included 12,244 subjects who replied to the question "Do you sleep during the daytime (take naps)?" with five response alternatives ranging from "no need" to "every or almost every day." Information on incident cases of diabetes was obtained by linkage to nationwide registers. Logistic regression models were used to obtain odds ratios (ORs) (95% confidence intervals) for incident type 2 diabetes risk in 1991-2004 by napping category. Adjustments were made for 11 socio-demographic and lifestyle covariates. For subjects aged 33-45 years at baseline, a questionnaire in 2011 provided information on prevalent diabetes. Thirty-four per cent had no need for napping, and 15% did so on ≥3 days weekly. There were 356 incident type 2 diabetes cases during the follow-up. Using the 'no need' category as the reference, the risk of type 2 diabetes was significantly increased only among those napping most frequently [OR 1.86 (1.29-2.67), age- and sex-adjusted]. After adjusting for other covariates, the results were essentially the same, but when adjusted for body mass index, the association decreased (to about 1.3) and was statistically non-significant. Analysis of 2011 self-reported type 2 diabetes was in line with the register data. Frequent napping is associated with future risk of type 2 diabetes. This association is largely explained by obesity. Copyright © 2015 Elsevier B.V. All rights reserved.

Genome mining-directed activation of a silent angucycline biosynthetic gene cluster in Streptomyces chattanoogensis.

PubMed

Zhou, Zhenxing; Xu, Qingqing; Bu, Qingting; Guo, Yuanyang; Liu, Shuiping; Liu, Yu; Du, Yiling; Li, Yongquan

2015-02-09

Genomic sequencing of actinomycetes has revealed the presence of numerous gene clusters seemingly capable of natural product biosynthesis, yet most clusters are cryptic under laboratory conditions. Bioinformatics analysis of the completely sequenced genome of Streptomyces chattanoogensis L10 (CGMCC 2644) revealed a silent angucycline biosynthetic gene cluster. The overexpression of a pathway-specific activator gene under the constitutive ermE* promoter successfully triggered the expression of the angucycline biosynthetic genes. Two novel members of the angucycline antibiotic family, chattamycins A and B, were further isolated and elucidated. Biological activity assays demonstrated that chattamycin B possesses good antitumor activities against human cancer cell lines and moderate antibacterial activities. The results presented here provide a feasible method to activate silent angucycline biosynthetic gene clusters to discover potential new drug leads. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Daytime napping, sleep duration and increased 8-year risk of type 2 diabetes in a British population.

PubMed

Leng, Y; Cappuccio, F P; Surtees, P G; Luben, R; Brayne, C; Khaw, K-T

2016-11-01

Few studies have prospectively examined the relationship between daytime napping and risk of type 2 diabetes. We aimed to study the effects of daytime napping and the joint effects of napping and sleep duration in predicting type 2 diabetes risk in a middle- to older-aged British population. In 1998-2000, 13 465 individuals with no known diabetes participating in the European Prospective Investigation into Cancer-Norfolk study reported daytime napping habit and 24-h sleep duration. Incident type 2 diabetes cases were identified through multiple data sources until 31 July 2006. After adjustment for age and sex, daytime napping was associated with a 58% higher diabetes risk. Further adjustment for education, marital status, smoking, alcohol intake, physical activity, comorbidities and hypnotic drug use had little influence on the association, but additional adjustment for BMI and Waist Circumference attenuated the Odds ratio (OR) (95% CI) to 1.30 (1.01, 1.69). The adjusted ORs (95% CI) associated with short and long sleep duration were 1.46 (1.10, 1.90) and 1.64 (1.16, 2.32), respectively. When sleep duration and daytime napping were examined together, the risk of developing diabetes more than doubled for those who took day naps and had less than 6 h of sleep, compared to those who did not nap and had 6-8 h of sleep. Daytime napping was associated with an increased risk of type 2 diabetes, particularly when combined with short sleep duration. Further physiological studies are needed to confirm the interaction between different domains of sleep in relation to diabetes risk. Copyright © 2016 The Italian Society of Diabetology, the Italian Society for the Study of Atherosclerosis, the Italian Society of Human Nutrition, and the Department of Clinical Medicine and Surgery, Federico II University. Published by Elsevier B.V. All rights reserved.

Comparing conventional Descriptive Analysis and Napping®-UFP against physiochemical measurements: a case study using apples.

PubMed

Pickup, William; Bremer, Phil; Peng, Mei

2018-03-01

The extensive time and cost associated with conventional sensory profiling methods has spurred sensory researchers to develop rapid method alternatives, such as Napping® with Ultra-Flash Profiling (UFP). Napping®-UFP generates sensory maps by requiring untrained panellists to separate samples based on perceived sensory similarities. Evaluations of this method have been restrained to manufactured/formulated food models, and predominantly structured on comparisons against the conventional descriptive method. The present study aims to extend the validation of Napping®-UFP (N = 72) to natural biological products; and to evaluate this method against Descriptive Analysis (DA; N = 8) with physiochemical measurements as an additional evaluative criterion. The results revealed that sample configurations generated by DA and Napping®-UFP were not significantly correlated (RV = 0.425, P = 0.077); however, they were both correlated with the product map generated based on the instrumental measures (P < 0.05). The finding also noted that sample characterisations from DA and Napping®-UFP were driven by different sensory attributes, indicating potential structural differences between these two methods in configuring samples. Overall, these findings lent support for the extended use of Napping®-UFP for evaluations of natural biological products. Although DA was shown to be a better method for establishing sensory-instrumental relationships, Napping®-UFP exhibited strengths in generating informative sample configurations based on holistic perception of products. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Global Identification of Genes Affecting Iron-Sulfur Cluster Biogenesis and Iron Homeostasis

PubMed Central

Hidese, Ryota; Kurihara, Tatsuo; Esaki, Nobuyoshi

2014-01-01

Iron-sulfur (Fe-S) clusters are ubiquitous cofactors that are crucial for many physiological processes in all organisms. In Escherichia coli, assembly of Fe-S clusters depends on the activity of the iron-sulfur cluster (ISC) assembly and sulfur mobilization (SUF) apparatus. However, the underlying molecular mechanisms and the mechanisms that control Fe-S cluster biogenesis and iron homeostasis are still poorly defined. In this study, we performed a global screen to identify the factors affecting Fe-S cluster biogenesis and iron homeostasis using the Keio collection, which is a library of 3,815 single-gene E. coli knockout mutants. The approach was based on radiolabeling of the cells with [2-14C]dihydrouracil, which entirely depends on the activity of an Fe-S enzyme, dihydropyrimidine dehydrogenase. We identified 49 genes affecting Fe-S cluster biogenesis and/or iron homeostasis, including 23 genes important only under microaerobic/anaerobic conditions. This study defines key proteins associated with Fe-S cluster biogenesis and iron homeostasis, which will aid further understanding of the cellular mechanisms that coordinate the processes. In addition, we applied the [2-14C]dihydrouracil-labeling method to analyze the role of amino acid residues of an Fe-S cluster assembly scaffold (IscU) as a model of the Fe-S cluster assembly apparatus. The analysis showed that Cys37, Cys63, His105, and Cys106 are essential for the function of IscU in vivo, demonstrating the potential of the method to investigate in vivo function of proteins involved in Fe-S cluster assembly. PMID:24415728

Genomics-driven discovery of the pneumocandin biosynthetic gene cluster in the fungus Glarea lozoyensis

PubMed Central

2013-01-01

Background The antifungal therapy caspofungin is a semi-synthetic derivative of pneumocandin B0, a lipohexapeptide produced by the fungus Glarea lozoyensis, and was the first member of the echinocandin class approved for human therapy. The nonribosomal peptide synthetase (NRPS)-polyketide synthases (PKS) gene cluster responsible for pneumocandin biosynthesis from G. lozoyensis has not been elucidated to date. In this study, we report the elucidation of the pneumocandin biosynthetic gene cluster by whole genome sequencing of the G. lozoyensis wild-type strain ATCC 20868. Results The pneumocandin biosynthetic gene cluster contains a NRPS (GLNRPS4) and a PKS (GLPKS4) arranged in tandem, two cytochrome P450 monooxygenases, seven other modifying enzymes, and genes for L-homotyrosine biosynthesis, a component of the peptide core. Thus, the pneumocandin biosynthetic gene cluster is significantly more autonomous and organized than that of the recently characterized echinocandin B gene cluster. Disruption mutants of GLNRPS4 and GLPKS4 no longer produced the pneumocandins (A0 and B0), and the Δglnrps4 and Δglpks4 mutants lost antifungal activity against the human pathogenic fungus Candida albicans. In addition to pneumocandins, the G. lozoyensis genome encodes a rich repertoire of natural product-encoding genes including 24 PKSs, six NRPSs, five PKS-NRPS hybrids, two dimethylallyl tryptophan synthases, and 14 terpene synthases. Conclusions Characterization of the gene cluster provides a blueprint for engineering new pneumocandin derivatives with improved pharmacological properties. Whole genome estimation of the secondary metabolite-encoding genes from G. lozoyensis provides yet another example of the huge potential for drug discovery from natural products from the fungal kingdom. PMID:23688303

A Nomadic Subtelomeric Disease Resistance Gene Cluster in Common Bean1[W

PubMed Central

David, Perrine; Chen, Nicolas W.G.; Pedrosa-Harand, Andrea; Thareau, Vincent; Sévignac, Mireille; Cannon, Steven B.; Debouck, Daniel; Langin, Thierry; Geffroy, Valérie

2009-01-01

The B4 resistance (R) gene cluster is one of the largest clusters known in common bean (Phaseolus vulgaris [Pv]). It is located in a peculiar genomic environment in the subtelomeric region of the short arm of chromosome 4, adjacent to two heterochromatic blocks (knobs). We sequenced 650 kb spanning this locus and annotated 97 genes, 26 of which correspond to Coiled-Coil-Nucleotide-Binding-Site-Leucine-Rich-Repeat (CNL). Conserved microsynteny was observed between the Pv B4 locus and corresponding regions of Medicago truncatula and Lotus japonicus in chromosomes Mt6 and Lj2, respectively. The notable exception was the CNL sequences, which were completely absent in these regions. The origin of the Pv B4-CNL sequences was investigated through phylogenetic analysis, which reveals that, in the Pv genome, paralogous CNL genes are shared among nonhomologous chromosomes (4 and 11). Together, our results suggest that Pv B4-CNL was derived from CNL sequences from another cluster, the Co-2 cluster, through an ectopic recombination event. Integration of the soybean (Glycine max) genome data enables us to date more precisely this event and also to infer that a single CNL moved from the Co-2 to the B4 cluster. Moreover, we identified a new 528-bp satellite repeat, referred to as khipu, specific to the Phaseolus genus, present both between B4-CNL sequences and in the two knobs identified at the B4 R gene cluster. The khipu repeat is present on most chromosomal termini, indicating the existence of frequent ectopic recombination events in Pv subtelomeric regions. Our results highlight the importance of ectopic recombination in R gene evolution. PMID:19776165

Evolutionary conservation of regulatory elements in vertebrate HOX gene clusters

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

Santini, Simona; Boore, Jeffrey L.; Meyer, Axel

2003-12-31

Due to their high degree of conservation, comparisons of DNA sequences among evolutionarily distantly-related genomes permit to identify functional regions in noncoding DNA. Hox genes are optimal candidate sequences for comparative genome analyses, because they are extremely conserved in vertebrates and occur in clusters. We aligned (Pipmaker) the nucleotide sequences of HoxA clusters of tilapia, pufferfish, striped bass, zebrafish, horn shark, human and mouse (over 500 million years of evolutionary distance). We identified several highly conserved intergenic sequences, likely to be important in gene regulation. Only a few of these putative regulatory elements have been previously described as being involvedmore » in the regulation of Hox genes, while several others are new elements that might have regulatory functions. The majority of these newly identified putative regulatory elements contain short fragments that are almost completely conserved and are identical to known binding sites for regulatory proteins (Transfac). The conserved intergenic regions located between the most rostrally expressed genes in the developing embryo are longer and better retained through evolution. We document that presumed regulatory sequences are retained differentially in either A or A clusters resulting from a genome duplication in the fish lineage. This observation supports both the hypothesis that the conserved elements are involved in gene regulation and the Duplication-Deletion-Complementation model.« less

Haplotype analysis of the apolipoprotein gene cluster on human chromosome 11

PubMed Central

Olivier, Michael; Wang, Xujing; Cole, Regina; Gau, Brian; Kim, Jessica; Rubin, Edward M.; Pennacchio, Len A.

2009-01-01

Members of the apolipoprotein gene cluster (APOA1/C3/A4/A5) on human chromosome 11q23 play an important role in lipid metabolism. Polymorphisms in both APOA5 and APOC3 are strongly associated with plasma triglyceride concentrations. The close genomic locations of these two genes as well as their functional similarity have hindered efforts to define whether each gene independently influences human triglyceride concentrations. In this study, we examined the linkage disequilibrium and haplotype structure of 49 SNPs in a 150-kb region spanning the gene cluster. We identified a total of five common APOA5 haplotypes with a frequency of greater than 8% in samples of northern European origin. The APOA5 haplotype block did not extend past the 7 SNPs in the gene and was separated from the other apolipoprotein gene in the cluster by a region of significantly increased recombination. Furthermore, one previously identified triglyceride risk haplotype of APOA5 (APOA5*3) showed no association with three APOC3 SNPs previously associated with triglyceride concentrations, in contrast to the other risk haplotype (APOA5*2), which was associated with all three minor APOC3 SNP alleles. These results highlight the complex genetic relationship between APOA5 and APOC3 and support the notion that APOA5 represents an independent risk gene affecting plasma triglyceride concentrations in humans. PMID:15081120

Daytime Napping and the Risk of Cardiovascular Disease and All-Cause Mortality: A Prospective Study and Dose-Response Meta-Analysis

PubMed Central

Yamada, Tomohide; Hara, Kazuo; Shojima, Nobuhiro; Yamauchi, Toshimasa; Kadowaki, Takashi

2015-01-01

Study Objectives: To summarize evidence about the association between daytime napping and the risk of cardiovascular disease and all-cause mortality, and to quantify the potential dose-response relation. Design: Meta-analysis of prospective cohort studies. Methods and Results: Electronic databases were searched for articles published up to December 2014 using the terms nap, cardiovascular disease, and all-cause mortality. We selected well-adjusted prospective cohort studies reporting risk estimates for cardiovascular disease and all-cause mortality related to napping. Eleven prospective cohort studies were identified with 151,588 participants (1,625,012 person-years) and a mean follow-up period of 11 years (60% women, 5,276 cardiovascular events, and 18,966 all-cause deaths). Pooled analysis showed that a long daytime nap (≥ 60 min/day) was associated with a higher risk of cardiovascular disease (rate ratio [RR]: 1.82 [1.22–2.71], P = 0.003, I2 = 37%) compared with not napping. All-cause mortality was associated with napping for ≥ 60 min/day (RR: 1.27 [1.11–1.45], P < 0.001, I2 = 0%) compared with not napping. In contrast, napping for < 60 min/day was not associated with cardiovascular disease (P = 0.98) or all-cause mortality (P = 0.08). Meta-analysis demonstrated a significant J-curve dose-response relation between nap time and cardiovascular disease (P for nonlinearity = 0.01). The RR initially decreased from 0 to 30 min/day. Then it increased slightly until about 45 min/day, followed by a sharp increase at longer nap times. There was also a positive linear relation between nap time and all-cause mortality (P for non-linearity = 0.97). Conclusions: Nap time and cardiovascular disease may be associated via a J-curve relation. Further studies are needed to confirm the efficacy of a short nap. Citation: Yamada T, Hara K, Shojima N, Yamauchi T, Kadowaki T. Daytime napping and the risk of cardiovascular disease and all-cause mortality: a prospective study and

New common program requirements for the resident physician workforce and the omission of strategic napping: A missed opportunity.

PubMed

Shnayder, Michelle M; St Onge, Joan E; Caban-Martinez, Alberto J

2017-09-01

Napping has known benefits for fatigue mitigation and improved alertness. However the Accreditation Council for Graduate Medical Education (ACGME) New Common Program Requirements recently removed the 16 h work limit for PGY1 residents and removed any suggestions of napping. We utilized a cross-sectional study design to administer a 44-item questionnaire in June 2016 to 858 residents and fellows at one large urban academic medical center. We assessed: 1) resident physician sentiment of work environment supportiveness for napping at work; and 2) agreement with 2011 ACGME guidelines on workweek hour limitations and strategic napping recommendations. While 89% of residents reported access to an on-call room at work, only 20% felt their work environment supported a culture of napping while at work. Over 76% expressed agreement with the 2011 ACGME work-hour restrictions. Strategies to support napping and well-being within the resident physician workforce and organizational setting are warranted. © 2017 Wiley Periodicals, Inc.

Improved efficiency in amplification of Escherichia coli o-antigen gene clusters using genome-wide sequence comparison

USDA-ARS?s Scientific Manuscript database

Background: In many bacteria including E. coli, genes encoding O-antigens are clustered in the chromosome, with a 39-bp JUMPstart sequence and gnd gene located upstream and downstream of the cluster, respectively. For determining the DNA sequence of the E. coli O-antigen gene cluster, one set of P...

A ground truth based comparative study on clustering of gene expression data.

PubMed

Zhu, Yitan; Wang, Zuyi; Miller, David J; Clarke, Robert; Xuan, Jianhua; Hoffman, Eric P; Wang, Yue

2008-05-01

Given the variety of available clustering methods for gene expression data analysis, it is important to develop an appropriate and rigorous validation scheme to assess the performance and limitations of the most widely used clustering algorithms. In this paper, we present a ground truth based comparative study on the functionality, accuracy, and stability of five data clustering methods, namely hierarchical clustering, K-means clustering, self-organizing maps, standard finite normal mixture fitting, and a caBIG toolkit (VIsual Statistical Data Analyzer--VISDA), tested on sample clustering of seven published microarray gene expression datasets and one synthetic dataset. We examined the performance of these algorithms in both data-sufficient and data-insufficient cases using quantitative performance measures, including cluster number detection accuracy and mean and standard deviation of partition accuracy. The experimental results showed that VISDA, an interactive coarse-to-fine maximum likelihood fitting algorithm, is a solid performer on most of the datasets, while K-means clustering and self-organizing maps optimized by the mean squared compactness criterion generally produce more stable solutions than the other methods.

Napping in older people 'at risk' of dementia: relationships with depression, cognition, medical burden and sleep quality.

PubMed

Cross, Nathan; Terpening, Zoe; Rogers, Naomi L; Duffy, Shantel L; Hickie, Ian B; Lewis, Simon J G; Naismith, Sharon L

2015-10-01

Sleep disturbance is prevalent in older adults, particularly so in those at a greater risk of dementia. However, so far the clinical, medical and neuropsychological correlates of daytime sleep have not been examined. The aims of this study were to investigate the characteristics and effects of napping using actigraphy in older people, particularly in those 'at risk' of dementia. The study used actigraphy and sleep diaries to measure napping habits in 133 older adults 'at risk' of dementia (mean age = 65.5 years, SD = 8.4 years), who also underwent comprehensive medical, psychiatric and neuropsychological assessment. When defined by actigraphy, napping was present in 83.5% (111/133) of participants; however, duration and timing varied significantly among subjects. Nappers had significantly greater medical burden and body mass index, and higher rates of mild cognitive impairment. Longer and more frequent naps were associated with poorer cognitive functioning, as well as higher levels of depressive symptoms, while the timing of naps was associated with poorer nocturnal sleep quality (i.e. sleep latency and wake after sleep onset). This study highlights that in older adults 'at risk' of dementia, napping is associated with underlying neurobiological changes such as depression and cognition. Napping characteristics should be more routinely monitored in older individuals to elucidate their relationship with psychological and cognitive outcomes. © 2015 European Sleep Research Society.

The Chloroplast atpA Gene Cluster in Chlamydomonas reinhardtii1

PubMed Central

Drapier, Dominique; Suzuki, Hideki; Levy, Haim; Rimbault, Blandine; Kindle, Karen L.; Stern, David B.; Wollman, Francis-André

1998-01-01

Most chloroplast genes in vascular plants are organized into polycistronic transcription units, which generate a complex pattern of mono-, di-, and polycistronic transcripts. In contrast, most Chlamydomonas reinhardtii chloroplast transcripts characterized to date have been monocistronic. This paper describes the atpA gene cluster in the C. reinhardtii chloroplast genome, which includes the atpA, psbI, cemA, and atpH genes, encoding the α-subunit of the coupling-factor-1 (CF1) ATP synthase, a small photosystem II polypeptide, a chloroplast envelope membrane protein, and subunit III of the CF0 ATP synthase, respectively. We show that promoters precede the atpA, psbI, and atpH genes, but not the cemA gene, and that cemA mRNA is present only as part of di-, tri-, or tetracistronic transcripts. Deletions introduced into the gene cluster reveal, first, that CF1-α can be translated from di- or polycistronic transcripts, and, second, that substantial reductions in mRNA quantity have minimal effects on protein synthesis rates. We suggest that posttranscriptional mRNA processing is common in C. reinhardtii chloroplasts, permitting the expression of multiple genes from a single promoter. PMID:9625716

Nap polygraphic recordings after partial sleep deprivation in patients with suspected epileptic seizures.

PubMed

Peraita-Adrados, R; Gutierrez-Solana, L; Ruiz-Falcó, M L; García-Peñas, J J

2001-02-01

A review of the literature shows that nap recordings make a significant contribution to epilepsy studies, providing evidence of specific EEG findings in patients suspected of having epilepsy. In addition, sleep deprivation can cause paroxysmal EEG activity and clinical seizures. We studied retrospectively 686 patients, 51.8% males and 48.2% females, who had experienced at least one episode classified from the clinical point of view as epileptic in origin. They were divided into six age groups. Patients underwent a two-hour (1 P.M.-3 P.M.) nap-video-polygraphic recording (EEG 13 channels using the standard 10-20 system, EOG, ECG, EMG and respiration), following a partial sleep deprivation (1 to 3 h) the night before. A second recording was made in 40 patients. In 35.3% of patients, a complete sleep cycle was obtained; in 64.6% sufficient light and deep NREM sleep was obtained, but not REM stage; in 9.3%, we only observed drowsiness and stage 1 of sleep, and this group was excluded from the analysis. Interictal and/or ictal epileptic discharges were observed during the first nap recording in 245 patients (40.4% of the sample). In addition, in 40 patients (11%) with normal or inconclusive first nap EEG, a second recording was able to demonstrate epileptic abnormalities in 35% of cases. Because of its good cost/benefit ratio and availability in most western laboratories, we consider the 'nap plus partial sleep deprivation' method as advantageous over other activation procedures.

FlyNap (Triethylamine) Increases the Heart Rate of Mosquitoes and Eliminates the Cardioacceleratory Effect of the Neuropeptide CCAP

PubMed Central

Chen, Weihan; Hillyer, Julián F.

2013-01-01

FlyNap (triethylamine) is commonly used to anesthetize Drosophila melanogaster fruit flies. The purpose of this study was to determine whether triethylamine is a suitable anesthetic agent for research into circulatory physiology and immune competence in the mosquito, Anopheles gambiae (Diptera: Culicidae). Recovery experiments showed that mosquitoes awaken from traditional cold anesthesia in less than 7 minutes, but that recovery from FlyNap anesthesia does not begin for several hours. Relative to cold anesthesia, moderate exposures to FlyNap induce an increase in the heart rate, a decrease in the percentage of the time the heart contracts in the anterograde direction, and a decrease in the frequency of heartbeat directional reversals. Experiments employing various combinations of cold and FlyNap anesthesia then showed that cold exposure does not affect basal heart physiology, and that the differences seen between the cold and the FlyNap groups are due to a FlyNap-induced alteration of heart physiology. Furthermore, exposure to FlyNap eliminated the cardioacceleratory effect of crustacean cardioactive peptide (CCAP), and reduced a mosquito’s ability to survive a bacterial infection. Together, these data show that FlyNap is not a suitable substitute to cold anesthesia in experiments assessing mosquito heart function or immune competence. Moreover, these data also illustrate the intricate biology of the insect heart. Specifically, they confirm that the neurohormone CCAP modulates heart rhythms and that it serves as an anterograde pacemaker. PMID:23875027

Resistance gene candidates identified by PCR with degenerate oligonucleotide primers map to clusters of resistance genes in lettuce.

PubMed

Shen, K A; Meyers, B C; Islam-Faridi, M N; Chin, D B; Stelly, D M; Michelmore, R W

1998-08-01

The recent cloning of genes for resistance against diverse pathogens from a variety of plants has revealed that many share conserved sequence motifs. This provides the possibility of isolating numerous additional resistance genes by polymerase chain reaction (PCR) with degenerate oligonucleotide primers. We amplified resistance gene candidates (RGCs) from lettuce with multiple combinations of primers with low degeneracy designed from motifs in the nucleotide binding sites (NBSs) of RPS2 of Arabidopsis thaliana and N of tobacco. Genomic DNA, cDNA, and bacterial artificial chromosome (BAC) clones were successfully used as templates. Four families of sequences were identified that had the same similarity to each other as to resistance genes from other species. The relationship of the amplified products to resistance genes was evaluated by several sequence and genetic criteria. The amplified products contained open reading frames with additional sequences characteristic of NBSs. Hybridization of RGCs to genomic DNA and to BAC clones revealed large numbers of related sequences. Genetic analysis demonstrated the existence of clustered multigene families for each of the four RGC sequences. This parallels classical genetic data on clustering of disease resistance genes. Two of the four families mapped to known clusters of resistance genes; these two families were therefore studied in greater detail. Additional evidence that these RGCs could be resistance genes was gained by the identification of leucine-rich repeat (LRR) regions in sequences adjoining the NBS similar to those in RPM1 and RPS2 of A. thaliana. Fluorescent in situ hybridization confirmed the clustered genomic distribution of these sequences. The use of PCR with degenerate oligonucleotide primers is therefore an efficient method to identify numerous RGCs in plants.

Two Gene Clusters Coordinate Galactose and Lactose Metabolism in Streptococcus gordonii

PubMed Central

Zeng, Lin; Martino, Nicole C.

2012-01-01

Streptococcus gordonii is an early colonizer of the human oral cavity and an abundant constituent of oral biofilms. Two tandemly arranged gene clusters, designated lac and gal, were identified in the S. gordonii DL1 genome, which encode genes of the tagatose pathway (lacABCD) and sugar phosphotransferase system (PTS) enzyme II permeases. Genes encoding a predicted phospho-β-galactosidase (LacG), a DeoR family transcriptional regulator (LacR), and a transcriptional antiterminator (LacT) were also present in the clusters. Growth and PTS assays supported that the permease designated EIILac transports lactose and galactose, whereas EIIGal transports galactose. The expression of the gene for EIIGal was markedly upregulated in cells growing on galactose. Using promoter-cat fusions, a role for LacR in the regulation of the expressions of both gene clusters was demonstrated, and the gal cluster was also shown to be sensitive to repression by CcpA. The deletion of lacT caused an inability to grow on lactose, apparently because of its role in the regulation of the expression of the genes for EIILac, but had little effect on galactose utilization. S. gordonii maintained a selective advantage over Streptococcus mutans in a mixed-species competition assay, associated with its possession of a high-affinity galactose PTS, although S. mutans could persist better at low pHs. Collectively, these results support the concept that the galactose and lactose systems of S. gordonii are subject to complex regulation and that a high-affinity galactose PTS may be advantageous when S. gordonii is competing against the caries pathogen S. mutans in oral biofilms. PMID:22660715

Effects of napping on sleepiness and sleep-related performance deficits in night-shift workers: a systematic review.

PubMed

Ruggiero, Jeanne S; Redeker, Nancy S

2014-04-01

Night-shift workers are prone to sleep deprivation, misalignment of circadian rhythms, and subsequent sleepiness and sleep-related performance deficits. The purpose of this narrative systematic review is to critically review and synthesize the scientific literature regarding improvements in sleepiness and sleep-related performance deficits following planned naps taken during work-shift hours by night workers and to recommend directions for future research and practice. We conducted a literature search using the Medline, PsychInfo, CINAHL, Cochrane Library, and Health and Safety Science Abstracts databases and included English-language quasi-experimental and experimental studies that evaluated the effects of a nighttime nap taken during a simulated or actual night-work shift. We identified 13 relevant studies, which consisted primarily of small samples and mixed designs. Most investigators found that, despite short periods of sleep inertia immediately following naps, night-shift napping led to decreased sleepiness and improved sleep-related performance. None of the studies examined the effects of naps on safety outcomes in the workplace. Larger-scale randomized clinical trials of night-shift napping and direct safety outcomes are needed prior to wider implementation.

The Genetic and Molecular Organization of the Dopa Decarboxylase Gene Cluster of Drosophila Melanogaster

PubMed Central

Stathakis, D. G.; Pentz, E. S.; Freeman, M. E.; Kullman, J.; Hankins, G. R.; Pearlson, N. J.; Wright, TRF.

1995-01-01

We report the complete molecular organization of the Dopa decarboxylase gene cluster. Mutagenesis screens recovered 77 new Df(2L)TW130 recessive lethal mutations. These new alleles combined with 263 previously isolated mutations in the cluster to define 18 essential genes. In addition, seven new deficiencies were isolated and characterized. Deficiency mapping, restriction fragment length polymorphism (RFLP) analysis and P-element-mediated germline transformation experiments determined the gene order for all 18 loci. Genomic and cDNA restriction endonuclease mapping, Northern blot analysis and DNA sequencing provided information on exact gene location, mRNA size and transcriptional direction for most of these loci. In addition, this analysis identified two transcription units that had not previously been identified by extensive mutagenesis screening. Most of the loci are contained within two dense subclusters. We discuss the effectiveness of mutagens and strategies used in our screens, the variable mutability of loci within the genome of Drosophila melanogaster, the cytological and molecular organization of the Ddc gene cluster, the validity of the one band-one gene hypothesis and a possible purpose for the clustering of genes in the Ddc region. PMID:8647399

Sequencing rare marine actinomycete genomes reveals high density of unique natural product biosynthetic gene clusters.

PubMed

Schorn, Michelle A; Alanjary, Mohammad M; Aguinaldo, Kristen; Korobeynikov, Anton; Podell, Sheila; Patin, Nastassia; Lincecum, Tommie; Jensen, Paul R; Ziemert, Nadine; Moore, Bradley S

2016-12-01

Traditional natural product discovery methods have nearly exhausted the accessible diversity of microbial chemicals, making new sources and techniques paramount in the search for new molecules. Marine actinomycete bacteria have recently come into the spotlight as fruitful producers of structurally diverse secondary metabolites, and remain relatively untapped. In this study, we sequenced 21 marine-derived actinomycete strains, rarely studied for their secondary metabolite potential and under-represented in current genomic databases. We found that genome size and phylogeny were good predictors of biosynthetic gene cluster diversity, with larger genomes rivalling the well-known marine producers in the Streptomyces and Salinispora genera. Genomes in the Micrococcineae suborder, however, had consistently the lowest number of biosynthetic gene clusters. By networking individual gene clusters into gene cluster families, we were able to computationally estimate the degree of novelty each genus contributed to the current sequence databases. Based on the similarity measures between all actinobacteria in the Joint Genome Institute's Atlas of Biosynthetic gene Clusters database, rare marine genera show a high degree of novelty and diversity, with Corynebacterium, Gordonia, Nocardiopsis, Saccharomonospora and Pseudonocardia genera representing the highest gene cluster diversity. This research validates that rare marine actinomycetes are important candidates for exploration, as they are relatively unstudied, and their relatives are historically rich in secondary metabolites.

Sequencing rare marine actinomycete genomes reveals high density of unique natural product biosynthetic gene clusters

PubMed Central

Schorn, Michelle A.; Alanjary, Mohammad M.; Aguinaldo, Kristen; Korobeynikov, Anton; Podell, Sheila; Patin, Nastassia; Lincecum, Tommie; Jensen, Paul R.; Ziemert, Nadine

2016-01-01

Traditional natural product discovery methods have nearly exhausted the accessible diversity of microbial chemicals, making new sources and techniques paramount in the search for new molecules. Marine actinomycete bacteria have recently come into the spotlight as fruitful producers of structurally diverse secondary metabolites, and remain relatively untapped. In this study, we sequenced 21 marine-derived actinomycete strains, rarely studied for their secondary metabolite potential and under-represented in current genomic databases. We found that genome size and phylogeny were good predictors of biosynthetic gene cluster diversity, with larger genomes rivalling the well-known marine producers in the Streptomyces and Salinispora genera. Genomes in the Micrococcineae suborder, however, had consistently the lowest number of biosynthetic gene clusters. By networking individual gene clusters into gene cluster families, we were able to computationally estimate the degree of novelty each genus contributed to the current sequence databases. Based on the similarity measures between all actinobacteria in the Joint Genome Institute's Atlas of Biosynthetic gene Clusters database, rare marine genera show a high degree of novelty and diversity, with Corynebacterium, Gordonia, Nocardiopsis, Saccharomonospora and Pseudonocardia genera representing the highest gene cluster diversity. This research validates that rare marine actinomycetes are important candidates for exploration, as they are relatively unstudied, and their relatives are historically rich in secondary metabolites. PMID:27902408

A Putative Gene Cluster from a Lyngbya wollei Bloom that Encodes Paralytic Shellfish Toxin Biosynthesis

PubMed Central

Mihali, Troco K.; Carmichael, Wayne W.; Neilan, Brett A.

2011-01-01

Saxitoxin and its analogs cause the paralytic shellfish-poisoning syndrome, adversely affecting human health and coastal shellfish industries worldwide. Here we report the isolation, sequencing, annotation, and predicted pathway of the saxitoxin biosynthetic gene cluster in the cyanobacterium Lyngbya wollei. The gene cluster spans 36 kb and encodes enzymes for the biosynthesis and export of the toxins. The Lyngbya wollei saxitoxin gene cluster differs from previously identified saxitoxin clusters as it contains genes that are unique to this cluster, whereby the carbamoyltransferase is truncated and replaced by an acyltransferase, explaining the unique toxin profile presented by Lyngbya wollei. These findings will enable the creation of toxin probes, for water monitoring purposes, as well as proof-of-concept for the combinatorial biosynthesis of these natural occurring alkaloids for the production of novel, biologically active compounds. PMID:21347365

Statistical indicators of collective behavior and functional clusters in gene networks of yeast

NASA Astrophysics Data System (ADS)

Živković, J.; Tadić, B.; Wick, N.; Thurner, S.

2006-03-01

We analyze gene expression time-series data of yeast (S. cerevisiae) measured along two full cell-cycles. We quantify these data by using q-exponentials, gene expression ranking and a temporal mean-variance analysis. We construct gene interaction networks based on correlation coefficients and study the formation of the corresponding giant components and minimum spanning trees. By coloring genes according to their cell function we find functional clusters in the correlation networks and functional branches in the associated trees. Our results suggest that a percolation point of functional clusters can be identified on these gene expression correlation networks.

Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana

PubMed Central

Reimegård, Johan; Kundu, Snehangshu; Pendle, Ali; Irish, Vivian F.; Shaw, Peter

2017-01-01

Abstract Co-expression of physically linked genes occurs surprisingly frequently in eukaryotes. Such chromosomal clustering may confer a selective advantage as it enables coordinated gene regulation at the chromatin level. We studied the chromosomal organization of genes involved in male reproductive development in Arabidopsis thaliana. We developed an in-silico tool to identify physical clusters of co-regulated genes from gene expression data. We identified 17 clusters (96 genes) involved in stamen development and acting downstream of the transcriptional activator MS1 (MALE STERILITY 1), which contains a PHD domain associated with chromatin re-organization. The clusters exhibited little gene homology or promoter element similarity, and largely overlapped with reported repressive histone marks. Experiments on a subset of the clusters suggested a link between expression activation and chromatin conformation: qRT-PCR and mRNA in situ hybridization showed that the clustered genes were up-regulated within 48 h after MS1 induction; out of 14 chromatin-remodeling mutants studied, expression of clustered genes was consistently down-regulated only in hta9/hta11, previously associated with metabolic cluster activation; DNA fluorescence in situ hybridization confirmed that transcriptional activation of the clustered genes was correlated with open chromatin conformation. Stamen development thus appears to involve transcriptional activation of physically clustered genes through chromatin de-condensation. PMID:28175342

Identifying conserved gene clusters in the presence of homology families.

PubMed

He, Xin; Goldwasser, Michael H

2005-01-01

The study of conserved gene clusters is important for understanding the forces behind genome organization and evolution, as well as the function of individual genes or gene groups. In this paper, we present a new model and algorithm for identifying conserved gene clusters from pairwise genome comparison. This generalizes a recent model called "gene teams." A gene team is a set of genes that appear homologously in two or more species, possibly in a different order yet with the distance of adjacent genes in the team for each chromosome always no more than a certain threshold. We remove the constraint in the original model that each gene must have a unique occurrence in each chromosome and thus allow the analysis on complex prokaryotic or eukaryotic genomes with extensive paralogs. Our algorithm analyzes a pair of chromosomes in O(mn) time and uses O(m+n) space, where m and n are the number of genes in the respective chromosomes. We demonstrate the utility of our methods by studying two bacterial genomes, E. coli K-12 and B. subtilis. Many of the teams identified by our algorithm correlate with documented E. coli operons, while several others match predicted operons, previously suggested by computational techniques. Our implementation and data are publicly available at euler.slu.edu/ approximately goldwasser/homologyteams/.

The Effect of Cognitive Activity on Sleep Maintenance in a Subsequent Daytime Nap.

PubMed

Arzilli, Cinzia; Cerasuolo, Mariangela; Conte, Francesca; Bittoni, Valentina; Gatteschi, Claudia; Albinni, Benedetta; Giganti, Fiorenza; Ficca, Gianluca

2018-01-25

The aim of this study is to assess the effects of a learning task on the characteristics of a subsequent daytime nap. Thirty-eight subjects were administered a control nap (C) and one preceded by a cognitive training session (TR). Relative to C, TR naps showed significantly increased sleep duration with decreased sleep latency, as well as significantly increased sleep efficiency due to reduced awakening frequency. Meaningful trends were also found toward an increase of Stage 2 sleep proportion and a reduction of Stage 1 sleep, percentage of wake after sleep onset (WASO), and frequency of state transitions. Our results indicate that presleep learning favors sleep propensity and maintenance, offering the possibility to explore planned cognitive training as a low-cost treatment for sleep impairments.

Molecular analysis of SCARECROW genes expressed in white lupin cluster roots

PubMed Central

Sbabou, Laila; Bucciarelli, Bruna; Miller, Susan; Liu, Junqi; Berhada, Fatiha; Filali-Maltouf, Abdelkarim; Allan, Deborah; Vance, Carroll

2010-01-01

The Scarecrow (SCR) transcription factor plays a crucial role in root cell radial patterning and is required for maintenance of the quiescent centre and differentiation of the endodermis. In response to phosphorus (P) deficiency, white lupin (Lupinus albus L.) root surface area increases some 50-fold to 70-fold due to the development of cluster (proteoid) roots. Previously it was reported that SCR-like expressed sequence tags (ESTs) were expressed during early cluster root development. Here the cloning of two white lupin SCR genes, LaSCR1 and LaSCR2, is reported. The predicted amino acid sequences of both LaSCR gene products are highly similar to AtSCR and contain C-terminal conserved GRAS family domains. LaSCR1 and LaSCR2 transcript accumulation localized to the endodermis of both normal and cluster roots as shown by in situ hybridization and gene promoter::reporter staining. Transcript analysis as evaluated by quantitative real-time-PCR (qRT-PCR) and RNA gel hybridization indicated that the two LaSCR genes are expressed predominantly in roots. Expression of LaSCR genes was not directly responsive to the P status of the plant but was a function of cluster root development. Suppression of LaSCR1 in transformed roots of lupin and Medicago via RNAi (RNA interference) delivered through Agrobacterium rhizogenes resulted in decreased root numbers, reflecting the potential role of LaSCR1 in maintaining root growth in these species. The results suggest that the functional orthologues of AtSCR have been characterized. PMID:20167612

A homeotic gene cluster patterns the anteroposterior body axis of C. elegans.

PubMed

Wang, B B; Müller-Immergluck, M M; Austin, J; Robinson, N T; Chisholm, A; Kenyon, C

1993-07-16

In insects and vertebrates, clusters of Antennapedia class homeobox (HOM-C) genes specify anteroposterior body pattern. The nematode C. elegans also contains a small cluster of HOM-C genes, one of which has been shown to specify positional identity. Here we show that two additional C. elegans HOM-C genes also specify positional identity and that together these three HOM-C genes function along the anteroposterior axis in the same order as their homologs in other organisms. Thus, HOM-C-based pattern formation has been conserved in nematodes despite the many differences in morphology and embryology that distinguish them from other phyla. Each C. elegans HOM-C gene is responsible for a distinct body region; however, where their domains overlap, two HOM-C genes can act together to specify the fates of individual cells.

Impact of the NAP-1 strain on disease severity, mortality, and recurrence of healthcare-associated Clostridium difficile infection.

PubMed

Bauer, Karri A; Johnston, Jessica E W; Wenzler, Eric; Goff, Debra A; Cook, Charles H; Balada-Llasat, Joan-Miquel; Pancholi, Preeti; Mangino, Julie E

2017-12-01

Studies are conflicting regarding the association of the North American pulsed-field gel electrophoresis type 1 (NAP1) strain in Clostridium difficile infection (CDI) and outcomes. We evaluated the association of NAP1 with healthcare-associated CDI disease severity, mortality, and recurrence at our academic medical center. Healthcare-associated CDI cases were identified from November 1, 2011 through January 31, 2013. Multivariable regression models were used to evaluate the associations of NAP1 with severe disease (based on the Hines VA severity score index), mortality, and recurrence. Among 5424 stool specimens submitted to the Clinical Microbiology Laboratory, 292 (5.4%) were positive for C. difficile by polymerase chain reaction (PCR) on or after hospital day 4; 70 (24%) of these specimens also tested positive for NAP1. During the study period, 247 (85%) patients had non-severe disease and 45 (15%) patients had severe disease. Among patients with non-severe disease, 65 (26%) had NAP1 and among patients with severe disease, 5 (11%) had NAP1. After controlling for potential confounders, NAP1 was not associated with an increased likelihood of severe disease (adjusted odds ratio [aOR] = 0.35; 95% confidence interval [CI], 0.13-0.93), in-hospital mortality (aOR = 1.02; 95% CI, 0.53-1.96), or recurrence (aOR = 1.16, 95% CI, 0.36-3.77). The NAP1 strain did not increase disease severity, mortality, or recurrence in this study, although the incidence of NAP1-positive healthcare associated-CDI was low. The role of strain typing in outcomes and treatment selection in patients with healthcare-associated CDI remains uncertain. Copyright © 2017 Elsevier Ltd. All rights reserved.

Clustering gene expression data based on predicted differential effects of GV interaction.

PubMed

Pan, Hai-Yan; Zhu, Jun; Han, Dan-Fu

2005-02-01

Microarray has become a popular biotechnology in biological and medical research. However, systematic and stochastic variabilities in microarray data are expected and unavoidable, resulting in the problem that the raw measurements have inherent "noise" within microarray experiments. Currently, logarithmic ratios are usually analyzed by various clustering methods directly, which may introduce bias interpretation in identifying groups of genes or samples. In this paper, a statistical method based on mixed model approaches was proposed for microarray data cluster analysis. The underlying rationale of this method is to partition the observed total gene expression level into various variations caused by different factors using an ANOVA model, and to predict the differential effects of GV (gene by variety) interaction using the adjusted unbiased prediction (AUP) method. The predicted GV interaction effects can then be used as the inputs of cluster analysis. We illustrated the application of our method with a gene expression dataset and elucidated the utility of our approach using an external validation.

Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury

PubMed Central

2010-01-01

Background Spinal cord injury leads to neurological dysfunctions affecting the motor, sensory as well as the autonomic systems. Increased excitability of motor neurons has been implicated in injury-induced spasticity, where the reappearance of self-sustained plateau potentials in the absence of modulatory inputs from the brain correlates with the development of spasticity. Results Here we examine the dynamic transcriptional response of motor neurons to spinal cord injury as it evolves over time to unravel common gene expression patterns and their underlying regulatory mechanisms. For this we use a rat-tail-model with complete spinal cord transection causing injury-induced spasticity, where gene expression profiles are obtained from labeled motor neurons extracted with laser microdissection 0, 2, 7, 21 and 60 days post injury. Consensus clustering identifies 12 gene clusters with distinct time expression profiles. Analysis of these gene clusters identifies early immunological/inflammatory and late developmental responses as well as a regulation of genes relating to neuron excitability that support the development of motor neuron hyper-excitability and the reappearance of plateau potentials in the late phase of the injury response. Transcription factor motif analysis identifies differentially expressed transcription factors involved in the regulation of each gene cluster, shaping the expression of the identified biological processes and their associated genes underlying the changes in motor neuron excitability. Conclusions This analysis provides important clues to the underlying mechanisms of transcriptional regulation responsible for the increased excitability observed in motor neurons in the late chronic phase of spinal cord injury suggesting alternative targets for treatment of spinal cord injury. Several transcription factors were identified as potential regulators of gene clusters containing elements related to motor neuron hyper-excitability, the manipulation

Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury.

PubMed

Ryge, Jesper; Winther, Ole; Wienecke, Jacob; Sandelin, Albin; Westerdahl, Ann-Charlotte; Hultborn, Hans; Kiehn, Ole

2010-06-09

Spinal cord injury leads to neurological dysfunctions affecting the motor, sensory as well as the autonomic systems. Increased excitability of motor neurons has been implicated in injury-induced spasticity, where the reappearance of self-sustained plateau potentials in the absence of modulatory inputs from the brain correlates with the development of spasticity. Here we examine the dynamic transcriptional response of motor neurons to spinal cord injury as it evolves over time to unravel common gene expression patterns and their underlying regulatory mechanisms. For this we use a rat-tail-model with complete spinal cord transection causing injury-induced spasticity, where gene expression profiles are obtained from labeled motor neurons extracted with laser microdissection 0, 2, 7, 21 and 60 days post injury. Consensus clustering identifies 12 gene clusters with distinct time expression profiles. Analysis of these gene clusters identifies early immunological/inflammatory and late developmental responses as well as a regulation of genes relating to neuron excitability that support the development of motor neuron hyper-excitability and the reappearance of plateau potentials in the late phase of the injury response. Transcription factor motif analysis identifies differentially expressed transcription factors involved in the regulation of each gene cluster, shaping the expression of the identified biological processes and their associated genes underlying the changes in motor neuron excitability. This analysis provides important clues to the underlying mechanisms of transcriptional regulation responsible for the increased excitability observed in motor neurons in the late chronic phase of spinal cord injury suggesting alternative targets for treatment of spinal cord injury. Several transcription factors were identified as potential regulators of gene clusters containing elements related to motor neuron hyper-excitability, the manipulation of which potentially could be

Transcriptional analysis of exopolysaccharides biosynthesis gene clusters in Lactobacillus plantarum.

PubMed

Vastano, Valeria; Perrone, Filomena; Marasco, Rosangela; Sacco, Margherita; Muscariello, Lidia

2016-04-01

Exopolysaccharides (EPS) from lactic acid bacteria contribute to specific rheology and texture of fermented milk products and find applications also in non-dairy foods and in therapeutics. Recently, four clusters of genes (cps) associated with surface polysaccharide production have been identified in Lactobacillus plantarum WCFS1, a probiotic and food-associated lactobacillus. These clusters are involved in cell surface architecture and probably in release and/or exposure of immunomodulating bacterial molecules. Here we show a transcriptional analysis of these clusters. Indeed, RT-PCR experiments revealed that the cps loci are organized in five operons. Moreover, by reverse transcription-qPCR analysis performed on L. plantarum WCFS1 (wild type) and WCFS1-2 (ΔccpA), we demonstrated that expression of three cps clusters is under the control of the global regulator CcpA. These results, together with the identification of putative CcpA target sequences (catabolite responsive element CRE) in the regulatory region of four out of five transcriptional units, strongly suggest for the first time a role of the master regulator CcpA in EPS gene transcription among lactobacilli.

Nap sleep spindle correlates of intelligence.

PubMed

Ujma, Péter P; Bódizs, Róbert; Gombos, Ferenc; Stintzing, Johannes; Konrad, Boris N; Genzel, Lisa; Steiger, Axel; Dresler, Martin

2015-11-26

Sleep spindles are thalamocortical oscillations in non-rapid eye movement (NREM) sleep, that play an important role in sleep-related neuroplasticity and offline information processing. Several studies with full-night sleep recordings have reported a positive association between sleep spindles and fluid intelligence scores, however more recently it has been shown that only few sleep spindle measures correlate with intelligence in females, and none in males. Sleep spindle regulation underlies a circadian rhythm, however the association between spindles and intelligence has not been investigated in daytime nap sleep so far. In a sample of 86 healthy male human subjects, we investigated the correlation between fluid intelligence and sleep spindle parameters in an afternoon nap of 100 minutes. Mean sleep spindle length, amplitude and density were computed for each subject and for each derivation for both slow and fast spindles. A positive association was found between intelligence and slow spindle duration, but not any other sleep spindle parameter. As a positive correlation between intelligence and slow sleep spindle duration in full-night polysomnography has only been reported in females but not males, our results suggest that the association between intelligence and sleep spindles is more complex than previously assumed.

Removal of Ca2+ and Zn2+ from aqueous solutions by zeolites NaP and KP.

PubMed

Yusof, Alias Mohd; Malek, Nik Ahmad Nizam Nik; Kamaruzaman, Nurul Asyikin; Adil, Muhammad

2010-01-01

Zeolites P in sodium (NaP) and potassium (KP) forms were used as adsorbents for the removal of calcium (Ca2+) and zinc (Zn2+) cations from aqueous solutions. Zeolite KP was prepared by ion exchange of K+ with Na+ which neutralizes the negative charge of the zeolite P framework structure. The ion exchange capacity of K+ on zeolite NaP was determined through the Freundlich isotherm equilibrium study. Characterization of zeolite KP was determined using infrared spectroscopy and X-ray diffraction (XRD) techniques. From the characterization, the structure of zeolite KP was found to remain stable after the ion exchange process. Zeolites KP and NaP were used for the removal of Ca and Zn from solution. The amount of Ca2+ and Zn2+ in aqueous solution before and after the adsorption by zeolites was analysed using the flame atomic absorption spectroscopy method. The removal of Ca2+ and Zn2+ followed the Freundlich isotherm rather than the Langmuir isotherm model. This result also revealed that zeolite KP adsorbs Ca2+ and Zn2+ more than zeolite NaP and proved that modification of zeolite NaP with potassium leads to an increase in the adsorption efficiency of the zeolite. Therefore, the zeolites NaP and KP can be used for water softening (Ca removal) and reducing water pollution/toxicity (Zn removal).

RubisCO Gene Clusters Found in a Metagenome Microarray from Acid Mine Drainage

PubMed Central

Guo, Xue; Yin, Huaqun; Cong, Jing; Dai, Zhimin; Liang, Yili

2013-01-01

The enzyme responsible for carbon dioxide fixation in the Calvin cycle, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), is always detected as a phylogenetic marker to analyze the distribution and activity of autotrophic bacteria. However, such an approach provides no indication as to the significance of genomic content and organization. Horizontal transfers of RubisCO genes occurring in eubacteria and plastids may seriously affect the credibility of this approach. Here, we presented a new method to analyze the diversity and genomic content of RubisCO genes in acid mine drainage (AMD). A metagenome microarray containing 7,776 large-insertion fosmids was constructed to quickly screen genome fragments containing RubisCO form I large-subunit genes (cbbL). Forty-six cbbL-containing fosmids were detected, and six fosmids were fully sequenced. To evaluate the reliability of the metagenome microarray and understand the microbial community in AMD, the diversities of cbbL and the 16S rRNA gene were analyzed. Fosmid sequences revealed that the form I RubisCO gene cluster could be subdivided into form IA and IB RubisCO gene clusters in AMD, because of significant divergences in molecular phylogenetics and conservative genomic organization. Interestingly, the form I RubisCO gene cluster coexisted with the form II RubisCO gene cluster in one fosmid genomic fragment. Phylogenetic analyses revealed that horizontal transfers of RubisCO genes may occur widely in AMD, which makes the evolutionary history of RubisCO difficult to reconcile with organismal phylogeny. PMID:23335778

Identification and characterization of the ergochrome gene cluster in the plant pathogenic fungus Claviceps purpurea.

PubMed

Neubauer, Lisa; Dopstadt, Julian; Humpf, Hans-Ulrich; Tudzynski, Paul

2016-01-01

Claviceps purpurea is a phytopathogenic fungus infecting a broad range of grasses including economically important cereal crop plants. The infection cycle ends with the formation of the typical purple-black pigmented sclerotia containing the toxic ergot alkaloids. Besides these ergot alkaloids little is known about the secondary metabolism of the fungus. Red anthraquinone derivatives and yellow xanthone dimers (ergochromes) have been isolated from sclerotia and described as ergot pigments, but the corresponding gene cluster has remained unknown. Fungal pigments gain increasing interest for example as environmentally friendly alternatives to existing dyes. Furthermore, several pigments show biological activities and may have some pharmaceutical value. This study identified the gene cluster responsible for the synthesis of the ergot pigments. Overexpression of the cluster-specific transcription factor led to activation of the gene cluster and to the production of several known ergot pigments. Knock out of the cluster key enzyme, a nonreducing polyketide synthase, clearly showed that this cluster is responsible for the production of red anthraquinones as well as yellow ergochromes. Furthermore, a tentative biosynthetic pathway for the ergot pigments is proposed. By changing the culture conditions, pigment production was activated in axenic culture so that high concentration of phosphate and low concentration of sucrose induced pigment syntheses. This is the first functional analysis of a secondary metabolite gene cluster in the ergot fungus besides that for the classical ergot alkaloids. We demonstrated that this gene cluster is responsible for the typical purple-black color of the ergot sclerotia and showed that the red and yellow ergot pigments are products of the same biosynthetic pathway. Activation of the gene cluster in axenic culture opened up new possibilities for biotechnological applications like the dye production or the development of new pharmaceuticals.

Clustering of time-course gene expression profiles using normal mixture models with autoregressive random effects

PubMed Central

2012-01-01

Background Time-course gene expression data such as yeast cell cycle data may be periodically expressed. To cluster such data, currently used Fourier series approximations of periodic gene expressions have been found not to be sufficiently adequate to model the complexity of the time-course data, partly due to their ignoring the dependence between the expression measurements over time and the correlation among gene expression profiles. We further investigate the advantages and limitations of available models in the literature and propose a new mixture model with autoregressive random effects of the first order for the clustering of time-course gene-expression profiles. Some simulations and real examples are given to demonstrate the usefulness of the proposed models. Results We illustrate the applicability of our new model using synthetic and real time-course datasets. We show that our model outperforms existing models to provide more reliable and robust clustering of time-course data. Our model provides superior results when genetic profiles are correlated. It also gives comparable results when the correlation between the gene profiles is weak. In the applications to real time-course data, relevant clusters of coregulated genes are obtained, which are supported by gene-function annotation databases. Conclusions Our new model under our extension of the EMMIX-WIRE procedure is more reliable and robust for clustering time-course data because it adopts a random effects model that allows for the correlation among observations at different time points. It postulates gene-specific random effects with an autocorrelation variance structure that models coregulation within the clusters. The developed R package is flexible in its specification of the random effects through user-input parameters that enables improved modelling and consequent clustering of time-course data. PMID:23151154

Afternoon Napping and Cognition in Chinese Older Adults: Findings from the China Health and Retirement Longitudinal Study Baseline Assessment.

PubMed

Li, Junxin; Cacchione, Pamela Z; Hodgson, Nancy; Riegel, Barbara; Keenan, Brendan T; Scharf, Mathew T; Richards, Kathy C; Gooneratne, Nalaka S

2017-02-01

To examine the cross-sectional associations between self-reported postlunch napping and structured cognitive assessments in Chinese older adults. Cross-sectional cohort study. China. Individuals aged 65 and older from the baseline national wave of the China Health and Retirement Longitudinal Study (CHARLS) (N = 2,974). Interview-based cognitive assessments of orientation and attention, episodic memory, visuospatial abilities, and a combined global cognition score incorporating these assessments. Other self-reported or interview-based assessments included postlunch napping duration, nighttime sleep duration, demographic characteristics, health habits, comorbidities, functional status and social activities. According to reported napping duration, older adults were categorized as non-nappers (0 minutes), short nappers (<30 minutes), moderate nappers (30-90 minutes), and extended nappers (>90 minutes). Postlunch napping was reporting in 57.7% of participants for a mean of 63 minutes. Cognitive function was significantly associated with napping (P < .001). Between-group comparisons showed that moderate nappers had better overall cognition than nonnappers (P < .001) or extended nappers (P = .01). Nonnappers also had significantly poorer cognition than short nappers (P = .03). In multiple regression analysis, moderate napping was significantly associated with better cognition than non- (P = .004), short (P = .04), and extended napping (P = .002), after controlling for demographic characteristics, body mass index, depression, instrumental activities of daily living, social activities, and nighttime sleep duration. A cross-sectional association was found between moderate postlunch napping and better cognition in Chinese older adults. The cross-sectional design and self-reported measures of sleep limited the findings. Longitudinal studies with objective napping measures are needed to further test this hypothesis. © 2016, Copyright the Authors Journal compilation © 2016

The association between daytime napping and risk of diabetes: a systematic review and meta-analysis of observational studies.

PubMed

Guo, Vivian Yawei; Cao, Bing; Wong, Carlos King Ho; Yu, Esther Yee Tak

2017-09-01

To investigate the association between daytime napping and prevalent/incident diabetes mellitus (DM) based on systematic review and meta-analytic data. The electronic databases of Embase, Medline, Pubmed and Web of Science were searched. Relevant studies were extracted by two reviewers independently. The associations between daytime napping (irrespective of duration), long nap (≥1 h/day) and short nap (<1 h/day), and risk of DM were assessed according to study types. Overall estimates were pooled using either fixed- or random-effect with inverse variance meta-analysis. Heterogeneity of included studies was assessed using the I 2 test and possible cause of the heterogeneity was examined by meta-regression analyses. Ten studies (four cross-sectional and six longitudinal cohort) comprising a total of 304,885 individuals and 20,857 cases of DM were included in the systematic review, with an average napping prevalence of 47%. Nappers were found to have increased risk of DM in both cross-sectional and cohort studies. However, significant heterogeneity was present. Long nap (≥1 h/day) was associated with both prevalent and incident DM; in particular, those with a daily nap over 1 h had a 31% increased risk of developing DM during follow-up (95% confidence interval: 2-67%). Conversely, no such association was found in individuals with short naps (<1 h/day) in cohort studies. Long daytime napping over 1 h per day was associated with increased risk of both prevalent and incident DM. Further studies are needed to confirm the findings. Copyright © 2017 Elsevier B.V. All rights reserved.

Self-reported Napping, Sleep Duration and Quality in the Lifestyle Interventions and Independence for Elders Pilot (LIFE-P) Study

PubMed Central

Picarsic, Jennifer L.; Glynn, Nancy W.; Taylor, Christopher A.; Katula, Jeffery; Goldman, Suzanne E.; Studenski, Stephanie; Newman, Anne B.

2010-01-01

OBJECTIVES To determine the prevalence of self-reported napping and its association with subjective nighttime sleep duration and quality, as measured by sleep-onset latency and sleep efficiency. DESIGN Cross-sectional study. SETTING Lifestyle Interventions and Independence for Elder’s Pilot Study. PARTICIPANTS Community-dwelling older adults (N=414), aged 70 to 89 years. MEASUREMENTS Self-report questionnaire on napping and sleep, derived from the Pittsburgh Sleep Quality Index (PSQI) scale. RESULTS A total of 54 percent of participants reported napping with mean nap duration of 55 minutes, (SD 41.2 minutes). Compared to non-nappers, nappers were more often men (37.3% vs. 23.8%, P = .003), African American (20.4% vs.14.4%, P = .06), or diabetic (28% vs. 14.3%, P = .007). Nappers and non-nappers had similar nighttime sleep duration and quality, but nappers spent about 10 percent of their 24-hour sleep occupied in napping. In a multivariate model, the odds of napping were higher for diabetics (OR: 1.9; 95% CI: 1.2–3.0) and men (OR: 1.9; 95% CI: 1.2–3.0)). In nappers, diabetes mellitus (β = 12.3 minutes, P =.005), male gender (β = 9.0 minutes, P = .04), higher BMI (β = 0.8 minutes, P = .02), and lower MMSE (β = 2.2, P = .03) were independently associated with longer nap duration. CONCLUSION Napping was a common practice in community-dwelling older adults and did not detract from nighttime sleep duration or quality. Given its high prevalence and association with diabetes, napping behavior should be assessed as part of sleep behavior, both in future research and in clinical practice. PMID:18662202

Self-reported napping and duration and quality of sleep in the lifestyle interventions and independence for elders pilot study.

PubMed

Picarsic, Jennifer L; Glynn, Nancy W; Taylor, Christopher A; Katula, Jeffrey A; Goldman, Suzanne E; Studenski, Stephanie A; Newman, Anne B

2008-09-01

To determine the prevalence of self-reported napping and its association with subjective nighttime sleep duration and quality, as measured according to sleep-onset latency and sleep efficiency. Cross-sectional study. Lifestyle Interventions and Independence for Elders Pilot Study. Community-dwelling older adults (N=414) aged 70 to 89. Self-report questionnaire on napping and sleep derived from the Pittsburgh Sleep Quality Index (PSQI) scale. Fifty-four percent of participants reported napping, with mean nap duration of 55.0+/-41.2 minutes. Nappers were more likely to be male (37.3% vs 23.8%, P=.003) and African American (20.4% vs 14.4%, P=.06) and to have diabetes mellitus (28% vs 14.3%, P=.007) than non-nappers. Nappers and non-nappers had similar nighttime sleep duration and quality, but nappers spent approximately 10% of their 24-hour sleep occupied in napping. In a multivariate model, the odds of napping were higher for subjects with diabetes mellitus (odds ratio (OR)=1.9, 95% confidence interval (CI)=1.2-3.0) and men (OR=1.9, 95% CI=1.2-3.0). In nappers, diabetes mellitus (beta=12.3 minutes, P=.005), male sex (beta=9.0 minutes, P=.04), higher body mass index (beta=0.8 minutes, P=.02), and lower Mini-Mental State Examination score (beta=2.2 minutes, P=.03) were independently associated with longer nap duration. Napping was a common practice in community-dwelling older adults and did not detract from nighttime sleep duration or quality. Given its high prevalence and association with diabetes mellitus, napping behavior should be assessed as part of sleep behavior in future research and in clinical practice.

The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster

PubMed Central

Bushley, Kathryn E.; Raja, Rajani; Jaiswal, Pankaj; Cumbie, Jason S.; Nonogaki, Mariko; Boyd, Alexander E.; Owensby, C. Alisha; Knaus, Brian J.; Elser, Justin; Miller, Daniel; Di, Yanming; McPhail, Kerry L.; Spatafora, Joseph W.

2013-01-01

The ascomycete fungus Tolypocladium inflatum, a pathogen of beetle larvae, is best known as the producer of the immunosuppressant drug cyclosporin. The draft genome of T. inflatum strain NRRL 8044 (ATCC 34921), the isolate from which cyclosporin was first isolated, is presented along with comparative analyses of the biosynthesis of cyclosporin and other secondary metabolites in T. inflatum and related taxa. Phylogenomic analyses reveal previously undetected and complex patterns of homology between the nonribosomal peptide synthetase (NRPS) that encodes for cyclosporin synthetase (simA) and those of other secondary metabolites with activities against insects (e.g., beauvericin, destruxins, etc.), and demonstrate the roles of module duplication and gene fusion in diversification of NRPSs. The secondary metabolite gene cluster responsible for cyclosporin biosynthesis is described. In addition to genes necessary for cyclosporin biosynthesis, it harbors a gene for a cyclophilin, which is a member of a family of immunophilins known to bind cyclosporin. Comparative analyses support a lineage specific origin of the cyclosporin gene cluster rather than horizontal gene transfer from bacteria or other fungi. RNA-Seq transcriptome analyses in a cyclosporin-inducing medium delineate the boundaries of the cyclosporin cluster and reveal high levels of expression of the gene cluster cyclophilin. In medium containing insect hemolymph, weaker but significant upregulation of several genes within the cyclosporin cluster, including the highly expressed cyclophilin gene, was observed. T. inflatum also represents the first reference draft genome of Ophiocordycipitaceae, a third family of insect pathogenic fungi within the fungal order Hypocreales, and supports parallel and qualitatively distinct radiations of insect pathogens. The T. inflatum genome provides additional insight into the evolution and biosynthesis of cyclosporin and lays a foundation for further investigations of the role

Gene cluster conservation provides insight into cercosporin biosynthesis and extends production to the genus Colletotrichum.

PubMed

de Jonge, Ronnie; Ebert, Malaika K; Huitt-Roehl, Callie R; Pal, Paramita; Suttle, Jeffrey C; Spanner, Rebecca E; Neubauer, Jonathan D; Jurick, Wayne M; Stott, Karina A; Secor, Gary A; Thomma, Bart P H J; Van de Peer, Yves; Townsend, Craig A; Bolton, Melvin D

2018-06-12

Species in the genus Cercospora cause economically devastating diseases in sugar beet, maize, rice, soy bean, and other major food crops. Here, we sequenced the genome of the sugar beet pathogen Cercospora beticola and found it encodes 63 putative secondary metabolite gene clusters, including the cercosporin toxin biosynthesis ( CTB ) cluster. We show that the CTB gene cluster has experienced multiple duplications and horizontal transfers across a spectrum of plant pathogenic fungi, including the wide-host range Colletotrichum genus as well as the rice pathogen Magnaporthe oryzae Although cercosporin biosynthesis has been thought to rely on an eight-gene CTB cluster, our phylogenomic analysis revealed gene collinearity adjacent to the established cluster in all CTB cluster-harboring species. We demonstrate that the CTB cluster is larger than previously recognized and includes cercosporin facilitator protein, previously shown to be involved with cercosporin autoresistance, and four additional genes required for cercosporin biosynthesis, including the final pathway enzymes that install the unusual cercosporin methylenedioxy bridge. Lastly, we demonstrate production of cercosporin by Colletotrichum fioriniae , the first known cercosporin producer within this agriculturally important genus. Thus, our results provide insight into the intricate evolution and biology of a toxin critical to agriculture and broaden the production of cercosporin to another fungal genus containing many plant pathogens of important crops worldwide. Copyright © 2018 the Author(s). Published by PNAS.

A scan statistic to extract causal gene clusters from case-control genome-wide rare CNV data.

PubMed

Nishiyama, Takeshi; Takahashi, Kunihiko; Tango, Toshiro; Pinto, Dalila; Scherer, Stephen W; Takami, Satoshi; Kishino, Hirohisa

2011-05-26

Several statistical tests have been developed for analyzing genome-wide association data by incorporating gene pathway information in terms of gene sets. Using these methods, hundreds of gene sets are typically tested, and the tested gene sets often overlap. This overlapping greatly increases the probability of generating false positives, and the results obtained are difficult to interpret, particularly when many gene sets show statistical significance. We propose a flexible statistical framework to circumvent these problems. Inspired by spatial scan statistics for detecting clustering of disease occurrence in the field of epidemiology, we developed a scan statistic to extract disease-associated gene clusters from a whole gene pathway. Extracting one or a few significant gene clusters from a global pathway limits the overall false positive probability, which results in increased statistical power, and facilitates the interpretation of test results. In the present study, we applied our method to genome-wide association data for rare copy-number variations, which have been strongly implicated in common diseases. Application of our method to a simulated dataset demonstrated the high accuracy of this method in detecting disease-associated gene clusters in a whole gene pathway. The scan statistic approach proposed here shows a high level of accuracy in detecting gene clusters in a whole gene pathway. This study has provided a sound statistical framework for analyzing genome-wide rare CNV data by incorporating topological information on the gene pathway.

Identification of the Coumermycin A1 Biosynthetic Gene Cluster of Streptomyces rishiriensis DSM 40489

PubMed Central

Wang, Zhao-Xin; Li, Shu-Ming; Heide, Lutz

2000-01-01

The biosynthetic gene cluster of the aminocoumarin antibiotic coumermycin A1 was cloned by screening of a cosmid library of Streptomyces rishiriensis DSM 40489 with heterologous probes from a dTDP-glucose 4,6-dehydratase gene, involved in deoxysugar biosynthesis, and from the aminocoumarin resistance gyrase gene gyrBr. Sequence analysis of a 30.8-kb region upstream of gyrBr revealed the presence of 28 complete open reading frames (ORFs). Fifteen of the identified ORFs showed, on average, 84% identity to corresponding ORFs in the biosynthetic gene cluster of novobiocin, another aminocoumarin antibiotic. Possible functions of 17 ORFs in the biosynthesis of coumermycin A1 could be assigned by comparison with sequences in GenBank. Experimental proof for the function of the identified gene cluster was provided by an insertional gene inactivation experiment, which resulted in an abolishment of coumermycin A1 production. PMID:11036020

Ethnic-specific associations of sleep duration and daytime napping with prevalent type 2 diabetes in postmenopausal women.

PubMed

Shadyab, Aladdin H; Kritz-Silverstein, Donna; Laughlin, Gail A; Wooten, Wilma J; Barrett-Connor, Elizabeth; Araneta, Maria Rosario G

2015-02-01

The objective of this study was to evaluate ethnic differences in the associations of nighttime sleep and daytime napping durations with prevalent type 2 diabetes. Samples of White (n = 908), Filipina (n = 330), and Black (n = 371) community-dwelling, postmenopausal women aged 50-86 years were evaluated with cross-sectional data obtained during 1992-1999 including self-reported duration of nighttime sleep and daytime napping, behaviors, medical history, and medication use. The prevalence of type 2 diabetes was evaluated with a 2-h 75-g oral glucose tolerance test. Overall, 10.9% of White, 37.8% of Filipina, and 17.8% of Black women had type 2 diabetes. Average sleep durations were 7.3, 6.3, and 6.6 h and napping durations were 16.8, 31.7, and 25.9 min for White, Filipina, and Black women, respectively. Sleep duration showed a significant (p < 0.01) nonlinear association with type 2 diabetes in Filipina women, with increased odds of diabetes at both low and high sleep durations independent of age, body mass index (BMI), triglyceride to high-density lipoprotein (HDL) ratio, hypertension, and daytime napping duration. Daytime napping duration was associated with type 2 diabetes only among White women; those napping ≥ 30 min/day had 74% (95% confidence interval (CI) = 10%, 175%) higher odds of diabetes compared to non-nappers independent of covariates including nighttime sleep duration. Results suggest ethnic-specific associations of nighttime sleep and daytime napping durations with type 2 diabetes. Copyright © 2014. Published by Elsevier B.V.

Napping: Do's and Don'ts for Healthy Adults

MedlinePlus

... fatigue or unexpected sleepiness Are about to experience sleep loss, for example, due to a long work shift Want to make planned naps part of your daily routine If you're ... or have a sleep disorder or other medical condition that's disrupting your ...

Gene structure and expression characteristic of a novel odorant receptor gene cluster in the parasitoid wasp Microplitis mediator (Hymenoptera: Braconidae).

PubMed

Wang, S-N; Shan, S; Zheng, Y; Peng, Y; Lu, Z-Y; Yang, Y-Q; Li, R-J; Zhang, Y-J; Guo, Y-Y

2017-08-01

Odorant receptors (ORs) expressed in the antennae of parasitoid wasps are responsible for detection of various lipophilic airborne molecules. In the present study, 107 novel OR genes were identified from Microplitis mediator antennal transcriptome data. Phylogenetic analysis of the set of OR genes from M. mediator and Microplitis demolitor revealed that M. mediator OR (MmedOR) genes can be classified into different subfamilies, and the majority of MmedORs in each subfamily shared high sequence identities and clear orthologous relationships to M. demolitor ORs. Within a subfamily, six MmedOR genes, MmedOR98, 124, 125, 126, 131 and 155, shared a similar gene structure and were tightly linked in the genome. To evaluate whether the clustered MmedOR genes share common regulatory features, the transcription profile and expression characteristics of the six closely related OR genes were investigated in M. mediator. Rapid amplification of cDNA ends-PCR experiments revealed that the OR genes within the cluster were transcribed as single mRNAs, and a bicistronic mRNA for two adjacent genes (MmedOR124 and MmedOR98) was also detected in female antennae by reverse transcription PCR. In situ hybridization experiments indicated that each OR gene within the cluster was expressed in a different number of cells. Moreover, there was no co-expression of the two highly related OR genes, MmedOR124 and MmedOR98, which appeared to be individually expressed in a distinct population of neurons. Overall, there were distinct expression profiles of closely related MmedOR genes from the same cluster in M. mediator. These data provide a basic understanding of the olfactory coding in parasitoid wasps. © 2017 The Royal Entomological Society.

Polymorphisms and linkage analysis for ICAM-1 and the selectin gene cluster

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

Vora, D.K.; Rosenbloom, C.L.; Cottingham, R.W.

1994-06-01

Genetic polymorphisms in leukocyte and endothelial cell adhesion molecules may be important variables with regard to susceptibility to multifactorial disease processes that include an inflammatory component. For this reason, polymorphisms were sought for intercellular adhesion molecule-1 (ICAM-1; gene symbol ICAM1) and for the three genes in the selectin cluster, P-selectin, L-selectin, and E-selectin (gene symbols SELP, SELL, and SELE, respectively). Two amino acid polymorphisms were identified for ICAM-1; Gly or Arg at codon 241 and Lys or Glu at codon 469. Dinucleotide repeat polymorphisms were identified in the 3{prime}-untranslated region for ICAM-1 and in intron 9 for P-selectin. Restriction fragmentmore » length polymorphisms were found using cDNAs for each of the three selectin genes as probes; E-selectin with BglII, P-selectin with ScaI, and L-selectin with HincII. Linkage analysis was performed for the selectin gene cluster and for ICAM-1 using the CEPH families; ICAM-1 is very tightly linked to the LDL receptor on chromosome 19, and the selectin cluster is linked to markers at chromosome 1q23. 41 refs., 2 tabs.« less

REM-Enriched Naps Are Associated with Memory Consolidation for Sad Stories and Enhance Mood-Related Reactivity.

PubMed

Gilson, Médhi; Deliens, Gaétane; Leproult, Rachel; Bodart, Alice; Nonclercq, Antoine; Ercek, Rudy; Peigneux, Philippe

2015-12-29

Emerging evidence suggests that emotion and affect modulate the relation between sleep and cognition. In the present study, we investigated the role of rapid-eye movement (REM) sleep in mood regulation and memory consolidation for sad stories. In a counterbalanced design, participants (n = 24) listened to either a neutral or a sad story during two sessions, spaced one week apart. After listening to the story, half of the participants had a short (45 min) morning nap. The other half had a long (90 min) morning nap, richer in REM and N2 sleep. Story recall, mood evolution and changes in emotional response to the re-exposure to the story were assessed after the nap. Although recall performance was similar for sad and neutral stories irrespective of nap duration, sleep measures were correlated with recall performance in the sad story condition only. After the long nap, REM sleep density positively correlated with retrieval performance, while re-exposure to the sad story led to diminished mood and increased skin conductance levels. Our results suggest that REM sleep may not only be associated with the consolidation of intrinsically sad material, but also enhances mood reactivity, at least on the short term.

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin

PubMed Central

Ing-Simmons, Elizabeth; Seitan, Vlad C.; Faure, Andre J.; Flicek, Paul; Carroll, Thomas; Dekker, Job; Fisher, Amanda G.; Lenhard, Boris

2015-01-01

In addition to mediating sister chromatid cohesion during the cell cycle, the cohesin complex associates with CTCF and with active gene regulatory elements to form long-range interactions between its binding sites. Genome-wide chromosome conformation capture had shown that cohesin's main role in interphase genome organization is in mediating interactions within architectural chromosome compartments, rather than specifying compartments per se. However, it remains unclear how cohesin-mediated interactions contribute to the regulation of gene expression. We have found that the binding of CTCF and cohesin is highly enriched at enhancers and in particular at enhancer arrays or “super-enhancers” in mouse thymocytes. Using local and global chromosome conformation capture, we demonstrate that enhancer elements associate not just in linear sequence, but also in 3D, and that spatial enhancer clustering is facilitated by cohesin. The conditional deletion of cohesin from noncycling thymocytes preserved enhancer position, H3K27ac, H4K4me1, and enhancer transcription, but weakened interactions between enhancers. Interestingly, ∼50% of deregulated genes reside in the vicinity of enhancer elements, suggesting that cohesin regulates gene expression through spatial clustering of enhancer elements. We propose a model for cohesin-dependent gene regulation in which spatial clustering of enhancer elements acts as a unified mechanism for both enhancer-promoter “connections” and “insulation.” PMID:25677180

Two Horizontally Transferred Xenobiotic Resistance Gene Clusters Associated with Detoxification of Benzoxazolinones by Fusarium Species

PubMed Central

Glenn, Anthony E.; Davis, C. Britton; Gao, Minglu; Gold, Scott E.; Mitchell, Trevor R.; Proctor, Robert H.; Stewart, Jane E.; Snook, Maurice E.

2016-01-01

Microbes encounter a broad spectrum of antimicrobial compounds in their environments and often possess metabolic strategies to detoxify such xenobiotics. We have previously shown that Fusarium verticillioides, a fungal pathogen of maize known for its production of fumonisin mycotoxins, possesses two unlinked loci, FDB1 and FDB2, necessary for detoxification of antimicrobial compounds produced by maize, including the γ-lactam 2-benzoxazolinone (BOA). In support of these earlier studies, microarray analysis of F. verticillioides exposed to BOA identified the induction of multiple genes at FDB1 and FDB2, indicating the loci consist of gene clusters. One of the FDB1 cluster genes encoded a protein having domain homology to the metallo-β-lactamase (MBL) superfamily. Deletion of this gene (MBL1) rendered F. verticillioides incapable of metabolizing BOA and thus unable to grow on BOA-amended media. Deletion of other FDB1 cluster genes, in particular AMD1 and DLH1, did not affect BOA degradation. Phylogenetic analyses and topology testing of the FDB1 and FDB2 cluster genes suggested two horizontal transfer events among fungi, one being transfer of FDB1 from Fusarium to Colletotrichum, and the second being transfer of the FDB2 cluster from Fusarium to Aspergillus. Together, the results suggest that plant-derived xenobiotics have exerted evolutionary pressure on these fungi, leading to horizontal transfer of genes that enhance fitness or virulence. PMID:26808652

Genome-wide DNA methylation analysis reveals estrogen-mediated epigenetic repression of metallothionein-1 gene cluster in breast cancer.

PubMed

Jadhav, Rohit R; Ye, Zhenqing; Huang, Rui-Lan; Liu, Joseph; Hsu, Pei-Yin; Huang, Yi-Wen; Rangel, Leticia B; Lai, Hung-Cheng; Roa, Juan Carlos; Kirma, Nameer B; Huang, Tim Hui-Ming; Jin, Victor X

2015-01-01

Recent genome-wide analysis has shown that DNA methylation spans long stretches of chromosome regions consisting of clusters of contiguous CpG islands or gene families. Hypermethylation of various gene clusters has been reported in many types of cancer. In this study, we conducted methyl-binding domain capture (MBDCap) sequencing (MBD-seq) analysis on a breast cancer cohort consisting of 77 patients and 10 normal controls, as well as a panel of 38 breast cancer cell lines. Bioinformatics analysis determined seven gene clusters with a significant difference in overall survival (OS) and further revealed a distinct feature that the conservation of a large gene cluster (approximately 70 kb) metallothionein-1 (MT1) among 45 species is much lower than the average of all RefSeq genes. Furthermore, we found that DNA methylation is an important epigenetic regulator contributing to gene repression of MT1 gene cluster in both ERα positive (ERα+) and ERα negative (ERα-) breast tumors. In silico analysis revealed much lower gene expression of this cluster in The Cancer Genome Atlas (TCGA) cohort for ERα + tumors. To further investigate the role of estrogen, we conducted 17β-estradiol (E2) and demethylating agent 5-aza-2'-deoxycytidine (DAC) treatment in various breast cancer cell types. Cell proliferation and invasion assays suggested MT1F and MT1M may play an anti-oncogenic role in breast cancer. Our data suggests that DNA methylation in large contiguous gene clusters can be potential prognostic markers of breast cancer. Further investigation of these clusters revealed that estrogen mediates epigenetic repression of MT1 cluster in ERα + breast cancer cell lines. In all, our studies identify thousands of breast tumor hypermethylated regions for the first time, in particular, discovering seven large contiguous hypermethylated gene clusters.

Regulatory Feedback Loop of Two phz Gene Clusters through 5′-Untranslated Regions in Pseudomonas sp. M18

PubMed Central

Li, Yaqian; Du, Xilin; Lu, Zhi John; Wu, Daqiang; Zhao, Yilei; Ren, Bin; Huang, Jiaofang; Huang, Xianqing; Xu, Yuhong; Xu, Yuquan

2011-01-01

Background Phenazines are important compounds produced by pseudomonads and other bacteria. Two phz gene clusters called phzA1-G1 and phzA2-G2, respectively, were found in the genome of Pseudomonas sp. M18, an effective biocontrol agent, which is highly homologous to the opportunistic human pathogen P. aeruginosa PAO1, however little is known about the correlation between the expressions of two phz gene clusters. Methodology/Principal Findings Two chromosomal insertion inactivated mutants for the two gene clusters were constructed respectively and the correlation between the expressions of two phz gene clusters was investigated in strain M18. Phenazine-1-carboxylic acid (PCA) molecules produced from phzA2-G2 gene cluster are able to auto-regulate expression itself and activate the expression of phzA1-G1 gene cluster in a circulated amplification pattern. However, the post-transcriptional expression of phzA1-G1 transcript was blocked principally through 5′-untranslated region (UTR). In contrast, the phzA2-G2 gene cluster was transcribed to a lesser extent and translated efficiently and was negatively regulated by the GacA signal transduction pathway, mainly at a post-transcriptional level. Conclusions/Significance A single molecule, PCA, produced in different quantities by the two phz gene clusters acted as the functional mediator and the two phz gene clusters developed a specific regulatory mechanism which acts through 5′-UTR to transfer a single, but complex bacterial signaling event in Pseudomonas sp. strain M18. PMID:21559370

Fatigue on the flight deck: the consequences of sleep loss and the benefits of napping.

PubMed

Hartzler, Beth M

2014-01-01

The detrimental effects of fatigue in aviation are well established, as evidenced by both the number of fatigue-related mishaps and numerous studies which have found that most pilots experience a deterioration in cognitive performance as well as increased stress during the course of a flight. Further, due to the nature of the average pilot's work schedule, with frequent changes in duty schedule, early morning starts, and extended duty periods, fatigue may be impossible to avoid. Thus, it is critical that fatigue countermeasures be available which can help to combat the often overwhelming effects of sleep loss or sleep disruption. While stimulants such as caffeine are typically effective at maintaining alertness and performance, such countermeasures do nothing to address the actual source of fatigue - insufficient sleep. Consequently, strategic naps are considered an efficacious means of maintaining performance while also reducing the individual's sleep debt. These types of naps have been advocated for pilots in particular, as opportunities to sleep either in the designated rest facilities or on the flight deck may be beneficial in reducing both the performance and alertness impairments associated with fatigue, as well as the subjective feelings of sleepiness. Evidence suggests that strategic naps can reduce subjective feelings of fatigue and improve performance and alertness. Despite some contraindications to implementing strategic naps while on duty, such as sleep inertia experienced upon awakening, both researchers and pilots agree that the benefits associated with these naps far outweigh the potential risks. This article is a literature review detailing both the health and safety concerns of fatigue among commercial pilots as well as benefits and risks associated with strategic napping to alleviate this fatigue. Published by Elsevier Ltd.

Performance Assessment of Kernel Density Clustering for Gene Expression Profile Data

PubMed Central

Zeng, Beiyan; Chen, Yiping P.; Smith, Oscar H.

2003-01-01

Kernel density smoothing techniques have been used in classification or supervised learning of gene expression profile (GEP) data, but their applications to clustering or unsupervised learning of those data have not been explored and assessed. Here we report a kernel density clustering method for analysing GEP data and compare its performance with the three most widely-used clustering methods: hierarchical clustering, K-means clustering, and multivariate mixture model-based clustering. Using several methods to measure agreement, between-cluster isolation, and withincluster coherence, such as the Adjusted Rand Index, the Pseudo F test, the r2 test, and the profile plot, we have assessed the effectiveness of kernel density clustering for recovering clusters, and its robustness against noise on clustering both simulated and real GEP data. Our results show that the kernel density clustering method has excellent performance in recovering clusters from simulated data and in grouping large real expression profile data sets into compact and well-isolated clusters, and that it is the most robust clustering method for analysing noisy expression profile data compared to the other three methods assessed. PMID:18629292

Short sleep duration and longer daytime napping are associated with non-alcoholic fatty liver disease in Chinese adults.

PubMed

Peng, Kui; Lin, Lin; Wang, Zhengyi; Ding, Lin; Huang, Ya; Wang, Po; Xu, Yu; Lu, Jieli; Xu, Min; Bi, Yufang; Wang, Weiqing; Chen, Yuhong; Ning, Guang

2017-09-01

Epidemiologic studies have reported conflicting results on the relationship between short sleep duration and non-alcoholic fatty liver disease (NAFLD). There are no previous studies investigating the effect of daytime napping on NAFLD. In the present study we examined the associations between NAFLD and both nightly sleep duration and daytime napping in a middle-aged and elderly Chinese population. This cross-sectional community-based population study was performed on 8559 individuals aged ≥40 years. Sleep duration and the duration of daytime napping were self-reported using a standardized questionnaire; NAFLD was diagnosed by ultrasonography. In this study sample, the overall prevalence of NAFLD was 30.4%. There was an inverse association between sleep duration and the risk of prevalent NAFLD. In multivariate analysis, the odds ratios (ORs) and 95% confidence intervals (CIs) of prevalent NAFLD for decreasing sleep duration categories (≥9, 8.1-9, 7.1-8, 6.1-7, and ≤6.1 h) were 1.00 (reference), 1.38 (1.13-1.70), 1.32 (1.08-1.61), 1.29 (1.04-1.60), and 1.66 (1.28-2.15), respectively (P trend  = 0.0073). Compared with participants without a daytime napping habit, nap takers with a longer nap duration (>0.5 h) had an increased risk of prevalent NAFLD (OR 1.22; 95% CI 1.06-1.41). The associations of sleep duration and daytime napping duration with NAFLD were generally consistent across different categories of age and obesity, metabolic syndrome, and insulin resistance status. Short sleep duration and longer daytime napping were associated with an increased risk of prevalent NAFLD in a middle-aged and elderly Chinese population. © 2016 Ruijin Hospital, Shanghai Jiaotong University School of Medicine and John Wiley & Sons Australia, Ltd.

Evolution of coding and non-coding genes in HOX clusters of a marsupial.

PubMed

Yu, Hongshi; Lindsay, James; Feng, Zhi-Ping; Frankenberg, Stephen; Hu, Yanqiu; Carone, Dawn; Shaw, Geoff; Pask, Andrew J; O'Neill, Rachel; Papenfuss, Anthony T; Renfree, Marilyn B

2012-06-18

The HOX gene clusters are thought to be highly conserved amongst mammals and other vertebrates, but the long non-coding RNAs have only been studied in detail in human and mouse. The sequencing of the kangaroo genome provides an opportunity to use comparative analyses to compare the HOX clusters of a mammal with a distinct body plan to those of other mammals. Here we report a comparative analysis of HOX gene clusters between an Australian marsupial of the kangaroo family and the eutherians. There was a strikingly high level of conservation of HOX gene sequence and structure and non-protein coding genes including the microRNAs miR-196a, miR-196b, miR-10a and miR-10b and the long non-coding RNAs HOTAIR, HOTAIRM1 and HOXA11AS that play critical roles in regulating gene expression and controlling development. By microRNA deep sequencing and comparative genomic analyses, two conserved microRNAs (miR-10a and miR-10b) were identified and one new candidate microRNA with typical hairpin precursor structure that is expressed in both fibroblasts and testes was found. The prediction of microRNA target analysis showed that several known microRNA targets, such as miR-10, miR-414 and miR-464, were found in the tammar HOX clusters. In addition, several novel and putative miRNAs were identified that originated from elsewhere in the tammar genome and that target the tammar HOXB and HOXD clusters. This study confirms that the emergence of known long non-coding RNAs in the HOX clusters clearly predate the marsupial-eutherian divergence 160 Ma ago. It also identified a new potentially functional microRNA as well as conserved miRNAs. These non-coding RNAs may participate in the regulation of HOX genes to influence the body plan of this marsupial.

Evolution of coding and non-coding genes in HOX clusters of a marsupial

PubMed Central

2012-01-01

Background The HOX gene clusters are thought to be highly conserved amongst mammals and other vertebrates, but the long non-coding RNAs have only been studied in detail in human and mouse. The sequencing of the kangaroo genome provides an opportunity to use comparative analyses to compare the HOX clusters of a mammal with a distinct body plan to those of other mammals. Results Here we report a comparative analysis of HOX gene clusters between an Australian marsupial of the kangaroo family and the eutherians. There was a strikingly high level of conservation of HOX gene sequence and structure and non-protein coding genes including the microRNAs miR-196a, miR-196b, miR-10a and miR-10b and the long non-coding RNAs HOTAIR, HOTAIRM1 and HOXA11AS that play critical roles in regulating gene expression and controlling development. By microRNA deep sequencing and comparative genomic analyses, two conserved microRNAs (miR-10a and miR-10b) were identified and one new candidate microRNA with typical hairpin precursor structure that is expressed in both fibroblasts and testes was found. The prediction of microRNA target analysis showed that several known microRNA targets, such as miR-10, miR-414 and miR-464, were found in the tammar HOX clusters. In addition, several novel and putative miRNAs were identified that originated from elsewhere in the tammar genome and that target the tammar HOXB and HOXD clusters. Conclusions This study confirms that the emergence of known long non-coding RNAs in the HOX clusters clearly predate the marsupial-eutherian divergence 160 Ma ago. It also identified a new potentially functional microRNA as well as conserved miRNAs. These non-coding RNAs may participate in the regulation of HOX genes to influence the body plan of this marsupial. PMID:22708672

Identification of the Regulator Gene Responsible for the Acetone-Responsive Expression of the Binuclear Iron Monooxygenase Gene Cluster in Mycobacteria ▿

PubMed Central

Furuya, Toshiki; Hirose, Satomi; Semba, Hisashi; Kino, Kuniki

2011-01-01

The mimABCD gene cluster encodes the binuclear iron monooxygenase that oxidizes propane and phenol in Mycobacterium smegmatis strain MC2 155 and Mycobacterium goodii strain 12523. Interestingly, expression of the mimABCD gene cluster is induced by acetone. In this study, we investigated the regulator gene responsible for this acetone-responsive expression. In the genome sequence of M. smegmatis strain MC2 155, the mimABCD gene cluster is preceded by a gene designated mimR, which is divergently transcribed. Sequence analysis revealed that MimR exhibits amino acid similarity with the NtrC family of transcriptional activators, including AcxR and AcoR, which are involved in acetone and acetoin metabolism, respectively. Unexpectedly, many homologs of the mimR gene were also found in the sequenced genomes of actinomycetes. A plasmid carrying a transcriptional fusion of the intergenic region between the mimR and mimA genes with a promoterless green fluorescent protein (GFP) gene was constructed and introduced into M. smegmatis strain MC2 155. Using a GFP reporter system, we confirmed by deletion and complementation analyses that the mimR gene product is the positive regulator of the mimABCD gene cluster expression that is responsive to acetone. M. goodii strain 12523 also utilized the same regulatory system as M. smegmatis strain MC2 155. Although transcriptional activators of the NtrC family generally control transcription using the σ54 factor, a gene encoding the σ54 factor was absent from the genome sequence of M. smegmatis strain MC2 155. These results suggest the presence of a novel regulatory system in actinomycetes, including mycobacteria. PMID:21856847

The Glucuronic Acid Utilization Gene Cluster from Bacillus stearothermophilus T-6

PubMed Central

Shulami, Smadar; Gat, Orit; Sonenshein, Abraham L.; Shoham, Yuval

1999-01-01

A λ-EMBL3 genomic library of Bacillus stearothermophilus T-6 was screened for hemicellulolytic activities, and five independent clones exhibiting β-xylosidase activity were isolated. The clones overlap each other and together represent a 23.5-kb chromosomal segment. The segment contains a cluster of xylan utilization genes, which are organized in at least three transcriptional units. These include the gene for the extracellular xylanase, xylanase T-6; part of an operon coding for an intracellular xylanase and a β-xylosidase; and a putative 15.5-kb-long transcriptional unit, consisting of 12 genes involved in the utilization of α-d-glucuronic acid (GlcUA). The first four genes in the potential GlcUA operon (orf1, -2, -3, and -4) code for a putative sugar transport system with characteristic components of the binding-protein-dependent transport systems. The most likely natural substrate for this transport system is aldotetraouronic acid [2-O-α-(4-O-methyl-α-d-glucuronosyl)-xylotriose] (MeGlcUAXyl3). The following two genes code for an intracellular α-glucuronidase (aguA) and a β-xylosidase (xynB). Five more genes (kdgK, kdgA, uxaC, uxuA, and uxuB) encode proteins that are homologous to enzymes involved in galacturonate and glucuronate catabolism. The gene cluster also includes a potential regulatory gene, uxuR, the product of which resembles repressors of the GntR family. The apparent transcriptional start point of the cluster was determined by primer extension analysis and is located 349 bp from the initial ATG codon. The potential operator site is a perfect 12-bp inverted repeat located downstream from the promoter between nucleotides +170 and +181. Gel retardation assays indicated that UxuR binds specifically to this sequence and that this binding is efficiently prevented in vitro by MeGlcUAXyl3, the most likely molecular inducer. PMID:10368143

Distribution of Suicin Gene Clusters in Streptococcus suis Serotype 2 Belonging to Sequence Types 25 and 28.

PubMed

Athey, Taryn B T; Vaillancourt, Katy; Frenette, Michel; Fittipaldi, Nahuel; Gottschalk, Marcelo; Grenier, Daniel

2016-01-01

Recently, we reported the purification and characterization of three distinct lantibiotics (named suicin 90-1330, suicin 3908, and suicin 65) produced by Streptococcus suis . In this study, we investigated the distribution of the three suicin lantibiotic gene clusters among serotype 2 S. suis strains belonging to sequence type (ST) 25 and ST28, the two dominant STs identified in North America. The genomes of 102 strains were interrogated for the presence of suicin gene clusters encoding suicins 90-1330, 3908, and 65. The gene cluster encoding suicin 65 was the most prevalent and mainly found among ST25 strains. In contrast, none of the genes related to suicin 90-1330 production were identified in 51 ST25 strains nor in 35/51 ST28 strains. However, the complete suicin 90-1330 gene cluster was found in ten ST28 strains, although some genes in the cluster were truncated in three of these isolates. The vast majority (101/102) of S. suis strains did not possess any of the genes encoding suicin 3908. In conclusion, this study indicates heterogeneous distribution of suicin genes in S. suis .

Form gene clustering method about pan-ethnic-group products based on emotional semantic

NASA Astrophysics Data System (ADS)

Chen, Dengkai; Ding, Jingjing; Gao, Minzhuo; Ma, Danping; Liu, Donghui

2016-09-01

The use of pan-ethnic-group products form knowledge primarily depends on a designer's subjective experience without user participation. The majority of studies primarily focus on the detection of the perceptual demands of consumers from the target product category. A pan-ethnic-group products form gene clustering method based on emotional semantic is constructed. Consumers' perceptual images of the pan-ethnic-group products are obtained by means of product form gene extraction and coding and computer aided product form clustering technology. A case of form gene clustering about the typical pan-ethnic-group products is investigated which indicates that the method is feasible. This paper opens up a new direction for the future development of product form design which improves the agility of product design process in the era of Industry 4.0.

Neighborhood socioeconomic status, sleep duration and napping in middle-to-old aged US men and women.

PubMed

Xiao, Qian; Hale, Lauren

2018-04-25

Earlier studies have linked neighborhood disadvantage with poor sleep outcomes. However, little is known about the association between changes in one's neighborhood over time and night sleep and napping. In over 300,000 middle-to-old aged Americans, we examined neighborhood socioeconomic status (SES) and change in neighborhood SES in relation to nocturnal sleep duration and napping. Nocturnal sleep duration and daytime napping were self-reported at baseline (1995-1996). Participants also reported baseline residential addresses, which were linked to US censuses. We derived a neighborhood SES index using census variables and calculated the baseline level and change (1990-2000) in neighborhood SES. Multinomial logistic regression was used to estimate the associations between neighborhood SES over time and nocturnal sleep and napping. Lower baseline neighborhood SES was associated short sleep, long sleep and napping. When compared with the highest quintile of neighborhood SES, the lowest was associated with 46% and 72% increase in relative risk (RR) of reporting very short (< 5 hours) sleep, 28% and 19% higher RR of long (≥9 hours) sleep and 95% and 85% increase in long (≥1 hours) nap in men and women, respectively. Moreover, a decrease in neighborhood SES was associated with higher RR of reporting very short sleep in women; while an improvement in neighborhood SES was associated with an increase in RR of long sleep in men. Neighborhood disadvantage and worsening neighborhood conditions were associated with unhealthy sleep behaviors. These results reinforce a growing literature on the potential importance of neighborhood context for understanding sleep health.

Infant Growth in Length Follows Prolonged Sleep and Increased Naps

PubMed Central

Lampl, Michelle; Johnson, Michael L.

2011-01-01

Study Objectives: The mechanisms underlying infant sleep irregularity are unknown. This study tests the hypothesis that sleep and episodic (saltatory) growth in infant length are temporally coupled processes. Study design: Daily parental diaries continuously recorded sleep onset and awakening for 23 infants (14 females) over 4-17 months (n = 5798 daily records). Multiple model-independent methods compared day-to-day sleep patterns and saltatory length growth. Measurements and Results: Approximate entropy (ApEn) quantified temporal irregularity in infant sleep patterns; breastfeeding and infant sex explained 44% of inter-individual variance (P = 0.001). Random effects mixed-model regression identified that saltatory length growth was associated with increased total daily sleep hours (P < 0.001) and number of sleep bouts (P = 0.001), with breastfeeding, infant sex, and age as covariates. Infant size and illness onset were non-contributory. CLUSTER analysis identified peaks in individual sleep of 4.5 more h and/or 3 more naps per day, compared to intervening intervals, that were non-randomly concordant with saltatory length growth for all individuals (P < 0.05), with a time lag of 0-4 days. Subject-specific probabilities of a growth saltation associated with sleep included a median odds ratio of 1.20 for each additional hour (n = 8, 95% CI 1.15 to 1.29) and 1.43 for each additional sleep bout (n = 12, 95% CI 1.21-2.03). Increased sleep bout duration predicted weight (P < 0.001) and abdominal skinfold accrual (P = 0.05) contingent on length growth, and truncal adiposity independent of growth (P < 0.001). Conclusions: Sleeping and length growth are temporally related biological processes, suggesting an integrated anabolic system. Infant behavioral state changes may reflect biological mechanisms underlying the timing and control of human growth. Citation: Lampl M; Johnson ML. Infant growth in length follows prolonged sleep and increased naps. SLEEP 2011

Intact cluster and chordate-like expression of ParaHox genes in a sea star

PubMed Central

2013-01-01

Background The ParaHox genes are thought to be major players in patterning the gut of several bilaterian taxa. Though this is a fundamental role that these transcription factors play, their activities are not limited to the endoderm and extend to both ectodermal and mesodermal tissues. Three genes compose the ParaHox group: Gsx, Xlox and Cdx. In some taxa (mostly chordates but to some degree also in protostomes) the three genes are arranged into a genomic cluster, in a similar fashion to what has been shown for the better-known Hox genes. Sea urchins possess the full complement of ParaHox genes but they are all dispersed throughout the genome, an arrangement that, perhaps, represented the primitive condition for all echinoderms. In order to understand the evolutionary history of this group of genes we cloned and characterized all ParaHox genes, studied their expression patterns and identified their genomic loci in a member of an earlier branching group of echinoderms, the asteroid Patiria miniata. Results We identified the three ParaHox orthologs in the genome of P. miniata. While one of them, PmGsx is provided as maternal message, with no zygotic activation afterwards, the other two, PmLox and PmCdx are expressed during embryogenesis, within restricted domains of both endoderm and ectoderm. Screening of a Patiria bacterial artificial chromosome (BAC) library led to the identification of a clone containing the three genes. The transcriptional directions of PmGsx and PmLox are opposed to that of the PmCdx gene within the cluster. Conclusions The identification of P. miniata ParaHox genes has revealed the fact that these genes are clustered in the genome, in contrast to what has been reported for echinoids. Since the presence of an intact cluster, or at least a partial cluster, has been reported in chordates and polychaetes respectively, it becomes clear that within echinoderms, sea urchins have modified the original bilaterian arrangement. Moreover, the sea star

Comparison of expression of secondary metabolite biosynthesis cluster genes in Aspergillus flavus, A. parasiticus, and A. oryzae.

PubMed

Ehrlich, Kenneth C; Mack, Brian M

2014-06-23

Fifty six secondary metabolite biosynthesis gene clusters are predicted to be in the Aspergillus flavus genome. In spite of this, the biosyntheses of only seven metabolites, including the aflatoxins, kojic acid, cyclopiazonic acid and aflatrem, have been assigned to a particular gene cluster. We used RNA-seq to compare expression of secondary metabolite genes in gene clusters for the closely related fungi A. parasiticus, A. oryzae, and A. flavus S and L sclerotial morphotypes. The data help to refine the identification of probable functional gene clusters within these species. Our results suggest that A. flavus, a prevalent contaminant of maize, cottonseed, peanuts and tree nuts, is capable of producing metabolites which, besides aflatoxin, could be an underappreciated contributor to its toxicity.

Comparison of Expression of Secondary Metabolite Biosynthesis Cluster Genes in Aspergillus flavus, A. parasiticus, and A. oryzae

PubMed Central

Ehrlich, Kenneth C.; Mack, Brian M.

2014-01-01

Fifty six secondary metabolite biosynthesis gene clusters are predicted to be in the Aspergillus flavus genome. In spite of this, the biosyntheses of only seven metabolites, including the aflatoxins, kojic acid, cyclopiazonic acid and aflatrem, have been assigned to a particular gene cluster. We used RNA-seq to compare expression of secondary metabolite genes in gene clusters for the closely related fungi A. parasiticus, A. oryzae, and A. flavus S and L sclerotial morphotypes. The data help to refine the identification of probable functional gene clusters within these species. Our results suggest that A. flavus, a prevalent contaminant of maize, cottonseed, peanuts and tree nuts, is capable of producing metabolites which, besides aflatoxin, could be an underappreciated contributor to its toxicity. PMID:24960201

A recently transferred cluster of bacterial genes in Trichomonas vaginalis - lateral gene transfer and the fate of acquired genes

PubMed Central

2014-01-01

Background Lateral Gene Transfer (LGT) has recently gained recognition as an important contributor to some eukaryote proteomes, but the mechanisms of acquisition and fixation in eukaryotic genomes are still uncertain. A previously defined norm for LGTs in microbial eukaryotes states that the majority are genes involved in metabolism, the LGTs are typically localized one by one, surrounded by vertically inherited genes on the chromosome, and phylogenetics shows that a broad collection of bacterial lineages have contributed to the transferome. Results A unique 34 kbp long fragment with 27 clustered genes (TvLF) of prokaryote origin was identified in the sequenced genome of the protozoan parasite Trichomonas vaginalis. Using a PCR based approach we confirmed the presence of the orthologous fragment in four additional T. vaginalis strains. Detailed sequence analyses unambiguously suggest that TvLF is the result of one single, recent LGT event. The proposed donor is a close relative to the firmicute bacterium Peptoniphilus harei. High nucleotide sequence similarity between T. vaginalis strains, as well as to P. harei, and the absence of homologs in other Trichomonas species, suggests that the transfer event took place after the radiation of the genus Trichomonas. Some genes have undergone pseudogenization and degradation, indicating that they may not be retained in the future. Functional annotations reveal that genes involved in informational processes are particularly prone to degradation. Conclusions We conclude that, although the majority of eukaryote LGTs are single gene occurrences, they may be acquired in clusters of several genes that are subsequently cleansed of evolutionarily less advantageous genes. PMID:24898731

Clustering by soft-constraint affinity propagation: applications to gene-expression data.

PubMed

Leone, Michele; Sumedha; Weigt, Martin

2007-10-15

Similarity-measure-based clustering is a crucial problem appearing throughout scientific data analysis. Recently, a powerful new algorithm called Affinity Propagation (AP) based on message-passing techniques was proposed by Frey and Dueck (2007a). In AP, each cluster is identified by a common exemplar all other data points of the same cluster refer to, and exemplars have to refer to themselves. Albeit its proved power, AP in its present form suffers from a number of drawbacks. The hard constraint of having exactly one exemplar per cluster restricts AP to classes of regularly shaped clusters, and leads to suboptimal performance, e.g. in analyzing gene expression data. This limitation can be overcome by relaxing the AP hard constraints. A new parameter controls the importance of the constraints compared to the aim of maximizing the overall similarity, and allows to interpolate between the simple case where each data point selects its closest neighbor as an exemplar and the original AP. The resulting soft-constraint affinity propagation (SCAP) becomes more informative, accurate and leads to more stable clustering. Even though a new a priori free parameter is introduced, the overall dependence of the algorithm on external tuning is reduced, as robustness is increased and an optimal strategy for parameter selection emerges more naturally. SCAP is tested on biological benchmark data, including in particular microarray data related to various cancer types. We show that the algorithm efficiently unveils the hierarchical cluster structure present in the data sets. Further on, it allows to extract sparse gene expression signatures for each cluster.

Identification of new genes in a cell envelope-cell division gene cluster of Escherichia coli: cell envelope gene murG.

PubMed Central

Salmond, G P; Lutkenhaus, J F; Donachie, W D

1980-01-01

We report the identification, cloning, and mapping of a new cell envelope gene, murG. This lies in a group of five genes of similar phenotype (in the order murE murF murG murC ddl) all concerned with peptidoglycan biosynthesis. This group is in a larger cluster of at least 10 genes, all of which are involved in some way with cell envelope growth. Images PMID:6998962

Prediagnosis Sleep Duration, Napping, and Mortality Among Colorectal Cancer Survivors in a Large US Cohort

PubMed Central

Arem, Hannah; Pfeiffer, Ruth; Matthews, Charles

2017-01-01

Abstract Study Objectives: Prediagnosis lifestyle factors can influence colorectal cancer (CRC) survival. Sleep deficiency is linked to metabolic dysfunction and chronic inflammation, which may contribute to higher mortality from cardiometabolic conditions and promote tumor progression. We hypothesized that prediagnosis sleep deficiency would be associated with poor CRC survival. No previous study has examined either nighttime sleep or daytime napping in relation to survival among men and women diagnosed with CRC. Methods: We examined self-reported sleep duration and napping prior to diagnosis in relation to mortality among 4869 CRC survivors in the NIH-AARP Diet and Health Study. Vital status was ascertained by linkage to the Social Security Administration Death Master File and the National Death Index. We examined the associations of sleep and napping with mortality using traditional Cox regression (total mortality) and Compositing Risk Regression (cardiovascular disease [CVD] and CRC mortality). Models were adjusted for confounders (demographics, cancer stage, grade and treatment, smoking, physical activity, and sedentary behavior) as well as possible mediators (body mass index and health status) in separate models. Results: Compared to participants reporting 7–8 hours of sleep per day, those who reported <5 hr had a 36% higher all-cause mortality risk (Hazard Ratio (95% Confidence Interval), 1.36 (1.08–1.72)). Short sleep (<5 hr) was also associated with a 54% increase in CRC mortality (Substitution Hazard Ratio (95% Confidence Interval), 1.54 (1.11–2.14)) after adjusting for confounders and accounting for competing causes of death. Compared to no napping, napping 1 hr or more per day was associated with significantly higher total and CVD mortality but not CRC mortality. Conclusion: Prediagnosis short sleep and long napping were associated with higher mortality among CRC survivors. PMID:28329353

Prediagnosis Sleep Duration, Napping, and Mortality Among Colorectal Cancer Survivors in a Large US Cohort.

PubMed

Xiao, Qian; Arem, Hannah; Pfeiffer, Ruth; Matthews, Charles

2017-04-01

Prediagnosis lifestyle factors can influence colorectal cancer (CRC) survival. Sleep deficiency is linked to metabolic dysfunction and chronic inflammation, which may contribute to higher mortality from cardiometabolic conditions and promote tumor progression. We hypothesized that prediagnosis sleep deficiency would be associated with poor CRC survival. No previous study has examined either nighttime sleep or daytime napping in relation to survival among men and women diagnosed with CRC. We examined self-reported sleep duration and napping prior to diagnosis in relation to mortality among 4869 CRC survivors in the NIH-AARP Diet and Health Study. Vital status was ascertained by linkage to the Social Security Administration Death Master File and the National Death Index. We examined the associations of sleep and napping with mortality using traditional Cox regression (total mortality) and Compositing Risk Regression (cardiovascular disease [CVD] and CRC mortality). Models were adjusted for confounders (demographics, cancer stage, grade and treatment, smoking, physical activity, and sedentary behavior) as well as possible mediators (body mass index and health status) in separate models. Compared to participants reporting 7-8 hours of sleep per day, those who reported <5 hr had a 36% higher all-cause mortality risk (Hazard Ratio (95% Confidence Interval), 1.36 (1.08-1.72)). Short sleep (<5 hr) was also associated with a 54% increase in CRC mortality (Substitution Hazard Ratio (95% Confidence Interval), 1.54 (1.11-2.14)) after adjusting for confounders and accounting for competing causes of death. Compared to no napping, napping 1 hr or more per day was associated with significantly higher total and CVD mortality but not CRC mortality. Prediagnosis short sleep and long napping were associated with higher mortality among CRC survivors. © Sleep Research Society 2017. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For

antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.

PubMed

Weber, Tilmann; Blin, Kai; Duddela, Srikanth; Krug, Daniel; Kim, Hyun Uk; Bruccoleri, Robert; Lee, Sang Yup; Fischbach, Michael A; Müller, Rolf; Wohlleben, Wolfgang; Breitling, Rainer; Takano, Eriko; Medema, Marnix H

2015-07-01

Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Resonant Proton Capture on Sodium-23 and Elemental Variations in Globular Cluster Stars

NASA Astrophysics Data System (ADS)

Cesaratto, John Michael

Globular clusters represent some of the oldest stellar bodies in the universe. As such, they are used as testing grounds for theories of stellar evolution and nucleosynthesis. Astronomical observations have shown star-to-star abundance variation in light-mass elements in all Galactic globular clusters. Standard stellar evolution models do not predict these variations. For instance, there exists a pronounced anticorrelation between Na and O in the cluster stars that is not observed in similar, isolated field stars. The current explanations for these observations are that a preexisting massive star could have polluted the interstellar medium where a younger star was born, or that stars undergo some additional mixing beyond dredge-up. Theoreticians rely on nuclear physics input in the form of thermonuclear reaction rates to edit or propose new theories predicting these abundance anomalies. The 23Na + p reaction is a bridge between the NeNa cycle and the MgAl cycle, but large uncertainties exist in the 23Na(p, gamma)24Mg reaction rate for burning temperatures relevant to red giant branch and asymptotic giant branch stars. The uncertainties arise from an expected, but unobserved resonance at Ecmr = 138 keV. A new high-intensity, low-energy electron cyclotron resonance (ECR) ion source at the Laboratory for Experimental Nuclear Astrophysics (LENA) has increased sensitivity for measuring this reaction. After many attempts and long measurement periods, a marginal signal (90% confidence level) has been observed from the resonance and a new strength has been established. This new strength marks a factor of 70 reduction from the previous strength upper limit. The strength has also been calculated as an upper limit at 95% confidence level. New reaction rates have been calculated for the 23Na(p, gamma)24Mg and 23 Na(p, alpha)20Ne reactions and the recommended value for the 23Na(p, gamma) 24Mg rate has been reduced by over an order of magnitude at T 9 = 0.07. This will have

Organization of the Escherichia coli K-12 gene cluster responsible for production of the extracellular polysaccharide colanic acid.

PubMed Central

Stevenson, G; Andrianopoulos, K; Hobbs, M; Reeves, P R

1996-01-01

Colanic acid (CA) is an extracellular polysaccharide produced by most Escherichia coli strains as well as by other species of the family Enterobacteriaceae. We have determined the sequence of a 23-kb segment of the E. coli K-12 chromosome which includes the cluster of genes necessary for production of CA. The CA cluster comprises 19 genes. Two other sequenced genes (orf1.3 and galF), which are situated between the CA cluster and the O-antigen cluster, were shown to be unnecessary for CA production. The CA cluster includes genes for synthesis of GDP-L-fucose, one of the precursors of CA, and the gene for one of the enzymes in this pathway (GDP-D-mannose 4,6-dehydratase) was identified by biochemical assay. Six of the inferred proteins show sequence similarity to glycosyl transferases, and two others have sequence similarity to acetyl transferases. Another gene (wzx) is predicted to encode a protein with multiple transmembrane segments and may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The first three genes of the cluster are predicted to encode an outer membrane lipoprotein, a phosphatase, and an inner membrane protein with an ATP-binding domain. Since homologs of these genes are found in other extracellular polysaccharide gene clusters, they may have a common function, such as export of polysaccharide from the cell. PMID:8759852

Work schedule and self-reported hypertension - the potential beneficial role of on-shift naps for night workers.

PubMed

Rotenberg, Lúcia; Silva-Costa, Aline; Vasconcellos-Silva, Paulo Roberto; Griep, Rosane Härter

2016-01-01

Data on the association between shift work and hypertension are controversial. Sleep restriction is hypothesized to be involved in this relationship. Since on-shift nap can partly compensate for sleep deprivation among night workers, this investigation is aimed at (i) comparing the prevalence of hypertension among workers considering both current and former night work, (ii) testing the association between on-shift naps and hypertension among night workers, and (iii) analyzing the influence of sleep complaints in the association between on-shift nap and hypertension. Nap was defined as a sleep episode with duration shorter than the average nighttime sleep. A cross-sectional study was performed at the 18 largest public hospitals in Rio de Janeiro, Brazil, in 2010-2011 (N = 2588 female registered nurses). Nurses were informally allowed to nap for up to three consecutive hours during working nights. Workers completed a multidimensional questionnaire including self-reported information on physician diagnosis of hypertension, napping, and sleep complaints (insomnia, diurnal sleepiness, and non-satisfactory sleep). Epidemiological and statistical treatment of data included binomial logistic regression and interaction tests. Higher chances of hypertension were observed for both current and former night workers compared with workers with no previous experience in night work, i.e. exclusive day workers (OR = 1.68; CI95% 1.22-2.33 and OR = 1.40; CI95% 1.01-1.96, respectively) after adjustment for age, race/ethnicity, physical activity, smoking, alcohol consumption, insomnia, weekly work hours, and BMI. Compared with exclusive day workers, both non-nappers and nappers were at a higher likelihood of reporting hypertension (OR = 1.93 CI95% 1.35-2.79 and OR = 1.41 CI95% 1.08-2.20, respectively). An interaction was observed between napping behavior and insomnia (p = 0.037). In the whole sample of night workers, the lower OR for nappers was confirmed when they were directly

Fatigue mitigation effects of en-route napping on commercial airline pilots flying international routes

NASA Astrophysics Data System (ADS)

Baldwin, Jarret Taylor

The introduction of ultra-long range commercial aircraft and the evolution of the commercial airline industry has provided new opportunities for air carriers to fly longer range international route segments while deregulation, industry consolidation, and the constant drive to reduce costs wherever possible has pressured airline managements to seek more productivity from their pilots. At the same time, advancements in the understanding of human physiology have begun to make their way into flight and duty time regulations and airline scheduling practices. In this complex and ever changing operating environment, there remains an essential need to better understand how these developments, and other daily realities facing commercial airline pilots, are affecting their fatigue management strategies as they go about their rituals of getting to and from their homes to work and performing their flight assignments. Indeed, the need for commercial airline pilots to have access to better and more effective fatigue mitigation tools to combat fatigue and insure that they are well rested and at the top of their game when flying long-range international route segments has never been greater. This study examined to what extent the maximum fatigue states prior to napping, as self-accessed by commercial airline pilots flying international route segments, were affected by a number of other common flight assignment related factors. The study also examined to what extent the availability of scheduled en-route rest opportunities, in an onboard crew rest facility, affected the usage of en-route napping as a fatigue mitigation strategy, and to what extent the duration of such naps affected the perceived benefits of such naps as self-accessed by commercial airline pilots flying international route segments. The study utilized an online survey tool to collect data on crew position, prior flight segments flown in the same duty period, augmentation, commuting, pre-flight rest obtained in the

Characterization of a Major Cluster of nif, fix, and Associated Genes in a Sugarcane Endophyte, Acetobacter diazotrophicus

PubMed Central

Lee, Sunhee; Reth, Alexander; Meletzus, Dietmar; Sevilla, Myrna; Kennedy, Christina

2000-01-01

A major 30.5-kb cluster of nif and associated genes of Acetobacter diazotrophicus (syn. Gluconacetobacter diazotrophicus), a nitrogen-fixing endophyte of sugarcane, was sequenced and analyzed. This cluster represents the largest assembly of contiguous nif-fix and associated genes so far characterized in any diazotrophic bacterial species. Northern blots and promoter sequence analysis indicated that the genes are organized into eight transcriptional units. The overall arrangement of genes is most like that of the nif-fix cluster in Azospirillum brasilense, while the individual gene products are more similar to those in species of Rhizobiaceae or in Rhodobacter capsulatus. PMID:11092875

Activation and comparative analysis of cryptic xiamycin gene cluster from marine-derived Streptomyces sp. FXJ 7.388.

PubMed

Uhong Lü, Yuhong; Liu, Xiaoli; Wang, Miao; Li, Yuanyuan; Liu, Ning; Bao, Yuxin; Liu, Minghao; Li, Xiaoqian; Wang, Yinyin; Qian, Shenyan; Yue, Changwu; Huang, Ying

2016-09-01

In order to obtain the natural products synthesized by the three putative xiamycin biosynthesis gene clusters which were predicted via antiSMASH during the genome mining of marine Streptomyces sp. FXJ 7.388, Streptomyces sp. FXJ 8.012, and Streptomyces olivaceus FXJ 7.023. Sixteen genes involved in xiamycin assembly, modification, and regulation with higher identity than the newest reported xiamycin biosynthetic gene cluster from marine Streptomyces sp. SCSIO 02999, Streptomyces sp. HKI0576, and Streptomyces sp. FXJ 7.388 were discovered via gene cluster comparative analysis. A ribosome engineering strategy was adopted to activate such cryptic gene clusters with different final concentrations antibiotics that act on the ribosome, and two indolosesquiterpenes were isolated from idlethaldose streptomycin-resistant Streptomyces sp. FXJ 7.388 strains. However, no such product was detected in Streptomyces sp. FXJ 8.012 and Streptomyces olivaceus FXJ 7.023 under the same treatment. This result suggested that these genes might hold the least gene content for xiamycin biosynthesis.

Genomic organization of the rat alpha 2u-globulin gene cluster.

PubMed

McFadyen, D A; Addison, W; Locke, J

1999-05-01

The alpha 2u-globulin are a group of similar proteins, belonging to the lipocalin superfamily of proteins, that are synthesized in a subset of secretory tissues in rats. The many alpha 2u-globulin isoforms are encoded by a multigene family that exhibits extensive homology. Despite a high degree of sequence identity, individual family members show diverse expression patterns involving complex hormonal, tissue-specific, and developmental regulation. Analysis suggests that there are approximately 20 alpha 2u-globulin genes in the rat genome. We have used fluorescence in situ hybridization (FISH) to show that the alpha 2u-globulin genes are clustered at a single site on rat Chromosome (Chr) 5 (5q22-24). Southern blots of rat genomic DNA separated by pulsed field gel electrophoresis indicated that the alpha 2u-globulin genes are contained on two NruI fragments with a total size of 880 kbp. Analysis of three P1 clones containing alpha 2u-globulin genes indicated that the alpha 2u-globulin genes are tandemly arranged in a head-to-tail fashion. The organization of the alpha 2u-globulin genes in the rat as a tandem array of single genes differs from the homologous major urinary protein genes in the mouse, which are organized as tandem arrays of divergently oriented gene pairs. The structure of these gene clusters may have consequences for the proposed function, as a pheromone transporter, for the protein products encoded by these genes.

Inference from clustering with application to gene-expression microarrays.

PubMed

Dougherty, Edward R; Barrera, Junior; Brun, Marcel; Kim, Seungchan; Cesar, Roberto M; Chen, Yidong; Bittner, Michael; Trent, Jeffrey M

2002-01-01

There are many algorithms to cluster sample data points based on nearness or a similarity measure. Often the implication is that points in different clusters come from different underlying classes, whereas those in the same cluster come from the same class. Stochastically, the underlying classes represent different random processes. The inference is that clusters represent a partition of the sample points according to which process they belong. This paper discusses a model-based clustering toolbox that evaluates cluster accuracy. Each random process is modeled as its mean plus independent noise, sample points are generated, the points are clustered, and the clustering error is the number of points clustered incorrectly according to the generating random processes. Various clustering algorithms are evaluated based on process variance and the key issue of the rate at which algorithmic performance improves with increasing numbers of experimental replications. The model means can be selected by hand to test the separability of expected types of biological expression patterns. Alternatively, the model can be seeded by real data to test the expected precision of that output or the extent of improvement in precision that replication could provide. In the latter case, a clustering algorithm is used to form clusters, and the model is seeded with the means and variances of these clusters. Other algorithms are then tested relative to the seeding algorithm. Results are averaged over various seeds. Output includes error tables and graphs, confusion matrices, principal-component plots, and validation measures. Five algorithms are studied in detail: K-means, fuzzy C-means, self-organizing maps, hierarchical Euclidean-distance-based and correlation-based clustering. The toolbox is applied to gene-expression clustering based on cDNA microarrays using real data. Expression profile graphics are generated and error analysis is displayed within the context of these profile graphics. A

The effects of napping on the risk of hypertension: a systematic review and meta-analysis.

PubMed

Cheungpasitporn, Wisit; Thongprayoon, Charat; Srivali, Narat; Vijayvargiya, Priya; Andersen, Carl A; Kittanamongkolchai, Wonngarm; Sathick, Insara J Jaffer; Caples, Sean M; Erickson, Stephen B

2016-11-01

The risk of hypertension in adults who regularly take a nap is controversial. The objective of this meta-analysis was to assess the associations between napping and hypertension. A literature search was performed using MEDLINE, EMbase and The Cochrane Database of Systematic Reviews from inception through October, 2015. Studies that reported relative risks, odd ratios or hazard ratios comparing the risk of hypertension in individuals who regularly take nap were included. Pooled risk ratios (RR) and 95% confidence interval (CI) were calculated using a random-effect, generic inverse variance method. Nine observational studies with 112,267 individuals were included in the analysis to assess the risk of hypertension in nappers. The pooled RR of hypertension in nappers was 1.13 with 95% CI (0.98 to 1.30). When meta-analysis was limited only to studies assessing the risk of hypertension in daytime nappers, the pooled RR of hypertension was 1.19 with 95% CI (1.06 to 1.35). The data on association between nighttime napping in individuals who work night shift and hypertension were limited, only one observational study reported reduced risk of hypertension in nighttime nappers with odds ratio of 0.79 with 95% CI (0.63 to 1.00). Our meta-analysis demonstrates a significant association between daytime napping and hypertension. Future study is needed to assess the potential benefits of HTN screening for daytime nappers. © 2016 Chinese Cochrane Center, West China Hospital of Sichuan University and John Wiley & Sons Australia, Ltd.

Clavine Alkaloids Gene Clusters of Penicillium and Related Fungi: Evolutionary Combination of Prenyltransferases, Monooxygenases and Dioxygenases

PubMed Central

Martín, Juan F.; Liras, Paloma

2017-01-01

The clavine alkaloids produced by the fungi of the Aspergillaceae and Arthrodermatacea families differ from the ergot alkaloids produced by Claviceps and Neotyphodium. The clavine alkaloids lack the extensive peptide chain modifications that occur in lysergic acid derived ergot alkaloids. Both clavine and ergot alkaloids arise from the condensation of tryptophan and dimethylallylpyrophosphate by the action of the dimethylallyltryptophan synthase. The first five steps of the biosynthetic pathway that convert tryptophan and dimethylallyl-pyrophosphate (DMA-PP) in chanoclavine-1-aldehyde are common to both clavine and ergot alkaloids. The biosynthesis of ergot alkaloids has been extensively studied and is not considered in this article. We focus this review on recent advances in the gene clusters for clavine alkaloids in the species of Penicillium, Aspergillus (Neosartorya), Arthroderma and Trychophyton and the enzymes encoded by them. The final products of the clavine alkaloids pathways derive from the tetracyclic ergoline ring, which is modified by late enzymes, including a reverse type prenyltransferase, P450 monooxygenases and acetyltransferases. In Aspergillus japonicus, a α-ketoglutarate and Fe2+-dependent dioxygenase is involved in the cyclization of a festuclavine-like unknown type intermediate into cycloclavine. Related dioxygenases occur in the biosynthetic gene clusters of ergot alkaloids in Claviceps purpurea and also in the clavine clusters in Penicillium species. The final products of the clavine alkaloid pathway in these fungi differ from each other depending on the late biosynthetic enzymes involved. An important difference between clavine and ergot alkaloid pathways is that clavine producers lack the enzyme CloA, a P450 monooxygenase, involved in one of the steps of the conversion of chanoclavine-1-aldehyde into lysergic acid. Bioinformatic analysis of the sequenced genomes of the Aspergillaceae and Arthrodermataceae fungi showed the presence of

Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in xanthomonas.

PubMed

Lu, Hong; Patil, Prabhu; Van Sluys, Marie-Anne; White, Frank F; Ryan, Robert P; Dow, J Maxwell; Rabinowicz, Pablo; Salzberg, Steven L; Leach, Jan E; Sonti, Ramesh; Brendel, Volker; Bogdanove, Adam J

2008-01-01

Xanthomonas is a large genus of plant-associated and plant-pathogenic bacteria. Collectively, members cause diseases on over 392 plant species. Individually, they exhibit marked host- and tissue-specificity. The determinants of this specificity are unknown. To assess potential contributions to host- and tissue-specificity, pathogenesis-associated gene clusters were compared across genomes of eight Xanthomonas strains representing vascular or non-vascular pathogens of rice, brassicas, pepper and tomato, and citrus. The gum cluster for extracellular polysaccharide is conserved except for gumN and sequences downstream. The xcs and xps clusters for type II secretion are conserved, except in the rice pathogens, in which xcs is missing. In the otherwise conserved hrp cluster, sequences flanking the core genes for type III secretion vary with respect to insertion sequence element and putative effector gene content. Variation at the rpf (regulation of pathogenicity factors) cluster is more pronounced, though genes with established functional relevance are conserved. A cluster for synthesis of lipopolysaccharide varies highly, suggesting multiple horizontal gene transfers and reassortments, but this variation does not correlate with host- or tissue-specificity. Phylogenetic trees based on amino acid alignments of gum, xps, xcs, hrp, and rpf cluster products generally reflect strain phylogeny. However, amino acid residues at four positions correlate with tissue specificity, revealing hpaA and xpsD as candidate determinants. Examination of genome sequences of xanthomonads Xylella fastidiosa and Stenotrophomonas maltophilia revealed that the hrp, gum, and xcs clusters are recent acquisitions in the Xanthomonas lineage. Our results provide insight into the ancestral Xanthomonas genome and indicate that differentiation with respect to host- and tissue-specificity involved not major modifications or wholesale exchange of clusters, but subtle changes in a small number of genes or

A novel harmony search-K means hybrid algorithm for clustering gene expression data

PubMed Central

Nazeer, KA Abdul; Sebastian, MP; Kumar, SD Madhu

2013-01-01

Recent progress in bioinformatics research has led to the accumulation of huge quantities of biological data at various data sources. The DNA microarray technology makes it possible to simultaneously analyze large number of genes across different samples. Clustering of microarray data can reveal the hidden gene expression patterns from large quantities of expression data that in turn offers tremendous possibilities in functional genomics, comparative genomics, disease diagnosis and drug development. The k- ¬means clustering algorithm is widely used for many practical applications. But the original k-¬means algorithm has several drawbacks. It is computationally expensive and generates locally optimal solutions based on the random choice of the initial centroids. Several methods have been proposed in the literature for improving the performance of the k-¬means algorithm. A meta-heuristic optimization algorithm named harmony search helps find out near-global optimal solutions by searching the entire solution space. Low clustering accuracy of the existing algorithms limits their use in many crucial applications of life sciences. In this paper we propose a novel Harmony Search-K means Hybrid (HSKH) algorithm for clustering the gene expression data. Experimental results show that the proposed algorithm produces clusters with better accuracy in comparison with the existing algorithms. PMID:23390351

A novel harmony search-K means hybrid algorithm for clustering gene expression data.

PubMed

Nazeer, Ka Abdul; Sebastian, Mp; Kumar, Sd Madhu

2013-01-01

Recent progress in bioinformatics research has led to the accumulation of huge quantities of biological data at various data sources. The DNA microarray technology makes it possible to simultaneously analyze large number of genes across different samples. Clustering of microarray data can reveal the hidden gene expression patterns from large quantities of expression data that in turn offers tremendous possibilities in functional genomics, comparative genomics, disease diagnosis and drug development. The k- ¬means clustering algorithm is widely used for many practical applications. But the original k-¬means algorithm has several drawbacks. It is computationally expensive and generates locally optimal solutions based on the random choice of the initial centroids. Several methods have been proposed in the literature for improving the performance of the k-¬means algorithm. A meta-heuristic optimization algorithm named harmony search helps find out near-global optimal solutions by searching the entire solution space. Low clustering accuracy of the existing algorithms limits their use in many crucial applications of life sciences. In this paper we propose a novel Harmony Search-K means Hybrid (HSKH) algorithm for clustering the gene expression data. Experimental results show that the proposed algorithm produces clusters with better accuracy in comparison with the existing algorithms.

Daytime Napping and the Risk of All-Cause and Cause-Specific Mortality: A 13-Year Follow-up of a British Population

PubMed Central

Leng, Yue; Wainwright, Nick W. J.; Cappuccio, Francesco P.; Surtees, Paul G.; Hayat, Shabina; Luben, Robert; Brayne, Carol; Khaw, Kay-Tee

2014-01-01

Epidemiologic studies have reported conflicting results on the relationship between daytime napping and mortality risk, and there are few data on the potential association in the British population. We investigated the associations between daytime napping and all-cause or cause-specific mortality in the European Prospective Investigation Into Cancer-Norfolk study, a British population-based cohort study. Among the 16,374 men and women who answered questions on napping habits between 1998 and 2000, a total of 3,251 died during the 13-year follow-up. Daytime napping was associated with an increased risk of all-cause mortality (for napping less than 1 hour per day on average, hazard ratio = 1.14, 95% confidence interval: 1.02, 1.27; for napping 1 hour or longer per day on average, hazard ratio = 1.32, 95% confidence interval: 1.04, 1.68), independent of age, sex, social class, educational level, marital status, employment status, body mass index, physical activity level, smoking status, alcohol intake, depression, self-reported general health, use of hypnotic drugs or other medications, time spent in bed at night, and presence of preexisting health conditions. This association was more pronounced for death from respiratory diseases (for napping less than 1 hour, hazard ratio = 1.40, 95% confidence interval: 0.95, 2.05; for napping 1 hour or more, hazard ratio = 2.56, 95% confidence interval: 1.34, 4.86) and in individuals 65 years of age or younger. Excessive daytime napping might be a useful marker of underlying health risk, particularly of respiratory problems, especially among those 65 years of age or younger. Further research is required to clarify the nature of the observed association. PMID:24685532

Daytime napping and the risk of all-cause and cause-specific mortality: a 13-year follow-up of a British population.

PubMed

Leng, Yue; Wainwright, Nick W J; Cappuccio, Francesco P; Surtees, Paul G; Hayat, Shabina; Luben, Robert; Brayne, Carol; Khaw, Kay-Tee

2014-05-01

Epidemiologic studies have reported conflicting results on the relationship between daytime napping and mortality risk, and there are few data on the potential association in the British population. We investigated the associations between daytime napping and all-cause or cause-specific mortality in the European Prospective Investigation Into Cancer-Norfolk study, a British population-based cohort study. Among the 16,374 men and women who answered questions on napping habits between 1998 and 2000, a total of 3,251 died during the 13-year follow-up. Daytime napping was associated with an increased risk of all-cause mortality (for napping less than 1 hour per day on average, hazard ratio = 1.14, 95% confidence interval: 1.02, 1.27; for napping 1 hour or longer per day on average, hazard ratio = 1.32, 95% confidence interval: 1.04, 1.68), independent of age, sex, social class, educational level, marital status, employment status, body mass index, physical activity level, smoking status, alcohol intake, depression, self-reported general health, use of hypnotic drugs or other medications, time spent in bed at night, and presence of preexisting health conditions. This association was more pronounced for death from respiratory diseases (for napping less than 1 hour, hazard ratio = 1.40, 95% confidence interval: 0.95, 2.05; for napping 1 hour or more, hazard ratio = 2.56, 95% confidence interval: 1.34, 4.86) and in individuals 65 years of age or younger. Excessive daytime napping might be a useful marker of underlying health risk, particularly of respiratory problems, especially among those 65 years of age or younger. Further research is required to clarify the nature of the observed association.

Identification of the Viridicatumtoxin and Griseofulvin Gene Clusters from Penicillium aethiopicum

PubMed Central

Chooi, Yit-Heng; Cacho, Ralph; Tang, Yi

2010-01-01

SUMMARY Penicillium aethiopicum produces two structurally interesting and biologically active polyketides: the tetracycline-like viridicatumtoxin 1 and the classic antifungal agent griseofulvin 2. Here, we report the concurrent discovery of the two corresponding biosynthetic gene clusters (vrt and gsf) by 454 shotgun sequencing. Gene deletions confirmed two nonreducing PKSs (NRPKS), vrtA and gsfA, are required for the biosynthesis of 1 and 2, respectively. Both PKSs share similar domain architectures and lack a C-terminal thioesterase domain. We identified gsfI as the chlorinase involved in the biosynthesis of 2, as deletion of gsfI resulted in the accumulation of decholorogriseofulvin 3. Comparative analysis with the P. chrysogenum genome revealed that both clusters are embedded within conserved syntenic regions of P. aethiopicum chromosomes. Discovery of the vrt and gsf clusters provided the basis for genetic and biochemical studies of the pathways. PMID:20534346

Daytime napping and mortality from all causes, cardiovascular disease, and cancer: a meta-analysis of prospective cohort studies.

PubMed

Zhong, Guochao; Wang, Yi; Tao, TieHong; Ying, Jun; Zhao, Yong

2015-07-01

The association between daytime napping and mortality remains controversial. We conducted a meta-analysis to examine the associations between daytime napping and the risks of death from all causes, cardiovascular disease (CVD), and cancer. PubMed and Embase databases were searched through 19 September 2014. Prospective cohort studies that provided risk estimates of daytime napping and mortality were eligible for our meta-analysis. Two investigators independently performed study screening and data extraction. A random-effects model was used to estimate the combined effect size. Subgroup analyses were conducted to identify potential effect modifiers. Twelve studies, involving 130,068 subjects, 49,791 nappers, and 19,059 deaths, were included. Our meta-analysis showed that daytime napping was associated with an increased risk of death from all causes [n = 9 studies; hazard ratio (HR), 1.22; 95% confidence interval (CI), 1.14-1.31; I(2) = 42.5%]. No significant associations between daytime napping and the risks of death from CVD (n = 6 studies; HR, 1.20; 95% CI, 0.96-1.50; I(2) = 75.0%) and cancer (n = 4 studies; HR, 1.07; 95% CI, 0.99-1.15; I(2) = 8.9%) were found. There were no significant differences in risks of all-cause and CVD mortality between subgroups stratified by the prevalence of napping, follow-up duration, outcome assessment, age, and sex. Daytime napping is a predictor of increased all-cause mortality but not of CVD and cancer mortality. However, our findings should be treated with caution because of limited numbers of included studies and potential biases. Copyright © 2015. Published by Elsevier B.V.

MeSH key terms for validation and annotation of gene expression clusters

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

Rechtsteiner, A.; Rocha, L. M.

2004-01-01

Integration of different sources of information is a great challenge for the analysis of gene expression data, and for the field of Functional Genomics in general. As the availability of numerical data from high-throughput methods increases, so does the need for technologies that assist in the validation and evaluation of the biological significance of results extracted from these data. In mRNA assaying with microarrays, for example, numerical analysis often attempts to identify clusters of co-expressed genes. The important task to find the biological significance of the results and validate them has so far mostly fallen to the biological expert whomore » had to perform this task manually. One of the most promising avenues to develop automated and integrative technology for such tasks lies in the application of modern Information Retrieval (IR) and Knowledge Management (KM) algorithms to databases with biomedical publications and data. Examples of databases available for the field are bibliographic databases c ntaining scientific publications (e.g. MEDLINE/PUBMED), databases containing sequence data (e.g. GenBank) and databases of semantic annotations (e.g. the Gene Ontology Consortium and Medical Subject Headings (MeSH)). We present here an approach that uses the MeSH terms and their concept hierarchies to validate and obtain functional information for gene expression clusters. The controlled and hierarchical MeSH vocabulary is used by the National Library of Medicine (NLM) to index all the articles cited in MEDLINE. Such indexing with a controlled vocabulary eliminates some of the ambiguity due to polysemy (terms that have multiple meanings) and synonymy (multiple terms have similar meaning) that would be encountered if terms would be extracted directly from the articles due to differing article contexts or author preferences and background. Further, the hierarchical organization of the MeSH terms can illustrate the conceptuallfunctional relationships of genes

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

PubMed Central

Blin, Kai; Duddela, Srikanth; Krug, Daniel; Kim, Hyun Uk; Bruccoleri, Robert; Lee, Sang Yup; Fischbach, Michael A; Müller, Rolf; Wohlleben, Wolfgang; Breitling, Rainer; Takano, Eriko

2015-01-01

Abstract Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software. PMID:25948579

A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits

PubMed Central

2011-01-01

Background First identified in fruit flies with temperature-sensitive paralysis phenotypes, the Drosophila melanogaster TipE locus encodes four voltage-gated sodium (NaV) channel auxiliary subunits. This cluster of TipE-like genes on chromosome 3L, and a fifth family member on chromosome 3R, are important for the optional expression and functionality of the Para NaV channel but appear quite distinct from auxiliary subunits in vertebrates. Here, we exploited available arthropod genomic resources to trace the origin of TipE-like genes by mapping their evolutionary histories and examining their genomic architectures. Results We identified a remarkably conserved synteny block of TipE-like orthologues with well-maintained local gene arrangements from 21 insect species. Homologues in the water flea, Daphnia pulex, suggest an ancestral pancrustacean repertoire of four TipE-like genes; a subsequent gene duplication may have generated functional redundancy allowing gene losses in the silk moth and mosquitoes. Intronic nesting of the insect TipE gene cluster probably occurred following the divergence from crustaceans, but in the flour beetle and silk moth genomes the clusters apparently escaped from nesting. Across Pancrustacea, TipE gene family members have experienced intronic nesting, escape from nesting, retrotransposition, translocation, and gene loss events while generally maintaining their local gene neighbourhoods. D. melanogaster TipE-like genes exhibit coordinated spatial and temporal regulation of expression distinct from their host gene but well-correlated with their regulatory target, the Para NaV channel, suggesting that functional constraints may preserve the TipE gene cluster. We identified homology between TipE-like NaV channel regulators and vertebrate Slo-beta auxiliary subunits of big-conductance calcium-activated potassium (BKCa) channels, which suggests that ion channel regulatory partners have evolved distinct lineage-specific characteristics

Establishment of the Inducible Tet-On System for the Activation of the Silent Trichosetin Gene Cluster in Fusarium fujikuroi