Comparative Genomics of 9 Novel Paenibacillus Larvae Bacteriophages

American Foulbrood Disease, caused by the bacterium Paenibacillus larvae, is one of the most destructive diseases of the honeybee, Apis mellifera. Our group recently published the sequences of 9 new phages with the ability to infect and lyse P. larvae. Here, we characterize the genomes of these P. larvae phages, compare them to each other and to other sequenced P. larvae phages, and putatively identify protein function. The phage genomes are 38–45 kb in size and contain 68–86 genes, most of which appear to be unique to P. larvae phages. We classify P. larvae phages into 2 main clusters and one singleton based on nucleotide sequence identity. Three of the new phages show sequence similarity to other sequenced P. larvae phages, while the remaining 6 do not. We identified functions for roughly half of the P. larvae phage proteins, including structural, assembly, host lysis, DNA replication/metabolism, regulatory, and host-related functions. Structural and assembly proteins are highly conserved among our phages and are located at the start of the genome. DNA replication/metabolism, regulatory, and host-related proteins are located in the middle and end of the genome, and are not conserved, with many of these genes found in some of our phages but not others. All nine phages code for a conserved N-acetylmuramoyl-L-alanine amidase. Comparative analysis showed the phages use the “cohesive ends with 30 overhang” DNA packaging strategy. This work is the first in-depth study of P. larvae phage genomics, and serves as a marker for future work in this area

New iron tetrazolate frameworks : synthesis temperature effect, thermal behaviour, Mössbauer and magnetic studies

The exploration of the FeF3/FeF2-Hamtetraz-HF system in dimethylformamide by solvothermal synthesis evidences two isostructural 3D hybrid fluoroferrates. They are prepared from the same starting mixture at two different synthesis temperatures: 120 °C for [Hdma]·(Fe4IIFeIIIF8(H2O)2(amtetraz)4) (1) and 140 °C for [Hdma]1.5·(Fe4.5IIFe0.5IIIF7(H2O)(HCOO)(amtetraz)4) (2). Both compounds are characterized by single crystal X-ray diffraction, X-ray thermodiffraction, TGA analysis, Mössbauer spectrometry and SQUID magnetometry. They crystallize in the monoclinic system and are built from two distinct chains connected by aminotetrazolate anions. The first chain ∞(FeIIFN4) is common to 1 and 2 and can be found in numerous fluorides. In the second chain ∞(Fe3X12) (X = F, N, O), iron cations adopt both valence states Fe(II)/Fe(III). The hydrolysis of DMF implies the formation of a [Hdma]+ cation and a (HCOO)− anion. The presence of Fe3+ in both phases is evidenced by 57Fe Mössbauer spectrometry. The magnetic properties are studied and two transitions from a paramagnetic regime to a long range ordered state below 30 K and 5 K are identified.PostprintPeer reviewe

Sleep characteristics and health-related quality of life in 9- to 11-year-old children from 12 countries

Introduction: Previous studies have linked short sleep duration, poor sleep quality, and late sleep timing with lower health-related quality of life (HRQoL) in children. However, almost all studies relied solely on self-reported sleep information, and most studies were conducted in high-income countries. To address these gaps, we studied both device-measured and self-reported sleep characteristics in relation to HRQoL in a sample of children from 12 countries that vary widely in terms of economic and human development. Methods: The study sample included 6,626 children aged 9-11 years from Australia, Brazil, Canada, China, Colombia, Finland, India, Kenya, Portugal, South Africa, the United Kingdom, and the United States. Waist-worn actigraphy was used to measure total sleep time, bedtime, wake-up time, and sleep efficiency on both weekdays and weekends. Children also reported ratings of sleep quantity and quality. HRQoL was measured by the KIDSCREEN-10 survey. Multilevel regression models were used to determine the relationships between sleep characteristics and HRQoL. Results: Results showed considerable variation in sleep characteristics, particularly duration and timing, across study sites. Overall, we found no association between device-measured total sleep time, sleep timing or sleep efficiency, and HRQoL. In contrast, self-reported ratings of poor sleep quantity and quality were associated with HRQoL. Conclusions: Self-reported, rather than device-based, measures of sleep are related to HRQoL in children. The discrepancy related to sleep assessment methods highlights the importance of considering both device-measured and self-reported measures of sleep in understanding its health effects

Proportion of children meeting recommendations for 24-hour movement guidelines and associations with adiposity in a 12-country study

Background: The Canadian 24-h movement guidelines were developed with the hope of improving health and future health outcomes in children and youth. The purpose of this study was to evaluate adherence to the 3 recommendations most strongly associated with health outcomes in new 24-h movement guidelines and their relationship with adiposity (obesity and body mass index z-score) across countries participating in the International Study of Childhood Obesity, Lifestyle and the Environment (ISCOLE). Methods: Cross-sectional results were based on 6128 children aged 9-11years from the 12 countries of ISCOLE. Sleep duration and moderate-to-vigorous physical activity (MVPA) were assessed using accelerometry. Screen time was measured through self-report. Body weight and height were measured. Body mass index (BMI, kgm2) was calculated, and BMI z-scores were computed using age- and sex-specific reference data from the World Health Organization. Obesity was defined as a BMI z-score>+2 SD. Meeting the overall 24-h movement guidelines was defined as: 9 to 11h/night of sleep, ≤2h/day of screen time, and at least 60min/day of MVPA. Age, sex, highest parental education and unhealthy diet pattern score were included as covariates in statistical models. Associations between meeting vs. not meeting each single recommendation (and combinations) with obesity were assessed with odds ratios calculated using generalized linear mixed models. A linear mixed model was used to examine the differences in BMI z-scores between children meeting vs. not meeting the different combinations of recommendations. Results: The global prevalence of children meeting the overall recommendations (all three behaviors) was 7%, with children from Australia and Canada showing the highest adherence (15%). Children meeting the three recommendations had lower odds ratios for obesity compared to those meeting none of the recommendations (OR=0.28, 95% CI 0.18-0.45). Compared to not meeting the 24-h movement recommendations either independently or combined, meeting them was significantly associated with a lower BMI z-score. Whenever the MVPA recommendation was included in the analysis the odds ratios for obesity were lower. Conclusions: For ISCOLE participants meeting these 3 healthy movement recommendations the odds ratios of being obese or having high BMI z-scores were lower. However, only a small percentage of children met all recommendations. Future efforts should aim to find promising ways to increase daily physical activity, reduce screen time, and ensure an adequate night's sleep in children. Trial registration: The International Study of Childhood Obesity, Lifestyle and the Environment (ISCOLE) was registered at ClinicalTrials.gov (Identifier NCT01722500) (October 29, 2012)

Regulation of death and differentiation of embryonic stem cells

Embryonic stem cells (ESCs) possess two notable traits: self-renewal, the ability to proliferate without senescence or quiescence, and pluripotency, the capacity to differentiate into nearly any cell type in the body. Whereas the transcriptional regulatory circuitry of self-renewal has been extensively characterized, the mechanisms underlying proper differentiation are less well known. My dissertation focuses on two pressing questions regarding the molecular regulation of cell fate. First, during differentiation, ~30% of ESCs undergo apoptosis, likely to cull cells that resist differentiation and thus allow the overall cell population to differentiate successfully. However, upstream regulators that control the endogenous rate of apoptosis are not known. Second, although it has been observed qualitatively that selecting appropriate seeding densities for cell culture is critical for proper differentiation, the effects of seeding density on global gene expression and cell fate specification have not yet been quantitatively measured. To address these questions, first, I investigate the dependence of mouse ESCs (mESCs) on the Hippo transcriptional effector Yap1 during differentiation. I show that genetic ablation of Yap1 substantially augments the rate of apoptosis during differentiation, but not self-renewal, regardless of intended cell fate. Mechanistically, I demonstrate that Yap1 regulates the transcription of anti- and pro-apoptotic genes. The absence of Yap1 results in heightened mitochondrial priming, leading to elevated activation of the endogenous apoptotic cascade. Finally, I demonstrate that ectopic expression of pro- and anti-apoptotic factors as well as the Yap1 paralog Taz allow for modulation of apoptosis during differentiation. To quantitatively address the effect of seeding density on global gene expression, I perform transcriptomic analysis of mESCs during both self-renewal and differentiation over a gradient of seeding densities. I show that a simple change in seeding density is sufficient to alter the expression of thousands of genes, including those involved in cell fate specification. I demonstrate that low seeding density facilitates more efficient mESC differentiation during LIF withdrawal due to enhanced upregulation of lineage markers. Notably, I uncover three transcriptional regulators (β-catenin, Tcf7l1, and Esrrb) that activate or repress many of these density-sensitive genes. Perturbation of a single density regulator is sufficient to shift gene expression patterns from a low density profile to a high density-like profile, and vice versa. My findings in this dissertation highlight the contributions of several transcription factors and co-regulators to fate specification in the context of programmed cell death and seeding density. Taken together, this work illustrates several molecular mechanisms of the regulation of mESC differentiationCellular and Molecular Biolog