Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary

Integrated transcriptome and proteome analysis unveils black tea polyphenols metabolic pathways in Saccharomyces cerevisiae

Kombucha is a fermented beverage produced through the fermentation of sweetened tea by a symbiotic community of bacteria and yeasts (SCOBY). Microbial fermentation in kombucha increases low-molecular-weight polyphenols contents, effectively improving the bioavailability and antioxidant properties. However, the biotransformation pathways of polymerized polyphenols remain poorly understood. This study combines polyphenol dynamics with transcriptomic and proteomic analyses to elucidate the metabolic pathways in Saccharomyces cerevisiae, a yeast frequently found in kombucha, during black tea broth fermentation. Firstly, profiles of polyphenols, particularly catechins were analyzed and key points of polyphenol changes kinetics were identified, then transcriptome and proteome of S. cerevisiae were examined. The overall omics data profile indicated the reduction in protein synthesis in S. cerevisiae, reflecting a shift in resource allocation, with energy focused more on metabolic activities rather than on growth. Specifically, enzymes related to biotransformation of polymerized polyphenols and hydrolyzing of glycoside polyphenols were extracted. For polymeric polyphenols, the upregulation of peroxidases (CCP1) and multicopper oxidases (FET3) suggests their role in the degradation of organic aromatic compounds. They also showed a strong correlation with catechin changes. Additionally, S. cerevisiae enzymes like monooxygenase (COQ6) likely contribute to the reductive cleavage of the O1-C2 bond in the C-ring of flavan-3-ols. Enzymes such as NADPH dehydrogenase 3 (OYE3) may be involved in catechin degradation in the later stages of fermentation. In addition, glycoside hydrolases, involved in breaking glycosidic bonds in polyphenol glycosides, were also identified. Based on these findings, the tea polyphenol biotransformation pathways in S. cerevisiae were mapped. This research provides a foundation for uncovering polyphenol metabolism pathways in starter cultures, designing new cultures to achieve predictable polyphenol profiles in kombucha, and enhancing its health benefits.

CD34+CD45+ cells promote alveolar macrophage efferocytosis to alleviate phosgene-induced acute lung injury in rats

Phosgene is still widely used in industrial production nowadays. However, as a toxic gas, accidental exposure to phosgene can lead to acute lung injury (ALI). Our team previously identified a cell subpopulation as CD34+CD45+ cells in the bronchoalveolar lavage fluid (BALF) of rats. CD34+CD45+ cells were demonstrated to possess stem cell properties and alleviate pulmonary inflammation during phosgene-induced acute lung injury (P-ALI). However, how CD34+CD45+ cells contribute to the anti-inflammatory process remains unexplored. Rats with P-ALI were intratracheally administered with CD34+CD45+ cells, and it was found that both the infiltration of macrophages and apoptotic cells were reduced in the lung tissues. The macrophages were polarized to an anti-inflammatory CD45+CD3-CD163+MHC-IIlo phenotype and restored efferocytosis efficiency, with a decreased level of inflammatory cytokines in the BALF. Moreover, it was observed that CD34+CD45+ cells promoted macrophage efferocytosis ex vivo and in vitro. Exosomes derived from CD34+CD45+ cells were further demonstrated to mediate the enhancement of macrophage efferocytosis. The small RNA sequencing analysis suggested that exosomal rno-miR-149-5p contributed to the effect. The transfection of rno-miR-149-5p mimic induced the enhancement of efferocytosis in macrophages as the exosomes did, while rno-miR-149-5p inhibitor attenuated the effect by exosomes. Our findings provide convincing evidence that CD34+CD45+ cells can alleviate ALI by enhancing macrophage efferocytosis, offering valuable insights into their therapeutic potential in managing chemical-induced acute lung injuries.

Gut microbiota dysbiosis triggered by salinity stress enhances systemic inflammation in spotted scat (Scatophagus argus)

As an ecological disturbance, salinity changes substantially impact aquatic organism health. Gut microbiota plays a pivotal role in host health and exhibits heightened sensitivity to environmental salinity stress; however, the potential correlative mechanisms between gut microbiota dysbiosis triggered by salinity changes and host health remain unclear. The present study conducted a 4-week stress experiment to investigate the precise impact of gut microbiota on the inflammatory response in Scatophagus argus under different salinities (0 ‰ [hyposaline group, HO], 25 ‰ [control group, CT], and 40 ‰ [hypersaline group, HE]). Our results revealed that both HO and HE stress significantly changed the relative abundances of Gram-negative bacteria and the impairment of intestinal barrier function. Subsequently, the levels of lipopolysaccharide (LPS) in the serum exhibited a significant increase, and the expression levels of genes (tlrs, myd88, irak1, irak4, and traf6) involving TLRs/MyD88/NF-κB signaling pathway and pro-inflammatory cytokines (il-6, il-8, il-1β, and tnf-α) in the representative immune organs were significantly upregulated. Conversely, the abundance of the anti-inflammatory gene (tgf-β1) and its protein contents in serum were decreased. Transplantation of the gut microbiota from S. argus exposed to varying salinities into germ-free Oryzias latipes resulted in an enhanced inflammatory response. Our results suggested that both HO and HE stress increased the presence of Gram-negative bacteria and disrupted the intestinal barrier, leading to elevated serum LPS and subsequent systemic inflammation in fish. These findings provide innovative insights into the influence of salinity manipulation strategies on the health of aquatic organisms, contributing to the mariculture management in coastal areas.

Carbon metabolism and partitioning in citrus leaves is determined by hybrid, cultivar and leaf type

The partitioning and metabolism of carbohydrates and lignin in leaves are essential for numerous physiological functions, growth and development of plants. This study was aimed to characterize these processes in four leaf types (i.e., autumn-, summer-, spring- and current-year spring shoots) of two citrus hybrids (loose-skin mandarin cultivars OP (i.e., cultivars 'Orah' (OR) Citrus reticulata Blanco and 'Ponkan' (PO) Citrus reticulata Blanco and the sweet orange cultivars NT 'Newhall navel orange' (NO) Citrus sinensis (L.) Osbeck and 'Tarocco' (TA) Citrus sinensis (L.) Osbeck) differing in fruit maturation under field conditions. For this purpose, we analyzed the levels of foliar structural, non-structural carbohydrates and lignin and the expression of related genes. Our results showed that the contents of structural, non-structural carbohydrates and lignin measured in the two hybrids and its partitioning were mostly determined by differences in gene expression recorded in hybrids, cultivars and leaf type. Particularly, differences between leaf types were largely attributed to up- and down-regulation of the expression of genes of cellulose synthesis, lignin precursor synthesis, the Calvin cycle, glycolysis, the tricarbonic acid and starch synthesis and degradation pathways. These differences between leaf types required more complex transcriptional regulation than differences between hybrids and cultivars. The present results indicated that the two citrus hybrids studied differed in the expression of structural, non-structural carbohydrates and lignin-related genes. Future studies have to show if the differences observed in foliar partitioning and metabolism of carbohydrates and lignin are translated into partitioning and metabolism of carbohydrates and lignin in the roots.

Poly-Lysine-Derived Carbon Quantum Dots Promote the Repair of Bone Defects in Osteomyelitis Through Antibacterial and Osteogenic Effects

Background

Osteomyelitis is a challenging clinical condition to manage effectively. In this study, we used ε-Poly (L-lysine) as the raw material to synthesize carbon quantum dots (PL-CQDs). These PL-CQDs possess antibacterial and osteogenesis ability, and are expected to improve the therapeutic effect of osteomyelitis.

Methods

PL-CQDs were synthesized via a dry heat-intermittent ultrasound method and characterized. The antibacterial efficacy of PL-CQDs was assessed using the spread plate method. The biological functions of PL-CQDs were evaluated through CCK-8 assays, scratch wound healing assay, osteogenic differentiation experiments, and transcriptome sequencing. In the in vivo experiments, the rats with osteomyelitis were evenly divided into five groups and treated with calcium sulfate containing different concentrations of PL-CQDs, and the therapeutic effects were evaluated by micro-CT and histology.

Results

PL-CQDs at concentrations of 200, 400, and 800 µg/mL exhibited no cytotoxicity and demonstrated the ability to kill methicillin-resistant Staphylococcus aureus and Escherichia coli. Additionally, PL-CQDs promoted the migration and osteogenic differentiation of mouse pre-osteoblasts (MC3T3-E1) cells. Transcriptome sequencing revealed that PL-CQDs significantly altered the ECM-receptor interaction signaling pathways and participated in biological processes such as the positive regulation of chondrocyte proliferation, collagen fiber organization, and regulation of fibroblast proliferation. Micro-CT and Masson staining results showed that the incorporation of PL-CQDs at different concentrations was beneficial to the repair of osteomyelitis defects, with the best repair in the PL-CQD50@CS group. Immunohistochemistry (CD31, DMP1) suggested that PL-CQDs facilitated the repair of osteomyelitis by enhancing matrix deposition and vascularization at the bone defect site.

Conclusion

PL-CQDs exhibit antibacterial and osteogenic properties and may serve as a potential alternative treatment for osteomyelitis.

Integrative analyses reveal Bna-miR397a-BnaLAC2 as a potential modulator of low-temperature adaptability in Brassica napus L

Brassica napus L. (B. napus) is a major edible oil crop grown around the southern part of China, which often faces cold stress, posing potential damage to vegetative tissues. To sustain growth and reproduction, a detailed understanding of fundamental regulatory processes in B. napus against long-term low temperature (LT) stress is necessary for breeders to adjust the level of LT adaption in a given region and is therefore of great economic importance. Till now, studies on microRNAs (miRNAs) in coping with LT adaption in B. napus are limited. Here, we performed an in-depth analysis on two B. napus varieties with distinct adaptability to LT stress. Through integration of RNA sequencing (RNA-seq) and small RNA-sequencing (sRNA-seq), we identified 106 modules comprising differentially expressed miRNAs and corresponding potential targets based on strong negative correlations between their dynamic expression patterns. Specifically, we demonstrated that Bna-miR397a post-transcriptionally regulates a LACCASE (LAC) gene, BnaLAC2, to enhance the adaption to LT stresses in B. napus by reducing the total lignin remodelling and ROS homeostasis. In addition, the miR397-LAC2 module was also proved to improve freezing tolerance of Arabidopsis, indicating a conserved role of miR397-LAC2 in Cruciferae plants. Overall, this work provides the first description of a miRNA-mediated-module signature for LT adaption and highlights the prominent role of laccase in future breeding programme of LT tolerant B. napus.

Transcriptomic signatures related to the immune priming of Ruditapes philippinarum in response to the re-infection of Vibrio anguillarum

Manila clam (Ruditapes philippinarum) is a commercially valuable bivalve species, but its susceptibility to pathogenic microorganisms in aquaculture limits the development of the shellfish industry. Immune priming has been previously found in other invertebrates, but not in the unique immune system of the R. philippinarum. In the present study, the survival rate of R. philippinarum after two consecutive injections of Vibrio anguillarum was recorded, and the mechanisms of immune priming was studied by transcriptome analysis of R. philippinarum after two consecutive stimulations of V. anguillarum. R. philippinarum was first injected with V. anguillarum with PBS control group (SA), and then injected with V. anguillarum again after seven days (AA) with PBS control group (SS). The log-rank test showed that the survival rate of the AA group after the second injection was significantly higher than that of the other control groups (P < 0.05). The analysis of hepatopancreatic bacterial load showed that the pathogen clearance efficiency of the AA group was significantly enhanced. The activities of alkaline phosphatase (AKP), acid phosphatase (ACP), antioxidant enzymes (SOD) and malondialdehyde (MDA) were significantly increased after V. anguillarum infection, and the secondary stimulation was significantly higher than the primary stimulation. In addition, transcriptome analysis results showed that a common 84 differentially expressed genes (DEGs) were up-regulated after the primary stimulation and secondary stimulation compared with the SS control group, including C-type mannose receptor 2 (MRC2), Ubiquitin-like protein ATG12 (Atg12) and Toll-like receptor 4 (TLR4). The results of transcriptome analysis were verified by qRT-PCR of fifteen immune-related DEGs. The results showed that the pattern recognition receptors (PRR)-related genes are involved in immune priming. This study provides novel insights into physiological and molecular evidences of the immune priming response in R. philippinarum.

Mechanisms of BpTT2 overexpression in enhancing cadmium tolerence of Broussonetia papyrifera

The development of cadmium-resistant plants has become a promising green biotechnology in the field of soil heavy metal remediation due to its advantages of low cost, wide adaptability and no secondary pollutants, it is the key to realize the application of this technology. In this study, we clarified the role of BpTT2 in Broussonetia papyrifera in response to Cd stress. Under the induction of 500 μmol/L CdCl2, the anti-Cd ability of BpTT2-overexpressed B. papyrifera was enhanced, and the accumulation of Cd was significantly reduced (P < 0.05). The plant height, biomass and total chlorophyll content of BpTT2-overexpressed B. papyrifera were significantly higher than those of non-transgenic lines (P < 0.001). Moreover, more substances related to ROS accumulation, such as MDA and H2O2, were detected in non-transgenic lines. Transcriptome sequencing showed that the AUX/IAA signal transduction gene (ARF5), ABA signal transduction genes (PP2C and SNRK2), protein kinase-related genes (PHOT1, WAKL4, PK1 and MPK3), ROS accumulation-related genes (RbohD and CAT1), and TFs family genes highly sensitive to Cd stress were significantly up-regulated in BpTT2-overexpressed B. papyrifera (P < 0.01). Notably, these genes regulate multiple signaling cascades simultaneously in the same protein family, which not only regulate plant signal transduction pathways, but also participate in the scavenging ROS and the feedback regulation of H2O2 signal. This study confirmed that the overexpression of BpTT2 can enhance the remediation effect of B. papyrifera on soil Cd pollution, which has important significance for better utilization of phytoremediation technology to treat heavy metal pollution.

Integrative whole-genome methylation and transcriptome analysis reveals epigenetic modulation of glucose metabolism by dietary berberine in blunt snout bream (Megalobrama amblycephala)

The present research was designed to explore the epigenetic mechanism by which dietary berberine (BBR) affects glucose metabolism in fish. Blunt snout bream (Megalobrama amblycephala) is susceptible to disturbances in glucose metabolism when subjected to prolonged high-carbohydrate diets. This study aimed to elucidate whether BBR can enhance glucose regulation in M. amblycephala via modulating DNA methylation levels. Fish (average weight of 20.36 ± 1.44 g) were administered a normal-carbohydrate diet (NC, 30 % carbohydrate), a high-carbohydrate diet (HC, 43 % carbohydrate), or a high-carbohydrate diet supplemented with 50 mg/kg berberine (HB) for 10 weeks. Subsequently, global DNA methylation level, whole-genome bisulfite sequencing (WGBS), RNA-seq, bisulfite sequencing PCR, and real-time quantitative PCR were employed to analyze the DNA methylation patterns and transcription results of the liver genome. The findings indicated that high carbohydrate diets induced glucose metabolism disorders in M. amblycephala, whereas BBR mitigated these metabolic disturbances by reducing methylation levels. WGBS results revealed that CG-type cytosine methylation predominated, and that DNA methylation mainly occurred in promoter, intron, and exon regions. Furthermore, analyses demonstrated a negative correlation between DNA methylation around the transcriptional start site and gene expression levels for 47 genes. Functional enrichment analysis revealed that these genes were associated with 60 KEGG pathways, including 12 genes implicated in the amelioration of insulin resistance, reduction of gluconeogenesis, and maintenance of glucose homeostasis. Consequently, we generated a comprehensive catalog of liver DNA methylation in M. amblycephala, which provides a foundational framework for future investigations into the epigenetic regulation of glucose metabolism by BBR.

Transcriptome analysis reveals molecular mechanism of Dosinia corrugata in response to acute heat stress

This study seeks to explore the molecular regulatory mechanism within Dosinia corrugata in response to extreme high-temperature conditions, aiming to enhance the sustainable development of the D. corrugata aquaculture industry. To identify heat-responsive genes and elucidate adaptive mechanisms, we conducted transcriptional profiling of D. corrugata gills after 12 h and 24 h of acute heat stress. At 12 h and 24 h under acute heat stress, we detected 6842 and 1112 differentially expressed genes (DEGs), respectively. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis revealed that co-enriched pathways at both time points included Apoptosis-multiple species, Ubiquitin-mediated proteolysis, Tumor Necrosis Factor (TNF) signaling pathway, and Retinoic acid-inducible Gene I (RIG-I)-like receptor signaling pathway in response to acute heat stress. It is noteworthy that at 12 h of acute heat stress, metabolic pathways were significantly enriched, while at 24 h, immune-related pathways showed significant enrichment. Based on the co-enrichment pathways identified at both time points during acute heat stress (12 h and 24 h), we constructed a potential regulatory network for differentially expressed genes under heat stress. This study offers valuable insights into comprehending the potential molecular regulatory mechanisms that underlie D. corrugata's response to elevated temperatures.

Genome-wide characterization of the TRP gene family and transcriptional expression profiles under different temperatures in gecko Hemiphyllodactylus yunnanensis

Temperature is closely linked to the life history of organisms, and thus thermoception is an important sensory mechanism. Transient receptor potential (TRP) ion channels are the key mediators of thermal sensation. In this study, we analyzed the sequence characteristics of TRPs in gecko Hemiphyllodactylus yunnanensis and compared the phylogenetic relationships of TRP family members among different Squamata species. In addition, we sequenced the transcriptome of skin and brain tissues of H. yunnanensis exposed to 12 °C (cold), 20 °C (cool), 28 °C (warm), and 36 °C (hot). The results showed that a total of 591 TRPs were identified in the genomes of 21 Squamate species, and these genes were classified into six subfamilies. Among them, 26 TRP genes were identified in H. yunnanensis and distributed on 13 chromosomes. Overall, TRP genes were conserved in squamates. Based on the transcriptome results, we found a total of 9 TRP genes expressed in the brain and skin of H. yunnanensis, of which six TRP genes were under positive selection. TRPP1L2, TRPP1L3, and TRPV1 were involved in heat-sensitive responses (> 36 °C), and TRPV3, TRPA1, and TRPM8 were involved in cold-sensitive responses (< 20 °C). TRPM8 and TRPP1L2 were important cold and heat sensors in H. yunnanensis, respectively.

Genomic insights into the evolution of Chinese sweetgum and its autumn leaf coloration

Chinese sweetgum (Liquidambar formosana) is valued as a source of resin and timber and is an important ornamental tree due to its showy fall foliage. Here, we report the chromosome-level assembly of the Chinese sweetgum genome. Phylogenomic analyses showed the basal phylogenetic position of Chinese sweetgum in core eudicots. Comparative genomic analyses revealed that the well-known gamma event in the common ancestors of core eudicots is evident in the Chinese sweetgum genome, and ancestral triplicated blocks resulting from that event are more intact in Chinese sweetgum than in grapevine (Vitis vinifera). Because of its conserved genome structure, very slow rate of evolution, and basal phylogenetic position, the Chinese sweetgum genome is a good reference for comparative genome studies. Further, we reconstructed the entire metabolic pathway for anthocyanins and potential regulatory networks of autumn leaf coloration of this species via metabolomics and transcriptomics. The transcription factors LfMYB69, basic helix-loop-helix (LfbHLH4), and WD40-repeat (LfWDR1) may collectively regulate the transcription of anthocyanin biosynthetic genes. The regulation of chalcone synthase genes (LfCHS1-3) and dihydroflavonol 4-reductase genes (LfDFR1-2) by the LfMYB69-LfbHLH4-LfWDR1 complex was confirmed by luciferase assays. Epigenomic analyses revealed that 5 structural genes, including LfCHS1, and 2 regulatory LfMYBs are epigenetically regulated. This study expands our understanding of autumn leaf coloration and provides valuable genomic resources for comparative biology, breeding, and biotechnology.

Integrative Proteome and Transcriptome Analyses Reveal the Metabolic Disturbance of the Articular Cartilage in Kashin-Beck Disease, an Endemic Arthritis

The objective of this study was to elucidate the proteomic and transcriptomic alterations within the cartilage in Kashin-Beck disease (KBD) compared to a normal control. We conducted a comparison of the expression profiles of proteins, mRNAs, and lncRNAs via data-independent acquisition (DIA) proteomics and transcriptome sequencing in six KBD individuals and six normal individuals. To facilitate the functional annotation enrichment analysis of the differentially expressed (DE) proteins, DE mRNAs, and DE lncRNAs, we employed bioinformatic analysis utilizing Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Additionally, we conducted integration analysis of multi-omics datasets using mixOmics. We revealed a distinct proteomic signature, highlighting 53 DE proteins, with notable alterations in the pathways related to tryptophan metabolism and microbial metabolism. Additionally, we identified 160 DE mRNAs, with the functional enrichment analysis uncovering pathways related to RNA metabolism and protein splicing. Furthermore, our analysis of the lncRNAs demonstrated biological processes involved in protein metabolism and cellular nitrogen compound metabolic processes. The integrative analysis uncovered significant correlations, including the positive correlation between superoxide dismutase 1 (SOD1) and mitochondrial import receptor subunit TOM6 homolog (TOMM6), and the negative correlation between C-X9-C motif-containing 1 (CMC1) and succinate-CoA ligase [GDP-forming] subunit beta, mitochondrial (SUCLG2). Our results provide novel insights into the molecular mechanisms underlying KBD.

Integrating exosome wide associations study and Mendelian randomization identified causal miRNAs for type 2 diabetes mellitus and its complications

BACKGROUND

Type 2 diabetes mellitus (T2DM) and its complications, including diabetic lower extremity arterial disease (DLEAD) and diabetic foot (DF), impose significant health burdens worldwide. However, the differential expression of microRNAs (miRNAs) between T2DM and its complications and its causal effects remain poorly understood.

METHODS

We conducted an exosome-wide association study (EWAS) comparing miRNA profiles between T2DM and its complications, including DLEAD and DF, without healthy controls. The significant miRNAs identified between DM and its complications were further validated by integrating cis-miRNA expression quantitative trait loci (cis-miR-eQTLs) and genome-wide association study (GWAS) summary data of T2DM and peripheral arterial disease (PAD) through two-sample Mendelian randomization (MR) analysis.

RESULTS

We identified several differential expressions of miRNAs between T2DM, DLEAD, and DF, such as hsa-miR-409-3p between T2DM and DLEAD, hsa-miR-543 between T2DM and DF and hsa-miR-206 between DLEAD and DF. The two sample MR analysis revealed potential causal relationships between dysregulated miRNAs and T2DM and its complications, such as hsa-miR-30b-3p and hsa-miR-30b-5p showed causal associations with T2DM and PAD respectively.

CONCLUSIONS

Our study elucidates the miRNA signatures associated with T2DM and its complications. These findings provide insights into the pathogenesis of T2DM and its complications and suggest potential therapeutic targets for intervention.

Dissection of genetic basis underlying heat stress response of Apis cerana

The honeybee Apis cerana as an important pollinator contributes significantly to ecological diversity. In recent years, it has been used as a common pollinator in greenhouses, but it is highly susceptible to heat stress, which affects its behavior, physiology, survival, and gene expression. Here, we conducted transcriptomic analysis to identify differentially expressed genes (DEGs) and reveal the associated biological processes in the queen head and ovary of honeybee A. cerana under different temperatures. Differential expression analysis revealed 116 DEGs (72 upregulated, 44 downregulated) in the head and 106 DEGs (78 upregulated, 28 downregulated) in the ovary after 24 h of heat stress. At 96 h, 29 DEGs (17 upregulated, 12 downregulated) were identified in the head, and 44 DEGs (34 upregulated, 10 downregulated) in the ovary. After 168 h, the number of DEGs increased significantly: 846 DEGs (567 upregulated, 279 downregulated) in the head, 479 DEGs (296 upregulated, 183 downregulated) in the ovary, and 582 DEGs (338 upregulated, 244 downregulated) in the thorax. DEGs associated with metabolic processes, signaling, and transport pathways were significantly altered under heat stress, potentially contributing to the reduced reproductive and growth capacity of bees. Additionally, genes related to antioxidant activity, nutrient metabolism, heat shock proteins, zinc finger proteins, and serine/threonine-protein kinases were differentially expressed across treatments. Overall, the head and ovaries of honeybee queens show a significant response to heat shock, and these responses are related to antioxidant genes, heat shock proteins, and metabolic regulation, our findings provide genetic information for the breeding of heat-resistant bee strains.

Transcriptomic Profiling of Paulownia fortunei (Seem.) Hemsl. Roots in Response to Chromium and Copper Stress

BACKGROUND

Soil heavy metal pollution by chromium (Cr) and copper (Cu) is a global environmental concern.

METHODS

This study evaluated Cr/Cu accumulation in Paulownia fortunei tissues and analyzed its root transcriptome under Cr and Cu stress to elucidate molecular response mechanisms.

RESULTS

Findings revealed significantly higher Cr and Cu accumulation capacity in roots compared to stems and leaves. Transcriptome sequencing identified 6017 and 2265 differentially expressed genes (DEGs) under Cr and Cu stress, respectively. These DEGs were primarily involved in redox reactions, stress responses, transcriptional regulation, transmembrane transport, and metabolism. Quantitative PCR of 20 selected genes validated dynamic expression changes under stress. Weighted Gene Co-expression Network Analysis (WGCNA) identified distinct co-expression modules associated with Cr and Cu. Hub gene analysis implicated Pfo_020668 and Pfo_019190 in Cr response, while Pfo_010312 and Pfo_000197 may enhance Cu tolerance via cell wall polysaccharide synthesis regulation. Pathways related to pyruvate metabolism and proteasome were significantly enriched under Cr stress, whereas amino acid metabolism pathways were prominent under Cu stress.

CONCLUSIONS

Differentially expressed transporter genes suggest potential roles in heavy metal uptake and transport. This transcriptomic analysis provides novel insights into P. fortunei's molecular responses to Cr and Cu stress, offering a foundation for utilizing this species in soil phytoremediation efforts.

Transcriptome profiling and alternative splicing analysis of skeletal muscle in Pseudocaranx dentex: insights into slow-twitch and fast-twitch muscle specialization

Alternative splicing (AS) plays a crucial role in regulating muscle type specialization characteristics in mammals but has been rarely explored in teleost. In this study, we combined Iso-Seq and RNA-Seq technologies to profile the transcriptome and AS landscape of slow-twitch muscle (SM) and fast-twitch muscle (FM) in a migratory teleost, Pseudocaranx dentex. We identified 24,096 full-length transcripts and 14,346 isoforms in SM, and 18,483 full-length transcripts and 10,541 isoforms in FM, revealing extensive transcript and isoform diversity. The 3086 differentially expressed transcripts (DETs) were found to contribute to metabolic and contractile differences between SM and FM. Additionally, we detected 5761 AS events in SM and 4543 in FM, with skipped exons (SE) and intron retention (IR) being the predominant AS types. Furthermore, 325 differentially AS genes (DASGs) were found to regulate differences in metabolic processes, organelles organization, cellular component organization, and microtubule-based processes. Importantly, transcripts of tnni2, capzb, neb, and pdlim5 produced by AS with significant expression differences between SM and FM were determined to associate with sarcomere assembly. This study provides the first comprehensive view of transcriptome complexity and splice variants in teleost skeletal muscle and sheds light on the molecular mechanisms underlying muscle type specialization through post-transcriptional regulation.

CIEC: Cross-tissue Immune Cell Type Enrichment and Expression Map Visualization for Cancer

Single-cell transcriptome sequencing technology has been applied to decode the cell types and functional states of immune cells, revealing their tissue-specific gene expression patterns and functions in cancer immunity. Comprehensive assessments of immune cells within and across tissues will provide us with a deeper understanding of the tumor immune system in general. Here, we present Cross-tissue Immune cell type or state Enrichment analysis of gene lists for Cancer (CIEC), the first web-based application that integrates database and enrichment analysis to estimate the cross-tissue immune cell types or states. CIEC version 1.0 consists of 480 samples covering primary tumor, adjacent normal tissue, lymph node, metastasis tissue, and peripheral blood from 323 cancer patients. By applying integrative analysis, we constructed an immune cell type/state map for each context, and adopted our previously developed Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology Based Annotation System (KOBAS) algorithm to estimate the enrichment for context-specific immune cell types/states. In addition, CIEC also provides an easy-to-use online interface for users to comprehensively analyze the immune cell characteristics mapped across multiple tissues, including expression map, correlation, similar gene detection, signature score, and expression comparison. We believe that CIEC will be a valuable resource for exploring the intrinsic characteristics of immune cells in cancer patients and for potentially guiding novel cancer-immune biomarker development and immunotherapy strategies. CIEC is freely accessible at http://ciec.gene.ac/.

Molecular mechanisms of s-methoprene-induced growth inhibition in Ephestia elutella (Hübner) (Lepidoptera: Pyralidae): insights from transcriptomic analysis

Ephestia elutella is a globally distributed storage pest, and its growth and development are regulated by juvenile hormones. To investigate the molecular mechanisms underlying the response of E. elutella larvae to the juvenile hormone analog s-methoprene, this study examined the effects of s-methoprene on the growth and development of E. elutella, explored the response of E. elutella to s-methoprene exposure by transcriptomic analysis, and confirmed its hub genes by RT-qPCR experiments. Larval mortality of E. elutella increased and adult emergence decreased with increasing exposure durations and doses of s-methoprene. After exposure at 5 × 10⁻⁵ mg/cm² of s-methoprene for 4 wk, a few of larvae pupated, but failed to emerge into adults, while at 50 × 10⁻⁵ mg/cm² for 4 wk, larvae were completely unable to pupate. Transcriptomic analysis identified 2,569 and 6,719 differentially expressed genes in the EE0 vs. EE5 and EE0 vs. EE50, respectively. Weighted Gene Co-expression Network Analysis identified 5 modules, with the yellow module most relevant to EE5. The genes in the yellow module were significantly enriched in biological processes. The Cluster-6182.18691, Cluster-6182.8343, Cluster-6182.28346, and Cluster-6182.21392 were hub genes in the yellow module. s-Methoprene directly or indirectly inhibited the growth and development of E. elutella larvae by affecting critical biological processes, such as hormonal regulation, etc. RT-qPCR validation confirmed the reliability of the transcriptomic data. This study provides important foundational data and theoretical insights into the molecular mechanisms of E. elutella in response to s-methoprene.

Comprehensive analysis of the transcriptome implicated in the immune response of Procambarus clarkii to Aeromonas hydrophila

In order to better understand the immune response of Procambarus clarkii to Aeromonas hydrophila injection, the transcriptome data of the gill tissue of P. clarkii were compared and analyzed. 1008 significant DEGs were identified in A. hydrophila infected and PBS control groups, including 411 up-regulated genes and 597 down-regulated genes. Endocytosis, phagocyte and lysosome were the most clustered pathways of DEGs in KEGG database. RNA-Seq results were validated through the verification of immune-related differentially expressed genes (DEGs), whose expression levels were assessed using quantitative real-time PCR (qRT-PCR). With the increase of treatment time of A. hydrophila, the total protein in gill of the treatment group showed a trend of increasing first, then decreasing and then increasing and decreasing. ACP and AKP both show a trend of rising first, then falling and then rising. The results of comprehensive research showed that crayfish infected with A. hydrophila caused damage to gill tissue, and the related immune genes were up-regulated and the immune mechanism was operated to protect the body from A. hydrophila. The differential gene MRC1 was screened through the transcriptome, and to further understand its impact, it was disrupted by RNAi technology, which showed a significant down-regulation of immune genes (TAB2, TLR3, ALF6, Lyso3, clotting factor G beta subunit-like and coagulation factor X-like) as well as genes downstream of the pathway (AP4E1, ARSB and TUBA1A). This study provides a theoretical basis for further exploring the immune adaptability of aquatic animals under bacterial infection.

The chimeric gene orf610a reduces cotton pollen fertility by impairing the assembly of ATP synthase

Cytoplasmic male sterility (CMS) serves as a pivotal tool for exploiting hybrid vigour and studying nuclear-cytoplasmic interactions. Despite its long-standing use in cotton breeding, the underlying mechanisms of the CMS-D2 system remain elusive. Our study unravelled the role of the mitochondrial chimeric gene orf610a in reducing fertility in cotton through its interaction with ATP synthase subunit D (atpQ). Using yeast two-hybrid, bimolecular luciferase complementation, and transgenic overexpression studies, we identified a unique interaction between orf610a and atpQ, which disturbs the assembly of ATP synthase. This interaction leads to a decrease in ATP levels, an increase in H2O2 production, and mitochondrial dysfunctions, which are associated with pollen abortion. Transcriptomic and biochemical analyses of three independent overexpression lines identified 1711 differentially expressed genes (DEGs), among which 10 were related to reactive oxygen species (ROS) and ATP production. Phenotypic analysis confirmed that orf610a expression causes abnormal anther development and reduced pollen viability, contributing to sterility. Notably, SEM and TEM analyses highlighted structural anomalies in the pollen of orf610a-overexpressing lines, supporting the detrimental impacts of altered ATP synthase function. Our findings suggest that orf610a's interaction with ATP synthase components disrupts normal mitochondrial function and energy production, leading to male sterility in cotton. Understanding the molecular interactions involved in CMS can aid in developing strategies to manipulate sterility for crop improvement, offering insights into mitochondrial-nuclear interactions that could impact future breeding programmes.

Energy metabolism, antioxidant defense system, metal transport, and ion homeostasis are key contributors to Cd tolerance in SSSL derived from wild rice

Cadmium (Cd) toxicity poses major challenges to rice cultivation, affecting plant growth and development. Wild rice and nanoparticles offer promising strategies to enhance Cd tolerance, yet little is known about their combined effects. This study evaluates the single segment substitution line (SG004) from Oryza glumaepatula (wild rice) and its response to Cd stress compared to cultivated rice (HJX74). Both genotypes were also treated with calcium oxide nanoparticles (np-CaO). Results showed that Cd exposure disrupts reactive oxygen species (ROS) metabolism in both lines, such as malondialdehyde (MDA) increases by 57 % in HJX74 compared to SG004. Moreover, SG004 exhibited a 26 % reduction in shoot length compared to 41 % in HJX74 and a 42 % decline in chlorophyll ab content versus 53 % in HJX74. Antioxidant activity such as glutathione (GSH) decreased 25 % more in HJX74 than SG004 under Cd toxicity. Additionally, SG004 had lower Cd accumulation in roots (70 %) and shoots (85 %) than HJX74, indicating its enhanced tolerance to Cd toxicity. The root cell cytology reveals several deformations in different organelles of HJX74 but less in SG004. RNAseq analysis identifies key pathways, including energy metabolism, antioxidant defense, metal transport, and ion homeostasis, which may be critical for SG004 enhanced tolerance. Notably, two distinct metallothionein-like genes (BGIOSGA019338, BGIOSGA035982), a peroxidase (BGIOSGA019133), ammonium (BGIOSGA008640, BGIOSGA008641, and potassium transporters (BGIOSGA030867), NRAMP1 (BGIOSGA025476), and an aluminum-activated malate transporter (BGIOSGA014531), showed differential expressions in SG004 under Cd stress. Genes within the substituted fragment, including those for peroxidase 25 (BGIOSGA002866), metallothionein (BGIOSGA002389), and reductase (BGIOSGA002387), are also upregulated in SG004, reinforcing the role of antioxidant and ion homeostasis pathways. The utilization of np-CaO alleviates Cd-induced stress in both genotypes, hence reinforcing the application of wild rice and nanoparticles to improve Cd tolerance.

BrCNGC12 and BrCNGC16 mediate Ca2+ absorption and transport to enhance resistance to tipburn in Chinese cabbage

Tipburn is a common physiological disorder in leafy vegetables, significantly impairing crop growth and commercial value. It is widely recognized that Ca2+ deficiency is a key factor triggering tipburn; however, the functions and regulatory mechanisms of genes conferring resistance remain largely unexplored. Through transcriptomic analysis of Chinese cabbage under normal (medium calcium, MCa) and Ca2+-deficient (low calcium, LCa) conditions, we observed that genes in the hormone and calcium signalling pathways exhibited significant responses to LCa stress. Among these, the cyclic nucleotide-gated ion channel (CNGC) genes BrCNGC12 and BrCNGC16, part of the calcium signalling pathway, were notably up-regulated and down-regulated, respectively, under LCa stress. Silencing BrCNGC12 in Chinese cabbage improves Ca2+ absorption and distribution, which strengthens tipburn resistance. Conversely, under LCa stress, heterologous expression of BrCNGC16 in Arabidopsis thaliana increases resistance to tipburn, whereas partial silencing of BrCNGC16 in Chinese cabbage diminishes resistance, with both outcomes linked to altered Ca2+ uptake and translocation. Additionally, overexpression of BrCNGC16 in Chinese cabbage promotes Ca2+ uptake and translocation, thereby enhancing resistance to tipburn and mitigating oxidative damage induced by Ca2+ deficiency. In conclusion, BrCNGC12 and BrCNGC16 play pivotal roles in tipburn resistance in Chinese cabbage, offering novel insights into the interplay between the calcium signalling pathway and tipburn resistance.

Potential mechanism of inhibitory effect of "medicine food homology" curcumin and its analogue EF24 on oral squamous cell carcinoma

BACKGROUND

Oral squamous cell carcinoma (OSCC) is one of the most common malignant tumors of head and neck with high incidence and poor prognosis. Curcumin, as a drug-food congener, has a broad spectrum of anticancer effects, and based on this property, we further focused on EF24, a small molecule compound using curcumin as a backbone, to study the effects of both in OSCC.

METHODS

Cell experiments were performed to test the inhibitory effect of curcumin and EF24 on OSCC cells. The potential mechanism was further analyzed by transcriptome sequencing, and the DEGs after drug treatment were determined. PPI networks were created using Cytoscape software.

RESULTS

Both curcumin and EF24 inhibit the viability, migration, and invasion, and induce apoptosis of OSCC cells and the IC50 of EF24 was much lower than that of curcumin. Analysis of DEGs identified 893 DEGs following curcumin treatment, of which 794 were up-regulated and 99 were down-regulated; 797 DEGs following EF24 treatment were identified, of which 665 were up-regulated and 132 were down-regulated. Curcumin and EF24 were found to down-regulate lipid metabolism by key enzymes that regulate fatty acid and cholesterol synthesis. Furthermore, the number of T cell CD4 + memory is up-regulated and the immune response is enhanced.

CONCLUSIONS

It is suggested that curcumin and EF24 inhibit the metabolic reprogramming of tumor cells and at the same time regulate TME, and improve the immunotherapy of tumors, which opens the way for the future treatment of OSCC with this approach alone or in conjunction with immune-checkpoint blocking.

GLR3.6T807I Mutation of Casuarina equisetifolia Is Associated With a Decreased JA Response to Insect Feeding by Lymantria xylina

Lymantria xylina is the most important defoliator, damaging the effective coastal windbreak tree species Casuarina equisetifolia. However, the underlying genetic mechanisms through which C. equisetifolia responds to L. xylina attacks remain unknown. Here, we compared the transcriptional, phytohormone and metabolic differences between susceptible (S) and resistant (R) C. equisetifolia cultivars in response to L. xylina feeding. The main L. xylina-induced resistance in C. equisetifolia was a jasmonate (JA) response and JA synthesis was highly induced by L. xylina feeding at both the transcriptional and metabolic levels, thus promoting flavonoid accumulation. The JA response was highly activated by L. xylina feeding on the R but not in the S cultivar, although the JA signalling pathway was intact in both cultivars. We found a single amino acid mutation in the homologues of glutamate receptor-like protein 3.6 (CeGLR3.6T807I) in the S cultivar. Compared with the GLR3.6 homologues in the R cultivar, phosphorylation of CeGLR3.6T807I was not induced by insect feeding, leading to a decreased JA response in the S cultivar. Collectively, this study provides new insights into the function of CeGLR3.6 in regulating the JA response of C. equisetifolia to L. xylina feeding.

Transcriptome analysis of the ovary and testis of the pearl oyster Pinctada fucata: Identification of genes and pathways involved in gonadal development

Pinctada fucata is a commercially vital species in global pearl aquaculture, producing high-quality pearls. To investigate the molecular regulatory mechanisms of gonadal development in P. fucata, transcriptome analysis was employed to compare expression profiles between testis and ovary across four key developmental stages. A total of 56.86 Gb of clean data was generated, including 392,510 circular consensus sequencing reads, among which 292,295 full-length non-chimeric (FLNC) sequences were identified. A transcript clustering analysis of FLNC reads revealed 89,645 high-quality consensus sequences. 17,646 gene loci were identified, including 8588 novel loci and 28,121 newly discovered transcripts, of which 17,350 were successfully annotated. The boundaries of 12,040 genes on the chromosomes were corrected, and 10,761 complete open reading frame sequences. 281 genes related to gonadal development were identified, including 186 genes with full-length cDNAs in the PacBio library. The study found that HUS1-like, MAD2A-X1, and BLM were stage-specifically upregulated during ovarian maturation, ensuring the accuracy of meiosis. Meanwhile, NR0B1, ETV7L-X5, and CAPRIN1-X2 promoted testicular maturation by regulating somatic cell differentiation and the germ cell microenvironment. KEGG enrichment analysis identified key pathways involved in gonadal development, including the ribosome, oxidative phosphorylation, DNA replication, and lysosome. Fatty acid metabolism was linked to ovarian maturation, while the FoxO and ErbB signaling pathways were associated with testicular maturation. These findings offer valuable insights into the molecular mechanisms regulating gonadal development in P. fucata and enhance genomic resources for this economically important species.

Analysis of regulatory networks provides new insights into the mechanism of rubber synthesis in Lactuca serriola

The rubber tree currently serves as the sole source of natural rubber (NR). However, its limited cultivation range and the increasing global NR demand necessitate the development of an alternative crop for NR production. This study reports that Lactuca serriola can produce high-quality NR suitable for industrial rubber demand. The rubber molecular weight of L. serriola exceeds 750 kg/mol, with NR production occurring throughout the entire plant. Furthermore, treatments with ethylene, methyl jasmonate (MeJA), and salicylic acid (SA) significantly increased rubber content in L. serriola. Transcriptome analysis revealed that ethylene and MeJA treatments affected gene expression associated with isopentenyl pyrophosphate (IPP) synthesis, while ethylene and SA treatments influenced gene expression involved in sucrose transportation and metabolism. Through Pearson correlation coefficient (PCC) analysis and virus-induced gene silencing, several transcription factors and LsCPTs/LsCPTL were identified as key regulators of rubber synthesis in L. serriola. Yeast two-hybrid and co-expression assays suggested that LsCPTL anchors LsCPT1 and LsCPT2 to the endoplasmic reticulum, forming a protein complex that regulates rubber synthesis. This study provides a preliminary analysis of the mechanism by which plant hormones regulate rubber synthesis in L. serriola, revealing its significant potential as an alternative to the rubber tree for NR production.

The genomic insights of intertidal adaptation in Bryopsis corticulans

Many marine green algae thrive in intertidal zones, adapting to complex light environments that fluctuate between low underwater light and intense sunlight. Exploring their genomic bases could help to comprehend the diversity of adaptation strategies in response to environmental pressures. Here, we developed a novel and practical strategy to assemble high-confidence algal genomes and sequenced a high-quality genome of Bryopsis corticulans, an intertidal zone macroalga in the Bryopsidales order of Chlorophyta that originated 678 million years ago. Comparative genomic analyses revealed a previously overlooked whole genome duplication event in a closely related species, Caulerpa lentillifera. A total of 100 genes were acquired through horizontal gene transfer, including a homolog of the cryptochrome photoreceptor CRY gene. We also found that all four species studied in Bryopsidales lack key photoprotective genes (LHCSR, PsbS, CYP97A3, and VDE) involved in the xanthophyll cycle and energy-dependent quenching processes. We elucidated that the expansion of light-harvesting antenna genes and the biosynthesis pathways for siphonein and siphonaxanthin in B. corticulans likely contribute to its adaptation to intertidal light conditions. Our study unraveled the underlying special genetic basis of Bryopsis' adaptation to intertidal environments, advancing our understanding of plant adaptive evolution.

Effects of ρ-hydroxybenzoic acid on metabolism and excretion of grapevine root

Autotoxicity is a significant contributor to replant disease, with phenolic acid autotoxins such as 4-HBA (ρ-hydroxybenzoic acid) influencing the structure of the rhizosphere microbial community by modifying the secretion characteristics of grapevine roots. In the study, 'Beta' grape seedlings were selected to investigate the regulatory mechanism of 4HBA on root metabolism and secreting characteristics. The results showed that the expression level of genes related to primary and secondary metabolism in the roots was affected by 100 μg mL-1 4-HBA treatment, and the genes related to starch and sucrose metabolism were generally down-regulated, and most genes encoding glycolytic pathway, amino acid pathway and phenylpropanoid biological pathway were up-regulated. A total of 142 metabolites were significantly changed after 100 μg mL-1 4-HBA treatment, of which 92 metabolites were significantly up-regulated and 50 metabolites were significantly down-regulated. 7 amino acids, 3 phenolic acids, 2 nucleotides, 2 flavonoids, 4 organic acids, and 9 fatty acids might be regulated by ABC transporter. Further research found that some metabolites regulated by ABC transporter affected the growth of Fusarium solani, a harmful fungus related to grape replant disease. Our research confirmed that 4-HBA not only alters root metabolism but also modifies the content of root exudates, among which ABC transporters playing a crucial role in the efflux process.

Identification of stay-green candidate gene TaTRNH1-3B and development of molecular markers related to chlorophyll content and yield in wheat (Triticum aestivum L.)

Functional stay-green characteristic is closely associated with delayed loss in photosynthetic function and increased crop yield. However, the development and application of functional molecular markers based on stay-green-related genes are limited. This study compared and analyzed the differences of SPAD values, photosynthetic parameters, fluorescence parameters, and antioxidant enzyme activities at 0, 10, 18, 22, 26, 30 and 34 days after anthesis, as well as agronomic traits at mature stage between a stay-green line, Tailv113 (TL113), and a non-stay-green cultivar, Jinmai39 (JM39). The results showed that TL113 had higher photosynthetic capacity, photosynthetic efficiency, antioxidant capacity and yield than JM39. Subsequently, a comparative transcriptome analysis was conducted on TL113 and JM39 at 0, 26, and 30 days after anthesis. Analysis showed that senescence-associated co-expressed genes (SCEGs) and stay-green-associated differentially expressed genes (SDEGs) jointly affected wheat leaf senescence, while SDEGs played an important role in the stay green differences between TL113 and JM39. By analyzing the SNP sites of the SDEGs from transcriptome sequencing, a nsSNP was found in the TaTRNH1-3B sequence between TL113 and JM39. Further analyzing the resequencing data published in the Wheat Union database, four linked SNP sites were identified in TaTRNH1-3B, which formed two haplotypes, TaTRNH1-3B-Hap1 and TaTRNH1-3B-Hap2. Based on the SNP at 373 bp (A/G), a CAPS molecular marker, TaTRNH1-3B-Nla III-CAPS, was developed to distinguish allelic variations (A/G). Association analysis between TaTRNH1-3B allelic variation and agronomic traits found that the accessions possessing TaTRNH1-3B-Hap1 (A) exhibited significantly higher SPAD values than those possessing TaTRNH1-3B-Hap2 (G) in 6 of 10 environments at the jointing stage and in 7 of 10 environments at the grain filling stage in Beijing. Similarly, the accessions possessing TaTRNH1-3B-Hap1 (A) exhibited significantly higher chlorophyll contents and yield than those possessing TaTRNH1-3B-Hap2 (G) in 3 environments in Taigu. Additionally, lines with TaTRNH1-3B-Hap1 (A) displayed higher SPAD values at 0, 15, and 20 days after anthesis in the two BC3F3 populations than those with TaTRNH1-3B-Hap2 (G). These results suggest that TaTRNH1-3B is associated with the stay-green and yield traits in wheat, and TaTRNH1-3B-Hap1 is a favorable stay-green haplotype. The newly developed molecular marker, TaTRNH1-3B-Nla III-CAPS, provide valuable information for wheat genetic improvement of stay-green and high-yield traits, and can be used to marker-assisted selection breeding.

Integrated analysis of transcriptome and metabolome reveals the molecular basis of quality differences in Alpinia oxyphylla Miq. From geo-authentic and non-authentic areas

Alpinia oxyphylla Miq., a well-accepted medicinal and edible plant in south China. The primary ingredients of this medicine vary significantly depending on their origin, which profoundly impacts its quality. In this study, a principal component analysis was performed on 17 different planting areas of A. oxyphylla, with nootkatone and kaempferol identified as representative sesquiterpenoids and flavonoids, respectively. To investigate the genes involved in nootkatone and kaempferol biosynthesis, a combined transcriptome and metabolome profiling was carried out on materials sourced from geo-authentic and non-authentic areas. The transcriptome analysis of these two types of accessions identified 96,691 unigenes, with 13,589 genes showing differential expression in both regions. Metabolome analysis revealed 2859 differentially accumulated metabolites across the four pairwise comparisons. Correlation analysis uncovered a number of genes, that associated with the differential biosynthesis of nootkatone and kaempferol in A. oxyphylla fruits from geo-authentic and non-authentic areas. Further investigation highlighted the candidate gene AoFMO1's ability to heterologously biosynthesize nootkatone in Arabidopsis thaliana leaves. This research lays the groundwork for a deeper understanding of the molecular mechanisms behind the authentication of A. oxyphylla's quality synthesis, and presents a comprehensive list of candidate genes for future functional studies to enhance the development of high-quality A. oxyphylla varieties rich in medicinal ingredients.

Serine Hydroxymethyltransferase Modulates Midgut Physiology in Aedes aegypti Through miRNA Regulation: Insights from Small RNA Sequencing and Gene Expression Analysis

Aedes aegypti mosquitoes are critical vectors of arboviruses, responsible for transmitting pathogens that pose significant public health challenges. Serine hydroxymethyltransferase (SHMT), a key enzyme in one-carbon metabolism, plays a vital role in various biological processes, including DNA synthesis, energy metabolism, and cell proliferation. Although SHMT is expressed at low levels in the midgut of Aedes aegypti, its silencing has been shown to inhibit blood meal digestion. The precise mechanisms by which SHMT regulates midgut physiology in mosquitoes remain poorly understood. In this study, we employed small RNA sequencing and quantitative PCR to identify differentially expressed miRNAs (DEMs) following SHMT downregulation. We focused on a subset of DEMs-miR-2940-5p, miR-2940-3p, miR-2941, and miR-306-5p-to explore their potential biological functions. To further elucidate the molecular mechanisms underlying the miRNA response to SHMT downregulation, we analyzed the expression levels of key genes involved in the miRNA biogenesis pathway. Our results demonstrated that several critical enzymes, including Drosha, Dicer1, and AGO1, exhibited significant changes in expression upon SHMT silencing. This study provides new insights into the molecular mechanisms through which SHMT influences the biological functions and nutritional metabolism of the mosquito midgut. By linking SHMT activity to miRNA regulation, our findings highlight a potential pathway by which SHMT modulates midgut physiology, offering a foundation for future research into mosquito biology and vector control strategies.

Transcriptome analysis reveals the mechanism of mixed oligosaccharides in the response of rice seedlings to abiotic stresses

Salinity and alkalinity stresses severely suppress rice seedling growth and substantially reduce rice yield; whereas the application of oligosaccharides as plant growth regulators has been demonstrated to remarkably enhance crop tolerance to abiotic stresses. To investigate the potential growth-promoting effects of KP-priming (mixed-oligosaccharides, 1.12 mg mL-1) on rice seedlings under salinity (100 mmol L-1 NaCl) and alkalinity (10 mmol L-1 Na2CO3) stresses, plant morphology and physiology assessments, and transcriptome analyses were performed. The KP-priming significantly improved rice seedling tolerance to salinity and alkalinity stresses, evidenced by increases in plant height, dry matter weight, and fresh weight, and improved root morphology (root length, surface area) and vitality by 10.27-89.06%. Leaf cell membrane stability was improved in KP-priming by increasing the soluble sugar content and superoxide dismutase, peroxidase, and catalase activities by 2.74-97.32%, and reducing accumulation of malondialdehyde and hydrogen peroxide by 17.67-49.70%. KP-priming treatment significantly enhanced leaf photosynthetic capacity through promoting photosynthetic pigments and maximum photochemical efficiency by 2.34-135.76%, and enhancing leaf stomatal aperture by 21.58-75.84%. Transcriptomic analysis revealed that differentially expressed genes in response to KP-priming under salt and alkaline stresses were predominantly associated with photosynthetic pathways. Total 4125 (salinity) and 1971 (alkalinity) DEGs were identified under stresses compared to KP-priming. Transcriptional profiling of KP-priming-treated leaves demonstrated significant up-regulation of key photosynthetic genes, including OsRBCS5, PGR5, Se5, OsPORA, GRA78, OsLhcb7, and OsPS1-F. This coordinated gene expression was functionally associated with enhanced leaf photosynthesis capacity and mitigated oxidative damage through improved electron transport and reactive oxygen species scavenging mechanisms. Our findings demonstrated that KP-priming initiated a self-regulatory mechanism in plants, orchestrating a dual protective response that simultaneously mitigated oxidative damage while enhancing photosynthetic efficiency and stress resilience. This study provided initial insights into using KP-priming to alleviate salinity and alkalinity stresses and its underlying molecular mechanisms, which is valuable for both field management practices and understanding rice tolerance to abiotic stresses.

Pathological and miRNA-mRNA Analyses Provide New Insights into the Immune Response of Clams to Vibrio Infection

Manila clam plays a crucial role in China's marine aquaculture industry. However, frequent vibriosis outbreaks severely hinder sustainable and healthy development of the shellfish aquaculture industry. This study indicated markedly decreased clam survival rates after 48 h of Vibrio alginolyticus challenge. Gill and hepatopancreas damage was investigated through histological observation. The activity of lysozyme in the gills and hepatopancreas peaked at 12 and 24 h, respectively. V. alginolyticus showed a maximum bacterial load in the gills and hepatopancreas at 12 and 24 h, respectively. Additionally, transcriptome sequencing of hepatopancreas revealed ten differentially expressed miRNAs in Va and Cn after 48 h infection with V. alginolyticus, corresponding to 100 target genes, with eight upregulated and two downregulated DE miRNAs. Gene ontology (GO) enrichment analysis identified 50 known miRNAs and 111 novel miRNAs, thereby predicting a total of 1840 target genes. KEGG analysis revealed significant changes in multiple signaling pathways, involving lysosomes, apoptosis, amino acid metabolism, and endocytosis, in response to V. alginolyticus stimulation. This study provided new information regarding the immune regulation mechanisms of R. philippinarum in response to V. alginolyticus stress.

Differential Cell Death Pathways Induced by Oxidative Stress in Multi-Organs of Amur Grayling (Thymallus grubii) Under Gradient Ammonia Stress

Ammonia nitrogen is a common contaminant in aquatic environments, and its potential toxicity to organisms has attracted extensive attention. However, few studies have comprehensively evaluated the negative impacts of ammonia stress on cold-water fish. In this study, liver, gill, and intestine specimens of Amur grayling (Thymallus grubii) from three treatment groups (control (0 mg/L), low ammonia (43.683 mg/L), and high ammonia (436.8 mg/L)), were collected for histological observation, biochemical examination, and transcriptomic, metabolomic, and intestinal microbiome analysis. Our results showed that excessive ammonia nitrogen blocked the normal immune function and compromised the integrity of liver and gill tissues through oxidative stress-mediated differential cell death pathways. Meanwhile, the multi-omics analysis revealed that ammonia exposure predominantly altered the carbohydrate, lipid, and amino acid metabolism modes. In addition, it was also demonstrated that ammonia nitrogen stress affected the composition of intestinal microbiota taxa. This study provides insights into the potential risks and hazards of ammonia stress on cold fish in natural waters and provides a reference for the environment control of the water quality in aquaculture.

Physiological and Transcriptomic Analyses Unveil the Preservation Mechanism of Streptomyces albulus Ah11601 Fermentation Broth on 'Shine Muscat' Grapes

BACKGROUND/OBJECTIVES

Grapes (Vitis vinifera), particularly 'Shine Muscat', are prone to postharvest quality loss mainly due to poor storage tolerance. Actinomycetes are microbial resources that produce secondary metabolites that exhibit notable functional properties.

METHODS

This study explored the use of Streptomyces albulus Ah11601 fermentation broth (SFB) as a postharvest treatment to preserve 'Shine Muscat' grape quality during 6 days of room temperature storage using physiological, transcriptomic, and bioinformatics analyses to elucidate the underlying regulatory mechanism.

RESULTS

The results demonstrated that, compared to the control group stored at room temperature (25 °C) for 6 days (6D), the SFB-treated group (T6D) presented a significant delay in the decrease in fruit hardness and vitamin C content. Further investigations revealed that the 6D treatment significantly elevated lipoxygenase activity, MDA content, O2- generation rate, and H2O2 levels. In addition, both the 6D and T6D treatments significantly increased the activities of SOD and APX. Functional enrichment analysis revealed that the upregulated DEGs in the 6D group were predominantly enriched in pathways such as phenylpropanoid biosynthesis; flavonoid biosynthesis; phenylalanine metabolism; and stilbenoid, diarylheptanoid, and gingerol biosynthesis. The downregulated DEGs were enriched primarily in the endoplasmic reticulum protein processing pathway. In the T6D group, the upregulated DEGs were predominantly enriched in the zeatin biosynthesis pathway. In addition, significant alterations in the expression of genes associated with the ethylene and abscisic acid signaling pathways were detected.

CONCLUSIONS

In conclusion, SFB treatment effectively mitigated the deterioration of the postharvest quality of 'Shine Muscat' grapes by preserving the cellular redox balance, regulating cytokinin and ethylene biosynthesis, and optimizing the regulation of ethylene and abscisic acid signaling.

Transcriptomic insights into the resistance mechanism of Penaeus vannamei against highly lethal Vibrio parahaemolyticus

Highly lethal Vibrio disease (HLVD) caused by a virulent strain of Vibrio parahaemolyticus (VpHLVD), which poses a significant threat to Penaeus vannamei post-larvae, leads to substantial mortality and economic losses. To address this challenge, researchers have recently isolated a highly disease-resistant strain of P. vannamei shrimp. However, the underlying mechanisms that could improve disease resistance require further investigation. Our study found that disease-resistant shrimp exhibited a remarkable ability to prevent VpHLVD invasion effectively. To unravel the genetic basis of this resistance, we conducted a transcriptomic analysis with susceptible and disease-resistant shrimp at various time points (0, 6, and 12 h) post-infection with VpHLVD. Differential gene expression (DEGs) analysis of uninfected shrimp revealed that disease-resistant individuals displayed higher expression of immune-related genes and pathways compared to their susceptible counterparts. Simultaneously, they exhibited lower expression of Vibrio toxin-binding genes and Vibrio colonization gene, indicating enhanced defense mechanisms in the resistant shrimp. Upon VpHLVD infection, DEGs analysis also showed that susceptible shrimp attempt to mount a similar immune response as the disease-resistant shrimp during the early stages of infection. However, as the infection progresses, the defense strategies diverge between the two groups, with the peak of gene response occurring later in the disease-resistant shrimp. Our findings indicated that disease-resistant shrimp did not experience significant stress during the early stages of infection and are capable of effectively enhancing their immune response in the middle and late stages of the infection. In summary, our study enhanced the understanding of the mechanisms employed by disease-resistant shrimp to combat Vibrio, and would help to develop effective strategies for disease prevention and control, ultimately reducing the impact of HLVD on shrimp aquaculture.

Integrated transcriptomic, transcriptional factors, and protein interaction reveal the regulatory mechanisms of flowering time in rice (Oryza sativa L.)

Appropriate flowering time is important for rice regional adaptation and optimum rice production, but little is known about the omics of heading date in rice. Here, we studied omics including transcriptome, proteome and transcriptional factors to identify regulatory genes related to flowering time. A total of 1402 differentially expressed genes (DEGs, 721 up-regulated and 681 down-regulated) were detected in wild and mutant. These transcripts are classified according to biological processes, cellular components, and molecular functions. Among these differentially expressed genes, many transcription factor genes demonstrated multiple regulatory pathways involved in flowering time. Gene expression analysis showed that Os03g0122600 (OsMADS50), Os08g0105000 (Ehd3), Os06g0275000 (Hd1) were expressed higher and Os06g0199500 (OsHAL3), Os06g0498800 (OsMFT1), Os08g0105000 (Ehd3), Os06g0157700 (Hd3a), and Os02g0731700 (Ghd2), were expressed lower in wild compared to mutant, which are the key genes that regulate the flowering in rice. In addition, Ghd7 interacted with Os10g30860 and Os12g08260 using yeast two-hybrid assay. We identified 28 potential Ghd7 transcriptional regulators using the transcription factor-centered yeast one hybrid (TF-Centered Y1H) assay. Taken together, this study developed a new set of genomic resources to identify and characterize genes, proteins, and motifs associated with flowering time.

Heat Stress Influences Immunity Through DUSP1 and HSPA5 Mediated Antigen Presentation in Chickens

The objective of this study was to elucidate the immune system response to heat stress in chickens. In this study, mRNA-seq was conducted on the spleen and bursa of experimental chickens, six differentially expressed genes associated with immunity were present in the spleen following immunization. Following exposure to heat stress, 15 differentially expressed genes related to immune and heat shock proteins were identified. Furthermore, the expression levels of DUSP1 and HSPA5 were significantly lower in the non-stressed group. With regard to the mechanism, overexpression of DUSP1 or HSPA5 resulted in no significant difference in MHC-I, MHC-II, and CD80 mRNA expression. However, following stimulation with LPS, mRNA expression of MHC-II, CD80, CD86, CD1C, IL1B, and TLR4 was significantly increased. Furthermore, the enhancement was observed to occur at an earlier stage than when LPS was stimulated alone, thereby facilitating the recognition of LPS by HD11. Following the inhibition of DUSP1 or HSPA5 and the stimulation of LPS, no significant alterations were detected. However, CD1C expression was notably diminished. In conclusion, DUSP1 and HSPA5 have been demonstrated to play important roles in immunity to heat stress by affecting antigen presentation. The present study provides a theoretical basis for the regulation mechanism of disease resistance in poultry.

C-type natriuretic peptide regulates lipid metabolism through a NPRB-PPAR pathway in the intramuscular and subcutaneous adipocytes in chickens

Natriuretic peptides (NPs) have an important role in lipid metabolism in skeletal muscle and adipose tissue in animals. C-type natriuretic peptide (CNP) is an important NP, but the molecular mechanisms that underlie its activity are not completely understood. Treatment of intramuscular fat (IMF) and subcutaneous fat (SCF) adipocytes with CNP led to decreased differentiation, promoted proliferation and lipolysis, and increased the expression of natriuretic peptide receptor B (NPRB) mRNA. Silencing natriuretic peptide C (NPPC) had the opposite results in IMF and SCF adipocytes. Transcriptome analysis found 665 differentially expressed genes (DEGs) in IMF adipocytes and 991 in SCF adipocytes. Seven genes in IMF adipocytes (FABP4, APOA1, ACOX2, ADIPOQ, CD36, FABP5, and LPL) and eight genes in SCF adipocytes (ACOX3, ACSL1, APOA1, CPT1A, CPT2, FABP4, PDPK1 and PPARα) are related to fat metabolism. Fifteen genes were found to be enriched in the peroxisome proliferator-activated receptor (PPAR) pathway. Integrated analysis identified 113 intersection genes in IMF and SCF adipocytes, two of which (APOA1 and FABP4) were enriched in the PPAR pathway. In conclusion, CNP may regulated lipid metabolism through the NPRB-PPAR pathway in both IMF and SCF adipocytes, FABP4 and APOA1 may be the key genes that mediated CNP regulation of fat deposition.

Effect of Heterologous Expression of Key Enzymes Involved in Astaxanthin and Lipid Synthesis on Lipid and Carotenoid Production in Aurantiochytrium sp

Aurantiochytrium sp., a heterotrophic microorganism, has received increasing attention for its high production of polyunsaturated fatty acids and has been widely applied in various industries. This study intended to optimize the carotenoid synthesis pathway in Aurantiochytrium sp. by metabolic engineering to increase the carotenoid content. Multi-sourced key enzyme genes involved in lipid synthesis (LPAAT and DGAT) and astaxanthin synthesis (crtZ and crtW) were selected to construct single-gene expression vectors and transformed into Aurantiochytrium sp. The results showed that the overexpression of LPAAT of Phaeodactylum tricornutum in Aurantiochytrium sp. caused an increase of 39.3% in astaxanthin, 424.7% in β-carotene, 901.8% in canthaxanthin, and 575.9% in lutein, as well as a down-regulation of 15.3% in the fatty acid content. Transcriptomics analysis revealed enhanced expression of genes involved in purine and amino acid metabolism in the transformed strains, and the down-regulation of the citric acid cycle led to an increase in the source of acetyl coenzyme A for the production of fatty acids. This study provides strong experimental evidence to support the application of increasing carotenoid levels in Aurantiochytrium sp.

Plasmodium Infection Modulates Host Inflammatory Response through circRNAs during the Intracellular Stage in Red Blood Cells

The integration of RNA- and DNA-based assays enables the investigation of disease dynamics, specifically assessing the role of asymptomatic or subclinical infections in malaria transmission. Circular RNAs (circRNAs), a distinct category of noncoding RNAs, are implicated in numerous pathogenic mechanisms. As of now, research has yet to explore circRNAs' function in malaria infection. The findings revealed that Plasmodium infection upregulated 60 circRNAs and downregulated 71 in BALB/c mice. We selected 11 differentially expressed (DE) circRNAs according to function prediction of target miRNA-mRNA and coding protein, and these were further confirmed by validation experiments. IRESfinder, GO, and KEGG evaluations indicated that 7 DE circRNAs possess protein-coding potential and are enriched in the MAPK signaling cascade. In P.y17XL-infected BALB/c mouse models, the findings substantiated that the dynamic characteristics of DE circRNAs correlated with inflammation, and the MAPK and NF-κB signaling cascades were activated, also contributing to the inflammatory reaction during malaria infection. This study establishes Plasmodium-induced circRNA expression as a novel mechanism by which the parasite modulates host immune signaling, advancing the understanding of Plasmodium-host cell interactions. In addition, 42 circRNAs were found in normal BALB/c mice, and 25 circRNAs were discovered in P.y17XL-infected BALB/c mice, excluding 1238 circRNAs shared by normal and P.y17XL-infected BALB/c mice. Plasmodium infection changes the expression profile of circRNAs in the host, and these altered circRNAs are involved in the inflammatory response during malaria infection. In addition, Plasmodium possibly regulates the reverse splicing of pre-mRNA or m6A modification of RNA, inducing the production of novel circRNAs in the host.

Ultrasound-activated nano-oxygen sensitizer for sonodynamic-radiotherapy of esophageal cancer

Background: owing to the intricate nature, variability, and persistent oxygen-deficient environment associated with esophageal cancer (EC) tissues, radiotherapy (RT) sometimes doesn't work as well because some cancer cells can resist the radiation to a certain extent. This can lead to the cancer coming back in the same spot or even making the treatment ineffective. The integration of RT with oxygenation strategies is a common approach in cancer treatment. The advent of oxygen-enhancing sonodynamic therapy (SDT), leveraging the cytotoxic effects of reactive oxygen species (ROS), has garnered significant attention as an innovative approach to inducing cell death. Methods: this study utilized nanobubbles (NBs) containing the acoustic sensitizer indocyanine green (ICG) to create a nanoplatform (ICG@O2 NBs) that incorporates oxygen-enhanced SDT and RT. Besides, NBs are paired with low-frequency ultrasound (LFUS), known as ultrasound-targeted nano-bubble destruction (UTND), for precise drug release and improved safety. Results: experimental findings, including JC-1/DCFH-DA assays, demonstrate that ICG@O2 NBs effectively enhance the performance of both RT and SDT. RNA sequencing (RNA-seq) demonstrated differential expression of mRNA and LncRNA prior to and after co-treatment. KEGG and GO pathway analysis were then conducted for enriching and recognizing target genes and pathways correlated with the sensitivity of RT, which were revealed to be remarkably clustered in RT-associated pathways. Conclusion: in vitro and in vivo investigations have indicated significant efficacy of synergistic treatments, highlighting the potential of combining NBs with SDT and RT for managing EC.

DNA methylation regulates somatic stress memory and mediates plasticity during acclimation to repeated sulfide stress in Urechis unicinctus

Stress memory is an adaptive mechanism that enables organisms to develop resilience in response to environmental changes. Among them, somatic stress memory is an important means for organisms to cope with contemporary repeated stress, and is accompanied by transcription memory. Sulfide is a common environmental pollutant; however, some organisms have adapted to survive in sulfur-rich environments. Urechis unicinctus is a sulfur-tolerant organism that enhances sulfide stress tolerance by establishing a somatic sulfide stress memory mechanism. However, the molecular mechanisms that regulate sulfide stress memory remain unclear. To explore whether epigenetics, which plays a role in the response of organisms to environmental stress, is involved in regulating somatic sulfide stress memory, we performed a combined analysis of DNA methylation and transcriptome data. We found that elevated levels of DNA methylation under repetitive sulfide stress regulated gene expression and resulted in enhanced sulfide stress tolerance in U. unicinctus, a phenomenon verified using DNA methylase inhibitors. Transcriptional memory can be induced in genes related to oxidative stress, regulation of autophagy, and maintenance of protein homeostasis by altering the level of DNA methylation to facilitate sulfide stress acclimation. Our results provide new insights into adaptive mechanisms to cope with environmental fluctuations.

Transcriptomic Characterization of miRNAs in Pyrrhalta aenescens Fairmaire in Response to 20-Hydroxyecdysone Treatment

BACKGROUND/OBJECTIVES

Pyrrhalta aenescens, a major pest of elm trees, causes extensive ecological and economic damage through rapid population growth and defoliation. Existing research mainly focuses on its biological traits and chemical control, with little knowledge about its reproductive development mechanisms, a key factor in population expansion. In other insects, the steroid hormone 20-hydroxyecdysone (20E) regulates development and reproduction via microRNA (miRNA)-mediated pathways, but this has not been studied in P. aenescens. This study aimed to systematically identify miRNAs responsive to 20E in P. aenescens and unravel their roles in regulating reproduction and metabolic pathways, providing foundational insights into hormone-miRNA crosstalk in this ecologically significant pest.

METHODS

Adult beetles (collected from Baotou, Inner Mongolia) were injected with 1.0 μg/μL 20E or control. Total RNA from three biological replicates (10 adults each) was sequenced, followed by miRNA identification, differential expression analysis, target prediction, and functional enrichment.

RESULTS

Small RNA sequencing identified 205 miRNAs (162 conserved, 43 novel), with 12 DEMs post-20E treatment. Target prediction linked these miRNAs to 7270 genes, including key regulators of the FoxO signaling pathway and MAPK signaling pathway. KEGG analysis highlighted lipid metabolism and stress response pathways.

CONCLUSIONS

This study revealed that 20E modulates miRNA networks to regulate FoxO and MAPK pathways in P. aenescens, suggesting hormonal control of lipid metabolism and developmental processes. As the first miRNA resource for this pest, our findings provide mechanistic insights into 20E-miRNA crosstalk and identify potential molecular targets for disrupting its reproductive biology, laying a foundation for eco-friendly pest control.

Machine learning-based characterization of PANoptosis-related biomarkers and immune infiltration in ulcerative colitis: A comprehensive bioinformatics analysis and experimental validation

Ulcerative colitis (UC) is a heterogeneous autoimmune condition. PANoptosis, a new form of programmed cell death, plays a role in inflammatory diseases. This study aimed to identify differentially expressed PANoptosis-related genes (PRGs) involved in immune dysregulation in UC. Three key PRGs-BIRC3, MAGED1, and PSME2 were found using weighted gene co-expression network analysis (WGCNA) and machine learning. Immune infiltration analysis revealed that these key PRGs were associated with neutrophils, CD8+ T cells, activated CD4 T cells, and NK cells. Moreover, these key PRGs were significantly enriched in pathways related to inflammatory bowel disease, the IL-17 signaling pathway, and NOD-like receptor signaling pathway. The expression levels of the key PRGs were validated in various datasets, animal models, and UC intestinal tissue samples. Our findings confirmed the involvement of PANoptosis in UC and predict hub genes and immune characteristics, providing new insights for further investigations into UC pathogenic mechanisms and therapeutic strategies.

Transcriptome profiling reveals the mechanism of fruit navel development in melon (Cucumis melo L.)

BACKGROUND

Melon is an important horticultural crop cultivated extensively worldwide. The size of the fruit navel, the terminal region of melon fruits, significantly influences the appearance quality of the fruit. However, the regulatory factors and molecular mechanisms governing the fruit navel development remain poorly understood in melon.

RESULTS

In this study, the regulators and mechanisms underlying fruit navel development were investigated through phenotypic analysis, RNA sequencing (RNA-seq) and RT-qPCR methods. The inbred line 'T03' and a big fruit navel mutant 'BFN' of melon were used as experimental materials. RNA-seq analysis identified 116 differentially expressed genes (DEGs), including 54 up-regulated and 62 down-regulated genes, in both the green bud (GB) and ovary at anthesis (OA) stages of the 'BFN' melon compared to the 'T03' melon. Functional enrichment analysis revealed that these 116 DEGs were significantly associated with "Sesquiterpenoid and triterpenoid biosynthesis", "Circadian rhythm-plant", "Galactose metabolism" and "Biosynthesis of various alkaloids" pathways. There were three (AP2/ERF, MYB and C2H2 types) and eight (AP2/ERF, MADS-box, homeobox domain and bZIP types) transcription factors presented in up-regulated and down-regulated DEGs, and their putative target genes were predicted. Based on KEGG and expression analyses, two terpene cyclase/mutase genes (MELO3 C001812 and MELO3 C004329) were identified as being involved in the "Sesquiterpenoid and triterpenoid biosynthesis" pathway, and their transcripts were significantly downregulated in all detected development stages (EGB, GB, GYB, YB and OA) of 'BFN' fruits compared with 'T03' fruits.

CONCLUSIONS

The findings of this study elucidate a fundamental regulatory mechanism underlying fruit navel formation, and identify two key negative regulators, MELO3C001812 and MELO3C004329, involved in the development of the fruit navel in melon.

Exosomes derived from mesenchymal stem cells ameliorate impaired glucose metabolism in myocardial Ischemia/reperfusion injury through miR-132-3p/PTEN/AKT pathway

Exosomes secreted by mesenchymal stem cells (MSCs) have been considered as a novel biological therapy for myocardial ischemia/reperfusion injury (MIRI). However, the underlying mechanism of exosomes has not been completely established, especially in the early stage of MIRI. In this study, we primarily investigated the protective effect of exosomes on MIRI from both in vitro and ex vivo perspectives. Bioinformatic analysis was conducted to identify exosomal miRNA associated with myocardial protection, Genes and proteins related to functional studies and myocardial energy metabolism were analyzed and evaluated using techniques such as Polymerase Chain Re-action (PCR), Western blotting, double luciferase biochemical techniques, flow cytometry assay, etc. It was discovered that exosomes ameliorated cardiomyocyte injury t by delivery of miR-132-3p.This process reduced the expression of Phosphatase and tensin homolog (PTEN) mRNA and protein, enhanced the expression of phosphorylated protein kinase (pAKT), regulated the insulin signaling pathway, facilitated intracellular Glucose transporter 4 (GLUT4) protein membrane translocation, and enhanced glucose uptake and Adenosine Triphosphate (ATP) production. This study confirmed, for the first time, that MSC-EXO can provide myocardial protection in the early stages of MIRI through miR-132/PTEN/AKT pathway. This research establishes a theoretical and experimental foundation for the clinical application of MSC-derived exosomes.

Urea Amidolyase as an Enzyme for Urea Utilisation in Phytoplankton: Functional Display in Chlamydomonas reinhardtii

Urea is an important source of nitrogen for many phytoplankton with the potential to stimulate harmful algal blooms, but the molecular machinery underpinning urea uptake and assimilation by algae is not fully understood. Urease (URE) is commonly regarded as the responsible enzyme, but urea amidolyase (UAL), albeit known to exist, has hardly been studied. Here, the species distribution, expression patterns and functional roles of UAL are examined. We found a widespread occurrence of UAL across six major phytoplankton lineages, along with evidence of a potential URE-independent evolutionary trajectory and lineage-specific losses. Quantitative analyses based on marine planktonic metagenomes and metatranscriptomes revealed that UAL is as prevalent as URE, but exhibits higher expression levels in phytoplankton than in bacteria, suggesting that UAL plays a crucial role in nitrogen nutrition in marine phytoplankton. Furthermore, using the CRISPR/Cas9 genome editing method and Chlamydomonas reinhardtii as the algal model, we showed that DUR2 in UAL is essential for urea utilisation, as its knockout completely abolishes the ability of algae to grow under urea as the sole nitrogen source. This study unveils an unappreciated mechanism in algae for utilising urea as a nutrient, underscores the need to consider both URE and UAL enzyme systems to model urea utilisation by algae and provides a crucial gene (DUR2) as a potential genetic marker for detecting the contribution of UAL to urea utilisation in phytoplankton.

CeJAZ3 suppresses longifolene accumulation in Casuarina equisetifolia, affecting the host preference of Anoplophora chinensis

BACKGROUND

Casuarina equisetifolia, a crucial species of coastal windbreaks, is highly susceptible to infestation by Anoplophora chinensis. This stem-boring pest poses a significant threat to the health and sustainability of Casuarina equisetifolia forests. Understanding the molecular mechanisms underlying the host preference of A. chinensis to Casuarina equisetifolia is essential for developing effective pest management strategies.

RESULTS

Through field surveys, we identified two cultivars of Casuarina equisetifolia that exhibited differing levels of host preference for A. chinensis. Further analysis of multi-omics data (phenomics, transcriptomics, and metabolomics) from these cultivars revealed that longifolene plays a significant role in attracting A. chinensis to Casuarina equisetifolia. Additionally, the jasmonic acid (JA) signaling pathway was found to suppress longifolene accumulation, primarily through the interaction between the jasmonate ZIM-domain (JAZ) proteins and the terpene synthase (TPS) gene. Moreover, we identified a critical JAZ component, CeJAZ3, whose overexpression led to the down-regulation of TPS expression levels and, consequently, a reduced release of longifolene.

CONCLUSION

We confirmed that the negative regulator of host preference, CeJAZ3, in the JA signaling pathway can suppress the expression of TPSs, thereby down-regulating the accumulation of longifolene in Casuarina equisetifolia and indirectly suppressing the attraction of host plants to A. chinensis, which provides a basis for the integrated management of A. chinensis. © 2024 Society of Chemical Industry.