Integrating Single-Cell and Spatial Transcriptomics Reveals Heterogeneity of Early Pig Skin Development and a Subpopulation with Hair Placode Formation.

The dermis and epidermis, crucial structural layers of the skin, encompass appendages, hair follicles (HFs), and intricate cellular heterogeneity. However, an integrated spatiotemporal transcriptomic atlas of embryonic skin has not yet been described and would be invaluable for studying skin-related diseases in humans. Here, single-cell and spatial transcriptomic analyses are performed on skin samples of normal and hairless fetal pigs across four developmental periods. The cross-species comparison of skin cells illustrated that the pig epidermis is more representative of the human epidermis than mice epidermis. Moreover, Phenome-wide association study analysis revealed that the conserved genes between pigs and humans are strongly associated with human skin-related diseases. In the epidermis, two lineage differentiation trajectories describe hair follicle (HF) morphogenesis and epidermal development. By comparing normal and hairless fetal pigs, it is found that the hair placode (Pc), the most characteristic initial structure in HFs, arises from progenitor-like OGN+/UCHL1+ cells. These progenitors appear earlier in development than the previously described early Pc cells and exhibit abnormal proliferation and migration during differentiation in hairless pigs. The study provides a valuable resource for in-depth insights into HF development, which may serve as a key reference atlas for studying human skin disease etiology using porcine models.

Ganoderma spore lipid ameliorates docetaxel, cisplatin, and 5-fluorouracil chemotherapy-induced damage to bone marrow mesenchymal stem cells and hematopoiesis.

BACKGROUND: A triplet chemotherapy regimen of docetaxel, cisplatin, and 5-fluorouracil (TPF) is used to treat head and neck squamous cell carcinoma; however, it is toxic to bone marrow mesenchymal stem cells (BMSCs). We previously demonstrated that Ganoderma spore lipid (GSL) protect BMSCs against cyclophosphamide toxicity. In this study, we investigated the protective effects of GSL against TPF-induced BMSCs and hematopoietic damage. METHODS: BMSCs and C57BL/6 mice were divided into control, TPF, co-treatment (simultaneously treated with GSL and TPF for 2 days), and pre-treatment (treated with GSL for 7 days before 2 days of TPF treatment) groups. In vitro, morphology, phenotype, proliferation, senescence, apoptosis, reactive oxygen species (ROS), and differentiation of BMSCs were evaluated. In vivo, peripheral platelets (PLTs) and white blood cells (WBCs) from mouse venous blood were quantified. Bone marrow cells were isolated for hematopoietic colony-forming examination. RESULTS: In vitro, GSL significantly alleviated TPF-induced damage to BMSCs compared with the TPF group, recovering their morphology, phenotype, proliferation, and differentiation capacity (p < 0.05). Annexin V/PI and senescence-associated ß-galactosidase staining showed that GSL inhibited apoptosis and delayed senescence in TPF-treated BMSCs (p < 0.05). GSL downregulated the expression of caspase-3 and reduced ROS formation (p < 0.05). In vivo, GSL restored the number of peripheral PLTs and WBCs and protected the colony-forming capacity of bone marrow cells (p < 0.05). CONCLUSIONS: GSL efficiently protected BMSCs from damage caused by TPF and recovered hematopoiesis.

Sophoridine Counteracts Obesity via Src-Mediated Inhibition of VEGFR Expression and PI3K/AKT Phosphorylation.

Sophoridine (SRP) is a natural quinolizidine alkaloid found in many traditional Chinese herbs, though its effect on adipose tissue is unclear. We improved serum lipid levels by administering SRP by gavage in high-fat diet (HFD)-fed C57BL/6 mice. After 11 weeks, SRP supplementation significantly reduced body weight gain and improved glucose homeostasis, while reducing subcutaneous fat and liver weight. SRP also inhibited cell proliferation and differentiation of 3T3-L1 cells. Proteomics analysis revealed that SRP inhibits adipocyte differentiation by interacting with Src, thereby suppressing vascular endothelial growth factor receptor 2 (VEGFR2) expression and PI3K/AKT phosphorylation. This study provides an empirical basis for the treatment of obesity with small molecules.

Genome-Wide Association Study on Reproductive Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs.

Reproductive traits have a key impact on production efficiency in the pig industry. It is necessary to identify the genetic structure of potential genes that influence reproductive traits. In this study, a genome-wide association study (GWAS) based on chip and imputed data of five reproductive traits, namely, total number born (TNB), number born alive (NBA), litter birth weight (LBW), gestation length (GL), and number of weaned (NW), was performed in Yorkshire pigs. In total, 272 of 2844 pigs with reproductive records were genotyped using KPS Porcine Breeding SNP Chips, and then chip data were imputed to sequencing data using two online software programs: the Pig Haplotype Reference Panel (PHARP v2) and Swine Imputation Server (SWIM 1.0). After quality control, we performed GWAS based on chip data and the two different imputation databases by using fixed and random model circulating probability unification (FarmCPU) models. We discovered 71 genome-wide significant SNPs and 25 potential candidate genes (e.g., SMAD4, RPS6KA2, CAMK2A, NDST1, and ADCY5). Functional enrichment analysis revealed that these genes are mainly enriched in the calcium signaling pathway, ovarian steroidogenesis, and GnRH signaling pathways. In conclusion, our results help to clarify the genetic basis of porcine reproductive traits and provide molecular markers for genomic selection in pig breeding.

Transcriptome, proteome and metabolome analysis provide insights on fat deposition and meat quality in pig.

Intramuscular fat (IMF) content, which is an important determinant of meat quality characteristics such as tenderness, juiciness and flavor, has long been a research hotspot. Chinese local pig breeds are famous for their excellent meat quality which is mainly reflected in the high IMF content, strong hydraulic system and et al. However, there are few analysis of meat quality by omics methods. In our study, we identified 12 different fatty acids, 6 different amino acids, 1,262 differentially expression genes (DEGs), 140 differentially abundant proteins (DAPs) and 169 differentially accumulated metabolites (DAMs) (p < 0.05) with metabolome, transcriptome, and proteome. It has been found that DEGs, DAPs and DAMs were enriched in the Wnt signaling pathway, PI3K-Akt signaling pathway, Rap1 signaling pathway, and Ras signaling pathway which were related to meat quality. Moreover, our Weighted genes co-expression network construction (WGCNA) showed RapGEF1 was the key gene related to IMF content and the RT-qPCR analysis was used to perform validation of the significant genes. In summary, our study provided both fundamental data and new insights to further uncover the secret of pig IMF content.

Dietary grape pomace extract supplementation improved meat quality, antioxidant capacity, and immune performance in finishing pigs.

In pig production, reducing production costs and improving immunity are important. Grape pomace, a good agricultural by-product, has been thrown away as food waste for a long time. Recently, we found that it could be used as a new source of pig feed. We investigated the effect of grape pomace on inflammation, gut barrier function, meat quality, and growth performance in finishing pigs. Our results indicated that treatment samples showed a significant decrease in water loss, IL-1ß, DAO, ROS, and MDA content (p < 0.05). IgA, IgG, IgM, CAT, T-AOC, SOD, and IFN-γ significantly increased compared with those in control samples (p < 0.05). Meanwhile, the relative mRNA expression of the tight junction protein occludin showed a significant difference (p < 0.05). Analysis of metagenomic sequencing indicated that grape pomace significantly decreased the relative abundance of Treponema and Streptococcus (p < 0.05). In summary, our results demonstrated that grape pomace could improve meat quality, alleviate inflammation, and decrease oxidative stress.

Regeneration of methylene blue-saturated biochar by synergistic effect of H2O2 desorption and peroxymonosulfate degradation.

Biochar, as an adsorbent, is widely used for the removal of organic pollutants in water body. Hence, after saturated adsorption, regeneration treatment is required to recover the adsorption performance of biochar. In this study, a biochar (P-GBC) prepared by phosphoric acid activation showed high adsorption capacity for methylene blue (MB) with the maximum adsorption capacity (Qm) of 599.66 mg/g. Then, regeneration treatments using 4 mM peroxymonosulfate (PMS), 0.2 M hydrogen peroxide (H2O2) and their mixture were used to regenerate MB-saturated biochar with regeneration efficiencies of 58.24%, 66.01% and 94.88%, respectively. Combining with degradation and quenching experiments, it is found that synergistic effect of H2O2 desorption and PMS degradation is responsible for the enhancement of regeneration efficiency of P-GBC in H2O2-PMS system and enables a high mineralization rate of 82.68% for the MB adsorbed on P-GBC. Furthermore, EPR tests indicate that singlet oxygen (1O2) is assigned as the primary activate species for the degradation of MB and XPS analyses confirm that graphite nitrogen and carbonyl on P-GBC are the main active sites for the activation of PMS. Compared with conventional regenerants, H2O2-PMS system has the advantages of low dosage, high mineralization efficiency, and easy accessibility, and is also effective, sustainable and environmentally friendly for the regeneration of organic pollutants-saturated biochar.

Low-Temperature Reduction Synthesis of γ-Fe2O3-x@biochar Catalysts and Their Combining with Peroxymonosulfate for Quinclorac Degradation.

Biochar loading mixed-phase iron oxide shows great advantages as a promising catalyst owing to its eco-friendliness and low cost. Here, γ-Fe2O3-x@biochar (E/Fe-N-BC) composite was successfully prepared by the sol-gel method combined with low-temperature (280 °C) reduction. The Scanning Electron Microscope (SEM) result indicated that γ-Fe2O3-x particles with the size of approximately 200 nm were well-dispersed on the surface of biochar. The CO derived from biomass pyrolysis is the main reducing component for the generation of Fe (II). The high content of Fe (II) contributed to the excellent catalytic performance of E/Fe-N-BC for quinclorac (QNC) degradation in the presence of peroxymonosulfate (PMS). The removal efficiency of 10 mg/L of QNC was 100% within 30 min using 0.3 g/L γ-Fe2O3-x@biochar catalyst and 0.8 mM PMS. The radical quenching experiments and electron paramagnetic resonance analysis confirmed that •OH and SO4•- were the main radicals during the degradation of QNC. The facile and easily mass-production of γ-Fe2O3-x@biochar with high catalytic activity make it a promising catalyst to activate PMS for the removal of organic pollutants.

Ablation of Tas1r1 Reduces Lipid Accumulation Through Reducing the de Novo Lipid Synthesis and Improving Lipid Catabolism in Mice.

Amino acid sensing plays an important role in regulating lipid metabolism by sensing amino acid nutrient disturbance. T1R1 (umami taste receptor, type 1, member 1) is a membrane G protein-coupled receptor that senses amino acids. Tas1r1-knockout (KO) mice were used to explore the function of umami receptors in lipid metabolism. Compared with wild-type (WT) mice, Tas1r1-KO mice showed decreased fat mass (P < 0.05) and adipocyte size, lower liver triglyceride (7.835 ± 0.809 vs 12.463 ± 0.916 mg/g WT, P = 0.013) and total cholesterol levels (0.542 ± 0.109 vs 1.472 ± 0.044 mmol/g WT, P < 0.001), and reduced lipogenesis gene expressions in adipose and liver tissues. Targeted liver amino acid metabolomics showed that the amino acid content of Tas1r1-KO mice was significantly decreased, which was consistent with the branched-chain ketoacid dehydrogenase protein levels. Proteomics analysis showed that the upregulated proteins were enriched in lipid and steroid metabolism pathways, and parallel reaction monitoring results illustrated that Tas1r1 ablation promoted lipid catabolism through oxysterol 7 α-hydroxylase and insulin-like growth factor binding protein 2. In summary, Tas1r1 disruption in mice could reduce lipid accumulation by reducing de novo lipid synthesis and improving lipid catabolism.

Screening the bioactive compound from Coptis chinensis inflorescence by immobilized peroxisome proliferator-activated receptor-gamma.

Coptis chinensis inflorescence is a by-product of Coptis chinensis Franch and riches in alkaloids. We screened the bioactive compounds in the by-product through an immobilized peroxisome proliferator-activated receptor gamma. The receptor was covalently immobilized on the macroporous silica gel through amino groups to generate the affinity stationary phase and was applied for screening. Berberine, palmatine, and jatrorrhizine were identified as the retained components of the herb on the affinity column. We evaluated the binding of the three bioactive compounds with the receptor by nonlinear chromatography and molecular docking. The affinities of the compounds to the receptor were (1.42 ± 0.10) ×108 /M, (4.88 ± 0.38) ×107 /M, and (1.65 ± 0.13) ×107 /M for berberine, palmatine, and jatrorrhizine, with dissociation rate constants of (17.70 ± 0.03) ×10-3 /S, (5.18 ± 0.25) ×10-2 /S, and (15.7 ± 0.05) ×10-2 /S, respectively. Cys285, Arg288, Ile326, Leu330, and His449 in the agonist binding pocket of the receptor participated in the formation of bioactive compound-receptor conjugates. These data indicated that the immobilized receptor is a reliable alternative for screening the bioactive compounds. In addition, Coptis chinensis inflorescence has the potential to be a source for drug discovery.

N, P, O-codoped biochar from phytoremediation residues: a promising cathode material for Li-S batteries.

Environment and energy are two key issues in today's society. In terms of environmental protection, the treatment of phytoremediation residues has become a key problem to be solved urgently, while for energy storage, it tends to utilize low-cost and high specific energy storage materials (i.e. porous carbon). In this study, the phytoremediation residues is applied to the storage materials with low-cost and high specific capacity. Firstly, the phosphorous acid assisted pyrolysis of oilseed rape stems from phytoremediation is effective in the removal of Zn, Cu, Cd and Cr from the derived biochar. Moreover, the derived biochar from phytoremediation residues shows abundant porous structure and polar groups (-O/-P/-N), and it can deliver 650 mAh g-1with 3.0 mg cm-2sulfur, and keeps 80% capacity after 200 cycles when employing it as a sulfur host for lithium-sulfur (Li-S) batteries. Hence, phosphorous acid assisted pyrolysis and application in Li-S battery is a promising approach for the disposal of phytoremediation residues, which is contributed to the environmental protection as well as energy storage.

Emerging disposal technologies of harmful phytoextraction biomass (HPB) containing heavy metals: A review.

Phytoextraction is an effective approach for remediation of heavy metal (HM) contaminated soil. After the enhancement of phytoextraction efficiency has been systematically investigated and illustrated, the harmless disposal and value-added use of harmful phytoextraction biomass (HPB) become the major issue to be addressed. Therefore, in recent years, a large number of studies have focused on the disposal technologies for HPB, such as composting, enzyme hydrolysis, hydrothermal conversion, phyto-mining, and pyrolysis. The present review introduces their operation process, reaction parameters, economic/ecological advantages, and especially the migration and transformation behavior of HMs/biomass. Since plenty of plants possess comparable extraction abilities for HMs but with discrepancy constitution of biomass, the phytoextraction process should be combined with the disposal of HPB after harvested in the future, and thus a grading handling strategy for HPB is also presented. Hence, this review is significative for disposing of HPB and popularizing phytoextraction technologies.

Emerging roles of circRNAs in regulating thermal and hypoxic stresses in Apostichopus japonicus (Echinodermata: Holothuroidea).

Some sea cucumbers are economically and ecologically important, but they are threatened by thermal and hypoxic stress in changing oceanographic conditions. We construct circRNAs profiles, reveal circRNAs characters, and illustrate the potential regulatory roles of circRNAs in one commercially important species of sea cucumber, Apostichopus japonicus. Reads are distributed in intergenic (44.14%), exonic (48.26%) and intronic (7.60%) regions of the genome. A total of 1684 circRNAs were identified, and the most common spliced length is 269 nt in the present study. In three treatments (HT [thermal stress], LO [hypoxic stress], and HL [combined thermal and hypoxic stress]), 24, 27 and 27 differentially expressed (DE) circRNAs were identified, respectively. Five novel DE-circRNAs commonly occur in these treatments (novel_circ_0003311, novel_circ_0000229, novel_circ_0003944, novel_circ_0001458 and novel_circ_0000707), and based on them, potential circRNA-miRNA binding pairs were predicted. Sanger sequencing, RNase R treatment experiment and qPCR validation identified the accuracy of the circRNAs. Key circRNAs identified in the present study were covalently closed and were more stable under RNase R treatment than linear RNAs. Based on function analysis, circRNAs could regulate metabolic process, signal transduction, and ion responses in A. japonicus when exposed to thermal and hypoxic stress, and 'regulation of response to stimulus' is a common gene ontology (GO) term that is significantly enriched in each treatment; GO terms for 'DNA' and 'stress' are commonly enriched in heat-related treatments (HT and HL); and GO terms for 'protein' are commonly enriched in hypoxia-related treatments (LO and HL). When environmentally stressed, 'metabolism,' 'transport and catabolism,' 'membrane transport,' and 'signal transduction' were significantly responded in sea cucumber based on KEGG analysis. We provide insights into circRNA functions in stress regulation and lay a foundation for invertebrate circRNA research.

Metabolomic analysis of white, green and purple morphs of sea cucumber Apostichopus japonicus during body color pigmentation process.

The sea cucumber Apostichopus japonicus is an important economic species owing to their high nutritive and medicinal value. Body color is one of the most important traits in the cultivation, which affects taste and market price of holothurian products. Pigmentation is an important stage of sea cucumber growth and development, in addition to achieving rare and beautiful coloration. In this study, UHPLC-QTOF/MS technique was performed to analyze the metabolome of white, green and purple A. japonicus body wall during the pigmentation process. A total of 2633 metabolites were identified. OPLS-DA clearly discriminated the body wall metabolites among the three color morphs. In addition, 13 annotated metabolites that could discriminate white, green and purple A. japonicus were screened out. KEGG metabolic pathway analysis revealed that "biosynthesis of unsaturated fatty acids" and "fatty acid biosynthesis" were closely related in the different color morphs. Furthermore, we performed comparative analysis of polysaccharide and saponin among white, green and purple A. japonicus. The results showed that the content of polysaccharide and saponin in purple A. japonicus was the highest, while that in white A. japonicus was the lowest. This study will provide valuable information for future studies on sea cucumber and the molecular mechanism underlying pigmentation and color polymorphism, and may contribute to support the culturing of desirable color morphs.

Sea cucumbers in a high temperature and low dissolved oxygen world: Roles of miRNAs in the regulation of environmental stresses.

The exacerbation of global warming has driven changes in environmental factors, including water temperature and oxygen concentration. The sea cucumber Apostichopus japonicus, an economically important aquatic animal, is constantly and directly challenged by heat and hypoxia. In this study, 12 small RNA libraries were constructed for this species, and a total of 21, 26 and 22 differentially expressed (DE) miRNAs were clarified in A. japonicus under thermal (26 °C), hypoxic (2 mg/L) and the combined stresses. Comparative miRNA sequencing analysis and real-time PCR were used to identify and validate the representative miRNAs, including Aja-miR-novel-299, Aja-let-7b-3p, Aja-miR-71b-5p, Aja-miR-novel-13218 and Aja-miR-2004 in response to high temperature, and Aja-miR-92b-3p, Aja-miR-210-5p and Aja-miR-novel-26331 in response to oxygen limitation. GO and KEGG pathway analysis revealed that the potential target genes of DE-miRNAs involved in biosynthesis, metabolism, immunity, cell growth and death, translation and signaling transduction. Key DE-miRNAs with potentially targeted genes associated with heat shock and hypoxia response were also determined. These results may help explaining the role of miRNA regulation in stress resistance, as well as the potential molecular regulation mechanism of the echinoderm A. japonicus in the context of global warming.

Combined Treatment with JFKD and Gefitinib Overcomes Drug Resistance in Non-Small Cell Lung Cancer.

BACKGROUND: Gefitinib is an important drug used to treat Non-Small Cell Lung Cancer (NSCLC) with EGFR activating mutations, but drug resistance restricts its clinical application. In this present study, combined Jin Fu Kang Decoction (JFKD) and gefitinib showed specific cytotoxicity to gefitinib-resistant cancer cells (PC-9/gef). OBJECTIVE: This study aimed to decipher the molecular mechanism of the JFKD on drug resistance when used together with Gefitinib and to find the contributing bio-active substance(s) in JFKD based on the putative mechanism. METHODS: To investigate the combined effect of gefitinib and JFKD, in vitro experiments were conducted on the established gefitinib-resistant PC-9 subclone, while in vivo experiments were conducted on the BALB/c nude mice with PC-9/gef xenografts. Western blot was used to evaluate the protein expression, and Ultra-Performance Liquid Chromatography (UPLC) coupled with quadrupole time-offlight Mass Spectrometry (MS) was used to detect the bio-active compounds of JFKD. RESULTS: The expression of the PTEN-relevant protein p-EGFR, p-Akt in vitro was inhibited more when combined JKFD and gefitinib were used, whereas the activities of PDCD4 and PTEN were increased; remarkably, in vivo experiments showed enhanced tumor growth inhibition when treated with this combination. Due to this combination, the effect on the gefitinib-resistant cell line, one of the JFKD-induced anti-cancer mechanisms, was found. To link the putative mechanism and the anticancer compounds in JFKD, 14 saponins and flavonoids were detected. CONCLUSION: The results suggested that a promising TCM-participated therapy can be established by the putative mechanism of the combined treatment in resistant NSCLC and screening the contributing bio-active substance(s) in JFKD is meaningful on new TCM formula discovery.

The role of BAMBI in regulating adipogenesis and myogenesis and the association between its polymorphisms and growth traits in cattle.

Bone morphogenic protein and activin membrane-bound inhibitor (BAMBI) is a transmembrane protein that affects the growth, development and muscle regeneration of the body by regulating the TGF-ß, BMP and Wnt signaling pathways. Studies have found that BAMBI has important regulatory functions in skeletal muscle and preadipocytes in vivo and in vitro. However, research on this protein in cattle is lacking. In this study, to determine the role of BAMBI in the growth and development of cattle, we first found that the expression of BAMBI in adipose tissue and longissimus muscle of newborn and adult Qinchuan beef cattle was significantly different. Then we showed that BAMBI knockdown promoted the differentiation of bovine preadipocytes and suppressed myoblast myogenesis, as indicated by the increased lipid droplets and the decreased myotubes, as well as the corresponding significant changes in the expression of PPARγ, C/EBPα, C/EBPß, FABP4, MyoD, MyoG and Myf6. Finally, to further verify the effect of BAMBI on the growth performance of cattle, we identified seven novel SNPs in the BAMBI genomic region, which were significantly correlated with one or more growth traits (p < 0.05). Furthermore, individuals with haplotype H1H4 (TC-GA-CT-CA-AT-AT-AG) had a higher body and carcass quality than those with other haplotypes (p < 0.05). In brief, BAMBI may be a functional gene for the differentiation of bovine preadipocytes and myoblasts, and variations in the BAMBI genomic region, especially the combined haplotype H1H4, may benefit marker-assisted selection in cattle.

Expression of RAD51 and Its Clinical Impact in Oral Squamous Cell Carcinoma.

PURPOSE: To examine the expression of RAD51 in oral squamous cell carcinoma (OSCC) and analyze its connection with pathological grade, clinical stage, and lymphatic metastasis potential. METHODS: For this study, 74 OSCC samples, 15 normal mucosa tissues, and 11 normal skin tissue samples were collected. RAD51 expression was investigated using immunohistochemistry. A follow-up visit was used to assess the prognosis of each patient. We compared RAD51 expression in oral mucosa epithelial cells (OMECs), keratinocytes, and tongue squamous cell carcinoma cells (TSCCs) by Western blot analysis. RESULTS: RAD51 expression was higher in tumor cells than in normal mucosal tissues. In addition, RAD51 expression was associated with higher tumor differentiation (P < 0.05). Also, RAD51 expression was higher (P < 0.05). Also, RAD51 expression was higher (P < 0.05). Also, RAD51 expression was higher (. CONCLUSION: A strong positive correlation was found between RAD51 expression and the degree of malignancy in OSCC patients, suggesting that RAD51 could be an excellent prognostic indicator for OSCC patients.

Transcriptome analysis of phototransduction-related genes in tentacles of the sea cucumber Apostichopus japonicus.

The sea cucumber Apostichopus japonicus (Selenka)is a typical nocturnal echinoderm, which is believed to be almost completely dependent on light intensity for the regulation of endogenous rhythms. Under conditions of high light intensity, this species shows clear evidence of light avoidance behavior, seeking out shaded areas of reef in which to reside. In this study, we performed RNA-Seq analysis to examine the tentacle transcriptome of A. japonicus specimens that had been subjected to dark and light (5 min and 1 h) conditions. We specifically focused on detecting genes involved in opsin-based light perception, including opsins and members of phototransduction-related pathways. On the basis of comparisons with both vertebrate and invertebrate phototransduction pathways, we determined that components of two of the main metazoan phototransduction pathways were altered in response to illumination. Among the key phototransduction-related genes in tentacles, we identified retinol dehydrogenase, members of the dehydrogenase/reductase family, and myosin III, and also detected a pair of visual pigment-like receptors, peropsin and peropsin-like, the homologous genes of which are believed to have the same function but show opposite expression patterns in response to different light environments. In general, the up-regulation of key genes in sea cucumber exposed to illumination indicated that the tentacles can respond to differences in the light environment at the molecular level.

The regulation mechanism of lncRNAs and mRNAs in sea cucumbers under global climate changes: Defense against thermal and hypoxic stresses.

The aquatic environment can be greatly impacted by thermal and hypoxic stresses, particularly caused by intensified global warming. Hence, there is an urgency to understand the response mechanisms of marine organisms to adverse environment. Although long non-coding RNAs (lncRNAs) are involved in many biological processes, their roles in stress responses still remain unclear. Here, differentially expressed (DE) lncRNAs and mRNAs were identified as responses to environmental stresses in the economically important sea cucumber, Apostichopus japonicus, and their potential roles were explored. Based on a total of 159, 355 and 495 significantly upregulated genes and 230, 518 and 647 significantly downregulated genes identified in the thermal, hypoxic and combination thermal + hypoxic stress treatments, respectively, we constructed DE-lncRNA-mRNA coexpression networks. Among the networks, eight shared pairs were identified from the three treatments, and based on the connectivity degree, MSTRG.27265, MSTRG.19729 and MSTRG.95524 were shown to be crucial lncRNAs. Among all the significantly changed lncRNAs identified by RT-qPCR and sequencing data, binding sites were found in four other lncRNAs (MSTRG.34610, MSTRG.10941, MSTRG.81281 and MSTRG.93731) with Aja-miR-2013-3p, a key miRNA that responds to hypoxia in sea cucumbers. The hypoxia-inducible factor (HIF-1α) was also shown as the possible targeted mRNA of Aja-miR-2013-3p. As indicated by a dual-luciferase reporter assay system, "HIF-1α gene/Aja-miR-2013-3p/MSTRG.34610" network and the "HIF-1α gene/Aja-miR-2013-3p/MSTRG.10941" network may play important roles in sea cucumbers under environmental stresses. Moreover, environmental stress altered the expression of multiple lncRNAs and mRNAs, thus affecting various biological processes in A. japonicus, including immunity, energy metabolism and the cell cycle. At the molecular level, more comprehensive responses were elicited by the combined thermal/hypoxic stress treatment than by individual stresses alone in sea cucumbers. This study lays the groundwork for future research on molecular mechanisms of echinoderm responses to thermal and hypoxic stress in the context of global climate changes.