Integrating Iso-seq and RNA-seq data for the reannotation of the greater amberjack genome.

The greater amberjack is a very important fishery species with high commercial value, and it is distributed worldwide. Transcriptome-based studies on S. dumerili have been limited by an inadequate reference genome and a lack of well-annotated full-length transcripts. In this study, a total of 12 tissues from juvenile and adult fish both sexes were collected for next-generation RNA sequencing (RNA-seq) and full-length isoform sequencing (Iso-seq). For Iso-seq, a total of 163,218, 149,716, and 189,169 high-quality unique transcript sequences were obtained, with an N50 of 5,441, 5,255, and 5,939, from juvenile, adult male and adult female S. dumerili, respectively. We integrated the Iso-seq and RNA-seq data to construct a comprehensive gene annotation and systematically profiled the dynamics of gene expression across the 12 tissues. Our gene models had greater detail and accuracy than those from NCBI and Ensembl, with more precise polyA locations. These resources serve as a foundation for functional genomic studies and provide valuable insights into the molecular mechanisms underlying the development, reproduction and commercial traits of amberjack.

Evolution and gene expression of matrix metalloproteinase gene family during gonadal development in Scatophagus argus.

BACKGROUND: During the reproductive cycle of Scatophagus argus (S. argus), their gonads undergo degeneration and re-maturation including the degradation of proteins in the extracellular matrix (ECM). Matrix metalloproteinases (MMPs), a family of zinc proteases, play a crucial role in ECM degradation. OBJECTIVE: Our aim was to identify the MMP gene family of S. argus and determine their gene expression levels across various stages of gonadal development. METHODS: The MMP gene family of S. argus in the genome was identified by using basic Local Alignment Search Tool (BLAST) and HMMER. Phylogenetic tree and synteny analysis were performed to investigate the evolutionary past of the MMP gene family. The gonads of 18 S. argus (9 males and 9 females) were dissected and a quantitative reverse transcription polymerase chain reaction (RT-qPCR) was conducted to investigate the expression levels of MMP genes across different stages of gonadal development. RESULTS: Twenty-three MMP family genes were identified in the genome of S. argus. We divided the MMP gene family into 4 categories and found that teleosts exhibit a higher MMP gene copy number relative to other vertebrates. By sampling S. argus at different stages of gonadal development, we observed an upregulation in relative expression levels of 11 MMP genes in the testis or ovary. Ten MMP genes (mmp2, 9, 14a, 15a, 15b, 16a, 17a, 23b and 24) showed higher mRNA expression in the testis compared to the ovary and mmp28 had higher expression during ovarian development. The tissue distribution results demonstrated that the gills exhibited the lowest relative expression level among all tissues examined. However, 6 genes (mmp2, 9, 14a, 15a, 15b, and 16a) had relatively high expression in all tissues. CONCLUSION: The result suggested that teleost-special whole genome duplication was mainly responsible for the formation of the MMP gene family in teleosts. Expression patterns of MMP genes indicated that mmp2, 9, 14a, 15a, 15b, 16a, 17a, 23b and 24 played a vital role in testicular development while mmp28 was more important for ovarian development. Limitaion: Further studies are needed to determine their protein expressions in gonadal development and precise mechanism in gonadal differentiation. The study enhances our understanding of the MMP gene family in evolution of teleost and provides valuable insights for further research on MMPs in S. argus.

Effects of Chronic Heat Stress on Growth, Apoptosis, Antioxidant Enzymes, Transcriptomic Profiles, and Immune-Related Genes of Hong Kong Catfish (Clarias fuscus).

Chronic heat stress can have detrimental effects on the survival of fish. This study aimed to investigate the impact of prolonged high temperatures on the growth, antioxidant capacity, apoptosis, and transcriptome analysis of Hong Kong catfish (Clarias fuscus). By analyzing the morphological statistics of C. fuscus subjected to chronic high-temperature stress for 30, 60, and 90 days, it was observed that the growth of C. fuscus was inhibited compared to the control group. The experimental group showed a significant decrease in body weight and body length compared to the control group after 60 and 90 days of high-temperature stress (p < 0.05, p < 0.01). A biochemical analysis revealed significant alterations in the activities of three antioxidant enzymes superoxide dismutase activity (SOD); catalase activity (CAT); glutathione peroxidase activity (GPx), the malondialdehyde content (MDA), and the concentrations of serum alkaline phosphatase (ALP); Aspartate aminotransferase (AST); and alanine transaminase (ALT) in the liver. TUNEL staining indicated stronger apoptotic signals in the high-temperature-stress group compared to the control group, suggesting that chronic high-temperature-induced oxidative stress, leading to liver tissue injury and apoptosis. Transcriptome analysis identified a total of 1330 DEGs, with 835 genes being upregulated and 495 genes being downregulated compared to the control group. These genes may be associated with oxidative stress, apoptosis, and immune response. The findings elucidate the growth changes in C. fuscus under chronic high temperature and provide insights into the underlying response mechanisms to a high-temperature environment.

Identification of Insulin-like Growth Factor (IGF) Family Genes in the Golden Pompano, Trachinotus ovatus: Molecular Cloning, Characterization and Gene Expression.

Insulin-like growth factors (IGFs) are hormones that primarily stimulate and regulate animal physiological processes. In this study, we cloned and identified the open reading frame (ORF) cDNA sequences of IGF family genes: the insulin-like growth factor 1 (IGF1), insulin-like growth factor 2 (IGF2), and insulin-like growth factor 3 (IGF3). We found that IGF1, IGF2, and IGF3 have a total length of 558, 648, and 585 base pairs (bp), which encoded a predicted protein with 185, 215, and 194 amino acids (aa), respectively. Multiple sequences and phylogenetic tree analysis showed that the mature golden pompano IGFs had been conserved and showed high similarities with other teleosts. The tissue distribution experiment showed that IGF1 and IGF2 mRNA levels were highly expressed in the liver of female and male fish. In contrast, IGF3 was highly expressed in the gonads and livers of male and female fish, suggesting a high influence on fish reproduction. The effect of fasting showed that IGF1 and mRNA expression had no significant difference in the liver but significantly decreased after long-term (7 days) fasting in the muscles and started to recover after refeeding. IGF2 mRNA expression showed no significant difference in the liver but had a significant difference in muscles for short-term (2 days) and long-term fasting, which started to recover after refeeding, suggesting muscles are more susceptible to both short-term and long-term fasting. In vitro incubation of 17ß-estradiol (E2) was observed to decrease the IGF1 and IGF3 mRNA expression level in a dose- (0.1, 1, and 10 µM) and time- (3, 6, and 12 h) dependent manner. In addition, E2 had no effect on IGF2 mRNA expression levels in a time- and dose-dependent manner. The effect of 17α-methyltestosterone (MT) in vitro incubation was observed to significantly increase the IGF3 mRNA expression level in a time- and dose-dependent manner. MT had no effect on IGF2 mRNA but was observed to decrease the IGF1 mRNA expression in the liver. Taken together, these data indicate that E2 and MT may either increase or decrease IGF expression in fish; this study provides basic knowledge and understanding of the expression and regulation of IGF family genes in relation to the nutritional status, somatic growth, and reproductive endocrinology of golden pompano for aquaculture development.

Analysis of risk factors for hypoglycemia in patients with gastrointestinal bleeding induced by somatostatin for injection and establishment of the prediction model.

OBJECTIVES: This study aimed to explore the risk factors of hypoglycemia in patients with gastrointestinal bleeding caused by somatostatin for injection and to establish a prediction model based on logistic regression combined with receiver operating characteristic (ROC) curve. MATERIALS AND METHODS: This retrospective study analyzed patients diagnosed with gastrointestinal bleeding and treated with somatostatin from January 2022 to May 2023 and collected hypoglycemic events. Univariate and multivariate logistic regression analysis were used to determine the independent influencing factors of somatostatin-induced hypoglycemia, and a prediction model was established. ROC analysis was used to evaluate the prediction model. RESULTS: A total of 331 patients were enrolled in this study, and 42 patients developed hypoglycemic events. Age and co-infection were found to be significant risk factors for hypoglycemia in patients with gastrointestinal bleeding induced by somatostatin. Binary logistic regression fitting established the hypoglycemia prediction model Logit (P) = -4.125+0.053Yage+1.366Yco-infection (co-infection: Xco-infection = 1, non-co-infection: Xno co-infection = 0), Hosmer-Lemeshow test results showed that the model had a good fit (χ2 = 10.552, df = 8, p = 0.228), and the AUC of the prediction model to predict the risk of hypoglycemia caused by somatostatin in patients with gastrointestinal bleeding was 0.744 (95% CI: 0.653 - 0.835, p < 0.001), the sensitivity was 57.14%, and the specificity was 93.77%. CONCLUSION: Among adult patients with gastrointestinal bleeding treated with somatostatin for injection, our study found that age and co-infection were significant risk factors for somatostatin-induced hypoglycemia in this patient population, and the fitted models had high predictive value in predicting the occurrence of hypoglycemia.

Molecular cloning of estrogen receptor and its function on vitellogenesis in pompano (Trachinotus ovatus).

Estrogen receptors (ERs) play a critical role in vitellogenesis (Vtgs). However, the contribution of each ER for the regulation of vtgs expression was not analyzed clearly in teleosts. In the present study, three ers isoforms (erα, erß1, and erß2) were cloned in pompano (Trachinotus ovatus). Real-time PCR and enzyme-linked immunosorbent assay (ELISA) was used to detect the effects of 17ß-estradiol (E2) on ERs and Vtgs in the liver of pompano. In vivo injection experiments showed that E2 significantly increased the expressions of ers and vtgs. ER broad spectrum antagonist Fulvestrant significantly attenuated the E2- induced up-regulation of ers and vtgs in a dose-dependent manner. ERα antagonist Methyl-piperidino pyrazole (MPP) significantly attenuated the up-regulation of erα, erß2, vtg-B and vtg-C, and promoted the expressions of erß1 and vtg-A. ERß antagonist Cyclofenil significantly inhibited the expressions of erß1, erß2, vtg-A and vtg-C, and promoted the expressions of erα and vtg-B. In addition, E2 significantly increased the protein level of Vtg, while Fulvestrant, MPP and Cyclofenil significantly inhibited the protein level of Vtg in a dose-dependent manner. Our results indicate that E2 may regulate the expression of each vtg with different subtypes of ERs, and shows a distinct compensatory expression effect on the regulation for ers and vtgs, which provides a theoretical basis for reproductive endocrinology study in pompano.

Pigment Identification and Gene Expression Analysis during Erythrophore Development in Spotted Scat (Scatophagus argus) Larvae.

Red coloration is considered an economically important trait in some fish species, including spotted scat, a marine aquaculture fish. Erythrophores are gradually covered by melanophores from the embryonic stage. Despite studies of black spot formation and melanophore coloration in the species, little is known about erythrophore development, which is responsible for red coloration. 1-phenyl 2-thiourea (PTU) is a tyrosinase inhibitor commonly used to inhibit melanogenesis and contribute to the visualization of embryonic development. In this study, spotted scat embryos were treated with 0.003% PTU from 0 to 72 h post fertilization (hpf) to inhibit melanin. Erythrophores were clearly observed during the embryonic stage from 14 to 72 hpf, showing an initial increase (14 to 36 hpf), followed by a gradual decrease (36 to 72 hpf). The number and size of erythrophores at 36 hpf were larger than those at 24 and 72 hpf. At 36 hpf, LC-MS and absorbance spectrophotometry revealed that the carotenoid content was eight times higher than the pteridine content, and ß-carotene and lutein were the main pigments related to red coloration in spotted scat larvae. Compared with their expression in the normal hatching group, rlbp1b, rbp1.1, and rpe65a related to retinol metabolism and soat2 and apoa1 related to steroid hormone biosynthesis and steroid biosynthesis were significantly up-regulated in the PTU group, and rh2 associated with phototransduction was significantly down-regulated. By qRT-PCR, the expression levels of genes involved in carotenoid metabolism (scarb1, plin6, plin2, apoda, bco1, and rep65a), pteridine synthesis (gch2), and chromatophore differentiation (slc2a15b and csf1ra) were significantly higher at 36 hpf than at 24 hpf and 72 hpf, except for bco1. These gene expression profiles were consistent with the developmental changes of erythrophores. These findings provide insights into pigment cell differentiation and gene function in the regulation of red coloration and contribute to selective breeding programs for ornamental aquatic animals.

A double-cycle echo state network topology for time series prediction.

Echo state network (ESN) has gained wide acceptance in the field of time series prediction, relying on sufficiently complex reservoir connections to remember the historical features of the data and using these features to obtain the outputs by a simple linear readout. However, the randomness of its input and reservoir connections pose negative impacts on the prediction performance and performance stability of the models, the complexity of reservoir connections brings high time consumption during network computing, and the presence of randomness and complexity makes the hardware implementation of the ESN difficult. In response, we propose a double-cycle ESN (DCESN) based on the Li-ESN model, which has fixed weights to improve prediction performance and performance stability and simpler reservoir connections compared to the classical ESN to reduce the time consumption. The existence of both greatly reduces the difficulty of hardware implementation of the ESN and provides many conveniences for the future application of the ESN. Experimental results on many widely used time series datasets show that the DCESN has comparable or even better prediction performance than the ESN and good robustness against noise and parameter fluctuations.

Comparative Transcriptome Analysis Reveals the Effect of Aurantiochytrium sp. on Gonadal Development in Zebrafish.

Aurantiochytrium sp. has received much attention as a potential resource for mass production of omega-3 fatty acids, which contribute to improved growth and reproduction in aquatic animals. In this study, we evaluated the gonadal index changes in zebrafish supplemented with 1-3% Aurantiochytrium sp. crude extract (TE) and the effects of ex vivo environmental Aurantiochytrium sp. on oocytes. 1% TE group showed significant improvement in the gonadal index, and both in vitro incubation and intraperitoneal injection promoted the maturation of zebrafish oocytes. In contrast, the transcriptome revealed 576 genes that were differentially expressed between the 1% TE group and the control group, including 456 up-regulated genes and 120 down-regulated genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathway analysis of differentially expressed genes indicated that Aurantiochytrium sp. potentially affects pathways such as lipid metabolism, immune regulation, and oocyte development in zebrafish. The results of this study enriched the knowledge of Aurantiochytrium sp. in regulating gonadal development in zebrafish and provided a theoretical basis for its application in aquaculture.

Bifunctional Cu(II)-containing PDA-PEI copolymer dots: Demonstration of a dual-mode platform for colorimetric-fluorescent detection of glyphosate in the environment.

The reliable and accurate detection of glyphosate is urgently demanded because it is related to food and environmental safety. In this contribution, a PDA-PEI/Cu2+ complex that possesses peroxidase-mimetic activity and stimulus-responsive fluorescence was fabricated by coordinating Cu2+ with polydopamine-polyethyleneimine copolymer dots (PDA-PEI CPDs). With the introduction of Cu2+, the fluorescence intensity of PDA-PEI CPDs dropped sharply owing to the electron transfer effect. As a peroxidase-mimicking nanozyme, the PDA-PEI/Cu2+ complex owns catalytic capacity to oxidize the colorless 3,3',5,5'-tetramethylbenzidine (TMB) into blue oxTMB, leading a further fluorescence quenching by internal filtering effect by oxTMB. Once the glyphosate participated, the fluorescence signal of PDA-PEI CPDs is recovered significantly because of the formation of more stable Glyp-Cu2+ complexes, meanwhile the peroxidase-mimicking activity of PDA-PEI/Cu2+ complex could be strongly hindered. According to this principle, a novel and extremely convenient 'turn off' colorimetric and 'turn on' fluorescence sensing platform can be established for dual-mode detection of glyphosate. The favorable sensitivity and selectivity and were verified in the analysis of glyphosate in the environment through the marriage of dual-signal sensing platform. The detection limit of the dual-mode glyphosate sensing platform was 103.82 ng/mL for colorimetric assay and 16.87 ng/mL for fluorescent assay, respectively. Satisfactory recoveries in the range of 96.40%-104.66% were obtained, indicating the potential of this method for application in complicated real sample. Thereby, this strategy broadens the applications of polydopamine nanomaterials and holds a promising application in determination of pesticide residues.

Green synthesis of Au@g-C3N4 nanocomposite using Hyssopus officinalis extract and its sensing application for vortioxetine determination.

Herein, we introduce a stable and green Au@g-C3N4 nanocomposite as a selective electrochemical sensor for vortioxetine (VOR) determination. The electrochemical behavior of VOR on the developed electrode was investigated through cyclic voltammetry (CV), differential pulse voltammetry (DPV), electrochemical impedance spectroscopy (EIS), and chronoamperometry. The Au@g-C3N4 nanocomposite was thoroughly observed by X-ray diffraction (XRD), energy-dispersive X-ray spectroscopy (EDX), Raman spectroscopy, and scanning electron microscopy. The Au@g-C3N4 nanocomposite had a higher conductivity and a narrower band gap than pure g-C3N4, causing higher electrochemical activity for VOR detection. Moreover, Au@g-C3N4 on the glassy carbon electrode (Au@g-C3N4/GCE) monitored a low level of VOR with high efficiency and low interference as an environmentally friendly processing approach. Interestingly, the as-fabricated sensor exhibited an ultrahigh selectivity for recognizing VOR with a detection limit (LOD) of 3.2 nM. Furthermore, the developed sensor was applied to determine VOR in pharmaceutical and biological samples, which indicated a high selectivity in the presence of interferences. This study suggests new insights into the phytosynthesis synthesis of nanomaterials with excellent biosensing applications.

Sensitive and Label-Free Colorimetric Detection of Glyphosate Based on the Suppression Peroxidase-Mimicking Activity of Cu(II) Ions.

The sensitive and accurate determination of glyphosate (Glyp) is urgently demanded because it is closely correlated with human health and environmental safety. In this work, we proposed a sensitive and convenient colorimetric assay by employing copper ion peroxidases for the detection of Glyp in the environment. Free Cu(II) ions displayed high peroxidase activity and can catalytically oxidize the colorless 3,3',5,5'-tetramethylbenzidine (TMB) into blue oxTMB, resulting in an obviously visible discoloration reaction. Once the Glyp is added, the ability of copper ions to mimic peroxidase can be largely suppressed because of the generation of Glyp-Cu2+ chelate. The favorable selectivity and sensitivity were demonstrated in the colorimetric analysis of Glyp. Furthermore, this rapid and sensitive method was successfully applied in the accurate and reliable determination of glyphosate in the real sample, holding promising applications in pesticide determination in the environment.

RNA Sequencing (RNA-Seq) Analysis Reveals Liver Lipid Metabolism Divergent Adaptive Response to Low- and High-Salinity Stress in Spotted Scat (Scatophagus argus).

Spotted scat (Scatophagus argus) can tolerate a wide range of salinity fluctuations. It is a good model for studying environmental salinity adaptation. Lipid metabolism plays an important role in salinity adaptation in fish. To elucidate the mechanism of lipid metabolism in the osmoregulation, the liver transcriptome was analyzed after 22 d culture with a salinity of 5 ppt (Low-salinity group: LS), 25 ppt (Control group: Ctrl), and 35 ppt (High-salinity group: HS) water by using RNA sequencing (RNA-seq) in spotted scat. RNA-seq analysis showed that 1276 and 2768 differentially expressed genes (DEGs) were identified in the LS vs. Ctrl and HS vs. Ctrl, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the pathways of steroid hormone biosynthesis, steroid biosynthesis, glycerophospholipid metabolism, glycerolipid metabolism, and lipid metabolism were significantly enriched in the LS vs. Ctrl. The genes of steroid biosynthesis (sqle, dhcr7, and cyp51a1), steroid hormone biosynthesis (ugt2a1, ugt2a2, ugt2b20, and ugt2b31), and glycerophospholipid metabolism (cept1, pla2g4a, and ptdss2) were significantly down-regulated in the LS vs. Ctrl. The pathways related to lipid metabolisms, such as fatty acid metabolism, fatty acid biosynthesis, peroxisome proliferator-activated receptor (PPAR) signaling pathway, adipocytokine signaling pathway, fatty acid degradation, and unsaturated fatty acid biosynthesis, were significantly enriched in the HS vs. Ctrl. The genes of unsaturated fatty acid biosynthesis (scd1, hacd3, fads2, pecr, and elovl1) and adipocytokine signaling pathway (g6pc1, socs1, socs3, adipor2, pck1, and pparα) were significantly up-regulated in the HS vs. Ctrl. These results suggest that the difference in liver lipid metabolism is important to adapt to low- and high-salinity stress in spotted scat, which clarifies the molecular regulatory mechanisms of salinity adaptation in euryhaline fish.

A chromosome-level genome assembly of Hong Kong catfish (Clarias fuscus) uncovers a sex-determining region.

BACKGROUND: Hong Kong catfish (Clarias fuscus) is an ecologically and economically important species that is widely distributed in freshwater regions of southern China. Hong Kong catfish has significant sexual growth dimorphism. The genome assembly of the Hong Kong catfish would facilitate study of the sex determination and evolution mechanism of the species. RESULTS: The first high-quality chromosome-level genome of the Hong Kong catfish was constructed. The total genome was 933.4 Mb, with 416 contigs and a contig N50 length of 8.52 Mb. Using high-throughput chromosome conformation capture (Hi-C) data, the genome assembly was divided into 28 chromosomes with a scaffold N50 length of 36.68 Mb. A total of 23,345 protein-coding genes were predicted in the genome, and 94.28% of the genes were functionally annotated in public databases. Phylogenetic analysis indicated that C. fuscus and Clarias magur diverged approximately 63.7 million years ago. The comparative genome results showed that a total of 60 unique, 353 expanded and 851 contracted gene families were identified in Hong Kong catfish. A sex-linked quantitative trait locus identified in a previous study was located in a sex-determining region of 30.26 Mb (0.02 to 30.28 Mb) on chromosome 13 (Chr13), the predicted Y chromosome. This QTL region contained 785 genes, of which 18 were identified as sex-related genes. CONCLUSIONS: This study is the first to report the chromosome-level genome assembly of Hong Kong catfish. The study provides an excellent genetic resource that will facilitate future studies of sex determination mechanisms and evolution in fish.

Etanercept ameliorates psoriasis progression through regulating high mobility group box 1 pathway.

BACKGROUND: As a common skin disease, psoriasis is related to inflammation and immune response. Due to the frequent recurrence of psoriasis, the treatment of psoriasis remains a clinical challenge. As an effective tumor necrosis factor-alpha (TNF-α) inhibitor, etanercept has been used for the treatment of psoriasis. However, some patients with psoriasis have no response to etanercept or discontinue treatment. To improve the therapeutic effect of etanercept, searching the potential biomarkers and investigating the related mechanisms of etanercept in the treatment of psoriasis are vital. MATERIALS AND METHODS: We stimulated HaCaT cells with lipopolysaccharide (LPS) to generate cellular psoriatic changes and established an imiquimod (IMQ)-induced psoriasis-like mouse model, and then used an etanercept to treat cell and mouse model. RESULTS: Etanercept alleviated IMQ-induced pathological changes and inflammation, and it also decreased the protein expression of high mobility group box 1 (HMGB1), receptor for advanced glycation end-products, and toll-like receptor 4. Moreover, the results of in vitro experiments showed that etanercept inhibited proliferation and inflammation, and promoted cell cycle arrest and apoptosis in LPS-treated HaCaT cells. Knockdown of HMGB1 further enhanced the inhibitory effects of etanercept on LPS-treated HaCaT cell viability and inflammation, while overexpression of HMGB1 notably reversed the inhibitory effects of etanercept on LPS-induced HaCaT cell viability and inflammation. CONCLUSION: Etanercept inhibited proliferation and inflammation and promoted cell cycle arrest and apoptosis in LPS-induced HaCaT cells, and etanercept ameliorated inflammation in a psoriasis-like mouse model.

Genome-Wide Identification and Characterization of Olfactory Receptor Genes in Silver Sillago (Sillago sihama).

Olfactory receptor (OR) genes are essential in the specific recognition of diverse stimuli in fish. In this study, a total of 141 OR genes were identified in silver sillago (Sillago sihama), a marine fish sensitive to environmental stimuli, including 112 intact genes, 26 truncated genes, and three pseudogenes. A phylogenetic tree analysis elucidated that the OR genes of S. sihama were classified into six groups, of which ß, γ, δ, ε, and ζ groups belonged to type I, and the η group belonged to type II. The type I OR genes contained almost all conserved motifs (n = 62), while type II OR genes mainly retained conserved motifs 7(3), 1, 10, 4, and 2 (n = 39). OR genes were mainly distributed on LG1, LG9, LG11, and LG12. Of all OR genes, 36.23% (50 genes) showed significant expansion in S. sihama. Ka/Ks analysis demonstrated that 227 sites were under purifying selection, while 12 sites were under positive selection, including eight genes in the OR2A12 gene subfamily. Sixty-one genes (44.20%) displayed differential expression under hypoxic stress. The identified OR genes explored the mechanism of environmental stress and ecological adaptation of S. sihama, and provided valuable genomic resources for further research on the olfaction of teleosts.

Effects of Natural and Synthetic Astaxanthin on Growth, Body Color, and Transcriptome and Metabolome Profiles in the Leopard Coralgrouper (Plectropomus leopardus).

Natural and synthetic astaxanthin can promote pigmentation in fish. In this study, the effects of dietary astaxanthin on growth and pigmentation were evaluated in leopard coralgrouper (Plectropomus leopardus). Fish were assigned to three groups: 0% astaxanthin (C), 0.02% natural astaxanthin (HP), and 0.02% synthetic astaxanthin (AS). Brightness (L*) was not influenced by astaxanthin. However, redness (a*) and yellowness (b*) were significantly higher for fish fed astaxanthin-containing diets than fish fed control diets and were significantly higher in the HP group than in the AS group. In a transcriptome analysis, 466, 33, and 32 differentially expressed genes (DEGs) were identified between C and HP, C and AS, and AS and HP, including various pigmentation-related genes. DEGs were enriched for carotenoid deposition and other pathways related to skin color. A metabolome analysis revealed 377, 249, and 179 differential metabolites (DMs) between C and HP, C and AS, and AS and HP, respectively. In conclusion, natural astaxanthin has a better coloration effect on P. leopardus, which is more suitable as a red colorant in aquaculture. These results improve our understanding of the effects of natural and synthetic astaxanthin on red color formation in fish.

BCU-Net: Bridging ConvNeXt and U-Net for medical image segmentation.

Medical image segmentation enables doctors to observe lesion regions better and make accurate diagnostic decisions. Single-branch models such as U-Net have achieved great progress in this field. However, the complementary local and global pathological semantics of heterogeneous neural networks have not yet been fully explored. The class-imbalance problem remains a serious issue. To alleviate these two problems, we propose a novel model called BCU-Net, which leverages the advantages of ConvNeXt in global interaction and U-Net in local processing. We propose a new multilabel recall loss (MRL) module to relieve the class imbalance problem and facilitate deep-level fusion of local and global pathological semantics between the two heterogeneous branches. Extensive experiments were conducted on six medical image datasets including retinal vessel and polyp images. The qualitative and quantitative results demonstrate the superiority and generalizability of BCU-Net. In particular, BCU-Net can handle diverse medical images with diverse resolutions. It has a flexible structure owing to its plug-and-play characteristics, which promotes its practicality.

Polyvinyl alcohol/polyacrylamide double-network hydrogel-based semi-dry electrodes for robust electroencephalography recording at hairy scalp for noninvasive brain-computer interfaces.

Objective.Reliable and user-friendly electrodes can continuously and real-time capture the electroencephalography (EEG) signals, which is essential for real-life brain-computer interfaces (BCIs). This study develops a flexible, durable, and low-contact-impedance polyvinyl alcohol/polyacrylamide double-network hydrogel (PVA/PAM DNH)-based semi-dry electrode for robust EEG recording at hairy scalp.Approach.The PVA/PAM DNHs are developed using a cyclic freeze-thaw strategy and used as a saline reservoir for semi-dry electrodes. The PVA/PAM DNHs steadily deliver trace amounts of saline onto the scalp, enabling low and stable electrode-scalp impedance. The hydrogel also conforms well to the wet scalp, stabilizing the electrode-scalp interface. The feasibility of the real-life BCIs is validated by conducting four classic BCI paradigms on 16 participants.Main results.The results show that the PVA/PAM DNHs with 7.5 wt% PVA achieve a satisfactory trade-off between the saline load-unloading capacity and the compressive strength. The proposed semi-dry electrode exhibits a low contact impedance (18 ± 8.9 kΩ at 10 Hz), a small offset potential (0.46 mV), and negligible potential drift (1.5 ± 0.4µV min-1). The temporal cross-correlation between the semi-dry and wet electrodes is 0.91, and the spectral coherence is higher than 0.90 at frequencies below 45 Hz. Furthermore, no significant differences are present in BCI classification accuracy between these two typical electrodes.Significance.Based on the durability, rapid setup, wear-comfort, and robust signals of the developed hydrogel, PVA/PAM DNH-based semi-dry electrodes are a promising alternative to wet electrodes in real-life BCIs.

Pacific white shrimp (Litopenaeus vannamei) vitelline membrane outer layer protein 1 (VMO1) is produced in the hepatopancreas and transported into ovarian oocytes during vitellogenesis.

In birds, vitelline membrane outer layer protein 1 (VMO1) is an exogenous protein that can be absorbed by eggs as a barrier to prevent the mixing of yolk and egg white. However, researches on VMO1 are limited in birds but not other non-avian species until now. In this study, we first identified a novel Vmo1 cDNA (Lv-Vmo1) in Pacific white shrimp (Litopenaeus vannamei), the most important cultured shrimp in the world. We further analyzed its gene organization, phylogenetic relationship and protein structure. The Lv-Vmo1 transcript was specifically expressed in the hepatopancreas without sexual dimorphism. During ovarian development in female, the hepatopancreatic Lv-Vmo1 mRNA levels showed a significant increase. By in situ hybridization, Lv-Vmo1 mRNA was present in three cell types of the hepatopancreas but neither oocytes nor follicle cells of the ovary. In contrast, immunofluorescence revealed that Lv-VMO1 protein was distributed in the cytoplasms of both hepatopancreatic cells and ovarian oocytes. Western blot showed that Lv-VMO1 protein was produced in the hepatopancreas and transported to the ovary via hemolymph circulation. Identification of a species-specific egg-entry guide protein is the key to the receptor-mediated ovarian transduction of cargo, a novel gene editing approach in oviparous animals. This study lays the mechanism for exogenous transport into penaeid shrimp eggs by VMO1, as a foundation for achieving exogenous protein-mediated incorporation into oocytes.