Genomic variation and biogeography of Antarctic haloarchaea

© 2018 The Author(s). Background: The genomes of halophilic archaea (haloarchaea) often comprise multiple replicons. Genomic variation in haloarchaea has been linked to viral infection pressure and, in the case of Antarctic communities, can be caused by intergenera gene exchange. To expand understanding of genome variation and biogeography of Antarctic haloarchaea, here we assessed genomic variation between two strains of Halorubrum lacusprofundi that were isolated from Antarctic hypersaline lakes from different regions (Vestfold Hills and Rauer Islands). To assess variation in haloarchaeal populations, including the presence of genomic islands, metagenomes from six hypersaline Antarctic lakes were characterised. Results: The sequence of the largest replicon of each Hrr. lacusprofundi strain (primary replicon) was highly conserved, while each of the strains' two smaller replicons (secondary replicons) were highly variable. Intergenera gene exchange was identified, including the sharing of a type I-B CRISPR system. Evaluation of infectivity of an Antarctic halovirus provided experimental evidence for the differential susceptibility of the strains, bolstering inferences that strain variation is important for modulating interactions with viruses. A relationship was found between genomic structuring and the location of variation within replicons and genomic islands, demonstrating that the way in which haloarchaea accommodate genomic variability relates to replicon structuring. Metagenome read and contig mapping and clustering and scaling analyses demonstrated biogeographical patterning of variation consistent with environment and distance effects. The metagenome data also demonstrated that specific haloarchaeal species dominated the hypersaline systems indicating they are endemic to Antarctica. Conclusion: The study describes how genomic variation manifests in Antarctic-lake haloarchaeal communities and provides the basis for future assessments of Antarctic regional and global biogeography of haloarchaea

Factors associated with food safety knowledge and practices among meat handlers in Bangladesh: a cross-sectional study.

Background Food handlers can play a vital role into reducing foodborne diseases by adopting appropriate food handling and sanitation practices in working plants. This study aimed to assess the factors associated with food safety knowledge and practices among meat handlers who work at butcher shops in Bangladesh. Methods A cross-sectional study was conducted among 300 meat handlers from January to March, 2021. Data were collected through in-person interviews using a structured questionnaire. The questionnaire consisted of three parts; socio-demographic characteristics, assessments of food safety knowledge, and food safety practices. A multiple logistic regression model was used to identify the factors associated with food safety knowledge and practices. Results Only 20% [95% confidence interval, (CI) 15.7–24.7] and 16.3% (95% CI 12.3–20.7) of the respondents demonstrated good levels of food safety knowledge and practices, respectively. The factors associated with good levels of food safety knowledge were: having a higher secondary education [adjusted odds ratio (AOR) = 4.57, 95% CI 1.11–18.76], income above 25,000 BDT/month (AOR = 10.52, 95% CI 3.43–32.26), work experience of > 10 years (AOR = 9.31, 95% CI 1.92–45.09), ≥ 8 h per day of work (AOR = 6.14, 95% CI 2.69–13.10), employed on a daily basis (AOR = 4.05, 95% CI 1.16–14.14), and having food safety training (AOR = 8.98 95% CI 2.16–37.32). Good food safety knowledge (AOR = 5.68, 95% CI 2.33–13.87) and working ≥ 8 h per day (AOR = 8.44, 95% CI 3.11–22.91) were significantly associated with a good level of food safety practice. Conclusions Poor knowledge and practices regarding food safety were found among Bangladeshi meat handlers. Findings may help public health professionals and practitioners develop targeted strategies to improve food safety knowledge and practices among this population. Such strategies may include education and sensitization on good food safety practices

First Year Physical Activity Findings From Turn up the Heat (Healthy Eating and Activity Time) in Summer Day Camps

Background Summer day camps (SDCs) serve 14 million children yearly in the U.S. and aim to provide participating children with 60 minutes of moderate-to-vigorous physical activity (MVPA). This study evaluated an intervention designed to increase the percent of children meeting this MVPA guideline. Design Two-group, pre-post quasi-experimental. Setting/Participants Twenty SDCs serving 1,830 children aged 5–12 years were assigned to MVPA intervention (n = 10) or healthy eating attention control (n = 10). Intervention The STEPs (Strategies to Enhance Practice) intervention is a capacity-building approach grounded in the Theory of Expanded, Extended and Enhanced Opportunities. Camp leaders and staff receive training to expand (e.g., introduction of activity breaks/active field trips), extend (e.g., schedule minimum of 3 hours/day for PA opportunities), and enhance (e.g., maximize MVPA children accumulate during schedule activity) activity opportunities. Camps in the comparison condition received support for improving the types of foods/beverages served. Main outcome measures Percent of children accumulating the 60min/d MVPA guideline at baseline (summer 2015) and post-test (summer 2016) measured via wrist-accelerometry. Results Multilevel logistic regression conducted fall 2016 indicated boys and girls attending intervention SDCs were 2.04 (95CI = 1.10,3.78) and 3.84 (95CI = 2.02,7.33) times more likely to meet the 60min/d guideline compared to boys and girls attending control SDCs, respectively. This corresponded to increases of +10.6% (78–89%) and +12.6% (69–82%) in the percentage of boys and girls meeting the guideline in intervention SDCs, respectively. Boys in comparison SDCs increased by +1.6% (81–83%) and girls decreased by -5.5% (76–71%). Process data indicated intervention SDCs successfully extended and enhanced PA opportunities, but were unable to expand PA opportunities, compared to control SDCs. Conclusions Although substantial proportions of children met the MVPA guideline at baseline, no SDCs ensured all children met the guideline. This intervention demonstrated that, with support, SDCs can help all children in attendance to accumulate their daily recommended 60min MVPA. Trial registration ClinicalTrials.gov NCT0216180

Unexpected host dependency of Antarctic Nanohaloarchaeota

In hypersaline environments, Nanohaloarchaeota (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaeota [DPANN] superphylum) are thought to be free-living microorganisms. We report cultivation of 2 strains of Antarctic Nanohaloarchaeota and show that they require the haloarchaeon Halorubrum lacusprofundi for growth. By performing growth using enrichments and fluorescence-activated cell sorting, we demonstrated successful cultivation of Candidatus Nanohaloarchaeum antarcticus, purification of Ca. Nha. antarcticus away from other species, and growth and verification of Ca. Nha. antarcticus with Hrr. lacusprofundi; these findings are analogous to those required for fulfilling Koch’s postulates. We use fluorescent in situ hybridization and transmission electron microscopy to assess cell structures and interactions; metagenomics to characterize enrichment taxa, generate metagenome assembled genomes, and interrogate Antarctic communities; and proteomics to assess metabolic pathways and speculate about the roles of certain proteins. Metagenome analysis indicates the presence of a single species, which is endemic to Antarctic hypersaline systems that support the growth of haloarchaea. The presence of unusually large proteins predicted to function in attachment and invasion of hosts plus the absence of key biosynthetic pathways (e.g., lipids) in metagenome assembled genomes of globally distributed Nanohaloarchaeota indicate that all members of the lineage have evolved as symbionts. Our work expands the range of archaeal symbiotic lifestyles and provides a genetically tractable model system for advancing understanding of the factors controlling microbial symbiotic relationships

Physical activity outcomes in afterschool programs: A group randomized controlled trial

Afterschool programs (ASPs) across the US are working towards achieving the standard of all children accumulating 30minutes of moderate-to-vigorous physical activity (MVPA) during program time. This study describes the two-year impact of an intervention designed to assist ASPs meeting the 30min/d MVPA standard

Identifying causes of low persistence of perennial ryegrass (Lolium perenne) dairy pasture using the Basic Grassland model (BASGRA)

Recent years have seen a decline in herbage production and tiller populations in New Zealand's perennial ryegrass (Lolium perenne) dairy pastures. One hypothesis is that modern genotypes are less suited to the warmer, drier weather experienced under changing climate patterns. In this study, a combination of long‐term trial data (2011–2017) and a process‐based pasture model (BASGRA) was used to explore the causes and possible mitigation of the observed production and population loss at three sites (dryland sites in Northland and Waikato and an irrigated site in Canterbury). Bayesian calibration was used to identify the model parameter sets that were consistent with the trial data and to identify differences in plant morphology and responses between sites. The model successfully simulated the observed differences in tiller numbers between the dryland sites, where populations and production declined rapidly after the second year and the irrigated site where populations and production were maintained. Analysis of the model calibrations along with preliminary scenario simulations suggests that increased tiller mortality associated with drought was the main cause of persistence failure at the dryland sites and that decreasing grazing pressure or breeding for tolerance to higher temperatures may not be successful in preventing this

The theory of expanded, extended, and enhanced opportunities for youth physical activity promotion

Background Physical activity interventions targeting children and adolescents (≤18 years) often focus on complex intra- and inter-personal behavioral constructs, social-ecological frameworks, or some combination of both. Recently published meta-analytical reviews and large-scale randomized controlled trials have demonstrated that these intervention approaches have largely produced minimal or no improvements in young people\u27s physical activity levels. Discussion In this paper, we propose that the main reason for previous studies\u27 limited effects is that fundamental mechanisms that lead to change in youth physical activity have often been overlooked or misunderstood. Evidence from observational and experimental studies is presented to support the development of a new theory positing that the primary mechanisms of change in many youth physical activity interventions are approaches that fall into one of the following three categories: (a) the expansion of opportunities for youth to be active by the inclusion of a new occasion to be active, (b) the extension of an existing physical activity opportunity by increasing the amount of time allocated for that opportunity, and/or (c) the enhancement of existing physical activity opportunities through strategies designed to increase physical activity above routine practice. Their application and considerations for intervention design and interpretation are presented. Summary The utility of these mechanisms, referred to as the Theory of Expanded, Extended, and Enhanced Opportunities (TEO), is demonstrated in their parsimony, logical appeal, support with empirical evidence, and the direct and immediate application to numerous settings and contexts. The TEO offers a new way to understand youth physical activity behaviors and provides a common taxonomy by which interventionists can identify appropriate targets for interventions across different settings and contexts. We believe the formalization of the TEO concepts will propel them to the forefront in the design of future intervention studies and through their use, lead to a greater impact on youth activity behaviors than what has been demonstrated in previous studies

Moving forward with backwards compatibility: Translating wrist accelerometer data

Purpose: To provide a means for calibrating raw acceleration data from wrist-worn accelerometers in relation to past estimates of children’s moderate-to-vigorous physical activity (MVPA) from a range of cut-points applied to hip-worn ActiGraph data. Methods: This is a secondary analysis of three studies with concurrent 7-day accelerometer wear at the wrist (GENEActiv) and hip (ActiGraph) in 238 children aged 9-12 years. The time spent above acceleration (ENMO) thresholds of 100, 150, 200, 250, 300, 350 and 400 mg from wrist acceleration data (<5 s epoch) was calculated for comparison to MVPA estimated from widely used children’s hip-worn ActiGraph MVPA cut-points (Freedson/Trost 1100 counts per minute (cpm); Pate 1680 cpm; Evenson 2296 cpm; Puyau 3200 cpm) with epochs of <5, 15 and 60 s. Results: The optimal ENMO thresholds for alignment with MVPA estimates from ActiGraph cut-points determined from 70% of the sample and cross-validated with the remaining 30% were: Freedson/Trost = ENMO 150+ mg, irrespective of ActiGraph epoch (ICC>0.65); Pate = ENMO 200+ mg, irrespective of ActiGraph epoch (ICC>0.67); Evenson = ENMO 250+ mg for 0.69) and ENMO 300+ mg for 60 s epochs (ICC=0.73); Puyau = ENMO 300+ mg for <5 s epochs (ICC=0.73), ENMO 350+ mg for 15 s epochs (ICC=0.73), ENMO 400+ mg for 60 s epochs (ICC=0.65). Agreement was robust with cross-validation ICCs=0.62-0.71 and means within ?7.8?±4.9% of MVPA estimates from ActiGraph cut-points, except Puyau 60 s epochs (ICC=0.42). Conclusion: Incremental ENMO thresholds enable children’s acceleration data measured at the wrist to be simply and directly compared, at a group level, to past estimates of MVPA from hip-worn ActiGraphs across a range of cut-points

Children’s moderate-to-vigorous physical activity on weekdays versus weekend days: a multi-country analysis

Abstract: Purpose: The Structured Days Hypothesis (SDH) posits that children’s behaviors associated with obesity – such as physical activity – are more favorable on days that contain more ‘structure’ (i.e., a pre-planned, segmented, and adult-supervised environment) such as school weekdays, compared to days with less structure, such as weekend days. The purpose of this study was to compare children’s moderate-to-vigorous physical activity (MVPA) levels on weekdays versus weekend days using a large, multi-country, accelerometer-measured physical activity dataset. Methods: Data were received from the International Children’s Accelerometer Database (ICAD) July 2019. The ICAD inclusion criteria for a valid day of wear, only non-intervention data (e.g., baseline intervention data), children with at least 1 weekday and 1 weekend day, and ICAD studies with data collected exclusively during school months, were included for analyses. Mixed effects models accounting for the nested nature of the data (i.e., days within children) assessed MVPA minutes per day (min/day MVPA) differences between weekdays and weekend days by region/country, adjusted for age, sex, and total wear time. Separate meta-analytical models explored differences by age and country/region for sex and child weight-status. Results/findings: Valid data from 15 studies representing 5794 children (61% female, 10.7 ± 2.1 yrs., 24% with overweight/obesity) and 35,263 days of valid accelerometer data from 5 distinct countries/regions were used. Boys and girls accumulated 12.6 min/day (95% CI: 9.0, 16.2) and 9.4 min/day (95% CI: 7.2, 11.6) more MVPA on weekdays versus weekend days, respectively. Children from mainland Europe had the largest differences (17.1 min/day more MVPA on weekdays versus weekend days, 95% CI: 15.3, 19.0) compared to the other countries/regions. Children who were classified as overweight/obese or normal weight/underweight accumulated 9.5 min/day (95% CI: 6.9, 12.2) and 10.9 min/day (95% CI: 8.3, 13.5) of additional MVPA on weekdays versus weekend days, respectively. Conclusions: Children from multiple countries/regions accumulated significantly more MVPA on weekdays versus weekend days during school months. This finding aligns with the SDH and warrants future intervention studies to prioritize less-structured days, such as weekend days, and to consider providing opportunities for all children to access additional opportunities to be active