Effect of the environment on horizontal gene transfer between bacteria and archaea
Background Horizontal gene transfer, the transfer and incorporation of genetic material between different species of organisms, has an important but poorly quantified role in the adaptation of microbes to their environment. Previous work has shown that genome size and the number of horizontally transferred genes are strongly correlated. Here we consider how genome size confuses the quantification of horizontal gene transfer because the number of genes an organism accumulates over time depends on its evolutionary history and ecological context (e.g., the nutrient regime for which it is adapted). Results We investigated horizontal gene transfer between archaea and bacteria by first counting reciprocal BLAST hits among 448 bacterial and 57 archaeal genomes to find shared genes. Then we used the DarkHorse algorithm, a probability-based, lineage-weighted method (Podell & Gaasterland, 2007), to identify potential horizontally transferred genes among these shared genes. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Interestingly, archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. However, high salt was not found to significantly affect the numbers of shared genes. Numbers of shared (genome size-corrected, reciprocal BLAST hits) and transferred genes (identified by DarkHorse) were strongly correlated. Thus archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. These horizontally transferred genes are over-represented by genes involved in energy conversion as well as the transport and metabolism of inorganic ions and amino acids. Conclusions Anaerobic and thermophilic bacteria share unusually large numbers of genes with archaea. This is mainly due to horizontal gene transfer of genes from the archaea to the bacteria. In general, these transfers are from archaea that live in similar oxygen and temperature conditions as the bacteria that receive the genes. Potential hotspots of horizontal gene transfer between archaea and bacteria include hot springs, marine sediments, and oil wells. Cold spots for horizontal transfer included dilute, aerobic, mesophilic environments such as marine and freshwater surface waters.
Fuchsman et al. (2017) Effect of the environment on horizontal gene transfer between bacteria and archaea. PeerJ 5:e3865 https://doi.org/10.7717/peerj.3865
Does silvoagropecuary landscape fragmentation affect the genetic diversity of the sigmodontine rodent Oligoryzomys longicaudatus?
Background Fragmentation of native forests is a highly visible result of human land-use throughout the world. In this study, we evaluated the effects of landscape fragmentation and matrix features on the genetic diversity and structure of Oligoryzomys longicaudatus, the natural reservoir of Hantavirus in southern South America. We focused our work in the Valdivian Rainforest where human activities have produced strong change of natural habitats, with an important number of human cases of Hantavirus. Methods We sampled specimens of O. longicaudatus from five native forest patches surrounded by silvoagropecuary matrix from Panguipulli, Los Rios Region, Chile. Using the hypervariable domain I (mtDNA), we characterized the genetic diversity and evaluated the effect of fragmentation and landscape matrix on the genetic structure of O. longicaudatus. For the latter, we used three approaches: (i) Isolation by Distance (IBD) as null model, (ii) Least-cost Path (LCP) where genetic distances between patch pairs increase with cost-weighted distances, and (iii) Isolation by Resistance (IBR) where the resistance distance is the average number of steps that is needed to commute between the patches during a random walk. Results We found low values of nucleotide diversity (π) for the five patches surveyed, ranging from 0.012 to 0.015, revealing that the 73 sampled specimens of this study belong to two populations but with low values of genetic distance (γST) ranging from 0.022 to 0.099. Likewise, we found that there are no significant associations between genetic distance and geographic distance for IBD and IBR. However, we found for the LCP approach, a significant positive relationship (r = 0.737, p = 0.05), with shortest least-cost paths traced through native forest and arborescent shrublands. Discussion In this work we found that, at this reduced geographical scale, Oligoryzomys longicaudatus shows genetic signs of fragmentation. In addition, we found that connectivity between full growth native forest remnants is mediated by the presence of dense shrublands and native forest corridors. In this sense, our results are important because they show how native forest patches and associated routes act as source of vector species in silvoagropecuary landscape, increasing the infection risk on human population. This study is the first approach to understand the epidemiological spatial context of silvoagropecuary risk of Hantavirus emergence. Further studies are needed to elucidate the effects of landscape fragmentation in order to generate new predictive models based on vector intrinsic attributes and landscape features.
Lazo-Cancino et al. (2017) Does silvoagropecuary landscape fragmentation affect the genetic diversity of the sigmodontine rodent Oligoryzomys longicaudatus?. PeerJ 5:e3842 https://doi.org/10.7717/peerj.3842
A prospective study of the motivational and health dynamics of Internet Gaming Disorder
The American Psychiatric Association has identified Internet Gaming Disorder (IGD) as a potential psychiatric condition and called for research to investigate its etiology, stability, and impacts on health and behavior. The present study recruited 5,777 American adults and applied self-determination theory to examine how motivational factors influence, and are influenced by, IGD and health across a six month period. Following a preregistered analysis plan, results confirmed our hypotheses that IGD criteria are moderately stable and that they and basic psychological need satisfaction have a reciprocal relationship over time. Results also showed need satisfaction promoted health and served as a protective factor against IGD. Contrary to what was hypothesized, results provided no evidence directly linking IGD to health over time. Exploratory analyses suggested that IGD may have indirect effects on health by way of its impact on basic needs. Implications are discussed in terms of existing gaming addiction and motivational frameworks.
Weinstein et al. (2017) A prospective study of the motivational and health dynamics of Internet Gaming Disorder. PeerJ 5:e3838 https://doi.org/10.7717/peerj.3838
Unraveling the diversification history of grasshoppers belonging to the “Trimerotropis pallidipennis” (Oedipodinae: Acrididae) species group: a hotspot of biodiversity in the Central Andes
The Andean Mountain range has been recognized as one of the biodiversity hotspots of the world. The proposed mechanisms for such species diversification, among others, are due to the elevation processes occurring during the Miocene and the intensive glacial action during the Pleistocene. In this study we investigated the diversification history of the grasshopper Trimerotropis pallidipennis species complex which shows a particularly wide latitudinal and altitudinal distribution range across the northern, central and southern Andes in South America. Many genetic lineages of this complex have been so far discovered, making it an excellent model to investigate the role of the central Andes Mountains together with climatic fluctuations as drivers of speciation. Phylogenetics, biogeographic and molecular clock analyses using a multi-locus dataset revealed that in Peru there are at least two, and possibly four genetic lineages. Two different stocks originated from a common ancestor from North/Central America—would have dispersed toward southern latitudes favored by the closure of the Panama Isthmus giving rise to two lineages, the coastal and mountain lineages, which still coexist in Peru (i.e., T. pallidipennis and T. andeana). Subsequent vicariant and dispersal events continued the differentiation process, giving rise to three to six genetic lineages (i.e., clades) detected in this study, which were geographically restricted to locations dispersed over the central Andes Mountains in South America. Our results provide another interesting example of “island diversification” motored by the topography plus unstable climatic conditions during the Pleistocene, pointing out the presence of a hotspot of diversification in the Andean region of Peru.
Guzmán et al. (2017) Unraveling the diversification history of grasshoppers belonging to the “Trimerotropis pallidipennis” (Oedipodinae: Acrididae) species group: a hotspot of biodiversity in the Central Andes. PeerJ 5:e3835 https://doi.org/10.7717/peerj.3835
The relationship between sustained attention and aerobic fitness in a group of young adults
Background A growing set of studies has shown a positive relationship between aerobic fitness and a broad array of cognitive functions. However, few studies have focused on sustained attention, which has been considered a fundamental cognitive process that underlies most everyday activities. The purpose of this study was to investigate the role of aerobic fitness as a key factor in sustained attention capacities in young adults. Methods Forty-four young adults (18–23 years) were divided into two groups as a function of the level of aerobic fitness (high-fit and low-fit). Participants completed the Psychomotor Vigilance Task (PVT) and an oddball task where they had to detect infrequent targets presented among frequent non-targets. Results The analysis of variance (ANOVA) showed faster responses for the high-fit group than for the low-fit group in the PVT, replicating previous accounts. In the oddball task, the high-fit group maintained their accuracy (ACC) rate of target detection over time, while the low-fit group suffered a significant decline of response ACC throughout the task. Discussion Importantly, the results show that the greater sustained attention capacity of high-fit young adults is not specific to a reaction time (RT) sustained attention task like the PVT, but it is also evident in an ACC oddball task. In sum, the present findings point to the important role of aerobic fitness on sustained attention capacities in young adults.
Ciria et al. (2017) The relationship between sustained attention and aerobic fitness in a group of young adults. PeerJ 5:e3831 https://doi.org/10.7717/peerj.3831
Extracorporeal life support with left ventricular decompression—improved survival in severe cardiogenic shock: results from a retrospective study
Objective Extracorporeal life support (ECLS) is a life-saving procedure used in the treatment of severe cardiogenic shock. Within this retrospective single centre study, we examined our experience in this critically ill patient cohort to assess outcomes and clinical parameters by comparison of ECLS with or without selective left ventricular decompression. Methods Between 2004 and 2014 we evaluated 48 adult patients with INTERMACS level 1 heart failure (age 49.7 ± 19.5 years), who received either central ECLS with (n = 20, 41.7%) or ECLS without (n = 28, 58.3%, including 10 peripheral ECLS) integrated left ventricular vent in our retrospective single centre trial. Results Follow up was 100% with a mean of 0.83 ± 1.85 years. Bridge to ventricular assist device was feasible in 29.2% (n = 14), bridge to transplant in 10.4% (n = 5) and bridge to recovery in 8.3% (n = 4). Overall 30-day survival was 37.5%, 6-month survival 27.1% and 1-year survival 25.0%. ECLS support with left ventricular decompression showed favourable 30-day survival compared to ECLS without left ventricular decompression (p = 0.034). Thirty-day as well as long-term survival did not differ between the subgroups (central ECLS with vent, ECLS without vent and peripheral ECLS without vent). Multivariate logistic regression adjusted for age and gender revealed ECLS without vent as independent factor influencing 30-day survival. Conclusion ECLS is an established therapy for patients in severe cardiogenic shock. Independent of the ECLS approach, 30-day mortality is still high but with superior 30-day survival for patients with ECLS and left ventricular venting. Moreover, by unloading the ventricle, left ventricular decompression may provide an important time window for recovery or further treatment, such as bridge to bridge or bridge to transplant.
Schmack et al. (2017) Extracorporeal life support with left ventricular decompression—improved survival in severe cardiogenic shock: results from a retrospective study. PeerJ 5:e3813 https://doi.org/10.7717/peerj.3813
Trichoplax adhaerens reveals a network of nuclear receptors sensitive to 9-cis-retinoic acid at the base of metazoan evolution
Trichoplax adhaerens, the only known species of Placozoa is likely to be closely related to an early metazoan that preceded branching of Cnidaria and Bilateria. This animal species is surprisingly well adapted to free life in the World Ocean inhabiting tidal costal zones of oceans and seas with warm to moderate temperatures and shallow waters. The genome of T. adhaerens (sp. Grell) includes four nuclear receptors, namely orthologue of RXR (NR2B), HNF4 (NR2A), COUP-TF (NR2F) and ERR (NR3B) that show a high degree of similarity with human orthologues. In the case of RXR, the sequence identity to human RXR alpha reaches 81% in the DNA binding domain and 70% in the ligand binding domain. We show that T. adhaerens RXR (TaRXR) binds 9-cis retinoic acid (9-cis-RA) with high affinity, as well as high specificity and that exposure of T. adhaerens to 9-cis-RA regulates the expression of the putative T. adhaerens orthologue of vertebrate L-malate-NADP+ oxidoreductase (EC 1.1.1.40) which in vertebrates is regulated by a heterodimer of RXR and thyroid hormone receptor. Treatment by 9-cis-RA alters the relative expression profile of T. adhaerens nuclear receptors, suggesting the existence of natural ligands. Keeping with this, algal food composition has a profound effect on T. adhaerens growth and appearance. We show that nanomolar concentrations of 9-cis-RA interfere with T. adhaerens growth response to specific algal food and causes growth arrest. Our results uncover an endocrine-like network of nuclear receptors sensitive to 9-cis-RA in T. adhaerens and support the existence of a ligand-sensitive network of nuclear receptors at the base of metazoan evolution.
Novotný et al. (2017) Trichoplax adhaerens reveals a network of nuclear receptors sensitive to 9-cis-retinoic acid at the base of metazoan evolution. PeerJ 5:e3789 https://doi.org/10.7717/peerj.3789
The World (of Warcraft) through the eyes of an expert
Negative correlations between pupil size and the tendency to look at salient locations were found in recent studies (e.g., Mathôt et al., 2015). It is hypothesized that this negative correlation might be explained by the mental effort put by participants in the task that leads in return to pupil dilation. Here we present an exploratory study on the effect of expertise on eye-movement behavior. Because there is no available standard tool to evaluate WoW players’ expertise, we built an off-game questionnaire testing players’ knowledge about WoW and acquired skills through completed raids, highest rated battlegrounds, Skill Points, etc. Experts (N = 4) and novices (N = 4) in the massively multiplayer online role-playing game World of Warcraft (WoW) viewed 24 designed video segments from the game that differ in regards with their content (i.e, informative locations) and visual complexity (i.e, salient locations). Consistent with previous studies, we found a negative correlation between pupil size and the tendency to look at salient locations (experts, r = − .17, p < .0001, and novices, r = − .09, p < .0001). This correlation has been interpreted in terms of mental effort: People are inherently biased to look at salient locations (sharp corners, bright lights, etc.), but are able (i.e., experts) to overcome this bias if they invest sufficient mental effort. Crucially, we observed that this correlation was stronger for expert WoW players than novice players (Z = − 3.3, p = .0011). This suggests that experts learned to improve control over eye-movement behavior by guiding their eyes towards informative, but potentially low-salient areas of the screen. These findings may contribute to our understanding of what makes an expert an expert.
Marzouki et al. (2017) The World (of Warcraft) through the eyes of an expert. PeerJ 5:e3783 https://doi.org/10.7717/peerj.3783
Multi-scale immunoepidemiological modeling of within-host and between-host HIV dynamics: systematic review of mathematical models
Objective The objective of this study is to conduct a systematic review of multi-scale HIV immunoepidemiological models to improve our understanding of the synergistic impact between the HIV viral-immune dynamics at the individual level and HIV transmission dynamics at the population level. Background While within-host and between-host models of HIV dynamics have been well studied at a single scale, connecting the immunological and epidemiological scales through multi-scale models is an emerging method to infer the synergistic dynamics of HIV at the individual and population levels. Methods We reviewed nine articles using the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) framework that focused on the synergistic dynamics of HIV immunoepidemiological models at the individual and population levels. Results HIV immunoepidemiological models simulate viral immune dynamics at the within-host scale and the epidemiological transmission dynamics at the between-host scale. They account for longitudinal changes in the immune viral dynamics of HIV+ individuals, and their corresponding impact on the transmission dynamics in the population. They are useful to analyze the dynamics of HIV super-infection, co-infection, drug resistance, evolution, and treatment in HIV+ individuals, and their impact on the epidemic pathways in the population. We illustrate the coupling mechanisms of the within-host and between-host scales, their mathematical implementation, and the clinical and public health problems that are appropriate for analysis using HIV immunoepidemiological models. Conclusion HIV immunoepidemiological models connect the within-host immune dynamics at the individual level and the epidemiological transmission dynamics at the population level. While multi-scale models add complexity over a single-scale model, they account for the time varying immune viral response of HIV+ individuals, and the corresponding impact on the time-varying risk of transmission of HIV+ individuals to other susceptibles in the population.
Dorratoltaj et al. (2017) Multi-scale immunoepidemiological modeling of within-host and between-host HIV dynamics: systematic review of mathematical models. PeerJ 5:e3877 https://doi.org/10.7717/peerj.3877
An exploration of strategies used by dressage horses to control moments around the center of mass when performing passage
Background Locomotion results from the generation of ground reaction forces (GRF) that cause translations of the center of mass (COM) and generate moments that rotate the body around the COM. The trot is a diagonally-synchronized gait performed by horses at intermediate locomotor speeds. Passage is a variant of the trot performed by highly-trained dressage horses. It is distinguished from trot by having a slow speed of progression combined with great animation of the limbs in the swing phase. The slow speed of passage challenges the horse’s ability to control the sagittal-plane moments around the COM. Footfall patterns and peak GRF are known to differ between passage and trot, but their effects on balance management, which we define here as the ability to control nose-up/nose-down pitching moments around the horse’s COM to maintain a state of equilibrium, are not known. The objective was to investigate which biomechanical variables influence pitching moments around the COM in passage. Methods Three highly-trained dressage horses were captured by a 10-camera motion analysis system (120 Hz) as they were ridden in passage over four force platforms (960 Hz). A full-body marker set was used to track the horse’s COM and measure balance variables including total body center of pressure (COP), pitching moments, diagonal dissociation timing, peak force production, limb protraction–retraction, and trunk posture. A total of twenty passage steps were extracted and partial correlation (accounting for horse) was used to investigate significant (P < 0.05) relationships between variables. Results Hindlimb mean protraction–retraction correlated significantly with peak hindlimb propulsive forces (R = 0.821; P < 0.01), mean pitching moments (R = 0.546, P = 0.016), trunk range of motion, COM craniocaudal location and diagonal dissociation time (P < 0.05). Discussion Pitching moments around the COM were controlled by a combination of kinematic and kinetic adjustments that involve coordinated changes in GRF magnitudes, GRF distribution between the diagonal limb pairs, and the moment arms of the vertical GRFs. The moment arms depend on hoof placements relative to the COM, which were adjusted by changing limb protraction–retraction angles. Nose-up pitching moments could also be increased by providing a larger hindlimb propulsive GRF.
Clayton et al. (2017) An exploration of strategies used by dressage horses to control moments around the center of mass when performing passage. PeerJ 5:e3866 https://doi.org/10.7717/peerj.3866