Understanding how genetic differentiation is structured across spatial scales is important to evolutionary and ecological research, particularly the interplay between fine-scale environmental heterogeneity and large-scale spatial variation. In the present study, heterogeneous microhabitats from nine intertidal locations along the Qingdao coast were examined to disentangle the effects of fine-scale environmental heterogeneity on genetic diversity in Mediterranean mussel Mytilus galloprovincialis. Double Digest Restriction-site Associated DNA sequencing (ddRAD-seq) was conducted to identify SNPs from 163 mussels randomly collected from three microhabitat types (bare rock, shallow tidal pool and deep tidal pool). Despite weak genetic differentiation among locations, distinct genetic divergence was detected among microhabitats, indicating that variation in immersion gradients during low tide exerts stronger effects on population structure than regional-scale geographic separation. Notably, the mean heterozygosity of all SNPs differed significantly between mussels inhabiting bare rock and deep tidal pool microhabitats, implying the action of balancing selection under contrasting immersion-related regimes. This study identified four SNPs significantly associated with immersion gradients, which were annotated to two candidate genes involved in metabolic regulation and rhythmic adjustment. In a summary, our results demonstrate that microhabitat heterogeneity plays a dominant role in maintaining genetic diversity and that immersion-driven environmental variation may shape genetic responses through balancing selection in M. galloprovincialis along the Qingdao coast. This study highlights the critical role of fine-scale environmental heterogeneity in shaping genetic variation and provides a genomic perspective for understanding how genetic diversity is maintained in intertidal organisms.
The utility of survival-related gene signatures in non-small cell lung cancer (NSCLC) is frequently limited by inconsistent study findings, attributed to methodological flaws, inadequate data, or poor universality of selected genes. To address this, we developed a novel approach to identify robust prognostic gene signatures from gene expression and clinical data of NSCLC adenocarcinoma patients, specifically selecting up- and down-regulated genes to enhance functional interpretability. We derived stage-specific up- and down-regulated signatures, rigorously validated for survival prediction across six independent datasets (three training and three testing cohorts). Univariate and multivariate Cox analyses showed that high expression of up-regulated signatures and low expression of down-regulated signatures consistently correlate with significantly poorer survival. Their independent prognostic value was confirmed even after adjusting for clinical covariates like age and sex, highlighting robustness. Validation via two microarray and one RNA-seq dataset verified consistent, explicit differential expression of signature genes between cancer and normal lung tissue. Functional enrichment (GSEA and GO) analyses revealed up-regulated signatures are linked to cancer pathways, cell proliferation (G2/M cycle, mitotic cycle, stem cell traits) and immune processes (T/B-cell immunity), while down-regulated signatures enrich for tumor suppressor functions and normal tissue homeostasis. Further TCGA data analysis demonstrated that the inverse correlation degree between up- and down-signature expressions directly relates to prognostic strength. This study offers valuable insights into NSCLC heterogeneity, provides robust tools for refining prognosis and guiding adjuvant therapy, and ultimately contributes to personalized medicine in lung cancer management.
The ocellaris clownfish (Amphiprion ocellaris) is a globally popular ornamental marine fish. The limited number of developed simple sequence repeat (SSR) markers in clownfish restricts further research. Recently, the sequenced A. ocellaris genome has enabled the development of large SSR markers. In this study, a total of 244441 SSRs in the A. ocellaris genome were identified and characterized. The total length of the SSRs was 8317543 base pairs (bp), which equates to 0.96
Asexual reproduction serves as a fundamental strategy toward rapid population expansion in many early diverging metazoans. Growing evidence indicates that microbial associations play an essential role in host asexual reproduction. However, community dynamics and functional traits of the microbiome during this process remain poorly understood. The upside-down jellyfish (Cassiopea xamachana)—a culturable cnidarian model—hosts photosynthetic obligate endosymbionts and a diverse array of bacterial communities. Here, we employed full-length 16S rRNA gene and Internal Transcribed Spacer 2 (ITS2) amplicon sequencing to investigate the diversity dynamics among bacterial and Symbiodiniaceae communities between two asexual reproductive modes: strobilation and planuloid reproduction. Comparative analyses revealed marked stage-specific changes in bacterial community composition and diversity under both modes, whereas those of Symbiodiniaceae remained relatively stable. Functional prediction based on 16S rRNA sequences indicated that bacterial recombination during strobilation may coincide with metabolic shifts toward nutrient biosynthesis, host-bacterial communications, and antiviral defense, which potentially support the host through non-feeding strobilae stages. Bacterial functions during planuloid reproduction were predicted to be enriched in nutrient biosynthesis. However, bacterial communities associated with newly formed polyps may promote host settlement and further development by participating in processes such as nitric oxide metabolism and nitrogen fixation. Collectively, these findings suggest that dynamic bacterial compositional restructuring may constitute a crucial strategy in supporting the host through different asexual reproductive modes, which pose distinct physiological challenges.
Hypoxia is a critical environmental stressor for aquatic organisms; it regulates gill remodeling and apoptosis in fish. Despite the commercial importance of the Japanese flounder (Paralichthys olivaceus), the molecular mechanisms underlying its hypoxic adaptability, particularly those involving epigenetic regulation and gene networks, remain poorly characterized. To address this issue, we subjected Japanese flounder to acute hypoxia ((2.39±0.84) mg/L DO) for 0 (control), 1, 6, and 24 h, which was followed by an integrated multi-omics analysis of gill tissue comprising RNA-seq and MethylRAD. We identified 319 CG-type and 969 CWG-type differentially methylated genes (DMGs) enriched in energy metabolism, immune signaling, and oxidative homeostasis. Transcriptomics revealed 6410 differentially expressed genes (DEGs) associated with apoptosis, ion transport, and metabolic reprogramming. Cross-omics integration pinpointed 59 consensus genes, with comparative analysis identifying four hypoxia-responsive ones: gpx1b, ero1a, rps23, and OTU domain-containing protein 4-like. Notably, promoter hypomethylation in gpx1b correlated with increased transcription. Dual-luciferase assays confirmed its HIF-1α-mediated transcriptional activation. Overexpression of gpx1b could partially attenuate apoptosis in gill cells. In summary, this study systematically delineated the epigenetic–transcriptional interplay that drives hypoxia adaptation in Japanese flounder, providing mechanistic insights into hypoxia response pathways and a molecular framework for breeding stress-resilient strains for aquaculture.
The Pacific oyster (Crassostrea gigas) is a key global aquaculture species. Tetraploid oysters are an essential broodstock for sustainable triploid production, yet their growth traits still need improvement. In this study, we successfully constructed 30 full-sib and 10 half-sib families of tetraploid Pacific oysters and reared them at three culture sites: Jiaonan, Rushan, and Rongcheng. We evaluated the genetic parameters of growth traits—shell height and wet weight—and then assessed the effects of genotype×environment interactions (G×E) on these traits. Additionally, the sex and ploidy composition of all tetraploid families was also examined. The heritability was moderate to high for shell height (0.39–0.44) and moderate for wet weight (0.32–0.36). For the same traits, genetic correlations between sites were moderate to high (0.55–0.80), indicating significant G×E effects. Tetraploid families reared in Rongcheng exhibited a strong male bias. Although chromosome loss was detected in all families at 360 d, the proportion of triploids and mosaic tetraploids was low (<10
The exercise and feeding capacity of sea urchins are pivotal factors influencing growth performance. In this study, a comprehensive 80-d feeding experiment was conducted to evaluate the effects of dietary vitamin B2 supplementation on the exercise and feeding performance of sea urchin Mesocentrotus nudus. Three experimental diets were formulated by supplementing graded levels of vitamin B2 (0, 15, and 30 mg/kg). Fresh kelp (Saccharina japonica) was used as the control diet. Each diet was randomly distributed to sea urchins cultured in three tanks with an initial average body weight of (3.63±0.02) g. The findings revealed that sea urchins fed with 15 mg/kg vitamin B2 showed markedly higher growth performance, feed intake, feeding speed, and Aristotle’s lantern (AL) reflex frequency. They also showed markedly shorter righting response time. The dietary level of 15 mg/kg vitamin B2 was found to significantly increase the collagen deposition in multiple tissues, including the spine joint, peristomial membrane (PM), AL muscle, and digestive tract. Meanwhile, sea urchins fed with 15 mg/kg vitamin B2 exhibited the most extensive and densely organized collagen fiber regions in the PM. Further study showed that 15 mg/kg vitamin B2 supplementation significantly upregulated the expression levels of COLP1α, TGFβR2, COLP2α, TGFβR1, COLP3α, and SNIP1 genes in the PM of sea urchins, while downregulated the expression level of MMP14. The results indicated that vitamin B2 promoted the exercise and feeding capacity of M. nudus by facilitating collagen production, potentially through activation of the TGF-β/Smad pathway.
Warming rate is regarded as a critical determinant of thermal tolerance. However, its role in shaping metabolic depression and the underlying molecular mechanisms remain poorly understood. Here, we examined how the fast and slow ramping rates influence cardiac performance and transcriptional and post-transcriptional regulations in the mudflat gastropod Batillaria attramentaria. Slow warming increased the prevalence of bimodal heart rate responses by driving transitions from unimodal cardiac performance, which is consistent with the deployment of metabolic depression. In contrast, fast warming predominantly produced unimodal responses and a stronger temperature dependence of heart rate. Despite similar cardiac breakpoints, the upper thermal limit of cardiac function was significantly lower under a slow warming rate, suggesting a trade-off between energy conservation and maximal performance. Transcriptomic analyses revealed that molecular stress responses were strongly warming rate-dependent. Rapid warming triggered early downregulation of peptide-mediated GPCR signaling, followed by induction of protein-folding chaperones and, at extreme temperatures, suppression of DNA repair and DNA duplex unwinding, consistent with accelerated regulatory breakdown. Under slow warming rate, translation-related processes were enriched near cardiac limits, while signatures of molecular dysfunction were largely absent. Alternative splicing analyses further revealed distinct regulatory strategies: gradual warming was associated with consistent enrichment of chromatin remodeling-related splicing, whereas rapid warming promoted spliceosome-related splicing and increased overlap between differentially expressed and spliced genes at high temperatures. Our findings demonstrate that warming rate determines the deployment of metabolic depression and its molecular regulation, thereby shapes thermal limits and vulnerability under climate change.
Under identical environmental conditions, spotted seabass (Lateolabrax maculatus) with an average weight of (4.3±0.02) g were fed a diet containing defatted Tenebrio molitor larvae meal (DTM; Tianchongyou F88) and exhibited divergent growth patterns. This study aimed to compare the differences between fast-growing (FG) and slow-growing (SG) individuals. The results revealed that the final body weight, weight gain rate, and specific growth rate were significantly higher in the FG group than in the SG group (P<0.05). Additionally, immune markers, including lysozyme, complement 3, and complement 4, were significantly higher in the FG group than in the SG group (P<0.05). Moreover, the FG group demonstrated a significant increase in total antioxidant capacity and superoxide dismutase activity compared to the SG group (P<0.05). Intestinal health was also improved in the FG group, with significantly greater intestinal villus number, height, and muscle layer thickness, indicating better intestinal tissue integrity. Furthermore, the FG group exhibited higher chitinase activity (P<0.05) and a greater number of goblet cells (P<0.05) than the SG group. In addition, the FG group had a higher abundance of potential probiotics, such as Bacillus and Paenibacillus, which may enhance the utilization of DTM by the spotted seabass. In conclusion, these findings suggest that the superior growth performance of the FG group can be attributed to improved intestinal health, enhanced immune function, and increased antioxidant capacity.
Vibrio parahaemolyticus is a major pathogen affecting shrimp aquaculture. Additionally, the extensive use of antibiotics for prophylaxis and treatment has led to the emergence of multidrug-resistant strains. This combination has created an urgent need to develop alternative control strategies, among which phage-based biocontrol is a promising approach. A novel bacteriophage, vB_VpaS_PP24 (PP24), which infects V. parahaemolyticus, was isolated by us in a previous study. It demonstrated potential to control this pathogen, making it a suitable candidate for phage-based biocontrol. In this study, we combined genomic, functional, and field approaches to assess the safety and efficacy of PP24 in controlling V. parahaemolyticus in shrimp aquaculture. Genomic and phylogenetic analyses based on the major capsid protein and DNA polymerase sequences indicated that PP24 shared high similarity with the Vibrio phage vB_VhaS-VHB1. Acute and subacute toxicity tests confirmed its safety. Critically, PP24 demonstrated potent in vitro lytic activity against the virulent V. parahaemolyticus strain VP8. In laboratory challenge trials, PP24 treatment significantly improved survival outcomes, reducing shrimp mortality from 55.56
To investigate the physiological response of Phascolosoma esculenta (Sipuncula: Phascolosomatidae) under zinc (Zn) stress and recovery, four Zn concentrations (0, 16.8, 33.6, and 84.0 mg/L) were applied according to the 96 h median lethal concentration (LC50). Then changes in intestinal Zn bioaccumulation, histological morphology, oxidative stress biomarkers, and microbial communities were assessed. The results showed a significant time- and dose-dependent increase in intestinal Zn accumulation, with no notable reduction during post-recovery, indicating that Zn is easily accumulated in the intestine. Histological examination revealed severe damage in the superior segment of the ascending intestine after 96 h of Zn stress, including goblet cell swelling, cilia shedding, increased granulocytes, and an incomplete of brush border. Notably, these injuries were exacerbated during the recovery phases. Moreover, Zn stress upregulated total antioxidant capacity (T-AOC) and altered superoxide dismutase (SOD) and catalase (CAT) activities, suggesting that the intestine is a primary target of Zn toxicity. Zn stress also disrupted intestinal microbial homeostasis, marked by a significant decrease in the relative abundance of Proteobacteria and an increase in Spirochaetota, potentially associate with metabolic dysregulation and inflammatory responses. After 96 h of recovery, the overall structure of the dominant bacterial returned to baseline levels; however, the genus Tenacibaculum, particularly Tenacibaculum litoreum and Tenacibaculum soleae, became significantly enriched, which may contribute to persistent intestinal impairment. In addition, Zn stress led to significant enrichment of signaling pathways associated with enzyme families, replication and repair, and immune system, indicating impaired enzymatic activity and immune function. In summary, acute Zn stress induced oxidative damage, disrupted intestinal microbial community homeostasis, and caused functional abnormalities in the intestine of P. esculenta.
To investigate the factors influencing the net mouth closing performance of the falling-net, this study fabricated a model net based on Tauti’s rule and conducted a series of flume tank tests. The results showed that the extrusion of netting by lead sinkers significantly hindered the sinking of the corresponding net mouth section, resulting in a left-right imbalance in the fishing gear shape. The net mouth distance decreased with sinking time, while the net mouth closing speed increased with fluctuations. The displacements of the upstream and downstream nodes along the current direction increased with longer shooting duration and higher current speed but decreased with higher hauling speed. In the late sinking stage, the net mouth distance increased with longer shooting duration and decreased with higher hauling speed and current speed. The average closing speed decreased with longer shooting duration and increased with higher hauling speed, current speed, and greater leadline weight. This study provides a reference for optimizing fishing operations and improving the structural design of fishing gear.
Wuzhizhou Island has one of the most biodiverse coral reef areas in Hainan; however, the molluscan diversity in its reef ecosystems remains poorly documented. This study presents the first comprehensive DNA barcoding evaluation of molluscan diversity in the northern coral reef ecosystems of Wuzhizhou Island. A total of 170 specimens were collected, from which 166 cytochrome c oxidase subunit I (COI) sequences were successfully obtained. Combined with morphological assessment, 122 species were identified. Among them, four species lacked molecular data, whereas the remaining species were assigned to 118 molecular operational taxonomic units (MOTUs), which included 95 gastropod, 22 bivalve, and 1 polyplacophoran species that was represented by a single COI sequence and was treated as an independent MOTU. Four of these species are newly recorded in China. Three delimitation methods (Automatic Barcode Gap Discovery, Assemble Species by Automatic Partitioning, and bPTP) demonstrated high consistency in species recognition and revealed a clear barcode gap, with mean congeneric distances 25 times greater than the intraspecific variation. Despite its utility for species identification, the COI gene fragment exhibited limited resolution for higher-level phylogeny, and the potential for misidentification was detected in public reference databases. These results confirm the benefit of DNA barcoding in reef mollusk surveys and provide a critical biodiversity baseline to support future conservation and restoration initiatives in tropical coral reef ecosystems.
Understanding spatiotemporal structures in ocean dynamic processes is critical for characterizing energy cascades that govern global heat redistribution, biogeochemical cycling, and climate variability. Multiscale oceanic dynamical processes exhibit intricate three-dimensional spatial structures and temporal variability. The comprehensive characterization of the dynamical signatures of the ocean remains challenging because of the spatiotemporal sparsity of ocean observations. The elliptical approximation (EA) model provides a generalized framework for representing spatiotemporal correlations by incorporating the mean advection and sweeping effects of shear currents, enabling spatiotemporal transformation. However, the applicability of the EA model to characterize spatiotemporal correlations has not been directly extended to ocean dynamics. In this study, we apply the EA model to analyze the vertical propagation characteristics of near-inertial internal waves (NIWs) in the Beaufort Sea, where NIWs dominate the energy spectrum. Analysis of high-resolution velocity time series shows that the sweeping velocity magnitude, which quantifies the energy associated with large-scale wave-induced advection of small-scale structures, is strongly correlated (a significant correlation exceeding 0.7) with local near-inertial energy levels. The directional components of the sweeping velocity are consistently aligned with the vertical propagation direction of near-inertial wave packets, indicating a robust link between the EA model parameters and near-inertial energy transport mechanisms. The results further reveal that elevated near-inertial energy levels indicate an intensified vertical propagation of NIWs. These findings validate the reliability of the EA model in shear-dominated oceanic environments and advance our quantitative understanding of the vertical propagation characteristics of NIWs. Moreover, the model is a potential diagnostic framework for systematically analyzing intricate spatiotemporal variability in other multiscale ocean dynamics and energy cascades.
Since the past few decades, nutrient dynamics in the Yellow Sea have undergone continuous change, specifically, an increase in the nitrogen:phosphorus ratio. This phenomenon has significantly influenced the relative growth rate (RGR), biomass production, and nutrient contents of macroalgae. This study investigated the response of four macroalgal species native to the Yellow Sea: Ulva pertusa, Ulva prolifera, Gracilariopsis longissima, and Grateloupia filicina. They were cultured in triplicate under six ambient N:P ratios—4:1, 8:1, 12:1, 16:1, 20:1, and 24:1. We observed that high N:P ratios (16:1–24:1) significantly limited the RGR and nutrient assimilation rate. However, an 8:1 ratio was optimal for macroalgal species. With an increase in N:P, the RGRs of U. pertusa, U. prolifera, and G. longissima were reduced by >50
The silver pomfret (Pampus argenteus) is a marine species with considerable economic value. The processes involved in gonadal maturation in P. argenteus are still mostly unclear, presenting obstacles to artificial breeding. The foxl2 gene is fundamental to the development of ovarian tissues, and its absence causes early ovarian failure and sex reversal. cyp19a1a encodes ovarian aromatase, a key enzyme responsible for estrogen biosynthesis by converting androgens into estrogens, and is essential for ovarian differentiation and maintenance in teleosts. This study aimed to elucidate the function of foxl2 in P. argenteus. Our results show that foxl2 expression was primarily observed in undifferentiated gonads and ovaries, with a notable increase during stages I and V of ovarian development, where it was predominantly localized in granulosa cells. Foxl2 seems to play a role in the initial stages of testicular development, with expression observed in stage I testes, where Foxl2 were primarily localized to the cytoplasm of spermatogonia. Immunofluorescence analysis of Foxl2 and Cyp19a1a protein distribution during gonadal development in P. argenteus revealed that Foxl2 was primarily localized to the cytoplasm of primary and previtellogenic oocytes, as well as in granulosa cells, while Cyp19a1a was detected predominantly in granulosa cells. The expression of foxl2 was markedly upregulated following treatment with estradiol (E2) and recombinant Cyp19a1a (rCyp19a1a). In summary, the evidence implies that foxl2, a gene with a female-specific expression pattern, may play an essential role in granulosa cell formation and estrogen production. Additionally, Foxl2 could have a complementary function with Cyp19a1a in P. argenteus.
Gracilaria textorii is a red alga that is known for its high agar content, which is influenced by environmental factors such as salinity. To investigate the putative key genes involved in the agar synthesis pathway of G. textorii, transcriptome sequencing was performed to analyze the differentially expressed genes (DEGs) in G. textorii cultivated under low (10), normal (30), and high (50) salinity conditions, and four DEGs within the agar synthesis pathway, including the glucose-6-phosphate isomerase (GPI), mannose-6-phosphate isomerase (MPI), UDP-galactose-4-epimerase (GALE), and GDP-D-mannose-3′,5′-epimerase (GME) genes, were identified. Concurrently, the agar content in G. textorii increased after 15 d of cultivation at salinities 10 and 50. To further elucidate the correlation between the agar synthesis pathway genes and agar accumulation, the GPI, MPI (MPI-1, MPI-2), GALE, and GME genes were cloned based on the transcriptome data. Subsequently, transcript levels of these four genes and agar accumulation were analyzed under five salinity conditions: 10, 20, 30 (control), 40, and 50. The results demonstrated a significantly positive correlation between the relative agar accumulation and differences in relative transcript levels of the four genes across the different salinity treatments. This suggests that these four genes may be key determinants of the agar content in G. textorii.
The circulation in the South China Sea (SCS) exhibits pronounced vertical coupling with distinct propagating features, yet the spatiotemporal characteristics of propagation and underlying dynamics remain poorly understood. Vertical coupling refers to the interaction and feedback processes occurring between different vertical water layers through dynamic momentum transfer. Using 30 years of simulated layer thickness from a realistic numerical model, we applied the Hilbert Empirical Orthogonal Function (HEOF) method to investigate these dynamics. We identified three dominant propagating modes that facilitate vertical interactions between the upper (0–600 m) and middle (600–1300 m) layers, collectively explaining a substantial portion of coherent variance between them. These modes represent important pathways for vertical energy transfer, potentially influencing circulation and water mass transformation. The first mode, a one year cycle, is linked to westward-propagating signals driven by Kuroshio intrusion and mesoscale eddy activity. Originating from the open ocean, these signals travel along the northern continental slope and induce delayed southwestward propagation in the intermediate layer, dynamically linking the two layers. The second mode has a two-year cycle associated with quasi-biennial oscillation’s modulation of summer monsoon intensity and onset, with southwestward propagation from southwest Taiwan to the eastern Vietnamese coast. The third mode, also annual, is primarily driven by the seasonal reversal of monsoon-forced western boundary currents and their interaction with topographically guided coastal flows, being most active along the SCS western boundary. These results reveal distinct, timescale-dependent mechanisms of vertical coupling in the SCS and highlight their roles in shaping circulation and water mass variability.
This study collected total suspended particulate aerosols in the Tian’e Ling area near Zhongshan Station in 2022. Nine trace elements (V, Mn, Fe, Ni, Cu, Zn, As, Cd, and Pb) were quantified using inductively coupled plasma–mass spectrometry. Enrichment factor calculations, multivariate analysis, and backward trajectory modeling were employed to characterize the spatiotemporal distribution and potential sources of these elements. The results revealed distinct seasonal variations in trace element concentrations within the atmospheric aerosols at Zhongshan Station, with higher levels observed in austral summer and lower levels in austral winter. Backward trajectory analyses identified three primary influencing factors: 1) resuspension of weathered crustal materials from the surrounding area; 2) anthropogenic emissions associated with research station operations; and 3) long-range atmospheric transport of particulate matter. In general, the contributions of Zhongshan Station to aerosol-bound heavy metals were comparable to those observed at other Antarctic research stations.
We previously identified two vertebrate peroxisome proliferator-activated receptor (PPAR) homologs, ScPPARa and ScPPARb, in Sinonovacula constricta. Here, we investigated their regulatory roles in the biosynthesis of long-chain polyunsaturated fatty acids (LC-PUFAs). Using bacteria expressing the respective dsRNA, we knocked down ScPPARa and ScPPARb transcription by about 50
