Search Results (2,086)

The mevalonate (MVA) pathway is a central metabolic route responsible for the biosynthesis of isoprenoids with broad biological and biotechnological relevance. Due to its importance, the MVA pathway has attracted increasing interest in studies of enzymatic regulation, structural biology, metabolic engineering, and synthetic biology, particularly in fungi. This review provides a comprehensive overview of the MVA pathway, addressing its distribution across different domains of life, evolutionary aspects, and metabolic organization, with emphasis in fungi. Special attention is given to the biochemical and structural characterization of MVA-pathway enzymes, including catalytic mechanisms, structural features, and regulatory processes. The methylerythritol phosphate pathway is also presented as an alternative route for isoprenoid precursor biosynthesis and discussed in terms of its taxonomic distribution and metabolic significance. Recent advances in synthetic biology, enzyme regulation, and pathway engineering are highlighted, emphasizing their contributions to metabolic engineering and synthetic biology. Special emphasis is given to fungi, in which the MVA pathway plays a central role in ergosterol biosynthesis, protein prenylation, and secondary metabolite production. Advances in the engineering of fungal cells, including Saccharomyces cerevisiae and other emerging fungal species, are discussed in the context of sustainable isoprenoid production. Finally, strategies for optimizing microbial production are presented, highlighting the importance of fungal synthetic biology in advancing biotechnological applications. Full article

Among myrmecophilous insects, beetles represent the most specialised and diverse group. Myrmecophily is a complex evolutionary strategy encompassing a wide spectrum of interactions with ants, ranging from occasional to obligate relationships, and from mutualistic associations (e.g., trophobionts) to fully parasitic symbioses (social parasites). One of the most remarkable examples of an obligate ant parasite is Paussus favieri Fairmaire,1851 (Carabidae, Paussinae, Paussini), a West-Mediterranean ant-nest beetle. This species spends most of its life inside the nests of Pheidole pallidula (Nylander, 1849) (Hymenoptera, Formicidae), where it exploits the colony’s most valuable resources (ant larvae, pupae, and tenerals) through a suite of sophisticated chemical and structural adaptations that allow it to evade detection and integrate seamlessly into the host colony. For these reasons, P. favieri has recently emerged as a key model organism for studying host–parasite interactions in eusocial systems. In this study, we investigated possible correlations between the nervous system of P. favieri and its remarkable morphological and behavioural adaptations, shedding light on how an extreme environment such as the ant nest may have shaped the beetle’s brain. Our results, although requiring more in-depth analysis, reveal an exceptional development of the central body and the antennal lobes, which rank among the largest recorded across all insect species studied to date. We also report two previously undescribed morphological asymmetries affecting the optic lobes and mushroom bodies. Together, these findings provide new insights into the neuroanatomy of carabid beetles and, more broadly, into the biology of a unique model of ant parasitism, advancing our understanding of the evolutionary adaptations that characterise the highly specialised Paussinae subfamily, laying down the basis for further analysis. Full article

Methylation of histone H3 at lysine 4 (H3K4me) is a key epigenetic mark in plants, governing transcriptional regulation, development, and stress adaptation. While the enzymes that deposit and remove this mark are well studied, how H3K4me signals are interpreted by reader proteins remains less understood. This review synthesizes recent advances in the molecular recognition of H3K4me states by plant reader domains, including PHD, BAH, CW, Tudor, and chromodomain modules. Unlike prior reviews that focused on writers and erasers or on stress-specific responses, we systematically examine the reader-side mechanisms, with particular emphasis on how distinct methylation states, including trimethylated (H3K4me3), dimethylated (H3K4me2), monomethylated (H3K4me1), and unmethylated H3K4, are discriminated and translated into chromatin-based outputs. These readers function as signaling hubs, integrating environmental and hormonal cues to regulate flowering, DNA repair, and stress memory, with implications for crop performance. However, fundamental gaps remain, including the identification of H3K4me1-specific readers, the structural basis for combinatorial histone mark recognition, and the evolutionary divergence of reader pathways between monocots and dicots. Our review provides a framework for understanding H3K4me reader biology and explores its potential for application in plant breeding. Full article

Wound healing is a fundamental biological process essential to maintaining structural integrity and survival across both plant and animal life. Despite the profound evolutionary distance separating these kingdoms, wound healing provides one of those momentous occasions when these biological universes collide, revealing significant evolutionary parallels in the core mechanisms of healing, despite clear molecular and physiological differences. However, two challenges have hindered systematic cross-kingdom comparisons. First, unlike animal wound healing, the major phases of plant wound healing have not been organized into a universally accepted classification. Second, no comparative framework exists for systematically comparing wound-healing processes across plant and animal kingdoms. To address these challenges, we developed a comparative classification framework that organizes wound healing into three functional phases: (1) bioelectrical signaling, (2) immune responses, and (3) tissue formation and remodeling. This classification defines the major phases of plant wound healing, while the comparative framework establishes a common basis for systematic cross-kingdom comparison. Through comparative analysis, multiple shared cellular and molecular mechanisms were identified. These findings led to a conceptual model termed the hybrid-wound healing system, integrating plant- and animal-derived regenerative responses and providing a theoretical basis for future bioinspired regenerative strategies. Within this system, living plant stem cells are proposed as central biological components that may potentially act as intelligent pharmaceutical microfactories, releasing bioactive molecules in suitable microenvironments. This approach represents a hypothetical future strategy requiring extensive preclinical validation to strategies based on extracts, conditioned media, extracellular vesicles, or isolated bioactive compounds. Collectively, this descriptive review establishes a conceptual foundation for future investigations in plant biology, wound healing, and regenerative medicine. Full article

Circulating tumor DNA (ctDNA) was initially conceived as a minimally invasive surrogate for interrogating cancer biology; however, three decades of evidence have demonstrated that plasma is not a passive reservoir of tumor-derived material, but rather a dynamic and biologically heterogeneous milieu in which multiple competing genomic signals coexist. This review explores the level of interpretive rigor required to translate ctDNA detection into clinically actionable precision oncology. Clonal hematopoiesis of indeterminate potential (CHIP) is discussed not as an occasional confounder, but as an intrinsic source of biological background noise, underscoring the critical importance of matched leukocyte sequencing to discriminate tumor-derived alterations from hematopoietic variants, particularly in older individuals and in patients previously exposed to cytotoxic therapies. The widespread assumption that variant allele frequency (VAF) directly reflects tumor burden is critically re-evaluated through the mathematical relationships linking VAF to tumor fraction, local copy-number architecture, and mutation multiplicity. Within this framework, estimation of cancer cell fraction (CCF) and probabilistic discrimination between clonal and subclonal events are examined, including the emergence of reversion mutations as molecular evidence of therapy-driven evolutionary adaptation. The review also addresses the central paradox of ultra-sensitive sequencing technologies: although unique molecular identifiers and duplex sequencing can extend analytical sensitivity below 0.01% VAF, sensitivity in the absence of contextual specificity risks conflating technical artifacts and biologically insignificant alterations with clinically meaningful disease. Equal emphasis is placed on pre-analytical variables, highlighting how sample collection, stabilization, and processing protocols define the upper limit of downstream analytical reliability. Beyond single-nucleotide variants, fragmentomic and methylation-based approaches are presented as complementary orthogonal dimensions capable of revealing tumor-associated signals even when mutational evidence is limited or absent. Longitudinal ctDNA assessment is argued to provide substantially greater biological and clinical insight than isolated static measurements, while robust clinical reporting is shown to depend on transparent disclosure of assay limitations, residual uncertainty related to CHIP, and structured bidirectional communication between molecular laboratories and treating clinicians. Ultimately, the transition from a biomarker-centered model toward an integrated systems-based framework, combining genomics, epigenomics, fragmentomics, and evolutionary modeling, emerges as the defining challenge for the next generation of liquid biopsy in precision oncology. Full article

The Zona Pellucida (ZP) and its structural analogs are evolutionarily ancient extracellular matrix components. These are essential for oocyte protection, species-specific gamete recognition, and prevention of polyspermy across Metazoa. Defined by the conserved ZP-domain—comprising ZP-N and ZP-C subdomains—these glycoproteins self-assemble into fibrillar matrices through tightly regulated polymerization. Mechanisms of the regulated polymerization involve furin cleavage, disulfide bonding, and hydrophobic interactions. Once considered a vertebrate innovation, the canonical ZP-domain—defined by its bipartite ZP-N/ZP-C architecture, eight conserved cysteine residues, and capacity for matrix polymerization—is now recognized as an ancient metazoan extracellular module, with homologs identified in basal lineages including Porifera, Cnidaria, and Placozoa. While ZP-like sequences have been reported in choanoflagellates such as Salpingoeca rosetta, these lack the complete canonical features and are considered distant structural relatives rather than true ZP-modules. There they function in cell adhesion and tissue integrity, suggesting an origin predating the evolution of specialized reproductive coats. Previous phylogenetic analyses across 97 metazoan species have revealed that vertebrate ZP genes arose from ancestral duplications of the canonical ZP-module. Accordingly, they give rise to eight subfamilies (ZP1–ZP4, ZPD, ZPAX, ZPX, ZPY), with lineage-specific expansions, losses, and pseudogenization reflecting adaptations to diverse reproductive strategies. Positive selection in sperm-binding regions of ZP2 and ZP3 drives a rapid adaptive evolution. It underscores coevolutionary arms races with sperm ligands, contributing to reproductive isolation and speciation. In invertebrates such as abalone and insects, ZP-domain proteins mediate analogous functions through lineage-specific elaborations, including tandem repeats and domain shuffling. Post-translational modifications, particularly glycosylation, fine-tune sperm receptor specificity and matrix stability. The functional transition from a general protective barrier in early metazoans to a sophisticated gamete recognition interface in vertebrates exemplifies modular evolution. This synthesis highlights the domain-level deep homology of ZP-domain proteins as a foundational element of metazoan extracellular matrices, repurposed through gene duplication, neofunctionalization, and selection to meet the demands of evolving reproductive modes. These insights bridge evolutionary biology, reproductive medicine, and developmental genetics. However, major gaps remain, including unresolved orthology between vertebrate and invertebrate ZP genes, the relative contribution of glycans versus protein backbone in sperm recognition, and the lack of functional evidence for canonical ZP-domain proteins in insects. Future studies integrating glycoproteomics, single-cell transcriptomics, and CRISPR-based models are needed to resolve these questions. Full article

Grassland foliar functional traits are closely linked to ecosystem functioning, biodiversity, and plant responses to environmental change. Hyperspectral remote sensing provides an efficient and non-destructive approach for mapping foliar traits, yet direct comparisons between UAV-based and airborne imaging spectroscopy remain limited. In this study, we evaluated the performance of UAV-based Nano and airborne Hyspex hyperspectral imagery for predicting ten foliar functional traits across experimental grassland plots at the Cedar Creek Ecosystem Science Reserve, USA. We further assessed the contributions of visible-to-near-infrared (VNIR) and shortwave infrared (SWIR) spectral regions, as well as the effects of spectral preprocessing approaches for minimizing confounding effects from canopy structure, illumination/viewing geometry, and soil background. Random Forest regression models were developed using plot-level average spectra derived from Nano and Hyspex imagery. Both UAV- and airborne-based imaging spectroscopy achieved moderate to high prediction accuracies for most foliar traits. High accuracies were obtained for non-structural carbohydrates (NSC), carotenoids, β-carotene, hemicellulose, and cellulose (R² = 0.66–0.82; NRMSE = 6–10%), while moderate accuracies were achieved for nitrogen, chlorophyll, and xanthophylls (R² = 0.51–0.74; NRMSE = 8–12%). In contrast, carbon and lignin consistently exhibited lower predictive performance (R² = 0.32–0.59; NRMSE = 9–15%). Despite covering only the VNIR spectral range, the UAV-based Nano imagery achieved accuracies comparable to those obtained using the airborne full-spectrum Hyspex imagery, indicating that high spatial resolution can partially compensate for limited spectral coverage by reducing soil background effects. The VNIR spectral region alone provided trait estimation accuracies comparable to those obtained using the full visible-to-shortwave infrared (VSWIR) spectrum, whereas SWIR wavelengths contributed only marginal improvements for a subset of structural traits. Among preprocessing approaches, vector normalization generally improved prediction performance by reducing the confounding effects of canopy structure and illumination/viewing geometry, whereas NIR_v-adjusted spectra provided limited benefits. Our findings demonstrate that UAV-based VNIR imaging spectroscopy can provide accurate and cost-effective estimation of grassland foliar functional traits. The results also highlight important trade-offs between spectral and spatial resolution in hyperspectral remote sensing and provide practical guidance for selecting imaging spectroscopy platforms and preprocessing approaches for grassland ecosystem monitoring. Full article

The carcinogenic liver fluke Opisthorchis viverrini underlies one of the world’s heaviest burdens of bile duct cancer, yet for decades it was treated as a single, genetically uniform parasite whose transmission was shaped mainly by environment and human behavior. However, advances in molecular biology have fundamentally reshaped this conceptual model. Evidence accumulated over the past three decades demonstrates that O. viverrini comprises geographically structured populations linked to hydrological connectivity, host distribution, and long-term evolutionary processes across interconnected river systems of mainland Southeast Asia, particularly within the Lower Mekong Basin. This review synthesizes research on the systematics and population structure of O. viverrini and its Bithynia snail hosts, tracing the transition from early allozyme studies to contemporary DNA-based and genomic approaches. Collectively, mitochondrial, nuclear, microsatellite, and intron markers reveal strong spatial structuring among parasite populations, while genetic patterns observed in snail hosts show partial geographic concordance with parasite population structure, suggesting that both may be influenced by shared hydrological organization, ecological isolation, and host connectivity across endemic aquatic systems. Population structure is strongly scale-dependent, with local panmixia often occurring within connected aquatic systems but pronounced differentiation emerging across broader geographic regions. Together, these findings indicate that transmission dynamics are shaped not only by environmental and behavioral factors, but also by evolutionary and landscape-level processes influencing host and parasite connectivity. Finally, we emphasize the increasing significance of population genomics and landscape genetics in understanding how transmission systems persist, disperse, reconnect, and respond to environmental change across endemic landscapes. Full article

KCTD proteins exhibit significant structural complexity, arising from their modular organization, oligomerization, and intricate biological partnerships. Although their biological importance has been assessed for two decades, the biochemical basis of their activities is only partially understood. This is certainly due to the limited structural information that was available until a few years ago. Fortunately, some recent insightful structural studies and the advent of machine-learning-based approaches are rapidly changing the scenario. By surveying the literature and structural databases and integrating this information with ad hoc 3D-structure predictions, we provide a detailed view of the structural biology of these proteins at different levels: individual domains, full-length oligomers, functional hetero-oligomers formed by different family members, and complexes with functional partners. Collectively, these surveys and analyses provide insights into the family’s evolutionary history and its structure–function relationships. The family-wide coverage of structural information also indicates the extent to which structural similarities are reflected in functional analogies. Finally, the potential functional implications of the intricate architecture of these multimeric proteins and the tendency of their members to hetero-oligomerize are discussed from a functional perspective. Full article

Whale watching is frequently presented as a benign form of wildlife interaction, yet its ethical and ecological acceptability depends on two conditions: vessel practices must minimize disturbance to free-ranging cetaceans, and tours must provide meaningful conservation-oriented education. This study assessed whale-watching operations in the New York City Metropolitan Area using three complementary frameworks: the Whale SENSE “On the Water” evaluation, the World Cetacean Alliance (WCA) Best Practice Guidance, and a Higher-Order Thinking Skills (HOTS) framework for interpretation. Eight trips representing the active full-time commercial sector in the study area were observed between May and November 2022. The results have revealed that certified operators generally performed better than uncertified operators, but the difference was not large enough to demonstrate that certification alone ensured welfare-protective practice. Educational content was often present but shallow, with limited discussion of cetacean threats, conservation measures, and legal protections, while higher-order engagement and multilingual accessibility were notably weak. Vessel behavior showed a similar pattern: certified operators achieved higher average scores, yet close approaches, inconsistent adherence to conservative speed and maneuvering guidance, and occasional unacceptable practices were still recorded. Overall, some operations still expose whales to avoidable disturbance and fail to meet the educational standards that give ecotourism its conservation value. Responsible whale watching should therefore be evaluated not only by whether vessels find whales and satisfy tourists, but also by whether operators demonstrably protect animal welfare and cultivate informed conservation attitudes. As such, this study offers a regionally novel benchmark for future comparative research, management evaluation, and the development of more responsible cetacean ecotourism. Full article

Introduction: The circum-Mediterranean region is a global biodiversity hotspot, hosting a highly distinctive freshwater fauna with a high degree of endemism and conservation concern. However, these ecosystems are increasingly threatened by biological invasions, particularly by non-native fish species, which represent a major driver of biodiversity loss. Objective: This study aims to compile a comprehensive and updated inventory of non-native inland fish species across the circum-Mediterranean region and to identify the main taxonomic, biogeographical, and socio-environmental drivers shaping their distribution. Methodology: We conducted an extensive review of the scientific literature, online databases (including EASIN, GISD, and CABI), and technical reports to compile records of non-native fish species across inland and transitional waters of Mediterranean-climate basins. Analyses focused on species composition, taxonomic representativeness, introduction pathways, native regions, and the relationship between species richness and selected environmental and socio-economic variables. Results: A total of 151 non-native fish species were recorded across the study area. Italy, Spain, Bosnia and Herzegovina, France, and Croatia exhibited the highest numbers of established species. Taxonomic representation was uneven, with Salmoniformes and Esociformes overrepresented among established non-native species, while Siluriformes and Characiformes were underrepresented. Most introductions originated from Europe, Asia, and North America, primarily through intentional releases and escape events. Non-native species richness was positively correlated with gross domestic product, precipitation, and the number of dams, highlighting the role of economic development and habitat modification in facilitating invasions. Conclusions: Biological invasions by non-native fishes are widespread across the Mediterranean basin and are strongly driven by human activities and environmental conditions. The high invasion levels observed in this biodiversity hotspot pose a significant threat to endemic freshwater faunas. These findings underscore the need for coordinated transnational management strategies, stricter regulation of introduction pathways, and prioritization of high-risk species to mitigate further impacts. Full article

Introduction: Squalius palaciosi (Doadrio, 1980; Leuciscidae) is a highly threatened freshwater fish species with an extremely restricted distribution, currently confined to a few tributaries on the right bank of the Guadalquivir River basin. During the 1980s, its populations were abundant and constituted a dominant component of local fish communities. However, multiple threats led to a drastic population decline, bringing the species to the brink of extinction. From an evolutionary perspective, S. palaciosi is particularly remarkable due to its polyploid condition and its potential involvement in hybridogenetic complexes, a rare phenomenon in the Iberian Peninsula. Hybridogenetic systems are well documented in its congeners Squalius alburnoides, widely distributed across Iberian river basins, and Squalius sp., restricted to the Guadiana basin. In these systems, the maternal lineage is shared (Squalius pyrenaicus), whereas the paternal lineage varies and remains unknown in S. palaciosi. Objective: This study aims to generate the first genomic data for S. palaciosi and to elucidate its evolutionary origin, as well as its mitochondrial and nuclear phylogenetic relationships within hybridogenetic complexes. Methodology: Genomic DNA was extracted from skeletal remains of preserved specimens housed in the fish collection of the National Museum of Natural Sciences (MNCN-CSIC) and subjected to Illumina short-read sequencing. After quality filtering, potential contaminant reads were removed. The complete mitochondrial genome and several nuclear gene fragments were assembled. Mitochondrial phylogenetic analyses were conducted using publicly available whole-genome sequencing data from Iberian freshwater fish species. Nuclear gene fragments were taxonomically assigned using BLAST analyses. Results: Phylogenetic analyses revealed that S. palaciosi is closely related at the mitochondrial level to S. alburnoides and S. tartessicus, with strong statistical support. BLAST-based taxonomic assignments of nuclear markers suggest the involvement of multiple Iberian freshwater fish species in the hybridogenetic origin of S. palaciosi. Conclusions: Our results provide novel insights into the evolutionary history of S. palaciosi and support a complex hybridogenetic origin involving multiple parental lineages. This study contributes to a better understanding of hybridogenetic speciation in freshwater fishes, a rare but evolutionarily significant process. Full article

Tertullian provocatively asked (circa 200 AD), “What indeed has Athens to do with Jerusalem? What concord is there between the Academy and the Church?” The relationship between formal philosophy and religion has been a contentious battleground ever since. It has historically come into sharpest focus in biology generally, and evolutionary theory specifically. Charles Darwin clearly won the day in the short-term. His evolutionary functionalism looked like an inglorious abandonment of time-honored metaphysical realism for positivist empirical reductionism with a concomitant horizontalization of perspective that has secularized and flattened the intellectual landscape. But more recently the rise of evo-devo (evolutionary developmental biology) and epigenetic factors have forced a reevaluation of his archrival, Richard Owen. This paper argues that the key to understanding Owen is rooted in his devout Anglicanism through his broad church theology which put Plato into the service of evolutionary theory only now beginning to receive our belated attention. The road to Owen’s evolutionary theory weaved its way from Athens through Jerusalem, finding itself in the contentious intersection of 19th-century Victorian science and religion. Inaccurately mapped by William Paley, Owen’s evolutionary structuralism offered an alternative through science, philosophy, and religion that is only now beginning to be appreciated. Full article