Class Families Research Articles

Aggregation-Prone Antimicrobial Peptides Target Gram-negative Bacterial Nucleic Acids and Protein Synthesis

Aggregation of antimicrobial peptides (AMPs) enhances their efficacy by destabilising the bacterial cell wall, membrane, and cytosolic proteins. Developing aggregation-prone AMPs offers a promising strategy to combat antibiotic resistance, though predicting such AMPs and understanding bacterial responses remain challenging. Octopus bimaculoides, a cephalopod species, lacks known AMP gene families, yet its protein fragments were used to predict AMPs via artificial intelligence tools. Four peptides (Oct-P1, Oct-P2, Oct-P3, and Oct-P4) were identified based on their aggregation propensity. Among them, Oct-P2 reduced the viability of Escherichia coli and Staphylococcus aureus by up to 90%, confirmed by confocal laser scanning microscopy and scanning electron microscopy. It further aggregated plasmid DNA in vitro, and the presence of extracellular DNA reduced their antibacterial activity. With knockout mutants, it revealed that Oct-P2 was internalised into bacterial cells, possibly through membrane transport proteins, enhancing its antibacterial effect. Aggregation-induced emission assays and molecular dynamics simulations revealed that Oct-P2 aggregates with transcription promoter DNA, inhibiting transcription and translation in vitro. This dual-target mechanism not only highlights the potential of Oct-P2 as a lead template for new antimicrobial drug development, but also opens a new window for discovering AMPs from protein fragments against the upcoming challenge of bacterial infections. Statement of significanceA popular strategy for identifying antimicrobial peptides (AMPs) in specific genomes uses the conserved regions of AMP families, but this strategy has limitations in organisms lacking classical AMP gene families, such as Octopus. Fragments from non-antimicrobial proteins serve as a rich source for the identification of new AMPs. In this study, we used artificial intelligence tools to search for potential candidate AMP sequences from non-antimicrobial proteins in Octopus bimaculoides. The successful identification of aggregation-prone AMPs was shown to decrease bacterial viability, increase permeability, and reduce biomass. One candidate, Oct-P2, kills the gram-negative bacteria E. coli by aggregating with DNA and inhibiting transcription and translation, suggesting a new intracellular mechanism of AMP activity.

The existence of real nine-dimensional manifolds which include classical one-parameter families of triply periodic minimal surfaces

Triply periodic minimal surfaces have been studied in many fields of natural science, and in particular, many one-parameter families of triply periodic minimal surfaces of genus three have been considered. In 1990s, the moduli theory of triply periodic minimal surfaces established by C. Arezzo and G. P. Pirola [1], [14], and they studied a relationship between the nullity of a minimal surface and the differential of its real period map from the viewpoint of complex geometry. The present paper develops their theory in terms of a real differential geometric aspect, and, by applying the classical transversal property to the real period map, we obtain the numerical evidence for the existence of real nine-dimensional manifolds of triply periodic minimal surfaces which include such one-parameter families. For each case that the transversal property fails, we give values of parameters from which new one-parameter families of triply periodic minimal surfaces issue.

On possible limit functions on a Fatou component in non-autonomous iteration

Abstract The possibilities for limit functions on a Fatou component for the iteration of a single polynomial or rational function are well understood and quite restricted. In non-autonomous iteration, where one considers compositions of arbitrary polynomials with suitably bounded degrees and coefficients, one should observe a far greater range of behavior. We show this is indeed the case and we exhibit a bounded sequence of quadratic polynomials which has a bounded Fatou component on which one obtains as limit functions every member of the classical Schlicht family of normalized univalent functions on the unit disc. The proof is based on quasiconformal surgery and the use of high iterates of a quadratic polynomial with a Siegel disc which closely approximate the identity on compact subsets. Careful bookkeeping using the hyperbolic metric is required to control the errors in approximating the desired limit functions and ensure that these errors ultimately tend to zero.

‘I love my class family’: Writing Realities and Relational Pedagogies

AbstractAsset‐based and relational pedagogies highlight the centrality of meaningful relationships and authenticity in teaching and learning. Foregrounding children's lived experiences, interests, and ways of knowing provides a focus for teachers to be responsive, both relationally and pedagogically. Writing workshop, as conceived in the 1980's by Donald Graves and Lucy Calkins, is a longstanding curricular structure that encourages young writers to engage with multiple tools and resources, including peers, as they compose. Through writing conferences and authors’ chairs, young writers attend to the practice of composing on paper/screen as well as how their message may be received. This study analyzes children's writing samples to underscore the presence of (a) writing identity, (b) critical literacy, (c) culturally sustaining pedagogy, (d) translanguaging, and (e) intertextuality. Chilldren's interactions with tools, peers, and others provide fertile ground for understanding the critical role of a humanizing and relational approach to teaching and learning. The following questions guide this study: (1) How is a writing realities framework reflected in young children's compositions? (2) What do children's writing artifacts reveal about relationality?

The crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase reveals active site features controlling catalytic specificity

Diterpenoid natural products serve critical functions in plant development and ecological adaptation and many diterpenoids have economic value as bioproducts. The family of class II diterpene synthases catalyzes the committed reactions in diterpenoid biosynthesis, converting a common geranylgeranyl diphosphate precursor into different bicyclic prenyl diphosphate scaffolds. Enzymatic rearrangement and modification of these precursors generates the diversity of bioactive diterpenoids. We report the crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase, GrTPS2, at 2.1 Å of resolution. GrTPS2 catalyzes the committed reaction in the biosynthesis of grindelic acid, which represents the signature metabolite in species of gumweed (Grindelia spp., Asteraceae). Grindelic acid has been explored as a potential source for drug leads and biofuel production. The GrTPS2 crystal structure adopts the conserved three-domain fold of class II diterpene synthases featuring a functional active site in the γβ-domain and a vestigial ɑ-domain. Substrate docking into the active site of the GrTPS2 apo protein structure predicted catalytic amino acids. Biochemical characterization of protein variants identified residues with impact on enzyme activity and catalytic specificity. Specifically, mutagenesis of Y457 provided mechanistic insight into the position-specific deprotonation of the intermediary carbocation to form the characteristic 7,13 double bond of 7,13-copalyl diphosphate.

Genome-Wide Identification and Characterization of the Aux/IAA Gene Family in Strawberry Species

Auxin is the first plant hormone found to play a dominant role in fruit growth, from fruit set to fruit ripening. Strawberry plants represent a suitable model for studying auxin’s biosynthesis, sensing, and signaling machinery. Aux/IAA genes are a classical rapid auxin-responsive family. However, the Aux/IAA gene family in Fragaria genus is poorly understood. In this study, a total of 287 Aux/IAA genes were identified in the eight strawberry genomes. Their physicochemical properties, domain structure, and cis-regulatory elements revealed the functional multiplicity of the strawberry Aux/IAAs. We used a phylogenetic analysis to classify these genes into 12 classes. In addition, based on synteny analysis, gene duplications, and calculation of the Ka/Ks ratio, we found that segmental duplications promote the evolution of Aux/IAAs in Fragaria species, which is followed by purifying selection. Furthermore, the expression pattern and protein–protein interaction network of these genes in Fragaria vesca revealed various tissue-specific expressions and probable regulatory functions. Taken together, these results provide basic genomic information and a functional analysis of these genes, which will serve to expand our understanding of the direction in which the Aux/IAA gene family is evolving in Fragaria species.

A survey of the Desulfuromonadia “cytochromome” provides a glimpse of the unexplored diversity of multiheme cytochromes in nature

BackgroundMultiheme cytochromes c (MHC) provide prokaryotes with a broad metabolic versatility that contributes to their role in the biogeochemical cycling of the elements and in energy production in bioelectrochemical systems. However, MHC have only been isolated and studied in detail from a limited number of species. Among these, Desulfuromonadia spp. are particularly MHC-rich. To obtain a broad view of the diversity of MHC, we employed bioinformatic tools to study the cytochromome encoded in the genomes of the Desulfuromonadia class.ResultsWe found that the distribution of the MHC families follows a different pattern between the two orders of the Desulfuromonadia class and that there is great diversity in the number of heme-binding motifs in MHC. However, the vast majority of MHC have up to 12 heme-binding motifs. MHC predicted to be extracellular are the least conserved and show high diversity, whereas inner membrane MHC are well conserved and show lower diversity. Although the most prevalent MHC have homologues already characterized, nearly half of the MHC families in the Desulforomonadia class have no known characterized homologues. AlphaFold2 was employed to predict their 3D structures. This provides an atlas of novel MHC, including examples with high beta-sheet content and nanowire MHC with unprecedented high numbers of putative heme cofactors per polypeptide.ConclusionsThis work illuminates for the first time the universe of experimentally uncharacterized cytochromes that are likely to contribute to the metabolic versatility and to the fitness of Desulfuromonadia in diverse environmental conditions and to drive biotechnological applications of these organisms.

The price of inequality: How state tax policies widen the wealth gap

State taxation has become particularly regressive in recent decades. Across the country, states have increasingly begun to rely on sales and consumption taxes to fund significant portions of their expenditures. Given that these taxes disproportionately hurt lower classes that spend a larger portion of their income on consumable goods and services, these trends widen wealth gaps. By replacing and reducing progressive income taxes with these regressive forms of taxation, levels of inequality have risen. This paper examines the impact of such state and local taxes on the levels of income inequality within each state. Through empirical analysis, it identifies a substantial and positive correlation between the regressivity of state tax codes, as measured by the relative tax burdens on different income brackets, and the levels of inequality, as quantified by the income share of the top 1%. In this study, I examine the relationship between state tax policies and income inequality in the United States. By analyzing the tax structures of different states, I identify a significant correlation between regressive taxes, that disproportionately burden the less wealthy, and increased income inequality. Using quantitative data from 2013 to 2019, I show that states that rely more on taxes that burden working class families, like sales and excise taxes, witness larger portions of wealth concentration within the top 1%. These findings suggest that tax policy at the state level significantly shapes wealth distribution and highlight the need for reforms to reduce inequality at the state level.

Coordinator and Young Adult Perceptions in Attracting and Retaining Chicago Youth in Out-of-School Time Programming

Youth from families with greater economic means have seen an increase in their participation in extracurricular activities, while the participation levels of youth from working class families have decreased. Knowing the benefits to youth participation in extracurricular activities, communities where youth of marginalized backgrounds reside have an obligation to engage their youth in activities offered through school and community out-of-school time programs. Interviews and focus groups with program coordinators and young adults were conducted to identify how youth in Chicago have been attracted, engaged, recruited, and retained in out-of-school time programs. Program aspects and strategies used to connect with youth and their families emerged, some of which have been previously found in the relevant literature to be positively related to youth outcomes, and some of which are specific to youth who identify as Latine and youth who identify as male. Practical implications and suggestions for future research are further discussed.

Pronunciation Challenges of Saudi Female EFL Learners: A Multidimensional Needs Analysis

Mastering English pronunciation poses persistent obstacles for Saudi learners pursuing higher education and careers reliant on strong oral skills. This mixed methods study explores female Saudi university students’ and vocational trainees’ self-reported experiences with pronunciation via questionnaires and interviews. Quantitative findings reveal ongoing segmental and suprasegmental difficulties, with consonant contrasts, vowel distinctions, and stress/rhythm issues most prevalent. Participants emphasize interconnected sociocultural variables influencing development, including class size, technology access, family support, teacher expertise, and learner confidence. Qualitative insights underscore pronunciation as a multifaceted process requiring aligned pedagogical responses. Recommendations center on specialized instructor training, personalized feedback techniques, targeted lessons, and technology integration. By capturing diverse learner perspectives, this research contributes an inclusive examination of needs to advance responsive policies and practices that optimize Saudi females’ pronunciation attainment. Findings affirm pronunciation as a complex yet critical developmental process necessitating comprehensive support structures.

Effect of Ramadan Fasting on Intestinal Microbiota and Fatty Acid Binding Protein 4 in Overweight and Obese Individuals.

Intermittent fasting is a nutritional strategy that focuses on when to eat, rather than what to eat. Although the effectiveness of intermittent fasting practices in many metabolic diseases is known, its effect on microbiota and its underlying mechanism has not yet been clarified. This study aimed to investigate the effect of Ramadan fasting, one of the intermittent fasting practices, on gut microbiota and fatty acid binding protein 4 (FABP4). The study involved 10 male volunteers, 6 of whom were overweight and 4 were obese. They fasted for an average of 14-15 hours daily from dawn to sunset during the 29-day Ramadan month between 23 March - 20 April 2023 and met the inclusion criteria. The participants' nutritional and physical activity status before and during Ramadan, as well as their anthropometric measurements before and after Ramadan, intestinal microbiota, transaminases, gamma-glutamyl transferase, C reactive protein, total cholesterol (C), high-density lipoprotein (HDL) C, low-density lipoprotein C, triglycerides (TG), and FABP4 levels, were evaluated within the scope of the study. The study found a statistically significant increase in both alpha and beta diversity in the intestinal microbiota following Ramadan fasting (p<0.05). The F/B ratio, Firmicutes phylum, Clostridia class, Clostridiales order, and Ruminococcaceae family exhibited statistically significant decreases, while the Bacteroidetes and Proteobacteria phyla, Bacteroidia, Alphaproteobacteria, and Erysipelotrichi classes, Bacteroidales, Erysipelotrichales, and Actinomycetales orders, Erysipelotrichaceae family and Prevotella genus, demonstrated statistically significant increases (p<0.05). Participants who achieved an average weight loss of 2.3±0.99 kg at the end of Ramadan showed a significant increase in HDL-C and a significant decrease in TG levels (p<0.05). Although FABP4 levels decreased after fasting, this difference was not statistically significant (p>0.05). Ramadan fasting induces weight loss, modifies gut microbiota, and improves blood lipid profile and FABP4 levels, suggesting the need for more extensive studies.

A Study of Home Environment, Academic Achievement and Parents Participation of Joint and Nuclear Family Students

In families the children are banned as un governance by parents. Children feel the life of lack. The facility in the family situation, environment, child development and stability learn to enable environment with time in the development and stability of the child, which facility is less in middle class families.

LGBT Agenda in Kazakhstan: Social and Psychological Aspect

The article defends the point of view according to which the increased acuteness of discussions around the LGBT agenda in Kazakhstan is due to the competition of several different socio-cultural codes, the bearers of which are citizens of Kazakhstan. It is proved that the existence of such competition is objective and is due to historical reasons. It is shown that the genesis of the widespread LGBT views reflects, among other things, the crisis of the classical monogamous family, which occurs for objective reasons. The main one of these reasons is the growing difference between the ages of social and biological maturation. It is shown that this crisis, among other things, gives rise to numerous psychological problems, forcing the population of Kazakhstan to increasingly turn to the services of practicing psychologists and psychoanalysts. It is shown that the resolution of accumulated contradictions can be realized through the introduction of modernized concepts in Kazakhstan that meet DEI. At the same time, the modernization of DEI should be based on the need to harmonize various socio-cultural codes on the platform of solving the geopolitical problems facing the Republic of Kazakhstan.

The personalization of smartphone use by mothers from low-class family in Palembang

The societal impact of technological advancements is profound, leading to significant transformations in the way people live. However, a significant proportion of the population continue to be marginalized and excluded. This study aims to examine the complex dynamics that shape the adoption and integration of technology into the daily lives of mothers from low class families. It also investigates how these mothers overcome challenges and leverage the opportunities presented by smartphones to benefit their lives. This study employs a constructivist paradigm and utilizes phenomenological approaches using social construction of technology framework. The data collection was done through in-depth interviews with 10 mothers in Palembang City who met the specified requirements for informants. This study shows that the social and economic factors are the primary factors behind technology appropriation process of mothers from low-class families. They strategically manage their use of mobile technology to meet the unique and particular demands of each home. The results of this study demonstrate that technology is not merely a functional instrument; it is also an entity that is embedded with social and cultural significance, making it inextricably linked to the social dynamics and gender context.

The impact of the pandemic on psychophysical well-being and quality of learning in the growth of adolescents (aged 11-13): a systematic review of the literature with a PRISMA method.

This study examines the social impact and psychological effects of the COVID-19 pandemic on the growth of adolescents students, aged 11-13, on well-being and learning. Said review, therefore, will consider all the report of scientific works published since 2020 on the following platforms: SCOPUS, PsycoInfo, and Web of Science. Specifically, the research has selected all studies concerning students aged 11-13. Furthermore, the authors have restricted the scope of the study to two fundamental aspects of the above-mentioned subjects, such as their physical and psychological well-being and didactic learning following the COVID-19 pandemic. The justification for choosing such themes lies in the fact that the SARS-CoV-2 pandemic and the ensuing measures adopted to curb its spread have had -and very likely will continue having- sizable repercussions in the life of each individual, especially in students considered, whose psychological and physical well-being has been considerably affected. In particular, during the peak of the pandemic and its subsequent phases, the various measures issued to limit contagion have completely compromised and disregarded the rights of children and youngsters. Suddenly, leisure, sport, play, relations, and socialization disappeared from their lives. Besides, in the early stages of the pandemic, remote teaching replaced face-to-face teaching, later to become an intermittent system in the red- and orange-labelled areas of the country. Consequently, such measures have severely limited opportunities for learning, growth, curiosity and creating relationships that are typical of both a school and outside environment. Concerning the well-being of the subjects considered, a review of the target literature indicates a wide range of psychological and physical disorders, such as malaise, eating and sleep disorders, addiction to games, internet, alcohol, and drugs. For what regards, instead, the realm of learning, most studies highlight a diminished school performance as the main implication of remote teaching. Furthermore, a remarkable number of studies reveals substantial social inequalities; specifically, students coming from middle class families have managed to maintain higher quality educational standards in a critical context such as the pandemic, while those students coming from socially disadvantaged families have had fewer learning opportunities both in terms of time and range of experiences (due to lack of electronic devices, Internet connectivity, homework, continuity of after-school activities). In summary, if the school system pre-COVID-19 already presented significant limitations in its ability to reduce existing social inequalities, school closures during lockdowns pose enormous challenges in developing effective policies to compensate learning losses and inequalities. Therefore, based on the results shown, the necessity arises of an emergency plan with social and educational objectives to restore those social, emotional, and cognitive abilities that are compromised. In general, it is the responsibility of countries and governments to guarantee the right to education in these difficult times, while avoiding any type of inequalities and establishing a digital learning system, that allows to face situations such as those generated by the Coronavirus, thus preventing those situations of serious anxiety and stress that have affected most subjects.

Symptoms of Attention Deficit Hyperactivity Disorder and Oral Health Problems among Children in Spain

Introduction: The aim of this study was to explore the association between symptoms of attention deficit hyperactivity disorder (ADHD) and oral health in a representative sample of the Spanish population aged 6–14 years. We also examined the contribution of several sociodemographic and behavioral determinants of children/adolescents and their family environment. Methods: A cross-sectional study involving 3,402 subjects aged between 6 and 14 years from the Spanish National Health Survey. The presence of ADHD symptoms was determined using the self-reported hyperactivity/inattention subscale of the Strength and Difficulties Questionnaire. Oral health was assessed using five indicators: caries, extraction, restorations, gingival bleeding, and the presence of teeth in poor condition (e.g., broken or misaligned). Logistic regressions were used to examine the association between the presence of ADHD symptoms and oral health indicators. These models were adjusted for sociodemographic factors, lifestyle variables, and oral hygiene behaviors relating to both the children and their parents. Results: Compared to children without ADHD symptoms, children with ADHD symptoms had a higher risk of caries (fully adjusted odds ratio: 2.16; 95% confidence interval: 1.66–2.82), extraction (1.42; 1.09–1.85), restoration (1.47; 1.19–1.82) and gingival bleeding (1.64; 1.11–2.41). The increased risk of caries was maintained when the analyses were restricted to middle/high social class families and children with low sugar intake, good oral hygiene behaviors and regular dental visits. Conclusions: Children with ADHD symptoms in Spain had worse oral health indicators than those without ADHD symptoms. Our results suggest that the association of ADHD symptoms with caries was independent of socioeconomic level, cariogenic diet, frequency of toothbrushing, and dental visits.

AARS Online: A collaborative database on the structure, function, and evolution of the aminoacyl-tRNA synthetases.

The aminoacyl-tRNA synthetases (aaRS) are a large group of enzymes that implement the genetic code in all known biological systems. They attach amino acids to their cognate tRNAs, moonlight in various translational and non-translational activities beyond aminoacylation, and are linked to many genetic disorders. The aaRS have a subtle ontology characterized by structural and functional idiosyncrasies that vary from organism to organism, and protein to protein. Across the tree of life, the 22 coded amino acids are handled by 16 evolutionary families of Class I aaRS and 21 families of Class II aaRS. We introduce AARS Online, an interactive Wikipedia-like tool curated by an international consortium of field experts. This platform systematizes existing knowledge about the aaRS by showcasing a taxonomically diverse selection of aaRS sequences and structures. Through its graphical user interface, AARS Online facilitates a seamless exploration between protein sequence and structure, providing a friendly introduction to the material for non-experts and a useful resource for experts. Curated multiple sequence alignments can be extracted for downstream analyses. Accessible at www.aars.online, AARS Online is a free resource to delve into the world of the aaRS.

Molecular Characterization of Odorant-Binding Protein Genes Associated with Host-Seeking Behavior in Oides leucomelaena.

The identification of odorant-binding proteins (OBPs) involved in host location by Oides leucomelaena (O. leucomelaena Weise, 1922, Coleoptera, Galerucinae) is significant for its biological control. Tools in the NCBI database were used to compare and analyze the transcriptome sequences of O. leucomelaena with OBP and other chemosensory-related proteins of other Coleoptera insects. Subsequently, MEGA7 was utilized for OBP sequence alignment and the construction of a phylogenetic tree, combined with expression profiling to screen for candidate antennae-specific OBPs. In addition, fumigation experiments with star anise volatiles were conducted to assess the antennae specificity of the candidate OBPs. Finally, molecular docking was employed to speculate on the binding potential of antennae-specific OBPs with star anise volatiles. The study identified 42 candidate OBPs, 8 chemosensory proteins and 27 receptors. OleuOBP3, OleuOBP5, and OleuOBP6 were identified as classic OBP family members specific to the antennae, which was confirmed by volatile fumigation experiments. Molecular docking ultimately clarified that OleuOBP3, OleuOBP5, and OleuOBP6 all exhibit a high affinity for β-caryophyllene among the star anise volatiles. We successfully obtained three antennae-specific OBPs from O. leucomelaena and determined their high-affinity volatiles, providing a theoretical basis for the development of attractants in subsequent stages.

Interval-Valued Multiobjective Programming Problems Based on Convex Cones

The new solution concepts of interval-valued multiobjective optimization problems using ordering cone are proposed in this paper. An equivalence relation is introduced to divide the collection of all bounded closed intervals into the equivalence classes. The family of all equivalence classes is also called a quotient set. In this case, this quotient set can turn into a vector space under some suitable settings for vector addition and scalar multiplication. The notions of ordering cone and partial ordering on a vector space are essentially equivalent. It means that an ordering in the quotient set can be defined to study the Pareto optimal solution in multiobjective optimization problems. In this paper, we consider the multiobjective optimization problem such that its coefficients are taken to be the bounded closed intervals. With the help of the convex cone, we can study the Pareto optimal solutions of the multiobjective optimization problem with interval-valued coefficients.

Recommended Tool Compounds for the Melanocortin Receptor (MCR) G Protein-Coupled Receptors (GPCRs).

The melanocortin receptors are a centrally and peripherally expressed family of Class A GPCRs with physiological roles, including pigmentation, steroidogenesis, energy homeostasis, and others yet to be fully characterized. There are five melanocortin receptor subtypes that, apart from the melanocortin-2 receptor (MC2R), are stimulated by a shared set of endogenous agonists. Until 2020, X-ray crystallographic and cryo-electron microscopic (cryo-EM) structures of these receptors were unavailable, and the investigation of their mechanisms of action and putative ligand-receptor interactions was driven by site-directed mutagenesis studies of the receptors and targeted structure-activity relationship (SAR) studies of the endogenous and derivative synthetic ligands. Synthetic derivatives of the endogenous agonist ligand α-MSH have evolved into a suite of powerful ligands such as NDP-MSH (melanotan I), melanotan II (MTII), and SHU9119. This suite of tool compounds now enables the study of the melanocortin receptors and serves as scaffolds for FDA-approved drugs, means of validating stably expressing melanocortin receptor cell lines, core ligands in assessing cryo-EM structures of active and inactive receptor complexes, and essential references for high-throughput discovery and mechanism of action studies. Herein, we review the history and significance of a finite set of these essential tool compounds and discuss how they are being utilized to further the field's understanding of melanocortin receptor physiology and greater druggability.