Functional immunogenomic diversity matters

Cyanobacteria rely on bicarbonate (HCO3-) as the primary inorganic carbon (Ci) source for photosynthesis in aquatic environments. To use this Ci source, cyanobacteria employ CO2 concentrating mechanisms that elevate cytoplasmic HCO3- via plasma membrane transporters, enhancing carboxylation by carboxysomal Rubisco. The sodium-dependent SbtA1 transporter family is well-characterized in freshwater cyanobacteria, but the related SbtA2 family, prevalent in marine α-cyanobacteria, remains uncharacterised. Here, we report functional characterisation of SbtA2 homologues from marine Synechococcus spp., which exhibit high Ci uptake flux with apparent chloride dependence and intermediate HCO3- affinity (K0.5 ≈ 150 µM), when assessed in E. coli. SbtA2 achieved internal Ci accumulation up to 24 mM within 30 seconds. Co-expression with the putative regulator SbtB2 reduced uptake activity, suggesting a regulatory role for this protein. These findings indicate that SbtA2 transporters contribute significantly to carbon acquisition in marine cyanobacteria. Given potential to enhance CO2 supply to Rubisco in C3 plants, we targeted SbtA2 to the tobacco chloroplast inner envelope membrane; however, this did not improve photosynthesis or growth. Our results highlight the functional diversity of cyanobacterial Ci transporters and suggest that additional components may be required for effective transfer of such systems into plant chloroplasts.

Taxonomic classification alone fails to capture the ecological and functional diversity of vaginal microbiomes, particularly those dominated by Gardnerella species. Using the expanded VIRGO2 gene catalog, we developed the vaginal inference of subspecies and typing algorithm (VISTA), a novel ortholog-based framework that defined metagenomic subspecies and 25 metagenomic community state types (mgCSTs), including six distinct Gardnerella-dominated profiles. The mgCSTs exhibit marked differences in species composition, functional gene content, transcriptional activity, and host immune responses. These findings reveal that Gardnerella predominance does not uniformly equate to dysbiosis and underscore the importance of functional context in shaping host-microbiome interactions. VISTA provides scalable classifiers and an interactive application to support mechanistic studies of vaginal microbiome function and its implications for reproductive health.IMPORTANCEThe vaginal microbiome plays a central role in reproductive and gynecologic health, yet its functional diversity and ecological organization remain poorly understood. Traditional 16S rRNA approaches provide only a partial view of this complexity, overlooking the strain-level variation that often determines microbial behavior and host outcomes. By applying metagenomic sequencing and scalable computational modeling, we developed the vaginal inference of subspecies and typing algorithm, a framework that defines gene-based subspecies and community state types across diverse populations. These classifications reveal new insights into the genomic and ecological foundations of vaginal community structure and offer a standardized resource for comparative and translational microbiome research. This work establishes the foundation for functionally informed diagnostics and precision interventions targeting women's reproductive health.

Colorectal cancer (CRC) remains a significant global health concern and is among the leading causes of cancer-related mortality. The disease often progresses to more advanced and treatment-resistant stages. By 2040, the incidence of CRC is projected to increase substantially worldwide, particularly in low- and middle-income countries. Despite the availability of various treatment modalities, CRC incidence remains elevated. Extracellular vesicles (EVs), including exosomes, microvesicles, and apoptotic bodies, represent a novel approach for CRC therapy and diagnosis. EVs possess distinct biological characteristics and exhibit both immunosuppressive and immunostimulatory properties within the tumour microenvironment. Tumour-derived EVs facilitate CRC progression and metastasis by transferring oncogenic proteins and microRNAs that promote epithelial-mesenchymal transition and alter recipient cell behaviour. Conversely, immune-derived EVs produced by dendritic cells, natural killer cells, T lymphocytes, B lymphocytes, and macrophages enhance anti-tumour immune responses and contribute to the elimination of cancer cells. Due to their stable encapsulation of nucleic acids, proteins, and lipids, EVs serve as highly sensitive and specific biomarkers for CRC diagnosis, prognosis, and therapeutic monitoring. Additionally, EVs have demonstrated both abscopal and bystander effects, highlighting their capacity to induce systemic antitumor responses. Recent advances in EV engineering, together with emerging technologies such as artificial intelligence, CRISPR/Cas9 genome editing, and chimeric antigen receptor (CAR)-T cell therapy, present new opportunities to optimise EV-based interventions and broaden their translational applications. Nevertheless, substantial challenges persist, including EV heterogeneity, technical barriers in isolation and characterisation, and limited understanding of their functional diversity. Addressing these limitations, particularly in the development of EV-based vaccines, enhancement of immunostimulatory properties, and further integration of artificial intelligence, will be essential for realising the full clinical potential of EVs in colorectal cancer management.

Introduction Industrial heritage revitalization is a key driver of urban renewal and industrial transformation in old industrial bases. However, there is a lack of systematic quantitative evidence at the regional scale regarding the spatial clustering of industrial heritage and the differentiated revitalization patterns across different urban typologies in Northeast China. Methods This study integrates national and provincial industrial heritage lists for Northeast China. It constructs five revitalization patterns—cultural exhibition, commercial development, landscape -park reuse, in-production activation, and static conservation—and applies GIS-based spatial statistical methods to analyze the spatial clustering characteristics and revitalization differentiation. Results The study reveals a “local clustering and overall dispersion” pattern, with high-density clusters around major urban agglomerations and industrial corridors. The urban typologies follow a policy-based classification into core cities, nodal cities, and resource-based cities. A clear “space–function coupling” differentiation is observed: core cities have the most diverse revitalization patterns, mainly dominated by cultural exhibition and commercial development; nodal cities show corridor-like distributions along transportation and industrial corridors, with in-production activation and exhibition functions interwoven; resource-based cities are primarily dominated by static conservation and landscape–park reuse. Discussion Further analysis suggests that population size and economic strength (GRP) influence revitalization choices and functional diversity. Based on the findings, the study proposes a “core–radiation–infill” regional activation pathway, offering quantitative evidence and differentiated policy implications for industrial heritage conservation, urban renewal, and industrial transformation in Northeast China.

Gene duplication and transposable element (TE) insertions are key drivers of genome evolution and have been linked to increased insecticide resistance in insects. The aim of this study was to characterize the distribution and potential impact of TEs within and near cytochrome P450 monooxygenase (CYP) genes in the invasive pest Drosophila suzukii compared with the non-pest Drosophila melanogaster . We performed in silico analyses of the CYP gene repertoire and genome architecture in D. suzukii and D. melanogaster . We identified ten duplicated CYP genes that are exclusive to D. suzukii and absent from its closely related species D. melanogaster . These duplications are enriched with TE fragments, predominantly Helitrons. Thirty-six percent of TE sequences within CYP genes and their flanking regions carry putative transcription-factor binding sites in D. suzukii , indicating a possible role in gene regulation. Building on the proposed model of Helitron-mediated exon shuffling, our findings suggest that these elements contribute to gene rearrangement, thereby potentially enhancing functional diversity. At the genome level, D. suzukii harbors a higher overall TE content than D. melanogaster , with a relative enrichment within CYP genes. The increased TE content may have enhanced genomic plasticity, thereby facilitating the species’ invasive success, rapid population growth, and ability to adapt to diverse habitats, such as native environments and agricultural fields.

Pseudomonas aeruginosa is a clinically significant, opportunistic pathogen adept at thriving in both host-associated and environmental settings. We sought to define the extent to which P. aeruginosa isolates specialize across niches using a comprehensive study of whole-genome sequencing with paired phenotypic characterization of 125 P. aeruginosa isolates from diverse clinical and environmental sites. We evaluated virulence-associated traits, including motility, cytotoxicity, biofilm formation, pyocyanin production, and antimicrobial resistance to eight antibiotics. Our results show that genomic diversity does not correlate with isolation source or most virulence phenotypes. Instead, we find that, in agreement with prior studies, the two major P. aeruginosa clades (groups A and B) clearly segregate by cytotoxicity, with group B strains showing significantly higher cytotoxicity than group A. Sequence analysis revealed previously uncharacterized alleles of genes encoding type III secretion effector proteins. We observed high variability among strains and isolation sources in the four assayed virulence phenotypes. Antimicrobial resistance was exclusively observed in clinical isolates, whereas it was absent in environmental isolates, reflecting antibiotic exposure-driven selection. Bacterial genome-wide association studies (GWAS) revealed an association between cytotoxicity and exoU presence, and we identified a novel exoU allelic variant with decreased cytotoxicity, demonstrating that functional diversity of well-characterized virulence factors may influence pathogenic outcomes. Overall, our analysis supports the hypothesis that the ability of P. aeruginosa to thrive across diverse niches is driven not by niche-specific accessory genes but by its core genome. Thus, P. aeruginosa isolates are capable of broad niche colonization without initial genetic adaptations.IMPORTANCEPseudomonas aeruginosa is a clinically significant opportunistic pathogen adept at thriving in both host-associated and environmental niches. A major gap in our understanding of this difficult-to-treat pathogen is whether niche specialization occurs in the context of human disease. Addressing this question is critical for guiding effective infection control strategies. Previous large-scale studies have focused solely on genotypic or phenotypic analyses; when paired, they have been limited to a single phenotypic assay or to a small number of isolates from one source, or relied on PCR-based methods targeting a restricted set of genes. To comprehensively uncover niche specialization and pathogenic versatility, we performed whole-genome sequencing and phenotypic characterization of five virulence-associated traits, including antimicrobial susceptibility of 125 clinical and environmental P. aeruginosa isolates. Our systems-level findings challenge reductionist models of bacterial niche specialization, instead supporting an integrated view where conserved genomic systems enable opportunistic pathogenesis across diverse environments.

Synthetic graphene nanoribbons (GNRs) have drawn significant attention due to their unique optical, electronic, and magnetic properties. Considerable efforts have been exerted in developing versatile synthetic methods to manipulate the architectures and properties of GNRs. However, these synthetic methodologies have still struggled to achieve a delicate control over the sequence and function of GNRs at the molecular level, thereby limiting their application potentials across a range of scientific and technological fields. Herein, we report a robust liquid-phase bottom-up synthesis strategy for the creation of sequence-regulated functional GNRs, enabling precise control over the side-chain sequence of GNRs. Using this approach, diversified sequence-regulated GNRs have been produced, demonstrating readily regulated hierarchical nanostructures and optical properties, attributing to their sequence-dependent molecular stacking mode. This liquid-phase bottom-up synthetic technology enabled the incorporation of the side-chain structural and functional diversity into GNRs, further holding great promise for optoelectronic and biomedical applications.

There is still a need for a better understanding of how abiotic/biotic factors affect the functional structure and composition of biological assemblages, given that living organisms are in constant interaction with their environment and with each other. Here, we present a comprehensive dataset of 31 functional traits of bacteria using information from BacDive, a bacterial diversity meta-database, as well as from the rrnDB and genomesizeR datasets. This updated version of the BactoTraits dataset, in addition to now offering more traits for more strains (97,721 strains with at least one trait described), makes R scripts available to the scientific community. These traits include physiological characteristics, metabolic processes, genome properties and biotope preferences. They could be inferred to the whole bacterial community thanks to taxonomic affiliation obtained from traditional high throughput 16S rRNA gene amplicon sequencing methods. This taxonomic affiliation is based on the regularly updated SILVA database and thus allows to study combinations of weighted mean trait profiles of bacterial communities at different taxonomic levels. BactoTraits can be used, for example, to improve predictions of ecological responses to natural/anthropogenic pressures and to support biomonitoring, management and conservation strategies. The R scripts, as well as the dataset encoded in BactoTraits, are available at: https://doi.org/10.24396/ORDAR-182.

Harnessing the Galanin paradox: A receptor- and circuit-based roadmap for precision neuromodulation.

Mycobacterium tuberculosis preferentially infects specific macrophage subsets in primate granulomas during the early stages of tuberculosis.

The association of the Wnt/β-catenin signaling pathway with Alzheimer's disease.

Nitrogen enrichment leads to diversity loss of plant community in grasslands, and it typically enhances productivity in short-term scale but decreases it in the long term. Short-term negative N effect on stability has generally beenprimarily attributed to species synchrony rather than species loss. However, the persistent species loss caused by long-term N enrichment may result in high population variability, ultimately contributing to variability in community productivity. Here, we report results of a 19year-long experiment that manipulated livestock exclusion and N enrichment in an alpine grassland to test their effects on species richness and stability of aboveground productivity through the years. Results demonstrated that the stability of aboveground productivity declined during the first non-overlapping 5year window which was primarily driven by increased species synchrony. In the second non-overlapping time window, decrease in stability was largely driven by compounded effects of persistent synchrony and amplified dominant species variability. In the third and fourth non-overlapping 5year windows, functional diversity loss and subordinate species variability contributed to a continued decline in stability. Mechanistically, the losses of species and functional diversity under different N forms shaped temporal patterns of synchrony and population variability, explaining decrease in stability. These findings reveal a time-dependent destabilization cascade, i.e., initial synchrony-driven fluctuations evolved into adual effect ofsynchronyanddominant species variability, ultimately disrupted by population variability. We posit that diversityhelp to sustains grassland functioningnot only byincreasing productivity, but alsoby maintaining adynamic balance betweensynchrony and population variability. This highlights the necessity of conserving plant diversity to secure ecosystem functioning under global change.

Straw return improves soil multifunctionality by altering functional microbial diversity and abundance

Functional diversity of dead wood promotes species-rich communities of fungi

Multilocus genetic and functional profiling of Indian-origin Lentinula edodes strains: Implications for cultivation and nutraceutical breeding.

Corrigendum to “Native forest cover, fragmentation, and seasonality shape functional diversity in forest bird communities” [For. Ecol. Manag. 598 (2025) 123201

Functional diversity enhances grassland productivity, but species identity drives performance

Writers and Readers of Sialylation in Immunoregulation in Cancer.

Spatial variability and microbiological and structural quality in sandy soil under managed functional diversity in integrated crop-livestock systems