Classification and function of small open reading frames

Small open reading frames (smORFs) of 100 codons or fewer are usually - if arbitrarily - excluded from proteome annotations. Despite this, the genomes of many metazoans, including humans, contain millions of smORFs, some of which fulfil key physiological functions. Recently, the transcriptome of Drosophila melanogaster was shown to contain thousands of smORFs of different classes that actively undergo translation, which produces peptides of mostly unknown function. Here, we present a comprehensive analysis of smORFs in flies, mice and humans. We propose the existence of several functional classes of smORFs, ranging from inert DNA sequences to transcribed and translated cis-regulators of translation and peptides with a propensity to function as regulators of membrane-associated proteins, or as components of ancient protein complexes in the cytoplasm. We suggest that the different smORF classes could represent steps in gene, peptide and protein evolution. Our analysis introduces a distinction between different peptide-coding classes of smORFs in animal genomes, and highlights the role of model organisms for the study of small peptide biology in the context of development, physiology and human disease

Global urban environmental change drives adaptation in white clover.

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale

Exploratory behavior is linked to stress physiology and social network centrality in free-living house finches (Haemorhous mexicanus)

Animal personality has been linked to individual variation in both stress physiology and social behaviors, but few studies have simultaneously examined covariation between personality traits, stress hormone levels, and behaviors in free-living animals. We investigated relationships between exploratory behavior (one aspect of animal personality), stress physiology, and social and foraging behaviors in wild house finches (Haemorhous mexicanus). We conducted novel environment assays after collecting samples of baseline and stress-induced plasma corticosterone concentrations from a subset of house finches. We then fitted individuals with Passive Integrated Transponder tags and monitored feeder use and social interactions at radio-frequency identification equipped bird feeders. First, we found that individuals with higher baseline corticosterone concentrations exhibit more exploratory behaviors in a novel environment. Second, more exploratory individuals interacted with more unique conspecifics in the wild, though this result was stronger for female than for male house finches. Third, individuals that were quick to begin exploring interacted more frequently with conspecifics than slow-exploring individuals. Finally, exploratory behaviors were unrelated to foraging behaviors, including the amount of time spent on bird feeders, a behavior previously shown to be predictive of acquiring a bacterial disease that causes annual epidemics in house finches. Overall, our results indicate that individual differences in exploratory behavior are linked to variation in both stress physiology and social network traits in free-living house finches. Such covariation has important implications for house finch ecology, as both traits can contribute to fitness in the wild

Design of a RCT evaluating the (cost-) effectiveness of a lifestyle intervention for male construction workers at risk for cardiovascular disease: the Health under Construction study

<p>Abstract</p> <p>Background</p> <p>Of all workers in Dutch construction industry, 20% has an elevated risk of cardiovascular disease (CVD). A major risk factor for CVD risk is an unhealthy lifestyle. The aim of our study is to design a lifestyle intervention for construction workers with an elevated CVD risk, and to evaluate its (cost-) effectiveness.</p> <p>Methods/Design</p> <p>In a RCT, 692 participants will be randomised to either the control or the intervention group. The control group will receive usual care. For the intervention group, a lifestyle intervention has been designed based on interviews and current literature. The intervention will last 6 months and will comprise 3 face-to-face and 4 telephone contacts, consisting of individual counselling aimed at increasing daily physical activity (PA) and improving dietary behaviour, and/or smoking cessation. Counselling will take place at the Occupational Health Service (OHS), and will be done according to motivational interviewing (MI). Additional written information about healthy lifestyle will also be provided to those in the intervention group. At baseline, after 6 and after 12 months, measurements will take place. Primary outcome variables will be the lifestyle behaviours of concern, i.e. daily PA, dietary intake, and smoking status. Secondary outcome variables will be body mass index (BMI), systolic and diastolic blood pressure, total and HDL blood cholesterol, Hba1c and cardio-respiratory fitness (CRF). Sickness absenteeism and cost-effectiveness will be assessed as well. Multilevel analysis will be performed to compare all outcome measures between the intervention group and the control group.</p> <p>Discussion</p> <p>By improving lifestyle, CVD risk may be lowered, yielding benefits for both employee and employer. If proven effective, this lifestyle intervention will be implemented on a larger scale within the Occupational Health Services in construction industry.</p> <p>Trial registration</p> <p>Current Controlled Trials ISRCTN60545588</p