Chromosome-Level Genome Assembly of the Blacktail Brush Lizard, Urosaurus nigricaudus, Reveals Dosage Compensation in an Endemic Lizard.

Urosaurus nigricaudus is a phrynosomatid lizard endemic to the Baja California Peninsula in Mexico. This work presents a chromosome-level genome assembly and annotation from a male individual. We used PacBio long reads and HiRise scaffolding to generate a high-quality genomic assembly of 1.87 Gb distributed in 327 scaffolds, with an N50 of 279 Mb and an L50 of 3. Approximately 98.4% of the genome is contained in 14 scaffolds, with 6 large scaffolds (334-127 Mb) representing macrochromosomes and 8 small scaffolds (63-22 Mb) representing microchromosomes. Using standard gene modeling and transcriptomic data, we predicted 17,902 protein-coding genes on the genome. The repeat content is characterized by a large proportion of long interspersed nuclear elements that are relatively old. Synteny analysis revealed some microchromosomes with high repeat content are more prone to rearrangements but that both macro- and microchromosomes are well conserved across reptiles. We identified scaffold 14 as the X chromosome. This microchromosome presents perfect dosage compensation where the single X of males has the same expression levels as two X chromosomes in females. Finally, we estimated the effective population size for U. nigricaudus was extremely low, which may reflect a reduction in polymorphism related to it becoming a peninsular endemic.

Genome-wide analysis of RNA-chromatin interactions in lizards as a mean for functional lncRNA identification.

BACKGROUND: Long non-coding RNAs (lncRNAs) are defined as transcribed molecules longer than 200 nucleotides with little to no protein-coding potential. LncRNAs can regulate gene expression of nearby genes (cis-acting) or genes located on other chromosomes (trans-acting). Several methodologies have been developed to capture lncRNAs associated with chromatin at a genome-wide level. Analysis of RNA-DNA contacts can be combined with epigenetic and RNA-seq data to define potential lncRNAs involved in the regulation of gene expression. RESULTS: We performed Chromatin Associated RNA sequencing (ChAR-seq) in Anolis carolinensis to obtain the genome-wide map of the associations that RNA molecules have with chromatin. We analyzed the frequency of DNA contacts for different classes of RNAs and were able to define cis- and trans-acting lncRNAs. We integrated the ChAR-seq map of RNA-DNA contacts with epigenetic data for the acetylation of lysine 16 on histone H4 (H4K16ac), a mark connected to actively transcribed chromatin in lizards. We successfully identified three trans-acting lncRNAs significantly associated with the H4K16ac signal, which are likely involved in the regulation of gene expression in A. carolinensis. CONCLUSIONS: We show that the ChAR-seq method is a powerful tool to explore the RNA-DNA map of interactions. Moreover, in combination with epigenetic data, ChAR-seq can be applied in non-model species to establish potential roles for predicted lncRNAs that lack functional annotations.

A Large-Scale Genome-Based Survey of Acidophilic Bacteria Suggests That Genome Streamlining Is an Adaption for Life at Low pH.

The genome streamlining theory suggests that reduction of microbial genome size optimizes energy utilization in stressful environments. Although this hypothesis has been explored in several cases of low-nutrient (oligotrophic) and high-temperature environments, little work has been carried out on microorganisms from low-pH environments, and what has been reported is inconclusive. In this study, we performed a large-scale comparative genomics investigation of more than 260 bacterial high-quality genome sequences of acidophiles, together with genomes of their closest phylogenetic relatives that live at circum-neutral pH. A statistically supported correlation is reported between reduction of genome size and decreasing pH that we demonstrate is due to gene loss and reduced gene sizes. This trend is independent from other genome size constraints such as temperature and G + C content. Genome streamlining in the evolution of acidophilic bacteria is thus supported by our results. The analyses of predicted Clusters of Orthologous Genes (COG) categories and subcellular location predictions indicate that acidophiles have a lower representation of genes encoding extracellular proteins, signal transduction mechanisms, and proteins with unknown function but are enriched in inner membrane proteins, chaperones, basic metabolism, and core cellular functions. Contrary to other reports for genome streamlining, there was no significant change in paralog frequencies across pH. However, a detailed analysis of COG categories revealed a higher proportion of genes in acidophiles in the following categories: "replication and repair," "amino acid transport," and "intracellular trafficking". This study brings increasing clarity regarding the genomic adaptations of acidophiles to life at low pH while putting elements, such as the reduction of average gene size, under the spotlight of streamlining theory.

After-Action Reviews and Long-Term Performance: An Experimental Examination in the Context of an Emergency Simulation.

OBJECTIVE: The present study examined the effectiveness of after-action reviews (AARs; also known as debriefing) in mitigating skill decay. BACKGROUND: Research on the long-term effectiveness of AARs is meager. To address this gap in the literature, we conducted an experimental study that also overcomes some research design issues that characterize the limited extant research. METHOD: Eighty-four participants were randomly assigned to an AAR or non-AAR condition and trained to operate a PC-based fire emergency simulator. During the initial acquisition phase, individuals in the AAR condition were allowed to review their performance after each practice session, whereas individuals in the non-AAR condition completed a filler task. About 12 weeks later, participants returned to the lab to complete four additional practice sessions using a similar scenario (i.e., the retention and reacquisition phase). RESULTS: The performance of participants in the AAR condition degraded more after nonuse but also recovered faster than the performance of participants in the non-AAR condition, although these effects were fairly small and not statistically significant. CONCLUSION: Consistent with the limited research on the long-term effectiveness of AARs, our findings failed to support their effectiveness as a decay-prevention intervention. Because the present study was conducted in a laboratory setting using a relatively small sample of undergraduate students, additional research is warranted. APPLICATION: Based on the results of the present study, we suggest some additional strategies that trainers might consider to support long-term skill retention when using AARs.

Molecular and Cellular Mechanisms Underlying Temperature-Dependent Sex Determination in Turtles.

The discovery in mammals that fetal testes are required in order to develop the male phenotype inspired research efforts to elucidate the mechanisms underlying gonadal sex determination and differentiation in vertebrates. A pioneer work in 1966 that demonstrated the influence of incubation temperature on sexual phenotype in some reptilian species triggered great interest in the environment's role as a modulator of plasticity in sex determination. Several chelonian species have been used as animal models to test hypotheses concerning the mechanisms involved in temperature-dependent sex determination (TSD). This brief review intends to outline the history of scientific efforts that corroborate our current understanding of the state-of-the-art in TSD using chelonian species as a reference.

A Large-Scale Multiple Genome Comparison of Acidophilic Archaea (pH ≤ 5.0) Extends Our Understanding of Oxidative Stress Responses in Polyextreme Environments.

Acidophilic archaea thrive in anaerobic and aerobic low pH environments (pH < 5) rich in dissolved heavy metals that exacerbate stress caused by the production of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), hydroxyl radical (·OH) and superoxide (O2-). ROS react with lipids, proteins and nucleic acids causing oxidative stress and damage that can lead to cell death. Herein, genes and mechanisms potentially involved in ROS mitigation are predicted in over 200 genomes of acidophilic archaea with sequenced genomes. These organisms are often be subjected to simultaneous multiple stresses such as high temperature, high salinity, low pH and high heavy metal loads. Some of the topics addressed include: (1) the phylogenomic distribution of these genes and what this can tell us about the evolution of these mechanisms in acidophilic archaea; (2) key differences in genes and mechanisms used by acidophilic versus non-acidophilic archaea and between acidophilic archaea and acidophilic bacteria and (3) how comparative genomic analysis predicts novel genes or pathways involved in oxidative stress responses in archaea and likely horizontal gene transfer (HGT) events.

The Effects of the 2016 Copa América Centenario Victory on Social Trust, Self-Transcendent Aspirations and Evaluated Subjective Well-Being: The Role of Identity With the National Team and Collective Pride in Major Sport Events.

Following a neo-Durkheimian perspective, major sporting events such as the World Cup or the America's Cup differ from other collective rituals because they promote interest throughout the nation due to their massiveness and international character. In order to increase the scientific knowledge related to these type of rituals, the aim of this study was to observe the effects that the Chilean victory in the 2016 Copa América Centenario had on social variables such as trust, self-transcendent aspirations, and evaluated subjective well-being (SWB) of both fans and non-fans. In addition, two longitudinal structural equation models (SEMs) were performed to estimate the effect of identity with the national team before the final match on evaluated SWB, trust, and self-transcendent aspirations post-final. A total of 648 Chilean participants (mean age = 38.58; SD = 10.96) answered the questionnaire before the final match. Out of these, 409 completed our measures after the final. The results show that fans presented higher scores in many of the studied variables before and after the final compared to non-fans. Identification with the national team (before the final) prospectively and significantly predicted pride in the national team and pride in the country (after the final). In addition, these two forms of collective pride mediated the relationship between identification with the national team (before the final) and evaluated SWB (after the final). The results are discussed emphasizing the importance of these kinds of specific massive rituals and their effects.

Expression Evolution of Ancestral XY Gametologs across All Major Groups of Placental Mammals.

Placental mammals present 180 million-year-old Y chromosomes that have retained a handful of dosage-sensitive genes. However, the expression evolution of Y-linked genes across placental groups has remained largely unexplored. Here, we expanded the number of Y gametolog sequences by analyzing ten additional species from previously unexplored groups. We detected seven remarkably conserved genes across 25 placental species with known Y repertoires. We then used RNA-seq data from 17 placental mammals to unveil the expression evolution of XY gametologs. We found that Y gametologs followed, on average, a 3-fold expression loss and that X gametologs also experienced some expression reduction, particularly in primates. Y gametologs gained testis specificity through an accelerated expression decay in somatic tissues. Moreover, despite the substantial expression decay of Y genes, the combined expression of XY gametologs in males is higher than that of both X gametologs in females. Finally, our work describes several features of the Y chromosome in the last common mammalian ancestor.

Sex determination systems in reptiles are related to ambient temperature but not to the level of climatic fluctuation.

BACKGROUND: Vertebrates exhibit diverse sex determination systems and reptiles stand out by having highly variable sex determinations that include temperature-dependent and genotypic sex determination (TSD and GSD, respectively). Theory predicts that populations living in either highly variable or cold climatic conditions should evolve genotypic sex determination to buffer the populations from extreme sex ratios, yet these fundamental predictions have not been tested across a wide range of taxa. RESULTS: Here, we use phylogenetic analyses of 213 reptile species representing 38 families (TSD = 101 species, GSD = 112 species) and climatic data to compare breeding environments between reptiles with GSD versus TSD. We show that GSD and TSD are confronted with the same level of climatic fluctuation during breeding seasons. However, TSD reptiles are significantly associated with warmer climates. We found a strong selection on the breeding season length that minimises exposure to cold and fluctuating climate. Phylogenetic path analyses comparing competing evolutionary hypotheses support that transitions in sex determination systems influenced the ambient temperature at which the species reproduces and nests. In turn, this interaction affects other variables such as the duration of the breeding season and life-history traits. CONCLUSIONS: Taken together, our results challenge long-standing hypotheses about the association between sex determination and climate variability. We also show that ambient temperature is important during breeding seasons and it helps explain the effects of sex determination systems on the geographic distribution of extant reptile species.

AciDB 1.0: a database of acidophilic organisms, their genomic information and associated metadata.

MOTIVATION: There are about 600 available genome sequences of acidophilic organisms (grow at a pH < 5) from the three domains of the Tree of Life. Information about acidophiles is scattered over many heterogeneous sites making it extraordinarily difficult to link physiological traits with genomic data. We were motivated to generate a curated, searchable database to address this problem. RESULTS: AciDB 1.0 is a curated database of sequenced acidophiles that enables researchers to execute complex queries linking genomic features to growth data, environmental descriptions and taxonomic information. AVAILABILITY AND IMPLEMENTATION: AciDB 1.0 is freely available online at: http://AciDB.cl. The source code is released under an MIT license at: https://gitlab.com/Hawkline451/acidb/.

Evolution of Predicted Acid Resistance Mechanisms in the Extremely Acidophilic Leptospirillum Genus.

Organisms that thrive in extremely acidic environments (≤pH 3.5) are of widespread importance in industrial applications, environmental issues, and evolutionary studies. Leptospirillum spp. constitute the only extremely acidophilic microbes in the phylogenetically deep-rooted bacterial phylum Nitrospirae. Leptospirilli are Gram-negative, obligatory chemolithoautotrophic, aerobic, ferrous iron oxidizers. This paper predicts genes that Leptospirilli use to survive at low pH and infers their evolutionary trajectory. Phylogenetic and other bioinformatic approaches suggest that these genes can be classified into (i) "first line of defense", involved in the prevention of the entry of protons into the cell, and (ii) neutralization or expulsion of protons that enter the cell. The first line of defense includes potassium transporters, predicted to form an inside positive membrane potential, spermidines, hopanoids, and Slps (starvation-inducible outer membrane proteins). The "second line of defense" includes proton pumps and enzymes that consume protons. Maximum parsimony, clustering methods, and gene alignments are used to infer the evolutionary trajectory that potentially enabled the ancestral Leptospirillum to transition from a postulated circum-neutral pH environment to an extremely acidic one. The hypothesized trajectory includes gene gains/loss events driven extensively by horizontal gene transfer, gene duplications, gene mutations, and genomic rearrangements.

The Reciprocal Relationship Between Gratitude and Life Satisfaction: Evidence From Two Longitudinal Field Studies.

Gratitude and life satisfaction are associated with several indicators of a good life (e.g., health, pro-social behavior, and relationships). However, how gratitude and life satisfaction relate to each other over time has remained unknown until now. Although a substantial body of research has tested the link from gratitude to life satisfaction, the reverse association remains unexplored. In addition, recent cross-cultural research has questioned the link between gratitude and subjective well-being in non-Western countries, suggesting that the benefits of gratitude may only prevail in Western societies. However, previous cross-cultural studies have only compared western (e.g., American) and eastern (e.g., Asian) cultures, but this simple contrast does not adequately capture the diversity in the world. To guide further theory and practice, we therefore extended previous cross-sectional and experimental studies, by testing the bi-directional longitudinal link between gratitude and life satisfaction in a Latin American context, aiming to establish temporal precedence. We assessed two adult samples from Chile, using three-wave cross-lagged panel designs with 1 month (Study 1, N = 725) and 3 months (Study 2, N = 1,841) between waves. Both studies show, for the first time, that gratitude and life satisfaction mutually predict each other over time. The reciprocal relationships suggest the existence of a virtuous circle of human well-being: higher levels of gratitude increase life satisfaction, which in turn increases gratitude, leading to a positive spiral. Key theoretical and practical implications for the dynamics of human flourishing and field of positive psychology are discussed.

Deciphering Ancestral Sex Chromosome Turnovers Based on Analysis of Male Mutation Bias.

The age of sex chromosomes is commonly obtained by comparing the substitution rates of XY gametologs. Coupled with phylogenetic reconstructions, one can refine the origin of a sex chromosome system relative to specific speciation events. However, these approaches are insufficient to determine the presence and duration of ancestral sex chromosome systems that were lost in some species. In this study, we worked with genomic and transcriptomic data from mammals and squamates and analyzed the effect of male mutation bias on X-linked sequences in these groups. We searched for signatures indicating whether monotremes shared the same sex chromosomes with placental mammals or whether pleurodonts and acrodonts had a common ancestral sex chromosome system. Our analyses indicate that platypus did not share the XY chromosomes with placental mammals, in agreement with previous work. In contrast, analyses of agamids showed that this lineage maintained the pleurodont XY chromosomes for several million years. We performed multiple simulations using different strengths of male mutation bias to confirm the results. Overall, our work shows that variations in substitution rates due to male mutation bias could be applied to uncover signatures of ancestral sex chromosome systems.

Corytophanids Replaced the Pleurodont XY System with a New Pair of XY Chromosomes.

Almost all lizard families in the pleurodont clade share the same XY system. This system was meticulously studied in Anolis carolinensis, where it shows a highly degenerated Y chromosome and a male-specific X chromosome dosage compensation mechanism. Corytophanids (casque-headed lizards) have been proposed as the only family in the pleurodont clade to lack the XY system. In this study, we worked with extensive genomic and transcriptomic data from Basiliscus vittatus, a member of the Corytophanidae family that inhabits the tropical rainforests of Mexico. We confirmed that B. vittatus underwent a sex chromosome system turnover, which consisted in the loss of the pleurodont XY system and the gain of a new pair of XY chromosomes that are orthologous to chicken chromosome 17. We estimated the origin of the sex chromosome system to have occurred ∼63 Ma in the ancestor of corytophanids. Moreover, we identified 12 XY gametologues with particular attributes, such as functions related to the membrane and intracellular trafficking, very low expression levels, blood specificity, and incomplete dosage compensation in males.

Revisiting the Link between Job Satisfaction and Life Satisfaction: The Role of Basic Psychological Needs.

The link between job satisfaction and life satisfaction has been extensively explored in the relevant literature. However, the great majority of past research has been carried out using cross-sectional analyses, and almost exclusively in the Western world. Moreover, the underlying psychological mechanisms explaining the link are not yet completely understood. Thus, we report the first research to date which uses both cross-sectional and longitudinal data among workers in Chile-a fast-developing Latin American economy-and which aims to tackle previous limitations. Three studies consistently support a positive link between the constructs. Study 1 (N = 636) found that higher job satisfaction predicted higher life satisfaction both contemporaneously and longitudinally, and vice versa, above and beyond several key control variables. Study 2 (N = 725) and Study 3 (N = 703) replicated Study 1 results, but tested for the first time the role of satisfaction of basic psychological needs (as stated by self-determination theory) in the job-life satisfaction link. This is the most novel contribution of our paper. Key implications not only for individual quality of life, but also for companies' human resource practices emerge from our findings.

Influencia de factores socioculturales en la imagen corporal desde la perspectiva de mujeres adolescentes / Influence of sociocultural factors on body image from the perspective of adolescent girls

Resumen: La imagen corporal es un tópico relevante en el desarrollo de la identidad durante la adolescencia, donde los factores sociales son decisivos en la determinación de las expectativas individuales. Este estudio describe y analiza la percepción que mujeres adolescentes tienen acerca de la influencia de los aspectos socioculturales en su imagen corporal. El enfoque de investigación fue cualitativo, exploratorio y descriptivo, basado en la teoría fundamentada. Se entrevistó a cinco mujeres adolescentes de entre 16 y 18 años de edad. Los resultados muestran que existe una experiencia de la imagen corporal caracterizada por sentimientos ambivalentes y diferentes grados de insatisfacción corporal. En general, las participantes sobrevaloran la importancia del aspecto físico y, específicamente, la delgadez es considerada signo de atractivo, éxito y perfección; prototipo estético que favorece la insatisfacción corporal. Los parámetros socioculturales percibidos como más influyentes fueron los medios masivos de comunicación, especialmente las redes sociales digitales, que superan a los pares y a la familia. Se concluye que el fortalecimiento de la capacidad de juicio crítico para discernir entre los ideales corporales y los cuerpos reales podría favorecer la prevención de problemas alimentarios en las mujeres adolescentes.

Abstract: Body image is a relevant topic in the development of identity during the adolescence, where social factors are significant in determining individual expectations. This study aims to describe and analyze the perception that female adolescents have about the influence of sociocultural factors on their own body image. This research has a qualitative, exploratory and descriptive approach based on the Grounded Theory. Five adolescent girls aged between 16 and 18 years were interviewed. Results show that body image is characterized by ambivalent feelings and different degrees of body dissatisfaction. In general, participants overvalue physical aspects, for instance, thinness is believed as a sign of attractiveness, success and perfection, prototype linked to body dissatisfaction. The more influential sociocultural parameters were mass media, especially online social networks, peers and family. It is concluded that strengthening critical judgment skills to distinguish between the ideal body and the real body could enhance the prevention of eating disturbances in adolescent women.

Parâmetros de desempenho de dezesseis equipamentos de irrigação por pivô central / Parameters of performance of sixteen center-pivot irrigation equipments

O tempo de uso de sistemas de irrigação por pivô central pode resultar em alteração de suas características hidráulicas, necessitando de avaliações periódicas para manter a uniformidade de distribuição de água em níveis aceitáveis. Objetivou-se, neste trabalho, avaliar as condições de funcionamento e desempenho de dezesseis pivôs centrais, localizados em onze municípios de Goiás e no Distrito Federal. Estimou-se o coeficiente de uniformidade de Heermann & Hein - CUH e uniformidade de distribuição - CUD, variação da lâmina coletada em relação à projetada e os fatores que interferem no desempenho dos equipamentos. Dos pivôs avaliados, quatro (25 por cento) apresentaram CUH inadequado (< 80 por cento) e três (18,75 por cento) apresentaram CUD inadequado (< 70 por cento). A lâmina média coletada foi superior à projetada em três e inferior em treze pivôs, com diferença maior que 10 por cento em apenas um pivô. A maioria dos pivôs avaliados necessita de manutenção para solucionar algum dos seguintes problemas: bocais com vazão diferente da considerada adequada para alguns intervalos dos equipamentos, emissores total ou parcialmente obstruídos ou danificados, ausência de pendurais, reguladores de pressão danificados, vazamentos em vários pontos da lateral e velocidade de deslocamento em campo diferente da indicada no relé porcentual.

The time of use of the center-pivot irrigation system may result in alteration of the hydraulic characteristics, frequent evaluations being needed to maintain the efficiency of water distribution at acceptable levels. The aim of this work was to evaluate the conditions of the use and the performance of sixteen center pivots, located in eleven municipal districts of Goiás State and Federal District, Brazil. The Heermann & Hein - CUH coefficient of uniformity and coefficient of distribution - CUD, variation between the collected and projected depth and verification of the main factors that influenced the performance were evaluated. Among the evaluated pivots, four (25 percent) presented inadequate CUH (< 80 percent) and three (18.75 percent) presented inadequate CUD (< 70 percent). The average depth applied was higher than the projected in three and lower in thirteen pivots, with the difference higher than 10 percent in only one pivot. Most of the evaluated pivots need maintenance to solve the following problems: emitters with flow rate different from the flow considered appropriate for some intervals of the equipments; emitters totally or partially clogged or damaged; absence of suspension strings; damaged pressure regulators; leaks in several points and speed displacement different from the observed on the relay percentile.

Comparative analysis of methodologies for the detection of horizontally transferred genes: a reassessment of first-order Markov models.

With the advent of larger genome databases detection of horizontal gene transfer events has been transformed into an increasingly important issue. Here we present a simple theoretical analysis based on the in silico artificial addition of known foreign genes from different prokaryotic groups into the genome of Escherichia coli K12 MG1655. Using this dataset as a control, we have tested the efficiency of four methodologies commonly employed to detect HTG (Horizontally transferred genes), which are based on (a) the codon adaptation index, codon usage, and GC percentage (CAI/GC); (b) a distributional profile (DP) approach made by a gene search in the closely related phylogenetic genomes; (c) a Bayesian model (BM); and (d) a first-order Markov model (MM). All methods exhibit limitations although, as shown here, the BM and the MM are better approximations. Moreover, the MM has demonstrated a more accurate rate of detections when genes from closely related organisms are evaluated. The application of the MM to detect recently transferred genes in the genomes of E. coli strains K12 MG1655, O157 EDL933, and Salmonella typhimurium, shows that these organisms have undergone a rather significant amount of HTG, most of which appear to be pseudogenes. Few of these sequences that have undergone HGT appear to have well defined functions and may be involved in the organism's adaptation.