Differences in size between first and replacement clutches match the seasonal decline in single clutches in Tree Swallows Tachycineta bicolor

© 2016 British Ornithologists' UnionThe seasonal decline in clutch size in birds can be a response to the environmentally conditioned decrease in prospects for offspring or a consequence of a lower physical ability of late-breeding females. To find out which of the explanations apply in Tree Swallows Tachycineta bicolor, we assessed whether replacement clutch size in this species is affected by an individual female's ability to lay a certain number of eggs. To do this, we measured the decline in clutch size as a function of laying date between first and replacement clutches in individuals that re-nested following natural failure, and compared this with the rate of decline in clutch size with laying date for Tree Swallows that laid only a single clutch in that season. Additionally, we assessed whether the clutch size and the rate of its seasonal decline varied across years. We accounted for the truncated and under-dispersed nature of clutch size data by using a Bayesian approach in the analysis. We found little variation in the rate of clutch size decline across years at our breeding site. Accounting for this seasonal decline in clutch size, mean clutch size was similar between single-time breeding females and those that laid replacement clutches, implying that the number of eggs laid on the second attempt by female Tree Swallows is determined by laying date, rather than by the female's physical ability to produce a clutch of a certain size

Intuitive Visualization and Analysis of Multi-Omics Data and Application to Escherichia coli Carbon Metabolism

Combinations of ‘omics’ investigations (i.e, transcriptomic, proteomic, metabolomic and/or fluxomic) are increasingly applied to get comprehensive understanding of biological systems. Because the latter are organized as complex networks of molecular and functional interactions, the intuitive interpretation of multi-omics datasets is difficult. Here we describe a simple strategy to visualize and analyze multi-omics data. Graphical representations of complex biological networks can be generated using Cytoscape where all molecular and functional components could be explicitly represented using a set of dedicated symbols. This representation can be used i) to compile all biologically-relevant information regarding the network through web link association, and ii) to map the network components with multi-omics data. A Cytoscape plugin was developed to increase the possibilities of both multi-omic data representation and interpretation. This plugin allowed different adjustable colour scales to be applied to the various omics data and performed the automatic extraction and visualization of the most significant changes in the datasets. For illustration purpose, the approach was applied to the central carbon metabolism of Escherichia coli. The obtained network contained 774 components and 1232 interactions, highlighting the complexity of bacterial multi-level regulations. The structured representation of this network represents a valuable resource for systemic studies of E. coli, as illustrated from the application to multi-omics data. Some current issues in network representation are discussed on the basis of this work

Personal endotoxin exposure in a panel study of school children with asthma

<p>Abstract</p> <p>Background</p> <p>Endotoxin exposure has been associated with asthma exacerbations and increased asthma prevalence. However, there is little data regarding personal exposure to endotoxin in children at risk, or the relation of personal endotoxin exposure to residential or ambient airborne endotoxin. The relation between personal endotoxin and personal air pollution exposures is also unknown.</p> <p>Methods</p> <p>We characterized personal endotoxin exposures in 45 school children with asthma ages 9-18 years using 376 repeated measurements from a PM_2.5active personal exposure monitor. We also assayed endotoxin in PM_2.5samples collected from ambient regional sites (N = 97 days) and from a subset of 12 indoor and outdoor subject home sites (N = 109 and 111 days, respectively) in Riverside and Whittier, California. Endotoxin was measured using the Limulus Amoebocyte Lysate kinetic chromogenic assay. At the same time, we measured personal, home and ambient exposure to PM_2.5mass, elemental carbon (EC), and organic carbon (OC). To assess exposure relations we used both rank correlations and mixed linear regression models, adjusted for personal temperature and relative humidity.</p> <p>Results</p> <p>We found small positive correlations of personal endotoxin with personal PM_2.5EC and OC, but not personal PM_2.5mass or stationary site air pollutant measurements. Outdoor home, indoor home and ambient endotoxin were moderately to strongly correlated with each other. However, in mixed models, personal endotoxin was not associated with indoor home or outdoor home endotoxin, but was associated with ambient endotoxin. Dog and cat ownership were significantly associated with increased personal but not indoor endotoxin.</p> <p>Conclusions</p> <p>Daily fixed site measurements of endotoxin in the home environment may not predict daily personal exposure, although a larger sample size may be needed to assess this. This conclusion is relevant to short-term exposures involved in the acute exacerbation of asthma.</p

Extending Epigenesis: From Phenotypic Plasticity to the Bio-Cultural Feedback

The paper aims at proposing an extended notion of epigenesis acknowledging an actual causal import to the phenotypic dimension for the evolutionary diversification of life forms. Section 1 offers introductory remarks on the issue of epigenesis contrasting it with ancient and modern preformationist views. In Section 2 we propose to intend epigenesis as a process of phenotypic formation and diversification a) dependent on environmental influences, b) independent of changes in the genomic nucleotide sequence, and c) occurring during the whole life span. Then, Section 3 focuses on phenotypic plasticity and offers an overview of basic properties (like robustness, modularity and degeneracy) that allows biological systems to be evolvable – i.e. to have the potentiality of producing phenotypic variation. Successively (Section 4), the emphasis is put on environmentally-induced modification in the regulation of gene expression giving rise to phenotypic variation and diversification. After some brief considerations on the debated issue of epigenetic inheritance (Section 5), the issue of culture (kept in the background of the preceding sections) is considered. The key point is that, in the case of humans and of the evolutionary history of the genus Homo at least, the environment is also, importantly, the cultural environment. Thus, Section 6 argues that a bio-cultural feedback should be acknowledged in the “epigenic” processes leading to phenotypic diversification and innovation in Homo evolution. Finally, Section 7 introduces the notion of “cultural neural reuse”, which refers to phenotypic/neural modifications induced by specific features of the cultural environment that are effective in human cultural evolution without involving genetic changes. Therefore, cultural neural reuse may be regarded as a key instance of the bio-cultural feedback and ultimately of the extended notion of epigenesis proposed in this work

Children’s residential exposure to selected allergens and microbial indicators: endotoxins and (1→3)-β-D-glucans

Objectives: The study was aimed at assessment of exposure to endotoxins, (1→3)-β-D-glucans and mite, cockroach, cat, dog allergens present in settled dust in premises of children as agents which may be significantly correlated with the occurrence of allergic symptoms and diseases in children. Materials and Methods: The study covered 50 homes of one- or two-year-old children in Poland. Samples of settled dust were taken from the floor and the child's bed. The levels of (1→3)-β-D-glucans (floor), endotoxins (floor) and allergens of mite, cat, dog and cockroach (floor and bed) were analyzed. Results: Average geometric concentrations (geometric standard deviation) of endotoxins, (1→3)-β-D-glucans, Der p1, Fel d1, Can f1 and Bla g1 in children homes were on the floor 42 166.0 EU/g (3.2), 20 478.4 ng/g (2.38), 93.9 ng/g (6.58), 119.8 ng/g (13.0), 288.9 ng/g (3.4), 0.72 U/g (4.4) and in their beds (only allergens) 597.8 ng/g (14.2), 54.1 ng/g (4.4), 158.6 ng/g (3.1) 0.6 U/g (2.9), respectively. When the floor was covered with the carpet, higher concentrations of endotoxins, (1→3)-β-D-glucans and allergens (each type) were found in the settled dust (p < 0.05). The trend was opposite in case of allergens (except dog) analyzed from bed dust and significantly higher concentrations were found in the rooms with smooth floor (p < 0.05). Conclusions: Among the analyzed factors only the type of floor significantly modified both the level of biological indicators and allergens. The results of this study could be the base for verifying a hypothesis that carpeting may have a protective role against high levels of cockroach, dog and cat allergens

Occupation and SARS-CoV-2 infection risk among 108 960 workers during the first pandemic wave in Germany

OBJECTIVE: The aim of this study was to identify the occupational risk for a SARS-CoV-2 infection in a nationwide sample of German workers during the first wave of the COVID-19 pandemic (1 February-31 August 2020). METHODS: We used the data of 108 960 workers who participated in a COVID follow-up survey of the German National Cohort (NAKO). Occupational characteristics were derived from the German Classification of Occupations 2010 (Klassifikation der Berufe 2010). PCR-confirmed SARS-CoV-2 infections were assessed from self-reports. Incidence rates (IR) and incidence rate ratios (IRR) were estimated using robust Poisson regression, adjusted for person-time at risk, age, sex, migration background, study center, working hours, and employment relationship. RESULTS: The IR was 3.7 infections per 1000 workers [95% confidence interval (CI) 3.3-4.1]. IR differed by occupational sector, with the highest rates observed in personal (IR 4.8, 95% CI 4.0-5.6) and business administration (IR 3.4, 95% CI 2.8-3.9) services and the lowest rates in occupations related to the production of goods (IR 2.0, 95% CI 1.5-2.6). Infections were more frequent among essential workers compared with workers in non-essential occupations (IRR 1.95, 95% CI 1.59-2.40) and among highly skilled compared with skilled professions (IRR 1.36, 95% CI 1.07-1.72). CONCLUSIONS: The results emphasize higher infection risks in essential occupations and personal-related services, especially in the healthcare sector. Additionally, we found evidence that infections were more common in higher occupational status positions at the beginning of the pandemic

EAACI position paper on occupational rhinitis

The present document is the result of a consensus reached by a panel of experts from European and non-European countries on Occupational Rhinitis (OR), a disease of emerging relevance which has received little attention in comparison to occupational asthma. The document covers the main items of OR including epidemiology, diagnosis, management, socio-economic impact, preventive strategies and medicolegal issues. An operational definition and classification of OR tailored on that of occupational asthma, as well as a diagnostic algorithm based on steps allowing for different levels of diagnostic evidence are proposed. The needs for future research are pointed out. Key messages are issued for each item