A bird's-eye view of chromosomic evolution in the Class Aves

Birds (Aves) are the most speciose of terrestrial vertebrates, displaying Class-specific characteristics yet incredible external phenotypic diversity. Critical to agriculture and as model organisms, birds have adapted to many habitats. The only extant examples of dinosaurs, birds emerged ~150 mya and >10% are currently threatened with extinction. This review is a comprehensive overview of avian genome (“chromosomic”) organization research based mostly on chromosome painting and BAC-based studies. We discuss traditional and contemporary tools for reliably generating chromosome-level assemblies and analyzing multiple species at a higher resolution and wider phylogenetic distance than previously possible. These results permit more detailed investigations into inter- and intrachromosomal rearrangements, providing unique insights into evolution and speciation mechanisms. The ‘signature’ avian karyotype likely arose ~250 mya and remained largely unchanged in most groups including extinct dinosaurs. Exceptions include Psittaciformes, Falconiformes, Caprimulgiformes, Cuculiformes, Suliformes, occasional Passeriformes, Ciconiiformes, and Pelecaniformes. The reasons for this remarkable conservation may be the greater diploid chromosome number generating variation (the driver of natural selection) through a greater possible combination of gametes and/or an increase in recombination rate. A deeper understanding of avian genomic structure permits the exploration of fundamental biological questions pertaining to the role of evolutionary breakpoint regions and homologous synteny blocks

Bird’s-eye view of chromosomic evolution in Class Aves

Birds (Aves) are the most speciose of terrestrial vertebrates, displaying Class-specific characteristics yet incredible external phenotypic diversity. Critical to agriculture and as model organisms, birds have adapted to many habitats. The only extant examples of dinosaurs, birds emerged ~150 mya and >10% are currently threatened with extinction

Dinosaurs

According to Britannica, dinosaurs are described as “Triceratops, contemporary birds, their most recent common ancestor and all of their descendants.” However, for biologists, it could be simpler to picture dinosaurs as reptiles with hind limbs held erect beneath the trunk, similar to how mammals’ hind limbs are held

Dinosaurs: comparative cytogenomics of their reptile cousins and avian descendants

Simple Summary Dinosaurs have been in scientific and popular culture since early fossil discoveries, but increased interest, particularly in their genomes, is expanding. Birds are reptiles, specifically theropod dinosaurs, meaning that if we compare the genomes of related reptile relations, we can get an idea of what the extinct dinosaur genomes looked like. In all animals/plants/fungi, we think of genome organization in terms of chromosomes. Genes sit on chromosomes and each cell of each individual of each species has its own unique organization. Every gene is in exactly the same spot on each chromosome, organized like continents and islands, with the genes as the cities/ towns/villages. All reptiles apart from crocodilians have both big and small chromosomes in their genomes but birds particularly so, like the Philippines or Polynesia. Birds have ~80 chromosomes (far more than most organisms) and this is very consistent in most species. Recent studies suggest that this pattern was probably established ~255 million years ago as it is also mostly present in some turtles. In other words, most dinosaurs probably had chromosomes (genome organization) like chickens or emus. In this paper, we present ideas of how this may have contributed to dinosaurs being so diverse in appearance and function. Abstract Reptiles known as dinosaurs pervade scientific and popular culture, while interest in their genomics has increased since the 1990s. Birds (part of the crown group Reptilia) are living theropod dinosaurs. Chromosome‐level genome assemblies cannot be made from long‐extinct biological material, but dinosaur genome organization can be inferred through comparative genomics of related extant species. Most reptiles apart from crocodilians have both macro‐ and microchromosomes; comparative genomics involving molecular cytogenetics and bioinformatics has established chromosomal relationships between many species . The capacity of dinosaurs to survive multiple extinction events is now well established, and birds now have more species in comparison with any other terrestrial vertebrate. This may be due, in part, to their karyotypic features, including a distinctive karyotype of around n = 40 (~10 macro and 30 microchromosomes). Similarity in genome organization in distantly related species suggests that the common avian ancestor had a similar karyotype to e.g., the chicken/emu/zebra finch. The close karyotypic similarity to the soft‐shelled turtle (n = 33) suggests that this basic pattern was mostly established before the Testudine–Archosaur divergence, ~255 MYA. That is, dinosaurs most likely had similar karyotypes and their extensive phenotypic variation may have been mediated by increased random chromosome segregation and genetic recombination, which is inherently higher in karyotypes with more and smaller chromosomes

Using the RE-AIM framework to evaluate physical activity public health programs in México

Background: Physical activity (PA) public health programming has been widely used in Mexico; however, few studies have documented individual and organizational factors that might be used to evaluate their public health impact. The RE-AIM framework is an evaluation tool that examines individual and organizational factors of public health programs. The purpose of this study was to use the RE-AIM framework to determine the degree to which PA programs in Mexico reported individual and organizational factors and to investigate whether reporting differed by the program's funding source. Methods: Public health programs promoting PA were systematically identified during 2008-2013 and had to have an active program website. Initial searches produced 23 possible programs with 12 meeting inclusion criteria. A coding sheet was developed to capture behavioral, outcome and RE-AIM indicators from program websites. Results: In addition to targeting PA, five (42%) programs also targeted dietary habits and the most commonly reported outcome was change in body composition (58%). Programs reported an average of 11.1 (±3.9) RE-AIM indicator items (out of 27 total). On average, 45% reported reach indicators, 34% reported efficacy/effectiveness indicators, 60% reported adoption indicators, 40% reported implementation indicators, and 35% reported maintenance indicators. The proportion of RE-AIM indicators reported did not differ significantly for programs that were government supported (M∈=∈10, SD∈=∈3.1) and programs that were partially or wholly privately or corporately supported (M∈=∈12.0, SD∈=∈4.4). Conclusion: While reach and adoption of these programs were most commonly reported, there is a need for stronger evaluation of behavioral and health outcomes before the public health impact of these programs can be established. © 2015 Jauregui et al.; licensee BioMed Central

Parent-perceived neighbourhood environment, parenting practices and preschool-aged children physical activity and screen time: a cross-sectional study of two culturally and geographically diverse cities

Background: Preschool-aged children’s physical activity (PA) and screen time (ST) are important health-related behaviours likely influenced by PA opportunities, parental perceptions of neighbourhood safety and parenting practices pertaining to PA and ST. How these factors interact to impact on young children’s PA and ST, and whether their effects are generalisable across cultures and geographical location is not known. This study addressed these knowledge gaps by conducting pooled analyses of comparable data from two culturally and geographically diverse samples – Chinese parent-child dyads from an ultra-dense city (Hong Kong, China) and Latino parent-child dyads from a low-density city (Houston, USA). Methods: The analytical sample consisted of 164 Hong Kong Chinese and 84 US Latino parent-child dyads with data on socio-demographic characteristics, parent-perceived neighbourhood destinations and facilities for children’s PA, physical and social safety-related neighbourhood attributes, PA-related parenting practices and child’s ST and accelerometer-assessed PA. Generalised linear models with robust standard errors accounting for neighbourhoodlevel clustering were used to estimate associations and interaction effects. Results: Hong Kong Chinese children accumulated less PA than US Latino children, although the latter had more ST. Hong Kong Chinese parents reported more parenting practices promoting inactivity. Neighbourhood PA opportunities were positively related to children’s PA only if parental perceptions of neighbourhood safety were favourable, and the associations of physical neighbourhood environment characteristics with children’s PA and ST depended on PA-related parenting practices. Community cohesion was positively related to children’s PA and negatively related to ST, while parental promotion of ST was positively associated with children’s ST. Correlates of children’s PA and ST did not differ by city. Conclusions: The substantial diferences in activity patterns between Hong Kong Chinese and US Latino preschoolaged children observed in this study are likely due to a combination of cultural and built environmental factors. However, the fact that no between-city differences in correlates of PA and ST were detected indicates that both populations of children are equally affected by parent-perceived neighbourhood environmental characteristics and parenting practices. Overall, this study highlights the importance of considering how various individual-, home- and neighbourhood physical and social factors interact to influence young children’s health-promoting activity levels

Conscientiousness and fruit and vegetable consumption: exploring behavioural intention as a mediator

Clear associations have emerged between conscientiousness and health behaviours, such that higher levels of conscientiousness are predictive of beneficial health behaviours. This study investigated the conscientiousness-fruit and vegetable consumption relationship and whether behavioural intention mediated this relationship. A large sample of adults (N = 2136) completed an online battery of questionnaires measuring conscientiousness, behavioural intentions to consume fruit and vegetables, together with self-reported behaviour. Correlation analysis revealed that conscientiousness and each of its facets were positively associated with behavioural intention and self-reported behaviour. Hierarchical multiple regression analyses revealed that after controlling for age, gender and education, total conscientiousness, and the facets of responsibility, industriousness, order and virtue predicted self-reported behaviour. Further analysis revealed that in line with the Theory of Planned Behaviour, behavioural intention fully mediated the conscientiousness-fruit and vegetable behaviour relationship. In conclusion, low levels of conscientiousness were found to be associated with lower fruit and vegetable intentions, with the latter also associated with fruit and vegetable consumption

Incidence, Reproductive Outcome, and Economic Impact of Reciprocal Translocations in the Domestic Pig

Pigs (Sus scrofa) have vast economic importance, with pork accounting for over 30% of the global meat consumption. Chromosomal abnormalities, and in particular reciprocal translocations (RTs), are an important cause of hypoprolificacy (litter size reduction) in pigs. However, these do not necessarily present with a recognizable phenotype and may cause significant economic losses for breeders when undetected. Here, we present a reappraisal of the incidence of RTs across several European pig herds, using contemporary methodology, as well as an analysis modelling the economic impact of these abnormalities. Molecular cytogenetic investigation was completed by karyotyping and/or multiprobe FISH (fluorescence in situ hybridisation) between 2016–2021, testing 2673 animals. We identified 19 types of chromosome abnormalities, the prevalence of these errors in the database was 9.1%, and the estimated incidence of de novo errors was 0.90%. Financial modelling across different scenarios revealed the potential economic impact of an undetected RT, ranging from £69,802 for an individual affected terminal boar in a commercial farm selling weaned pigs, to £51,215,378 for a genetics company with an undetected RT in a dam line boar used in a nucleus farm. Moreover, the added benefits of screening by FISH instead of karyotyping were estimated, providing a strong case for proactive screening by this approach

Comparative mapping of the macrochromosomes of eight avian species provides further insight into their phylogenetic relationships and avian karyotype evolution

Avian genomes typically consist of ~10 pairs of macro- and ~30 pairs of microchromosomes. While inter-chromosomally, a pattern emerges of very little change (with notable exceptions) throughout evolution, intrachromosomal changes remain relatively poorly studied. To rectify this, here we use a pan-avian universally hybridising set of 74 chicken bacterial artificial chromosome (BAC) probes on the macrochromosomes of eight bird species: common blackbird, Atlantic canary, Eurasian woodcock, helmeted guinea fowl, houbara bustard, mallard duck, and rock dove. A combination of molecular cytogenetic, bioinformatics, and mathematical analyses allowed the building of comparative cytogenetic maps, reconstruction of a putative Neognathae ancestor, and assessment of chromosome rearrangement patterns and phylogenetic relationships in the studied neognath lineages. We observe that, as with our previous studies, chicken appears to have the karyotype most similar to the ancestor; however, previous reports of an increased rate of intrachromosomal change in Passeriformes (songbirds) appear not to be the case in our dataset. The use of this universally hybridizing probe set is applicable not only for the re-tracing of avian karyotype evolution but, potentially, for reconstructing genome assemblies

Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework

© 2019 Author(s). As molecular scientists have made progress in their ability to engineer nanoscale molecular structure, we face new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs from the familiar mechanics of everyday objects because it involves a complicated, highly correlated, and three-dimensional many-body dynamical choreography which is often nonintuitive even for highly trained researchers. We recently described how interactive molecular dynamics in virtual reality (iMD-VR) can help to meet this challenge, enabling researchers to manipulate real-time MD simulations of flexible structures in 3D. In this article, we outline various efforts to extend immersive technologies to the molecular sciences, and we introduce "Narupa," a flexible, open-source, multiperson iMD-VR software framework which enables groups of researchers to simultaneously cohabit real-time simulation environments to interactively visualize and manipulate the dynamics of molecular structures with atomic-level precision. We outline several application domains where iMD-VR is facilitating research, communication, and creative approaches within the molecular sciences, including training machines to learn potential energy functions, biomolecular conformational sampling, protein-ligand binding, reaction discovery using "on-the-fly" quantum chemistry, and transport dynamics in materials. We touch on iMD-VR's various cognitive and perceptual affordances and outline how these provide research insight for molecular systems. By synergistically combining human spatial reasoning and design insight with computational automation, technologies such as iMD-VR have the potential to improve our ability to understand, engineer, and communicate microscopic dynamical behavior, offering the potential to usher in a new paradigm for engineering molecules and nano-architectures