Search Results (92)

Fishes represent an extremely diverse group of organisms, both within and among species. This diversity reflects their association with the environment and resources like habitat and food. Here, examples from diverse life histories of fishes are used to illustrate the significance of the patterns and processes involved in the ongoing dynamic relationships organisms have with their environment. This exploration relates directly to an ongoing paradigm shift in evolutionary biology, where organismal development is at the core. This paper applies knowledge of phenotypic plasticity and transgenerational plasticity in fishes in concert with biosemiotics to explain this kind of approach. It is concluded that the role of signals and cues involved in organismal interpretation and responses to changing conditions play a key role in understanding how new opportunities for development and evolution become realised through complex pathways influencing phenotypic variation within and across generations. Because of their diversity and responsiveness, especially in developmental and life history strategies, fishes are excellent subjects to study this further both theoretically and empirically. Full article

Silk production is a classic example of a domestication trait, yet the cell-type-specific driver of its enhancement in the silkworm Bombyx mori remains unresolved. To address this, we integrated extensive bulk RNA-seq data with a single-nucleus RNA-seq atlas of silk glands (SGs) from domestic B. mori and wild B. mandarina for deconvolution analysis. This identified phenotype-associated cell subpopulations (Scissor+ and Scissor− cells) that enrich in B. mori and B. mandarina, respectively. Transcriptomic characterization revealed that B. mori SG cells exhibit a pervasive “pro-synthesis” transcriptional state, with concerted upregulation of silk protein genes and metabolic pathways. Conversely, B. mandarina cells maintained a “protective–adaptive” state, enriched for stress response and xenobiotic metabolism genes. Pseudotime analysis further delineated the cell state transitions, pinpointing key dynamic gene expression linked to high silk yield. Our findings demonstrate that domestication reshaped the silk gland cellular landscape, promoting a systemic shift toward a synthesis-optimized cell state. This study offers a new framework at the cellular level to elucidate the evolution of complex traits under selection. Full article

Enteroviruses (EVs), particularly those within the species Enterovirus A and B, represent a significant global public health burden, especially in infants and young children. While often causing self-limiting hand, foot, and mouth disease (HFMD), certain serotypes can lead to severe neurological and cardiopulmonary complications. This comprehensive review focuses on the major pathogenic serotypes, including enterovirus A71 (EV-A71), coxsackievirus A16 (CV-A16), coxsackievirus A6 (CV-A6), coxsackievirus B3 (CV-B3), and enterovirus D68 (EV-D68). We began by reconstructing a phylogenetic tree based on VP1 protein sequences, elucidating the genetic relationships and evolutionary patterns among these serotypes, which underpin their diverse antigenicity and epidemiology. Building upon this genetic foundation, the review then provides a detailed synthesis of their distinct pathogenesis, highlighting the five-phase clinical progression from exanthematous phase to convalescence, and their unique tropisms for target organs such as the central nervous system and heart. Progressing to the molecular mechanisms, a critical component of this work is a systematic summary of the specific host receptors that mediate viral entry, including SCARB2 for EV-A71 and CV-A16, sialic acid and ICAM-5 for EV-D68, and CAR/CD55 for CV-B3, explaining the mechanistic basis for their tissue specificity and pathogenicity. Finally, to translate these insights into clinical applications, we critically evaluate the current landscape of vaccine development, noting the high efficacy (~90%) of inactivated EV-A71 vaccines in Asia and the significant global success of poliovirus vaccines, while also addressing the stark lack of cross-protective or licensed vaccines for other prevalent serotypes like CV-A16, CV-A6, and EV-D68. The review concludes that the high genetic diversity and serotype-specific immunity of enteroviruses pose a major challenge, necessitating a concerted shift towards the development of broad-spectrum vaccines and therapeutics informed by an integrated understanding of viral evolution, receptor usage, and pathogenesis. Full article

The internal transcribed spacer (ITS) is one of the most extensively utilized in the taxonomy of the genus Morus due to its generally concerted evolution. Although non-concerted evolution of nuclear ribosomal DNA (nrDNA) has been reported in some species, genome-wide nrDNA characteristics in the genus Morus remain poorly understood. In this study, 158 single-nucleotide polymorphisms (SNPs) and 15 insertions and deletions (InDels) were identified within the nrDNA regions of 542 mulberry accessions representing sixteen Morus species. These wide occurrences of heterogeneous SNPs and InDels revealed the intra-individual polymorphism within the nrDNA region of Morus, indicating the incomplete concerted evolution of nrDNA. Notably, 66 out of 158 SNPs and 13 out of 15 InDels were localized within the ITS regions (ITS1-5.8S-ITS2), indicating a high degree of polymorphism in the ITS, which was further validated through classical cloning and Sanger sequencing methodologies. The 13/16 bp InDel located in the ITS1 region was utilized to develop a rapid and reliable cleaved amplified polymorphic sequence (CAPS) marker-based method for distinguishing M. alba and M. notabilis from other Morus species, eliminating the need for a clone-based sequencing step or comparative phenotypic analysis. Phylogenetic analysis based on nrDNA SNPs from 542 mulberry accessions revealed six distinct clades, corresponding to the six Morus species. These findings offer novel new insights into the taxonomy, conservation, and breeding improvement of Morus species. Full article

The global burden of hepatitis B virus (HBV) remains high, with ongoing concerted efforts to eliminate viral hepatitis as a public health concern by 2030. The absence of curative treatment against HBV makes it an active area of research to further study HBV pathogenesis. In vitro cell culture systems are essential in exploration of molecular mechanisms for HBV propagation and the development of therapeutic targets for antiviral agents. The lack of an efficient cell culture system is one of the challenges limiting the development and study of novel antiviral strategies for HBV infection. However, the evolution of cell culture systems to study HBV pathogenesis and treatment susceptibility in vitro has made a significant contribution to public health. The currently available cell culture systems to grow HBV have their advantages and limitations, requiring further optimization. The discovery of sodium taurocholate co-transporting polypeptide (NTCP) as a receptor for HBV was a major breakthrough for the development of a robust cell model, allowing the study of de novo HBV infection through NTCP expression in the HepG2 hepatoma cell line. This review is aimed at highlighting the evolution of cell culture systems to study HBV pathogenesis and in vitro treatment susceptibility. Full article

Viral infections impose a significant burden on global public health and the economy. This study examines the current state of CRISPR-Cas system research, focusing on their applications in viral detection and their evolution over recent years. A bibliometric analysis and systematic review were conducted using articles published between 2019 and 2024, retrieved from Web of Science, Scopus, and PubMed databases. Out of 2713 identified articles, 194 were included in the analysis. The findings reveal substantial growth in scientific output related to CRISPR-Cas systems, with the United States leading in research and development in this field. The rapid increase in CRISPR-Cas research during this period underscores its immense potential to transform viral diagnostics. With advantages such as speed, precision, and suitability for deployment in resource-limited settings, CRISPR-Cas systems outperform many traditional diagnostic methods. The concerted efforts of scientists worldwide further highlight the promising future of this technology. CRISPR-Cas systems are emerging as a powerful alternative, offering the possibility of expedited and accessible point-of-care testing and paving the way for more equitable and effective diagnostics on a global scale. Full article

Tandem repeats in eukaryotic genomes exhibit intrinsic instability that drives rapid evolutionary diversification. However, their evolutionary dynamics in allopolyploid species such as the water hyacinth (Pontederia crassipes or Eichhornia crassipes) remain largely unexplored. Our study used integrated genomic and cytogenetic analyses of this allotetraploid species to characterize five representative tandem repeats, revealing distinct genomic distribution patterns and copy number polymorphisms. The highly abundant centromeric tandem repeat, putative CentEc, was co-localized with the centromeric retrotransposon CREc, indicating conserved centromeric architecture. Remarkably, putative CentEc sequences showed high sequence conservation (91–100%) despite subgenome divergence, indicative of active concerted evolution. Fluorescence in situ hybridization (FISH) analysis showed ubiquitous telomeric repeats across all chromosomes, while an interstitial chromosome region tandem repeat (ICREc) displayed chromosome-specific localization, both exhibiting copy number variation. Furthermore, differential rDNA organization was observed. 5S rDNA was detected on a single chromosome pair, whereas 35S rDNA exhibited multichromosomal distribution with varying intensities. A comparative analysis of subgenome-specific rDNA sequences revealed substantial heterogeneity in both 5S and 35S rDNA units, suggesting subgenome-biased evolutionary trajectories. Collectively, these findings elucidate the structural and evolutionary significance of tandem repeats in shaping the water hyacinth genome, highlighting mechanisms of concerted evolution and subgenome-biased adaptation in invasive polyploids. Full article

Autonomous vessels are becoming paramount to ocean transportation, while they also face complex risks in dynamic marine environments. Machine learning plays a crucial role in enhancing maritime safety by leveraging its data analysis and predictive capabilities. However, there has been no review grounded in bibliometric analysis in this field. To explore the research evolution and knowledge frontier in the field of maritime safety for autonomous shipping, a bibliometric analysis was conducted using 719 publications from the Web of Science database, covering the period from 2000 up to May 2024. This study utilized VOSviewer, alongside traditional literature analysis methods, to construct a knowledge network map and perform cluster analysis, thereby identifying research hotspots, evolution trends, and emerging knowledge frontiers. The findings reveal a robust cooperative network among journals, researchers, research institutions, and countries or regions, underscoring the interdisciplinary nature of this research domain. Through the review, we found that maritime safety machine learning methods are evolving toward a systematic and comprehensive direction, and the integration with AI and human interaction may be the next bellwether. Future research will concentrate on three main areas: evolving safety objectives towards proactive management and autonomous coordination, developing advanced safety technologies, such as bio-inspired sensors, quantum machine learning, and self-healing systems, and enhancing decision-making with machine learning algorithms such as generative adversarial networks (GANs), hierarchical reinforcement learning (HRL), and federated learning. By visualizing collaborative networks, analyzing evolutionary trends, and identifying research hotspots, this study lays a groundwork for pioneering advancements and sets a visionary angle for the future of safety in autonomous shipping. Moreover, it also facilitates partnerships between industry and academia, making for concerted efforts in the domain of USVs. Full article

Ubiquitylation is a post-translational modification that modulates protein function and stability. It is orchestrated by the concerted action of three types of enzymes, with substrate specificity governed by ubiquitin ligases (E3s), which may exist as single proteins or as part of multi-protein complexes. Although Cullin (CUL) proteins lack intrinsic enzymatic activity, they participate in the formation of active ubiquitin ligase complexes, known as Cullin-Ring ubiquitin Ligases (CRLs), through their association with ROC1 or ROC2, along with substrate adaptor and receptor proteins. Mammalian genomes encode several CUL proteins (CUL1–9), each contributing to distinct CRLs. Among these CUL proteins, CUL1, CUL3, and CUL4 are believed to be the most ancient and evolutionarily conserved from yeast to mammals, with CUL4 uniquely duplicated in vertebrates. Genetic evidence strongly implicates CUL4-based ubiquitin ligases (CRL4s) in chromatin regulation across various species and suggests that, in vertebrates, CRL4s have also acquired a cytosolic role, which is facilitated by a cytosol-localizing paralog of CUL4. Substrates identified through biochemical studies have elucidated the molecular mechanisms by which CRL4s regulate chromatin and cytosolic processes. The substantial body of knowledge on CUL4 biology amassed over the past two decades provides a unique opportunity to explore the functional evolution of CRL4. In this review, we synthesize the available structural, genetic, and biochemical data on CRL4 from various model organisms and discuss the conserved and novel functions of CRL4s. Full article

Background/Objectives: Accipitridae mitogenomes exhibit unique structural variations, including duplicated control regions (CRs) that undergo gradual degeneration into pseudo-CRs, revealing a complex evolutionary landscape. However, annotation of this characteristic in a subset of accipitrid genomes is lacking. Due to the taxonomic diversity of Accipitridae and the presence of understudied species, comprehensive mitogenomic studies are essential. This study sought to expand and investigate the evolutionary characteristics of Accipitridae mitogenomes. Methods: A comparative analysis was conducted using the newly acquired complete mitogenomes of Haliastur indus and Accipiter badius poliopsis along with 22 available accipitrid mitogenomes. Codon usage, selective pressure, phylogenetic relationships, and structural variations were comparatively analyzed. Results: Accipitrid mitogenomes showed a strong AT bias with adenine preference. Most protein-coding genes (PCGs) were under purifying selection except for ND3, which underwent positive selection. The ATP8 gene exhibited relaxed purifying selection on codon usage patterns and showed high genetic variation. Selection for ATP8 and ND3 genes was specific to certain clades of accipitrids. Gene order re-examination revealed both non-degenerate CRs and highly degenerate CR2 fragments in the Accipitridae family. Non-degenerate CRs were found in early diverging species, such as Elanus caeruleus and Pernis ptilorhynchus orientalis, while more recent lineages had highly degenerate CR2 fragments with missing conserved element. Repeat motifs and sequence variations were observed in the functional CR. Conclusions: These findings suggest that ATP8 and ND3 genes reflect metabolic adaptations, while CRs indicate potential diversification of these accipitrid species. This study provides valuable insights into mitochondrial genome evolution within the Accipitridae family. Full article

This research study computationally examined the thermal decomposition of three molecules, 3,6-dihydro-2H-pyran, 4-methyl-3,6-dihydro-2H-pyran, and 2,6-dimethyl-3,6-dihydro-2H-pyran, using the PBE0/6-311+G(d,p) level of theory and a concerted mechanism with a 6-member cyclic transition state. For this analysis, kinetic and thermodynamic parameters were calculated for reactions within a temperature range of 584 to 633 K and compared with experimental data. Our results revealed that methyl substituents at 2, 4, and 6 positions decrease the activation free energy of the molecules. Even though the evaluated reactions exhibited high absolute synchronicity, significant differences were observed regarding the extent of their bond evolution. Full article

Land degradation poses a significant global challenge, adversely affecting soil quality and diminishing the productivity of arable land, which, in turn, impacts food production and ecosystem services. This degradation manifests in various forms, including soil compaction, salinity, nutrient depletion, loss of biodiversity, and contamination, ultimately rendering soil unproductive and exacerbating climate change. Given the challenges arising from conventional farming practices and climate change, there is an urgent necessity to develop agricultural systems that not only enhance agronomic efficiency but also improve environmental performance. This study focuses on addressing food security in Africa by investigating the role of land restoration and biodiversity in sustainable food systems through a comprehensive bibliometric analysis for documents between 2010 to 2023, identifying 64 relevant documents. The analysis reveals insights into the most-cited documents and thematic evolution, underscoring the significant contributions from Ethiopia and advocating for collaborative efforts among African nations. Key themes identified include “climate change”, “food security”, “biodiversity conservation”, and “agroecosystems”, all highlighting the importance of sustainable agricultural practices. The study anticipates a continued prioritization of agroecosystems, smart agriculture, and biodiversity conservation to tackle food security challenges in the face of climate change. Collaboration, investment in research, and practical initiatives emerge as essential components for achieving sustainable food security and mitigating climate change impacts in Africa. This research provides valuable insights into the current landscape and future trends regarding the contributions of land restoration and biodiversity to food systems in Africa, emphasizing the critical need for concerted efforts to address these pressing issues. Full article

Although there have been concerted efforts to integrate Tibetan Buddhist monastic education into the Indian university system since the 1960s, the attainment of academic accreditation has tended to require significant curricular trade-offs. The majority of Tibetan Buddhist monastic colleges have therefore eschewed the potential advantages of academic accreditation—including greater opportunities for monastic graduates in universities and other secular contexts—in order to preserve the rigour of traditional scholastic programmes. However, through its affiliation to the University of Mysore in 2022, the Geluk monastery of Sera Je is now able to award accredited Bachelor of Arts (BA) degrees even without making significant changes in practice to its traditional curriculum and pedagogy. This article examines the structure and content of Sera Je’s new programmes and contextualises what may prove to be a landmark development against the backdrop of previous attempts to negotiate the boundary between Tibetan Buddhist monastic education and university education in India. It suggests that the accreditation of research programmes raises further challenges in addition to those associated with the accreditation of taught programmes. Nonetheless, the urgency of solving these longstanding issues appears to have been heightened by a developing crisis in Tibetan Buddhist monastic recruitment. In investigating the topic of academic accreditation, this article throws light on an issue that has driven notable evolutions in Tibetan Buddhist monastic education in India but has previously received little scholarly attention. Full article

Defect engineering, by adjusting the surface charge and active sites of CoP catalysts, significantly enhances the efficiency of the oxygen evolution reaction (OER). We have developed a new Co_1−xP_v catalyst that has both cobalt defects and phosphorus vacancies, demonstrating excellent OER performance. Under both basic and acidic media, the catalyst incurs a modest overvoltage, with 238 mV and 249 mV needed, respectively, to attain a current density of 10 mA cm⁻². In the practical test of alkaline electrocatalytic water splitting (EWS), the Co_1−xP_v || Pt/C EWS shows a low cell voltage of 1.51 V and superior performance compared to the noble metal-based EWS (RuO₂ || Pt/C, 1.66 V). This catalyst’s exceptional catalytic efficiency and longevity are mainly attributed to its tunable electronic structure. The presence of cobalt defects facilitates the transformation of Co²⁺ to Co³⁺, while phosphorus vacancies enhance the interaction with oxygen species (*OH, *O, *OOH), working in concert to improve the OER efficiency. This strategy offers a new approach to designing transition metal phosphide catalysts with coexisting metal defects and phosphorus vacancies, which is crucial for improving energy conversion efficiency and catalyst performance. Full article

The lack of a universally accepted definition of a pandemic hinders a comprehensive understanding of and effective response to these global health crises. Current definitions often lack quantitative criteria, rendering them vague and limiting their utility. Here, we propose a refined definition that considers the likelihood of susceptible individuals contracting an infectious disease that culminates in widespread global transmission, increased morbidity and mortality, and profound societal, economic, and political consequences. Applying this definition retrospectively, we identify 22 pandemics that occurred between 165 and 2024 AD and were caused by a variety of diseases, including smallpox (Antonine and American), plague (Justinian, Black Death, and Third Plague), cholera (seven pandemics), influenza (two Russian, Spanish, Asian, Hong Kong, and swine), AIDS, and coronaviruses (SARS, MERS, and COVID-19). This work presents a comprehensive analysis of past pandemics caused by both emerging and re-emerging pathogens, along with their epidemiological characteristics, societal impact, and evolution of public health responses. We also highlight the need for proactive measures to reduce the risk of future pandemics. These strategies include prioritizing surveillance of emerging zoonotic pathogens, conserving biodiversity to counter wildlife trafficking, and minimizing the potential for zoonotic spillover events. In addition, interventions such as promoting alternative protein sources, enforcing the closure of live animal markets in biodiversity-rich regions, and fostering global collaboration among diverse stakeholders are critical to preventing future pandemics. Crucially, improving wildlife surveillance systems will require the concerted efforts of local, national and international entities, including laboratories, field researchers, wildlife conservationists, government agencies and other stakeholders. By fostering collaborative networks and establishing robust biorepositories, we can strengthen our collective capacity to detect, monitor, and mitigate the emergence and transmission of zoonotic pathogens. Full article