The sea–land transition is one of the most dramatic evolutionary changes and requires an adaptive genetic response to salinity changes and osmotic stress. Here, we used multi-species genomes and multi-tissue transcriptomes of the talitrid crustaceans, a living sea–land transition model, to investigate the adaptive genetic changes and osmoregulatory organs that facilitated their salinity adaptation. Genomic analyses detected numerous osmoregulatory genes in terrestrial talitrids undergoing gene family expansions and positive selection. Gene expression comparisons among species and tissues confirmed the gill being the primary organ responsible for ion transport and identified the genetic expression variation that enable talitrids to adapt to marine and land habitats. V-type H⁺-ATPases related to H⁺ transport play a crucial role in land adaptations, while genes related to the transport of inorganic ions (Na⁺, K⁺, Cl⁻) are upregulated in marine habitats. Our results demonstrate that talitrids have divergent genetic responses to salinity change that led to the uptake or excretion of ions in the gills and promoted habitat adaptation. These findings suggest that detecting gene expression changes in talitrids presents promising potential as a biomarker for salinity monitoring.

Phycobilisomes (PBS), the primary light-harvesting complexes in cyanobacteria, are degraded under nitrogen starvation to provide nitrogen for cell growth. This study reveals that carbon supply is a critical prerequisite for PBS degradation under nitrogen deficiency in Synechococcus sp. PCC 7002. Even under nitrogen-deficient conditions, PBS degradation is inhibited in the absence of sufficient carbon. We demonstrate that both the nblAB-mediated PBS-degradation pathway and the ccmLMNK operon-mediated CO₂-concentrating mechanism are essential for PBS degradation. Furthermore, our findings highlight the critical role of PBS degradation in cyanobacterial adaptation to high C/N conditions. Mutant strains (Mut-nblA and Mut-nblB) deficient in PBS degradation exhibited impaired adaptation to high C/N conditions, as evidenced by their inability to thrive in high NaHCO₃ (nitrogen-free) or CO₂ (low-nitrogen) environments. While these mutants displayed a greener phenotype under high C/N conditions compared to the wild type, they exhibited extensive cellular damage, and significant downregulation of photosynthesis-related genes. These results provide novel insights into the carbon-dependent regulation of PBS degradation and its essential role in cyanobacterial C/N balance, highlighting its significance for their adaptation to fluctuating environmental conditions.

Astome ciliates live in the digestive tract of a broad spectrum of marine, freshwater, and terricolous annelids. In aquatic lumbriculid and criodrilid oligochaetes collected in Central Europe, we rediscovered three insufficiently known astomes: Hoplitophrya secans, Mesnilella clavata, and Buchneriella criodrili. Their morphology was studied using in vivo observation, protargol, and dry silver nitrate impregnation. Multiple nuclear and mitochondrial molecular markers were used to determine their phylogenetic positions and reconstruct their evolutionary history. According to our phylogenetic analyses: (1) mouthless ciliates isolated from annelids form a robustly supported monophylum within the class Oligohymenophorea, (2) the progenitor of astomes invaded the digestive tract of marine polychaetes during the Paleozoic era, (3) lumbricid earthworms likely served as a source of astomes for criodrilid, almid, and megascolecid earthworms, (4) the ancestral host of the earthworm-dwelling astome clade led an endogeic lifestyle, and (5) there were multiple independent transfers of astomes from endogeic to epigeic and anecic earthworms. These findings support previous views of the annelid phylogeny, suggesting that astomes reside and evolve in tandem with annelids for several hundred million years.

Sex determination and differentiation play crucial biological roles in sexual reproduction in vertebrates, including zebrafish. Nevertheless, the intricate molecular mechanisms governing these processes have remained enigmatic. In this study, we showed a pivotal role played by zinc finger GATA-like protein-1 (Zglp-1) in sex differentiation in zebrafish. Our findings revealed that homozygous mutants having no Zglp-1 exhibited a female-to-male sex reversal, ultimately resulting in the development of fertile males. Within the pivotal phase of sexual differentiation, zglp-1^−/− zebrafish demonstrated a gene expression pattern that was skewed toward a male phenotype. Notably, the expression of amh was upregulated, while the expression of cyp19a1a was not sustained. Furthermore, our data revealed a direct interaction between the zinc fingers of Zglp-1 and Sf-1, which inhibited the ability of Sf-1 to activate the amh promoter. This interaction was crucial for regulating sex differentiation. Moreover, we observed alterations in gonadal cell proliferation and apoptosis in zglp-1^−/− zebrafish, which partially contributed to the sexual fate selection. Overall, our findings firmly established Zglp-1 as a crucial regulator of sex differentiation in zebrafish, offering deep insights into the intricate molecular mechanisms that govern sex determination and differentiation in vertebrates.

As dynamic and functionally active organelles, lipid droplets (LDs) mainly function in lipid anabolism, while recent studies showed that mammalian LDs also actively participated in innate immunity; however, the specific roles and regulation mechanism remain relatively unexplored, and the existing studies were mainly limited to mammals. In the present study, we first found that Vibrio harveyi, a serious pathogen in marine environment, could induce LDs accumulation in the liver of obscure puffer Takifugu obscurus on the histology, morphology and molecular levels, and the induction mainly conducted by promoting the synthesis of neutral lipids. Moreover, the antibacterial activity of LD proteins was significantly enhanced upon V. harveyi stimulation, and showed broad-spectrum characteristic. While the inhibition of LDs formation downregulated the expression of immune-related genes and immune signaling elements, highlighting the potential critical roles of LDs during the bacterial infection. The isolated LDs from obscure puffer liver were examined via proteomic analyses, and the data supported the conservative property of LDs from bacteria to humans, and revealed that numerous innate immune system-related components were enriched on the surface of LDs. These results will deepen the understanding of LDs biology and host immune defense mechanism, shedding light on the new strategies for the development of anti-infective therapies.

Annual bay scallops are commercially significant bivalve species for fisheries and aquaculture, but their small size and severe inbreeding depression impede the development of their industry. Some interspecific hybrids of bay scallops and peruvian scallops show longer lifespans and significantly greater sizes, which may result from the longevity genes in the latter (7–10 years). Sirtuins (SIRTs) play pivotal roles in the genetic control of aging in various model species and human beings. However, the role of SIRTs in longevity has not been systematically studied in aquatic animals. In this study, different gene numbers, sequences, structures and tandem duplications of SIRTs were first identified between the two scallops through genome-wide analysis. Cloning and characteristics of the SIRT1 and SIRT6 ORFs revealed dramatic variations in amino acids between the two scallops, which may cause intrinsic differences in function for longevity regulation. In particular, the amino acid variations in the N-terminus may auto-regulate conformations, causing intrinsic differences in catalytic activity for longevity regulation. The robust expression of SIRT1 and SIRT6-2 in peruvian scallops suggested they may exert a role in extending the lifespan. Nutrient restriction (NR) could promote lifespan in terrestrial model organisms, and the SIRTs and their related genes responded to NR for longevity in scallops; peruvian scallops showed a higher ability of autophagy. This study provides potential biomarkers for breeding long-lived larger scallop hybrids for the sustainability of aquaculture. Moreover, the genetic variation during evolution in the two scallops provides a foundation for further research on the longevity function of the SIRTs.

MS/MS-based molecular networking is an effective strategy to rapidly dereplicate known compounds and to guide the discovery process for new and novel natural products. In the present study, the chemical diversity of indole diterpenoids from the marine-derived fungus Penicillium sp. N4-3 was investigated using molecular networking techniques. Guided by this information, targeted isolation resulted in two new indole diterpenoids shearinines R and S (1, 2) and an oxidative artifact shearinine T (3), together with the verification of two known analogs (4, 5). Furthermore, five indole diterpenoids (6−10), including three putatively new ones, shearinines U−W (6, 9, 10), were predicted from the molecular ion cluster by the combination of GNPS molecular networking and manual analysis of MS/MS fragmentation clusters. Shearinines T (3) and W (10) are characterized by an oxidative cleavage of the C-2–C-18 double bond. Feature fragment ions of these shearinines revealed two type of dominant ions related to the indole moiety and the breaking of C-9 side chain or Ring I. Compound 1 showed antibacterial activities against a panel of pathogenic bacteria with IC₅₀ values ranging from 6.34 to 47.96 μg/mL and inhibited the growth of the human hepatic (HepG2) and gastric (SGC-7901) cancer cells lines with IC₅₀ values of 6.27 and 19.16 μg/mL, respectively.

An investigation of the mangrove-derived fungus Penicillium sp. DM27 led to the isolation of 19 new compounds, including three pairs of piperidinone enantiomers ( ±)-1, ( ±)-2, and ( ±)-3, two pairs of pyrrolidinone enantiomers ( ±)-4 and ( ±)-5, and nine pyrrolidine derivatives 6−14. The structures of 1−14 were elucidated through NMR and HRESIMS analysis, coupled with experimental and calculated ECD spectroscopy and the modified Mosher method. Quantitative real time PCR and Western bolt analyses revealed that 11 blocked EMT in TGF-β1-treated HK-2 cells and suppressed fibroblast activation in TGF-β1-stimulated NIH-3T3 cells. Molecular simulations demonstrated that compound 11 could dock ADAM17, showing a high negative binding affinity. Additionally, the overexpression of ADAM17 by lentiviral infection triggered renal tubular EMT, while compound 11 suppressed this process. Overall, our research suggests that pyrrolidine derivatives may be potential therapeutic agents for the treatment of fibrotic kidney disease.

Tumor necrosis factor receptor superfamily member 4 (TNFRSF4), also known as OX40, plays a crucial role in the regulation of T-cell immune responses under normal physiological conditions. Abnormal expression of OX40 and its cognate ligand OX40L (TNFSF4) have been associated with various autoimmune diseases, indicating that blocking the OX40/OX40L pathway could be a promising strategy for the treatment of a broad range of T cell-mediated autoimmune diseases. Here, we screened and characterized a fully human anti-OX40 antibody (JY007) from a naïve human scFv phage library. JY007 has an affinity constant of 7.71 nmol/L and effectively inhibited the OX40-OX40L interaction at both molecular and cellular levels, with IC₅₀ values of 1.088 and 10.12 nmol/L, respectively. Furthermore, JY007 demonstrated the ability to deplete activated T lymphocytes through antibody-dependent cellular cytotoxicity (ADCC) activity, with an EC₅₀ of 5.592 pmol/L. The combination of ADCC and its antagonist activity against OX40 suggests potential efficacy in suppressing inflammatory responses mediated by the OX40/OX40L pathway. Additionally, we employed molecular docking, site-directed mutagenesis, and competitive ELISA to pinpoint the epitopes on OX40. The results revealed that JY007 binds to Pro³⁷, Ser³⁸, and Asp⁴⁰ of OX40. Interestingly, we also found that the most potent anti-OX40 antibody drug in the clinical stage, KHK4083, binds to different OX40 amino-acid residues, including Asp⁷⁴, Lys⁸², Asp¹¹⁷, Ser¹¹⁸, Tyr¹¹⁹, and Lys¹²⁰. This divergence suggests that the novel monoclonal antibody JY007 holds promise as a potential therapeutic option for patients with atopic dermatitis and may find broad applications in the treatment of autoimmune diseases.

In this study, we investigated the molecular recognition mechanisms of shark-derived single-domain antibodies (ssdAbs) targeting fluoroquinolones using an integrated approach that combines in silico homologous modeling, molecular dynamics simulations, molecular docking, and alanine scanning mutagenesis. Three ssdAbs—2E6, 1N9, and 1O17—specific to enrofloxacin, norfloxacin, and ofloxacin, respectively, were selected based on previous work. Through AlphaFold2 and GalaxyWEB, the protein structures of these ssdAbs were predicted and optimized, followed by molecular dynamics simulations to emulate realistic protein behavior in a solvent environment. Molecular docking, alanine scanning mutagenesis, and subsequent verifications identified 30N and 93W of 2E6; 30N, 89R, 98Y, and 99D of 1N9; 100W and 101R of 1O17, all located within the complementarity determining region 3 loop, as critical for antigen binding. These residues primarily interact with their targets through hydrogen bonds, salt bridges, π–π stackings, and cation–π interactions. This study revealed, for the first time, the binding mechanism of ssdAbs to fluoroquinolones from a theoretical perspective, emphasizing the importance of aromatic and polar residues in recognizing characteristic epitopes, such as the carboxyl group at the C3 position and the 1-piperazinyl group at the C7 position. Our findings provide valuable insights for the rational design and enhancement of ssdAbs for detecting small molecule hazards in aquaculture.

This study demonstrated the design of whey protein isolate (WPI)-mannose (Man) conjugates with triphenylphosphonium bromide (TPP) through self-assembly to prepare macrophage and mitochondrion dual-targeting astaxanthin (AXT) nanoparticles (AXT@TPP-WPI-Man). The nanoparticles displayed spherical structures with a well-dispersed size of approximately 206.1 ± 39.2 nm, with good biocompatibility, stability, and targeting capabilities. In vitro experiments demonstrated the specific accumulation of AXT@TPP-WPI-Man in mitochondria and exhibited good targeting ability toward macrophages. The AXT@TPP-WPI-Man effectively reduced reactive oxygen species and preserved the normal mitochondrial membrane potential. The AXT@TPP-WPI-Man treated ulcerative colitis mice exhibited a 52.32% increase in colon length with significant improvement in weight loss, disease activity index scores, and reduced release of inflammatory cytokines. Immunofluorescence staining indicated AXT@TPP-WPI-Man alleviated ulcerative colitis by reducing M1 polarization in colonic macrophages while promoting M2 polarization. The dual-targeting AXT@TPP-WPI-Man has the potential to improve astaxanthin bioavailability, presenting a promising delivery method for the treatment of ulcerative colitis.

Sacoglossan sea slugs have attracted considerable scientific attention due to their capacity to retain functional macroalgal chloroplasts inside their cells. This endosymbiotic association is nutritionally relevant for these organisms and represents an interesting research issue for biotechnological applications. The Caribbean species Elysia crispata can integrate chloroplasts from different macroalgal species. The lipidome of chloroplasts includes lipid classes unique to these photosynthetic organelles. Specialized lipids, such as the glycolipids MGDG, DGDG, and SQDG, are essential for maintaining the integrity of both the thylakoid membranes and the overall chloroplast membrane structure. Additionally, lipids are a diverse group of biomolecules playing essential roles at nutritional and physiological levels. A combined approach using LC–HR-MS and MS/MS was employed to determine the polar lipid profile of the photosynthetic sea slug E. crispata from two habitats in the north-western tropical Atlantic (Sistema Arrecifal Veracruzano and Mahahual) and two different feeding conditions (fed and after 1 week of starvation). Significant differences were identified in the abundance of structural and signalling phospholipids (PC, PI, PG, PS, CL) suggesting different nutritional states between populations. The composition of glycolipids demonstrated a clear separation by habitat, but not by feeding conditions. The lower abundance of glycolipids in the Mahahual samples suggests a lower density of chloroplasts in their tissues compared to Veracruz individuals. These results corroborate that 1 week of starvation is insufficient to initiate the degradation of plastid membranes. This study confirms the advantages of using lipidomics as a tool to enhance our knowledge of the ecology of marine invertebrates.

Heterotrophic bacterial production and respiration, two important contributors to carbon cycling, play an important role in global biogeochemical cycles. However, recent research suggests that these two processes may be decoupled, and the underlying changes in community structure and their interactions remain unclear. In this study, two research expeditions to the North Pacific Subtropical Gyre (NPSG) during the summer and winter of 2020–2021 revealed seasonal shifts in bacterial metabolism and community structure in response to environmental factors. The findings indicated notable seasonal fluctuations in bacterial abundance and production in the surface waters. Both peaked in winter compared to summer. Alterations in bacterial abundance that were further evident at the community level demonstrated significant seasonal differences in bacterial community structure and diversity and revealed, in particular, the intricacy of the networks and interactions among bacterial communities in winter. Bacterial respiration displayed no significant seasonal variations and was decoupled from bacterial abundance and production. The implication was that bacterial production did not directly dictate bacterial respiration. Specific taxa exerted a more substantial influence on bacterial respiration, potentially including groups with high respiration rates but relatively low abundance, thus challenging the notion that highly abundant taxa are invariably the most metabolically active. Moreover, the interplay between different bacterial taxa and their interactions may also impact the overall strength of bacterial community respiration. These findings significantly enhance our understanding of the decoupling between bacterial production and respiration, which is crucial for unraveling the complex mechanisms underlying carbon cycling and energy flow in marine ecosystems.