Moving beyond the overrated perception of harbors as polluted ecosystems: unexpected high diversity of meio- and macro-benthic communities in the Port of Dunkirk, France.

SST interneurons facilitate dendritic calcium signaling via tonic activation of α5-GABA receptors.

Unraveling acridine degradation mechanisms in PAH-contaminated soils using DNA-SIP combined with metagenomics and soil transcriptomics.

Ionophore susceptibility of Eimeria zaria: First characterisation in a cryptic Eimeria species of chickens.

The subtelomeric regions of eukaryotic chromosomes harbor repeated elements that contribute to genomic plasticity and adaptation. In Saccharomyces cerevisiae, the Y′ elements represent a major class of subtelomeric repeats; yet, their diversity and evolutionary dynamics remain incompletely characterized. Here, we analyzed Y′ elements across 54 S. cerevisiae strains using high-quality telomere-to-telomere genome assemblies. We detected 893 high-confidence Y′ elements, which we classified into 12 major clusters, revealing a broader structural diversity than previously described, including canonical short (∼5.2 kb) and long (∼6.7 kb) elements, intermediate-size classes (mid1 and mid2), and a novel family containing CA-rich repeats. Sequence analyses showed that open reading frames, including those encoding the putative Y′-Help1 helicase, are highly conserved within clusters, suggesting selective maintenance of functional sequences. The distribution of Y′ elements varied widely across strains and chromosome extremities, with some strains lacking Y′ entirely and others, such as the clinical ADI isolate, carrying up to 149 copies. Interstitial telomeric sequences were variably associated with Y′ elements and tandem Y′ repeats, potentially facilitating recombination and amplification. Analysis of telomere length data further revealed that the presence of long Y′ elements, but not Y′ elements from other clusters, at the subtelomere is correlated with shorter telomeres at the same chromosome end. Our results provide the most comprehensive catalog of S. cerevisiae Y′ elements to date, uncovering unexpected structural and sequence diversity, and a potentially functional role in telomere length regulation.

Epithelial-to-mesenchymal transition (EMT) is a central driver of cancer cell plasticity, enabling invasion, immune evasion, therapeutic resistance and metastasis. Rather than a binary switch, EMT comprises a continuum of transient, reversible states that endow tumor cells with distinct functional properties. Recent technological advances have revealed an unexpected diversity of EMT states across tumor contexts, with implications for disease progression and therapy response. In this Review, we synthesize emerging evidence on EMT heterogeneity and dynamics during cancer progression, examine how new methodologies have increased our understanding of the process and outline therapeutic challenges and opportunities.

Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are structurally diverse natural products that possess a range of bioactivities, often acting as antibiotics, antifungals, or metallophores. In RiPP biosynthesis, different modifying enzymes install an array of chemical motifs onto a precursor peptide. A recently described RiPP-modifying enzyme, ChrH, catalyzes a remarkably complex reaction on its precursor peptide that results in a macrocycle, heterocycle, and S-methyl group. By leveraging comparative genomics, we demonstrate that the products from a subfamily of enzymes related to ChrH display unexpected structural diversity, including the production of unmethylated macrocyclic congeners and C-terminally modified proteins over 30 kDa in size. Several of these precursors contain a signal peptide, sending them for downstream maturation by the bacterial lipoprotein biosynthetic pathway. Like bacterial lipoproteins, such peptides are modified by addition of a diacylglycerol (DAG) group to the N-terminal cysteine residue along with acylation of the N-terminal amine. Genome mining reveals that these RiPP-lipoprotein hybrids, which we term DAG-RiPPs, are widespread across bacterial phyla and are likely involved in different biological roles. Together, these results highlight a maturation paradigm for membrane-bound RiPPs and lay the foundation for the future discovery and bioengineering of other RiPP-lipoprotein hybrids.

Bodo is a cosmopolitan genus of free-living bacterivorous single-celled flagellates in the class Kinetoplastea. Genus Bodo is considered the closest free-living lineage to the parasitic lineages Trypanosoma and Leishmania, the causative agents of the human diseases sleeping sickness, Chagas disease and leishmaniasis. Currently, a single genome exists for the one formally described species in the genus, Bodo saltans. Previous studies on B. saltans have shown that it is dependent on an endosymbiotic bacterium from the order Holosporales, ‘Candidatus Bodocaedibacter vickermanii’. Using single-cell sequencing, we isolated, sequenced and assembled genomes for seven uncultured Bodo spp. cells from a freshwater sample from Royal Leamington Spa, UK. Using comparative genomics, we show that these seven cells represent three potentially novel Bodo species exhibiting unexpected levels of diversity at the genome level. Our results indicate that small subunit ribosomal DNA sequencing, often used to classify Bodo flagellates, is insufficient for determining species delimitation in this genus. In addition, we recovered a Holosporales bacterium genome from all seven Bodo spp. cells. Surprisingly, these seven endosymbionts also represent three novel species, congruent with the phylogeny of the host and exhibiting lineage-specific adaptations. This diversity and host–symbiont association would be indistinguishable in routinely used metabarcoding or bulk sequencing pipelines, thus demonstrating the power of single-cell sequencing to reveal diversity within lineages of microbial eukaryotes.

Protein N-glycosylation is a fundamental post-translational modification that regulates protein stability, trafficking, and molecular interactions, yet its diversity and functional significance remain poorly understood in hemimetabolous, phloem-feeding insects. The green peach aphid, Myzus persicae, is a globally important polyphagous pest and vector of numerous plant viruses, making it an ideal system for investigating the physiological and ecological roles of glycosylation. Here, we present the first comprehensive glycoproteomic characterization of M. persicae using high-resolution LC-MS/MS. We identified 43 distinct N-glycan compositions distributed across 446 glycoproteins and 1819 unique glycopeptides. The aphid N-glycome was dominated by oligomannose structures (74%), but also exhibited an unexpectedly high proportion of hybrid (14%) and complex (12%) glycans, contrasting sharply with the > 90% oligomannose dominance reported for holometabolous insects. The most abundant glycans were HexNAc(2)Hex(6) (13%), HexNAc(2)Hex(5) (11%), HexNAc(4)Hex(3) (10%), and the fucosylated paucimannose HexNAc(2)Hex(3)Fuc(1) (10%). Functional enrichment analyses revealed that glycosylation preferentially targets proteins involved in metabolism, detoxification, extracellular processes, and host-plant and virus interactions. Together, these results uncover previously unrecognized N-glycan complexity in a hemimetabolous insect and suggest that expanded hybrid and complex glycosylation may support hemimetabolous development, phloem-feeding specialization, and vector competence. This study establishes a foundational glycoproteomic resource for aphids and provides new insights into glycan-mediated mechanisms with implications for insect physiology, ecology, and the development of glycosylation-targeted pest management strategies.

Imine-linked two-dimensional covalent organic frameworks (2D COFs) are commonly considered structurally simple materials, yet precise structure determination by X-ray diffraction remains challenging due to the difficulty of obtaining large single crystals. Here, we show that a single-atom change in the aldehyde substituent is sufficient to switch both pore architecture and lattice symmetry in a prototypical 2D COF system. Comparing the widely studied TAPB-DMPDA (COF-OMe) with its -SMe analogue (COF-SMe), we establish a bimodal mesoporous framework for COF-OMe and a unimodal one for COF-SMe through a combination of advanced imaging and diffraction techniques alongside finely sampled gas/vapor physisorption, which resolves two-step capillary processes exclusively in COF-OMe. Electron ptychography reveals previously unrecognized structural features in COF-OMe and enables refinement of its model to propeller-like 1,3,5-tris(4-aminophenyl)benzene nodes with unusually large dihedral angles. Simulated electrostatic potential and X-ray diffraction pattern based on the refined model reproduce the experimental data with high fidelity. COF-SMe undergoes a symmetry reduction from hexagonal to triclinic during kinetic-to-thermodynamic phase evolution, driven by subtle interlayer slippage and intralayer distortion while retaining a single pore type. Together, these results uncover unexpected structural diversity and substituent-governed flexibility in 2D COFs, underscoring the need for state-of-the-art characterization to reassess long-accepted structural models.

Specialized metabolites play key roles in ecological interactions and stress responses, yet their diversification remains poorly understood in many crop species. In the Brassica genus, most metabolomic studies have focused on a limited number of compound classes, thereby underestimating the breadth of chemical variation and its evolutionary significance. Here, we use untargeted metabolomics combined with genomic resources to explore how metabolic diversity, enlarged through CuCl2 inductive treatments, can be systematically analysed to uncover novel biochemical features and generate testable hypotheses on biochemical innovation across a diverse panel of divergent Brassica species, as well as within species. Using a diverse panel of 10 B. oleracea and 10 B. rapa accessions, we constructed a curated metabolomic dataset integrating root and shoot metabolomes from plants grown under optimal conditions and exposed to CuCl₂-induced stress responses, followed by manual compound annotation. Available genomic data were used to support mechanistic interpretations of the observed variation among accessions. This approach enabled the exploration of a wide array of Brassica metabolites, notably by incorporating underexplored classes such as megastigmanes, phenolamides, and tetra/pentahexosylated acylated flavonoids. We uncovered pronounced inter- and intraspecific metabolic signatures, revealing distinct evolutionary trajectories between the two species. Strikingly, we detected distinct classes of blumenol derivatives across Brassica species, a plant genus considered non-mycorrhizal. This finding extends the known occurrence of these compounds and raises new questions about their biological roles. In addition, we link variation in glucosinolate chain-length chemotypes to specific mutations and structural variants in MAM genes, illustrating how metabolomic patterns can guide mechanistic genomic investigations. Together, these results show how a curated metabolomic dataset can simultaneously serve as a reference framework and as a driver for hypothesis-oriented research. By connecting metabolic variation to genomic features, our study provides a basis for functional investigations and offers new opportunities to exploit specialized metabolic traits in breeding programs aimed at improving stress resilience and ecological performance in Brassica crops.

The pyruvate dehydrogenase complex (PDHc) is a universally conserved multienzyme system that converts pyruvate into acetyl-CoA for entry into the tricarboxylic acid cycle and for NADH production. Its central scaffold, the dihydrolipoyl transacetylase (E2p), forms an oligomeric inner core that recruits pyruvate dehydrogenase (E1p) and dihydrolipoyl dehydrogenase (E3). All previously characterized PDHc assemblies adopt either an octahedral 24-mer or an icosahedral 60-mer E2p core, each constructed from trimeric building blocks. We recently showed that the Mycobacterium tuberculosis (Mtb) E2p protein DlaT also functions as the core of the pathogen’s peroxynitrite reductase/peroxidase complex. Here, using cryo-EM, we demonstrate that DlaT assembles into discrete hexamers and dodecamers at micromolar concentrations, which approximate intracellular DlaT concentrations in Mtb. Structure-guided mutagenesis combined with in vitro activity assays indicates that the hexamer represents the functional E2p core of the Mtb PDHc. This noncanonical architecture arises from unique interfaces between DlaT trimers that preclude formation of the classic spherical 24- or 60-mer structures. We propose that this specialized E2p organization enables Mtb to regulate metabolic activities and to remodel the E2p core for engagement in the peroxynitrite reductase/peroxidase antioxidant pathway under stress. Our findings reveal an unexpected diversity in PDHc architecture and uncover a distinct organization principle for the core metabolic complex in mycobacteria.

Unexpected diversity and a wide distribution of paedogenetic gall midges of the genus Heteropeza (Diptera: Cecidomyiidae) in Japan

Abstract A new genus is described for the rare species “Eigenmannia” guchereauae, originally described in Distocyclus but later transferred to Eigenmannia despite its morphology being incongruent with that genus. The description is based on recently collected material from the upper Tapanahony River in Suriname, part of the Maroni basin to which the species is endemic. Osteological and meristic features, together with multilocus phylogenetic analyses (COI, CytB, Rag1), support recognition of this lineage as distinct, and sister to Archolaemus. The new genus appears most morphologically similar to Archolaemus, but is distinguished chiefly by its lack of a free orbital margin. This recognition expands the number of sternopygid genera to eight and highlights the Guiana Shield as a center of gymnotiform endemism. Our findings underscore the importance of continued exploration of poorly studied regions such as the upper Tapanahony, which continues to reveal unexpected diversity and biogeographic complexity in Neotropical electric fishes.

Spectral diversity of vertebrate retinal photoisomerase RGRs.

Powdery mildew is a persistent disease affecting the cultivation of Rosa, a genus of substantial horticultural and economic value worldwide. Despite more than a century of study, the true diversity of powdery mildews infecting roses has remained unclear, largely due to the long-standing and overly broad application of the name Podosphaera pannosa. To reassess this system, we conducted an extensive investigation of powdery mildew specimens infecting Rosa. A total of 112 collections were examined, including recently gathered material from 23 provinces, historical types, representative specimens from the Herbarium Mycologicum Academiae Sinicae (HMAS), China, and a neotype specimen from Germany. Morphological observations combined with phylogenetic analyses (ITS, 28S, and IGS rDNA) resolved several long-standing taxonomic problems and revealed unexpected diversity within the rose powdery mildew complex. Molecular data from Erysiphe rosae provide the first phylogenetic evidence supporting the synonymy of Medusosphaera with Erysiphe. Sphaerotheca rosae, previously treated as a synonym of P. pannosa, is reinstated as a distinct species as Podosphaera rosae comb. nov., and a previously unrecognized lineage is described as Podosphaera rosae-xanthinae sp. nov. In addition, earlier varieties of E. simulans are shown to lack diagnostic morphological or genetic characters and are no longer supported. Taken together, these results demonstrate that powdery mildews on Rosa represent a complex of five species across two genera, structured by host phylogeny. Clear patterns of host preference and distribution indicate a history of co-evolution and ecological differentiation driven by host availability. This study fundamentally revises our understanding of rose powdery mildews, revealing a level of taxonomic and evolutionary complexity much greater than previously recognized and highlighting Rosa as a key host lineage in the diversification of the Erysiphaceae.

Transfer RNA (tRNA) modifications tune translation rates and codon optimality, thereby optimizing co-translational protein folding. However, the mechanisms by which tRNA modifications modulate codon optimality and trigger phenotypes remain unclear. Here, we show that ribosomes stall at specific modification-dependent codon pairs in wobble uridine modification (U34) mutants. This triggers ribosome collisions and a coordinated hierarchical response of cellular quality control pathways. High-resolution ribosome profiling reveals an unexpected functional diversity of U34 modifications during decoding. For instance, 5-carbamoylmethyluridine (ncm5U) exhibits distinct effects at the A and P sites. Importantly, ribosomes only slow down at a fraction of codons decoded by hypomodified tRNA, and the decoding speed of most codons remains unaffected. However, the translation speed of a codon largely depends on the identity of A- and P-site codons. Stalling at modification-dependent codon pairs induces ribosome collisions, triggering ribosome-associated quality control (RQC) and preventing protein aggregation by degrading aberrant nascent peptides and messenger RNAs. Inactivation of RQC stimulates the expression of molecular chaperones that remove protein aggregates. Our results demonstrate that loss of tRNA modifications primarily disrupts translation rates of suboptimal codon pairs, showing the coordinated regulation and adaptability of cellular surveillance systems. These systems ensure efficient and accurate protein synthesis and maintain protein homeostasis.

The family Boletaceae (Boletales) comprises ecologically and economically vital macrofungi with a global distribution in forest ecosystems. Although China is recognized as a biodiversity hotspot for Boletaceae due to its floristic and topographic complexity, its taxonomy remains incompletely understood with numerous new taxa awaiting discovery. Morphological examinations and multi-locus phylogenetic analysis (28S, TEF1, RPB1, and RPB2) were integrated using specimens collected from subtropical and tropical China. Studies have demonstrated that three novel genera (Boletellopsis, Chenrenyua, Sudongpoa) were established to accommodate four newly identified species (C. longispora, C. verrucosa, S. rubicarpos, S. rubripes) and one previously described taxon (B. elata). Twenty-two additional taxa were described, comprising fourteen new species in the genera Aureoboletus and Hemileccinum, viz. A. applanatus, A. atrotomentosus, A. canceriformis, A. exiguisquamatus, A. hainanensis, A. macrocarpus, A. magniporus, A. pallidorubellus, A. phaeosquamus, A. urceopileus, H. brunneoalbum, H. dilutibrunneum, H. lutosum, and H. verrucatum. Taxonomic clarifications resolved the A. solus complex into five species; confirmed the phylogenetic distinctness of A. pallidorubellus from A. rubellus; and synonymized A. pseudorussellii with A. wusangongii and H. squamipes with H. parvum. These findings significantly advance Boletaceae systematics, revealing substantial undocumented diversity in China and providing critical data for fungal conservation and sustainable resource utilization. Keys to accepted species of Aureoboletus and Hemileccinum in China were also provided.

The naked mole-rat Heterocephalus, a hairless, subterranean rodent from the Horn of Africa, has attracted scientific interest due to its cooperative breeding, poikilothermy, longevity, resistance to cancer, and tolerance to pain and hypoxia, among others. Genomic analyses of H. glaber, traditionally considered a single species, reveal three highly divergent lineages. One of these, identified as H. phillipsi Thomas 1885, shows deep genetic divergence (~4.1 Ma) and distinct morphology, notably reduced third molars, warranting recognition as a distinct species. The remaining two lineages, previously designated as the subspecies H. g. glaber Rüppell 1842 and H. g. ansorgei Thomas 1903, diverged around 2.3 Ma and their morphological differentiation is less pronounced. Each of the lineages occupies distinct environmental conditions, with H. phillipsi inhabiting extremely harsh habitats. The finding of an unexpected diversity within this key biomedical model opens new avenues across various fields of research.

DNA barcoding of museum-vouchered samples collected from fish markets reveals an unexpected diversity of consumed gastropods in Vietnam