Distinct Domain Of Life Research Articles

Machine learning classification of archaea and bacteria identifies novel predictive genomic features

BackgroundArchaea and Bacteria are distinct domains of life that are adapted to a variety of ecological niches. Several genome-based methods have been developed for their accurate classification, yet many aspects of the specific genomic features that determine these differences are not fully understood. In this study, we used publicly available whole-genome sequences from bacteria (N=2546\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$N=2546$$\\end{document}) and archaea (N=109\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$N=109$$\\end{document}). From these, a set of genomic features (nucleotide frequencies and proportions, coding sequences (CDS), non-coding, ribosomal and transfer RNA genes (ncRNA, rRNA, tRNA), Chargaff’s, topological entropy and Shannon’s entropy scores) was extracted and used as input data to develop machine learning models for the classification of archaea and bacteria.ResultsThe classification accuracy ranged from 0.993 (Random Forest) to 0.998 (Neural Networks). Over the four models, only 11 examples were misclassified, especially those belonging to the minority class (Archaea). From variable importance, tRNA topological and Shannon’s entropy, nucleotide frequencies in tRNA, rRNA and ncRNA, CDS, tRNA and rRNA Chargaff’s scores have emerged as the top discriminating factors. In particular, tRNA entropy (both topological and Shannon’s) was the most important genomic feature for classification, pointing at the complex interactions between the genetic code, tRNAs and the translational machinery.ConclusionstRNA, rRNA and ncRNA genes emerged as the key genomic elements that underpin the classification of archaea and bacteria. In particular, higher nucleotide diversity was found in tRNA from bacteria compared to archaea. The analysis of the few classification errors reflects the complex phylogenetic relationships between bacteria, archaea and eukaryotes.

The Development and Initial Validation of the Multidimensional Fairness Scale

Research in psychology, sociology, economics, and other disciplines investigating social justice has identified associations between fair treatment and human well-being. However, the lack of a practical and valid instrument for measuring individual experiences of fair treatment in multiple areas of life has limited the ability to understand the relationship between fairness and wellness. The purpose of these studies was to develop and establish the initial psychometric properties and convergent validity of a scale measuring personal experiences of fairness across various life domains. Development and validation occurred across three studies. Scale development in Study 1 included the generation of items, item revision, and analysis of content validity. A review of existing literature and qualitative data derived from focus group discussions informed the initial pool of items. Cognitive interviews and expert input aided in analysis of content validity and revision of items. Study 2 consisted of confirmatory factor analyses to evaluate the performance of items and determine the underlying factor structure of the scale. In Study 3, factor analyses were used to evaluate convergent validity with other fairness-related instruments. Results of the first study supported the conceptualization of fairness along a social-ecological spectrum: experiences of fairness existed in multiple distinct life domains (e.g., interpersonal, occupational, community). Results from the second study revealed a bifactor model with one general Fairness factor and four Interpersonal, Occupational, Community, and Societal ecological group factors. Results from the third study suggested acceptable convergent validity among some subscales and other established instruments, while also suggesting that refinements to the Community fairness subscale might improve the scale. The final 12-item scale demonstrated good reliability. Results of this study produced an instrument able to measure individual experiences of fair treatment across four life domains.

The role of core self-evaluations and ego-resiliency in predicting resource losses and gains in the face of the COVID-19 crisis: the perspective of conservation of resources theory.

The purpose of the present study was to investigate, through the lens of conservation of resources theory, the predictive role of 2 positive personality traits in the form of core self-evaluations (CSE) and ego-resiliency (ER) in resource losses and gains triggered by the COVID-19 crisis. The 2 personality traits, constituting positive person-related resources, were examined in relation to resource losses and gains in both general and distinct life domains: hedonistic and vital, spiritual, family, economic and political, and finally power and prestige. The findings from a nationwide sample of 1000 working adults (65% women; age M±SD 38.93±10.9 years) indicated that CSE negatively predicted resource losses, whereas ER served as a positive predictor of resource gains. The predictive role of personality traits was demonstrated both for resource losses and gains in general and in different life domains. The results of this study highlight in particular the role of CSE as a protective factor of resource losses, and the role of ER as a promotive factor of resource gains, suggesting that both traits might evoke divergent resilience responses when facing prolonged stressful life events. Int J Occup Med Environ Health. 2023;36(4):551-62.

The Effect of Neuropathic Pain on Psychological Well-Being of An Individual

This comprehensive study delves into the intricate relationship between neuropathic pain and psychological well-being among individuals while exploring the multifaceted influences of pain severity, gender, socio-economic class, and potential gender-based disparities. Employing a cross-sectional design, data were meticulously gathered from a sample of 110 participants within a medical facility. To assess neuropathic pain and psychological well-being, the study thoughtfully employed self-report measures, notably the DN4 Questionnaire for pain assessment and the Satisfaction with Life Scale for evaluating psychological well-being. The findings of this study unveiled a robust and statistically significant negative correlation between neuropathic pain and psychological well-being (r = -0.87, p = 0.02). This compelling correlation indicates that as the severity of neuropathic pain escalates, psychological well-being tends to markedly diminish. This relationship was further corroborated through linear regression analysis, demonstrating that for each incremental unit increase in neuropathic pain, there is a corresponding decrease of 0.87 units in psychological well-being (p = 0.001). Furthermore, this study unearthed noteworthy negative correlations between neuropathic pain and distinct domains of life, encompassing general activity, mood, normal work, relationships, sleep and enjoyment in life. These correlations illuminate that as the severity of neuropathic pain intensifies, individuals encounter impediments in various facets of their lives, including their daily activities, emotional states, work performance, social interactions, sleep quality, and overall life satisfaction. Notably, the socio-economic class emerged as a salient factor influencing well-being, with individuals in the middle class exhibiting significantly higher well-being scores when compared to their counterparts in the lower socioeconomic class (F = 5.770, p = 0.004). Intriguingly, gender did not wield a substantial impact on either well-being or pain levels in this study's context. The profound implications of these findings underscore the imperative necessity for the development and implementation of comprehensive pain management strategies, as well as robust psychosocial support systems tailored to individuals grappling with neuropathic pain. Future avenues of research should consider adopting longitudinal study designs to gain insights into the evolution of these relationships over time and should also explore nuanced cultural and gender-related factors that might further elucidate the complex interplay between pain experiences and psychological well-being.

Personal Experiences of Age Discrimination in Different Life Domains: Determinants and Consequences

Age discrimination is pervasive in society which bears far-reaching consequences for individuals in terms of decreased psychological and physical health. Age discrimination can be experienced in different life-domains and perceived as a social (others’ experiences) or as a personal phenomenon (own experiences). Our first goal was to examine country- and age-related differences in personal experiences of age discrimination in distinct life domains, reported by 2,817 participants aged 40 to 90 years from the US, China, Germany, the Czech Republic, and Taiwan. As another goal, we investigated the impact of age discrimination on life satisfaction. Personal age discrimination was domain-specific, with more experiences reported in the family, work, and personality domains. Personal age discrimination increased with age and was higher in China and Taiwan. Age discrimination negatively predicted life satisfaction. This negative effect was more pronounced if age discrimination was experienced in domains with high subjective importance.

The brief daily stressors screening tool: An introduction and evaluation.

The present study introduces a short screening instrument for the measurement of experienced general daily stressors across different life domains that can be used in large-scale studies. The brief daily stressors screening tool (BDSST) assesses the experience of general daily stressors in eight distinct life domains. General daily stressors are indicated for the past 12-months on a five-point Likert scale. The present study evaluates the BDSST in two successive studies. The first study was conducted in a representative German sample (n = 7,849). The second study was conducted to assess one-month-retest-stability in another representative German sample (n = 1,294). The BDSST shows promising psychometric properties. It has a skewed positive distribution, internal consistency and stability are acceptable and its one-factor structure was confirmed in a bifactor confirmatory factor analysis. The BDSST is a reliable and valid short instrument for the assessment of experienced general daily stressors in large-scale studies and routine clinical practise. For in-depth clinical assessment, it can be used to identify relevant life domains for further investigation.

The Lazy Life of Lipid-Linked Oligosaccharides in All Life Domains.

Lipid-linked oligosaccharides (LLOs) play an important role in the N-glycosylation pathway as the donor substrate of oligosaccharyltransferases (OSTs), which are responsible for the en bloc transfer of glycan chains onto a nascent polypeptide. The lipid component of LLO in both eukarya and archaea consists of a dolichol, and an undecaprenol in prokarya, whereas the number of isoprene units may change between species. Given the potential relevance of LLOs and their related enzymes to diverse biotechnological applications, obtaining reliable LLO models from distinct domains of life could support further studies on complex formation and their processing by OSTs, as well as protein engineering on such systems. In this work, molecular modeling techniques, such as quantum mechanics calculations, molecular dynamics simulations, and metadynamics were employed to study eukaryotic (Glc3-Man9-GlcNAc2-PP-Dolichol), bacterial (Glc1-GalNAc5-Bac1-PP-Undecaprenol), and archaeal (Glc1-Man1-Gal1-Man1-Glc1-Gal1-Glc1-P-Dolichol) LLOs in membrane bilayers. Microsecond molecular dynamics simulations and metadynamics calculations of LLOs revealed that glycan chains are more prone to interact with the membrane lipid head groups, while the PP linkages are positioned at the lipid phosphate head groups level. The dynamics of isoprenoid chains embedded within the bilayer are described, and membrane dynamics and related properties are also investigated. Overall, there are similarities regarding the structure and dynamics of the eukaryotic, the bacterial, and the archaeal LLOs in bilayers, which can support the comprehension of their association with OSTs. These data may support future studies on the transferring mechanism of the oligosaccharide chain to an acceptor protein.

The Effects of Life Domains on Cyberbullying and Bullying: Testing the Generalizability of Agnew’s Integrated General Theory

In 2005, Robert Agnew published his book Why Criminals Offend in which he synthesized an array of theoretical predictors of crime and delinquency into a parsimonious integrated general theory. He argued that delinquency is influenced by mechanisms found in five distinct life domains: self, family, peer, school, and work. Using longitudinal data from South Korea, the current research tested the generalizability of Agnew’s theory by applying it to bullying and cyberbullying. Results from a negative binomial regression model provided mixed support for Agnew’s theory as a general theory of crime. The significant effects of life domains were found to differ across types of bullying.

Chronic Stress in Vocational and Intimate Partner Domains as Predictors of Depressive Symptoms After Breast Cancer Diagnosis.

After cancer diagnosis, depressive symptoms are elevated on average and decline over time, but substantial variability is apparent. Few studies have examined to what extent chronic stress in distinct life domains affects depressive symptoms. Chronic stress in vocational and intimate partner life domains, and their interaction, were tested as predictors of depressive symptoms after breast cancer diagnosis. Women (N = 460) completed validated interviews regarding chronic stress in specific life domains shortly after diagnosis and a measure of depressive symptoms every 6 weeks for 6 months. In latent growth curve modeling analyses, greater chronic stress in work (b = 2.90; p < .001) and intimate partner domains (b = 1.38, p = .02) was associated with higher depressive symptoms at study entry (intercept), and greater work stress predicted faster recovery from depressive symptoms over time (b = -0.10; p = .01). The two domains of chronic stress also interacted significantly on depressive symptoms at study entry (b = -1.54; p < .02) and over time (b = 0.14; p < .001). Greater work stress was associated with higher depressive symptoms at study entry regardless of intimate partner stress, but greater intimate partner stress was associated with higher depressive symptoms when work stress was low. The decline over 6 months in initially elevated depressive symptoms predicted by high work stress was significantly steeper when intimate partner stress was low. Targeting interventions to recently diagnosed breast cancer patients living with chronically stressful vocational and intimate partner life circumstances could be worthwhile.

Internet use and well-being: A survey and a theoretical framework

How does Internet use affect well-being? This paper presents a survey of the literature investigating this question, and it develops a framework to analyze both positive effects and potential risks. We point out four distinct channels through which Internet can shape well-being: it changes time use patterns, creates new activities, facilitates access to information, and acts as powerful communication tool. We show how these four channels impact well-being in distinct domains of life. A central point emerging from the literature review is that the effects of Internet on well-being are mediated by a set of personal characteristics that are specific to each individual: psychological functioning, capabilities, and framing conditions (culture and beliefs). Hence, it is the interaction between human beings’ activities in distinct domains of life and their own personal characteristics that explains why the use of Internet has stronger positive effects for some individuals and social groups than others.

Patchwork giant viruses reignite debate over origin of viruses Patchwork giant viruses reignite debate over domains of life Patchwork giant viruses spark debate over the tree of life

The Klosneuviruses contradict the theory that viruses make up a distinct domain of life, but not everyone is convinced.

The Structure, Function and Roles of the Archaeal ESCRT Apparatus.

Although morphologically resembling bacteria, archaea constitute a distinct domain of life with a closer affiliation to eukaryotes than to bacteria. This similarity is seen in the machineries for a number of essential cellular processes, including DNA replication and gene transcription. Perhaps surprisingly, given their prokaryotic morphology, some archaea also possess a core cell division apparatus that is related to that involved in the final stages of membrane abscission in vertebrate cells, the ESCRT machinery.

Exploring Spatio-temporal Dynamics of Cellular Automata for Pattern Recognition in Networks.

Network science is an interdisciplinary field which provides an integrative approach for the study of complex systems. In recent years, network modeling has been used for the study of emergent phenomena in many real-world applications. Pattern recognition in networks has been drawing attention to the importance of network characterization, which may lead to understanding the topological properties that are related to the network model. In this paper, the Life-Like Network Automata (LLNA) method is introduced, which was designed for pattern recognition in networks. LLNA uses the network topology as a tessellation of Cellular Automata (CA), whose dynamics produces a spatio-temporal pattern used to extract the feature vector for network characterization. The method was evaluated using synthetic and real-world networks. In the latter, three pattern recognition applications were used: (i) identifying organisms from distinct domains of life through their metabolic networks, (ii) identifying online social networks and (iii) classifying stomata distribution patterns varying according to different lighting conditions. LLNA was compared to structural measurements and surpasses them in real-world applications, achieving improvement in the classification rate as high as 23%, 4% and 7% respectively. Therefore, the proposed method is a good choice for pattern recognition applications using networks and demonstrates potential for general applicability.

Perceptions of Links Between Quality of Life Areas: Implications for Measurement and Practice

Quality of life (QoL) measures frequently conceptualise QoL as having distinct life domains. However, research suggests that there may be overlap. In this study, perceptions of links between life areas are explored. At time one, 143 participants in Khon Kaen, Thailand completed the “Global Person Generated Index” (GPGI), nominating up to five areas important to QoL. Participants then described why they perceived areas as important. Frequencies of links mentioned between areas were recorded. At time two, 42 participants completed the GPGI and were then asked to visually represent the areas of life with circles, overlapping, containing other circles or unconnected to show the interrelationships. Descriptions of the life areas often spontaneously included links with other life areas. “Money” was the most commonly linked area, followed by “job or work” and family. Diagrams representing the relationships between life areas showed diversity. All participants linked at least one area. About 26% presented at least one area as independent. Participants in this sample generally viewed their QoL as composed of some inter-related areas. This has implications for QoL measurement, suggesting data to capture inter-relating domains should be collected. The use of a mixed methods approach to understanding QoL is recommended. Implications for practice are also highlighted, as interventions aimed at one area of QoL will likely impact on others, in ways we currently do not measure.

Bioanalytical tools for the discovery of eukaryotic glycoproteins applied to the analysis of bacterial glycoproteins

The commonly accepted theory that prokaryotes lack the ability to glycosylate their proteins has been disproved recently. The field of bacterial glycoprotein research is no longer considered novel owing to the rapid progress in analytical technologies and genome sequencing that has been made in the last few years. Enhanced interest in glycoprotein discovery in bacteria can be explained by a proven correlation between the presence of glycosylation and bacterial pathogenicity. Eukaryotic and prokaryotic organisms’ features share certain similarities. However, with respect to inherent differences between these two distinct domains of life, the use of bioanalytical tools for glycoprotein analysis in eukaryotic systems often needs modification to be applied successfully to bacteria. In this article, we draw attention to the differences between eukaryotic and prokaryotic glycoproteins. We also focus on the main bottlenecks that may be encountered in the search for glycosylation in concrete bacterium and outline a possible work-flow for the exploration of glycoproteins in bacteria.

Archaeal genetics — the third way

For decades, archaea were misclassified as bacteria because of their prokaryotic morphology. Molecular phylogeny eventually revealed that archaea, like bacteria and eukaryotes, are a fundamentally distinct domain of life. Genome analyses have confirmed that archaea share many features with eukaryotes, particularly in information processing, and therefore can serve as streamlined models for understanding eukaryotic biology. Biochemists and structural biologists have embraced the study of archaea but geneticists have been more wary, despite the fact that genetic techniques for archaea are quite sophisticated. It is time for geneticists to start asking fundamental questions about our distant relatives.

Control Judgements across the Lifespan

Given the inconsistent findings in the literature, we examined age-cohort differences in various personal control judgements over the lifespan ( N = 1623; ages 14-85). For three distinct life domains (personal, social, and societal), participants rated their amount of personal control, the goal importance, the degree of control striving, and, in comparison with same-aged peers, their relative control in each domain. Within this broad lifespan range, the developmental trends showed, as expected, different trajectories depending upon the type of control dimension and the nature of the life domain. The differential nature of these age-cohort trends have important implications for understanding the inconsistent findings reported in the literature, namely, that depending on the nature of the life domain, the type of control dimension, and the age range tested, the trajectories can either increase, decrease, or remain stable. These trends are discussed with reference to various metatheoretical perspectives on lifespan development and control-related judgements.

Bioenergetics of the Archaea.

In the late 1970s, on the basis of rRNA phylogeny, Archaea (archaebacteria) was identified as a distinct domain of life besides Bacteria (eubacteria) and Eucarya. Though forming a separate domain, Archaea display an enormous diversity of lifestyles and metabolic capabilities. Many archaeal species are adapted to extreme environments with respect to salinity, temperatures around the boiling point of water, and/or extremely alkaline or acidic pH. This has posed the challenge of studying the molecular and mechanistic bases on which these organisms can cope with such adverse conditions. This review considers our cumulative knowledge on archaeal mechanisms of primary energy conservation, in relationship to those of bacteria and eucarya. Although the universal principle of chemiosmotic energy conservation also holds for Archaea, distinct features have been discovered with respect to novel ion-transducing, membrane-residing protein complexes and the use of novel cofactors in bioenergetics of methanogenesis. From aerobically respiring Archaea, unusual electron-transporting supercomplexes could be isolated and functionally resolved, and a proposal on the organization of archaeal electron transport chains has been presented. The unique functions of archaeal rhodopsins as sensory systems and as proton or chloride pumps have been elucidated on the basis of recent structural information on the atomic scale. Whereas components of methanogenesis and of phototrophic energy transduction in halobacteria appear to be unique to Archaea, respiratory complexes and the ATP synthase exhibit some chimeric features with respect to their evolutionary origin. Nevertheless, archaeal ATP synthases are to be considered distinct members of this family of secondary energy transducers. A major challenge to future investigations is the development of archaeal genetic transformation systems, in order to gain access to the regulation of bioenergetic systems and to overproducers of archaeal membrane proteins as a prerequisite for their crystallization.

Working and recreating with machines: Outdoor recreation choices among machine‐tool workers in western Pennsylvania

The relationship between work and leisure has most often been described in terms of three basic models. First, the spillover model suggests that one's choice of leisure is affected by interests and attitudes developed during work. Second, the compensation model holds that leisure choices are the opposite of one's work activities, thus providing satisfaction not realized in the work context. Third, according to the segmentation model, work and leisure are distinct life domains and do not interact. Occasionally, a fourth perspective is added: Work and leisure are mutually influential. Evidence for the first three perspectives is mixed. Moreover, there is a units‐of‐analysis problem in studying work and leisure; that is, what about work and leisure is comparable? A patterned socialization model of work and leisure that encompasses and augments these perspectives is presented in this article. Evidence from the outdoor recreation activities of a sample of workers in the machining and tooling industries of west...