Search Results (151)

Complex wastewater matrices hinder the efficacy of conventional treatment methods due to the presence of various inorganic and organic pollutants, along with their intricate interactions. Leveraging the synergy between algae and bacteria, algal–bacterial symbiosis (ABS) systems offering an evolutionary and highly effective approach. The ABS system demonstrates 10–30% higher removal efficiency than conventional biological/physicochemical methods under identical conditions, especially at low C/N ratios. Recent advances in biology techniques and big data analytics have deepened our understanding of the synergistic mechanisms involved. Despite the system’s considerable promise, challenges persist concerning complex pollution scenarios and scaling it for industrial applications, particularly regarding system design, environmental adaptability, and stable operation. In this review, we explore the current forms and operational modes of ABS systems, discussing relevant mechanisms in various wastewater treatment contexts. Furthermore, we examine the advantages and limitations of ABS systems in treating complex wastewater matrices, highlighting challenges and proposing future directions. Full article

New theologies developed in tandem with evolutionary biology during the nineteenth century, which have been called metaphysical evolutionisms and evolutionary theologies. A subset of these theologies analyzed here were developed by thinkers who accepted biological science but rejected both biblical creationism and materialist science. Tools from the cognitive science of religion, including conceptual metaphor theory (CMT) and blending theory, also known as conceptual integration theory (CIT), can help to explain the development of these systems and their transformation between the nineteenth and the twentieth centuries. The analysis focuses on several stable and popular blends of ideas, which have continued with some alteration into the twenty-first century. The three blends evaluated here are Progressive Soul Evolution, Salvation is Evolution, and Evolution is Therapy. Major contributors to these blends are the theosophist and theologian Helena P. Blavatsky and psychologist Frederic W. H. Myers, both influenced by the spiritualist movement, particularly the ideas of the spiritualist and biologist Alfred Russel Wallace. The influence of these blends can be seen in the twentieth-century “Aquarian Frontier,” a group of 145 thinkers and organizations identified in 1975 by counterculture historian Theodore Roszak. Part of the appeal of these blends may be seen in their use of metaphors, including the Great Chain of Being and A Purposeful Life is a Journey. The application of the polysemic term evolution in a sense that does much of the theological work of salvation in Christianity can in part be explained by applying the principles of blending theory, including the vital relation “achieve a human scale,” as well as compressions of time and identity. These blends have been successful because they meet the needs of a population who are friendly towards science but disenchanted with traditional religions. The blends provide a satisfying new theology that extends beyond death for a subset of adherents, particularly in the New Age and spiritual but not religious (SBNR) movements, who combine the agency of self-directed “evolution” with the religious concepts of grace and transcendence. Full article

The recent discovery of TIGR-Tas (Tandem Interspaced Guide RNA-Targeting Systems) marks a major advance in the field of genome editing, introducing a new class of compact, programmable DNA-targeting systems that function independently of traditional CRISPR-Cas pathways. TIGR-Tas effectors use a novel dual-spacer guide RNA (tigRNA) to recognize both strands of target DNA without requiring a protospacer adjacent motif (PAM). These Tas proteins introduce double-stranded DNA cuts with characteristic 8-nucleotide 3′ overhangs and are significantly smaller than Cas9, offering delivery advantages for in vivo editing. Structural analyses reveal homology to box C/D snoRNP proteins, suggesting a previously unrecognized evolutionary lineage of RNA-guided nucleases. This review positions TIGR-Tas at the forefront of a new wave of RNA-programmable genome-editing technologies. In parallel, I provide comparative insight into the diverse and increasingly modular CRISPR-Cas systems, including Cas9, Cas12, Cas13, and emerging effectors like Cas3, Cas10, CasΦ, and Cas14. While the CRISPR-Cas universe has revolutionized molecular biology, TIGR-Tas systems open a complementary and potentially more versatile path for programmable genome manipulation. I discuss mechanistic distinctions, evolutionary implications, and potential applications in human cells, synthetic biology, and therapeutic genome engineering. Full article

Automated generative design is increasingly used across engineering disciplines to accelerate innovation and reduce costs. Generative design offers the prospect of simplifying manual design tasks by exploring the efficacy of solutions automatically. However, existing generative design frameworks rely heavily on expensive optimisation procedures and often produce customised solutions, lacking reusable generative rules that transfer across different problems. This work presents a bioinspired generative design algorithm utilising the concept of evolutionary development (EvoDevo). This evolves a set of developmental rules that can be applied to different engineering problems to rapidly develop designs without the need to run full optimisation procedures. In this approach, an initial design is decomposed into simple entities called cells, which independently control their local growth over a development cycle. In biology, the growth of cells is governed by a gene regulatory network (GRN), but there is no single widely accepted model for this in artificial systems. The GRN responds to the state of the cell induced by external stimuli in its environment, which, in this application, is the loading regime on a bridge truss structure (but can be generalised to any engineering structure). Two GRN models are investigated: graph neural network (GNN) and graph-based Cartesian genetic programming (CGP) models. Both GRN models are evolved using a novel genetic search algorithm for parameter search, which can be re-used for other design problems. It is revealed that the CGP-based method produces results similar to those obtained using the GNN-based methods while offering more interpretability. In this work, it is shown that this EvoDevo approach is able to produce near-optimal truss structures via growth mechanisms such as moving vertices or changing edge features. The technique can be set up to provide design automation for a range of engineering design tasks. Full article

As distant hybridization has profound implications for evolutionary biology, aquaculture, and biodiversity conservation, this study aims to elucidate patterns of maternal inheritance, genetic divergence, and phylogenetic relationships by synthesizing mitochondrial genome (mitogenome) data from 74 distant hybrid fish species. These hybrids span diverse taxa, including 48 freshwater and 26 marine species, with a focus on Cyprinidae (n = 35) and Epinephelus (n = 14), representing the most frequently hybridized groups in freshwater and marine systems, respectively. Mitogenome lengths were highly conserved (15,973 to 17,114 bp); however, the genetic distances between hybrids and maternal species varied from 0.001 to 0.17, with 19 hybrids (25.7%) showing distances >0.02. Variable sites in these hybrids were randomly distributed but enriched in hypervariable regions, such as the D-loop and NADH dehydrogenase subunits 1, 3 and 6 (ND2, ND3, and ND6) genes, likely reflecting maternal inheritance (reported in Cyprinus carpio × Carassius auratus). Moreover, these genes were under purifying selection pressure, revealing their conserved nature. Phylogenetic reconstruction using complete mitogenomes revealed three distinct clades in hybrids: (1) Acipenseriformes, (2) a freshwater cluster dominated by Cypriniformes and Siluriformes, and (3) a marine cluster comprising Centrarchiformes, Pleuronectiformes, Scombriformes, Cichliformes, Anabantiformes, Tetraodontiformes, Perciformes, and Salmoniformes. The prevalence of Cyprinidae hybrids underscores their importance in aquaculture for hybridization, where traits such as rapid growth and disease resistance are enhanced. In contrast, marine hybrids are valued for their market value and adaptability. While mitogenome data robustly support maternal inheritance in most cases, exceptions suggest complex mechanisms, such as doubly uniparental inheritance (DUI), in distantly related crosses. Moreover, AT-skew of genes in hybrids revealed a paternal leakage of traits in mitogenomes. This study also highlights ecological risks, such as genetic swamping in native populations, emphasizing the need for responsible hybridization practices. These findings advance our understanding of the role of hybridization in fish evolution and aquaculture, providing a genomic framework and policy recommendations for optimizing breeding programs, hybrid introduction, and mitigating conservation challenges. Full article

Consciousness remains one of the most critical yet least understood functions of the brain, not only in humans but also in certain highly organized animal species. In this review, we propose treating consciousness as an emergent, goal-directed informational system organized by the subjective “self” as an active system-forming factor. We present an integrative theoretical–systems framework in which subjectivity functions as system-forming factor of consciousness (SFF) throughout biological evolution. Beginning with proto-conscious invertebrates, we trace progressive elaborations of working and long-term memory, the refinement of behavioral programs, and the emergence of an internal arbiter capable of resolving competing drives. In endothermic vertebrates, subjectivity acquires distinct functional features—sensory filtering, causal reasoning, and adaptive arbitration—underpinned by increasingly complex neural architectures. This evolutionary trajectory culminates in humans, where subjectivity attains its highest level of organization through culturally mediated networks. Although the framework does not assume any specific neural substrate, it provides a testable roadmap linking evolutionary biology, information theory, and quantitative modeling. By clarifying why consciousness arose and how subjectivity shapes complex networks, this perspective also lays the groundwork for exploring possible nonbiological extensions of subjectivity. Full article

Invasive species often defy theoretical expectations, successfully establishing and spreading despite reduced propagule pressure and limited genetic diversity. What genomic mechanisms underpin this paradox? How do adaptive processes and host–pathogen interactions shape invasion outcomes? And which genes drive resistance and modulate pathogen virulence? Here, we address these questions using a model of co-invasion: the Asian topmouth gudgeon (Pseudorasbora parva) and its fungal parasite the Rosette agent (Sphaerothecum destruens), a system with profound ecological and economic consequences. Here by (1) mapping the reads obtained by Illumina sequencing on a previously deposited P. parva genome from Germany, (2) identifying SNPs and (3) creating a consensus sequence, we generated the first whole genome of an invasive P. parva population in France and compared it to a German population to explore patterns of genetic diversity, local adaptation, and potential signatures of pathogen resistance. Despite historical bottlenecks, our results reveal unexpectedly high levels of genomic diversity between these invasive populations. We identify candidate loci linked to immune function and provide insights into the evolutionary dynamics of co-introduction. These findings offer a rare window into how invasive species maintain adaptability and how pathogens may co-evolve during range expansion. Beyond advancing our understanding of invasion biology, the genomic resources generated here pave the way for translational approaches, including the development of genome-editing strategies aimed at mitigating the impact of invasive species and their associated pathogens. This work marks a critical step toward unraveling the complex interplay between genetics, ecology, and evolution in biological invasions. Full article

The yeast metabolic and evolutionary engineering, especially Saccharomyces cerevisiae, plays a significant role in the enhancement of its industrial applications in food, beverage, and biofuel production. This review integrates genetic engineering, systems biology, and evolutionary principles to optimize yeast performance, adaptability, and productivity. The key strategies which enable targeted genome modifications to improve substrate utilization, stress tolerance, and the biosynthesis of valuable metabolites such as flavor compounds, organic acids, vitamins, and antioxidants, including precise gene editing, notably CRISPR-Cas9. The metabolic pathway optimization through gene overexpression, deletion, and heterologous pathway integration, supported by multi-omics analyses and the Subcellular compartmentalization of metabolic pathways, which enhances biosynthetic efficiency. This review then discusses evolutionary engineering and global transcription machinery engineering by leveraging natural selection and global gene regulation to improve complex traits. The exploration of non-Saccharomyces species and genome shuffling expands the genetic toolkit for strain development. Emerging approaches, including machine learning and synthetic biology, are accelerating rational strain design. By critically synthesizing these diverse methodologies, this review highlights current advancements, identifies key challenges, and outlines future directions in engineering robust yeast strains for sustainable food biotechnology. Full article

Hans Selye’s stress concept, first introduced in the 1930s, has undergone substantial evolution, extending beyond biology and medicine to influence diverse academic disciplines. Initially, Selye’s General Adaptation Syndrome (GAS) described nonspecific physiological responses to stressors exclusively in mammals, without addressing other biological systems. Consequently, the concept of stress developed independently in biology and medicine, shaped by distinct physiological contexts. This review provides a historical overview of stress research, highlights both parallels and divergences between the stress responses of plants and animals, and integrates insights from traditional Eastern philosophies. We propose an updated GAS framework that incorporates the dynamic balance among reactive oxygen species (ROS), reactive nitrogen species (RNS), and reactive sulfur species (RSS) within the broader context of oxidative stress. We highlight the ionotropic glutamate receptor (iGluR) family and the transient receptor potential (TRP) channel superfamily as minimal molecular architectures for achieving GAS. This perspective expands the classical stress paradigm, providing new insights into redox biology, interspecies stress adaptation, and evolutionary physiology. Full article

The non-random usage of synonymous codons encoding the same amino acid—referred to as codon usage bias (CUB)—varies substantially across genomes and significantly affects translational efficiency by modulating transcriptional and post-transcriptional processes. In chloroplast genomes, the optimization of CUB is critical for improving the efficacy of genetic engineering approaches. However, comprehensive analyses of CUB in Fagopyrum chloroplast genomes remain scarce. In this study, we performed an in-depth comparative analysis of codon usage patterns in the chloroplast genomes of nine Fagopyrum species. Our results revealed a marked AT-rich nucleotide composition, with base content in the order T > A > C > G. We identified 23 optimal codons and 29 high-frequency codons, most of which ended with A or U. Correlation analyses demonstrated that codon usage is strongly influenced by nucleotide skewness (GC and AT skews), protein properties (such as amino acid composition and the number of synonymous codons), and gene expression levels. Neutrality plot analysis (PR2 bias) and evaluations based on the effective number of codons (ENc) indicated that both mutational pressure and natural selection contribute to shaping CUB, with natural selection identified as the predominant evolutionary force. Comparative analyses with four model organisms indicated that Arabidopsis thaliana shares the highest codon usage compatibility with Fagopyrum chloroplast genomes, highlighting its suitability as a potential heterologous expression system. Phylogenetic reconstruction based on codon usage profiles yielded a fully resolved topology with 100% bootstrap support at all nodes, reinforcing the utility of codon usage data in evolutionary inference. This study elucidates the evolutionary determinants of codon usage variation in Fagopyrum plastomes and provides a robust methodological foundation for codon optimization in chloroplast-based synthetic biology. The validated codon adaptation metrics offer promising tools for improving heterologous protein expression and guiding transgene design in advanced breeding strategies. Full article

Type IV pili (T4Ps) are multifunctional surface fibers essential for bacterial motility, adhesion, and virulence, found across Gram-negative and Gram-positive bacteria and archaea. Detailed descriptions of T4P structural biology are allowing progress in understanding T4P biogenesis. Secretins, large outer membrane channels, are crucial for T4P extrusion in Gram-negative bacteria. Using cryo-EM and AlphaFold, we modeled the structure of BfpB, the secretin of the Bundle-Forming Pilus (BFP) of enteropathogenic Escherichia coli. BfpB exhibits a unique 17-fold symmetry, correlating with the thicker BFP filaments, and diverging from the 12–15 subunits typical of T4P, type 2 secretion (T2S), and type 3 secretion (T3S) systems. Additionally, we identified an extended β-hairpin loop in the N3 domain, resembling features of distantly related T3SS secretins, and an N-terminal helix where a C-terminal S-domain is seen in some T2S and T3S secretins. These findings reveal evolutionary parallels and structural adaptations in secretins, highlighting the link between oligomerization and pilus structure. This work advances our understanding of T4P biogenesis, secretin evolution, and bacterial secretion systems, offering insights into pathogenic diversity and future research directions. Full article

Metabolism, the network of biochemical reactions that powers life, arose under conditions radically different from those on Earth today. Investigating its origins reveals how initially simple chemical processes gradually integrated nucleic acid and then protein catalysts, becoming progressively more complex and regulated until they evolved into the enzyme-rich systems observed in modern organisms. Here, we integrate multiple perspectives on the origin of metabolism, focusing primarily on an evolutionary trajectory from an RNA-based world, where ribozymes, metal ions, coenzymes, small peptides, and other small organic molecules worked in concert, to enzyme-driven metabolic networks. We also address the longstanding debates on whether these early metabolic pathways were largely autotrophic or heterotrophic, and consider so-called “pre-metabolisms” (non-enzymatic networks) as an alternative conceptual framework. We discuss key examples such as the Wood–Ljungdahl (W–L) pathway and the reverse tricarboxylic acid (TCA) cycle, both posited to function under early Earth conditions. Finally, we examine how the environment (e.g., minerals, clays, hydrothermal vents) shaped early metabolism, describe unresolved questions about the Last Common Ancestor’s catalytic repertoire and propose future directions that link geochemical insights with molecular biology and synthetic approaches. Full article

The cross-species transmission of influenza viruses represents a critical link in the pandemic of zoonotic diseases. This mechanism involves multi-level interactions, including viral genetic adaptability, host–receptor compatibility, and ecological drivers. Recent studies have highlighted the essential role of mutations in hemagglutinin and neuraminidase in overcoming host barriers, while elucidating the differences in the distribution of host sialic acid receptors. Furthermore, the “mixer” function of intermediate hosts, such as pigs, plays a significant role in viral redistribution. Advances in high-throughput sequencing and structural biology technologies have gradually resolved key molecular markers and host restriction factors associated with these viruses. However, challenges remain in understanding the dynamic evolutionary patterns of virus–host interaction networks, developing real-time early warning capabilities for cross-species transmission, and formulating broad-spectrum prevention and control strategies. Moving forward, it is essential to integrate multidisciplinary approaches to establish a multi-level defense system, leveraging the ‘One Health’ monitoring network, artificial intelligence prediction models, and new vaccine research and development to address the ongoing threat of cross-species transmission of influenza viruses. This paper systematically reviews the research progress and discusses bottlenecks in this field, providing a theoretical foundation for optimizing future prevention and control strategies. Full article

Cartilage is a crucial component of the vertebrate skeletal system, providing structural integrity, flexibility, and adaptive functions across species. In teleost fish, cartilage exhibits significant morphological and functional diversity, providing specialized biomechanical properties essential for aquatic life. This study presents a detailed histological, immunohistochemical, and ultrastructural investigation of cartilage in molly fish (Poecilia sphenops), identifying five distinct types of cartilage: hyaline-cell, scleral, cell-rich hyaline, elastic cell-rich, and matrix-rich hyaline cartilage. Histological staining techniques revealed notable differences in cellular architecture and composition of the extracellular matrix among the cartilage types. Immunohistochemical analysis demonstrated the expression of S100 protein and acetylcholinesterase (Ach), suggesting their involvement in cartilage regulation and maintenance. Endochondral ossification was observed in the head and gill arches. Electron microscopy provided detailed insights into chondrocyte morphology, interactions between cartilage and the perichondrium, and interactions between telocytes and fibroblasts. The findings enhance our understanding of skeletal adaptations in teleost fish, emphasizing the functional diversity of cartilage in aquatic environments. This study contributes to evolutionary biology and may have implications for regenerative medicine and biomaterials research. Full article

In this review dedicated to the great protistologist Edouard Chatton (1883–1947), I wanted to highlight the originality and remarkable diversity of some dinoflagellate protists through the lens of cell biology. Their fossilized traces date back to more than 538 million years (Phanerozoic eon). However, they may be much older because acritarchs from the (Meso) Proterozoic era (1500 million years ago) could be their most primitive ancestors. Here, I described several representative examples of the various lifestyles of free-living (the autotrophic thecate Prorocentrum micans Ehrenberg and the heterotrophic athecate Noctiluca scintillans McCartney and other “pseudo-noctilucidae”, as well as the thecate Crypthecodinium cohnii Biecheler) and of parasitic dinoflagellates (the mixotroph Syndinium Chatton). Then, I compared the different dinoflagellate mitotic systems and reported observations on the eyespot (ocelloid), an organelle that is present in the binucleated Glenodinium foliaceum Stein and in some Warnowiidae dinoflagellates and can be considered an evolutionary marker. The diversity and innovations observed in mitosis, meiosis, reproduction, sexuality, cell cycle, locomotion, and nutrition allow us to affirm that dinoflagellates are among the most innovative unicells in the Kingdom Protista. Full article