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Heat shock proteins (HSPs) are a class of highly conserved proteins that play an important role in biological responses to various environmental stresses. The mariculture of Thamnaconus septentrionalis, a burgeoning aquaculture species in China, frequently encounters stressors such as extreme temperatures, salinity variations, and elevated ammonia levels. However, systematic identification and analysis of the HSP70 and HSP90 gene families in T. septentrionalis remain unexplored. This study conducted the first genome-wide identification of 12 HSP70 and 4 HSP90 genes in T. septentrionalis, followed by a comprehensive analysis including phylogenetics, gene structure, conserved domains, chromosomal localization, and expression profiling. Expression analysis from RNA-seq data across various tissues and developmental stages revealed predominant expression in muscle, spleen, and liver, with the highest expression found during the tailbud stage, followed by the gastrula, neurula, and juvenile stages. Under abiotic stress, most HSP70 and HSP90 genes were upregulated in response to high temperature, high salinity, and low salinity, notably hspa5 during thermal stress, hspa14 in high salinity, and hsp90ab1 under low salinity conditions. Ammonia stress led to a predominance of downregulated HSP genes in the liver, particularly hspa2, while upregulation was observed in the gills, especially for hsp90b1. Quantitative real-time PCR analysis corroborated the expression levels under environmental stresses, validating their involvement in stress responses. This investigation provides insights into the molecular mechanisms of HSP70 and HSP90 in T. septentrionalis under stress, offering valuable information for future functional studies of HSPs in teleost evolution, optimizing aquaculture techniques, and developing stress-resistant strains. [ABSTRACT FROM AUTHOR]

Chinese cabbage (Brassica rapa L. ssp. Pekinensis) in the genus Brassica of the family Brassicaceae (Cruciferae) originates from China and is one of the most consumed leafy vegetables in East Asian countries. The leaf color is tightly linked with its growth, development, and yield. By screening an EMS mutagenized population of Chinese cabbage inbred line A03, we identified a yellowgreen leaf mutant ygl. This mutant developed abnormal ultrastructure in chloroplasts. Transcriptome and Gene Ontology (GO) analyses unveiled that abiotic stress response and glucan metabolism pathways were enriched in ygl compared to A03. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis reveals that differentially expressed genes were mainly associated with plant hormone signal transduction, photosynthesis, and starch and sucrose metabolism. In ygl, the expression of some photosynthetic pathway genes was significantly up-regulated, while the transcription of key genes related to carbon fixation, starch syntheses, and sugar metabolism pathways, such as RBCS1A, APS1, APL3, and SUS1, was markedly down-regulated. We also found a similar reduction trend in mRNA levels of IAA19, IAA29, and ARR4 associated with auxin and cytokinin pathways. Taken together, we uncovered transcriptional profiles for some important genes that may be responsible for leaf color development, and such gene expression repertoire may be useful for further investigation into the phenotype-to-genotype link in the ygl mutant Chinese cabbage. [ABSTRACT FROM AUTHOR]

Background: Triple-negative breast cancer (TNBC) is the most heterogenous and aggressive subtype of breast cancer. Chemotherapy remains the standard treatment option for patients with TNBC owing to the unavailability of acceptable targets and biomarkers in clinical practice. Novel biomarkers and targets for patient stratification and treatment of TNBC are urgently needed. It has been reported that the overexpression of DNA damage-inducible transcript 4 gene (DDIT4) is associated with resistance to neoadjuvant chemotherapy and poor prognosis in patients with TNBC. In this study, we aimed to identify novel biomarkers and therapeutic targets using RNA sequencing (RNA-seq) and data mining using data from public databases. Methods: RNA sequencing (RNA-Seq) was performed to detect the different gene expression patterns in the human TNBC cell line HS578T treated with docetaxel or doxorubicin. Sequencing data were further analyzed by the R package "edgeR" and "clusterProfiler" to identify the profile of differentially expressed genes (DEGs) and annotate gene functions. The prognostic and predictive value of DDIT4 expression in patients with TNBC was further validated by published online data resources, including TIMER, UALCAN, Kaplan–Meier plotter, and LinkedOmics, and GeneMANIA and GSCALite were used to investigate the functional networks and hub genes related to DDIT4, respectively. Results: Through the integrative analyses of RNA-Seq data and public datasets, we observed the overexpression of DDIT4 in TNBC tissues and found that patients with DDIT4 overexpression showed poor survival outcomes. Notably, immune infiltration analysis showed that the levels of DDIT4 expression correlated negatively with the abundance of tumor-infiltrating immune cells and immune biomarker expression, but correlated positively with immune checkpoint molecules. Furthermore, DDIT4 and its hub genes (ADM, ENO1, PLOD1, and CEBPB) involved in the activation of apoptosis, cell cycle, and EMT pathways. Eventually, we found ADM, ENO1, PLOD1, and CEBPB showed poor overall survival in BC patients. Conclusion: In this study, we found that DDIT4 expression is associated with the progression, therapeutic efficacy, and immune microenvironment of patients with TNBC, and DDIT4 would be as a potential prognostic biomarker and therapeutic target. These findings will help to identify potential molecular targets and improve therapeutic strategies against TNBC. [ABSTRACT FROM AUTHOR]

Cytokines can be induced by pathogen stimulation for the information exchange between cells, and their expression patterns indicate the response status of cells. In the present study, the expression patterns of ten cytokines (Cg IL17–1, −2, −3, −4, −5, −6, Cg TNF-1/2, Cg TGF-β and Cg IFNLP) in haemocytes were analyzed in the Pacific oyster Crassostrea gigas after Vibrio splendidus stimulation in the indoor and outdoor experiments to compare the induction patterns of different cytokines and evaluate the response status of haemocytes. After the indoor V. splendidus immersion stimulation, the mRNA abundances of six cytokines (Cg IL17–1, −3, −4, −5, Cg TGF-β and Cg IFNLP) in haemocytes were significantly downregulated at 48 h compared with that in the control group, among which Cg IL17–4 was the most down-regulated with 0.009-fold of that in the control group (p < 0.05). The mRNA abundances of Cg IL17–2, Cg IL17–6, Cg TNF-1 and Cg TNF-2 showed no significant change at 48 h compared with that in the control group. The apoptosis rate of haemocytes reached the maximum level of 1.138% at 48 h after the stimulation. In the oysters cultured outdoor from April to September 2021, the mRNA abundances of all ten cytokines in haemocytes were found to decrease in June (0.270-fold on average) and increase in July (5.402-fold on average) compared with those in May. After the in situ V. splendidus immersion stimulation in the outdoor cultured oysters in June and July, seven cytokines (Cg IL17–1, Cg IL17–2, Cg IL17–4, Cg IL17–5, Cg TNF-1, Cg TGF-β and Cg IFNLP) exhibited upregulated mRNA abundance in June, while in July, the mRNA abundances of five cytokines (Cg IL17–1, Cg IL17–3, Cg TNF-2, Cg TGF-β, and Cg IFNLP) remained constant, and four cytokines (Cg IL17–2, Cg IL17–4, Cg IL17–5 and Cg TNF-1) were suppressed after the stimulation. Cg IL17–4 had the highest fold-change in mRNA abundance among all cytokines in June after the stimulation, which was 85.599-fold compared with that in the control group (p < 0.05). The score of haemocyte response status (SH) was evaluated using the mRNA abundance database of all ten cytokines. It decreased to 124.860 at 48 h after the indoor V. splendidus stimulation, and it decreased to 66.793 in June and increased to 451.092 in July in the cultured oysters prior to the stimulation. Collectively, the expression patterns of ten cytokines in haemocytes varied against bacterial stimulation, among which Cg IL17–4 was found to response the most significantly, and SH indicated by the mRNA abundances of cytokines suggested an abnormal response status of haemocytes in the oysters at 48 h after indoor V. splendidus stimulation and the oysters cultured outdoor during June and July. These findings will further our understanding of the cytokine variation and haemocyte response of the Pacific oyster against bacterial stimulation. • Cg IL17-4 exrhibited the most significant response after stimulation in ten cytokines. • A formula was established to evaluate haemocyte response status using cytokine data. • The bacterial stimulation for 48 h resulted in abnormal response status of haemocytes. • Abnormal response status of haemocytes occurred in cultured oysters in June and July. [ABSTRACT FROM AUTHOR]

Danhong Huayu Koufuye (DHK), a traditional Chinese prescription, is used to treat central retinal vein occlusion clinically. We previously reported that DHK prevented diabetic retinopathy (DR) in rats. Moreover, we found that it protected endothelial cells from hyperglycemia-induced apoptosis through antioxidation and anti-inflammation. Here, we investigated whether antioxidative and anti-inflammatory activities of DHK contributed to its therapeutic effect on DR in streptozotocin- (STZ-) induced diabetic rats. DHK significantly blocked the breakdown of the blood-retinal barrier (BRB) and increased the thickness of the inner nuclear layer (INL), as well as suppressed the swelling of the ganglion cell layer (GCL) in diabetic retinas. DHK remarkably increased the activities of superoxide dismutase (SOD) and glutathione peroxidase (GPx) in plasma, and decreased serum level of nitric oxide (NO). Moreover, DHK markedly reduced the serum levels of vascular endothelial growth factor (VEGF) and intercellular adhesion molecule-1 (ICAM-1). Furthermore, DHK significantly downregulated protein expressions of VEGF and inducible NO synthase (iNOS) and mRNA expression of ICAM-1 in retinas. These results suggest that the antioxidative and anti-inflammatory activities of DHK may be important mechanisms involved in the protective effect of DHK on DR in STZ-induced diabetic rats. [ABSTRACT FROM AUTHOR]

Background: Aflatoxin B1 (AFB1) exposure is a crucial factor to initiate hepatocellular carcinoma (HCC). However, comprehensive microRNA (miRNA)‐message RNA (mRNA) regulatory network regarding AFB1‐associated HCC is still lacking. This work was aimed to identify miRNA‐mRNA network in primary human hepatocytes after AFB1 exposure. Methods: A miRNA expression dataset GSE71540 obtained from the gene expression omnibus (GEO) was used to identify differentially expressed miRNAs (DEMs) after AFB1 exposure using GEO2R. Target genes of these DEMs were identified using TargetScan V_7.2, miRDB, PITA, miRanda, and miRTarBase. Gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed at Database for Annotation, Visualization and Integrated Discovery (DAVID). miRNA‐mRNA regulatory network was established by analyzing three enriched KEGG pathways significantly correlated with HCC onset and then visualized at CytoScape. Results: In this work, nine upregulated and nine downregulated DEMs were identified. Functional enrichment analyses showed that these predicted target genes were significantly associated with cancer development. Analysis of three enriched pathways related to the onset of HCC identified 13 and nine target genes for upregulated DEMs and downregulated DEMs, respectively. Subsequently, the miRNA‐mRNA regulatory networks were constructed. Conclusions: In conclusion, miRNA‐mRNA regulatory network was established, which will help to understand the mechanism underlying the AFB1‐induced onset of HCC. [ABSTRACT FROM AUTHOR]

Caspases are cysteinyl aspartate-specific proteinases, playing critical roles in apoptotic pathway to induce apoptosis and inflammatory response. In this study, the expanded repertoire of Caspases was revealed in the Pacific oyster Crassostrea gigas , and a total of 30 Caspases were identified from the genomic and stress-induced transcriptomic databases of the Pacific oyster. They were clustered into Cg Caspase-2/9, Cg Caspase-8/10, Cg Caspase-3/6/7, Cg Caspase-Cg, and Cg Caspase-L. Cg Caspase-Cg subgroup was found to be specifically expanded after a positive selection in oyster with average Ka/Ks of 0.50. The mRNA expression of CgCaspase-Cg-5 was found to be obviously induced against various bacterial and viral stimulations or environmental stresses. The relative expression level of CgCaspase-Cg-5 in haemocytes increased and reached the peak at 6 h after Vibrio splendidus stimulation, which was 5.57-fold of that in the control group (p < 0.01). In the oysters whose CgCaspase-Cg-5 expression was knocked down, the mRNA expression of apoptosis-related genes including CgBcl2 , CgBax , CgCaspase3 and CgCaspase9 changed significantly at 12 h after V. splendidus stimulation. The expression of CgBax , CgCaspase3 and CgCaspase9 decreased, which was 0.64-fold (p < 0.05), 0.53-fold (p < 0.05) and 0.62-fold (p < 0.01), while the expression of CgBcl2 increased, which was 2.81-fold (p < 0.01) of that in the EGFP-dsRNA group, respectively. Meanwhile, the apoptotic rate of haemocytes (1.90 ± 0.71%) significantly decreased compared to that in the EGFP-dsRNA group (5.40 ± 0.72%) (p < 0.05), and the histological damages of widened cell spacing, gill filament swelling and loose cytoplasm were observed in the Cg Caspase-Cg-5-knockdown oysters after V. splendidus stimulation. Collectively, Cg Caspase-Cg subgroup was specifically expanded in oyster and some bivalve species, and species-specific Cg Caspase-Cg-5 regulated the mRNA expression of the apoptosis-related genes to induce haemocyte apoptosis in the early stage of immune response. This provided insight into the evolutionary and functional characteristics of Caspase repertoire in the Pacific oyster and highlighted the important role of Cg Caspase-Cg-5 in the response to pathogen infection and environmental stresses. • Five subgroups of Caspases were identified in the Pacific oyster. • Cg Caspase-Cgs were found to expand in the Pacific oyster after a positive selection. • Cg Caspase-Cg-5 was induced against various biotic and abiotic stresses. • The apoptosis-related genes expressed differently in Cg Caspase-Cg-5-RNAi oysters. • Apoptotic rate of haemocytes decreased significantly in Cg Caspase-Cg-5-RNAi oysters. [ABSTRACT FROM AUTHOR]